Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015282.1 Kokia drynarioides strain JFW-HI SEQ_130327, 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: 423680
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 323 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:18057 original size:14 final size:14
Alignment explanation
Indices: 18038--18067 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18028 GAATAAATCT
18038 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
18052 TTAATTAATTAAAA
1 TTAATTAAATAAAA
18066 TT
1 TT
18068 TTTAAACCCT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:18410 original size:18 final size:16
Alignment explanation
Indices: 18379--18422 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
18369 AGTTTAAGGT
*
18379 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
18396 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
18410 TTAAAAATTTATT
1 TTAAAAATTTATT
18423 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:18706 original size:32 final size:32
Alignment explanation
Indices: 18665--18726 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
18655 TCGAGTTGGC
*
18665 GCTTGATTGGCTCGTGACACCAACTTAATCGT
1 GCTTGATTGGCTCGAGACACCAACTTAATCGT
*
18697 GCTTGATTGGCTTGAGACACCAACTTAATC
1 GCTTGATTGGCTCGAGACACCAACTTAATC
18727 AAGGCTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (32 bp):
GCTTGATTGGCTCGAGACACCAACTTAATCGT
Found at i:23133 original size:19 final size:18
Alignment explanation
Indices: 23100--23139 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
23090 ATGAAAAGCA
* *
23100 AAATAAAATATAGAGCGC
1 AAATAAAATAAAGAGCCC
23118 AAATAAAATAAAAGAGCCC
1 AAATAAAAT-AAAGAGCCC
23137 AAA
1 AAA
23140 CAAAGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (18 bp):
AAATAAAATAAAGAGCCC
Found at i:23432 original size:26 final size:28
Alignment explanation
Indices: 23403--23472 Score: 90
Period size: 26 Copynumber: 2.6 Consensus size: 28
23393 ATTCAAGTAT
23403 AATGAATGAAATTTTTAA-TAAAAAT-A
1 AATGAATGAAATTTTTAATTAAAAATAA
* * *
23429 AATGAATGAATTTTTTAATTGACAATAA
1 AATGAATGAAATTTTTAATTAAAAATAA
*
23457 AATGGATGAAATTTTT
1 AATGAATGAAATTTTT
23473 TACGTGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 17 0.46
27 5 0.14
28 15 0.41
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (28 bp):
AATGAATGAAATTTTTAATTAAAAATAA
Found at i:26336 original size:7 final size:7
Alignment explanation
Indices: 26324--26356 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
26314 GTGGTTCAGA
26324 TGATGAT
1 TGATGAT
26331 TGATGAT
1 TGATGAT
26338 TGATGAT
1 TGATGAT
26345 TGATGAT
1 TGATGAT
26352 TGATG
1 TGATG
26357 TATTTTGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.42
Consensus pattern (7 bp):
TGATGAT
Found at i:32283 original size:13 final size:13
Alignment explanation
Indices: 32265--32289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32255 TCCTCTCTTT
32265 TTTTTGCTCTGTA
1 TTTTTGCTCTGTA
32278 TTTTTGCTCTGT
1 TTTTTGCTCTGT
32290 TTTGAGCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.16, T:0.64
Consensus pattern (13 bp):
TTTTTGCTCTGTA
Found at i:32662 original size:18 final size:18
Alignment explanation
Indices: 32624--32660 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
32614 AAAAACTAGA
*
32624 TAAAATATCTAAAATATT
1 TAAAATATATAAAATATT
32642 TAAAATAATATAAAATATT
1 TAAAAT-ATATAAAATATT
32661 AATATTAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATATATAAAATATT
Found at i:35082 original size:22 final size:22
Alignment explanation
Indices: 35049--35091 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35039 TCTTGTGGAC
*
35049 ATAATAATTGAAGTTTAGTGTG
1 ATAATAATTGAAATTTAGTGTG
*
35071 ATAATTAA-TGAAATTTGGTGT
1 ATAA-TAATTGAAATTTAGTGT
35092 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (22 bp):
ATAATAATTGAAATTTAGTGTG
Found at i:48936 original size:18 final size:18
Alignment explanation
Indices: 48913--48990 Score: 79
Period size: 20 Copynumber: 4.2 Consensus size: 18
48903 CTAATAAGGT
48913 ATTATAAAAATT-TTAGAA
1 ATTATAAAAATTATTA-AA
*
48931 ATTATAGATAAATTAATAAA
1 ATTATA-A-AAATTATTAAA
48951 ATTATAAAAACTTATTAAA
1 ATTATAAAAA-TTATTAAA
*
48970 ATGATTAAAAA-TATTAAA
1 ATTA-TAAAAATTATTAAA
48988 ATT
1 ATT
48991 TTATGACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
18 18 0.35
19 12 0.24
20 19 0.37
21 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (18 bp):
ATTATAAAAATTATTAAA
Found at i:48970 original size:10 final size:9
Alignment explanation
Indices: 48913--48990 Score: 59
Period size: 9 Copynumber: 8.3 Consensus size: 9
48903 CTAATAAGGT
*
48913 ATTATAAAA
1 ATTATTAAA
48922 ATT-TTAGAA
1 ATTATTA-AA
*
48931 ATTATAGATAA
1 ATTAT-TA-AA
*
48942 ATTAATAAA
1 ATTATTAAA
*
48951 ATTATAAAA
1 ATTATTAAA
48960 ACTTATTAAA
1 A-TTATTAAA
*
48970 ATGATTAAA
1 ATTATTAAA
*
48979 AATATTAAA
1 ATTATTAAA
48988 ATT
1 ATT
48991 TTATGACAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
8 2 0.04
9 34 0.64
10 10 0.19
11 7 0.13
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (9 bp):
ATTATTAAA
Found at i:50388 original size:8 final size:8
Alignment explanation
Indices: 50377--50401 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
50367 AGAAAATTAT
50377 TTAATAAA
1 TTAATAAA
50385 TTAATAAA
1 TTAATAAA
50393 TTAATAAA
1 TTAATAAA
50401 T
1 T
50402 ATAAGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTAATAAA
Found at i:50412 original size:13 final size:13
Alignment explanation
Indices: 50394--50418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50384 ATTAATAAAT
50394 TAATAAATATAAG
1 TAATAAATATAAG
50407 TAATAAATATAA
1 TAATAAATATAA
50419 TTATATTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
TAATAAATATAAG
Found at i:57376 original size:50 final size:50
Alignment explanation
Indices: 57231--57383 Score: 132
Period size: 50 Copynumber: 3.1 Consensus size: 50
57221 GGGTTCACCA
* ** * *
57231 TTGTGACTTAAACCTTTCCCCTTC-AAATCTTCGTGGTACTGGATTCGCCG
1 TTGTAACTTAAACCTTT-CCCTTCTTGATCTTTGTGGTACTGGATCCGCCG
** * * * **
57281 TTGTGGCTTAAATCTTTCCCTTCTTG-TCTTCTGAGGTTCACGATCCGCCG
1 TTGTAACTTAAACCTTTCCCTTCTTGATCTT-TGTGGTACTGGATCCGCCG
* *
57331 TTGTAACTTAAACCTTT-CCTTTTTGTATCTTTGTGGTACTGGATCCGTCG
1 TTGTAACTTAAACCTTTCCCTTCTTG-ATCTTTGTGGTACTGGATCCGCCG
57381 TTG
1 TTG
57384 CAGTCTAGAT
Statistics
Matches: 80, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
49 17 0.21
50 59 0.74
51 4 0.05
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (50 bp):
TTGTAACTTAAACCTTTCCCTTCTTGATCTTTGTGGTACTGGATCCGCCG
Found at i:57620 original size:100 final size:100
Alignment explanation
Indices: 57503--57699 Score: 268
Period size: 100 Copynumber: 2.0 Consensus size: 100
57493 TTTTTGTCAT
* ** **
57503 GTCTCTAAGGTACAAGGTTTGCTGTTGCGACTTAAACCCTTCCCTTTCGTATCTTTACGGTACTG
1 GTCTCTAAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTCGTATCTTTACAATACTG
*
57568 GATCCGCCATTGCTATCTTAAATCTTTCCCGTAAA
66 GATCCGCCATTGCGATCTTAAATCTTTCCCGTAAA
* * * * *
57603 GTCTCTGAGGTATAAGGTTCGCCATTGCGACTTACACCCTTCCCTTTTGTATCTTTGCAATACTG
1 GTCTCTAAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTCGTATCTTTACAATACTG
* * *
57668 GATCCGCCGTTGCGGTCTTAGATCTTTCCCGT
66 GATCCGCCATTGCGATCTTAAATCTTTCCCGT
57700 CATGTTTCAT
