Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014767.1 Kokia drynarioides strain JFW-HI SEQ_129807, 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: 313945
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 871 characters in sequence are not A, C, G, or T
Found at i:1638 original size:72 final size:72
Alignment explanation
Indices: 1548--1817 Score: 319
Period size: 72 Copynumber: 3.8 Consensus size: 72
1538 TTATTTGGAC
* *
1548 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAGCAC
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTAGGCAATATGAGTCGACTTAGCAC
*
1613 TTTTTAT
66 TTTTGAT
* * * * * *
1620 GCATCTTATAACAATTTGAGTGGTCCAATTCCAAATTGGTTATGCCATATGAGTGGACTAAACAC
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTAGGCAATATGAGTCGACTTAGCAC
1685 TTTTGAT
66 TTTTGAT
** * *
1692 GTTTCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTT-GGACAATATGAGTCGAC-TAGAC
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTAGG-CAATATGAGTCGACTTAG-C
*
1755 AATTTTGAT
64 ACTTTTGAT
** * ** * *
1764 GTTTCTTATAATAAAATGAGTGGCCCAATTCCAAATTGTTTGGGCAATATGAGT
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTAGGCAATATGAGT
1818 GCTCTGAGGT
Statistics
Matches: 174, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
71 2 0.01
72 170 0.98
73 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (72 bp):
GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTAGGCAATATGAGTCGACTTAGCAC
TTTTGAT
Found at i:1814 original size:144 final size:144
Alignment explanation
Indices: 1551--1818 Score: 360
Period size: 144 Copynumber: 1.9 Consensus size: 144
1541 TTTGGACGCA
* * *
1551 TCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAGCACTTT
1 TCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCAATTT
* ** * * *
1616 TTATGCATCTTATAACAATTTGAGTGGTCCAATTCCAAATTGGTTATGCCATATGAGTGGACTAA
66 TGATGCATCTTATAACAAAATGAGTGGCCCAATTCCAAATTGGTTAGGCAATATGAGTGGACTAA
1681 ACACTTTTGATGTT
131 ACACTTTTGATGTT
* *
1695 TCTTATAATAATTTGAGTGGCCCAATTCCAAATTGCTT-GGACAATATGAGTCGAC-TAGACAAT
1 TCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACTTAG-CAAT
** * * *
1758 TTTGATGTTTCTTATAATAAAATGAGTGGCCCAATTCCAAATTGTTTGGGCAATATGAGTG
64 TTTGATGCATCTTATAACAAAATGAGTGGCCCAATTCCAAATTGGTTAGGCAATATGAGTG
1819 CTCTGAGGTT
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
143 4 0.04
144 102 0.96
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (144 bp):
TCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCAATTT
TGATGCATCTTATAACAAAATGAGTGGCCCAATTCCAAATTGGTTAGGCAATATGAGTGGACTAA
ACACTTTTGATGTT
Found at i:3473 original size:20 final size:21
Alignment explanation
Indices: 3439--3518 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 21
3429 AATTTTTAAA
*
3439 AAATATAAGTTTTGAAATTTTT
1 AAATATTA-TTTTGAAATTTTT
3461 ATAA-A-TATTTTG-AA-TTTT
1 A-AATATTATTTTGAAATTTTT
*
3479 AAATATTATTTTGAAATTTTG
1 AAATATTATTTTGAAATTTTT
*
3500 AAA-ATTATTTT-AATTTTTT
1 AAATATTATTTTGAAATTTTT
3519 TGTAATTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
17 2 0.04
18 6 0.12
19 15 0.31
20 15 0.31
21 7 0.14
22 2 0.04
23 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (21 bp):
AAATATTATTTTGAAATTTTT
Found at i:3478 original size:19 final size:20
Alignment explanation
Indices: 3448--3510 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
3438 AAAATATAAG
3448 TTTTGAAATTTTTATAAA-TA
1 TTTTGAAATTTTTA-AAATTA
3468 TTTTG-AA-TTTTAAATATTA
1 TTTTGAAATTTTTAAA-ATTA
*
3487 TTTTGAAATTTTGAAAATTA
1 TTTTGAAATTTTTAAAATTA
3507 TTTT
1 TTTT
3511 AATTTTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 2 0.05
18 6 0.16
19 9 0.24
20 15 0.39
21 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTTGAAATTTTTAAAATTA
Found at i:3493 original size:39 final size:39
Alignment explanation
Indices: 3439--3516 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
3429 AATTTTTAAA
*
3439 AAATATAAGTTTTGAAATTTTTATAAA-TATTTTGAATTTT
1 AAATATAAGTTTTGAAATTTTGA-AAATTATTTT-AATTTT
*
3479 AAATATTA-TTTTGAAATTTTGAAAATTATTTTAATTTT
1 AAATATAAGTTTTGAAATTTTGAAAATTATTTTAATTTT
3517 TTTGTAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 9 0.26
39 19 0.54
40 7 0.20
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (39 bp):
AAATATAAGTTTTGAAATTTTGAAAATTATTTTAATTTT
Found at i:3647 original size:28 final size:28
Alignment explanation
Indices: 3603--3656 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
3593 AAATCTTTTT
*
3603 AATAATATAAAACATAAGA-AATATTAAA
1 AATAATATAAAAAATAA-ATAATATTAAA
3631 AATAA-ATAAATAAATAAATAATATTA
1 AATAATATAAA-AAATAAATAATATTA
3657 TAGAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (28 bp):
AATAATATAAAAAATAAATAATATTAAA
Found at i:7338 original size:2 final size:2
Alignment explanation
Indices: 7331--7366 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7321 NNNNNNNNNN
7331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7367 CCATATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10394 original size:12 final size:12
Alignment explanation
Indices: 10377--10402 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10367 TTTGAAAAAT
10377 ATAAAAATATTA
1 ATAAAAATATTA
10389 ATAAAAATATTA
1 ATAAAAATATTA
10401 AT
1 AT
10403 TAATTATATA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAAAAATATTA
Found at i:11280 original size:30 final size:31
Alignment explanation
Indices: 11244--11314 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
11234 ACCAACATTT
11244 ACTCAACTTTAACCTCAAAG-AAAAATAGTC
1 ACTCAACTTTAACCTCAAAGAAAAAATAGTC
* * *
11274 ACTCAACTTTGACTTCAATGAAAAAATAGTC
1 ACTCAACTTTAACCTCAAAGAAAAAATAGTC
*
11305 ACTTAACTTT
1 ACTCAACTTT
11315 CAAAAACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 17 0.47
31 19 0.53
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (31 bp):
ACTCAACTTTAACCTCAAAGAAAAAATAGTC
Found at i:12584 original size:28 final size:29
Alignment explanation
Indices: 12521--12586 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
12511 ATGTTAATTC
*
12521 GTGACTGATTTATCATTTTTTGATAACGTTA
1 GTGACTGATTTAT-ATTTTTT-ATAAAGTTA
*
12552 ATGACTGATTTAT-TTTTTT-TAAAGTTGA
1 GTGACTGATTTATATTTTTTATAAAGTT-A
12580 GTGACTG
1 GTGACTG
12587 TGTTGTCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 6 0.19
28 7 0.23
29 6 0.19
31 12 0.39
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (29 bp):
GTGACTGATTTATATTTTTTATAAAGTTA
Found at i:12919 original size:15 final size:17
Alignment explanation
Indices: 12889--12930 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
12879 TAGTAAAAAT
12889 ATAATTTTATTATTTTA
1 ATAATTTTATTATTTTA
*
12906 ATAA-TTTA-TATTTTT
1 ATAATTTTATTATTTTA
12921 ATAAATTTTA
1 AT-AATTTTA
12931 AATAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTTATTATTTTA
Found at i:12927 original size:16 final size:17
Alignment explanation
Indices: 12888--12928 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
12878 ATAGTAAAAA
*
12888 TATAATTTTATTATTTT
1 TATAAATTTATTATTTT
*
12905 AAT-AATTTA-TATTTT
1 TATAAATTTATTATTTT
12920 TATAAATTT
1 TATAAATTT
12929 TAAATAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 8 0.40
16 10 0.50
17 2 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAAATTTATTATTTT
Found at i:13487 original size:17 final size:16
Alignment explanation
Indices: 13465--13506 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
13455 AGCTATTAAG
13465 TTTTTTTATAT-AAAGT
1 TTTTTTTAT-TCAAAGT
13481 TTTTTTTATTCGAAAGT
1 TTTTTTTATTC-AAAGT
13498 TTTTTTTAT
1 TTTTTTTAT
13507 CCATGATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.04
16 9 0.38
17 14 0.58
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTTTTATTCAAAGT
Found at i:14435 original size:34 final size:34
Alignment explanation
Indices: 14387--14469 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
14377 ACAAAAGTCC
*
14387 AATTAAACAATATTTGAATAAGGTAAAAGGTAAAA
1 AATTAAA-AATATTTGAATAAGATAAAAGGTAAAA
