Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013503.1 Kokia drynarioides strain JFW-HI SEQ_128529, 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: 97835
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:4042 original size:33 final size:33
Alignment explanation
Indices: 4000--4067 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
3990 CTGATCTCTT
4000 TTCCTTACAACTTTCATCATGCAATGAAGGTGC
1 TTCCTTACAACTTTCATCATGCAATGAAGGTGC
4033 TTCCTTACAACTTTCATCATGCAATGAAGGTGC
1 TTCCTTACAACTTTCATCATGCAATGAAGGTGC
4066 TT
1 TT
4068 TACTCATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (33 bp):
TTCCTTACAACTTTCATCATGCAATGAAGGTGC
Found at i:6046 original size:23 final size:23
Alignment explanation
Indices: 5924--6045 Score: 138
Period size: 23 Copynumber: 5.2 Consensus size: 23
5914 ACCCTAGCGC
*
5924 GCTCTCCGTTTAGCAC-GTCTCGT
1 GCTCTCCGTTTAGCACTGTGT-GT
5947 GCTCTCCGTTATTAGCACTGTGTGT
1 GCTCTCCG-T-TTAGCACTGTGTGT
* *
5972 GCTCTCCGATTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACTGTGTGT
* * *
5995 GCTCTCCGATTAGTACTTTGTGT
1 GCTCTCCGTTTAGCACTGTGTGT
* *
6018 GCTCTTCTTTTAGCACTGTGTGT
1 GCTCTCCGTTTAGCACTGTGTGT
6041 GCTCT
1 GCTCT
6046 TTGTTGCCCA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 66 0.76
24 1 0.01
25 17 0.20
26 3 0.03
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTCTCCGTTTAGCACTGTGTGT
Found at i:11848 original size:25 final size:23
Alignment explanation
Indices: 11743--11863 Score: 154
Period size: 23 Copynumber: 5.3 Consensus size: 23
11733 TGCTGGGTAA
* *
11743 CGGAGAGCACACAAAGTGTTAAA
1 CGGAGAGCACACAAAGTGCTAAT
* * *
11766 CGAAGAGTACACAAAGTACTAAT
1 CGGAGAGCACACAAAGTGCTAAT
11789 CGGAGAGCACACAAAGTGCTAAT
1 CGGAGAGCACACAAAGTGCTAAT
11812 CGGAGAGCACACACAA-TGCTAAT
1 CGGAGAGCACACA-AAGTGCTAAT
* * *
11835 CGAAGAGCAAACACAGTGCTAAT
1 CGGAGAGCACACAAAGTGCTAAT
11858 CGGAGA
1 CGGAGA
11864 CCGCGCTAAG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
22 1 0.01
23 81 0.96
24 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (23 bp):
CGGAGAGCACACAAAGTGCTAAT
Found at i:13904 original size:20 final size:20
Alignment explanation
Indices: 13865--13918 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
13855 AGTCTTCAAG
* *
13865 GTATCGGTAGAACTATAGTT
1 GTATCGGTAGAAGTAGAGTT
*
13885 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTAGAGTT
*
13905 CTA-CAGGTAGAAGT
1 GTATC-GGTAGAAGT
13919 CTCACTAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (20 bp):
GTATCGGTAGAAGTAGAGTT
Found at i:20309 original size:43 final size:43
Alignment explanation
Indices: 20258--20360 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
20248 AGTCATAGGT
* * * *
20258 TCTTCCATTTACAAATAATCCTATGCTCTTGACGAAACACAAG
1 TCTTCCATTTATAAATAATCCTACGCTCCTCACGAAACACAAG
* * ** *
20301 TCTTCCATTTGTAAATAATCCTACGCTCCTCCCGAGTCATAAG
1 TCTTCCATTTATAAATAATCCTACGCTCCTCACGAAACACAAG
20344 TCTTCCATTTATAAATA
1 TCTTCCATTTATAAATA
20361 TTTTTATGCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (43 bp):
TCTTCCATTTATAAATAATCCTACGCTCCTCACGAAACACAAG
Found at i:20625 original size:21 final size:21
Alignment explanation
Indices: 20584--20626 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
20574 ATCTATCAAA
**
20584 TAAATCATTCAATTTTCTCAT
1 TAAATCATTCAATTTAATCAT
20605 TAAATCATGT-AATTTAATCAT
1 TAAATCAT-TCAATTTAATCAT
20626 T
1 T
20627 TAGTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAATCATTCAATTTAATCAT
Found at i:27212 original size:19 final size:19
Alignment explanation
Indices: 27154--27213 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
27144 AAATTTAAAG
* *
27154 AAATATATAAAAGTAATAA
1 AAATATATAAAAATATTAA
* * *
27173 AAATACATAAATAT-TTTA
1 AAATATATAAAAATATTAA
*
27191 AAATGTATAAAAATATTAA
1 AAATATATAAAAATATTAA
27210 AAAT
1 AAAT
27214 TTACCTTCCT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATATATAAAAATATTAA
