Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012867.1 Kokia drynarioides strain JFW-HI SEQ_127881, 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: 163096
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:616 original size:16 final size:17
Alignment explanation
Indices: 595--678 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 17
585 GTTTTTGGAC
* *
595 TTTTAATTTAA-TTAAG
1 TTTTAATTAAATTTAAA
* *
611 TTTTAAATCAATTTAAA
1 TTTTAATTAAATTTAAA
628 TTTTAATTAAATTTAAA
1 TTTTAATTAAATTTAAA
*
645 TTTTAAAAGATAAATTTAAA
1 TTTT--AA-TTAAATTTAAA
* *
665 TTTAAAATAAATTT
1 TTTTAATTAAATTT
679 GAATAAATTC
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.16
17 31 0.54
18 2 0.04
19 2 0.04
20 13 0.23
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTTAATTAAATTTAAA
Found at i:631 original size:17 final size:17
Alignment explanation
Indices: 606--678 Score: 83
Period size: 17 Copynumber: 4.1 Consensus size: 17
596 TTTAATTTAA
* *
606 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATAAAT
*
623 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
640 TTAAATTTTAAAAGATAAAT
1 TTAAATTTT--AA-ATAAAT
*
660 TTAAATTTAAAATAAAT
1 TTAAATTTTAAATAAAT
677 TT
1 TT
679 GAATAAATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
17 31 0.65
18 2 0.04
19 2 0.04
20 13 0.27
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:635 original size:6 final size:6
Alignment explanation
Indices: 620--670 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
610 GTTTTAAATC
* **
620 AATTTA AATTTT AA-TTA AATTTA AATTTTAA AAGATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AA-TTT-A AATTTA AATTTA AATTTA
669 AA
1 AA
671 ATAAATTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
5 4 0.11
6 25 0.69
7 4 0.11
8 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:3956 original size:98 final size:97
Alignment explanation
Indices: 3774--3964 Score: 249
Period size: 98 Copynumber: 1.9 Consensus size: 97
3764 TTTGTCGATT
* * * *
3774 TTTTCTTAAGAATGTTTCGTTCCTTTTGACGCGAAGTAGAATGACAACCTAAGCACCTCACTCCG
1 TTTTCTTAAGAATGTTTAG-TCCTTTTGACGCGAAGTAGAATAACAACCCAAGCACCCCACTCCG
* * *
3839 ATTACTTAGCTCAACACACTCCCAATTTCGTTA
65 ATTACTCAACCCAACACACTCCCAATTTCGTTA
* *
3872 TTTTCTTAAGAATGTATTAG-CCATTTTGACGCGAATTGGAATAACAACCCAAGCACCCCACTCC
1 TTTTCTTAAGAATGT-TTAGTCC-TTTTGACGCGAAGTAGAATAACAACCCAAGCACCCCACTCC
* *
3936 GATTACTCAACCCAAGACACTCCTAATTT
64 GATTACTCAACCCAACACACTCCCAATTT
3965 TTTATTATCC
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
97 2 0.03
98 75 0.94
99 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (97 bp):
TTTTCTTAAGAATGTTTAGTCCTTTTGACGCGAAGTAGAATAACAACCCAAGCACCCCACTCCGA
TTACTCAACCCAACACACTCCCAATTTCGTTA
Found at i:4741 original size:16 final size:15
Alignment explanation
Indices: 4714--4760 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
4704 AACATGCAAG
4714 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
*
4729 AAGAATGAAAATAAATA
1 AA-AATAAAAATAAA-A
4746 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
4761 TTGGTTGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.11
16 22 0.79
17 3 0.11
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:21425 original size:20 final size:19
Alignment explanation
Indices: 21397--21435 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21387 TCTAACCTTT
21397 CTTTACATTCGTGTTATTTA
1 CTTTACATT-GTGTTATTTA
* *
21417 CTTTTCATTGTTTTATTTA
1 CTTTACATTGTGTTATTTA
21436 TATTTTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.62
Consensus pattern (19 bp):
CTTTACATTGTGTTATTTA
Found at i:31643 original size:9 final size:9
Alignment explanation
Indices: 31631--31667 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
31621 AACAATTTTA
31631 AAATAAATT
1 AAATAAATT
*
31640 AAAT-AGTT
1 AAATAAATT
31648 -AATAAATT
1 AAATAAATT
31656 AAATAAATT
1 AAATAAATT
31665 AAA
1 AAA
31668 AATTAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 3 0.12
8 6 0.25
9 15 0.62
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAATAAATT
Found at i:31670 original size:16 final size:16
Alignment explanation
Indices: 31632--31672 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
31622 ACAATTTTAA
*
31632 AATAAATTAAATAGTT
1 AATAAATTAAATAATT
31648 AATAAATTAAATAAATT
1 AATAAATTAAAT-AATT
31665 AA-AAATTA
1 AATAAATTA
31673 GAAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AATAAATTAAATAATT
Found at i:33295 original size:66 final size:66
Alignment explanation
