Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, 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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 64
Found at i:3431 original size:21 final size:20
Alignment explanation
Indices: 3402--3444 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
3392 TTAGGGTCTA
*
3402 GTAGGGGTTTCGAAACCTATT
1 GTAGAGGTTTCGAAACCT-TT
*
3423 GTAGAGGTTTTGAAACCTTT
1 GTAGAGGTTTCGAAACCTTT
3443 GT
1 GT
3445 GAAAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (20 bp):
GTAGAGGTTTCGAAACCTTT
Found at i:5359 original size:47 final size:47
Alignment explanation
Indices: 5280--5372 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
5270 TCACAATTAT
5280 TTTCAATATTTATTATTCTTGCATTATTTATTTATGTATTTATTTAG
1 TTTCAATATTTATTATTCTTGCATTATTTATTTATGTATTTATTTAG
* * *
5327 TTTCAATTTTTTATTATTCTTTCATTA-TTATTTATTTATTTATTTA
1 TTTCAA-TATTTATTATTCTTGCATTATTTATTTATGTATTTATTTA
5373 TTTATTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
47 24 0.57
48 18 0.43
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (47 bp):
TTTCAATATTTATTATTCTTGCATTATTTATTTATGTATTTATTTAG
Found at i:5390 original size:19 final size:17
Alignment explanation
Indices: 5303--5395 Score: 63
Period size: 19 Copynumber: 5.4 Consensus size: 17
5293 TATTCTTGCA
5303 TTATTTA-TTT-ATGTAT
1 TTATTTATTTTCAT-TAT
* *
5319 TTATTTAGTTTCAATTTT
1 TTATTTATTTTC-ATTAT
5337 TTA-TTATTCTTTCATTA-
1 TTATTTA-T-TTTCATTAT
5354 TTATTTA-TTT-ATTTAT
1 TTATTTATTTTCA-TTAT
5370 TTATTTATTTTCAATTCAT
1 TTATTTATTTTC-ATT-AT
5389 TTATTTA
1 TTATTTA
5396 CTTTGTTAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
14 1 0.02
15 6 0.10
16 14 0.23
17 12 0.19
18 13 0.21
19 16 0.26
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (17 bp):
TTATTTATTTTCATTAT
Found at i:5395 original size:4 final size:4
Alignment explanation
Indices: 5303--5379 Score: 65
Period size: 4 Copynumber: 19.5 Consensus size: 4
5293 TATTCTTGCA
*
5303 TTAT TTAT TTAT GTAT TTAT TTAGT TTCAAT TT-T TTA- TTAT TCT-T
1 TTAT TTAT TTAT TTAT TTAT TTA-T TT--AT TTAT TTAT TTAT T-TAT
*
5348 TCA- TTA- TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
5380 TCAATTCATT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
3 11 0.18
4 42 0.69
5 4 0.07
6 3 0.05
7 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:8192 original size:42 final size:41
Alignment explanation
Indices: 8130--8249 Score: 168
Period size: 42 Copynumber: 2.8 Consensus size: 41
8120 TGAATATTAT
8130 TGATGTTGATTTTATTTAGACTTATTGAGACTTATTAGTGTTA
1 TGATGTT-A-TTTATTTAGACTTATTGAGACTTATTAGTGTTA
* * * *
8173 TGGTGTTATTTATTTTAGACTTATTGAGAATTAATGGTGTTA
1 TGATGTTATTTA-TTTAGACTTATTGAGACTTATTAGTGTTA
8215 TGATGTTATTTAATTTAGACTTATTGAGACTTATT
1 TGATGTTATTT-ATTTAGACTTATTGAGACTTATT
8250 TGATAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.06
42 57 0.84
43 7 0.10
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (41 bp):
TGATGTTATTTATTTAGACTTATTGAGACTTATTAGTGTTA
Found at i:12709 original size:11 final size:11
Alignment explanation
Indices: 12693--12720 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12683 TAAACATCGT
12693 TTGTTCAACAG
1 TTGTTCAACAG
12704 TTGTTCAACAG
1 TTGTTCAACAG
12715 TTGTTC
1 TTGTTC
12721 TCTTGAATTC
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:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (11 bp):
TTGTTCAACAG
Found at i:13250 original size:20 final size:20
Alignment explanation
Indices: 13225--13267 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13215 ACTAAGAGCC
*
13225 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
13245 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
13265 CAT
1 CAT
13268 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:20537 original size:21 final size:20
Alignment explanation
Indices: 20508--20550 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
20498 TTAGGGTCTA
*
20508 GTAGGGGTTTCGAAACCTATT
1 GTAGAGGTTTCGAAACCT-TT
*
20529 GTAGAGGTTTTGAAACCTTT
1 GTAGAGGTTTCGAAACCTTT
20549 GT
1 GT
20551 GAAAATTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (20 bp):
GTAGAGGTTTCGAAACCTTT
Found at i:22426 original size:4 final size:4
Alignment explanation
Indices: 22417--22513 Score: 80
Period size: 4 Copynumber: 24.8 Consensus size: 4
22407 TATTCTTGCA
*
22417 TTAT TTAT TTAT GTAT TTAT TTAGT TTCAAT TT-T TTA- TTAT TCT-T
1 TTAT TTAT TTAT TTAT TTAT TTA-T TT--AT TTAT TTAT TTAT T-TAT
* * *
22462 TCA- TTA- TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA- TCAT TCAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
22507 TTAT TTA
1 TTAT TTA
22514 CTTTGTTAGA
Statistics
Matches: 78, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
3 13 0.17
4 57 0.73
5 4 0.05
6 3 0.04
7 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:22456 original size:48 final size:47
Alignment explanation
Indices: 22393--22486 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 47
22383 TCACAATTAT
22393 TTTCAATATTTTATTATTCTTGCATTATTTATTTATGTATTTATTTAG
1 TTTCAATATTTTATTATTCTTGCATTA-TTATTTATGTATTTATTTAG
* * *
22441 TTTCAATTTTTTATTATTCTTTCATTATTATTTATTTATTTATTTA
1 TTTCAATATTTTATTATTCTTGCATTATTATTTATGTATTTATTTA
22487 TTTATTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
47 18 0.42
48 25 0.58
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.66
Consensus pattern (47 bp):
TTTCAATATTTTATTATTCTTGCATTATTATTTATGTATTTATTTAG
Found at i:25303 original size:42 final size:41
Alignment explanation
Indices: 25241--25360 Score: 168
Period size: 42 Copynumber: 2.8 Consensus size: 41
25231 TGAATATTAT
25241 TGATGTTGATTTTATTTAGACTTATTGAGACTTATTAGTGTTA
1 TGATGTT-A-TTTATTTAGACTTATTGAGACTTATTAGTGTTA
* * * *
25284 TGGTGTTATTTATTTTAGACTTATTGAGAATTAATGGTGTTA
1 TGATGTTATTTA-TTTAGACTTATTGAGACTTATTAGTGTTA
25326 TGATGTTATTTAATTTAGACTTATTGAGACTTATT
1 TGATGTTATTT-ATTTAGACTTATTGAGACTTATT
25361 TGATAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.06
42 57 0.84
43 7 0.10
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (41 bp):
TGATGTTATTTATTTAGACTTATTGAGACTTATTAGTGTTA
Found at i:29816 original size:11 final size:11
Alignment explanation
Indices: 29800--29827 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
29790 TAAACATCGT
29800 TTGTTCAACAG
1 TTGTTCAACAG
29811 TTGTTCAACAG
1 TTGTTCAACAG
29822 TTGTTC
1 TTGTTC
29828 TCTTGAATTC
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:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (11 bp):
TTGTTCAACAG
Found at i:30357 original size:20 final size:20
Alignment explanation
Indices: 30332--30374 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
30322 ACTAAGAGCC
*
30332 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
30352 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
30372 CAT
1 CAT
30375 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:36865 original size:21 final size:20
Alignment explanation
Indices: 36836--36878 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
36826 TTAGGGTCTA
*
36836 GTAGGGGTTTCGAAACCTATT
1 GTAGAGGTTTCGAAACCT-TT
*
36857 GTAGAGGTTTTGAAACCTTT
1 GTAGAGGTTTCGAAACCTTT
36877 GT
1 GT
36879 GAAAATTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (20 bp):
GTAGAGGTTTCGAAACCTTT
Found at i:38743 original size:4 final size:4
Alignment explanation
Indices: 38734--38824 Score: 86
Period size: 4 Copynumber: 23.8 Consensus size: 4
38724 TATTCTTGCA
* * *
38734 TTAT TTAT TTAT GTAT TTAT TTAGT TTCAA TT-T TTA- TTA- TTCT TTA-
1 TTAT TTAT TTAT TTAT TTAT TTA-T TT-AT TTAT TTAT TTAT TTAT TTAT
*
38780 TTAT TTAT TTA- TTAT TTA- TTAT TTAT TTAT TTAT TCAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
38825 CTTTGTTAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
3 16 0.22
4 50 0.69
5 5 0.07
6 1 0.01
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:38783 original size:46 final size:45
Alignment explanation
Indices: 38712--38799 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 45
38702 TCACAATTAT
38712 TTTCAATATTTTTATTCTTGCATTATTTATTTATGTATTTATTTAG
1 TTTCAATATTTTTATTCTTGCATTATTTATTTAT-TATTTATTTAG
* *
38758 TTTCAATTTTTATTATTCTT-TATTATTTATTTATTATTTATT
1 TTTCAATATTT-TTATTCTTGCATTATTTATTTATTATTTATT
38800 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
45 8 0.21
46 23 0.59