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (100 bp):
GTCTCTAAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTCGTATCTTTACAATACTG
GATCCGCCATTGCGATCTTAAATCTTTCCCGTAAA
Found at i:58913 original size:6 final size:6
Alignment explanation
Indices: 58904--58989 Score: 54
Period size: 6 Copynumber: 14.0 Consensus size: 6
58894 CCTCGACCTC
* *
58904 TCTTTT TCTTTT TCTTTTT TCTCTTT T-TTTAT TATTTT AT-TATT T-TTTT
1 TCTTTT TCTTTT TC-TTTT TCT-TTT TCTTT-T TCTTTT -TCTTTT TCTTTT
* *
58953 TGTTTT TCCTTTT TCTTCT TCTTTT T-TCTTT TCTTTT
1 TCTTTT T-CTTTT TCTTTT TCTTTT TCT-TTT TCTTTT
58990 ATTCATTGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
5 8 0.12
6 38 0.58
7 20 0.30
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:58922 original size:7 final size:7
Alignment explanation
Indices: 58906--58984 Score: 56
Period size: 7 Copynumber: 11.4 Consensus size: 7
58896 TCGACCTCTC
58906 TTTTTC-
1 TTTTTCT
58912 TTTTTCT
1 TTTTTCT
58919 TTTTTCT
1 TTTTTCT
*
58926 CTTTT-T
1 TTTTTCT
* *
58932 TTATTAT
1 TTTTTCT
*
58939 TTTATTAT
1 TTT-TTCT
*
58947 TTTTTTT
1 TTTTTCT
*
58954 GTTTTTCC
1 -TTTTTCT
58962 TTTTTC-
1 TTTTTCT
*
58968 TTCTTCT
1 TTTTTCT
58975 TTTTTCT
1 TTTTTCT
58982 TTT
1 TTT
58985 CTTTTATTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
6 15 0.25
7 32 0.54
8 12 0.20
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:58930 original size:9 final size:8
Alignment explanation
Indices: 58912--58989 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 8
58902 TCTCTTTTTC
58912 TTTTTCTT
1 TTTTTCTT
58920 TTTTCTCTT
1 TTTT-TCTT
*
58929 TTTTTATT
1 TTTTTCTT
* *
58937 ATTTTATT
1 TTTTTCTT
*
58945 ATTTTTTTT
1 -TTTTTCTT
58954 GTTTTTCCTT
1 -TTTTT-CTT
58964 TTTCTTCTT
1 TTT-TTCTT
*
58973 CTTTT-TT
1 TTTTTCTT
*
58980 CTTTTCTT
1 TTTTTCTT
58988 TT
1 TT
58990 ATTCATTGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
7 7 0.12
8 19 0.33
9 27 0.47
10 4 0.07
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:64214 original size:18 final size:19
Alignment explanation
Indices: 64193--64250 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
64183 ATATGTTAAA
*
64193 AATATTTTAATTATAT-TT
1 AATATTTTAATTAAATATT
* *
64211 AATAATTTAAATAAATATT
1 AATATTTTAATTAAATATT
* *
64230 ATTATTTTACATTAATTATT
1 AATATTTTA-ATTAAATATT
64250 A
1 A
64251 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 13 0.42
19 9 0.29
20 9 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTTTAATTAAATATT
Found at i:64238 original size:37 final size:37
Alignment explanation
Indices: 64195--64266 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
64185 ATGTTAAAAA
64195 TATTTTA-ATTATATT-TAATAATTTAAATAAATATTAT
1 TATTTTACATTA-ATTATAATAATTTAAA-AAATATTAT
*
64232 TATTTTACATTAATTATTATAATTTAAAAAATATT
1 TATTTTACATTAATTATAATAATTTAAAAAATATT
64267 TAATTCACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (37 bp):
TATTTTACATTAATTATAATAATTTAAAAAATATTAT
Found at i:64257 original size:19 final size:18
Alignment explanation
Indices: 64212--64271 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
64202 ATTATATTTA
64212 ATAATTTAAATAAATATT
1 ATAATTTAAATAAATATT
* * *
64230 ATTATTTTACATTAATTATT
1 A-TAATTTA-AATAAATATT
64250 ATAATTTAAA-AAATATT
1 ATAATTTAAATAAATATT
64267 -TAATT
1 ATAATT
64272 CACATATGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 2 0.06
19 12 0.35
20 9 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAATTTAAATAAATATT
Found at i:64956 original size:16 final size:16
Alignment explanation
Indices: 64937--64982 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
64927 TTTTAAATAA
64937 TTTTTATTATTTTTAC
1 TTTTTATTATTTTTAC
*
64953 TTTTTATT-TTATTTAT
1 TTTTTATTATT-TTTAC
64969 TTTTTATTATTTTT
1 TTTTTATTATTTTT
64983 CACTCACATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTATTATTTTTAC
Found at i:67994 original size:23 final size:22
Alignment explanation
Indices: 67968--68040 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
67958 AAAGCTCGTG
67968 TTATAGCAAAAAGTTTGTCAATA
1 TTATA-CAAAAAGTTTGTCAATA
* * * *
67991 TTATACCAAATGTTTGTTATAAA
1 TTATACAAAAAGTTTGTCA-ATA
* *
68014 TTATA-ACAAAGCTTGTCAATA
1 TTATACAAAAAGTTTGTCAATA
68035 TTATAC
1 TTATAC
68041 TAATAACAAC
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
21 7 0.18
22 19 0.50
23 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (22 bp):
TTATACAAAAAGTTTGTCAATA
Found at i:68039 original size:21 final size:21
Alignment explanation
Indices: 67977--68039 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
67967 GTTATAGCAA
*
67977 AAAGTTTGTCAATATTATACC
1 AAAGTTTGTCAATATTATAAC
* *
67998 AAATGTTTGTTATAAATTATAAC
1 AAA-GTTTGTCA-ATATTATAAC
*
68021 AAAGCTTGTCAATATTATA
1 AAAGTTTGTCAATATTATA
68040 CTAATAACAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 10 0.29
22 13 0.38
23 11 0.32
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAGTTTGTCAATATTATAAC
Found at i:68861 original size:29 final size:30
Alignment explanation
Indices: 68829--68900 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
68819 TAATTTTAAT
68829 TTAAAATTATTTTTTAAAAT-ATAAAATTA
1 TTAAAATTATTTTTTAAAATAATAAAATTA
68858 TTAAAATTATTTTTTTAAAATAATAAAATTA
1 TTAAAATTA-TTTTTTAAAATAATAAAATTA
68889 TT-AAA-TATTTTT
1 TTAAAATTATTTTT
68901 AATTTCTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
28 5 0.12
29 11 0.27
30 14 0.34
31 11 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAAAATTATTTTTTAAAATAATAAAATTA
Found at i:68874 original size:30 final size:31
Alignment explanation
Indices: 68829--68900 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 31
68819 TAATTTTAAT
68829 TTAAAATTA-TTTTTTAAAAT-ATAAAATTA
1 TTAAAATTATTTTTTTAAAATAATAAAATTA
68858 TTAAAATTATTTTTTTAAAATAATAAAATTA
1 TTAAAATTATTTTTTTAAAATAATAAAATTA
68889 TT-AAA-TATTTTT
1 TTAAAATTATTTTT
68901 AATTTCTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
29 16 0.39
30 14 0.34
31 11 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAAAATTATTTTTTTAAAATAATAAAATTA
Found at i:70687 original size:15 final size:15
Alignment explanation
Indices: 70664--70705 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
70654 AACTCTTTCT
*
70664 AAAACTGTTTTTTTG
1 AAAAGTGTTTTTTTG
*
70679 AAAAGTGTTTTTTTT
1 AAAAGTGTTTTTTTG
*
70694 AAAAGTATTTTT
1 AAAAGTGTTTTT
70706 GAGAAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (15 bp):
AAAAGTGTTTTTTTG
Found at i:71267 original size:11 final size:11
Alignment explanation
Indices: 71248--71303 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
71238 GACTGGGCCT
*
71248 TTTTTAATTTA
1 TTTTAAATTTA
71259 TTTTAAATTTGA
1 TTTTAAATTT-A
71271 -TTTAAATTTAA
1 TTTTAAATTT-A
* *
71282 ATTTAAATTGA
1 TTTTAAATTTA
*
71293 TATTAAATTTA
1 TTTTAAATTTA
71304 AATTGAATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:71282 original size:17 final size:16
Alignment explanation
Indices: 71276--71323 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
71266 TTTGATTTAA
71276 ATTTAAATTTAAATTG
1 ATTTAAATTTAAATTG
71292 ATATTAAATTTAAATTG
1 AT-TTAAATTTAAATTG
* *
71309 AATTCAATTTAAATT
1 ATTTAAATTTAAATT
71324 AAAAAGTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (16 bp):
ATTTAAATTTAAATTG
Found at i:71288 original size:23 final size:23
Alignment explanation