Indices: 33221--33352 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
33211 TTTTTGGATG
*
33221 GTAAGTTATAGCAATCTTGTGCCTTATTTCATGTTTATCAAGTTTCCACTTTAACAATTTGTTTA
1 GTAAGTTATAGCAATCTTGTGCCTTATTTCATGTTTATCAAGTTGCCACTTTAACAATTTGTTTA
33286 C
66 C
* *
33287 GTAAGTTATAGCAATCTTGTGCCTTATTTCATGTTTATCAAGTTGCGACTTTAACCATTTGTTTA
1 GTAAGTTATAGCAATCTTGTGCCTTATTTCATGTTTATCAAGTTGCCACTTTAACAATTTGTTTA
33352 C
66 C
33353 AAAATGGAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.45
Consensus pattern (66 bp):
GTAAGTTATAGCAATCTTGTGCCTTATTTCATGTTTATCAAGTTGCCACTTTAACAATTTGTTTA
C
Found at i:59972 original size:27 final size:27
Alignment explanation
Indices: 59912--59972 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
59902 TCAAAATAAT
*
59912 AATAAGATAAAATAAACTAAGTTTATA
1 AATAAGCTAAAATAAACTAAGTTTATA
59939 AATAAGCTAAAATAAACTAAGTTTATA
1 AATAAGCTAAAATAAACTAAGTTTATA
59966 AATAAGC
1 AATAAGC
59973 CTTCGAATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (27 bp):
AATAAGCTAAAATAAACTAAGTTTATA
Found at i:61162 original size:23 final size:22
Alignment explanation
Indices: 61128--61171 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
61118 GTTTGACTTT
*
61128 GGTTTGGTTTGGTTTTTAAAAG
1 GGTTTGGTTTGGGTTTTAAAAG
61150 GGTTTGGGTTTGGGTTTTAAAA
1 GGTTT-GGTTTGGGTTTTAAAA
61172 TTGGGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (22 bp):
GGTTTGGTTTGGGTTTTAAAAG
Found at i:63338 original size:42 final size:42
Alignment explanation
Indices: 63288--63370 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
63278 GAGATAAAAT
63288 TACAAGAATGTAAACCGAACAACAATGAGTCAGAAAATAAAC
1 TACAAGAATGTAAACCGAACAACAATGAGTCAGAAAATAAAC
63330 TACAAGAATGTAAACCGAACAACAATGAGTCAGAAAATAAA
1 TACAAGAATGTAAACCGAACAACAATGAGTCAGAAAATAAA
63371 AAACTAGGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.14
Consensus pattern (42 bp):
TACAAGAATGTAAACCGAACAACAATGAGTCAGAAAATAAAC
Found at i:63751 original size:14 final size:16
Alignment explanation
Indices: 63727--63767 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
63717 TGCAATATAT
*
63727 TTCTCCTCTTTTC-TC
1 TTCTTCTCTTTTCTTC
63742 TT-TTCTCTTTTCTTC
1 TTCTTCTCTTTTCTTC
63757 TTCTT-TCTTTT
1 TTCTTCTCTTTT
63768 TTTTCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 9 0.39
15 12 0.52
16 2 0.09
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTTCTCTTTTCTTC
Found at i:77112 original size:68 final size:68
Alignment explanation
Indices: 76993--77315 Score: 342
Period size: 68 Copynumber: 4.8 Consensus size: 68
76983 TTTAACACAA
* * *
76993 CACATATTAATCACATTTAATCACATTAGTCACATGAATATATCAGCATTTATCACATCAGATAT
1 CACAT-TTAGTCACATTTAATCACATTAGTCACATGAATATTTCAGCATTTATCACATCACATAT
77058 TAAT
65 TAAT
* ** *
77062 CACATTTAGTCACATTTAATCTCATTAGTCACGCGAATATTTTAGCATTTATCACATCACATATT
1 CACATTTAGTCACATTTAATCACATTAGTCACATGAATATTTCAGCATTTATCACATCACATATT
77127 AAT
66 AAT
* * * * *
77130 AACATTTAGTCACATTTAATCACATATAATCACATTAATATTTCAACATTTACCACATCACA-AT
1 CACATTTAGTCACATTTAATCACAT-TAGTCACATGAATATTTCAGCATTTATCACATCACATA-
*
77194 TTAGT
64 TTAAT
* * *
77199 CACATTTAGTCACATTTAAT--C---A-T---ATGAATATTTCATCATTTATCGCATCATATATT
1 CACATTTAGTCACATTTAATCACATTAGTCACATGAATATTTCAGCATTTATCACATCACATATT
77255 AAT
66 AAT
* * * * * *
77258 CACATTTAGTCACATTAAATCACATATAATCGCATTAATATTTCAACATTTATAACAT
1 CACATTTAGTCACATTTAATCACAT-TAGTCACATGAATATTTCAGCATTTATCACAT
77316 TAATATTTAA
Statistics
Matches: 212, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
59 47 0.22
60 1 0.00
61 1 0.00
62 1 0.00
63 1 0.00
65 1 0.00
66 1 0.00
67 1 0.00
68 80 0.38
69 78 0.37
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (68 bp):
CACATTTAGTCACATTTAATCACATTAGTCACATGAATATTTCAGCATTTATCACATCACATATT
AAT
Found at i:77146 original size:10 final size:10
Alignment explanation
Indices: 77117--77220 Score: 64
Period size: 10 Copynumber: 9.4 Consensus size: 10
77107 CATTTATCAC
77117 ATCACATATTA
1 ATCACAT-TTA
*
77128 ATAACATTTA
1 ATCACATTTA
*
77138 GTCACATTTA
1 ATCACATTTA
*
77148 ATCACATATA
1 ATCACATTTA
77158 ATCACATTAATA
1 ATCACATT--TA
*
77170 TTTCAACATTTACCA
1 -ATC-ACATTT---A
77185 CATCACAATTTA
1 -ATCAC-ATTTA
*
77197 GTCACATTTA
1 ATCACATTTA
*
77207 GTCACATTTA
1 ATCACATTTA
77217 ATCA
1 ATCA
77221 TATGAATATT
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
10 44 0.59
11 10 0.14
12 4 0.05
13 2 0.03
14 7 0.09
15 7 0.09
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (10 bp):
ATCACATTTA
Found at i:77229 original size:59 final size:58