47 8 0.21
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (45 bp):
TTTCAATATTTTTATTCTTGCATTATTTATTTATTATTTATTTAG
Found at i:41584 original size:42 final size:41
Alignment explanation
Indices: 41519--41641 Score: 174
Period size: 42 Copynumber: 2.9 Consensus size: 41
41509 ACATTGAATA
41519 TTATGATGTTGATTTTATTTAGACTTATTGAGACTTATTAGTG
1 TTATGATGTT-A-TTTATTTAGACTTATTGAGACTTATTAGTG
* * * *
41562 TTATGGTGTTATTTATTTTAGACTTATTGAGAATTAATGGTG
1 TTATGATGTTATTTA-TTTAGACTTATTGAGACTTATTAGTG
41604 TTATGATGTTATTTAATTTAGACTTATTGAGACTTATT
1 TTATGATGTTATTT-ATTTAGACTTATTGAGACTTATT
41642 TGATAATATG
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
41 4 0.06
42 57 0.80
43 10 0.14
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (41 bp):
TTATGATGTTATTTATTTAGACTTATTGAGACTTATTAGTG
Found at i:44875 original size:16 final size:17
Alignment explanation
Indices: 44851--44883 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
44841 ACGTGTATAC
*
44851 TTCCTTCCATT-GTGGT
1 TTCCCTCCATTGGTGGT
44867 TTCCCTCCATTGGTGGT
1 TTCCCTCCATTGGTGGT
44884 CGAGTTAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.27, G:0.21, T:0.45
Consensus pattern (17 bp):
TTCCCTCCATTGGTGGT
Found at i:48819 original size:16 final size:16
Alignment explanation
Indices: 48777--48819 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
48767 TGATATTACA
48777 TAATTTTAAATTGTAGT
1 TAATTTT-AATTGTAGT
* *
48794 TAAATGTAATTGTAGT
1 TAATTTTAATTGTAGT
*
48810 TACTTTTAAT
1 TAATTTTAAT
48820 CCAATTGTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (16 bp):
TAATTTTAATTGTAGT
Found at i:56234 original size:20 final size:20
Alignment explanation
Indices: 56209--56256 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
56199 CCAGTTTTGT
56209 CGGTTCTTAGCCGATTCTTC
1 CGGTTCTTAGCCGATTCTTC
56229 CGGTTCTTAGCCGATTCTTC
1 CGGTTCTTAGCCGATTCTTC
*
56249 TGGTTCTT
1 CGGTTCTT
56257 TACCCCTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.08, C:0.27, G:0.21, T:0.44
Consensus pattern (20 bp):
CGGTTCTTAGCCGATTCTTC
Found at i:57061 original size:33 final size:33
Alignment explanation
Indices: 57017--57081 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
57007 TATTCAAGCA
*
57017 TAAAATTGAG-TTTTGACAAATGAGACTTTAAT
1 TAAAATTGAGTTTTTGACAAATGAGACCTTAAT
57049 TAAAATTTGAGTTTTTGACAAATGAGACCTTAA
1 TAAAA-TTGAGTTTTTGACAAATGAGACCTTAA
57082 AGAAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 5 0.17
33 5 0.17
34 20 0.67
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (33 bp):
TAAAATTGAGTTTTTGACAAATGAGACCTTAAT
Found at i:57707 original size:21 final size:20
Alignment explanation
Indices: 57682--57721 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
57672 TAAAGTTAAC
57682 AAATA-TATATCATTATAAAAT
1 AAATATTATA-CATT-TAAAAT
57703 AAATATTATACATTTAAAA
1 AAATATTATACATTTAAAA
57722 CATAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATTATACATTTAAAAT
Found at i:58252 original size:9 final size:9
Alignment explanation
Indices: 58202--58426 Score: 105
Period size: 9 Copynumber: 24.0 Consensus size: 9
58192 GACACATTTA
58202 ATATATTATT
1 ATATATTA-T
*
58212 ATATAGTAT
1 ATATATTAT
58221 ATTATAGTGTAT
1 A-TATA-T-TAT
58233 ATATATATAT
1 ATATAT-TAT
58243 ATATATTAT
1 ATATATTAT
*
58252 A-A-CTTAT
1 ATATATTAT
58259 ATAT-TATAGT
1 ATATAT-TA-T
58269 ATATATATACT
1 ATATAT-TA-T
58280 ATATATTAT
1 ATATATTAT
58289 -TATTATTAT
1 ATA-TATTAT
58298 -TATATTAT
1 ATATATTAT
58306 AGTATATTTAT
1 A-TATA-TTAT
* *
58317 ATGTATTGT
1 ATATATTAT
*
58326 ATGTA-TAT
1 ATATATTAT
58334 ATCATATT-T
1 AT-ATATTAT
*
58343 ATATTTTAT
1 ATATATTAT
58352 ATAT-TGGTAT
1 ATATAT--TAT
* *
58362 GTGTATTAT
1 ATATATTAT
58371 ATAGTATTAT
1 ATA-TATTAT
58381 ATATTATTAT
1 ATA-TATTAT
58391 -TATTATTAT
1 ATA-TATTAT
58400 -TATTATTAT
1 ATA-TATTAT
58409 -TATTATTAT
1 ATA-TATTAT
58418 -TATTATTAT
1 ATA-TATTAT
58427 TTTATATTTA
Statistics
Matches: 181, Mismatches: 15, Indels: 39
0.77 0.06 0.17
Matches are distributed among these distances:
7 5 0.03
8 20 0.11
9 75 0.41
10 56 0.31
11 21 0.12
12 4 0.02
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (9 bp):
ATATATTAT
Found at i:58274 original size:40 final size:39
Alignment explanation
Indices: 58202--58318 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 39
58192 GACACATTTA
* *
58202 ATATATTATTAT-A-TAGTATATTATAGTGTATATATAT
1 ATATATTATTATAATTATTATATTATAGTATATATATAT
58239 ATATATATATTATAACTTA-TATATTATAGTATATATATACT
1 ATATAT-TATTATAA-TTATTATATTATAGTATATATATA-T
* *
58280 ATATATTATTATTATTATTATATTATAGTATATTTATAT
1 ATATATTATTATAATTATTATATTATAGTATATATATAT
58319 GTATTGTATG
Statistics
Matches: 71, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
37 6 0.08
38 6 0.08
39 5 0.07
40 45 0.63
41 9 0.13
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (39 bp):
ATATATTATTATAATTATTATATTATAGTATATATATAT
Found at i:58373 original size:2 final size:2
Alignment explanation
Indices: 58202--58355 Score: 77
Period size: 2 Copynumber: 81.0 Consensus size: 2
58192 GACACATTTA
*
58202 AT AT AT -T AT -T AT AT AGT AT AT -T AT AGT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT
58243 AT AT AT -T AT A- ACT -T AT AT AT -T AT AGT AT AT AT AT ACT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT A-T AT
*
58282 AT AT -T AT -T AT -T AT -T AT -T AT AT -T AT AGT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * * *
58319 GT AT -T GT AT GT AT AT AT CAT AT TT AT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
58356 TGGTATGTGT
Statistics
Matches: 118, Mismatches: 12, Indels: 44
0.68 0.07 0.25
Matches are distributed among these distances:
1 15 0.13
2 92 0.78
3 11 0.09
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (2 bp):
AT
Found at i:58390 original size:3 final size:3
Alignment explanation
Indices: 58365--58431 Score: 100
Period size: 3 Copynumber: 22.0 Consensus size: 3
58355 TTGGTATGTG
*
58365 TAT TAT ATAG TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58412 TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT
58432 ATTTATTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 2 0.03
3 52 0.88
4 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:63661 original size:33 final size:33
Alignment explanation
Indices: 63609--63726 Score: 157
Period size: 33 Copynumber: 3.6 Consensus size: 33
63599 TGCTGCTGGC
*
63609 AATGGAAGACCAGCAGTTGTAGGTTCTGCGGGA
1 AATGGAAGATCAGCAGTTGTAGGTTCTGCGGGA
*
63642 AATGGAAGATCAGCTGTTGTAGGTTCTGC-GGA
1 AATGGAAGATCAGCAGTTGTAGGTTCTGCGGGA
* ** * *
63674 CAATGGCAGATCAGCTTTTGTAGGTTCTGTGGGC
1 -AATGGAAGATCAGCAGTTGTAGGTTCTGCGGGA
63708 AATGGAAGATCAGCAGTTG
1 AATGGAAGATCAGCAGTTG
63727 CTCCTTTGCC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 3 0.04
33 69 0.93
34 2 0.03
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.26
Consensus pattern (33 bp):
AATGGAAGATCAGCAGTTGTAGGTTCTGCGGGA
Found at i:71885 original size:21 final size:19
Alignment explanation
Indices: 71833--71883 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
71823 CTATCATTAA
71833 TTATAATATATATTAAATG
1 TTATAATATATATTAAATG
71852 TTATAATATATATTAAATG
1 TTATAATATATATTAAATG
71871 TTATAATATATAT
1 TTATAATATATAT
71884 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
TTATAATATATATTAAATG
Found at i:74024 original size:15 final size:15
Alignment explanation
Indices: 74006--74039 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
73996 ACAGTTAGAG
74006 ACTCAACAAAACAAT
1 ACTCAACAAAACAAT
* *
74021 ACTCTATAAAACAAT
1 ACTCAACAAAACAAT
74036 ACTC
1 ACTC
74040 TATAGTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (15 bp):
ACTCAACAAAACAAT
Found at i:74040 original size:15 final size:15
Alignment explanation
Indices: 74013--74043 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
74003 GAGACTCAAC
74013 AAAACAATACTCTAT
1 AAAACAATACTCTAT
74028 AAAACAATACTCTAT
1 AAAACAATACTCTAT
74043 A
1 A
74044 GTTAGGTGTC
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:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAACAATACTCTAT
Found at i:86125 original size:12 final size:12
Alignment explanation
Indices: 86095--86138 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
86085 CATTTTCCAC
86095 TTTCATATTCAT
1 TTTCATATTCAT
**
86107 TCACATATTCAT
1 TTTCATATTCAT
86119 TTTCATATTCCAT