Found at i:34427 original size:8 final size:8
Alignment explanation
Indices: 34413--34450 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
34403 TATTTATTTT
34413 ATTTTATA
1 ATTTTATA
*
34421 GTTTTATA
1 ATTTTATA
34429 ATTTTATA
1 ATTTTATA
34437 ATTTTATAA
1 ATTTTAT-A
34446 ATTTT
1 ATTTT
34451 TTTATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
ATTTTATA
Found at i:35513 original size:73 final size:72
Alignment explanation
Indices: 35394--35529 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 72
35384 TTTTCATTAA
* * * * * * *
35394 ATTTGGTAGATTTTTAGTTTGATTTTAGAAACTAATATAAATTAGTATCTAAATGTTAATTTAGC
1 ATTTGGTAGATTTTTAGTTTAATTTGACAAACTAAGACAAAGTAGTATCTAAATATTAATTTAGC
35459 AAAAAAT
66 AAAAAAT
* * *
35466 ATTTGGTAATATTTTTAGTTTAATTTGACAAATTAAGACAAAGTAGTATCTATATATTAATTTA
1 ATTTGGT-AGATTTTTAGTTTAATTTGACAAACTAAGACAAAGTAGTATCTAAATATTAATTTA
35530 AATAATTGCA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
72 7 0.13
73 46 0.87
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (72 bp):
ATTTGGTAGATTTTTAGTTTAATTTGACAAACTAAGACAAAGTAGTATCTAAATATTAATTTAGC
AAAAAAT
Found at i:35565 original size:23 final size:22
Alignment explanation
Indices: 35529--35574 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
35519 ATATTAATTT
* *
35529 AAATAATTGCAATATTTAAATAA
1 AAATAATTGAAATAATT-AATAA
*
35552 AAATAATTTAAATAATTAATAA
1 AAATAATTGAAATAATTAATAA
35574 A
1 A
35575 TTACGGTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATAATTGAAATAATTAATAA
Found at i:36886 original size:6 final size:6
Alignment explanation
Indices: 36875--36904 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
36865 CCCACAATGT
*
36875 GAATAA GAATAA GAATAA GAATAA AAATAA
1 GAATAA GAATAA GAATAA GAATAA GAATAA
36905 AAAGACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (6 bp):
GAATAA
Found at i:39096 original size:19 final size:19
Alignment explanation
Indices: 39072--39118 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
39062 TAGTTTAGCC
39072 TAAAAATTATAAAA-TTAA
1 TAAAAATTATAAAACTTAA
** *
39090 TTAAAAACCATAAAACTTTA
1 -TAAAAATTATAAAACTTAA
39110 TAAAAATTA
1 TAAAAATTA
39119 AATTATGTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATTATAAAACTTAA
Found at i:46346 original size:21 final size:20
Alignment explanation
Indices: 46321--46362 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
46311 TTTCTTATGT
*
46321 AATTATTTAATCTCTTAACAA
1 AATTACTTAATCTCTT-ACAA
*
46342 AATTACTTAATTTCTTACAA
1 AATTACTTAATCTCTTACAA
46362 A
1 A
46363 TTTTGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTACTTAATCTCTTACAA
Found at i:46391 original size:20 final size:20
Alignment explanation
Indices: 46338--46393 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 20
46328 TAATCTCTTA
* *
46338 ACAAAATTACTTAATTTCTT
1 ACAAAAATACTTAATTTCAT
*
46358 AC--AAAT-TTTGAATTTCAT
1 ACAAAAATACTT-AATTTCAT
46376 ACAAAAATACTTAATTTC
1 ACAAAAATACTTAATTTC
46394 TAATAGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
17 2 0.07
18 12 0.43
20 12 0.43
21 2 0.07
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (20 bp):
ACAAAAATACTTAATTTCAT
Found at i:46700 original size:19 final size:20
Alignment explanation
Indices: 46662--46700 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46652 AAATGATTGA
*
46662 ATTGAATCTCTTACACAATT
1 ATTGAATCCCTTACACAATT
46682 ATTGAATCCCTTA-ACAATT
1 ATTGAATCCCTTACACAATT
46701 TTAATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTGAATCCCTTACACAATT
Found at i:46769 original size:20 final size:19
Alignment explanation
Indices: 46745--46833 Score: 65
Period size: 20 Copynumber: 4.5 Consensus size: 19
46735 CTAAACTACT
46745 AAATCTCTTAAACAATTAC
1 AAATCTCTTAAACAATTAC
*
46764 ACAATCTTTTAAAC-ATTAC
1 A-AATCTCTTAAACAATTAC
* *
46783 TTAATTTCTTACAA-AATTAC
1 -AAATCTCTTA-AACAATTAC
* *
46803 TAAATTTCTTAAACTATTATC
1 -AAATCTCTTAAACAATTA-C
*
46824 AAATTTCTTA