Alignment explanation
Indices: 77133--77282 Score: 192
Period size: 59 Copynumber: 2.6 Consensus size: 58
77123 TATTAATAAC
* * *
77133 ATTTAGTCACATTTAATCACATATAATCACATTAATATTTCAACATTTACCACATCACA
1 ATTTAGTCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTACCACATCA-A
* * * * *
77192 ATTTAGTCACATTTAGTCACATTTAATCATATGAATATTTCATCATTTATCGCATCAT
1 ATTTAGTCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTACCACATCAA
* *
77250 ATATTAATCACATTTAGTCACATTAAATCACAT
1 AT-TTAGTCACATTTAGTCACATTTAATCACAT
77283 ATAATCGCAT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 2 0.03
59 77 0.97
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (58 bp):
ATTTAGTCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTACCACATCAA
Found at i:77255 original size:128 final size:126
Alignment explanation
Indices: 77060--77309 Score: 365
Period size: 128 Copynumber: 2.0 Consensus size: 126
77050 TCAGATATTA
* * * *
77060 ATCACATTTAGTCACATTTAATCTCATTAGTCACGCGAATATTTTAGCATTTATCACATCACATA
1 ATCACATTTAGTCACATTTAATCACATTAATCACACGAATATTTCAGCATTTATCACATCACATA
*
77125 TTAATAACATTTAGTCACATTTAATCACATATAATCACATTAATATTTCAACATTTACCAC
66 TTAATAACATTTAGTCACATTAAATCACATATAATCACATTAATATTTCAACATTTACCAC
* * * * * *
77186 ATCACAATTTAGTCACATTTAGTCACATTTAATCATATGAATATTTCATCATTTATCGCATCATA
1 ATCAC-ATTTAGTCACATTTAATCACA-TTAATCACACGAATATTTCAGCATTTATCACATCACA
* *
77251 TATTAATCACATTTAGTCACATTAAATCACATATAATCGCATTAATATTTCAACATTTA
64 TATTAATAACATTTAGTCACATTAAATCACATATAATCACATTAATATTTCAACATTTA
77310 TAACATTAAT
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
126 5 0.05
127 19 0.17
128 85 0.78
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (126 bp):
ATCACATTTAGTCACATTTAATCACATTAATCACACGAATATTTCAGCATTTATCACATCACATA
TTAATAACATTTAGTCACATTAAATCACATATAATCACATTAATATTTCAACATTTACCAC
Found at i:77293 original size:20 final size:20
Alignment explanation
Indices: 77255--77295 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
77245 ATCATATATT
* *
77255 AATCACATTTAGTCACATTA
1 AATCACATATAATCACATTA
*
77275 AATCACATATAATCGCATTA
1 AATCACATATAATCACATTA
77295 A
1 A
77296 TATTTCAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (20 bp):
AATCACATATAATCACATTA
Found at i:77340 original size:23 final size:23
Alignment explanation
Indices: 77314--77357 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
77304 CATTTATAAC
*
77314 ATTAATATTTAAGCATAAATCAT
1 ATTAACATTTAAGCATAAATCAT
77337 ATTAACATTTAAGCATAAATC
1 ATTAACATTTAAGCATAAATC
77358 GAACCCCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (23 bp):
ATTAACATTTAAGCATAAATCAT
Found at i:78365 original size:3 final size:3
Alignment explanation
Indices: 78345--78412 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
78335 ATCAAACACG
* * * * *
78345 ATA ATGA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATC CTC AGA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
78391 ATA ATA AGA ATA ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
78413 CGATTTATAG
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:78561 original size:5 final size:5
Alignment explanation
Indices: 78551--78611 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
78541 AAAATTGCAA
* *
78551 AAAAT AAAAT AAATAA AACAAT GATAAT AAAAT AAAAT --AAT AAAAT
1 AAAAT AAAAT AAA-AT AA-AAT -AAAAT AAAAT AAAAT AAAAT AAAAT
78597 AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT
78612 TAAGAAGGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
3 3 0.06
5 35 0.74
6 7 0.15
7 2 0.04
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:78567 original size:27 final size:27
Alignment explanation
Indices: 78531--78595 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
78521 AAGGAAAAAC
*
78531 AAATACTAAAAAAATTG-CAA-AAAATA
1 AAATAATAAAAAAA-TGACAATAAAATA
* *
78557 AAATAAATAAAACAATGATAATAAAATA
1 AAAT-AATAAAAAAATGACAATAAAATA
78585 AAATAATAAAA
1 AAATAATAAAA
78596 TAAAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 6 0.18
27 17 0.52
28 10 0.30
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (27 bp):
AAATAATAAAAAAATGACAATAAAATA
Found at i:78592 original size:13 final size:13
Alignment explanation
Indices: 78551--78603 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
78541 AAAATTGCAA
78551 AAAATAAAATAAAT
1 AAAATAAAAT-AAT
* *
78565 AAAACAATGATAAT
1 AAAATAA-AATAAT
78579 AAAATAAAATAAT
1 AAAATAAAATAAT
78592 AAAATAAAATAA
1 AAAATAAAATAA
78604 AATAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 17 0.50