1 TTTCATATT-CAT
*
86132 GTTCATA
1 TTTCATA
86139 ATAAGTACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTCATATTCAT
Found at i:86252 original size:19 final size:19
Alignment explanation
Indices: 86163--86257 Score: 118
Period size: 19 Copynumber: 5.0 Consensus size: 19
86153 ATTTCAGAAT
* *
86163 TTATTTCCAGACTCATAAC
1 TTATTTTCAGACTCATAGC
* *
86182 TTATTTCCAGACTCATAAC
1 TTATTTTCAGACTCATAGC
86201 TTATTTTCAGACTCATAGC
1 TTATTTTCAGACTCATAGC
* *
86220 TTATTGTCAGATTCATAGC
1 TTATTTTCAGACTCATAGC
* *
86239 TTATTTTCAAATTCATAGC
1 TTATTTTCAGACTCATAGC
86258 CAATGCATAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 70 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (19 bp):
TTATTTTCAGACTCATAGC
Found at i:87632 original size:7 final size:7
Alignment explanation
Indices: 87617--87695 Score: 68
Period size: 7 Copynumber: 11.3 Consensus size: 7
87607 CTTTATAATG
*
87617 AACCTTA
1 AACCCTA
87624 AACCCTA
1 AACCCTA
87631 AACCCTA
1 AACCCTA
*
87638 AACCTTA
1 AACCCTA
**
87645 AACTTTA
1 AACCCTA
*
87652 AGCCCTA
1 AACCCTA
***
87659 AATATTA
1 AACCCTA
87666 AACCCTA
1 AACCCTA
87673 AACCCTA
1 AACCCTA
**
87680 AACAATA
1 AACCCTA
87687 AACCCTA
1 AACCCTA
87694 AA
1 AA
87696 TTATACTTAC
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (7 bp):
AACCCTA
Found at i:87641 original size:21 final size:21
Alignment explanation
Indices: 87621--87695 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
87611 ATAATGAACC
*
87621 TTAAACCCTAAACCCTAAACC
1 TTAAACCCTAAACCCTAAACA
** * *
87642 TTAAACTTTAAGCCCTAAATA
1 TTAAACCCTAAACCCTAAACA
87663 TTAAACCCTAAACCCTAAACA
1 TTAAACCCTAAACCCTAAACA
*
87684 ATAAACCCTAAA
1 TTAAACCCTAAA
87696 TTATACTTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (21 bp):
TTAAACCCTAAACCCTAAACA
Found at i:87760 original size:7 final size:7
Alignment explanation
Indices: 87748--87793 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
87738 GTCATTGTAA
*
87748 TAAACCT
1 TAAACCC
87755 TAAACCC
1 TAAACCC
87762 TAAACCC
1 TAAACCC
87769 TAAACCC
1 TAAACCC
**
87776 TAAACTA
1 TAAACCC
87783 TAAACCC
1 TAAACCC
87790 TAAA
1 TAAA
87794 TCTAATTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:92781 original size:20 final size:20
Alignment explanation
Indices: 92756--92798 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
92746 ACTAAGAGCC
*
92756 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
92776 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
92796 CAT
1 CAT
92799 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:98452 original size:18 final size:18
Alignment explanation
Indices: 98429--98466 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
98419 GCCATACTTG
98429 ATAGGCACCAAAGTCATT
1 ATAGGCACCAAAGTCATT
98447 ATAGGCACCAAAGTCATT
1 ATAGGCACCAAAGTCATT
98465 AT
1 AT
98467 TCACACTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (18 bp):
ATAGGCACCAAAGTCATT
Found at i:103281 original size:17 final size:17
Alignment explanation
Indices: 103259--103304 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
103249 TCGAGTTTGA
103259 TTCGAGCTTGAATCTAG
1 TTCGAGCTTGAATCTAG
103276 TTCGAGCTTGAATCTAG
1 TTCGAGCTTGAATCTAG
103293 --CGAGCTTGAATC
1 TTCGAGCTTGAATC
103305 GAGCTCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.41
17 17 0.59
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (17 bp):
TTCGAGCTTGAATCTAG
Found at i:103926 original size:12 final size:12
Alignment explanation
Indices: 103911--103935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
103901 ACTTTCCATT
103911 TAACTACCTTTA
1 TAACTACCTTTA
103923 TAACTACCTTTA
1 TAACTACCTTTA
103935 T
1 T
103936 GAATTCTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACTACCTTTA
Found at i:105467 original size:32 final size:32
Alignment explanation
Indices: 105426--105493 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
105416 GGGTATTACA
*
105426 CCTTGGGTAGGCTCTTAGGCCCCAAGGTACTC
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTC
105458 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTC
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTC
105490 CCTT
1 CCTT
105494 AGGTTGTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.25
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTC
Found at i:116009 original size:19 final size:21
Alignment explanation
Indices: 115982--116030 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
115972 CATAAATGAC
* *
115982 ATCGATACCGTAAT-AG-AGT
1 ATCGGTACCATAATAAGAAGT
116001 ATCGGTACCATAATACAGAAGT
1 ATCGGTACCATAATA-AGAAGT
116023 ATCGGTAC
1 ATCGGTAC
116031 TGAGAGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.48
21 2 0.08
22 11 0.44
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCGGTACCATAATAAGAAGT
Found at i:116540 original size:45 final size:45
Alignment explanation
Indices: 116485--116726 Score: 349
Period size: 45 Copynumber: 5.4 Consensus size: 45
116475 ATATATTTTC
* * *
116485 GATGCACATAAATGAAATGCGTAACGGTGTATTGAAGGCATGAAAG
1 GATGC-CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
* * *
116531 GATGCCATAAATAAAATGCATAACGGTGCATTAAAGTCATGAAAA
1 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
* * **
116576 AATGACATAAATGAAATGCATAACAATGCATTAAAGGCATGAAAG
1 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
116621 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
1 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
* * * *
116666 AATGCTATAAATGAAATGCATAACGGTGCATTACAGGCATGCAAG
1 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
116711 GATGCCATAAATGAAA
1 GATGCCATAAATGAAA
116727 ATAATGAATA
Statistics
Matches: 173, Mismatches: 23, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
45 168 0.97
46 5 0.03
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (45 bp):
GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
Found at i:122023 original size:20 final size:18
Alignment explanation
Indices: 121981--122023 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
121971 GATGAAATTA
**
121981 GTATCGATACATAGGTGG
1 GTATCGATACATAGGAAG
121999 GTATCGATACCATGAGGAAG
1 GTATCGATA-CAT-AGGAAG
122019 GTATC
1 GTATC
122024 AATATATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 3 0.14
20 9 0.43
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (18 bp):
GTATCGATACATAGGAAG
Found at i:122206 original size:22 final size:22
Alignment explanation
Indices: 122164--122206 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
122154 ATACTGAAAG
*
122164 GAAGTATCAGTATCATAGTATA
1 GAAGTATCAGTACCATAGTATA
*
122186 GAAGTATC-GATACCATGGTAT
1 GAAGTATCAG-TACCATAGTAT
122207 GGGTACCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (22 bp):
GAAGTATCAGTACCATAGTATA
Found at i:122622 original size:45 final size:45
Alignment explanation
Indices: 122558--122793 Score: 382
Period size: 45 Copynumber: 5.2 Consensus size: 45
122548 TTTTGATCCA
*
122558 CATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
122603 CATAAATGAAATGTATAACGGTGCATTAAAGGCATGAAAGGATAC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
122648 CATAAATGAAATGCATAACAGTGTATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
122693 CATAAATAAAATGCATAACGGTGCATTAAAGGCATAAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
122738 CATAAATGAAATGCATAACGGTGCATTACAGGCATGAAAAGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
122783 CATGAATGAAA
1 CATAAATGAAA
122794 ATAATAAATA
Statistics
Matches: 175, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 175 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.21
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:131820 original size:3 final size:3
Alignment explanation
Indices: 131812--131892 Score: 105
Period size: 3 Copynumber: 26.7 Consensus size: 3
131802 TAAACAAATA
131812 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AACCT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T
131861 AAT -AT AAT AAAT AAT AAT -AT AAAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AA
131893 AAACTATATA
Statistics
Matches: 71, Mismatches: 0, Indels: 14
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.08
3 57 0.80
4 5 0.07
5 3 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:131942 original size:22 final size:22
Alignment explanation