1 AAATCTCTTA
46834 CAAAAATACT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
19 15 0.26
20 42 0.72
21 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCTCTTAAACAATTAC
Found at i:49587 original size:36 final size:34
Alignment explanation
Indices: 49547--49662 Score: 92
Period size: 36 Copynumber: 3.3 Consensus size: 34
49537 GAAACATCTG
*
49547 AAGTAATATGCATCCATCGCTCATTGGTATAAACT
1 AAGTAATATGCA-CCAACGCTCATTGGTATAAACT
* * **
49582 AAAGTAATGTATGC-CCAACACTCATTGGAAT-GTCT
1 -AAGTAA--TATGCACCAACGCTCATTGGTATAAACT
* *
49617 GAAGTAATATGCACCCAACGCTTATCGGTATAAATCT
1 -AAGTAATATGCA-CCAACGCTCATTGGTATAAA-CT
49654 AAGTAATAT
1 AAGTAATAT
49663 CCAGCATTCA
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
33 5 0.08
35 21 0.34
36 29 0.47
37 2 0.03
38 5 0.08
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (34 bp):
AAGTAATATGCACCAACGCTCATTGGTATAAACT
Found at i:49618 original size:71 final size:71
Alignment explanation
Indices: 49486--49660 Score: 199
Period size: 71 Copynumber: 2.5 Consensus size: 71
49476 ATTTTTCCAA
** * * * * *
49486 CACCCAACGCTCATCAATACAAATCGAAATAATGTGTGCCTAACACTCATCGAAACATCTGAAGT
1 CACCCAACGCTCATCGGTATAAATCTAAGTAATGTATGCCCAACACTCATCGAAACATCTGAAGT
49551 AATATG
66 AATATG
* * * * * **
49557 CATCCATCGCTCATTGGTATAAA-CTAAAGTAATGTATGCCCAACACTCATTGGAATGTCTGAAG
1 CACCCAACGCTCATCGGTATAAATCT-AAGTAATGTATGCCCAACACTCATCGAAACATCTGAAG
49621 TAATATG
65 TAATATG
*
49628 CACCCAACGCTTATCGGTATAAATCTAAGTAAT
1 CACCCAACGCTCATCGGTATAAATCTAAGTAAT
49661 ATCCAGCATT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
70 1 0.01
71 81 0.96
72 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (71 bp):
CACCCAACGCTCATCGGTATAAATCTAAGTAATGTATGCCCAACACTCATCGAAACATCTGAAGT
AATATG
Found at i:52325 original size:30 final size:31
Alignment explanation
Indices: 52289--52347 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
52279 TAAAAATGTA
*
52289 ATTTTTAAAA-GATTAAATCAAAATTTTATC
1 ATTTTTAAAAGGATCAAATCAAAATTTTATC
* *
52319 ATTTTTAAAAGGATCAAATTATAATTTTA
1 ATTTTTAAAAGGATCAAATCAAAATTTTA
52348 CTTTTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTTTTAAAAGGATCAAATCAAAATTTTATC
Found at i:57444 original size:39 final size:40
Alignment explanation
Indices: 57358--57452 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
57348 ACAAGTCTCT
*
57358 TTCAAAAGGTGTCCATCCAATATGAAAACGTCTGTGACTT
1 TTCAAAAGGTGTCCATCCAATATGAAAACGTCTGTGACTC
* **
57398 TTCAAAAGGTATCCATCCAATATGAAAGGGT-TGTGACTC
1 TTCAAAAGGTGTCCATCCAATATGAAAACGTCTGTGACTC
57437 TTCAAAAGGTGTCCAT
1 TTCAAAAGGTGTCCAT
57453 TGAGTGAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 22 0.44
40 28 0.56
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (40 bp):
TTCAAAAGGTGTCCATCCAATATGAAAACGTCTGTGACTC
Found at i:62383 original size:39 final size:40
Alignment explanation
Indices: 62296--62394 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 40
62286 TGGGACAAGT
62296 CTCTTCTAAAAGGTGTCCATCCAATATGAAAAGGATTGTGA
1 CTCTTC-AAAAGGTGTCCATCCAATATGAAAAGGATTGTGA
* *
62337 CTTTTCAAAAGGTGTCCATCCAATATG-AAAGGGTTGTGA
1 CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGATTGTGA
*
62376 CTCTTCAAAATGTGTCCAT
1 CTCTTCAAAAGGTGTCCAT
62395 TGAGTACATA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 28 0.52
40 21 0.39
41 5 0.09
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (40 bp):
CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGATTGTGA
Found at i:65505 original size:28 final size:28
Alignment explanation
Indices: 65474--65565 Score: 71
Period size: 28 Copynumber: 3.1 Consensus size: 28
65464 TTTTAATGAA
65474 TTTAATTTAATAATTATCTAGATAATAT
1 TTTAATTTAATAATTATCTAGATAATAT
* * *
65502 TTT-A-TTAACTTAATATACTATGAGATATTAAA
1 TTTAATTTAA--TAAT-TA-TCT-AGATAAT-AT
* *
65534 TTTAATATAATATTTATCTAGATAATAT
1 TTTAATTTAATAATTATCTAGATAATAT
65562 TTTA
1 TTTA
65566 TTAATTTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