14 15 0.44
15 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:78606 original size:18 final size:18
Alignment explanation
Indices: 78549--78608 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
78539 AAAAAATTGC
78549 AAAA-AATAAAAT-AAAT
1 AAAATAATAAAATAAAAT
* *
78565 AAAACAATGATAATAAAAT
1 AAAATAAT-AAAATAAAAT
78584 AAAATAATAAAATAAAAT
1 AAAATAATAAAATAAAAT
78602 AAAATAA
1 AAAATAA
78609 AATTAAGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 4 0.11
17 3 0.08
18 20 0.53
19 11 0.29
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATAATAAAATAAAAT
Found at i:78607 original size:28 final size:28
Alignment explanation
Indices: 78551--78611 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
78541 AAAATTGCAA
* *
78551 AAAATAAAATAAATAAAACAATGATAAT
1 AAAATAAAATAAATAAAAAAATGAAAAT
78579 AAAATAAAAT-AATAAAATAAAAT-AAAAT
1 AAAATAAAATAAAT-AAA-AAAATGAAAAT
78607 AAAAT
1 AAAAT
78612 TAAGAAGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 22 0.76
29 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (28 bp):
AAAATAAAATAAATAAAAAAATGAAAAT
Found at i:78610 original size:23 final size:24
Alignment explanation
Indices: 78551--78611 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
78541 AAAATTGCAA
78551 AAAATAAAAT-AAATAAAACAATG
1 AAAATAAAATAAAATAAAACAATG
*
78574 ATAATAAAATAAAATAATAA-AAT-
1 AAAATAAAATAAAATAA-AACAATG
78597 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
78612 TAAGAAGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 23 0.68
24 9 0.26
25 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAATAAAATAAAATAAAACAATG
Found at i:80158 original size:36 final size:36
Alignment explanation
Indices: 80118--80381 Score: 377
Period size: 36 Copynumber: 7.3 Consensus size: 36
80108 TTAGCATAAT
*
80118 ATATTCACTGTCACATGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
** * *
80154 ATATTTTTTGTCTCATGGCATGAATAACATACTCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * *
80190 ATATTTATTGTCACATAGCATGAATAACATGCCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
80226 ATATTTACCGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
80262 ATATTTATTGTCACATGGCATGAATAACATACCAAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
80298 ATATTTACTGTCACATGACATGAATAACATACCAAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
80334 ATATTTACTGTC-CTATGGCATGAATAACATACCCAC
1 ATATTTACTGTCAC-ATGGCATGAATAACATACCCAC
*
80370 ATATTTATTGTC
1 ATATTTACTGTC
80382 TCAATAGTCA
Statistics
Matches: 203, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
35 1 0.00
36 202 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (36 bp):
ATATTTACTGTCACATGGCATGAATAACATACCCAC
Found at i:95814 original size:28 final size:28
Alignment explanation
Indices: 95782--95838 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
95772 TATGTAAGTG
95782 TGATAGAAGGTTATTTATATATGAATAT
1 TGATAGAAGGTTATTTATATATGAATAT
95810 TGATAGAAGGTTATTTATATATGAATAT
1 TGATAGAAGGTTATTTATATATGAATAT
95838 T
1 T
95839 CTAATTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.44
Consensus pattern (28 bp):
TGATAGAAGGTTATTTATATATGAATAT
Found at i:97657 original size:15 final size:15
Alignment explanation
Indices: 97634--97663 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
97624 TTTATATTAA
97634 TTTTAATTTAATATT
1 TTTTAATTTAATATT
*
97649 TTTTTATTTAATATT
1 TTTTAATTTAATATT
97664 CTATATATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATTTAATATT
Found at i:97798 original size:16 final size:16
Alignment explanation
Indices: 97754--97789 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
97744 TATGTCTTAT
97754 AAATAATATAATATATAA
1 AAATAATA-AA-ATATAA
97772 AAATAATAAAATATAA
1 AAATAATAAAATATAA
97788 AA
1 AA
97790 CATTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAATAAAATATAA
Found at i:100183 original size:31 final size:31
Alignment explanation
Indices: 100148--100206 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
100138 TTTTTTAAAT
100148 AATTAAAT-TAAAATTTTATCATTT-TTAAGGA
1 AATT-AATGTAAAATTTTATC-TTTATTAAGGA
*
100179 AATTAATGTACAATTTTATCTTTATTAA
1 AATTAATGTAAAATTTTATCTTTATTAA
100207 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (31 bp):
AATTAATGTAAAATTTTATCTTTATTAAGGA
Found at i:100927 original size:20 final size:20
Alignment explanation
Indices: 100890--100942 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
100880 AATATATAAT
* *
100890 AAATT-TTTGGAATTTTTGA