Indices: 131906--131955 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
131896 CTATATATCA
* *
131906 TATATATTATATTTTCAGAAAC
1 TATATAATATATTTTCAAAAAC
* *
131928 TATATAATATGTTTTCAAAAAT
1 TATATAATATATTTTCAAAAAC
131950 TATATA
1 TATATA
131956 TATTATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATAATATATTTTCAAAAAC
Found at i:132085 original size:35 final size:35
Alignment explanation
Indices: 132046--132136 Score: 148
Period size: 35 Copynumber: 2.6 Consensus size: 35
132036 TTTTTTAACT
*
132046 ATATATTATATGTTTTCAAAAATATTTTCAAAACC
1 ATATATTATACGTTTTCAAAAATATTTTCAAAACC
*
132081 ATATATTATACGTTTTCAAAAATATTTTTAAAACC
1 ATATATTATACGTTTTCAAAAATATTTTCAAAACC
132116 ATAT-TATATACGTTTTCAAAA
1 ATATAT-TATACGTTTTCAAAA
132137 TCATATTATA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
34 1 0.02
35 52 0.98
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (35 bp):
ATATATTATACGTTTTCAAAAATATTTTCAAAACC
Found at i:132106 original size:91 final size:90
Alignment explanation
Indices: 131951--132192 Score: 226
Period size: 91 Copynumber: 2.6 Consensus size: 90
131941 TTCAAAAATT
* * *
131951 ATATATATTATATATGTTTTCAAAAATCGTTTTAAAAACCATATA-TATA-TATTCAAAAC-TAT
1 ATATATA-T-TATATGTTTTCAAAAAT-ATTTTCAAAACCATATATTATAGTTTTCAAAACATAT
* ** * *
132013 ATTAT-ATACGTTTTTAAAAACCGTTTTTTA
63 -TTATAAAACCATATTAAAAA-CG-TTTTCA
132043 ACTATATATTATATGTTTTCAAAAATATTTTCAAAACCATATATTATACGTTTTCAAAA-ATATT
1 A-TATATATTATATGTTTTCAAAAATATTTTCAAAACCATATATTATA-GTTTTCAAAACATATT
* * *
132107 TTTAAAACCATATTATATACGTTTTCA
64 TATAAAACCATATTAAAAACGTTTTCA
* *
132134 AAATCATATTATATATTTTCAAAAATATTTTCAAAACCATAT-TATATATGTTTTCAAAA
1 ATAT-ATATTATATGTTTTCAAAAATATTTTCAAAACCATATAT-TATA-GTTTTCAAAA
132193 GTATGTTAAA
Statistics
Matches: 128, Mismatches: 14, Indels: 17
0.81 0.09 0.11
Matches are distributed among these distances:
90 18 0.14
91 77 0.60
92 7 0.05
93 26 0.20
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (90 bp):
ATATATATTATATGTTTTCAAAAATATTTTCAAAACCATATATTATAGTTTTCAAAACATATTTA
TAAAACCATATTAAAAACGTTTTCA
Found at i:132152 original size:21 final size:21
Alignment explanation
Indices: 132102--132157 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 21
132092 GTTTTCAAAA
*
132102 ATATTTTTAAAACCATATTAT
1 ATATTTTCAAAACCATATTAT
*
132123 ATACGTTTTCAAAATCATATTAT
1 ATA--TTTTCAAAACCATATTAT
132146 ATATTTTCAAAA
1 ATATTTTCAAAA
132158 ATATTTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.39
23 19 0.61
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATTTTCAAAACCATATTAT
Found at i:132154 original size:56 final size:57
Alignment explanation
Indices: 132070--132192 Score: 187
Period size: 56 Copynumber: 2.2 Consensus size: 57
132060 TTCAAAAATA
*
132070 TTTTCAAAACCATATATTATACGTTTTCAAAAATATTTTTAAAACCATATTATATACG
1 TTTTCAAAACCATATATTATAC-TTTTCAAAAATATTTTCAAAACCATATTATATACG
* *
132128 TTTTCAAAATCATAT-TATATA-TTTTCAAAAATATTTTCAAAACCATATTATATATG
1 TTTTCAAAACCATATAT-TATACTTTTCAAAAATATTTTCAAAACCATATTATATACG
132184 TTTTCAAAA
1 TTTTCAAAA
132193 GTATGTTAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 42 0.69
57 1 0.02
58 18 0.30
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.43
Consensus pattern (57 bp):
TTTTCAAAACCATATATTATACTTTTCAAAAATATTTTCAAAACCATATTATATACG
Found at i:132175 original size:33 final size:34
Alignment explanation
Indices: 132128--132215 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 34
132118 ATTATATACG
*
132128 TTTTCAAAATCATATTATATA-TTTTCAAAAATA
1 TTTTCAAAACCATATTATATAGTTTTCAAAAATA
*
132161 TTTTCAAAACCATATTATATATGTTTTCAAAAGTA
1 TTTTCAAAACCATATTATATA-GTTTTCAAAAATA
* *
132196 TGTT-AAAATCTATATTATAT
1 TTTTCAAAA-CCATATTATAT
132216 GATTATGTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 20 0.42
34 4 0.08
35 24 0.50
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (34 bp):
TTTTCAAAACCATATTATATAGTTTTCAAAAATA
Found at i:132211 original size:91 final size:91
Alignment explanation
Indices: 132048--132215 Score: 259
Period size: 91 Copynumber: 1.8 Consensus size: 91
132038 TTTTAACTAT
* *
132048 ATATTATATGTTTTCAAAAATATTTTCAAAACCATATATTATACGTTTTCAAAAATATTTTTAAA
1 ATATTATATATTTTCAAAAATATTTTCAAAACCATATATTATACGTTTTCAAAAATATTGTTAAA
132113 ACCATATTATATACGTTTTCAAAATC
66 ACCATATTATATACGTTTTCAAAATC
* *
132139 ATATTATATATTTTCAAAAATATTTTCAAAACCATAT-TATATATGTTTTCAAAAGTA-TGTTAA
1 ATATTATATATTTTCAAAAATATTTTCAAAACCATATAT-TATACGTTTTCAAAAATATTGTTAA
*
132202 AATCTATATTATAT
65 AA-CCATATTATAT
132216 GATTATGTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
90 8 0.11
91 62 0.89
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (91 bp):
ATATTATATATTTTCAAAAATATTTTCAAAACCATATATTATACGTTTTCAAAAATATTGTTAAA
ACCATATTATATACGTTTTCAAAATC
Found at i:132987 original size:21 final size:19
Alignment explanation
Indices: 132955--132994 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
132945 CCGAAAATAT
*
132955 TAAAAATTTAATGTTTTAAA
1 TAAAAATATAAT-TTTTAAA
132975 TAAAAATAATAATTTTTAAA
1 TAAAAAT-ATAATTTTTAAA
132995 GTGATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAAATATAATTTTTAAA
Found at i:143123 original size:19 final size:19
Alignment explanation
Indices: 143093--143148 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
143083 AAAAGAAGAA
*
143093 AATATAATAAAATATAAAT
1 AATAAAATAAAATATAAAT
* * *
143112 GGATAAAA-AAAATACACAT
1 -AATAAAATAAAATATAAAT
143131 AATAAAATAAAATATAAA
1 AATAAAATAAAATATAAA
143149 GCAATGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 6 0.21
19 17 0.61
20 5 0.18
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATATAAAT
Found at i:144913 original size:12 final size:12
Alignment explanation
Indices: 144887--144931 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
144877 AAGAAAAATG
144887 TAATA-AATATA
1 TAATATAATATA
*
144898 TAATATAATTTA
1 TAATATAATATA
144910 TAATATAAATATA
1 TAATAT-AATATA
144923 TATATATAA
1 TA-ATATAA
144932 GGACGAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 9 0.31
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:145133 original size:20 final size:20
Alignment explanation
Indices: 145108--145147 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
145098 GTGAGGTTGA
145108 GTGAAATTGAAATCGAACTC
1 GTGAAATTGAAATCGAACTC
145128 GTGAAATTGAAATCGAACTC
1 GTGAAATTGAAATCGAACTC
145148 AGAGTTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
GTGAAATTGAAATCGAACTC
Found at i:145402 original size:105 final size:105
Alignment explanation
Indices: 145205--145838 Score: 1187
Period size: 105 Copynumber: 6.0 Consensus size: 105
145195 CGTTGTGAAG
* * *
145205 CTGAAATTGGGTAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGAAATTGAG-AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
145270 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
145311 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
145376 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
145416 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
145481 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGCAACTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
145521 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
145586 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
145626 CTGAAATTGAGAAACGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
145691 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
145731 CTGAAATTAAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
145796 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
145836 CTG
1 CTG
145839 GGTAAAACCT
Statistics
Matches: 517, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
105 507 0.98
106 10 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:146661 original size:59 final size:60
Alignment explanation
Indices: 146573--146686 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 60
146563 TTTTCTCTTC
* ** *
146573 TTTTTTCTCTTTTTTCTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCA-CCTAAACGTT
1 TTTTTTCTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAACGTT
* * * *
146632 TTTTTTTTTTTTTTTTTTTTTTAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTTCTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
146687 GCGAAGTATT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 41 0.89
60 5 0.11