Indices: 71260--71307 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
71250 TTTAATTTAT
71260 TTTAAATTTGAT-TTAAATTTAAA
1 TTTAAA-TTGATATTAAATTTAAA
71283 TTTAAATTGATATTAAATTTAAA
1 TTTAAATTGATATTAAATTTAAA
71306 TT
1 TT
71308 GAATTCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAAATTGATATTAAATTTAAA
Found at i:71323 original size:6 final size:6
Alignment explanation
Indices: 71260--71307 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
71250 TTTAATTTAT
* * *
71260 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA TTGATA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
71306 TT
1 TT
71308 GAATTCAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 27 0.79
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:73362 original size:26 final size:24
Alignment explanation
Indices: 73333--73403 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 24
73323 TTTATATTTT
73333 ATTTCTTTAACAATAATAAAAATATA
1 ATTT-TTTAA-AATAATAAAAATATA
*
73359 ATTTTTCTAAAAATTATAAAAATATAA
1 ATTTTT-T-AAAATAATAAAAATAT-A
*
73386 ATTATTT-AAATAATAAAA
1 ATTTTTTAAAATAATAAAA
73404 TTACATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 10 0.26
25 2 0.05
26 19 0.49
27 8 0.21
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTTTTTAAAATAATAAAAATATA
Found at i:74266 original size:45 final size:45
Alignment explanation
Indices: 74202--74289 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
74192 TTATTTAACA
74202 TAGTACCTGGGTTGGGTAGGGTCACCTTAGGAAGAAAATCAAACT
1 TAGTACCTGGGTTGGGTAGGGTCACCTTAGGAAGAAAATCAAACT
74247 TAGTACCTGGGTTGGGTAGGGTCACCTTAGGAAGAAAATCAAA
1 TAGTACCTGGGTTGGGTAGGGTCACCTTAGGAAGAAAATCAAA
74290 GTAAACGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.24
Consensus pattern (45 bp):
TAGTACCTGGGTTGGGTAGGGTCACCTTAGGAAGAAAATCAAACT
Found at i:82444 original size:12 final size:12
Alignment explanation
Indices: 82427--82458 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
82417 ATATTGTCTC
82427 GTTAAAAATCTT
1 GTTAAAAATCTT
82439 GTTAAAAATCTT
1 GTTAAAAATCTT
*
82451 ATTAAAAA
1 GTTAAAAA
82459 AAATTGACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (12 bp):
GTTAAAAATCTT
Found at i:91351 original size:18 final size:17
Alignment explanation
Indices: 91330--91386 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
91320 TTTTATGATT
91330 TTTAATAATTTTTATAA
1 TTTAATAATTTTTATAA
91347 GTTTACAT-ATTTTTA-ACA
1 -TTTA-ATAATTTTTATA-A
*
91365 TTTTAATAGTTTTTATAA
1 -TTTAATAATTTTTATAA
91383 TTTA
1 TTTA
91387 TTTACAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 7 0.21
18 23 0.70
19 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (17 bp):
TTTAATAATTTTTATAA
Found at i:93067 original size:22 final size:21
Alignment explanation
Indices: 93026--93069 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
93016 GTAAGTTCTA
**
93026 TTTTTTAAAAAGTTAAAATAT
1 TTTTTTAAAAAAATAAAATAT
93047 TTTTTTAAAAAAATAATAATAT
1 TTTTTTAAAAAAATAA-AATAT
93069 T
1 T
93070 CCAATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTTTAAAAAAATAAAATAT
Found at i:95052 original size:43 final size:44
Alignment explanation
Indices: 94999--95087 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 44
94989 TTTGAAATAA
* * * *
94999 AATAAAAGTTGAGATAATTATACATTTAAAAA-AATTATAATTT
1 AATAAAAGTTGAGACAATTAGACATCTAAAAACAATTAAAATTT
* * *
95042 AATAGAAGTTGTGACAATTAGAGATCTAAAAACAATTAAAATTT
1 AATAAAAGTTGAGACAATTAGACATCTAAAAACAATTAAAATTT
95086 AA
1 AA
95088 ATTAATATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 26 0.68
44 12 0.32
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (44 bp):
AATAAAAGTTGAGACAATTAGACATCTAAAAACAATTAAAATTT
Found at i:96475 original size:23 final size:21
Alignment explanation
Indices: 96433--96547 Score: 68
Period size: 23 Copynumber: 5.2 Consensus size: 21
96423 TTTTGGTACT
* * *
96433 TTTTTATTGTTTTGGTTGTTG
1 TTTTTGTTGTTTTTGCTGTTG
*
96454 TTTTCATGTTGTTTTTGCTGTTA
1 TTTT--TGTTGTTTTTGCTGTTG
* ** *
96477 TTTTTGTTGCTCTTTTGTTACTA
1 TTTTTGTTG-T-TTTTGCTGTTG
**
96500 TTTTTGTTGTTTTTAATGTTG
1 TTTTTGTTGTTTTTGCTGTTG
* *
96521 TTTTGCTGTTATTTTTGCTGCTG
1 TTTT--TGTTGTTTTTGCTGTTG
96544 TTTT
1 TTTT
96548 GATTGTTATT
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
21 19 0.26
22 2 0.03
23 51 0.71
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (21 bp):
TTTTTGTTGTTTTTGCTGTTG
Found at i:96512 original size:55 final size:55
Alignment explanation
Indices: 96448--96567 Score: 161
Period size: 55 Copynumber: 2.2 Consensus size: 55
96438 ATTGTTTTGG
* *
96448 TTGTTGTTTTCATGTTGTTTTTGCTGTTATTTTTGTTGCTCTTTTG-TTACTATTT
1 TTGTTGTTTTAATGTTG-TTTTGCTGTTATTTTTGCTGCTCTTTTGATTACTATTT
* **
96503 TTGTTGTTTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTGTTTTGATTGTTATTT
1 TTGTTG-TTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTCTTTTGATTACTATTT
*
96559 TTATTGTTT
1 TTGTTGTTT
96568 GGATGTTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
55 35 0.61
56 22 0.39
ACGTcount: A:0.08, C:0.07, G:0.17, T:0.68
Consensus pattern (55 bp):
TTGTTGTTTTAATGTTGTTTTGCTGTTATTTTTGCTGCTCTTTTGATTACTATTT
Found at i:98811 original size:25 final size:23
Alignment explanation
Indices: 98747--98816 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 23
98737 GTTAATTGAT
98747 TAATATTTTATATTTGATATTTA
1 TAATATTTTATATTTGATATTTA
*
98770 T-TTAATTTTATCCATTTGATATTTA
1 TAAT-ATTTTAT--ATTTGATATTTA
98795 TAAATATTTTTATATTT-ATATT
1 T-AATA-TTTTATATTTGATATT
98817 AAATATGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 1 0.03
23 8 0.21
24 5 0.13
25 17 0.44
26 1 0.03
27 7 0.18
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (23 bp):
TAATATTTTATATTTGATATTTA
Found at i:99662 original size:31 final size:31
Alignment explanation
Indices: 99627--99686 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
99617 CCAATCCAAT
*
99627 GACTTAAAT-AAAATTATTTGAATAGTTCAGC
1 GACTTAAATGAAAACT-TTTGAATAGTTCAGC
99658 GACTTAAATGAAAACTTTTGAATAGTTCA
1 GACTTAAATGAAAACTTTTGAATAGTTCA
99687 TTAACCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
GACTTAAATGAAAACTTTTGAATAGTTCAGC
Found at i:100637 original size:14 final size:14
Alignment explanation
Indices: 100620--100650 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
100610 AGGGTTTAAA
100620 AAATTTAATTAATT
1 AAATTTAATTAATT
*
100634 AAATTTATTTAATT
1 AAATTTAATTAATT
100648 AAA
1 AAA
100651 GATTTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:102602 original size:12 final size:12
Alignment explanation
Indices: 102585--102621 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
102575 GTTTATTAAG
102585 TAATTAATAATA
1 TAATTAATAATA
102597 TAATTAATAATA
1 TAATTAATAATA
*
102609 -AATAAATAA-A
1 TAATTAATAATA
102619 TAA
1 TAA
102622 ATAAAAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 10 0.43
12 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATTAATAATA
Found at i:103660 original size:30 final size:29
Alignment explanation
Indices: 103613--103699 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 29
103603 CGAAACTTCC
*
103613 AAAAATTCCAATTTTACCCCTAAATTTCA
1 AAAAATTCCATTTTTACCCCTAAATTTCA
* * * *
103642 AAAAA-TCTCATTTTTTACCTCGAAACTTCC
1 AAAAATTC-CA-TTTTTACCCCTAAATTTCA
* *
103672 AAAAATTCCATTTTTACCCTTGAATTTC
1 AAAAATTCCATTTTTACCCCTAAATTTC