**
14422 AATTAAAAATATTTGGGTAAGATAAAAGGTAAAA
1 AATTAAAAATATTTGAATAAGATAAAAGGTAAAA
14456 AATTAAAAATATTT
1 AATTAAAAATATTT
14470 AGGTTTAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 38 0.84
35 7 0.16
ACGTcount: A:0.57, C:0.01, G:0.13, T:0.29
Consensus pattern (34 bp):
AATTAAAAATATTTGAATAAGATAAAAGGTAAAA
Found at i:16335 original size:31 final size:32
Alignment explanation
Indices: 16277--16350 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 32
16267 TTACAATATG
*
16277 ATCACTGAACTATTTGAAAGTTTTTTATTTAA
1 ATCACTGAACTATTCGAAAGTTTTTTATTTAA
* * *
16309 TTCATTGAATTATTCGAAA-TTTTTTATTTAA
1 ATCACTGAACTATTCGAAAGTTTTTTATTTAA
16340 ATCACTGAACT
1 ATCACTGAACT
16351 GATAAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 20 0.57
32 15 0.43
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (32 bp):
ATCACTGAACTATTCGAAAGTTTTTTATTTAA
Found at i:29455 original size:5 final size:5
Alignment explanation
Indices: 29445--29478 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
29435 ATGGAAACAG
*
29445 ATAAT ATAAT ATAAT ATAAT ATAAAT ATATT ATA
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATA
29479 TTAATAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:30652 original size:233 final size:233
Alignment explanation
Indices: 30239--30706 Score: 891
Period size: 233 Copynumber: 2.0 Consensus size: 233
30229 ACATTAATTC
30239 AACCAGGAGCTTAAATAATAGTATAAACATACAATTGATGGAAATAATCAAATATGCATAATAAA
1 AACCAGGAGCTTAAATAATAGTATAAACATACAATTGATGGAAATAATCAAATATGCATAATAAA
*
30304 ATTAAAATATATAAAAAATCTAAATGAAGCTTTAGATGTGCAGTAAGTTAAAAGTTTTATTAATA
66 ATTAAAATATATAAAAAATCTAAATGAAGCTTTAGATGTGCAGTAAGTTAAAAGTTTTACTAATA
30369 CAATTTGTTCGGGTTCATATCCCACCATATGTATATTTTTATTAATTTTTTTAAATAAAAATATT
131 CAATTTGTTCGGGTTCATATCCCACCATATGTATATTTTTATTAATTTTTTTAAATAAAAATATT
30434 AAGATACCATCGAATAATTTAACTTATTTTAATTAAGA
196 AAGATACCATCGAATAATTTAACTTATTTTAATTAAGA
*
30472 AACCAGGAGCTTAAATAATAGTATAAACATACAATTGATGGAAATAATCAAATATGCATAATATA
1 AACCAGGAGCTTAAATAATAGTATAAACATACAATTGATGGAAATAATCAAATATGCATAATAAA
*
30537 ATTAAAATGTATAAAAAATCTAAATGAAGCTTTAGATGTGCAGTAAGTTAAAAGTTTTACTAATA
66 ATTAAAATATATAAAAAATCTAAATGAAGCTTTAGATGTGCAGTAAGTTAAAAGTTTTACTAATA
*
30602 CAATTTGTTCGGGTTCATATCCCACCATATGTATATTTTTATTGATTTTTTTAAATAAAAATATT
131 CAATTTGTTCGGGTTCATATCCCACCATATGTATATTTTTATTAATTTTTTTAAATAAAAATATT
*
30667 AAGATACCATCGAATAATTTAACTTATTTTGATTAAGA
196 AAGATACCATCGAATAATTTAACTTATTTTAATTAAGA
30705 AA
1 AA
30707 AAATATTTTC
Statistics
Matches: 230, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
233 230 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.36
Consensus pattern (233 bp):
AACCAGGAGCTTAAATAATAGTATAAACATACAATTGATGGAAATAATCAAATATGCATAATAAA
ATTAAAATATATAAAAAATCTAAATGAAGCTTTAGATGTGCAGTAAGTTAAAAGTTTTACTAATA
CAATTTGTTCGGGTTCATATCCCACCATATGTATATTTTTATTAATTTTTTTAAATAAAAATATT
AAGATACCATCGAATAATTTAACTTATTTTAATTAAGA
Found at i:36245 original size:11 final size:11
Alignment explanation
Indices: 36231--36325 Score: 57
Period size: 11 Copynumber: 8.7 Consensus size: 11
36221 ATATTCCAAC
*
36231 AATAACAATAA
1 AATAATAATAA
36242 AATAATAATAA
1 AATAATAATAA
* *
36253 CATAATAATGA
1 AATAATAATAA
* *
36264 AATGATAACAA
1 AATAATAATAA
** * *
36275 AATAACGAGAG
1 AATAATAATAA
* *
36286 AACAAAAATAA
1 AATAATAATAA
* *
36297 AATAACAACAA
1 AATAATAATAA
*
36308 AACAATAA-AA
1 AATAATAATAA
36318 AATAATAA
1 AATAATAA
36326 CATTTTTTTT
Statistics
Matches: 61, Mismatches: 23, Indels: 1
0.72 0.27 0.01
Matches are distributed among these distances:
10 9 0.15
11 52 0.85
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.17
Consensus pattern (11 bp):
AATAATAATAA
Found at i:47591 original size:24 final size:24
Alignment explanation
Indices: 47563--47613 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
47553 AAAAATAATT
* * *
47563 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTCAGTTG
*
47587 TTTCAATTAGACTCTGTTCAGTTG
1 TTTCAATTAAACTCTGTTCAGTTG
47611 TTT
1 TTT
47614 GAGTCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTCAGTTG
Found at i:49573 original size:24 final size:24
Alignment explanation
Indices: 49545--49595 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
49535 AGAAATAATC
* *
49545 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
49569 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
49593 TTT
1 TTT
49596 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:49797 original size:29 final size:29
Alignment explanation
Indices: 49760--49824 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
49750 ACGTTTTGAG
*
49760 AGTTCTTTATTTTTTGGTTTTTGGGGTTT
1 AGTTTTTTATTTTTTGGTTTTTGGGGTTT
49789 AGTTTTTTATTTTTTGGTTTTTGGGGTTT
1 AGTTTTTTATTTTTTGGTTTTTGGGGTTT
49818 AGTTTTT
1 AGTTTTT
49825 ATCTTCATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.08, C:0.02, G:0.23, T:0.68
Consensus pattern (29 bp):
AGTTTTTTATTTTTTGGTTTTTGGGGTTT
Found at i:66574 original size:20 final size:19
Alignment explanation
Indices: 66536--66597 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
66526 AAACTTTAAA
*
66536 AAATAATTTTTATATTTTT
1 AAATAATTTTAATATTTTT
66555 AAATAATTTTAATGATTTTT
1 AAATAATTTTAAT-ATTTTT
*
66575 AATGTAATTTTGAAT-TTTTT
1 AA-ATAATTTT-AATATTTTT
66595 AAA
1 AAA
66598 ATTTAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 12 0.32
20 15 0.41
21 7 0.19
22 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
AAATAATTTTAATATTTTT
Found at i:75990 original size:17 final size:16
Alignment explanation
Indices: 75970--76003 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
75960 AAAATTTCAT
*
75970 AATTAATTTTTAAATTA
1 AATTAATATTT-AATTA
75987 AATTAATATTTAATTA
1 AATTAATATTTAATTA
76003 A
1 A
76004 CTAATAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAATATTTAATTA
Found at i:84616 original size:42 final size:43
Alignment explanation
Indices: 84546--84631 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
84536 GGGTGGTGGT
* * *
84546 GCGGTAGGTGGTGCAGGAGGACTGGCTCTAATTGGGGCAGGAG
1 GCGGTAGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGGAG
*
84589 GCGGT-GGTGGTGGAGGAGAACTAGCTCTAATCGGGGCAGGAG
1 GCGGTAGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGGAG
84631 G
1 G
84632 TTCTGGAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 34 0.87
43 5 0.13
ACGTcount: A:0.20, C:0.14, G:0.49, T:0.17
Consensus pattern (43 bp):
GCGGTAGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGGAG
Found at i:90675 original size:53 final size:52
Alignment explanation
Indices: 90598--90706 Score: 121
Period size: 53 Copynumber: 2.1 Consensus size: 52
90588 TATAGTCCCT
* * * * * *
90598 TTAAAATAATAAATTTTTAATTTAAACCTT-TTATAATTTATAAAATTTTAAA
1 TTAAAATAATAAAATTATAATTT-AACCTTCTCAAAAATTATAAAAATTTAAA
* *
90650 TTAATAATAATAAAATTATATTTTAACCTTCTCAAAAATTATAAAAATTTAAT
1 TTAA-AATAATAAAATTATAATTTAACCTTCTCAAAAATTATAAAAATTTAAA
90703 TTAA
1 TTAA
90707 CATTTTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
52 10 0.21
53 37 0.79
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.45
Consensus pattern (52 bp):
TTAAAATAATAAAATTATAATTTAACCTTCTCAAAAATTATAAAAATTTAAA
Found at i:90706 original size:31 final size:31
Alignment explanation
Indices: 90655--90724 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
90645 TTAAATTAAT
* *
90655 AATAAT-AAAATTATATTTTAACCTTCTCAAA
1 AATAATAAAAATTATAATTTAACATT-TCAAA
* *
90686 AATTATAAAAATT-TAATTTAACATTTTAAA
1 AATAATAAAAATTATAATTTAACATTTCAAA
90716 AATAATAAA
1 AATAATAAA
90725 GTTGTACACT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 12 0.36
31 15 0.45
32 6 0.18
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (31 bp):
AATAATAAAAATTATAATTTAACATTTCAAA
Found at i:99828 original size:17 final size:17
Alignment explanation
Indices: 99774--99828 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
99764 CCCTTTACTT
* *
99774 TTAACCTTCCATCTTCT
1 TTAACCTTTCATCTTCC
*
99791 TTAACCTTTC-T-TGACC