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (60 bp):
TTTTTTCTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAACGTT
Found at i:156078 original size:10 final size:10
Alignment explanation
Indices: 156053--156086 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
156043 AACGTTAGTA
*
156053 AAATAGAAAT
1 AAATAAAAAT
*
156063 AGATAAAAAT
1 AAATAAAAAT
156073 AAATAAAAAT
1 AAATAAAAAT
156083 AAAT
1 AAAT
156087 GGTAAACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:158935 original size:12 final size:12
Alignment explanation
Indices: 158909--158953 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
158899 AAGAAAAATG
158909 TAATA-AATATA
1 TAATATAATATA
*
158920 TAATATAATTTA
1 TAATATAATATA
158932 TAATATAAATATA
1 TAATAT-AATATA
158945 TATATATAA
1 TA-ATATAA
158954 GGACGAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 9 0.31
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:159238 original size:12 final size:13
Alignment explanation
Indices: 159223--159254 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
159213 TTATCGAAAA
159223 TATTATTATTT-T
1 TATTATTATTTGT
159235 TATTATT-TTTGT
1 TATTATTATTTGT
159247 TATTATTA
1 TATTATTA
159255 GAAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 15 0.83
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TATTATTATTTGT
Found at i:168114 original size:23 final size:23
Alignment explanation
Indices: 168057--168114 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
168047 CTCGTATAAC
* *
168057 TGCACCGAAGTACCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAA
*
168080 TGCACCGAAGTGCCATGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAA
*
168103 TGCACCGTAGTG
1 TGCACCGAAGTG
168115 TCATATAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAA
Found at i:168885 original size:21 final size:21
Alignment explanation
Indices: 168861--168909 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
168851 AATTTAGTCT
168861 TAGTGTATCGGTACCCATTTA
1 TAGTGTATCGGTACCCATTTA
*
168882 TAGTGTATCGGTACCTATTTA
1 TAGTGTATCGGTACCCATTTA
168903 TAGTGTA
1 TAGTGTA
168910 CCGATATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (21 bp):
TAGTGTATCGGTACCCATTTA
Found at i:173444 original size:21 final size:21
Alignment explanation
Indices: 173418--173462 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
173408 GATTTCTGGG
* *
173418 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
173439 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
173460 CAA
1 CAA
173463 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:175204 original size:23 final size:22
Alignment explanation
Indices: 175148--175211 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
175138 TGGACATCAA
*
175148 TCTAC-GGCACTACGGTGCAAT
1 TCTACGGGCACTTCGGTGCAAT
175169 TCTACGGGCACTTCGGTGCAAT
1 TCTACGGGCACTTCGGTGCAAT
175191 TCTACGGGGCACTTCGGTGCA
1 TCTAC-GGGCACTTCGGTGCA
175212 TTTATACGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 5 0.12
22 20 0.50
23 15 0.38
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (22 bp):
TCTACGGGCACTTCGGTGCAAT
Found at i:182486 original size:92 final size:90
Alignment explanation
Indices: 182328--182511 Score: 278
Period size: 92 Copynumber: 2.0 Consensus size: 90
182318 TTTGTCAATT
* * * * * *
182328 TAATGTTGGTTTTGTTGTCAAACTCTTGAGTGAATTAATGTTCAAGTCTTTTTACAAGACAGAGG
1 TAATGTTAGTATTGTTGTCAAACCCTTGAGTGAATTAATGTTCAAGTCTTATCACAAGACAAAGG
*
182393 TAGTTTTTTTAAATTAATCTGGCCAAG
66 TAGTTTTTTT-AATTAATCTAG-CAAG
182420 TAATGTTAGTATTGTTGTCAAACCCTTGAGTGAATTAATGTTCAAGTCTTATCACAAGACAAAGG
1 TAATGTTAGTATTGTTGTCAAACCCTTGAGTGAATTAATGTTCAAGTCTTATCACAAGACAAAGG
*
182485 TAGTTTTTTTTATTAATCTAGCAAG
66 TAGTTTTTTTAATTAATCTAGCAAG
182510 TA
1 TA
182512 TAATACAATA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 6 0.07
91 9 0.11
92 69 0.82
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.40
Consensus pattern (90 bp):
TAATGTTAGTATTGTTGTCAAACCCTTGAGTGAATTAATGTTCAAGTCTTATCACAAGACAAAGG
TAGTTTTTTTAATTAATCTAGCAAG
Found at i:191429 original size:14 final size:14
Alignment explanation
Indices: 191383--191420 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
191373 CGTTGGGCAT
*
191383 CCGAAGCCATCCGA
1 CCGAGGCCATCCGA
*
191397 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
191411 CCGAGGCCAT
1 CCGAGGCCAT
191421 TCGAGCGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:191517 original size:29 final size:29
Alignment explanation
Indices: 191476--191577 Score: 158
Period size: 29 Copynumber: 3.7 Consensus size: 29
191466 GAGGAGCAGG
191476 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
191505 AGGAGTGCATGGCGACCTACAAGGT--CT
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
191532 AGGAGTGC--GGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
191559 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
191578 TGCTGGGAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
25 15 0.23
27 17 0.26
29 34 0.52
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:194802 original size:15 final size:15
Alignment explanation
Indices: 194782--194812 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
194772 TTTTCCTGTA
194782 ACACTCTTTGTGGGC
1 ACACTCTTTGTGGGC
194797 ACACTCTTTGTGGGC
1 ACACTCTTTGTGGGC
194812 A
1 A
194813 AAACTTCTTA
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:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (15 bp):
ACACTCTTTGTGGGC
Found at i:196756 original size:350 final size:349
Alignment explanation
Indices: 196115--196816 Score: 1242
Period size: 350 Copynumber: 2.0 Consensus size: 349
196105 GTGGTAGAAA
* **
196115 TAAAAGATAAGAATTAGAAAAAAGATTTATAGTAGTTCAACTTTCTCAATCAAAGTCTACATTCA
1 TAAAAGATAAGAATTAGAAAAAAGATCTATAGTAGTTCAACTTTCTCAATCAAAGTCTACAACCA
196180 CTACCTTAGCTCCACACTAAGGATTTCAACAAATTCACTATTTTTTCTTTCTTTTTCTAGGCTCA
66 CTACCTTAGCTCCACACTAAGGATTTCAACAAATTCACTATTTTTTCTTTCTTTTTCTAGGCTCA
* * *
196245 AGAGTAACCTTTACAACTCTCTAGTTTTCAAGGATAAACTATAATCACTCCCCTTTTACAAATGA
131 AGAGTAACCCTTACAACTCTCTAGTTTTCAAGGATAAACTATAACCACTCCCCTTTTACAAAGGA
*
196310 TAAGAAATGTAAACAAGAAACCTCACAAGGTAGGTGTTTACAAAGATTTAAGCTCACAAGAATAA
196 TAAGAAATGTAAACAAGAAACCTCACAAGGTAGATGTTTACAAAGATTTAAGCTCACAAGAATAA
* *
196375 AAACAAAAGATATTCAATTAAACTCTGTACACTTATGTGCAAGATAAAAATGAAGGAAATATGAA
261 AAACAAAAGATATTCAATTAAACTATGTACACTTATGTGCAAGATAAAAATGAAGGAAATAGGAA
196440 TAAAAACTCTTTTCTCTTGATCTC
326 TAAAAACTCTTTTCTCTTGATCTC
* * *
196464 TAAAAGATAAGAATTAGAAACAAGATCTATAGTGGTTCGACTTTCTCAATCAAAGTCTACAACCA
1 TAAAAGATAAGAATTAGAAAAAAGATCTATAGTAGTTCAACTTTCTCAATCAAAGTCTACAACCA
* *
196529 CTATCTTAGCTCCATACTAAGGATTTCAACAAATTCACTAATTTTTTCTTTCTTTTTCTAGGCTC
66 CTACCTTAGCTCCACACTAAGGATTTCAACAAATTCACT-ATTTTTTCTTTCTTTTTCTAGGCTC
*
196594 AAGAGTAACCCTTACAACTCTTTAGTTTTCAAGGATAAACTATAACCACTCCCCTTTTACAAAGG
130 AAGAGTAACCCTTACAACTCTCTAGTTTTCAAGGATAAACTATAACCACTCCCCTTTTACAAAGG
*
196659 ATAAGAAATGTAAACAAGAAACCTCACAAGGTAGATGTTTCCAAAGATTTAAGCTCACAAGAATA
195 ATAAGAAATGTAAACAAGAAACCTCACAAGGTAGATGTTTACAAAGATTTAAGCTCACAAGAATA
*
196724 AAAACAAAAGATATTCAATTAAACTATGTACACTTCTGTGCAAGATAAAAATGAAGGAAATAGGA
260 AAAACAAAAGATATTCAATTAAACTATGTACACTTATGTGCAAGATAAAAATGAAGGAAATAGGA
196789 ATAAAAACTCTTTTCTCTTGATCTC
325 ATAAAAACTCTTTTCTCTTGATCTC
196814 TAA
1 TAA
196817 GCTTAGAAAG
Statistics
Matches: 335, Mismatches: 17, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
349 96 0.29
350 239 0.71
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (349 bp):
TAAAAGATAAGAATTAGAAAAAAGATCTATAGTAGTTCAACTTTCTCAATCAAAGTCTACAACCA
CTACCTTAGCTCCACACTAAGGATTTCAACAAATTCACTATTTTTTCTTTCTTTTTCTAGGCTCA
AGAGTAACCCTTACAACTCTCTAGTTTTCAAGGATAAACTATAACCACTCCCCTTTTACAAAGGA
TAAGAAATGTAAACAAGAAACCTCACAAGGTAGATGTTTACAAAGATTTAAGCTCACAAGAATAA
AAACAAAAGATATTCAATTAAACTATGTACACTTATGTGCAAGATAAAAATGAAGGAAATAGGAA
TAAAAACTCTTTTCTCTTGATCTC
Found at i:196993 original size:20 final size:19
Alignment explanation
Indices: 196965--197015 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
196955 GCACATGCAA
*
196965 TTTCAAAACTTTGAAGAAAG
1 TTTCGAAACTTTG-AGAAAG
196985 TTTCGAAACTTTTGAGAAAG
1 TTTCGAAAC-TTTGAGAAAG
197005 TTTCGAAACTT
1 TTTCGAAACTT
197016 AATGAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 23 0.79
21 4 0.14
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (19 bp):