103700 CAAGAATCCT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 2 0.04
29 20 0.44
30 21 0.47
31 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCTAAATTTCA
Found at i:103700 original size:29 final size:29
Alignment explanation
Indices: 103609--103715 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 29
103599 TCCCCGAAAC
* * *
103609 TTCCAAAAATTCCAATTTTACCCCTAAAT
1 TTCCAAAAATTCCATTTTTACCCTTGAAT
* * *
103638 TT-CAAAAAATCTCATTTTTTA-CCTCGAAAC
1 TTCCAAAAATTC-CA-TTTTTACCCTTG-AAT
103668 TTCCAAAAATTCCATTTTTACCCTTGAAT
1 TTCCAAAAATTCCATTTTTACCCTTGAAT
*
103697 TTCCAAGAA-TCCTATTTTT
1 TTCCAAAAATTCC-ATTTTT
103716 GACCTCAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
28 11 0.18
29 28 0.45
30 15 0.24
31 8 0.13
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCTTGAAT
Found at i:103726 original size:29 final size:28
Alignment explanation
Indices: 103609--103736 Score: 82
Period size: 29 Copynumber: 4.4 Consensus size: 28
103599 TCCCCGAAAC
* *
103609 TTCCAAAAATTCC-AATTTTACCCCTAAAT
1 TTCCAAAAA-TCCTATTTTTACCTC-AAAT
* *
103638 TTCAAAAAAT-CTCATTTTTTACCTCGAAAC
1 TTCCAAAAATCCT-A-TTTTTACCTC-AAAT
**
103668 TTCCAAAAATTCC-ATTTTTACCCTTGAAT
1 TTCCAAAAA-TCCTATTTTTA-CCTCAAAT
*
103697 TTCCAAGAATCCTATTTTTGACCTCAAATT
1 TTCCAAAAATCCTATTTTT-ACCTCAAA-T
*
103727 TTCCCAAAAT
1 TTCCAAAAAT
103737 TTCTATTTCA
Statistics
Matches: 76, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
27 1 0.01
28 4 0.05
29 36 0.47
30 33 0.43
31 1 0.01
32 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (28 bp):
TTCCAAAAATCCTATTTTTACCTCAAAT
Found at i:103737 original size:59 final size:59
Alignment explanation
Indices: 103603--103721 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 59
103593 TAAAGGTCCC
*
103603 CGAAACTTCCAAAAATTCCAATTTTACCCCTAAATTTCAAAAAATCTCATTTTTTACCT
1 CGAAACTTCCAAAAATTCCAATTTTACCCCTAAATTTCAAAAAATCTCATTTTTGACCT
* * * * *
103662 CGAAACTTCCAAAAATTCCATTTTTACCCTTGAATTTCCAAGAATC-CTATTTTTGACCT
1 CGAAACTTCCAAAAATTCCAATTTTACCCCTAAATTTCAAAAAATCTC-ATTTTTGACCT
103721 C
1 C
103722 AAATTTTCCC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 1 0.02
59 52 0.98
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
CGAAACTTCCAAAAATTCCAATTTTACCCCTAAATTTCAAAAAATCTCATTTTTGACCT
Found at i:105342 original size:18 final size:18
Alignment explanation
Indices: 105309--105343 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105299 TTTCTTTATA
*
105309 TATTTTTTAGATTTTTTT
1 TATTTTTTAGAATTTTTT
*
105327 TATTTTTTATAATTTTT
1 TATTTTTTAGAATTTTT
105344 AAAAATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TATTTTTTAGAATTTTTT
Found at i:110490 original size:29 final size:29
Alignment explanation
Indices: 110458--110513 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
110448 GTAACACTTG
110458 TAAACAAAAAAAATA-TTTAGGTACCAAAA
1 TAAA-AAAAAAAATAGTTTAGGTACCAAAA
* *
110487 TAAAAAAATATATAGTTTAGGTACCAA
1 TAAAAAAAAAAATAGTTTAGGTACCAA
110514 TTTATCAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (29 bp):
TAAAAAAAAAAATAGTTTAGGTACCAAAA
Found at i:125365 original size:22 final size:22
Alignment explanation
Indices: 125341--125382 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
125331 TATCAAATAA
125341 AAAAT-AAA-TTAAATTATGTAT
1 AAAATGAAATTTAAA-TATGTAT
125362 AAAATGAAATTTAAATATGTA
1 AAAATGAAATTTAAATATGTA
125383 AATACATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAATGAAATTTAAATATGTAT
Found at i:126329 original size:22 final size:22
Alignment explanation
Indices: 126301--126348 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
126291 AATAGCGGTT
*
126301 GATGTGACCCTTGGTCCAATAG
1 GATGTGACCCTTGATCCAATAG
*
126323 GATGTGATCCTTGATCCAATAG
1 GATGTGACCCTTGATCCAATAG
126345 GATG
1 GATG
126349 GGAACAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (22 bp):
GATGTGACCCTTGATCCAATAG
Found at i:137212 original size:21 final size:21
Alignment explanation
Indices: 137188--137233 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
137178 CTCCTTATCT
* * *
137188 TCATCTTCATCATCAAAGTCA
1 TCATCTTCACCAACAAAATCA
*
137209 TCATCTTTACCAACAAAATCA
1 TCATCTTCACCAACAAAATCA
137230 TCAT
1 TCAT
137234 TATTATTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (21 bp):
TCATCTTCACCAACAAAATCA
Found at i:137500 original size:222 final size:219
Alignment explanation
Indices: 137103--137545 Score: 570
Period size: 222 Copynumber: 2.0 Consensus size: 219
137093 TATCAGCCTT
*
137103 ATCCTCCTTAGCAACATCATCAGGAATCACATCATTATGACCAGAAATGCCTCCACCACTGCCAT
1 ATCCCCCTTAGCAACATCATCAGGAATCACATCATTATGACCAGAAATGCCTCCACCACTGCCAT
* *
137168 CATCATTACCCTCCTTATCTTCATCTTCATCATCAAAGTCATCATCTTTACCAACAAAATCATCA
66 CATCATCACCCTCC---TCTTCATCTTCATCATCAAAGTCATCATCCTTACCAACAAAATCATCA
* **
137233 TTATTATTAACATTATCTTGATTAAAACCAGCATCCTCTGATACTCCGTTACCATTGCCATATAT
128 TCATTATTAACATTATCTTGATTAAAACCAGCATCCTCTGATACTCCGGCACCATTGCCATATAT
* * *
137298 ATGATATTCTTCATTCGCTTCATCCTC
193 ACGAAATTCTTCATTAGCTTCATCCTC
* **
137325 ATCCCCCTTATCAACATCATCAGGAATCACATCATTATCATAATGACCAGAAATGCCTCTGCCAC
1 ATCCCCCTTAGCAACATCATCAGGAATCACATC---AT--T-ATGACCAGAAATGCCTCCACCAC
* * *
137390 TGCCATCATCATCACCCT-C-C-TCATCTTCATCATCAAAGTCATCGTCCTTACCATCAACATCA
60 TGCCATCATCATCACCCTCCTCTTCATCTTCATCATCAAAGTCATCATCCTTACCAACAAAATCA
* * * * *
137452 TCGTCATTATTAAC-TGTGTCTTGATTAAAACCGGCATCCTCTGATACTCCGGCATCATTTCCAT
125 TCATCATTATTAACAT-TATCTTGATTAAAACCAGCATCCTCTGATACTCCGGCACCATTGCCAT
* *
137516 TTATACGAAATTCTTTATTAGCTTCATCCT
189 ATATACGAAATTCTTCATTAGCTTCATCCT
137546 ACACCAATTT
Statistics
Matches: 192, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
221 1 0.01
222 148 0.77
223 1 0.01
225 2 0.01
227 2 0.01
228 38 0.20
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (219 bp):
ATCCCCCTTAGCAACATCATCAGGAATCACATCATTATGACCAGAAATGCCTCCACCACTGCCAT
CATCATCACCCTCCTCTTCATCTTCATCATCAAAGTCATCATCCTTACCAACAAAATCATCATCA
TTATTAACATTATCTTGATTAAAACCAGCATCCTCTGATACTCCGGCACCATTGCCATATATACG
AAATTCTTCATTAGCTTCATCCTC
Found at i:138433 original size:27 final size:25
Alignment explanation
Indices: 138389--138441 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
138379 TGAATTTTAA
*
138389 TTTTATAAAATTATATATATAAATTT
1 TTTTATAAAAATATATATA-AAATTT
138415 TTTTATGAAAAATATATATAAAATTT
1 TTTTAT-AAAAATATATATAAAATTT
138441 T
1 T
138442 GATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTATAAAAATATATATAAAATTT
Found at i:143996 original size:18 final size:19
Alignment explanation
Indices: 143973--144019 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
143963 CTTTTATTTA
*
143973 AAAATATATAAAAA-TATG
1 AAAATATATAAAAACTATC
*
143991 AAAATATAAAAAAACTATC
1 AAAATATATAAAAACTATC
144010 AAAATA-ATAA
1 AAAATATATAA
144020 CAGTAGTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAATATATAAAAACTATC
Found at i:144916 original size:2 final size:2
Alignment explanation
Indices: 144909--144939 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
144899 AACCAATTTA
*
144909 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
144940 ATTTTTAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:158342 original size:59 final size:59
Alignment explanation
Indices: 158270--158388 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
158260 TCTTTCTCTA
158270 CCACATGCCGTCTTTAATTTGTTTGCCTTCAAACGTTTGTCACCACCTGGGGAAAATAG