26 4 0.08
27 1 0.02
28 12 0.25
29 8 0.17
30 4 0.08
31 8 0.17
32 7 0.15
33 1 0.02
34 3 0.06
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (28 bp):
TTTAATTTAATAATTATCTAGATAATAT
Found at i:65576 original size:31 final size:31
Alignment explanation
Indices: 65475--65578 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
65465 TTTAATGAAT
*
65475 TTAATTTAATAATTATCTAGATAATATTTTA
1 TTAATTTAATATTTATCTAGATAATATTTTA
* * **
65506 TTAACTTAATA--TA-CTATGA-GATATTAAA
1 TTAATTTAATATTTATCTA-GATAATATTTTA
*
65534 TTTAATATAATATTTATCTAGATAATATTTTA
1 -TTAATTTAATATTTATCTAGATAATATTTTA
65566 TTAATTTAATATT
1 TTAATTTAATATT
65579 AATGTGATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 9 0.16
29 13 0.23
31 26 0.46
32 9 0.16
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (31 bp):
TTAATTTAATATTTATCTAGATAATATTTTA
Found at i:70239 original size:25 final size:26
Alignment explanation
Indices: 70190--70239 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
70180 CTTCTTATAA
*
70190 TATTTTATAATATATTTTTAGTTTTT
1 TATTTTATAATATATTTTTAATTTTT
70216 TATTTT-TAATA-ATTTTTATATTTT
1 TATTTTATAATATATTTTTA-ATTTT
70240 GAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 9 0.41
26 6 0.27
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TATTTTATAATATATTTTTAATTTTT
Found at i:70279 original size:25 final size:25
Alignment explanation
Indices: 70195--70282 Score: 67
Period size: 25 Copynumber: 3.5 Consensus size: 25
70185 TATAATATTT
*
70195 TATAATATATTTTTAGT-TTTT-TATT
1 TATAATAT-TTTTTA-TATTTTATATA
* *
70220 TTTAATAATTTTTATATTTTGA-A-A
1 TATAATATTTTTTATATTTT-ATATA
* *
70244 AATTATAATTTTTTATATTTTATATA
1 TATAAT-ATTTTTTATATTTTATATA
70270 TATAATATTTTTT
1 TATAATATTTTTT
70283 GCAATTTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
23 1 0.02
24 14 0.29
25 28 0.58
26 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TATAATATTTTTTATATTTTATATA
Found at i:70375 original size:19 final size:19
Alignment explanation
Indices: 70348--70390 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
70338 TTTTTATAAT
70348 TTTTATATAATCTTTATGA
1 TTTTATATAATCTTTATGA
* * *
70367 TTTTCTATATTTTTTATGA
1 TTTTATATAATCTTTATGA
70386 TTTTA
1 TTTTA
70391 AATATAAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTATATAATCTTTATGA
Found at i:72575 original size:40 final size:40
Alignment explanation
Indices: 72530--72901 Score: 239
Period size: 40 Copynumber: 9.4 Consensus size: 40
72520 CCCAAGGTCG
*
72530 GGGTAAGAGATTTGATGATCTTCAATCTGCTCTC-TGGTTA
1 GGGTAAGAGATTGGATGATCTTCAATCTGC-CTCATGGTTA
* * * * * *
72570 AGGTAAAAGATTGAAT--TGCTTTAATCTGCCCCATGGTTG
1 GGGTAAGAGATTGGATGAT-CTTCAATCTGCCTCATGGTTA
* * *
72609 GGGTAAGAGATCGAATGATCTTCAATCTGCTCTC-TAGTTA
1 GGGTAAGAGATTGGATGATCTTCAATCTGC-CTCATGGTTA
* **
72649 GGGTAAAAGATTGGAT--TGCTTCAATCTGCCTCATGGTCG
1 GGGTAAGAGATTGGATGAT-CTTCAATCTGCCTCATGGTTA
* * * *
72688 GGGTAAGAGATCGGATGATCTTCAATTTACCTTATGGTTA
1 GGGTAAGAGATTGGATGATCTTCAATCTGCCTCATGGTTA
* * * * * **
72728 GAGTAAAAGATTGAAT--TGCTTCAATCTGCCCCATAGTCG
1 GGGTAAGAGATTGGATGAT-CTTCAATCTGCCTCATGGTTA
* * * *
72767 GGGTAAGAGATTAGATGGTCTTCAATTTGCCCTC-TAGTTA
1 GGGTAAGAGATTGGATGATCTTCAATCTG-CCTCATGGTTA
* * *
72807 GGATAAAAGATTGGAT--TGCTTCAATCTGCCTCATGG-TC
1 GGGTAAGAGATTGGATGAT-CTTCAATCTGCCTCATGGTTA
* ** * *
72845 GAGGTAAAAGATCAGATGACCTTCAATATGTCCTC-TGGTTA
1 G-GGTAAGAGATTGGATGATCTTCAATCTG-CCTCATGGTTA
*
72886 GGGTAAAAGATTGGAT
1 GGGTAAGAGATTGGAT
72902 TGCTTCAATT
Statistics
Matches: 252, Mismatches: 60, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
38 15 0.06
39 105 0.42
40 118 0.47
41 14 0.06
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (40 bp):
GGGTAAGAGATTGGATGATCTTCAATCTGCCTCATGGTTA
Found at i:72607 original size:39 final size:39
Alignment explanation
Indices: 72549--72915 Score: 220
Period size: 39 Copynumber: 9.3 Consensus size: 39