TTTCGAAACTTTGAGAAAG
Found at i:197024 original size:19 final size:19
Alignment explanation
Indices: 196979--197034 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
196969 AAAACTTTGA
*
196979 AGAAAGTTTCGAAACTTTT
1 AGAAAGTTTCGAAACTTAT
196998 GAGAAAGTTTCGAAACTTA-
1 -AGAAAGTTTCGAAACTTAT
* *
197017 ATGAAAGTATCAAAACTT
1 A-GAAAGTTTCGAAACTT
197035 TTAAACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 14 0.44
20 17 0.53
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (19 bp):
AGAAAGTTTCGAAACTTAT
Found at i:197188 original size:20 final size:20
Alignment explanation
Indices: 197145--197201 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
197135 TTATGGGTGC
* **
197145 AAAGTTTTGAAACT-TTTGT
1 AAAGTTTCGAAACTCTTAAT
197164 AAAGTTTCGAAACTCTTAAT
1 AAAGTTTCGAAACTCTTAAT
*
197184 AAAGTTTCAAAACTCTTA
1 AAAGTTTCGAAACTCTTA
197202 CAAAGTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTAAT
Found at i:197211 original size:20 final size:20
Alignment explanation
Indices: 197164--197214 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
197154 AAACTTTTGT
* *
197164 AAAGTTTCGAAACTCTTAAT
1 AAAGTTTCAAAACTCTTAAC
197184 AAAGTTTCAAAACTCTT-AC
1 AAAGTTTCAAAACTCTTAAC
197203 AAAGTTTTCAAA
1 AAAG-TTTCAAA
197215 CTATGAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAGTTTCAAAACTCTTAAC
Found at i:197309 original size:11 final size:11
Alignment explanation
Indices: 197293--197329 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
197283 ATTTAAAAAG
197293 TTTTAAACACA
1 TTTTAAACACA
197304 TTTTAAACAC-
1 TTTTAAACACA
*
197314 -TTTAAACATA
1 TTTTAAACACA
197324 TTTTAA
1 TTTTAA
197330 TTAACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTTAAACACA
Found at i:199133 original size:23 final size:22
Alignment explanation
Indices: 199066--199121 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
199056 GTGGAATTCA
*
199066 AAGGGTGGTACCAGTACTAGTTG
1 AAGGG-GGTATCAGTACTAGTTG
199089 AAGGGGGTATCAGTACTAGTTG
1 AAGGGGGTATCAGTACTAGTTG
199111 AAGGGGGTATC
1 AAGGGGGTATC
199122 GATATTGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.25
Consensus pattern (22 bp):
AAGGGGGTATCAGTACTAGTTG
Found at i:199812 original size:21 final size:21
Alignment explanation
Indices: 199788--199901 Score: 90
Period size: 21 Copynumber: 5.2 Consensus size: 21
199778 GAGGGTCTTG
*
199788 TGTGGTCCTTAGGGACAATTA
1 TGTGGTCCTTCGGGACAATTA
199809 TGTGG-CACTTCGGTG-CAAACTTA
1 TGTGGTC-CTTCGG-GAC-AA-TTA
* *
199832 TGTGGTCATTCGGGACAAATA
1 TGTGGTCCTTCGGGACAATTA
* *
199853 TGTGGTACTTCGGCG-CAAACCTA
1 TGTGGTCCTTCGG-GAC-AA-TTA
*
199876 TGTGGTCATTCGGGACAATTA
1 TGTGGTCCTTCGGGACAATTA
199897 TGTGG
1 TGTGG
199902 CACTTAAGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.01
21 32 0.43
22 12 0.16
23 28 0.38
24 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (21 bp):
TGTGGTCCTTCGGGACAATTA
Found at i:199832 original size:23 final size:21
Alignment explanation
Indices: 199804--199906 Score: 88
Period size: 23 Copynumber: 4.7 Consensus size: 21
199794 CCTTAGGGAC
199804 AATTATGTGGCACTTCGGTGCA
1 AATTATGTGGCACTTCGG-GCA
199826 AACTTATGTGGTCA-TTCGGGACA
1 AA-TTATGTGG-CACTTCGGG-CA
*
199849 AA-TATGTGGTACTTCGGCGCA
1 AATTATGTGGCACTTCGG-GCA
*
199870 AACCTATGTGGTCA-TTCGGG-A
1 AA-TTATGTGG-CACTTCGGGCA
199891 CAATTATGTGGCACTT
1 -AATTATGTGGCACTT
199907 AAGTACAAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
20 3 0.04
21 26 0.38
22 7 0.10
23 29 0.43
24 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (21 bp):
AATTATGTGGCACTTCGGGCA
Found at i:199855 original size:44 final size:44
Alignment explanation
Indices: 199788--199906 Score: 184
Period size: 44 Copynumber: 2.7 Consensus size: 44
199778 GAGGGTCTTG
* * * *
199788 TGTGGTCCTTAGGGACAATTATGTGGCACTTCGGTGCAAACTTA
1 TGTGGTCATTCGGGACAATTATGTGGCACTTCGGCGCAAACCTA
* *
199832 TGTGGTCATTCGGGACAAATATGTGGTACTTCGGCGCAAACCTA
1 TGTGGTCATTCGGGACAATTATGTGGCACTTCGGCGCAAACCTA
199876 TGTGGTCATTCGGGACAATTATGTGGCACTT
1 TGTGGTCATTCGGGACAATTATGTGGCACTT
199907 AAGTACAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (44 bp):
TGTGGTCATTCGGGACAATTATGTGGCACTTCGGCGCAAACCTA
Found at i:201175 original size:21 final size:21
Alignment explanation
Indices: 201150--201192 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
201140 ATTCGACAGA
*
201150 TGAAGCAAGAATTCATGAGCT
1 TGAAGAAAGAATTCATGAGCT
201171 TGAAGAAAGAATTCATGAGCT
1 TGAAGAAAGAATTCATGAGCT
201192 T
1 T
201193 AAAGTAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.26
Consensus pattern (21 bp):
TGAAGAAAGAATTCATGAGCT
Found at i:205539 original size:25 final size:25
Alignment explanation
Indices: 205506--205557 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
205496 AAAAAACACA
*
205506 CAAATAACCAAAACATCCAAAT-ATT
1 CAAACAACC-AAACATCCAAATCATT
*
205531 CAAACAACCAAATATCCAAATCATT
1 CAAACAACCAAACATCCAAATCATT
205556 CA
1 CA
205558 TCAAAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (25 bp):
CAAACAACCAAACATCCAAATCATT
Found at i:205541 original size:16 final size:16
Alignment explanation
Indices: 205506--205550 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
205496 AAAAAACACA
* *
205506 CAAATAACCAAAACATC
1 CAAATATCC-AAACAAC
*
205523 CAAATATTCAAACAAC
1 CAAATATCCAAACAAC
205539 CAAATATCCAAA
1 CAAATATCCAAA
205551 TCATTCATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.16
Consensus pattern (16 bp):
CAAATATCCAAACAAC
Found at i:213412 original size:44 final size:44
Alignment explanation
Indices: 213346--213442 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 44
213336 CAACTCAACG
* *
213346 ATATCGATAATGTCCTAGGAGTATCGATACTACTTTGTATAGTA
1 ATATCGATAACGTCCTAGGAGTATCGATACTACTATGTATAGTA
*
213390 ATATCGATACCGTCC-AGTGAGTATCGATACTACTATGTATAGTA
1 ATATCGATAACGTCCTAG-GAGTATCGATACTACTATGTATAGTA
*
213434 GTATCGATA
1 ATATCGATA
213443 TCGAACATGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 2 0.04
44 46 0.96
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (44 bp):
ATATCGATAACGTCCTAGGAGTATCGATACTACTATGTATAGTA
Found at i:213438 original size:24 final size:23
Alignment explanation
Indices: 213365--213442 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 23
213355 ATGTCCTAGG
213365 AGTATCGATACTACTTTGTATAGT
1 AGTATCGATACTAC-TTGTATAGT
* **
213389 AATATCGATAC--C--GTCCAGT
1 AGTATCGATACTACTTGTATAGT
213408 GAGTATCGATACTACTATGTATAGT
1 -AGTATCGATACTACT-TGTATAGT
213433 AGTATCGATA
1 AGTATCGATA
213443 TCGAACATGG
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 5 0.12
20 10 0.24
22 2 0.05
24 20 0.48
25 5 0.12
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (23 bp):
AGTATCGATACTACTTGTATAGT
Found at i:215569 original size:20 final size:21
Alignment explanation
Indices: 215521--215573 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
215511 TTAAAAGGGT
*
215521 GGTATCTATACTAGTTGAAGGA
1 GGTATCGATACTAGTTG-AGGA
215543 GGTATCGATACTGAGTTG-GGA
1 GGTATCGATACT-AGTTGAGGA
215564 -GTATCGATAC
1 GGTATCGATAC
215574 CAAGGGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.34
21 3 0.10
22 11 0.38
23 5 0.17
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.30
Consensus pattern (21 bp):
GGTATCGATACTAGTTGAGGA
Found at i:216268 original size:44 final size:43
Alignment explanation
Indices: 216219--216349 Score: 172
Period size: 44 Copynumber: 3.0 Consensus size: 43
216209 AGTCGAGGGT
* *
216219 CTTATGTAGTCCTTAGGGACAATTATGTGGCACTTCGGTTCAAA
1 CTTATGTGGT-CTTAGGGACAATTATGTGGCACTTCGGTGCAAA
* * *
216263 CTTATGTGGTTCTTTGTGACAATTATGTGGCACTTCAGTGCAAA
1 CTTATGTGG-TCTTAGGGACAATTATGTGGCACTTCGGTGCAAA
* * *
216307 CCTATGTGGTCTTCGGGATAATTATGTGGCACTTCGGTGCAAA
1 CTTATGTGGTCTTAGGGACAATTATGTGGCACTTCGGTGCAAA
216350 TTACGAGCTG
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
43 30 0.39
44 45 0.59
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (43 bp):
CTTATGTGGTCTTAGGGACAATTATGTGGCACTTCGGTGCAAA
Found at i:216343 original size:21 final size:21
Alignment explanation
Indices: 216234--216343 Score: 71
Period size: 21 Copynumber: 5.1 Consensus size: 21
216224 GTAGTCCTTA
216234 GGGACAATTATGTGGCACTTC
1 GGGACAATTATGTGGCACTTC
** ** *
216255 GGTTCAAACTTATGTGGTTCTTT
1 GGGAC-AA-TTATGTGGCACTTC
*
216278 GTGACAATTATGTGGCACTTC
1 GGGACAATTATGTGGCACTTC
* * *