1 CCACATGCCGTCTTTAATTTGTTTGCCTTCAAACGTTTGTCACCACCTGGGGAAAATAG
158329 CCACATGCCGTCTTTAATTTGTTTGCCTTCAAACGTTTGTCACCACCTGGGGAAAATAG
1 CCACATGCCGTCTTTAATTTGTTTGCCTTCAAACGTTTGTCACCACCTGGGGAAAATAG
158388 C
1 C
158389 TTAAATAGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (59 bp):
CCACATGCCGTCTTTAATTTGTTTGCCTTCAAACGTTTGTCACCACCTGGGGAAAATAG
Found at i:163810 original size:17 final size:19
Alignment explanation
Indices: 163788--163836 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
163778 TATATTGATA
163788 AATATTAAATTAT-A-TTT
1 AATATTAAATTATCATTTT
*
163805 AATATTAAAATAATCATTTT
1 AATATT-AAATTATCATTTT
163825 AATATTAAATTA
1 AATATTAAATTA
163837 ATAAAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 6 0.22
19 6 0.22
20 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTAAATTATCATTTT
Found at i:165036 original size:21 final size:21
Alignment explanation
Indices: 164993--165035 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
164983 ATTCAGAATG
* *
164993 TTATTAGATTATATATTATTT
1 TTATTAAATTATATATCATTT
165014 TTATTAAATTATAT-TCATTT
1 TTATTAAATTATATATCATTT
165034 TT
1 TT
165036 TTTATACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATTAAATTATATATCATTT
Found at i:165163 original size:15 final size:15
Alignment explanation
Indices: 165130--165182 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
165120 TGAATTGTTA
165130 ATTACAAATTTATTTC
1 ATTAC-AATTTATTTC
165146 ATTACAATTT-TTTAC
1 ATTACAATTTATTT-C
*
165161 ATTACAATTATATTTT
1 ATTACAATT-TATTTC
165177 ATTACA
1 ATTACA
165183 GTTTTATTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.09
15 15 0.45
16 12 0.36
17 3 0.09
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTACAATTTATTTC
Found at i:189596 original size:30 final size:30
Alignment explanation
Indices: 189562--189619 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
189552 TAATAATGAG
189562 TAAGCTTGTCCATATCCAAGTATAATACTA
1 TAAGCTTGTCCATATCCAAGTATAATACTA
189592 TAAGCTTGTCCATATCCAAGTATAATAC
1 TAAGCTTGTCCATATCCAAGTATAATAC
189620 AAATAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (30 bp):
TAAGCTTGTCCATATCCAAGTATAATACTA
Found at i:194767 original size:25 final size:23
Alignment explanation
Indices: 194709--194773 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
194699 CTCAATCCTT
* *
194709 CTTTGTTCTCTCTCCTTCTCGTCC
1 CTTTGTTCTCTCT-CTTCACGCCC
**
194733 CTTT-CCCTCTCTACTTCACGCCTC
1 CTTTGTTCTCTCT-CTTCACGCC-C
194757 CTTTGTTCTCTCTCTTC
1 CTTTGTTCTCTCTCTTC
194774 CTCTTCTCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
23 13 0.41
24 13 0.41
25 6 0.19
ACGTcount: A:0.03, C:0.43, G:0.06, T:0.48
Consensus pattern (23 bp):
CTTTGTTCTCTCTCTTCACGCCC
Found at i:197243 original size:133 final size:133
Alignment explanation
Indices: 196867--197246 Score: 595
Period size: 133 Copynumber: 2.9 Consensus size: 133
196857 GTGGAAATGG
* *
196867 CTGAGAGTGATAAGCTCAACATGTCCCACAACATATGCATGTTCAATGTAATGTAATTTGAAATC
1 CTGAGAGTGATGAGCTCAACATGTCCCATAACATATGCATGTTCAATGTAATGTAATTTGAAATC
*
196932 CCAAAAACAGCTTTTGGCTAGCCCTCCTCATCCTAGATGTAGATTCCTAGGGTGGATGAAAGTGA
66 CCAAAAACAGCTTTTGGCTAGCCCTCCTCATCCTAGATGTAGATTTCTAGGGTGGATGAAAGTGA
196997 TGA
131 TGA
* *
197000 CTGAGAGTGATGAGCTCAACATGTCCCATGACATATGCAAGTTCAATGTAATGTAATTTGAAATC
1 CTGAGAGTGATGAGCTCAACATGTCCCATAACATATGCATGTTCAATGTAATGTAATTTGAAATC
* *
197065 CCAAAAACAGCTTTTGGTTAGTCCTCCTCATCCTAGATGTAGATTTCTAGGGTGGATGAAAGTGA
66 CCAAAAACAGCTTTTGGCTAGCCCTCCTCATCCTAGATGTAGATTTCTAGGGTGGATGAAAGTGA
197130 TGA
131 TGA
* ** * *
197133 CTGAGAGTGATGAGCTCAATATG-CCCTATTCCATATGCATGTTCAATGTAAGGCAATTTGGAAA
1 CTGAGAGTGATGAGCTCAACATGTCCC-ATAACATATGCATGTTCAATGTAATGTAATTT-GAAA
*
197197 -CCCAAAAACAGCTTTTGGCTAGCCCTCCTCAT-CTCAGATGAAGATTTCTA
64 TCCCAAAAACAGCTTTTGGCTAGCCCTCCTCATCCT-AGATGTAGATTTCTA
197247 CAGTGGTTGC
Statistics
Matches: 228, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
132 5 0.02
133 219 0.96
134 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (133 bp):
CTGAGAGTGATGAGCTCAACATGTCCCATAACATATGCATGTTCAATGTAATGTAATTTGAAATC
CCAAAAACAGCTTTTGGCTAGCCCTCCTCATCCTAGATGTAGATTTCTAGGGTGGATGAAAGTGA
TGA
Found at i:202855 original size:17 final size:18
Alignment explanation
Indices: 202835--202877 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
202825 CAATAATCTG
202835 ATTATTTATATAATTT-T
1 ATTATTTATATAATTTCT
* *
202852 ATTATATAATATATTTTCT
1 ATTAT-TTATATAATTTCT
202871 ATTATTT
1 ATTATTT
202878 TTATTGGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTATTTATATAATTTCT
Found at i:208810 original size:19 final size:20
Alignment explanation
Indices: 208776--208813 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
208766 TAAAAAAATT
*
208776 TAAATATTATATAAAAAGAG
1 TAAATATTATAAAAAAAGAG
208796 TAAATATT-TAAAAAAAGA
1 TAAATATTATAAAAAAAGA
208814 AATTTCGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
TAAATATTATAAAAAAAGAG
Found at i:210496 original size:56 final size:57
Alignment explanation
Indices: 210395--210509 Score: 214
Period size: 56 Copynumber: 2.0 Consensus size: 57
210385 AACTTAGTTG
*
210395 ATTAACGGGCGTAGCTATAAAATTTTTTAGGGTTAAAATTAAATTATAATTTTTACA
1 ATTAACGGGCGTAGCTATAAAATATTTTAGGGTTAAAATTAAATTATAATTTTTACA
210452 ATTAACGGGCGTAGCTATAAAA-ATTTTAGGGTTAAAATTAAATTATAATTTTTACA
1 ATTAACGGGCGTAGCTATAAAATATTTTAGGGTTAAAATTAAATTATAATTTTTACA
210508 AT
1 AT
210510 ATTAAAAATA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 35 0.61
57 22 0.39
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (57 bp):
ATTAACGGGCGTAGCTATAAAATATTTTAGGGTTAAAATTAAATTATAATTTTTACA
Found at i:210550 original size:24 final size:23
Alignment explanation
Indices: 210489--210562 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 23
210479 AGGGTTAAAA
* *
210489 TTAAATTATA-ATTTTTACAATA
1 TTAAATTATATATTTTTATAATT
* *
210511 TTAAA-AATATAATTTTATAATT
1 TTAAATTATATATTTTTATAATT
210533 TTAATATTATATATTTTTATAAATT
1 TTAA-ATTATATATTTTTAT-AATT
210558 TTAAA
1 TTAAA
210563 AAATTAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.07
22 18 0.43
23 1 0.02
24 12 0.29
25 8 0.19
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAATTATATATTTTTATAATT
Found at i:210551 original size:46 final size:45
Alignment explanation
Indices: 210489--210586 Score: 112
Period size: 46 Copynumber: 2.2 Consensus size: 45
210479 AGGGTTAAAA
* *
210489 TTAA-ATTATAATTTTTA-CAATATT-AAAAATATAATTTTATAATT
1 TTAATATTATAATTTTTATAAATATTAAAAAAT-TAA-ATTATAATT
*
210533 TTAATATTATATATTTTTATAAATTTTAAAAAATTAAATTATAATT
1 TTAATATTATA-ATTTTTATAAATATTAAAAAATTAAATTATAATT
*
210579 TTATTATT
1 TTAATATT
210587 TTTAGAAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 4 0.09
45 6 0.13
46 22 0.48
47 8 0.17
48 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (45 bp):
TTAATATTATAATTTTTATAAATATTAAAAAATTAAATTATAATT
Found at i:217559 original size:40 final size:40
Alignment explanation
Indices: 217504--217587 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
217494 GGATGATGAG
217504 AGTATAACATGGAATGCATGCTTGAGATGTATACATTTCA
1 AGTATAACATGGAATGCATGCTTGAGATGTATACATTTCA
217544 AGTATAACATGGAATGCATGCTTGAGATGTATACATTTCA
1 AGTATAACATGGAATGCATGCTTGAGATGTATACATTTCA
217584 AGTA
1 AGTA
217588 ACTTTCAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (40 bp):