1 AAATTATTTTGAATATTTGA
100909 AAATTATTTTGAATATTTGA
1 AAATTATTTTGAATATTTGA
*
100929 AATTTATTTTGAAT
1 AAATTATTTTGAAT
100943 TGTTTTGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (20 bp):
AAATTATTTTGAATATTTGA
Found at i:106833 original size:16 final size:16
Alignment explanation
Indices: 106788--106838 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
106778 AGTAATATAT
*
106788 TTTTTCTGCTT-TTCTC
1 TTTTTCTTCTTCTT-TC
*
106804 TTTTTCTT-TGCTTTC
1 TTTTTCTTCTTCTTTC
106819 TTTTTCTTCTTCTTT-
1 TTTTTCTTCTTCTTTC
106834 TTTTT
1 TTTTT
106839 ATACGTGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTTCTTCTTCTTTC
Found at i:107416 original size:17 final size:17
Alignment explanation
Indices: 107396--107438 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
107386 AAATGAACTA
107396 ACAAGTAAAATGAAACG
1 ACAAGTAAAATGAAACG
* *
107413 ACAAGTAAAATGCAATG
1 ACAAGTAAAATGAAACG
*
107430 ACAATTAAA
1 ACAAGTAAA
107439 TGAGATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.16
Consensus pattern (17 bp):
ACAAGTAAAATGAAACG
Found at i:116297 original size:43 final size:43
Alignment explanation
Indices: 116236--116372 Score: 170
Period size: 43 Copynumber: 3.2 Consensus size: 43
116226 GAATCACTTG
* *
116236 ATGTATAAATGGAAGACTCATGTATTGGGATGAGCATGAGATT
1 ATGTATAAATGGAAGACTCATGTATCGGGAAGAGCATGAGATT
* *
116279 ATGTATAAATGGAAGACTCGTG-ACTCAGGAAGAGCATGAGATT
1 ATGTATAAATGGAAGACTCATGTA-TCGGGAAGAGCATGAGATT
* * * *
116322 ATGTTTAAA-GGAAGACTTATGTCTCGAGAAGAGCATGAGATT
1 ATGTATAAATGGAAGACTCATGTATCGGGAAGAGCATGAGATT
*
116364 ATGTTTAAA
1 ATGTATAAA
116373 AGAATAGTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
42 37 0.45
43 45 0.55
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (43 bp):
ATGTATAAATGGAAGACTCATGTATCGGGAAGAGCATGAGATT
Found at i:116353 original size:42 final size:41
Alignment explanation
Indices: 116267--116470 Score: 182
Period size: 42 Copynumber: 5.0 Consensus size: 41
116257 GTATTGGGAT
* ** *
116267 GAGCATGAGATTATGTATAAATGGAAGACTCGTGACTCAGGAA
1 GAGCATGAGATTATGTTTAAA-GGAAGACTTATGTCTC-GGAA
116310 GAGCATGAGATTATGTTTAAAGGAAGACTTATGTCTCGAGAA
1 GAGCATGAGATTATGTTTAAAGGAAGACTTATGTCTCG-GAA
* * * * *
116352 GAGCATGAGATTATGTTTAAAAGAATAGTTATGTCTTGGTA
1 GAGCATGAGATTATGTTTAAAGGAAGACTTATGTCTCGGAA
* * * * * *
116393 GAGCATAAGA-T-TGTTTAAAAGAATAGTTATGTCTTGGTA
1 GAGCATGAGATTATGTTTAAAGGAAGACTTATGTCTCGGAA
* *
116432 GAGCATAAGA-T-TGTTTAAAAAGGAAGACTTATGACTCGG
1 GAGCATGAGATTATGTTT--AAAGGAAGACTTATGTCTCGG
116471 TCGGAGCATA
Statistics
Matches: 143, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 44 0.31
40 1 0.01
41 28 0.20
42 50 0.35
43 20 0.14
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.30
Consensus pattern (41 bp):
GAGCATGAGATTATGTTTAAAGGAAGACTTATGTCTCGGAA
Found at i:116415 original size:39 final size:41
Alignment explanation
Indices: 116309--116451 Score: 186
Period size: 39 Copynumber: 3.6 Consensus size: 41
116299 TGACTCAGGA
* * * * * *
116309 AGAGCATGAGATTATGTTTAAAGGAAGACTTATGTCTCGAGA
1 AGAGCATAAGATTATGTTTAAAAGAATAGTTATGTCTTG-GT
*
116351 AGAGCATGAGATTATGTTTAAAAGAATAGTTATGTCTTGGT
1 AGAGCATAAGATTATGTTTAAAAGAATAGTTATGTCTTGGT
116392 AGAGCATAAGA-T-TGTTTAAAAGAATAGTTATGTCTTGGT
1 AGAGCATAAGATTATGTTTAAAAGAATAGTTATGTCTTGGT
116431 AGAGCATAAGA-T-TGTTTAAAA
1 AGAGCATAAGATTATGTTTAAAA
116452 AGGAAGACTT
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 48 0.51
40 1 0.01
41 11 0.12
42 35 0.37
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (41 bp):
AGAGCATAAGATTATGTTTAAAAGAATAGTTATGTCTTGGT
Found at i:122606 original size:15 final size:15
Alignment explanation
Indices: 122586--122614 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
122576 TTTCCATTTG
122586 TCAAGAATACCCTTC
1 TCAAGAATACCCTTC
122601 TCAAGAATACCCTT
1 TCAAGAATACCCTT
122615 GATTTACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (15 bp):
TCAAGAATACCCTTC
Found at i:138986 original size:12 final size:12
Alignment explanation
Indices: 138969--138994 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
138959 TGTTATCATG
138969 ATGAATGCTATT
1 ATGAATGCTATT
138981 ATGAATGCTATT
1 ATGAATGCTATT
138993 AT
1 AT
138995 TTATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:140842 original size:270 final size:269
Alignment explanation
Indices: 140331--141038 Score: 820
Period size: 270 Copynumber: 2.6 Consensus size: 269
140321 TGAGCTAATT
* *
140331 TTTTTTTGTCTATCATTTAAAATATTAAATCTTTTT-GACTGATTTCAAATGATT-TCTTTTGGG