1 TTAACCTTTCATCT-TCC
99807 TTTAACCTTTCATCTTCC
1 -TTAACCTTTCATCTTCC
99825 TTAA
1 TTAA
99829 TTTTTCATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 1 0.03
16 2 0.07
17 23 0.77
18 3 0.10
19 1 0.03
ACGTcount: A:0.20, C:0.31, G:0.02, T:0.47
Consensus pattern (17 bp):
TTAACCTTTCATCTTCC
Found at i:102870 original size:25 final size:25
Alignment explanation
Indices: 102830--102888 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
102820 CAAATCTAAC
*
102830 TTTT-AATTTTTAAATTTTAATTTA
1 TTTTAAATTTTTAAATTTAAATTTA
*
102854 TTTTAAATTTTTGAATTTAAATTTA
1 TTTTAAATTTTTAAATTTAAATTTA
102879 TTTTAAATTT
1 TTTTAAATTT
102889 GAATTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTAAATTTTTAAATTTAAATTTA
Found at i:102882 original size:17 final size:17
Alignment explanation
Indices: 102862--102914 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
102852 TATTTTAAAT
102862 TTTTGAATTTAAATTTA
1 TTTTGAATTTAAATTTA
* *
102879 TTTTAAATTTGAATTTA
1 TTTTGAATTTAAATTTA
* *
102896 TTTTGAATTAAAAATTA
1 TTTTGAATTTAAATTTA
102913 TT
1 TT
102915 AATATTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTTGAATTTAAATTTA
Found at i:103588 original size:3 final size:3
Alignment explanation
Indices: 103580--103666 Score: 52
Period size: 3 Copynumber: 29.0 Consensus size: 3
103570 TTAAAACGTC
** * * * * *
103580 AAT AAT AAT AAT AAT TGT AAT AAT AAGT AAT ATT AAA AAC AGT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
** *
103626 AAT AAT AAT TTT TA- AAT AAT AAT AAT AATT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
103667 CGAAGAGCCA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
2 3 0.05
3 55 0.86
4 6 0.09
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:104839 original size:30 final size:29
Alignment explanation
Indices: 104786--105113 Score: 310
Period size: 29 Copynumber: 11.2 Consensus size: 29
104776 GGAGGTCCCT
** *
104786 AAACTGTCCAAAAATTATATTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCTCG
* *
104816 AAACTTCCAAAAATTCTATTTTTGACATCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
104846 AAACTTCCAAAAATTCCATTTTTACCACCG
1 AAACTTCCAAAAATTCCATTTTTACC-TCG
*
104876 -AACTTCCAAAAATTCCATTTTTGACC-CC
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
104904 AAATTTCCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* *
104933 AAACTTTC-GAAATTCCATTTTTTACCTCG
1 AAACTTCCAAAAATTCCA-TTTTTACCTCG
*
104962 AAATTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* *
104992 -AACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* * *
105020 AAACCTCCAAAATTTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* * *
105050 AAACTTTCAAAAATTACCATTTTTCCCCCG
1 AAACTTCCAAAAATT-CCATTTTTACCTCG
* * *
105080 -GA-TGTCCAAAAACTCCATTTTCAACCTCG
1 AAACT-TCCAAAAATTCCATTTT-TACCTCG
105109 AAACT
1 AAACT
105114 CTCAAAATTA
Statistics
Matches: 247, Mismatches: 34, Indels: 33
0.79 0.11 0.11
Matches are distributed among these distances:
28 25 0.10
29 142 0.57
30 71 0.29
31 9 0.04
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:104997 original size:116 final size:118
Alignment explanation
Indices: 104782--105073 Score: 382
Period size: 116 Copynumber: 2.5 Consensus size: 118
104772 CCCTGGAGGT
* * * *
104782 CCCTAAACTGTCCAAAAATT--ATATTTTGACCTCGAAACTTCCAAAAATTCTATTTTTGACATC
1 CCCTAAAC-CTCCAAAAATTCCAT-TTTTGACCTCAAAACTTTCAAAAATTCCATTTTTGACATC
104845 GAAACTTCCAAAAATTCCATTTTTACCACCGAACTTCCAAAAATTCCATTTTTGAC
64 GAAACTTCCAAAAATTCCATTTTTACCACCGAACTTCCAAAAATTCCATTTTT-AC
** * * *
104901 CCC-AAATTTCCAAAAATTCCATTTTT-ACCCTC-AAACTTTC-GAAATTCCATTTTTTACCTCG
1 CCCTAAACCTCCAAAAATTCCATTTTTGA-CCTCAAAACTTTCAAAAATTCCATTTTTGACATCG
*
104962 AAATTTCCAAAAATTCCATTTTTACC-CTCGAACTTCCAAAAATTCCATTTTTAC
65 AAACTTCCAAAAATTCCATTTTTACCAC-CGAACTTCCAAAAATTCCATTTTTAC
*
105016 CCCTAAACCTCCAAAATTTCCATTTTTGACCTCAAAACTTTCAAAAATTACCATTTTT
1 CCCTAAACCTCCAAAAATTCCATTTTTGACCTCAAAACTTTCAAAAATT-CCATTTTT
105074 CCCCCGGATG
Statistics
Matches: 152, Mismatches: 12, Indels: 18
0.84 0.07 0.10
Matches are distributed among these distances:
115 6 0.04
116 90 0.59
117 27 0.18
118 16 0.11
119 13 0.09
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (118 bp):
CCCTAAACCTCCAAAAATTCCATTTTTGACCTCAAAACTTTCAAAAATTCCATTTTTGACATCGA
AACTTCCAAAAATTCCATTTTTACCACCGAACTTCCAAAAATTCCATTTTTAC
Found at i:105209 original size:27 final size:27
Alignment explanation
Indices: 105177--105230 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
105167 AACTTTCTCG
105177 AAATTACCATTTTGCCCCCGAGAATCC
1 AAATTACCATTTTGCCCCCGAGAATCC
*
105204 AAATTACCATTTTGCCCCCGAGTATCC
1 AAATTACCATTTTGCCCCCGAGAATCC
105231 GAAAAGTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (27 bp):
AAATTACCATTTTGCCCCCGAGAATCC
Found at i:107698 original size:28 final size:28
Alignment explanation
Indices: 107663--107720 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
107653 ACTATCCATG
*
107663 AAACTATAAATATATACTAAAAACTTAT
1 AAACTATAAATACATACTAAAAACTTAT
*
107691 AAACTATAAATACATATTAAAAACTTAT
1 AAACTATAAATACATACTAAAAACTTAT
107719 AA
1 AA
107721 TAAAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (28 bp):
AAACTATAAATACATACTAAAAACTTAT
Found at i:111170 original size:14 final size:14
Alignment explanation
Indices: 111151--111180 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
111141 ATGTGATTTG
*
111151 AATAAAAATATTAA
1 AATAAAAATAATAA
111165 AATAAAAATAATAA
1 AATAAAAATAATAA
111179 AA
1 AA
111181 AATAGAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAAAATAATAA
Found at i:113796 original size:228 final size:229
Alignment explanation
Indices: 113312--113879 Score: 910
Period size: 228 Copynumber: 2.5 Consensus size: 229
113302 GTAGTGATAC
* * *
113312 AACACATGCACAAAGATGCTTTG-AATATTAATAACTAAGAAAGGCACATCCATGAGAACTCGA-
1 AACACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCGAC
113375 ATGAGACTGTGGACGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGCAAGCTTC
66 A--AGACTGTGGACGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGCAAGCTTC
* * *
113440 ACTACTGTGCCAAAATGTAAATCAAAATCTAACTATTTAGGAGCTTAAATTCTGGATAATGATAA
129 ACCACTATGCCAAAATGTAAATC-AAATCTAACTATTTAGGAGCTTAAATTCTAGATAATGATAA
** *
113505 ACTCAATTGCGAACCATCGGGGATCTCCGTATCATTA
193 ACTCAATTGCGAACCATCAAGGATCTCCATATCATTA
* *
113542 AACACATGCACAGAGATGCTTTGAAATATTGATAACTAAGAAAGACACATGCATG-GTGACTCGA
1 AACACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAG-GACTCGA
*
113606 CAAGACTGTGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGCAAGCTTCA
65 CAAGACTGTGGACGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGCAAGCTTCA
* *
113671 CCACTATGCCAAAATGTAAATC-AATCTAACTATTTAGGAGCTTAAGTTCTATATAATGATAAAC
130 CCACTATGCCAAAATGTAAATCAAATCTAACTATTTAGGAGCTTAAATTCTAGATAATGATAAAC
*
113735 TCAATTGCGAACCATCAAGTATCTCCATATCATTA
195 TCAATTGCGAACCATCAAGGATCTCCATATCATTA
113770 AACACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCGAA
1 AACACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCG-A
* *
113835 CAAGACTTTGGACGGCCAAAACAAATTATATAAAGCTAGAAGAGA
65 CAAGACTGTGGACGGCCAAAACAAATGATATAAAGCTAGAAGAGA
113880 GCTTCACTAA
Statistics
Matches: 313, Mismatches: 20, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
228 129 0.41
229 44 0.14
230 105 0.34
231 34 0.11
232 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (229 bp):
AACACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCGAC
AAGACTGTGGACGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGCAAGCTTCAC
CACTATGCCAAAATGTAAATCAAATCTAACTATTTAGGAGCTTAAATTCTAGATAATGATAAACT
CAATTGCGAACCATCAAGGATCTCCATATCATTA
Found at i:115994 original size:2 final size:2
Alignment explanation
Indices: 115987--116026 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
115977 ATATAATCAC
115987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116027 TAAAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117347 original size:22 final size:24
Alignment explanation