AGTATAACATGGAATGCATGCTTGAGATGTATACATTTCA
Found at i:219586 original size:2 final size:2
Alignment explanation
Indices: 219579--219603 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
219569 AGCTAATTTA
219579 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 A
219604 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219673 original size:2 final size:2
Alignment explanation
Indices: 219666--219700 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
219656 NNNNNNNNNN
219666 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
219701 AGAAAACAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:220582 original size:17 final size:19
Alignment explanation
Indices: 220547--220583 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
220537 CCGAGTTAGT
220547 TATTTTTATAAATTATTAA
1 TATTTTTATAAATTATTAA
220566 TATTTTTA-AAATT-TTAA
1 TATTTTTATAAATTATTAA
220583 T
1 T
220584 TTTGATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTTATAAATTATTAA
Found at i:222085 original size:6 final size:6
Alignment explanation
Indices: 222069--222100 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
222059 CAATATTTAC
222069 TTTATTT TTTATT TTTATT TTTATT TTTATT T
1 TTTA-TT TTTATT TTTATT TTTATT TTTATT T
222101 CAGTCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:222792 original size:21 final size:23
Alignment explanation
Indices: 222768--222815 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
222758 TTCAATAATC
*
222768 TTTATTATTAATAAAA-GT-TAA
1 TTTATTATTAACAAAACGTGTAA
*
222789 TTTATTCTTAACAAAACGTGTAA
1 TTTATTATTAACAAAACGTGTAA
222812 TTTA
1 TTTA
222816 ATCTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 2 0.09
23 7 0.30
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (23 bp):
TTTATTATTAACAAAACGTGTAA
Found at i:223145 original size:21 final size:21
Alignment explanation
Indices: 223111--223154 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
223101 AAATGAAATT
*
223111 AAAATATAATAGAAAAATAAAA
1 AAAATATAAAAG-AAAATAAAA
*
223133 AAAATA-AAAAGAAACTAAAA
1 AAAATATAAAAGAAAATAAAA
223153 AA
1 AA
223155 CAAAAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAATATAAAAGAAAATAAAA
Found at i:224435 original size:30 final size:31
Alignment explanation
Indices: 224401--224472 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 31
224391 TAAAATGATT
*
224401 ATTAAATTGTT-TGAAAGTTTTATTTAAATC
1 ATTAAATTGTTCAGAAAGTTTTATTTAAATC
* * * *
224431 ATTAAACTATTCAGAAATTTTTATTTAAGTC
1 ATTAAATTGTTCAGAAAGTTTTATTTAAATC
* *
224462 AGTAAGTTGTT
1 ATTAAATTGTT
224473 AAGTTTTTTT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTAAATTGTTCAGAAAGTTTTATTTAAATC
Found at i:226562 original size:15 final size:15
Alignment explanation
Indices: 226542--226573 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
226532 TGGGAACTCC
*
226542 GGAATGTATGGTGGT
1 GGAATGTATGGCGGT
226557 GGAATGTATGGCGGT
1 GGAATGTATGGCGGT
226572 GG
1 GG
226574 CCTTGGTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.50, T:0.28
Consensus pattern (15 bp):
GGAATGTATGGCGGT
Found at i:230642 original size:3 final size:3
Alignment explanation
Indices: 230634--230658 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
230624 ACGTTTGGAA
230634 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
230659 TGAGATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:230790 original size:23 final size:23
Alignment explanation
Indices: 230758--230822 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 23
230748 ATAAAATTTA
* *
230758 ATCTTCAATTTTATTTTTTTAAT
1 ATCTTGAATTTAATTTTTTTAAT
230781 ATCTTGAATTTAATTTTTTTTAAT
1 ATCTTGAATTTAA-TTTTTTTAAT
230805 ATTCTTGAATTTAATTTT
1 A-TCTTGAATTTAATTTT
230823 GAATGTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 11 0.29
24 15 0.39
25 12 0.32
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (23 bp):
ATCTTGAATTTAATTTTTTTAAT
Found at i:230810 original size:25 final size:24
Alignment explanation
Indices: 230758--230822 Score: 96
Period size: 25 Copynumber: 2.7 Consensus size: 24
230748 ATAAAATTTA
* *
230758 ATCTTCAATTTTA-TTTTTTTAAT
1 ATCTTGAATTTAATTTTTTTTAAT
230781 ATCTTGAATTTAATTTTTTTTAAT
1 ATCTTGAATTTAATTTTTTTTAAT
230805 ATTCTTGAATTTAATTTT
1 A-TCTTGAATTTAATTTT
230823 GAATGTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 11 0.29
24 11 0.29
25 16 0.42
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (24 bp):
ATCTTGAATTTAATTTTTTTTAAT
Found at i:231277 original size:30 final size:30
Alignment explanation
Indices: 231242--231304 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
231232 ATCATTTGAA
*
231242 TAATTTATATTTTTATAATTTTTAA-AGTAT
1 TAATTTAAATTTTTATAATTTTTAAGAG-AT
*
231272 TAATTTAAATTTTTATTATTTTTAAGAGAT
1 TAATTTAAATTTTTATAATTTTTAAGAGAT
231302 TAA
1 TAA
231305 AATATAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (30 bp):
TAATTTAAATTTTTATAATTTTTAAGAGAT
Found at i:231316 original size:30 final size:30
Alignment explanation
Indices: 231247--231317 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
231237 TTGAATAATT
* **
231247 TATATTTTTATAATTTTTAAAGTATTAATT
1 TATAATTTTATAATTTTTAAAGTATTAAAA
*
231277 TA-AATTTTTATTATTTTTAAGAG-ATTAAAA
1 TATAA-TTTTATAATTTTTAA-AGTATTAAAA
231307 TATAATTTTAT
1 TATAATTTTAT
231318 CTTTATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 1 0.03
30 29 0.85
31 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.56
Consensus pattern (30 bp):
TATAATTTTATAATTTTTAAAGTATTAAAA
Found at i:236880 original size:197 final size:197
Alignment explanation
Indices: 236508--236865 Score: 461
Period size: 197 Copynumber: 1.8 Consensus size: 197
236498 TTATGTGTTT
*
236508 TGGGATTTTGTTGCACTCTTTGCCCTTTGTGAAATTGAATCCCATTCTATATCAAATGGAAACTA
1 TGGGATTTTGTTGCACTCTTTGCCCTTTGTGAAATTGAATCCCATTCTATAGC-AATGGAAACTA
* * * * *
236573 ATTGGTATCTCCAACCTAGTACTTTATTAGCTTGTTCAAGAACCTTAAAGCATTCTTGATCTTAT
65 AATGGTAGCTCCAACATAGTAATTTATTAGCTTGTTCAAGAACCTTAAAGCATTCTTGATCATAT
*** * *
236638 ATAATGGATCCTCTGGAATTTTAAAGGTTGAAACTACTCTGAATTTGCGGTTAGATTAGTATGCT
130 ATAAAACATCCACCGGAATTTTAAAGGTTGAAACTACTCTGAATTTGCGGTTAGATTAGTATGCT
236703 TTG
195 TTG
* ** *
236706 TGGGA-TTTGTTGCACTCTTTGCCCTTTTTGAAATTGAATTTCATTCTGTAGC-ATGGAAACTAA
1 TGGGATTTTGTTGCACTCTTTGCCCTTTGTGAAATTGAATCCCATTCTATAGCAATGGAAACTAA
* *
236769 ATGGTAGCTCCAATCTATAGTAATTTATTAGCTTGTTCAGGAGA-CTTAAAGCATTGTTGATCAT
66 ATGGTAGCTCCAA-C-ATAGTAATTTATTAGCTTGTTCAAGA-ACCTTAAAGCATTCTTGATCAT
* * * **
236833 ATGTAAAACATTCACCGGACTTTTTGAGGTTGA
128 ATATAAAACATCCACCGGAATTTTAAAGGTTGA
236866 GATTTCTGTG
Statistics
Matches: 135, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
195 22 0.16
196 1 0.01
197 106 0.79
198 6 0.04
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (197 bp):
TGGGATTTTGTTGCACTCTTTGCCCTTTGTGAAATTGAATCCCATTCTATAGCAATGGAAACTAA
ATGGTAGCTCCAACATAGTAATTTATTAGCTTGTTCAAGAACCTTAAAGCATTCTTGATCATATA
TAAAACATCCACCGGAATTTTAAAGGTTGAAACTACTCTGAATTTGCGGTTAGATTAGTATGCTT
TG
Found at i:246525 original size:29 final size:28
Alignment explanation
Indices: 246486--246553 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
246476 TTTCTAAAAA
246486 TTTTAGAATTTAA-TTTTTATACTTTTAT
1 TTTTAGAATTTAATTTTTTAT-CTTTTAT
*
246514 TTTTAGAGATTTAATTTTTTATTTTTTA-
1 TTTTAGA-ATTTAATTTTTTATCTTTTAT
*