72539 ATTTGATGAT
*
72549 CTTCAATCTGCTCTC-TGGTTAAGGTAAAAGATTGAATTG
1 CTTCAATCTGC-CTCATGGTTGAGGTAAAAGATTGAATTG
* * * * *
72588 CTTTAATCTGCCCCATGGTTGGGGTAAGAGATCGAA-TG
1 CTTCAATCTGCCTCATGGTTGAGGTAAAAGATTGAATTG
* *
72626 ATCTTCAATCTGCTCTC-TAGTT-AGGGTAAAAGATTGGATTG
1 --CTTCAATCTGC-CTCATGGTTGA-GGTAAAAGATTGAATTG
* * * * *
72667 CTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGA-TG
1 CTTCAATCTGCCTCATGGTTGAGGTAAAAGATTGAATTG
* * *
72705 ATCTTCAATTTACCTTATGGTT-AGAGTAAAAGATTGAATTG
1 --CTTCAATCTGCCTCATGGTTGAG-GTAAAAGATTGAATTG
* * * * * *
72746 CTTCAATCTGCCCCATAGTCGGGGTAAGAGATT-AGATGG
1 CTTCAATCTGCCTCATGGTTGAGGTAAAAGATTGA-ATTG
* * *
72785 TCTTCAATTTGCCCTC-TAGTT-AGGATAAAAGATTGGATTG
1 -CTTCAATCTG-CCTCATGGTTGAGG-TAAAAGATTGAATTG
* *
72825 CTTCAATCTGCCTCATGGTCGAGGTAAAAGA-TCAGA-TG
1 CTTCAATCTGCCTCATGGTTGAGGTAAAAGATTGA-ATTG
* *
72863 ACCTTCAATATGTCCTC-TGGTT-AGGGTAAAAGATTGGATTG
1 --CTTCAATCTG-CCTCATGGTTGA-GGTAAAAGATTGAATTG
*
72904 CTTCAATTTGCC
1 CTTCAATCTGCC
72916 CCATTTCAAC
Statistics
Matches: 249, Mismatches: 52, Indels: 55
0.70 0.15 0.15
Matches are distributed among these distances:
38 19 0.08
39 112 0.45
40 102 0.41
41 16 0.06
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (39 bp):
CTTCAATCTGCCTCATGGTTGAGGTAAAAGATTGAATTG
Found at i:72627 original size:79 final size:79
Alignment explanation
Indices: 72492--72919 Score: 458
Period size: 79 Copynumber: 5.4 Consensus size: 79
72482 TAGTTTTAGG
* * * * *
72492 GGTAAAAGACT-AGATTGTTTCAATCTACCCCAAGGTCGGGGTAAGAGATTTG-ATGATCTTCAA
1 GGTAAAAGATTGA-ATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGA-TCGAATGATCTTCAA
72555 TCTGCTCTCTGGTTAA
64 TCTGCTCTCTGGTTAA
* *
72571 GGTAAAAGATTGAATTGCTTTAATCTGCCCCATGGTTGGGGTAAGAGATCGAATGATCTTCAATC
1 GGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGATCTTCAATC
* *
72636 TGCTCTCTAGTTAG
66 TGCTCTCTGGTTAA
* * * *
72650 GGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGATGATCTTCAATT
1 GGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGATCTTCAATC
* *
72715 TAC-CTTATGGTT-A
66 TGCTC-TCTGGTTAA
* * *
72728 GAGTAAAAGATTGAATTGCTTCAATCTGCCCCATAGTCGGGGTAAGAGAT-TAGATGGTCTTCAA
1 G-GTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGA-ATGATCTTCAA
* * *
72792 TTTGCCCTCTAGTT-A
64 TCTGCTCTCTGGTTAA
* * * * *
72807 GGATAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGAGGTAAAAGATC-AGATGACCTTCAA
1 GG-TAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGA-ATGATCTTCAA
* *
72871 TATG-TCCTCTGGTTAG
64 TCTGCT-CTCTGGTTAA
* *
72887 GGTAAAAGATTGGATTGCTTCAATTTGCCCCAT
1 GGTAAAAGATTGAATTGCTTCAATCTGCCCCAT
72920 TTCAACTTTA
Statistics
Matches: 298, Mismatches: 41, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
78 5 0.02
79 289 0.97
80 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (79 bp):
GGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGAATGATCTTCAATC
TGCTCTCTGGTTAA
Found at i:72789 original size:158 final size:157
Alignment explanation
Indices: 72491--72919 Score: 549
Period size: 158 Copynumber: 2.7 Consensus size: 157
72481 ATAGTTTTAG
* * * * * * **
72491 GGGTAAAAGACTAGATTGTTTCAATCTACCCCAAGGTCGGGGTAAGAGATTTGATGATCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
* * * * *
72556 CTGCTCTCTGGTTA-AGGTAAAAGATTGAATTGCTTTAATCTGCCCCATGGTTGGGGTAAGAGAT
66 TTCCT-TCTGGTTAGA-GTAAAAGATTGAATTGCTTCAATCTGCCCCATAGTCGGGGTAAGAGAT
* *
72620 CGAATGATCTTCAATCTGCTCTCTAGTTA
129 AGAATGATCTTCAATCTGCCCTCTAGTTA
*
72649 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGATGATCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
*
72714 TTACCTTATGGTTAGAGTAAAAGATTGAATTGCTTCAATCTGCCCCATAGTCGGGGTAAGAGATT
66 TT-CCTTCTGGTTAGAGTAAAAGATTGAATTGCTTCAATCTGCCCCATAGTCGGGGTAAGAGA-T
* *
72779 AG-ATGGTCTTCAATTTGCCCTCTAGTTA
129 AGAATGATCTTCAATCTGCCCTCTAGTTA
* * * *
72807 GGATAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGAGGTAAAAGATCAGATGACCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