Indices: 117287--117348 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
117277 AAACGTATAA
*
117287 TAAAATTATTTAAAAATAAATTAT
1 TAAAATTACTTAAAAATAAATTAT
117311 TAAATATTACTTAAAAA-AAATT-T
1 TAAA-ATTACTTAAAAATAAATTAT
*
117334 TAAAATTACATAAAA
1 TAAAATTACTTAAAA
117349 GTTATAATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 10 0.29
23 5 0.14
24 9 0.26
25 11 0.31
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAATTACTTAAAAATAAATTAT
Found at i:119527 original size:19 final size:19
Alignment explanation
Indices: 119505--119548 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
119495 TTATTTTGAG
*
119505 AATTAAAATTTATTA-CAT
1 AATTAAAATTAATTATCAT
*
119523 CAATTAATATTAATTATCAT
1 -AATTAAAATTAATTATCAT
119543 AATTAA
1 AATTAA
119549 CTGTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTAAAATTAATTATCAT
Found at i:131305 original size:139 final size:139
Alignment explanation
Indices: 131053--131312 Score: 349
Period size: 139 Copynumber: 1.9 Consensus size: 139
131043 TGTTTGTGCG
* * *
131053 CATAAAACAAACAATTTTATAAAGCAAATTTAAAGTGTGGTTTTATTGCAAACGTACAGGTCAAT
1 CATAAAACAAACAATTTTATAAAGCAAATTTAAAGTGCGATTTTACTGCAAACGTACAGGTCAAT
* * **
131118 TGTAATATTTATAGTGTTATAATAAAACATTAAAGTATTCCAAGGATAGAACCCAACAGCGTTGC
66 TGTAATATTTATAGTGTAACAATAAAACACCAAAGTATTCCAAGGATAGAACCCAACAGCGTTGC
131183 GCTTTTGCA
131 GCTTTTGCA
* * * *
131192 CATAAAACAAACGATTTTATAAAGCAAATTTAAAGTGCGATTTTACTGCAAGCGTATAGGTCAGT
1 CATAAAACAAACAATTTTATAAAGCAAATTTAAAGTGCGATTTTACTGCAAACGTACAGGTCAAT
* * * ** * * *
131257 TGTGATATTTGTATTGTAACAATGGAACACCGAAGTATTCCAATGATAGAATCCAA
66 TGTAATATTTATAGTGTAACAATAAAACACCAAAGTATTCCAAGGATAGAACCCAA
131313 AGGAGTCGAC
Statistics
Matches: 102, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
139 102 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (139 bp):
CATAAAACAAACAATTTTATAAAGCAAATTTAAAGTGCGATTTTACTGCAAACGTACAGGTCAAT
TGTAATATTTATAGTGTAACAATAAAACACCAAAGTATTCCAAGGATAGAACCCAACAGCGTTGC
GCTTTTGCA
Found at i:139588 original size:33 final size:33
Alignment explanation
Indices: 139546--139611 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
139536 CGTGGAAGAA
139546 AACTGGCAAATTTCTGTTCATACGGCTATTATC
1 AACTGGCAAATTTCTGTTCATACGGCTATTATC
* *
139579 AACTGGCAAATTTTTGTTCCTACGGCTATTATC
1 AACTGGCAAATTTCTGTTCATACGGCTATTATC
139612 CTGCTGTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (33 bp):
AACTGGCAAATTTCTGTTCATACGGCTATTATC
Found at i:146385 original size:17 final size:17
Alignment explanation
Indices: 146360--146392 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
146350 AAGATTAAAA
*
146360 TGAATTTAATTATCAAG
1 TGAACTTAATTATCAAG
146377 TGAACTTAATTATCAA
1 TGAACTTAATTATCAA
146393 ATTCAGGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (17 bp):
TGAACTTAATTATCAAG
Found at i:147721 original size:23 final size:25
Alignment explanation
Indices: 147677--147722 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
147667 AAATAAAATT
*
147677 TTAAAAATATAATACATCAAATACA
1 TTAAAAATATAATAAATCAAATACA
*
147702 TTAAAAATA-ATTAAAT-AAATA
1 TTAAAAATATAATAAATCAAATA
147723 TTTCCCAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 5 0.26
25 9 0.47
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (25 bp):
TTAAAAATATAATAAATCAAATACA
Found at i:148873 original size:12 final size:12
Alignment explanation
Indices: 148858--148898 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
148848 GTTCAATTAT
148858 ATGTTCATGAAC
1 ATGTTCATGAAC
148870 ATGTTCATTG-A-
1 ATGTTCA-TGAAC
*
148881 ATGTTCGTGAAC
1 ATGTTCATGAAC
148893 ATGTTC
1 ATGTTC
148899 GGTTAAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
10 2 0.08
11 7 0.28
12 14 0.56
13 2 0.08
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (12 bp):
ATGTTCATGAAC
Found at i:148891 original size:23 final size:24
Alignment explanation
Indices: 148835--148898 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
148825 TCATTACCAT
*
148835 TGTTCGTGAATATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
*
148859 TGTTCATGAACATGTTC-ATTGA-A
1 TGTTCGTGAACATGTTCAATT-ATA
148882 TGTTCGTGAACATGTTC
1 TGTTCGTGAACATGTTC
148899 GGTTAAGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 20 0.56
24 16 0.44
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:151897 original size:25 final size:25
Alignment explanation
Indices: 151808--151921 Score: 111
Period size: 25 Copynumber: 4.4 Consensus size: 25
151798 CCAAAAATTA
* *
151808 GCTCTAACGAGCCCAGACAGATTATC
1 GCTCTTACGAG-CCAGACAGAATATC
* *
151834 GCTCTTTCGAGCCAGAATTCAGAATATT
1 GCTCTTACGAGCCAG-A--CAGAATATC
*
151862 GCTCTTTCGAGCCAGACAGAATATC
1 GCTCTTACGAGCCAGACAGAATATC
* * * *
151887 ACTCATACGAGCCAAACAAAATATC
1 GCTCTTACGAGCCAGACAGAATATC
151912 GCTCTTACGA
1 GCTCTTACGA
151922 TCCAACATTC
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
25 40 0.55
26 10 0.14
27 1 0.01
28 22 0.30
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (25 bp):
GCTCTTACGAGCCAGACAGAATATC
Found at i:156186 original size:17 final size:19
Alignment explanation
Indices: 156157--156192 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
156147 GTGACGGTGA
156157 CGGAGAGTGTCTT-CATGG
1 CGGAGAGTGTCTTCCATGG
156175 CGGAGA-TGTCTTCCATGG
1 CGGAGAGTGTCTTCCATGG
156193 TACAGAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.28
Consensus pattern (19 bp):
CGGAGAGTGTCTTCCATGG
Found at i:162941 original size:21 final size:21
Alignment explanation
Indices: 162917--162957 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
162907 CATCATTTAT
* *
162917 TTATGCTTTATATTTATTTGA
1 TTATACTTTATAATTATTTGA
*
162938 TTATACTTTTTAATTATTTG
1 TTATACTTTATAATTATTTG
162958 GACATGTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (21 bp):
TTATACTTTATAATTATTTGA
Found at i:163351 original size:15 final size:15
Alignment explanation
Indices: 163331--163361 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
163321 AGCGGTCATT
163331 GTATCCCTGCTTTAA
1 GTATCCCTGCTTTAA
163346 GTATCCCTGCTTTAA
1 GTATCCCTGCTTTAA
163361 G
1 G
163362 AGGCAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (15 bp):
GTATCCCTGCTTTAA
Found at i:163729 original size:25 final size:25
Alignment explanation
Indices: 163670--163723 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
163660 GCTTAGGCTT
* *
163670 ATTAACAAGATTTGAATAATGAACA
1 ATTAAAAAAATTTGAATAATGAACA
* *
163695 TTTAAAAAAATTTGAATGATGAA-A
1 ATTAAAAAAATTTGAATAATGAACA
163719 ATTAA
1 ATTAA
163724 TGAAAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.31
Consensus pattern (25 bp):
ATTAAAAAAATTTGAATAATGAACA
Found at i:168678 original size:24 final size:24
Alignment explanation
Indices: 168646--168696 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
168636 AAATTTGTAA
168646 TTAAATTGATATTGATAATTTT-TT
1 TTAAATTGATATTGA-AATTTTATT
* *
168670 TTAATTTGATATTTAAATTTTATT
1 TTAAATTGATATTGAAATTTTATT
168694 TTA
1 TTA
168697 GTTTAGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTAAATTGATATTGAAATTTTATT
Found at i:185611 original size:133 final size:131
Alignment explanation
Indices: 185164--185637 Score: 521
Period size: 133 Copynumber: 3.6 Consensus size: 131
185154 CATCTTTGTC
* * **
185164 AAGTTT-AAGTCTTTTGTTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGTTCCTATGTT
1 AAGTTTCAAGTCTTTTGCTCCAATGGGTTCAAAGTTTTTCTTCC-TTTTTGTTGGTTGGTATGTT
** * * * *
185228 CTTTGTTATAATTGTGCTTTTCTGTAATGTGTATCTTCAAGTCTATTGAATTTTTGAGCTTTTGT
65 CTTTGTTATAATTGTAATTTGCTGTAATGTGTAGCTTCAATTCTATT-AAATTTTGAGCTTTTGT
185293 TGA
129 TGA
* * * *
185296 AAGTTTCAAGTCTTTTACTCCAATGGGTTCTAAGTTTTTCTTTCTTTTTTGTTGGTTTGTA--TT
1 AAGTTTCAAGTCTTTTGCTCCAATGGGTTCAAAGTTTTTC-TTCCTTTTTGTTGGTTGGTATGTT
* * *
185359 CTTTGTTATAATTATAATTTGCTGTAATATGTAGATTCAATTCTATTAAATTTT-AGCTTTTGTT
65 CTTTGTTATAATTGTAATTTGCTGTAATGTGTAGCTTCAATTCTATTAAATTTTGAGCTTTTGTT
185423 GA
130 GA
*** ** *
185425 AAGTTT-AAGTCTTTTGCTCCAATGGGTT-ATAAGTTGCACTTTTTTTTTCTTGGTTGGTATGTT