216299 AGTG-CAAACCTATGTGG-TCTTC
1 -GGGAC-AA-TTATGTGGCACTTC
*
216321 GGGATAATTATGTGGCACTTC
1 GGGACAATTATGTGGCACTTC
216342 GG
1 GG
216344 TGCAAATTAC
Statistics
Matches: 65, Mismatches: 17, Indels: 14
0.68 0.18 0.15
Matches are distributed among these distances:
20 7 0.11
21 25 0.38
22 13 0.20
23 20 0.31
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (21 bp):
GGGACAATTATGTGGCACTTC
Found at i:217654 original size:24 final size:24
Alignment explanation
Indices: 217627--217688 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
217617 TCAAACTTGC
*
217627 CATGTCCTATCCTTTCATACCTGA
1 CATGTCCCATCCTTTCATACCTGA
*
217651 CATGTCCCAT-CTTTCATACTTGA
1 CATGTCCCATCCTTTCATACCTGA
217674 CATGTCCCATCCTTT
1 CATGTCCCATCCTTT
217689 AGCACTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 22 0.63
24 13 0.37
ACGTcount: A:0.19, C:0.34, G:0.08, T:0.39
Consensus pattern (24 bp):
CATGTCCCATCCTTTCATACCTGA
Found at i:225581 original size:59 final size:57
Alignment explanation
Indices: 225470--225587 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 57
225460 AATAGATGGA
* *
225470 TAAGTGTCCTATCAAACCCTCCTAGTCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCAATGAAAAGGAAAACTCGATAATATGACTC
* *
225527 TAAGTGTCCTATCGAACCCTTCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
1 TAAGTGTCCTATCAAACCCTCCTAGT--CAATGAAAAGGAAAACTCGATAATATGACTC
225586 TA
1 TA
225588 TTCAACCCTC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 24 0.44
59 31 0.56
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (57 bp):
TAAGTGTCCTATCAAACCCTCCTAGTCAATGAAAAGGAAAACTCGATAATATGACTC
Found at i:232919 original size:22 final size:22
Alignment explanation
Indices: 232888--232942 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
232878 AACACTCTAT
*
232888 GGTGAGTCACCACCATAGGTCC
1 GGTGACTCACCACCATAGGTCC
232910 GGTGACTCACCACCATAGGTCC
1 GGTGACTCACCACCATAGGTCC
232932 GGTGACTCACC
1 GGTGACTCACC
232943 GGATTTCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (22 bp):
GGTGACTCACCACCATAGGTCC
Found at i:233791 original size:18 final size:18
Alignment explanation
Indices: 233770--233859 Score: 62
Period size: 18 Copynumber: 4.9 Consensus size: 18
233760 TATGTTAGTC
233770 ATTAATTATTATAATAAG
1 ATTAATTATTATAATAAG
* *
233788 ATTAATTATAAT-AT-TG
1 ATTAATTATTATAATAAG
*
233804 GTATAATT-TTATATATTAAG
1 AT-TAATTATTATA-A-TAAG
*
233824 TTTAATT-TTATAATATAG
1 ATTAATTATTATAATA-AG
233842 TATTACATTATTATAATA
1 -ATTA-ATTATTATAATA
233860 GGACTATAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
16 5 0.09
17 9 0.16
18 15 0.27
19 14 0.25
20 5 0.09
21 8 0.14
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTAATTATTATAATAAG
Found at i:240273 original size:57 final size:56
Alignment explanation
Indices: 240185--240298 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 56
240175 AACCTTGCTC
240185 GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGATAAAATCCTTCTTGTGAA
1 GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGAT-AAATCCTTCTTGTGAA
* *
240242 GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCTTTCTTTTGAA
1 GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAA
240298 G
1 G
240299 TGTTTCAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 15 0.27
57 40 0.73
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (56 bp):
GAGATCTGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCCTTCTTGTGAA
Found at i:240593 original size:8 final size:8
Alignment explanation
Indices: 240580--240614 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
240570 TAAAGGATTG
240580 ATACATTC
1 ATACATTC
240588 ATACATTC
1 ATACATTC
240596 ATACATTC
1 ATACATTC
240604 ATACATTC
1 ATACATTC
240612 ATA
1 ATA
240615 AAGGATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATTC
Found at i:241200 original size:20 final size:20
Alignment explanation
Indices: 241175--241243 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
241165 TTTCTCACGA
*
241175 ATTTGTAAAGCCTTTGGGTC
1 ATTTGTAAAGCCTTCGGGTC
241195 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTTCGGGTC
241215 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTTCGGGTC
241235 ATTTGTAAA
1 ATTTGTAAA
241244 ATACTTTGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTTGTAAAGCCTTCGGGTC
Found at i:244410 original size:29 final size:29
Alignment explanation
Indices: 244368--244426 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
244358 TAATTTTCAT
*
244368 AACTAAATTGATGTAAGCAGTGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
244397 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
244426 A
1 A
244427 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:249077 original size:28 final size:29
Alignment explanation
Indices: 249024--249081 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 29
249014 ATTTTCACCT
249024 AACTAAATGATGTAAAGCAATGACATCAA
1 AACTAAATGATGTAAAGCAATGACATCAA
249053 AACTAAATTGA-GT-AAGCAATGACATCAA
1 AACTAAA-TGATGTAAAGCAATGACATCAA
249081 A
1 A
249082 TTAATTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 16 0.57
29 9 0.32
30 3 0.11
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (29 bp):
AACTAAATGATGTAAAGCAATGACATCAA
Found at i:253292 original size:19 final size:19
Alignment explanation
Indices: 253234--253293 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
253224 TTGATTGAAT
253234 ATAATTAAATTTATGAAAA
1 ATAATTAAATTTATGAAAA
* * * *
253253 AT-ACT-GATAT-TGAATA
1 ATAATTAAATTTATGAAAA
*
253269 TTAATTAAATTTATGAAAA
1 ATAATTAAATTTATGAAAA
253288 ATAATT
1 ATAATT
253294 GAACTAAATT
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
16 6 0.21
17 5 0.18
18 5 0.18
19 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (19 bp):
ATAATTAAATTTATGAAAA
Found at i:254543 original size:2 final size:2
Alignment explanation
Indices: 254538--254568 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
254528 AAACTCTTGA
254538 AT AT AT -T 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
254569 TAGTGGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:255484 original size:16 final size:15
Alignment explanation
Indices: 255465--255494 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
255455 TTTTTATAAA
255465 TAAAAATATTATTTTC
1 TAAAAATATT-TTTTC
255481 TAAAAATATTTTTT
1 TAAAAATATTTTTT
255495 AAAAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAAAATATTTTTTC
Found at i:257597 original size:21 final size:21
Alignment explanation
Indices: 257573--257615 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
257563 AATATGTCTC
*
257573 AAGTGGAGAACTTG-TTTGTTG
1 AAGTGAAGAA-TTGTTTTGTTG
*
257594 AAGTGAATAATTGTTTTGTTG
1 AAGTGAAGAATTGTTTTGTTG
257615 A
1 A
257616 GTTTAGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.42
Consensus pattern (21 bp):
AAGTGAAGAATTGTTTTGTTG
Found at i:262860 original size:22 final size:21
Alignment explanation
Indices: 262818--262869 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
262808 ATTCTGACTA
262818 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
262839 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGA-TTTCCCAAAT
*
262860 TCGCAATGCG
1 TCGCATTGCG
262870 GTTACATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:262863 original size:21 final size:20
Alignment explanation
Indices: 262817--262892 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
262807 GATTCTGACT
262817 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
262837 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
* * * **
262859 ATCGCAATGCGGTTACATAA
1 ATCGCATTGCGATTTCCCAA
*
262879 ATCGCAATGCGATT
1 ATCGCATTGCGATT
262893 ACGTAAATCG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.43
21 18 0.39
22 8 0.17
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:263092 original size:20 final size:20
Alignment explanation
Indices: 262856--263087 Score: 383
Period size: 20 Copynumber: 11.6 Consensus size: 20
262846 GCGATTTTCC
*
262856 TAAATCGCAATGCGGTTACA
1 TAAATCGCAATGCGGTTACG
*
262876 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGGTTACG
*
262896 TAAATCGCAATGAGGTTACG
1 TAAATCGCAATGCGGTTACG
*
262916 TAAATTGCAATGCGGTTACG
1 TAAATCGCAATGCGGTTACG
262936 TAAATCGCAATGCGGTTACG
1 TAAATCGCAATGCGGTTACG
*
262956 TAAATCGCAATGCAGTTACG
1 TAAATCGCAATGCGGTTACG
*