* * *
72872 ATGTCC-TCTGGTTAGGGTAAAAGATTGGATTGCTTCAATTTGCCCCAT
66 -T-TCCTTCTGGTTAGAGTAAAAGATTGAATTGCTTCAATCTGCCCCAT
72920 TTCAACTTTA
Statistics
Matches: 239, Mismatches: 27, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
158 230 0.96
159 8 0.03
160 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (157 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
TTCCTTCTGGTTAGAGTAAAAGATTGAATTGCTTCAATCTGCCCCATAGTCGGGGTAAGAGATAG
AATGATCTTCAATCTGCCCTCTAGTTA
Found at i:73875 original size:37 final size:37
Alignment explanation
Indices: 73821--73900 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
73811 CCCATCTTTT
*
73821 TTTTATTTGAGCAGCCCTTTACATGTTTTCAACTCAAC
1 TTTT-TTTGAGCAGCCCTTTACAGGTTTTCAACTCAAC
* ***
73859 TTTTTTTGAGCCGCCCTTTGTGGGTTTTCAACTCAAC
1 TTTTTTTGAGCAGCCCTTTACAGGTTTTCAACTCAAC
73896 TTTTT
1 TTTTT
73901 CTTTTTTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 33 0.89
38 4 0.11
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (37 bp):
TTTTTTTGAGCAGCCCTTTACAGGTTTTCAACTCAAC
Found at i:78947 original size:31 final size:31
Alignment explanation
Indices: 78901--78973 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
78891 CGTCTTTCTC
*
78901 AAACTTT-T-AATGCATGAAAATGCAATGCA
1 AAACTTTATGAATGCATGAAAATACAATGCA
* *
78930 AAACTTTATGAATGCATGAAAATACGATGCG
1 AAACTTTATGAATGCATGAAAATACAATGCA
*
78961 AAATTTTATGAAT
1 AAACTTTATGAAT
78974 ACATATGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 7 0.18
30 1 0.03
31 30 0.79
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (31 bp):
AAACTTTATGAATGCATGAAAATACAATGCA
Found at i:79998 original size:11 final size:11
Alignment explanation
Indices: 79982--80009 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
79972 GCACAGAAGT
79982 GAAAACTTGAC
1 GAAAACTTGAC
79993 GAAAACTTGAC
1 GAAAACTTGAC
80004 GAAAAC
1 GAAAAC
80010 ATAGGTACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (11 bp):
GAAAACTTGAC
Found at i:81549 original size:63 final size:63
Alignment explanation
Indices: 81450--81613 Score: 283
Period size: 63 Copynumber: 2.6 Consensus size: 63
81440 TTTGTTATTT
* *
81450 ATTTATTTATCTATATTCATAAAATACTAAATAAATAATAAAACAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
* **
81513 ATTTATTTATTTATATTCATACAATAATAAATAAATAATAAAACAAAATTAATATTATTTTTT
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
81576 ATTTATTTATTTATATTCATAAAATAATAAATAAATAA
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAA
81614 AAATGATAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 95 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (63 bp):
ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
Found at i:82464 original size:3 final size:3
Alignment explanation
Indices: 82450--82481 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
82440 AGTTATGCAA
*
82450 AAG AAT AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
82482 ATGGAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:82529 original size:3 final size:3
Alignment explanation
Indices: 82521--82658 Score: 104
Period size: 3 Copynumber: 46.0 Consensus size: 3
82511 TTATTGTGGG
* * * * *
82521 AGA AGA AGA AGGA GGA GGA GGA GGA AG- AGA AGA AGA TGA AGA AGA
1 AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * *
82566 AGA AGA AGG AGA AGG AGA AGG AGA AGA AGG AGA A-A AGGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA
* * *
82611 AGG AGA AGG AGA A-A GAGA AGG AGA AGCA A-A AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA -AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA
82656 AGA
1 AGA
82659 GAAAAAATGG
Statistics
Matches: 109, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
2 7 0.06
3 95 0.87
4 7 0.06
ACGTcount: A:0.57, C:0.01, G:0.41, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:82576 original size:39 final size:37