1 AAGTTTCAAGTCTTTTGCTCCAATGGGTTCA-AAGTTTTTCTTCCTTTTTGTTGGTTGGTATGTT
* * * ** *
185488 CTTTGTGTTATAATTGTAATCTGCTGAAATGGGTAGCTTTTATTCTTTTAAAATTTTGAGCTTTT
65 C-TT-TGTTATAATTGTAATTTGCTGTAATGTGTAGCTTCAATTCTATT-AAATTTTGAGCTTTT
185553 GTTGA
127 GTTGA
* * * *
185558 AA-TTTCATGTCCTTTGCTCCAATAGGTTCAAATTTTTTCTTCCTTTTTGTTGGTTGGTATGTTC
1 AAGTTTCAAGTCTTTTGCTCCAATGGGTTCAAAGTTTTTCTTCCTTTTTGTTGGTTGGTATGTTC
*
185622 TTTGTTGTAATGTGTA
66 TTTGTTATAAT-TGTA
185638 GATTCAAGTC
Statistics
Matches: 288, Mismatches: 42, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
127 17 0.06
128 27 0.09
129 21 0.07
130 8 0.03
131 84 0.29
132 22 0.08
133 105 0.36
134 4 0.01
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.53
Consensus pattern (131 bp):
AAGTTTCAAGTCTTTTGCTCCAATGGGTTCAAAGTTTTTCTTCCTTTTTGTTGGTTGGTATGTTC
TTTGTTATAATTGTAATTTGCTGTAATGTGTAGCTTCAATTCTATTAAATTTTGAGCTTTTGTTG
A
Found at i:189537 original size:19 final size:19
Alignment explanation
Indices: 189515--189593 Score: 74
Period size: 19 Copynumber: 4.2 Consensus size: 19
189505 AAAAAAAAAA
189515 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
* *
189534 AAAATTTAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
**
189553 AAAATTCAAAATTTTTTTT
1 AAAATTCAAAATAATTTTT
*
189572 AAAGATT-ATAA-AATTTTT
1 AAA-ATTCAAAATAATTTTT
189590 AAAA
1 AAAA
189594 AATTTTCCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.02
18 12 0.24
19 30 0.61
20 6 0.12
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:189557 original size:38 final size:39
Alignment explanation
Indices: 189513--189597 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 39
189503 ACAAAAAAAA
189513 AAAAAATTCAAAATAATTTTTAAA-ATT-TAAAATATTT
1 AAAAAATTCAAAATAATTTTTAAAGATTATAAAATATTT
** *
189550 ATAAAAATTCAAAATTTTTTTTAAAGATTATAAAATTTTT
1 A-AAAAATTCAAAATAATTTTTAAAGATTATAAAATATTT
189590 AAAAAATT
1 AAAAAATT
189598 TTCCATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 1 0.02
38 21 0.50
39 10 0.24
40 10 0.24
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (39 bp):
AAAAAATTCAAAATAATTTTTAAAGATTATAAAATATTT
Found at i:203186 original size:3 final size:3
Alignment explanation
Indices: 203178--203218 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
203168 ATCATTAAGA
*
203178 AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
203219 TGATTCACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:204847 original size:36 final size:36
Alignment explanation
Indices: 204777--204848 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
204767 AAAATAGTAA
*
204777 CAAAAATTAACAATAAAACAAGTGTTATACAATATC
1 CAAAAATTAACAATAAAACAAGTGTAATACAATATC
* *
204813 CAAACATTAACAA-AAAA-ATAGTAGTAATATAATATC
1 CAAAAATTAACAATAAAACA-AGT-GTAATACAATATC
204849 GAAATGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 1 0.03
35 7 0.23
36 23 0.74
ACGTcount: A:0.57, C:0.12, G:0.06, T:0.25
Consensus pattern (36 bp):
CAAAAATTAACAATAAAACAAGTGTAATACAATATC
Found at i:204895 original size:22 final size:21
Alignment explanation
Indices: 204870--204917 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
204860 AAAACAAAGG
* *
204870 CAAAAAATGGGGAAAACAATAA
1 CAAAAAAT-GGAAAAACAACAA
*
204892 CAAAACATGGAAAAACAACAA
1 CAAAAAATGGAAAAACAACAA
204913 CAAAA
1 CAAAA
204918 CAATAGGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.67, C:0.15, G:0.12, T:0.06
Consensus pattern (21 bp):
CAAAAAATGGAAAAACAACAA
Found at i:205674 original size:15 final size:15
Alignment explanation
Indices: 205650--205682 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
205640 AACCGAATCG
205650 AAATTTTATAAA-TA
1 AAATTTTATAAATTA
205664 AAATGTTTATAAATTA
1 AAAT-TTTATAAATTA
205680 AAA
1 AAA
205683 AGATGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATTTTATAAATTA
Found at i:205946 original size:132 final size:131
Alignment explanation
Indices: 205785--206025 Score: 374
Period size: 132 Copynumber: 1.8 Consensus size: 131
205775 AATTGAACAT
* * * *
205785 GGGACTCAATGATAAAATCATTATTATTTAACCATGAGAGTTGATATGTTAAAAACATTAATTAA
1 GGGACTCAATGATAAAATCATTATTATTTAACCAAGAGAGCTAATATATTAAAAACATTAATT-A
* *
205850 AAAATAATAAAAAGCTTAAAACAATATGAAATAAAAAATATAAATGTGGGTGAGAATAATCAAAC
65 AAAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAATGTGGGTGAGAATAATCAAAC
205915 TC
130 TC
* *
205917 GGGACTCAATGATATAATCATTATTATTTAACCAAGAGAGCTAATATATTAAAAGCATTAATTAA
1 GGGACTCAATGATAAAATCATTATTATTTAACCAAGAGAGCTAATATATTAAAAACATTAATTAA
* * *
205982 AAATAATAAAAAGGTTAAAACCACATGAAATAAATAATACAAAT
66 AAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAAT
206026 ACGAGTAGGA
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
131 41 0.42
132 57 0.58
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (131 bp):
GGGACTCAATGATAAAATCATTATTATTTAACCAAGAGAGCTAATATATTAAAAACATTAATTAA
AAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAATGTGGGTGAGAATAATCAAACT
C
Found at i:210972 original size:30 final size:29
Alignment explanation
Indices: 210938--211019 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 29
210928 ACTCGAGATG
*
210938 AAAATGAAATTTTAAAGAAGTTCGGGGGTT
1 AAAATGTAATTTTAAA-AAGTTCGGGGGTT
* * *
210968 AAAATGTGATTTTGGAAAAGTTTGGGGGTT
1 AAAATGTAATTTT-AAAAAGTTCGGGGGTT
210998 AAAATGTAATTTTAGAAAAGTT
1 AAAATGTAATTTTA-AAAAGTT
211020 TAAGGGTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
30 42 0.95
31 2 0.05
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTAAAAAGTTCGGGGGTT
Found at i:211009 original size:60 final size:59
Alignment explanation
Indices: 210945--211244 Score: 298
Period size: 60 Copynumber: 5.0 Consensus size: 59
210935 ATGAAAATGA
*** * * ** *
210945 AATTTTAAAGAAGTTCGGGGGTTAAAATGTGATTTTGGAAAAGTTTGGGGGTTAAAATGT
1 AATTTTAAA-AAGTTTAAGGGTCAAAATATGATTTTGGAAAAGTTTAAGGGTTAAAATAT
211005 AATTTTAGAAAAGTTTAAGGGTCAAAATATGATTTTGGAAAAGTTTAAGGGTTAAAATAT
1 AATTTTA-AAAAGTTTAAGGGTCAAAATATGATTTTGGAAAAGTTTAAGGGTTAAAATAT
* * ** * * *
211065 AATTTTGGAAAAGTTTAGGGGTCAAAAATATGATTTTAAAAAAGTTTGAGGGTCAAAAACAT
1 AATTTT-AAAAAGTTTAAGGGTC-AAAATATGATTTTGGAAAAGTTTAAGGGT-TAAAATAT
* * * *
211127 GATTTTAAAAAAGTTTAAGGGTCAAAATATAATTTT-GAAAATTTTTAGGGGTTAAAATAT
1 AATTTT-AAAAAGTTTAAGGGTCAAAATATGATTTTGGAAAA-GTTTAAGGGTTAAAATAT
** **
211187 AATTTTAAAAAAAATTAAGGGTCAAAATATGATTTTATAAAAGTTT-AGAGGTTAAAAT
1 AATTTT-AAAAAGTTTAAGGGTCAAAATATGATTTTGGAAAAGTTTAAG-GGTTAAAAT
211245 GACAAACCAA
Statistics
Matches: 200, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
59 1 0.00
60 123 0.62
61 51 0.25
62 25 0.12
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (59 bp):
AATTTTAAAAAGTTTAAGGGTCAAAATATGATTTTGGAAAAGTTTAAGGGTTAAAATAT
Found at i:211101 original size:31 final size:30
Alignment explanation
Indices: 210962--211244 Score: 264
Period size: 30 Copynumber: 9.4 Consensus size: 30
210952 AAGAAGTTCG
* * * *
210962 GGGGTTAAAATGTGATTTTGGAAAAGTTTG
1 GGGGTCAAAATATGATTTTAGAAAAGTTTA
* * *
210992 GGGGTTAAAATGTAATTTTAGAAAAGTTTA
1 GGGGTCAAAATATGATTTTAGAAAAGTTTA
* *
211022 AGGGTCAAAATATGATTTTGGAAAAGTTTA
1 GGGGTCAAAATATGATTTTAGAAAAGTTTA
* * * *
211052 AGGGTTAAAATATAATTTTGGAAAAGTTTA
1 GGGGTCAAAATATGATTTTAGAAAAGTTTA
*
211082 GGGGTCAAAAATATGATTTTAAAAAAGTTT-
1 GGGGTC-AAAATATGATTTTAGAAAAGTTTA
* *
211112 GAGGGTCAAAAACATGATTTTAAAAAAGTTTA
1 G-GGGTC-AAAATATGATTTTAGAAAAGTTTA
* * *
211144 AGGGTCAAAATATAATTTT-GAAAATTTTTA
1 GGGGTCAAAATATGATTTTAGAAAA-GTTTA
* * * **
211174 GGGGTTAAAATATAATTTTAAAAAAAATTA
1 GGGGTCAAAATATGATTTTAGAAAAGTTTA
* *
211204 AGGGTCAAAATATGATTTTATAAAAGTTTA
1 GGGGTCAAAATATGATTTTAGAAAAGTTTA
* *
211234 GAGGTTAAAAT
1 GGGGTCAAAAT
211245 GACAAACCAA
Statistics
Matches: 213, Mismatches: 35, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
29 4 0.02
30 152 0.71
31 57 0.27
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (30 bp):
GGGGTCAAAATATGATTTTAGAAAAGTTTA
Found at i:215784 original size:2 final size:2
Alignment explanation