246542 TTTTAAAATTTA
1 TTTTAGAATTTA
246554 TATTCAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 5 0.14
28 13 0.36
29 11 0.31
30 7 0.19
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTAGAATTTAATTTTTTATCTTTTAT
Found at i:246530 original size:15 final size:14
Alignment explanation
Indices: 246486--246532 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
246476 TTTCTAAAAA
246486 TTTTAGAATTTAAT
1 TTTTAGAATTTAAT
* * *
246500 TTTTATACTTTTAT
1 TTTTAGAATTTAAT
246514 TTTTAGAGATTTAAT
1 TTTTAGA-ATTTAAT
246529 TTTT
1 TTTT
246533 TATTTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTAGAATTTAAT
Found at i:248505 original size:30 final size:30
Alignment explanation
Indices: 248443--248515 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
248433 TACAGTTTAT
* *
248443 ATTTTTA-TATTTTTAATAGATTAAATTAA
1 ATTTTTATTATTTTGAATAGATAAAATTAA
*
248472 ATTTTTATTATTTTGAATGGATAAAATGT-A
1 ATTTTTATTATTTTGAATAGATAAAAT-TAA
248502 ATTTTATCATTATT
1 ATTTT-T-ATTATT
248516 AATTTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 7 0.19
30 22 0.59
31 2 0.05
32 6 0.16
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (30 bp):
ATTTTTATTATTTTGAATAGATAAAATTAA
Found at i:250872 original size:20 final size:20
Alignment explanation
Indices: 250831--250872 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
250821 GTCAAAATAT
* *
250831 AATTTTGTTATTAATATTAA
1 AATTTTGTTATAAATATAAA
250851 AATTTT-TTATAAACTATAAA
1 AATTTTGTTATAAA-TATAAA
250871 AA
1 AA
250873 CACTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
AATTTTGTTATAAATATAAA
Found at i:252243 original size:17 final size:17
Alignment explanation
Indices: 252213--252246 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
252203 ACAAATGCTT
252213 TTAAAATAATAACAAAA
1 TTAAAATAATAACAAAA
252230 TTAATAATAA-AACAAAA
1 TTAA-AATAATAACAAAA
252247 GTTATACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
TTAAAATAATAACAAAA
Found at i:255078 original size:31 final size:31
Alignment explanation
Indices: 255043--255107 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
255033 AGGTCCGCCC
* * *
255043 ATATTA-ATTTTTTTATTTTTTAAAAATATTT
1 ATATTATATTATTTTAATATTTAAAAAT-TTT
*
255074 ATATTATATTATTTTAATATTTAATAATTTT
1 ATATTATATTATTTTAATATTTAAAAATTTT
255105 ATA
1 ATA
255108 CATTTTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATATTATATTATTTTAATATTTAAAAATTTT
Found at i:259000 original size:25 final size:24
Alignment explanation
Indices: 258966--259012 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
258956 AAATTTTGAT
*
258966 AAAAAAATATTTTTAAATTGTAAA
1 AAAAAAATATTTTTAAAATGTAAA
258990 AAAAATAATATTTTTAAAATGTA
1 AAAAA-AATATTTTTAAAATGTA
259013 GATCTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
AAAAAAATATTTTTAAAATGTAAA
Found at i:261545 original size:7 final size:7
Alignment explanation
Indices: 261533--261563 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
261523 GGATACGATT
261533 TGAGTAC
1 TGAGTAC
261540 TGAGTAC
1 TGAGTAC
*
261547 CGAGTAC
1 TGAGTAC
261554 TGAGTAC
1 TGAGTAC
261561 TGA
1 TGA
261564 CTGTGCTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (7 bp):
TGAGTAC
Found at i:263663 original size:6 final size:6
Alignment explanation
Indices: 263652--263701 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
263642 TATGTTGACT
*
263652 CCACCG CCACCG CCACCG CCACCG CCACCG ---CCG CCACCG CCACCA
1 CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG
263697 CCACC
1 CCACC
263702 TCCTCCTCTG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
3 3 0.08
6 37 0.93
ACGTcount: A:0.18, C:0.68, G:0.14, T:0.00
Consensus pattern (6 bp):
CCACCG
Found at i:263675 original size:18 final size:18
Alignment explanation
Indices: 263652--263701 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 18
263642 TATGTTGACT
263652 CCACCGCCACCGCCACCG
1 CCACCGCCACCGCCACCG
263670 CCACCGCCACCG---CCG
1 CCACCGCCACCGCCACCG
*
263685 CCACCGCCACCACCACC
1 CCACCGCCACCGCCACC
263702 TCCTCCTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.50
18 14 0.50
ACGTcount: A:0.18, C:0.68, G:0.14, T:0.00
Consensus pattern (18 bp):
CCACCGCCACCGCCACCG
Found at i:263687 original size:9 final size:9
Alignment explanation
Indices: 263655--263698 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
263645 GTTGACTCCA
263655 CCGCCACCG
1 CCGCCACCG
* * *
263664 CCACCGCCA
1 CCGCCACCG
263673 CCGCCACCG
1 CCGCCACCG
263682 CCGCCACCG
1 CCGCCACCG
*
263691 CCACCACC
1 CCGCCACC
263699 ACCTCCTCCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (9 bp):
CCGCCACCG
Found at i:263687 original size:21 final size:21
Alignment explanation
Indices: 263652--263701 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
263642 TATGTTGACT
* *
263652 CCACCGCCACCGCCACCGCCA
1 CCACCACCGCCGCCACCGCCA
*
263673 CCGCCACCGCCGCCACCGCCA
1 CCACCACCGCCGCCACCGCCA
263694 CCACCACC
1 CCACCACC
263702 TCCTCCTCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.68, G:0.14, T:0.00
Consensus pattern (21 bp):
CCACCACCGCCGCCACCGCCA
Found at i:269320 original size:31 final size:31
Alignment explanation
Indices: 269255--269357 Score: 145
Period size: 31 Copynumber: 3.4 Consensus size: 31
269245 GATTAAGTTA
* * * * *
269255 ACAAAACAATCACTCAACTT-TGAAAATGTG
1 ACAAAACAGTCACTAAAGTTATTAAAAAGTG
269285 ACAAAACAGTCACTAAAGTTATTAAAAAGTG
1 ACAAAACAGTCACTAAAGTTATTAAAAAGTG
269316 ACAAAACAGTCACTAAAGTTATTAAAAAGTG
1 ACAAAACAGTCACTAAAGTTATTAAAAAGTG
*
269347 ACAAAATAGTC
1 ACAAAACAGTC
269358 CTCTTGTTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
30 17 0.26
31 49 0.74
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAGTTATTAAAAAGTG
Found at i:270371 original size:30 final size:31
Alignment explanation
Indices: 270308--270374 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
270298 AAGAGGATTA
* *
270308 TTTTGTCACTTTTCGATAACTTTAGTGATTG
1 TTTTGTCACTTTTCGATAACTTGAGTGACTG
*
270339 TTTTGTCACATTTTC-A-AAGTTGAGTGACTG
1 TTTTGTCAC-TTTTCGATAACTTGAGTGACTG
270369 TTTTGT
1 TTTTGT
270375 TACACATAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.53
31 10 0.31
32 5 0.16
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (31 bp):
TTTTGTCACTTTTCGATAACTTGAGTGACTG
Found at i:272727 original size:22 final size:21
Alignment explanation
Indices: 272697--272737 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
272687 TTGAATATAT
* *
272697 AAATTATATTTTAAATATTAAA
1 AAATAATATTATAAA-ATTAAA
272719 AAATAATATTATAAAATTA
1 AAATAATATTATAAAATTA
272738 TATATTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATAATATTATAAAATTAAA
Found at i:278811 original size:18 final size:18
Alignment explanation
Indices: 278790--278825 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
278780 TTGAAAAAAA
278790 TATAAAT-TTTGTAATTTT
1 TATAAATATTT-TAATTTT
278808 TATAAATATTTTAATTTT
1 TATAAATATTTTAATTTT
278826 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATAAATATTTTAATTTT
Found at i:279010 original size:23 final size:23
Alignment explanation
Indices: 278965--279010 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
278955 CTTGAAACTT
* * *
278965 GAATGACTTATTTGAGTTTACTC
1 GAATGACTTATTCGAATTGACTC
*
278988 GAATTACTTATTCGAATTGACTC
1 GAATGACTTATTCGAATTGACTC
279011 AAATAATTCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (23 bp):