1 TTTTTTTATCTTTCATTTAAAATATTAAAT-TTTTTAGACTGATTTCAAATGATTATC-TTTGGG
* ** ** * *
140394 TTTGTAAGAAGAA-TTATAAATATGATTGCC-CACTTGAATGCTGTTATAAGGCACGAGTTTTTG
64 TTTGTAAGAAGAACTT-CAAATATGGCTGCCACAC--GCTTGCTGTTACAAGGCACGAG-TTTCG
* * * * ** * ** *
140457 GAACCTCATTTC-TGGGTAAAGGAAGTGCAC-TCATCGGTGGAACGGATGTCGTAGACTGATTTG
125 GAACCTCATTTCTTGGG-AGAGGAAGCGC-CTTCATCGATGGAACAGACATCGAAGACCAATTGG
* **
140520 GAACGATGGGTTTCTAGGGCATTGATGTATTTATCAACACAAATAGGTTTTAACAAACAAGTTCA
188 GAACGATAGGTTTCTAGGGCATCAATGTATTTATCAACACAAATAGGTTTTAAC-AACAAGTTCA
* *
140585 AAAAAATACTGAAACTAA
252 AAAAAACAATGAAACTAA
* * *
140603 TTTTTTTATCTTTCATTTAAAATATTAAATTTTTTATACTAATTTCAAACGATTATCTTTGGGTT
1 TTTTTTTATCTTTCATTTAAAATATTAAATTTTTTAGACTGATTTCAAATGATTATCTTTGGGTT
* * * *
140668 TGTAAGAAGAACTTCAAATATGGCTGCCACACGCTTTCTGTTGCAAGGAACGAGTTTCGAAACCT
66 TGTAAGAAGAACTTCAAATATGGCTGCCACACGCTTGCTGTTACAAGGCACGAGTTTCGGAACCT
* *
140733 CATTTCTTGGGAGAGGAAGCGCCTTTATCGATTGAACAGACATCGAAGACCAATTGGGAACGATA
131 CATTTCTTGGGAGAGGAAGCGCCTTCATCGATGGAACAGACATCGAAGACCAATTGGGAACGATA
* *
140798 GGTTTCTAGGGCATCAATGTATTTATCAATACAAATATGTTTTAACAACAAGTTCAAAAAAACAA
196 GGTTTCTAGGGCATCAATGTATTTATCAACACAAATAGGTTTTAACAACAAGTTCAAAAAAACAA
**
140863 TGATGCTAA
261 TGAAACTAA
* * *
140872 TTTTTTCTACCTTTCATTTAAAATATTAAATATTTTAGACTGATTTCAAATGATTACCTTTGGGT
1 TTTTTT-TATCTTTCATTTAAAATATTAAATTTTTTAGACTGATTTCAAATGATTATCTTTGGGT
* * * * * *
140937 TTATAAGAAGAACTGCAAATATGGCTTCCACAAGCTTGCGGTTACAAAGCACGAG-TTCTGGAAC
65 TTGTAAGAAGAACTTCAAATATGGCTGCCACACGCTTGCTGTTACAAGGCACGAGTTTC-GGAAC
* *
141001 CTCGTTT-TTGGGGAGAGGAAGCGCCTTCATCGGTGGAA
129 CTCATTTCTT-GGGAGAGGAAGCGCCTTCATCGATGGAA
141039 TGGACGTCGA
Statistics
Matches: 370, Mismatches: 57, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
269 36 0.10
270 229 0.62
271 25 0.07
272 73 0.20
273 7 0.02
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (269 bp):
TTTTTTTATCTTTCATTTAAAATATTAAATTTTTTAGACTGATTTCAAATGATTATCTTTGGGTT
TGTAAGAAGAACTTCAAATATGGCTGCCACACGCTTGCTGTTACAAGGCACGAGTTTCGGAACCT
CATTTCTTGGGAGAGGAAGCGCCTTCATCGATGGAACAGACATCGAAGACCAATTGGGAACGATA
GGTTTCTAGGGCATCAATGTATTTATCAACACAAATAGGTTTTAACAACAAGTTCAAAAAAACAA
TGAAACTAA
Found at i:141621 original size:17 final size:17
Alignment explanation
Indices: 141575--141640 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 17
141565 ATATATATGG
**
141575 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* **
141592 AGATGCAGCGACAATAA
1 AAATGCAATGACAATAA
*
141609 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
* * *
141626 TAATGTAAGGACAAT
1 AAATGCAATGACAAT
141641 TATACTATAG
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:149130 original size:25 final size:24
Alignment explanation
Indices: 149080--149147 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
149070 GTCTTCCAAA
* *
149080 AATTAAGCTCATACGAGCCCAAATAG
1 AATT-AGCTCTTAAGAG-CCAAATAG
149106 AATTAGCTCTTAAGAGCCAATATAG
1 AATTAGCTCTTAAGAGCCAA-ATAG
* *
149131 -GTTAGCTCTTATGAGCC
1 AATTAGCTCTTAAGAGCC
149148 TAGATAGAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 19 0.51
25 14 0.38
26 4 0.11
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (24 bp):
AATTAGCTCTTAAGAGCCAAATAG
Found at i:149154 original size:24 final size:24
Alignment explanation
Indices: 149108--149154 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
149098 CCAAATAGAA
*
149108 TTAGCTCTTAAGAGCCAATATAGG
1 TTAGCTCTTAAGAGCCAAGATAGG
* *
149132 TTAGCTCTTATGAGCCTAGATAG
1 TTAGCTCTTAAGAGCCAAGATAG
149155 AGTTTAACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (24 bp):
TTAGCTCTTAAGAGCCAAGATAGG
Found at i:151217 original size:31 final size:31
Alignment explanation
Indices: 151145--151230 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
151135 AATGTGTAAT
*
151145 TGTATACATG-AATTTTAA-TTTGATGCAAT
1 TGTATACATGAAATTTTAATTTTGATGCAAA
* * * *
151174 TTTATACGTGAAATTTTAATTTTGGTTCAAA
1 TGTATACATGAAATTTTAATTTTGATGCAAA
* *
151205 TGTATACTTGAAATTTAAATTTTGAT
1 TGTATACATGAAATTTTAATTTTGAT
151231 TTAATCATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
29 8 0.17
30 8 0.17
31 30 0.65
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48
Consensus pattern (31 bp):
TGTATACATGAAATTTTAATTTTGATGCAAA
Found at i:152962 original size:11 final size:11
Alignment explanation
Indices: 152943--152986 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
152933 TTTTTTTAAA
*
152943 TTTAGATTTAT
1 TTTAAATTTAT
*
152954 TTTAAATTTGGT
1 TTTAAATTT-AT
*
152966 TTTAAATTTAA