Indices: 215777--215813 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
215767 ATATGTTTTA
215777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
215814 ATAAATCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:215998 original size:2 final size:2
Alignment explanation
Indices: 215989--216026 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
215979 CTCTCTCAAT
215989 TA TA -A 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 TA TA T
216027 TAAATGGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:217718 original size:105 final size:105
Alignment explanation
Indices: 217596--217800 Score: 241
Period size: 105 Copynumber: 2.0 Consensus size: 105
217586 AACAACACCA
* * *
217596 GGCTCAATGTCTCGCTTTCTCATCGCGTCAACAATATCCT-CAGCTTGAGAGACCATCCCATCCT
1 GGCTCAATGCCTCGCTTTCTCATCACGTCAACAATAT-CTACAGCTTGAGAAACCATCCCATCCT
* * * *
217660 TGCAATGTGCATCAACCAATGTATTGTATGTGACAACATTG
65 TGCAAAGTGCATCAACCAATATATTATACGTGACAACATTG
* * * * * * * *
217701 GGCTCAATGCCTTGCTTTCTCATCATGTCAACGATCTCTACAGCTTTAGAAATCATGCCTTCCTT
1 GGCTCAATGCCTCGCTTTCTCATCACGTCAACAATATCTACAGCTTGAGAAACCATCCCATCCTT
* *
217766 GCAAAGTGCATCGATCAATATATTATACGTGACAA
66 GCAAAGTGCATCAACCAATATATTATACGTGACAA
217801 TATCAAGAGA
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
104 2 0.02
105 80 0.98
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (105 bp):
GGCTCAATGCCTCGCTTTCTCATCACGTCAACAATATCTACAGCTTGAGAAACCATCCCATCCTT
GCAAAGTGCATCAACCAATATATTATACGTGACAACATTG
Found at i:219561 original size:18 final size:18
Alignment explanation
Indices: 219540--219601 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
219530 TGTCAAATAA
*
219540 TATTTCTAATATTTT-TAT
1 TATTTATAAT-TTTTATAT
219558 TATTTATAATTTTTATAT
1 TATTTATAATTTTTATAT
219576 T-TTTAT-A-TTTTATA-
1 TATTTATAATTTTTATAT
*
219590 TATTTAAAATTT
1 TATTTATAATTT
219602 AAAAGTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 1 0.03
15 11 0.29
16 2 0.05
17 11 0.29
18 13 0.34
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATAATTTTTATAT
Found at i:219570 original size:15 final size:16
Alignment explanation
Indices: 219552--219601 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
219542 TTTCTAATAT
219552 TTTTAT-TATTTATAA
1 TTTTATATATTTATAA
*
219567 TTTT-TATATTTTTATA
1 TTTTATATATTTATA-A
*
219583 TTTTATATATTTAAAA
1 TTTTATATATTTATAA
219599 TTT
1 TTT
219602 AAAAGTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 11 0.38
16 9 0.31
17 8 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATATATTTATAA
Found at i:219580 original size:24 final size:25
Alignment explanation
Indices: 219539--219594 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
219529 ATGTCAAATA
*
219539 ATATTTCTAATATTTTTAT-TATTTAT
1 ATATTT-TTATATTTTTATAT-TTTAT
219565 A-ATTTTTATATTTTTATATTTTAT
1 ATATTTTTATATTTTTATATTTTAT
219589 ATATTT
1 ATATTT
219595 AAAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 17 0.63
25 9 0.33
26 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (25 bp):
ATATTTTTATATTTTTATATTTTAT
Found at i:220226 original size:23 final size:22
Alignment explanation
Indices: 220200--220257 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
220190 ATAAAAAGAA
220200 TTATATTGTTGTTTTGTTGT-TT
1 TTATATTGTT-TTTTGTTGTGTT
*
220222 TT-TATTG-TTTTGGTTGTTGTT
1 TTATATTGTTTTTTGTTG-TGTT
220243 TTAGTATTGTTTTTT
1 TTA-TATTGTTTTTT
220258 ACTATTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 7 0.24
20 2 0.07
21 9 0.31
22 2 0.07
23 5 0.17
24 4 0.14
ACGTcount: A:0.09, C:0.00, G:0.19, T:0.72
Consensus pattern (22 bp):
TTATATTGTTTTTTGTTGTGTT
Found at i:220239 original size:19 final size:19
Alignment explanation
Indices: 220208--220296 Score: 68
Period size: 19 Copynumber: 4.9 Consensus size: 19
220198 AATTATATTG
220208 TTGTTTT-GTTGTTTTTTA
1 TTGTTTTGGTTGTTTTTTA
220226 TTGTTTTGGTTGTTGTTTTA
1 TTGTTTTGGTTGTT-TTTTA
*
220246 --G---T-ATTGTTTTTTA
1 TTGTTTTGGTTGTTTTTTA
* *
220259 CTATTTTGG-TGCTTTTTTA
1 TTGTTTTGGTTG-TTTTTTA
220278 TTGTTTTGGTTGTTATTTT
1 TTGTTTTGGTTGTT-TTTT
220297 GGTGCTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
13 5 0.09
14 5 0.09
15 1 0.02
18 11 0.20
19 22 0.40
20 11 0.20
ACGTcount: A:0.08, C:0.02, G:0.19, T:0.71
Consensus pattern (19 bp):
TTGTTTTGGTTGTTTTTTA
Found at i:220241 original size:22 final size:23
Alignment explanation
Indices: 220213--220255 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
220203 TATTGTTGTT
*
220213 TTGTTGTTTT-TTATTGTTTTGG
1 TTGTTGTTTTAGTATTGTTTTGG
220235 TTGTTGTTTTAGTATTGTTTT
1 TTGTTGTTTTAGTATTGTTTT
220256 TTACTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.07, C:0.00, G:0.21, T:0.72
Consensus pattern (23 bp):
TTGTTGTTTTAGTATTGTTTTGG
Found at i:220253 original size:33 final size:30
Alignment explanation
Indices: 220205--220284 Score: 83
Period size: 33 Copynumber: 2.6 Consensus size: 30
220195 AAGAATTATA
* *
220205 TTGTTGTTTTGTTGTTTTTTATTGTTTTGG
1 TTGTTGTTTTGTTGTTTTTTACTATTTTGG
220235 TTGTTGTTTTAGTATTGTTTTTTACTATTTTGG
1 TTGTTGTTTT-G--TTGTTTTTTACTATTTTGG
*
220268 -TGCTT-TTTTATTGTTTT
1 TTG-TTGTTTTGTTGTTTT
220285 GGTTGTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
29 7 0.16
30 10 0.23
31 1 0.02
32 6 0.14
33 19 0.44
ACGTcount: A:0.07, C:0.03, G:0.19, T:0.71
Consensus pattern (30 bp):
TTGTTGTTTTGTTGTTTTTTACTATTTTGG
Found at i:220308 original size:52 final size:52
Alignment explanation
Indices: 220211--220329 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
220201 TATATTGTTG
* *
220211 TTTTGTTGTTTTTTATTGTTTTGGTTGTTGTTTTAGTA-TTGTTTTTTACTA
1 TTTTGGTGTTTTTTATTGTTTTGGTTGTTATTTTAGTATTTGTTTTTTACTA
* * *
220262 TTTTGGTGCTTTTTTATTGTTTTGGTTGTTATTTTGGTGCTTT-TTTTTTACTG
1 TTTTGGTG-TTTTTTATTGTTTTGGTTGTTATTTTAGT-ATTTGTTTTTTACTA
*
220315 TTTTAGTGTTGTTTT
1 TTTTGGTGTT-TTTT
220330 TGCTATTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
51 7 0.12
52 29 0.50
53 20 0.34
54 2 0.03
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.70
Consensus pattern (52 bp):
TTTTGGTGTTTTTTATTGTTTTGGTTGTTATTTTAGTATTTGTTTTTTACTA
Found at i:220317 original size:34 final size:33
Alignment explanation
Indices: 220260--220327 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 33
220250 TGTTTTTTAC
*
220260 TATTTTGGTGCTTTTTTATTGTTTT-G-GTTGT
1 TATTTTGGTGCTTTTTTACTGTTTTAGTGTTGT
220291 TATTTTGGTGCTTTTTTTTTACTGTTTTAGTGTTGT
1 TATTTTGGTGC---TTTTTTACTGTTTTAGTGTTGT
220327 T
1 T
220328 TTTGCTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 11 0.35
34 13 0.42
35 1 0.03
36 6 0.19
ACGTcount: A:0.07, C:0.04, G:0.21, T:0.68
Consensus pattern (33 bp):
TATTTTGGTGCTTTTTTACTGTTTTAGTGTTGT
Found at i:220360 original size:12 final size:12
Alignment explanation
Indices: 220321--220378 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
220311 ACTGTTTTAG
*
220321 TGTTGTTTTTGC
1 TGTTATTTTTGC
*
220333 TATTATTTTTGC
1 TGTTATTTTTGC
*
220345 TGTTATTTTTGT
1 TGTTATTTTTGC
*
220357 TGTT-GTTTTGC
1 TGTTATTTTTGC
*
220368 CGTTATTTTTG
1 TGTTATTTTTG
220379 TAGTTGTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 8 0.22
12 29 0.78
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:220365 original size:23 final size:23
Alignment explanation
Indices: 220339--220389 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
220329 TTGCTATTAT
* *
220339 TTTTGCTGTTATTTTTGTTGTTG
1 TTTTGCCGTTATTTTTGTAGTTG
220362 TTTTGCCGTTATTTTTGTAGTTG
1 TTTTGCCGTTATTTTTGTAGTTG
220385 TTTTG
1 TTTTG
220390 GTTGTTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.67
Consensus pattern (23 bp):
TTTTGCCGTTATTTTTGTAGTTG
Found at i:220366 original size:35 final size:36
Alignment explanation
Indices: 220321--220395 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
220311 ACTGTTTTAG
* *
220321 TGTTGTTTTTGCTATTATTTTTGCT-GTTATTTTTGT
1 TGTTGTTTTTGCCATTATTTTTG-TAGTTATTTTGGT
* *
220357 TGTTG-TTTTGCCGTTATTTTTGTAGTTGTTTTGGT
1 TGTTGTTTTTGCCATTATTTTTGTAGTTATTTTGGT
220392 TGTT
1 TGTT