262976 TAAATCGCAATGTGGTTACG
1 TAAATCGCAATGCGGTTACG
262996 TAAATCGCAATGCGGTTACG
1 TAAATCGCAATGCGGTTACG
263016 TAAATCGCAATGCGGTTACG
1 TAAATCGCAATGCGGTTACG
263036 TAAATCGCAATGCGGTTACG
1 TAAATCGCAATGCGGTTACG
**
263056 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGGTTACG
*
263076 TAAATTGCAATG
1 TAAATCGCAATG
263088 TGAATCTGAC
Statistics
Matches: 198, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 198 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (20 bp):
TAAATCGCAATGCGGTTACG
Found at i:263756 original size:20 final size:20
Alignment explanation
Indices: 263719--263776 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
263709 GATTCTTGCG
**
263719 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
263739 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
**
263759 TTGCGATTTTCATTTTCG
1 TTGCGATAGTCATTTTCG
263777 TGTTGCGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:263777 original size:20 final size:20
Alignment explanation
Indices: 263748--263787 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
263738 ATTGCGATAG
263748 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
263768 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
263788 AAAGTTTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.55
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:263795 original size:20 final size:20
Alignment explanation
Indices: 263752--263795 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
263742 CGATAGTCAT
** *
263752 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
263772 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
263792 TTTC
1 TTTC
263796 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:265695 original size:20 final size:20
Alignment explanation
Indices: 265670--265753 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
265660 AGAATAGTTT
265670 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
265690 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
265706 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* * *
265724 ACTATTGTAATGCGAAAACG
1 ACTATCGCAATGCGAAAATG
265744 ACTATCGCAA
1 ACTATCGCAA
265754 CGAAAGAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 7 0.14
16 4 0.08
17 4 0.08
18 4 0.08
20 32 0.63
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:265825 original size:20 final size:20
Alignment explanation
Indices: 265800--265866 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
265790 GATTATCTCG
**
265800 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
265820 TTGCGATAGTCATTTTCTCA
1 TTGCGATAGTCATTTTCGCA
*
265840 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
265860 TTGCGAT
1 TTGCGAT
265867 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:266441 original size:21 final size:21
Alignment explanation
Indices: 266350--266454 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
266340 AACTCACCTG
*
266350 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
266372 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
266392 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
266413 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
266434 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
266455 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:266447 original size:42 final size:42
Alignment explanation
Indices: 266347--266457 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
266337 CCCAACTCAC
* * * *
266347 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
266389 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
266431 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
266458 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:267749 original size:14 final size:14
Alignment explanation
Indices: 267730--267765 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
267720 ATTGTTTAAT
267730 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
267744 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
267758 TGATTTGT
1 TGATTTGT
267766 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:267955 original size:34 final size:33
Alignment explanation
Indices: 267867--267962 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
267857 AAAACAGACT
* **
267867 ATCGCAACGCGGAAATGATTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
267901 ATCGCAATGCGAAATGAAAATCACAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
267934 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
267963 CGAAACTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:268161 original size:33 final size:33
Alignment explanation
Indices: 268115--268182 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
268105 TCGCAACGCG
**
268115 GAAATGACTATCGCAACGAGAGAATAGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATAGCAATGC
* * *
268148 GAAATGAAAATCGCAACGAGTGAATCGCATTGC
1 GAAATGAAAATCGCAACGAGAGAATAGCAATGC
268181 GA
1 GA
268183 TTCACTCGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATAGCAATGC
Found at i:268219 original size:19 final size:19
Alignment explanation
Indices: 268195--268236 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
268185 CACTCGTTGT
268195 GATTTTCATTTCGCATTGA
1 GATTTTCATTTCGCATTGA
*
268214 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGA
268233 GATT
1 GATT
268237 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGA
Found at i:268234 original size:52 final size:54
Alignment explanation
Indices: 268172--268289 Score: 150
Period size: 52 Copynumber: 2.2 Consensus size: 54
268162 AACGAGTGAA
* ** **
268172 TCGCATTGCGATTCACTCGTTGTGATTTTCATTT-CGCATTGAGATTTTC-ATT
1 TCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCGCATTGAGATAGTCAATT
* *
268224 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATAGTCAATT
1 TCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCGCATTGAGATAGTCAATT
*
268278 CCGCATTGCGAT
1 TCGCATTGCGAT
268290 AATCATTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 30 0.54
53 12 0.21
54 14 0.25
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (54 bp):
TCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCGCATTGAGATAGTCAATT
Found at i:268268 original size:20 final size:20
Alignment explanation
Indices: 268243--268329 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
268233 GATTCTCTCG
268243 TTGCGATAGTCATTTCCGCA
1 TTGCGATAGTCATTTCCGCA
*
268263 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTCCGCA
* * **
268283 TTGCGATAATCATTTACGTG
1 TTGCGATAGTCATTTCCGCA
* *
268303 CTGCGATAGTCATATT-CGCG
1 TTGCGATAGTCAT-TTCCGCA
268323 TTGCGAT
1 TTGCGAT
268330 TTCTGCGTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 54 0.96
21 2 0.04
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCA
Found at i:271662 original size:20 final size:20
Alignment explanation
Indices: 271649--271718 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
271639 CAGAATCTCG
*
271649 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTAATCGCA
*
271669 TTGCGATTTACGTAATCGCT
1 TTGCGATTTACGTAATCGCA
271689 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
271709 TTGCGATTTA
1 TTGCGATTTA
271719 GGAAAATCAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 1 0.02
20 45 0.98
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:279960 original size:23 final size:22
Alignment explanation
Indices: 279899--279976 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
279889 TTCGGCGCTA
* *
279899 GGTATCGATACCCCCTTGCA-TG
1 GGTACCGATACCCCCTT-TAGTG
* * *
279921 GGTACCAATTCCTCCTTTAAGTG
1 GGTACCGATACCCCCTTT-AGTG
*
279944 GGTACCGATACCCCC-TT-GAG
1 GGTACCGATACCCCCTTTAGTG
279964 GGTACCGATACCC
1 GGTACCGATACCC
279977 TCCACGGGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 15 0.33
22 16 0.36
23 14 0.31
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.26
Consensus pattern (22 bp):
GGTACCGATACCCCCTTTAGTG
Found at i:282277 original size:12 final size:13
Alignment explanation
Indices: 282249--282281 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
282239 AGGGGGAGTA
*
282249 ATTTCAAAACTTG
1 ATTTCAAAACATG
282262 ATTTCAAAA-ATG
1 ATTTCAAAACATG
282274 ATTTCAAA
1 ATTTCAAA
282282 TTAGAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (13 bp):
ATTTCAAAACATG
Done.