1 TTTAAATTTAT
152977 TTTAAATTTA
1 TTTAAATTTA
152987 AATTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:152969 original size:17 final size:17
Alignment explanation
Indices: 152927--152962 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
152917 CCGGGTCCCT
*
152927 TTTAAATTT-TTTTAAA
1 TTTAGATTTATTTTAAA
152943 TTTAGATTTATTTTAAA
1 TTTAGATTTATTTTAAA
152960 TTT
1 TTT
152963 GGTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTAGATTTATTTTAAA
Found at i:152980 original size:5 final size:6
Alignment explanation
Indices: 152937--152992 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
152927 TTTAAATTTT
* * ***
152937 TTTAAA TTTAGA TTT-AT TTTAAA TTTGGT TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
152983 TTTAAA TTTA
1 TTTAAA TTTA
152993 TTATAAAGTC
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
5 8 0.21
6 30 0.79
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:152990 original size:12 final size:11
Alignment explanation
Indices: 152941--152992 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
152931 AATTTTTTTA
*
152941 AATTTAGATTT
1 AATTTAAATTT
*
152952 ATTTTAAATTT
1 AATTTAAATTT
**
152963 GGTTTTAAATTT
1 -AATTTAAATTT
152975 AATTTAAATTT
1 AATTTAAATTT
152986 AAATTTA
1 -AATTTA
152993 TTATAAAGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 18 0.53
12 16 0.47
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:153038 original size:14 final size:13
Alignment explanation
Indices: 152998--153044 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
152988 ATTTATTATA
152998 AAGTCC-AATTAC
1 AAGTCCAAATTAC
153010 AAAAGTCCAAATTAC
1 --AAGTCCAAATTAC
*
153025 ATGTCCAAATTTAC
1 AAGTCCAAA-TTAC
153039 AAGTCC
1 AAGTCC
153045 GATTGGGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 8 0.28
14 15 0.52
15 6 0.21
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (13 bp):
AAGTCCAAATTAC
Found at i:153753 original size:3 final size:3
Alignment explanation
Indices: 153650--153742 Score: 89
Period size: 3 Copynumber: 31.0 Consensus size: 3
153640 AATAAGACTT
** *
153650 TAA TAA TAA TAA TGG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * ** *
153698 TAC TAA T-A TCAT TAA TAA TAT TAA TAA CGA CAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
153743 ACATTAATAA
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
2 2 0.03
3 70 0.96
4 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:154793 original size:30 final size:28
Alignment explanation
Indices: 154757--155125 Score: 328
Period size: 29 Copynumber: 13.0 Consensus size: 28
154747 CCCTGGATGT
* *
154757 CCCTAAACTATTCAAAAATTGCATTTTTA
1 CCCTAAACT-TCCAAAAATTCCATTTTTA
154786 CCTCTAAACTTCC-AAAATTCCATTTTTGA
1 CC-CTAAACTTCCAAAAATTCCATTTTT-A
* *
154815 CCCCAAAACTTCCAAAAATTCAATTTTTA
1 -CCCTAAACTTCCAAAAATTCCATTTTTA
*
154844 CCCTCGAACTTCCAAAAATTCCATTTTTGA
1 CCCT-AAACTTCCAAAAATTCCATTTTT-A
154874 ---T---C--CCAAAAATTCCATTTTTA
1 CCCTAAACTTCCAAAAATTCCATTTTTA
* *
154894 CCC-AAACTTCCAAAAATTTCATTATTGA
1 CCCTAAACTTCCAAAAATTCCATT-TTTA
* **
154922 CCTCGAAACTTCCAAAAATTAAATTTTTA
1 CC-CTAAACTTCCAAAAATTCCATTTTTA
** *
154951 CCCCCCAACTTCC-AAAATTCCATTTTGA
1 -CCCTAAACTTCCAAAAATTCCATTTTTA
* *
154979 CCCCAAAACTTCAAAAAATTCCATTTTTA
1 -CCCTAAACTTCCAAAAATTCCATTTTTA
*
155008 CCCTCGAACTTCCAAAAATTCCATTTTTAA
1 CCCT-AAACTTCCAAAAATTCCATTTTT-A
* *
155038 CCTCAAAACTTCTAAAAATTCCATTTTTAA
1 CC-CTAAACTTCCAAAAATTCCATTTTT-A
* *
155068 CCTCAAAACTTCCAAAAATTCAATTTTTA
1 CC-CTAAACTTCCAAAAATTCCATTTTTA
*
155097 CCCTCAAACTTCTAAAAATTCCATTTTTA
1 CCCT-AAACTTCCAAAAATTCCATTTTTA
155126 ACCCCAAAAA
Statistics
Matches: 285, Mismatches: 32, Indels: 46
0.79 0.09 0.13
Matches are distributed among these distances:
20 1 0.00
21 17 0.06
23 1 0.00
25 1 0.00
27 14 0.05
28 47 0.16
29 108 0.38
30 95 0.33
31 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTCCATTTTTA
Found at i:154871 original size:59 final size:59
Alignment explanation
Indices: 154769--155133 Score: 388
Period size: 59 Copynumber: 6.4 Consensus size: 59
154759 CTAAACTATT
*
154769 CAAAAATTGCATTTTTA-CCTCTAAACTTCC-AAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * *
154827 CAAAAATTCAATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTG--------A-TCC
1 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * * *
154877 CAAAAATTCCATTTTTA-CC-CAAACTTCCAAAAATTTCATTATTGACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