220396 TAGATGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 1 0.03
35 28 0.82
36 5 0.15
ACGTcount: A:0.07, C:0.05, G:0.21, T:0.67
Consensus pattern (36 bp):
TGTTGTTTTTGCCATTATTTTTGTAGTTATTTTGGT
Found at i:229215 original size:12 final size:14
Alignment explanation
Indices: 229198--229230 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
229188 CAATTACTCA
229198 TAAATTA-TTATT-
1 TAAATTATTTATTG
229210 TAAATTATTTATTG
1 TAAATTATTTATTG
229224 TAAATTA
1 TAAATTA
229231 GTTCACAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 5 0.26
14 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TAAATTATTTATTG
Found at i:230190 original size:7 final size:7
Alignment explanation
Indices: 230178--230222 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
230168 AAAGACGAGA
230178 GAGGAGT
1 GAGGAGT
230185 GAGGAGT
1 GAGGAGT
230192 GAGGAGT
1 GAGGAGT
230199 GAGGAGT
1 GAGGAGT
230206 GAGGAGT
1 GAGGAGT
230213 GAGGAGT
1 GAGGAGT
230220 GAG
1 GAG
230223 AAGAAAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.29, C:0.00, G:0.58, T:0.13
Consensus pattern (7 bp):
GAGGAGT
Found at i:231447 original size:29 final size:29
Alignment explanation
Indices: 231388--231446 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
231378 TTTAGTTTAA
*
231388 TGTGTAATTTTATACATTAATTTTGATTT
1 TGTGTAATTTTATACATAAATTTTGATTT
* *
231417 TGTGTAATTTTATATATAAAATTTTTATTT
1 TGTGTAATTTTATACAT-AAATTTTGATTT
231447 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (29 bp):
TGTGTAATTTTATACATAAATTTTGATTT
Found at i:231671 original size:29 final size:27
Alignment explanation
Indices: 231605--231671 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 27
231595 ATTTTTCATG
231605 TGTATAATTGCACCAAATCAAAGTTGA
1 TGTATAATTGCACCAAATCAAAGTTGA
*
231632 TGTATTAAATTGCACATTAAATCAAAG-TGCA
1 TGTA-T-AATTGCAC--CAAATCAAAGTTG-A
231663 TGTATAATT
1 TGTATAATT
231672 TTGAGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 4 0.12
28 1 0.03
29 12 0.35
30 3 0.09
31 14 0.41
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAGTTGA
Found at i:234485 original size:29 final size:29
Alignment explanation
Indices: 234443--234509 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
234433 TGAATATGCT
*
234443 TAAATTAAGACAAAATTAATATACCATTG
1 TAAATTAACACAAAATTAATATACCATTG
234472 TAAATTAACACAAAATTAATATACCATTG
1 TAAATTAACACAAAATTAATATACCATTG
234501 TAAATTAAC
1 TAAATTAAC
234510 TCATTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (29 bp):
TAAATTAACACAAAATTAATATACCATTG
Found at i:246045 original size:69 final size:69
Alignment explanation
Indices: 245932--246070 Score: 235
Period size: 69 Copynumber: 2.0 Consensus size: 69
245922 TTATATTTTG
* *
245932 AGGGATATTTGAGTTCACATACATGATTTTAATCATTAAAAAAATACAATTGTAATAATGAGATA
1 AGGGATATTTGAGTTCACATACATGATTTTAATCATTAAAAAAATACAATGGTAACAATGAGATA
245997 AAAT
66 AAAT
*
246001 AGGGATATTTGAGTTCACAT-CGATGATTTTAATCATTAAGAAAATACAATGGTAACAATGAGAT
1 AGGGATATTTGAGTTCACATAC-ATGATTTTAATCATTAAAAAAATACAATGGTAACAATGAGAT
246065 AAAAT
65 AAAAT
246070 A
1 A
246071 TAGTTGAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.02
69 65 0.98
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (69 bp):
AGGGATATTTGAGTTCACATACATGATTTTAATCATTAAAAAAATACAATGGTAACAATGAGATA
AAAT
Found at i:246365 original size:16 final size:16
Alignment explanation
Indices: 246344--246375 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
246334 CTTGATCTTG
246344 GATAGTTAAAGCCTAC
1 GATAGTTAAAGCCTAC
246360 GATAGTTAAAGCCTAC
1 GATAGTTAAAGCCTAC
246376 TTCAAGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (16 bp):
GATAGTTAAAGCCTAC
Found at i:246805 original size:30 final size:30
Alignment explanation
Indices: 246769--246831 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
246759 ACTTAACAAG
246769 CAAATGCCTCTAAAACT-ATAACAAAATTAA
1 CAAATGCCTCTAAAA-TAATAACAAAATTAA
*
246799 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
246829 CAA
1 CAA
246832 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.56, C:0.17, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:248667 original size:23 final size:22
Alignment explanation
Indices: 248635--248740 Score: 70
Period size: 25 Copynumber: 4.5 Consensus size: 22
248625 ACATTAGCGC
* *
248635 GCCCTTTGTTCAGCACTGTGTGT
1 GCCCTCTGTTCAGCACT-TATGT
*
248658 GCCCTCTGTTATTAGCACTTCATGT
1 GCCCTCTG-T-TCAGCACTT-ATGT
*
248683 GCCCTCTGATT-AGCACTTTGTGT
1 GCCCTCTG-TTCAGCAC-TTATGT
* *
248706 GCCTTCTATTACCCAGCACTTATGT
1 GCCCTCTGTT---CAGCACTTATGT
248731 GCCCTCTGTT
1 GCCCTCTGTT
248741 AAGTACTTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
22 2 0.03
23 21 0.32
24 5 0.08
25 32 0.49
26 5 0.08
ACGTcount: A:0.13, C:0.29, G:0.19, T:0.39
Consensus pattern (22 bp):
GCCCTCTGTTCAGCACTTATGT
Found at i:248683 original size:25 final size:24
Alignment explanation
Indices: 248646--248741 Score: 88
Period size: 25 Copynumber: 3.9 Consensus size: 24
248636 CCCTTTGTTC
*
248646 AGCACTGTGTGTGCCCTCTGTTATT
1 AGCACT-TATGTGCCCTCTGTTATT
248671 AGCACTTCATGTGCCCTCTG--ATT
1 AGCACTT-ATGTGCCCTCTGTTATT
* * * **
248694 AGCACTTTGTGTGCCTTCTATTACCC
1 AGCAC-TTATGTGCCCTCTGTTA-TT
248720 AGCACTTATGTGCCCTCTGTTA
1 AGCACTTATGTGCCCTCTGTTA
248742 AGTACTTCGG
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
23 17 0.30
24 3 0.05
25 32 0.56
26 5 0.09
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.38
Consensus pattern (24 bp):
AGCACTTATGTGCCCTCTGTTATT
Found at i:248706 original size:48 final size:48
Alignment explanation
Indices: 248646--248738 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
248636 CCCTTTGTTC
* **
248646 AGCACTGTGTGTGCCCTCTGTTA-TTAGCACTTCATGTGCCCTCTGATT
1 AGCACTGTGTGTGCCCTCTATTACCCAGCACTT-ATGTGCCCTCTGATT
* *
248694 AGCACTTTGTGTGCCTTCTATTACCCAGCACTTATGTGCCCTCTG
1 AGCACTGTGTGTGCCCTCTATTACCCAGCACTTATGTGCCCTCTG
248739 TTAAGTACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 32 0.82
49 7 0.18
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.37
Consensus pattern (48 bp):
AGCACTGTGTGTGCCCTCTATTACCCAGCACTTATGTGCCCTCTGATT
Found at i:251819 original size:95 final size:95
Alignment explanation
Indices: 251656--251945 Score: 528
Period size: 95 Copynumber: 3.1 Consensus size: 95
251646 CTGAGGTAAG
* * *
251656 AAGTTTTCTAGGTTTGGTCGGTTATTATAGAGGATTTGTTTAAGGTTTTTCCATGATTGCGTTGC
1 AAGTTTTCTAGGTTTGGTCGGTTATTATAGAAGATTTGTTTAAGGATTTTCCATGATTGCATTGC
251721 CTTTAACGAGGCTATTGCAAAAAGATGTGA
66 CTTTAACGAGGCTATTGCAAAAAGATGTGA
251751 AAGTTTTCTAGGTTTGGTCGGTTATTATAGAAGATTTGTTTAAGGATTTTCCATGATTGCATTGC
1 AAGTTTTCTAGGTTTGGTCGGTTATTATAGAAGATTTGTTTAAGGATTTTCCATGATTGCATTGC
*
251816 CTTTAACGAGGCTATTGCAATAAGATGTGA
66 CTTTAACGAGGCTATTGCAAAAAGATGTGA
251846 AAGTTTTCTAGGTTTGGTCGGTTATTATAGAAGATTTGTTTAAGGATTTTCCATGATTGCATTGC
1 AAGTTTTCTAGGTTTGGTCGGTTATTATAGAAGATTTGTTTAAGGATTTTCCATGATTGCATTGC
*
251911 TTTTAACGAGGCTATTGCAAAAAGATGTG-
66 CTTTAACGAGGCTATTGCAAAAAGATGTGA
251940 AAGTTT
1 AAGTTT
251946 GAATGGGATG
Statistics
Matches: 189, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
94 6 0.03
95 183 0.97
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (95 bp):
AAGTTTTCTAGGTTTGGTCGGTTATTATAGAAGATTTGTTTAAGGATTTTCCATGATTGCATTGC
CTTTAACGAGGCTATTGCAAAAAGATGTGA
Found at i:255727 original size:25 final size:23
Alignment explanation
Indices: 255677--255779 Score: 125
Period size: 23 Copynumber: 4.4 Consensus size: 23
255667 GTTGAGCAAT
* *
255677 AGAGGGCACACAAAGTACTAATC
1 AGAGGGCACACAAAGTGCTAAAC
255700 AGAGGGCACACAAAGTGCTTATAAC
1 AGAGGGCACACAAAGTGC-TA-AAC
*
255725 AGAGGGCACACACAGTGCTAAAC
1 AGAGGGCACACAAAGTGCTAAAC
** * *
255748 AGAGGGCACGGAACGTGCTAAAT
1 AGAGGGCACACAAAGTGCTAAAC
255771 AGAGGGCAC
1 AGAGGGCAC
255780 GCTAGTGTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
23 47 0.67
24 4 0.06
25 19 0.27
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.12
Consensus pattern (23 bp):
AGAGGGCACACAAAGTGCTAAAC