Alignment explanation
Indices: 82523--82657 Score: 155
Period size: 39 Copynumber: 3.5 Consensus size: 37
82513 ATTGTGGGAG
* *
82523 AAGAAGAAGGAGGAGGAGGAGGAAGAGAAGAAGATGAA
1 AAGAAGAAGAAGGAGAAGGAGGAAGAGAAGAAGA-GAA
82561 GAAGAAGAAGAAGGAGAAGGA-GAAGGAGAAGAAGGAGAA
1 -AAGAAGAAGAAGGAGAAGGAGGAA-GAGAAGAA-GAGAA
* *
82600 AAGGAAGAAGAAGGAGAAGGAGAAAGAGAAGGAGAAGCAA
1 AA-GAAGAAGAAGGAGAAGGAGGAAGAGAAGAAG-AG-AA
*
82640 AAGAAGAAGAAGAAGAAG
1 AAGAAGAAGAAGGAGAAG
82658 AGAAAAAATG
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
38 6 0.07
39 71 0.84
40 8 0.09
ACGTcount: A:0.57, C:0.01, G:0.41, T:0.01
Consensus pattern (37 bp):
AAGAAGAAGAAGGAGAAGGAGGAAGAGAAGAAGAGAA
Found at i:83043 original size:47 final size:47
Alignment explanation
Indices: 82946--83045 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 47
82936 AATATGGTTT
* * * **
82946 TTGTTGTTTAAATGAAAAACCAACTTATGTGATAATTGGTATTGTTG
1 TTGTTGTTGAAATGAAAAACCAACTTATGTGATAATTAGTACTGGGG
*
82993 TTGTTGTTGAAATGGAAAACCAACTTATGTGACT-ATTAGTACTGGGG
1 TTGTTGTTGAAATGAAAAACCAACTTATGTGA-TAATTAGTACTGGGG
83040 TTGTTG
1 TTGTTG
83046 AAATGGATCG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 45 0.98
48 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (47 bp):
TTGTTGTTGAAATGAAAAACCAACTTATGTGATAATTAGTACTGGGG
Found at i:83133 original size:42 final size:41
Alignment explanation
Indices: 83084--83184 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 41
83074 TTTAAAGGAG
* *
83084 TCTTTGCTTCTTTGAATCGATTGTTTGTTATTTTAAATTGAT
1 TCTTTGCTTCTTT-AATCGATTGTTTATTATTTTAAATCGAT
* * *
83126 TCTTTGCTTATTTCAATTGATTGTTTATTGTTTTAAATCGAT
1 TCTTTGCTTCTTT-AATCGATTGTTTATTATTTTAAATCGAT
83168 TCTTTGCTTCTTTAATC
1 TCTTTGCTTCTTTAATC
83185 TATTCATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 3 0.06
42 48 0.94
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (41 bp):
TCTTTGCTTCTTTAATCGATTGTTTATTATTTTAAATCGAT
Found at i:83181 original size:21 final size:21
Alignment explanation
Indices: 83084--83182 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
83074 TTTAAAGGAG
*
83084 TCTTTGCTTCTTTGAATCGAT
1 TCTTTGCTTCTTTAAATCGAT
* * *
83105 TGTTTG-TTATTTTAAATTGAT
1 TCTTTGCTT-CTTTAAATCGAT
* * *
83126 TCTTTGCTTATTTCAATTGAT
1 TCTTTGCTTCTTTAAATCGAT
* * *
83147 TGTTT-ATTGTTTTAAATCGAT
1 TCTTTGCTT-CTTTAAATCGAT
83168 TCTTTGCTTCTTTAA
1 TCTTTGCTTCTTTAA
83183 TCTATTCATT
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
20 4 0.07
21 51 0.86
22 4 0.07
ACGTcount: A:0.19, C:0.11, G:0.12, T:0.58
Consensus pattern (21 bp):
TCTTTGCTTCTTTAAATCGAT
Found at i:83488 original size:42 final size:42
Alignment explanation
Indices: 83393--83497 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
83383 TGTTTATTTT
* * * * * *
83393 TTTTAAATTGAGTCTTTGCCTCTTTGAAACAATTGTTTGTTG
1 TTTTAAATCGATTCTTTGCTTATTTCAAACAATTATTTGTTG
*
83435 TTTTAAATCGATTCTTTGCTTATTTCAATCAATTATTTGTTG
1 TTTTAAATCGATTCTTTGCTTATTTCAAACAATTATTTGTTG
*
83477 TTTTAAATCGATTTTTTGCTT
1 TTTTAAATCGATTCTTTGCTT
83498 CTTTAATTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.54
Consensus pattern (42 bp):
TTTTAAATCGATTCTTTGCTTATTTCAAACAATTATTTGTTG
Found at i:83538 original size:20 final size:20
Alignment explanation
Indices: 83428--83542 Score: 97
Period size: 21 Copynumber: 5.6 Consensus size: 20
83418 GAAACAATTG
83428 TTTGTTGTTTTAAATCGATTC
1 TTTGTTG-TTTAAATCGATTC
* * * *
83449 TTTGCTTATTTCAATCAATTA
1 TTTG-TTGTTTAAATCGATTC
*
83470 TTTGTTGTTTTAAATCGATTT
1 TTTGTTG-TTTAAATCGATTC
* *
83491 TTTGCTTCTTT-AATTGATTC
1 TTTG-TTGTTTAAATCGATTC
* * *
83511 ATTATTGTTTGAATCGATTC
1 TTTGTTGTTTAAATCGATTC
83531 TTTGTTGTTTAA
1 TTTGTTGTTTAA
83543 CTTGATTCAA
Statistics
Matches: 72, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
19 5 0.07
20 28 0.39
21 35 0.49
22 4 0.06
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.57
Consensus pattern (20 bp):
TTTGTTGTTTAAATCGATTC