** * *
154934 CAAAAATTAAATTTTTACCCCCCAACTTCC-AAAATTCCA-TTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * * *
154991 AAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * *
155050 TAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTCAATTTTT-ACCCTC-AAACTTC
1 CAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTTGACCC-CAAAACTTC
*
155109 TAAAAATTCCATTTTTAACCC-CAAA
1 CAAAAATTCCATTTTT-ACCCTCAAA
155134 AATTCCATTT
Statistics
Matches: 260, Mismatches: 29, Indels: 36
0.80 0.09 0.11
Matches are distributed among these distances:
48 22 0.08
49 2 0.01
50 18 0.07
51 1 0.00
56 1 0.00
57 57 0.22
58 44 0.17
59 90 0.35
60 25 0.10
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
Found at i:154879 original size:21 final size:19
Alignment explanation
Indices: 154855--154899 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 19
154845 CCTCGAACTT
154855 CCAAAAATTCCATTTTTGATC
1 CCAAAAATTCCATTTTT-A-C
154876 CCAAAAATTCCATTTTTAC
1 CCAAAAATTCCATTTTTAC
154895 CCAAA
1 CCAAA
154900 CTTCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 17 0.71
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (19 bp):
CCAAAAATTCCATTTTTAC
Found at i:154948 original size:78 final size:80
Alignment explanation
Indices: 154799--155144 Score: 292
Period size: 89 Copynumber: 4.2 Consensus size: 80
154789 CTAAACTTCC
*
154799 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCAATTTTTACCCTCGAACTTCCAAAAATT
1 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCAATTTTGACCCTCGAACTTCCAAAAATT
**
154864 CCATTTTTGATCCCA
66 AAATTTTTGATCCCA
154879 AAAATTCCATTTTT-A-CCC-AAACTTCCAAAAATTTC-ATTATTGA-CCTCGAAACTTCCAAAA
1 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAA-TTCAATT-TTGACCCTCG-AACTTCCAAAA
*
154939 ATTAAATTTTT-ACCCCCCAA
63 ATTAAATTTTTGA--TCCC-A
* * *
154959 CTTCCAAAATTCCA-TTTTGACCCCAAAACTTCAAAAAATTCCATTTTTACCCTCGAACTTCCAA
1 -----AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCAATTTTGACCCTCGAACTTCCAA
** *
155023 AAATTCCATTTTTAACCTCAAAACTTCTA
61 AAATTAAATTTTTGA--TC----C--C-A
* * * * *
155052 AAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTCAATTTTTACCCTCAAACTTCTAAAAATT
1 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCAATTTTGACCCTCGAACTTCCAAAAATT
** * *
155117 CCATTTTTAACCCCA
66 AAATTTTTGATCCCA
155132 AAAATTCCATTTT
1 AAAATTCCATTTT
155145 ACCCTCGAAC
Statistics
Matches: 225, Mismatches: 17, Indels: 48
0.78 0.06 0.17
Matches are distributed among these distances:
77 22 0.10
78 29 0.13
79 4 0.02
80 29 0.13
81 1 0.00
83 1 0.00
84 4 0.02
85 10 0.04
86 29 0.13
87 25 0.11
88 9 0.04
89 59 0.26
91 1 0.00
93 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (80 bp):
AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCAATTTTGACCCTCGAACTTCCAAAAATT
AAATTTTTGATCCCA
Found at i:155168 original size:49 final size:50
Alignment explanation
Indices: 155079--155173 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 50
155069 CTCAAAACTT
* *
155079 CCAAAAATTCAATTTTTACCCTCAAACTTCTAAAAATTCCATTTTTAACC
1 CCAAAAATTCAATTTTTACCCTCAAACCTCCAAAAATTCCATTTTTAACC
* * *
155129 CCAAAAATTCCA-TTTTACCCTCGAACCTCCAAAATTTCCATTTTT
1 CCAAAAATTCAATTTTTACCCTCAAACCTCCAAAAATTCCATTTTT
155174 GACACCGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 29 0.73
50 11 0.28
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (50 bp):
CCAAAAATTCAATTTTTACCCTCAAACCTCCAAAAATTCCATTTTTAACC
Found at i:155241 original size:58 final size:58
Alignment explanation
Indices: 155130--155262 Score: 130
Period size: 58 Copynumber: 2.3 Consensus size: 58
155120 TTTTTAACCC
** * * *
155130 CAAAAATTCCATTTTACCCTCGAACCTCCAAAATTTCCATTTTTGACACCGAAATTTT
1 CAAAAATTCCATTTTACCCTCGAACCTCCAAAAACTCCATTTTCGACACCGAAACTCT
* * **
155188 CAAAAATTACCATTTTGCCC-CGGATGTCCAAAAACTCCATTTTCGAC-CTCGAAACTCT
1 CAAAAATT-CCATTTTACCCTCGAACCTCCAAAAACTCCATTTTCGACAC-CGAAACTCT
155246 C-AAAATTCTC-TTTTACC
1 CAAAAATTC-CATTTTACC
155263 TCAAATGTCT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
56 7 0.11
57 8 0.13
58 37 0.60
59 10 0.16
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (58 bp):
CAAAAATTCCATTTTACCCTCGAACCTCCAAAAACTCCATTTTCGACACCGAAACTCT
Found at i:156889 original size:22 final size:21
Alignment explanation
Indices: 156848--156890 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
156838 CCTAGAGAAA
*
156848 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
156869 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
156891 GCAGGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Done.