Found at i:255766 original size:48 final size:46
Alignment explanation
Indices: 255677--255779 Score: 125
Period size: 48 Copynumber: 2.2 Consensus size: 46
255667 GTTGAGCAAT
*
255677 AGAGGGCACACAAAGTACTAATCAGAGGGCACACAAAGTGCTTATAAC
1 AGAGGGCACACAAAGTACTAAACAGAGGGCACACAAAGTGC-TA-AAC
* * ** * *
255725 AGAGGGCACACACAGTGCTAAACAGAGGGCACGGAACGTGCTAAAT
1 AGAGGGCACACAAAGTACTAAACAGAGGGCACACAAAGTGCTAAAC
255771 AGAGGGCAC
1 AGAGGGCAC
255780 GCTAGTGTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 11 0.23
47 2 0.04
48 35 0.73
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.12
Consensus pattern (46 bp):
AGAGGGCACACAAAGTACTAAACAGAGGGCACACAAAGTGCTAAAC
Found at i:258539 original size:25 final size:25
Alignment explanation
Indices: 258486--258539 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
258476 GTTGGGCAAC
* *
258486 AGAGAGCACGCGAAGTGCTAATAAT
1 AGAGAGCACGAGAAGTGCTAATAAG
*
258511 AGAGAGCACGAGACGTGCTAA-ACAG
1 AGAGAGCACGAGAAGTGCTAATA-AG
258536 AGAG
1 AGAG
258540 CACACACAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.41, C:0.17, G:0.31, T:0.11
Consensus pattern (25 bp):
AGAGAGCACGAGAAGTGCTAATAAG
Found at i:258541 original size:23 final size:23
Alignment explanation
Indices: 258483--258586 Score: 95
Period size: 23 Copynumber: 4.4 Consensus size: 23
258473 AGTGTTGGGC
*
258483 AACAGAGAGCACGCGA-AGTGCTAA
1 AACAGAGAGCACAC-ACAGTGCT-A
* *
258507 TAATAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
** *
258531 AACAGAGAGCACACACAGTATTG
1 AACAGAGAGCACACACAGTGCTA
*
258554 AATAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
258577 AACAGAGAGC
1 AACAGAGAGC
258587 GTACTAGTGT
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
22 3 0.05
23 42 0.67
24 1 0.02
25 17 0.27
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:260830 original size:27 final size:27
Alignment explanation
Indices: 260792--260846 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
260782 TGAAATTGAG
260792 AAGGGCATTAAGGGTATAATAGGTATT
1 AAGGGCATTAAGGGTATAATAGGTATT
260819 AAGGGCATTAAGGGTATAATAGGTATT
1 AAGGGCATTAAGGGTATAATAGGTATT
260846 A
1 A
260847 GGTATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.29, T:0.29
Consensus pattern (27 bp):
AAGGGCATTAAGGGTATAATAGGTATT
Found at i:261723 original size:8 final size:8
Alignment explanation
Indices: 261710--261738 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
261700 ATTTCAACGG
261710 ATTTTTTA
1 ATTTTTTA
261718 A-TTTTTA
1 ATTTTTTA
261725 ATTTTTTA
1 ATTTTTTA
261733 ATTTTT
1 ATTTTT
261739 CATGATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTA
Found at i:261730 original size:15 final size:15
Alignment explanation
Indices: 261710--261738 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
261700 ATTTCAACGG
261710 ATTTTTTAATTTTTA
1 ATTTTTTAATTTTTA
261725 ATTTTTTAATTTTT
1 ATTTTTTAATTTTT
261739 CATGATTCTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTTAATTTTTA
Found at i:264788 original size:14 final size:15
Alignment explanation
Indices: 264765--264797 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
264755 ATAAATAAAT
*
264765 AAATAGAAAAA-TAA
1 AAATAAAAAAATTAA
264779 AAATAAAAAAATTAA
1 AAATAAAAAAATTAA
264794 AAAT
1 AAAT
264798 TGGGTTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAAAAAAATTAA
Found at i:271837 original size:21 final size:22
Alignment explanation
Indices: 271796--271837 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
271786 GTTAATATTG
*
271796 TCAATGTAATCAAACTTAAATA
1 TCAATGTAATCAAAATTAAATA
*
271818 TCAATGTACT-AAAATTAAAT
1 TCAATGTAATCAAAATTAAAT
271838 CAAAAGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (22 bp):
TCAATGTAATCAAAATTAAATA
Found at i:275413 original size:24 final size:24
Alignment explanation
Indices: 275381--275427 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
275371 ATGACTAATG
*
275381 AAAAAAAATA-ATATGACAACTTTC
1 AAAAAAAATATA-ATAACAACTTTC
*
275405 AAAATAAATATAATAACAACTTT
1 AAAAAAAATATAATAACAACTTT
275428 ATCCCTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAAAAATATAATAACAACTTTC
Found at i:285644 original size:28 final size:26
Alignment explanation
Indices: 285577--285649 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
285567 CGAAGTACTT
* *
285577 AACAGTAAGCACACAAGTGCTGGGGA
1 AACAATAAGCACACAAGTGCTAGGGA
285603 AACAATAAGCACACAAGTGCTAGGGA
1 AACAATAAGCACACAAGTGCTAGGGA
285629 AACAATAAGCACACACAGTGC
1 AACAATAAGCACACA-AGTGC
285650 AATCCAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 39 0.89
27 5 0.11
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (26 bp):
AACAATAAGCACACAAGTGCTAGGGA
Found at i:285663 original size:23 final size:23
Alignment explanation
Indices: 285631--285676 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
285621 GCTAGGGAAA
285631 CAATAAGCACACACAGTGCAATC
1 CAATAAGCACACACAGTGCAATC
*
285654 CAATAGGCACACACAGTGCAATC
1 CAATAAGCACACACAGTGCAATC
285677 AGTAGGTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.13
Consensus pattern (23 bp):
CAATAAGCACACACAGTGCAATC
Found at i:285688 original size:22 final size:22
Alignment explanation
Indices: 285637--285740 Score: 93
Period size: 23 Copynumber: 4.6 Consensus size: 22
285627 GAAACAATAA
*
285637 GCACACACAGTGCAATCCAATAG
1 GCACACACAGTGCAAT-CAGTAG
285660 GCACACACAGTGCAATCAGTAG
1 GCACACACAGTGCAATCAGTAG
** * *
285682 GTGCACATAGCGCAAATCAGTAG
1 GCACACACAGTGC-AATCAGTAG
* *
285705 GCACACGA-AGTGCGAAACAGTAA
1 GCACAC-ACAGTGC-AATCAGTAG
*
285728 GCACACAAAGTGC
1 GCACACACAGTGC
285741 GAAATAGTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
22 15 0.22
23 51 0.76
24 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.12
Consensus pattern (22 bp):
GCACACACAGTGCAATCAGTAG
Found at i:285725 original size:23 final size:23
Alignment explanation
Indices: 285699--285775 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
285689 TAGCGCAAAT
*
285699 CAGTAGGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
285722 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
* * *
285745 TAGTAAACACATGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
285768 TAGTAAGC
1 CAGTAAGC
285776 GCGCTAACAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:287153 original size:14 final size:14
Alignment explanation
Indices: 287134--287169 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
287124 TCTAAAATTT
287134 TCACTTAAAATATC
1 TCACTTAAAATATC
287148 TCACTTAAAATATC
1 TCACTTAAAATATC
287162 TCACTTAA
1 TCACTTAA
287170 GAAAAATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (14 bp):
TCACTTAAAATATC
Found at i:301065 original size:17 final size:18
Alignment explanation
Indices: 301031--301065 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
301021 ATTTTAATGT
301031 TTATAAAATTGAAATTTTA
1 TTATAAAATT-AAATTTTA
301050 TTATAAAATT-AATTTT
1 TTATAAAATTAAATTTT
301066 TTTAGTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATAAAATTAAATTTTA
Found at i:301511 original size:19 final size:17
Alignment explanation
Indices: 301459--301518 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
301449 TATATTAAAA
* *
301459 TTTATATATTTTATAAT
1 TTTAAATATTTTTTAAT
*
301476 TTTAATTA-TTTTTAAT
1 TTTAAATATTTTTTAAT
301492 TATTAAATATTTTTTGAATT
1 T-TTAAATATTTTTT-AA-T
301512 TTTAAAT
1 TTTAAAT
301519 TTTAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 8 0.23
17 12 0.34
18 5 0.14
19 8 0.23
20 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTAAATATTTTTTAAT
Found at i:312542 original size:33 final size:33
Alignment explanation
Indices: 312505--312570 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
312495 TTAAGTATTT
*
312505 ATAATCACTT-CAAATATATCGTGTTGAGTTGTG
1 ATAATCA-TTACAAATATATCGTGTTGAATTGTG
* * *
312538 ATAATTATTATAAATATGTCGTGTTGAATTGTG
1 ATAATCATTACAAATATATCGTGTTGAATTGTG
312571 GCAAAGTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (33 bp):
ATAATCATTACAAATATATCGTGTTGAATTGTG
Done.