Found at i:91033 original size:29 final size:29
Alignment explanation
Indices: 90996--91053 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
90986 GTAATCCCTT
* * * *
90996 TTTTTTTAATTAATTATGTAAATAATTTA
1 TTTTTTTAATCAAATACGAAAATAATTTA
91025 TTTTTTTAATCAAATACGAAAATAATTTA
1 TTTTTTTAATCAAATACGAAAATAATTTA
91054 AAATCTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTTTTTAATCAAATACGAAAATAATTTA
Found at i:92208 original size:28 final size:28
Alignment explanation
Indices: 92173--92229 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
92163 CTAAAGATTT
*
92173 TAAATTATTT-TCGTATTTAATAAAAAAA
1 TAAATTATTTAT-GTAATTAATAAAAAAA
*
92201 TAAATTATTTATGTAATTAATTAAAAAA
1 TAAATTATTTATGTAATTAATAAAAAAA
92229 T
1 T
92230 TTACTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (28 bp):
TAAATTATTTATGTAATTAATAAAAAAA
Found at i:92845 original size:4 final size:4
Alignment explanation
Indices: 92831--92916 Score: 68
Period size: 4 Copynumber: 21.2 Consensus size: 4
92821 AAATAAACGG
* * *
92831 GAAA TAAA GAAA GAAAA GAAG GAAA GAAA GAAA GAAT GAGAA GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * * *
92881 G-AA GAAT GAGAG GAAA GAAA G-AA TAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
92917 GTAATGTGTT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
3 5 0.08
4 49 0.77
5 10 0.16
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (4 bp):
GAAA
Found at i:92855 original size:21 final size:22
Alignment explanation
Indices: 92830--92903 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
92820 CAAATAAACG
*
92830 GGAAATAAAGAAAGAA-AAGAA
1 GGAAAGAAAGAAAGAATAAGAA
*
92851 GGAAAGAAAGAAAGAATGAGAA
1 GGAAAGAAAGAAAGAATAAGAA
*
92873 -GAAAGAAAG-AAGAATGAG-A
1 GGAAAGAAAGAAAGAATAAGAA
92892 GGAAAGAAAGAA
1 GGAAAGAAAGAA
92904 TAAGGAAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.38
21 25 0.52
22 4 0.08
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (22 bp):
GGAAAGAAAGAAAGAATAAGAA
Found at i:92858 original size:17 final size:20
Alignment explanation
Indices: 92836--92903 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
92826 AACGGGAAAT
92836 AAAGAAAGAA-AA-GA-AGG
1 AAAGAAAGAAGAATGAGAGG
*
92853 AAAGAAAGAAAGAATGAGAAG
1 AAAGAAAG-AAGAATGAGAGG
92874 AAAGAAAGAAGAATGAGAGG
1 AAAGAAAGAAGAATGAGAGG
92894 AAAGAAAGAA
1 AAAGAAAGAA
92904 TAAGGAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
17 8 0.18
18 2 0.04
19 2 0.04
20 23 0.51
21 10 0.22
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (20 bp):
AAAGAAAGAAGAATGAGAGG
Found at i:92887 original size:20 final size:19
Alignment explanation
Indices: 92831--92916 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 19
92821 AAATAAACGG
*
92831 GAAATAAAGAAAGAA-AA-
1 GAAAGAAAGAAAGAAGAAT
*
92848 GAAGGAAAGAAAGAAAGAAT
1 GAAAGAAAGAAAG-AAGAAT
92868 GAGAAGAAAGAAAGAAGAAT
1 GA-AAGAAAGAAAGAAGAAT
* * *
92888 GAGAGGAAAGAAAGAATAAG
1 GA-AAGAAAGAAAGAAGAAT
92908 GAAAGAAAG
1 GAAAGAAAG
92917 GTAATGTGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
17 11 0.19
18 2 0.03
19 8 0.14
20 27 0.47
21 10 0.17
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (19 bp):
GAAAGAAAGAAAGAAGAAT
Found at i:96160 original size:45 final size:44
Alignment explanation
Indices: 96042--96177 Score: 182
Period size: 45 Copynumber: 3.0 Consensus size: 44
96032 AGGAGGAATA
* * * * **
96042 GAGTATCGCGATGGCTCGTCAAACTCAGCCTGATATCCTTCCCTT
1 GAGTATTGCG-TGGCTCATCAAACTGAGGCTGATATCCTTGGCTT
* *
96087 GAGTATTGCGTGGCTCATCAAATTGAGGCTAATATCCTTGGCTT
1 GAGTATTGCGTGGCTCATCAAACTGAGGCTGATATCCTTGGCTT
96131 GAGTATTGCAGTGGCTCATCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGC-GTGGCTCATCAAACTGAGGCTGATATCCTTGGCTT
96176 GA
1 GA
96178 TGAGCTATGC
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 36 0.45
45 44 0.55
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (44 bp):
GAGTATTGCGTGGCTCATCAAACTGAGGCTGATATCCTTGGCTT
Done.