GAATGACTTATTCGAATTGACTC
Found at i:279711 original size:25 final size:25
Alignment explanation
Indices: 279683--279730 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
279673 TACTGAGATT
279683 TTAAA-ATTAAATATTTTTGAATATA
1 TTAAATATTAAAT-TTTTTGAATATA
* *
279708 TTAAATATTACATTTTTTTAATA
1 TTAAATATTAAATTTTTTGAATA
279731 ACAACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAAATATTAAATTTTTTGAATATA
Found at i:279725 original size:26 final size:24
Alignment explanation
Indices: 279683--279730 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
279673 TACTGAGATT
279683 TTAAAATTAAATATTTTTGAATATA
1 TTAAAATTAAATATTTTT-AATATA
* *
279708 TTAAATATTACATTTTTTTAATA
1 TTAAA-ATTAAATATTTTTAATA
279731 ACAACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTAAAATTAAATATTTTTAATATA
Found at i:294089 original size:2 final size:2
Alignment explanation
Indices: 294082--294116 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
294072 TATCATTTAC
294082 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
294117 TTGTTGTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:302861 original size:8 final size:8
Alignment explanation
Indices: 302850--302891 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
302840 TTAATTAATT
302850 TTTTAAAA
1 TTTTAAAA
302858 TTTTAAAA
1 TTTTAAAA
302866 TTTTAAAA
1 TTTTAAAA
*
302874 TATATAAAA
1 T-TTTAAAA
302883 TTATTAAAA
1 TT-TTAAAA
302892 ATATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 18 0.60
9 12 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TTTTAAAA
Found at i:302881 original size:17 final size:17
Alignment explanation
Indices: 302850--302899 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
302840 TTAATTAATT
*
302850 TTTTAAAAT-TTTAAAA
1 TTTTAAAATATATAAAA
302866 TTTTAAAATATATAAAA
1 TTTTAAAATATATAAAA
302883 TTATTAAAA-ATATAAAA
1 TT-TTAAAATATATAAAA
302900 AATATAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 9 0.29
17 16 0.52
18 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAAATATATAAAA
Found at i:302883 original size:9 final size:9
Alignment explanation
Indices: 302870--302913 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
302860 TTAAAATTTT
302870 AAAATATATA
1 AAAATATA-A
* *
302880 AAATTATTA
1 AAAATATAA
302889 AAAATATAA
1 AAAATATAA
302898 AAAATATAA
1 AAAATATAA
302907 AAAATAT
1 AAAATAT
302914 TTTTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 24 0.80
10 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATATAA
Found at i:302900 original size:18 final size:19
Alignment explanation
Indices: 302861--302913 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
302851 TTTAAAATTT
302861 TAAAATT-TT-AAAATATA
1 TAAAATTATTAAAAATATA
302878 TAAAATTATTAAAAATATA
1 TAAAATTATTAAAAATATA
* *
302897 -AAAAATATAAAAAATAT
1 TAAAATTATTAAAAATAT
302914 TTTTTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 7 0.22
18 17 0.53
19 8 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAATTATTAAAAATATA
Found at i:303570 original size:48 final size:46
Alignment explanation
Indices: 303478--303570 Score: 107
Period size: 48 Copynumber: 2.0 Consensus size: 46
303468 TATTCTTTTC
* * *
303478 TCTTCCTTCTTTCTCTCTTTTTTTTCTTCTCTTTTTAACTTTTCTAA
1 TCTTCCTTCTTTCTCTCTTTTTTTTATTCTATGTTT-ACTTTTCTAA
*
303525 TCTTCCATTTTTTCTCTCTCTTTTTTTATTCTATGTTT-CTCTTTCT
1 TCTTCC-TTCTTTCTCTCT-TTTTTTTATTCTATGTTTACT-TTTCT
303571 TCTCCTTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
47 8 0.21
48 16 0.41
49 15 0.38
ACGTcount: A:0.08, C:0.25, G:0.01, T:0.67
Consensus pattern (46 bp):
TCTTCCTTCTTTCTCTCTTTTTTTTATTCTATGTTTACTTTTCTAA
Found at i:305935 original size:21 final size:21
Alignment explanation
Indices: 305883--305935 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
305873 TCATATTTGT
*
305883 TATTCTCTTTTCTTTCTCATA
1 TATTCTCTTTTATTTCTCATA
* * *
305904 T-TTGATTTTTTATTTTTCATA
1 TATT-CTCTTTTATTTCTCATA
305925 TATTCTCTTTT
1 TATTCTCTTTT
305936 TCTTTCCCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTCTCTTTTATTTCTCATA
Found at i:309275 original size:15 final size:15
Alignment explanation
Indices: 309244--309286 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
309234 AAGGTATAAC
309244 AAAAGCAAAAG-AATG
1 AAAAG-AAAAGAAATG
* *
309259 AAAGGAAATGAAATG
1 AAAAGAAAAGAAATG
309274 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
309287 ATATATGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAGAAATG
Found at i:315259 original size:2 final size:2
Alignment explanation
Indices: 315254--315279 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
315244 AATTTTTTAA
315254 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
315280 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:315776 original size:17 final size:18
Alignment explanation
Indices: 315756--315802 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
315746 TGTTAGTGGG
315756 TTTTATTAAAAAATA-TA
1 TTTTATTAAAAAATATTA
*
315773 TTTTATTTATAAAAGTATTA
1 TTTTA-TTA-AAAAATATTA
*
315793 TTTTAATAAA
1 TTTTATTAAA
315803 TATATTTCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.20
18 5 0.20
19 8 0.32
20 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTATTAAAAAATATTA
Found at i:315808 original size:17 final size:17
Alignment explanation
Indices: 315756--315809 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
315746 TGTTAGTGGG
*
315756 TTTTATTAAAAAATATA
1 TTTTATTAATAAATATA
*
315773 TTTTATTTATAAA-AGTA
1 TTTTATTAATAAATA-TA
315790 TTATT-TTAATAAATATA
1 TT-TTATTAATAAATATA
315807 TTT
1 TTT
315810 CGTGTCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 2 0.06
17 26 0.84
18 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTTATTAATAAATATA
Found at i:330321 original size:40 final size:40
Alignment explanation
Indices: 330276--330356 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
330266 AGACATAAAC
*
330276 TTGTGTTCAGGTGTCTATACTTACTCAAGCCTGAGTAACA
1 TTGTGTTCAGGTCTCTATACTTACTCAAGCCTGAGTAACA
330316 TTGTGTTCAGGTCTCTATACTTACTCAAGCCTGAGTAACA
1 TTGTGTTCAGGTCTCTATACTTACTCAAGCCTGAGTAACA
330356 T
1 T
330357 AGATTCCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (40 bp):
TTGTGTTCAGGTCTCTATACTTACTCAAGCCTGAGTAACA
Found at i:333324 original size:16 final size:16
Alignment explanation
Indices: 333303--333333 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
333293 TTTGCATTAA
333303 TAAAATTTTAATTTAT
1 TAAAATTTTAATTTAT
*
333319 TAAAATTTTATTTTA
1 TAAAATTTTAATTTA
333334 ATATGATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAAATTTTAATTTAT
Found at i:334819 original size:2 final size:2
Alignment explanation
Indices: 334812--334836 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
334802 TTAAATTTTA
334812 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 A
334837 AGTTACAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:339562 original size:2 final size:2
Alignment explanation
Indices: 339551--339580 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
339541 CAATTTATTA
339551 AT AT -T 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 A
339581 GGAGGAACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344550 original size:15 final size:15
Alignment explanation
Indices: 344530--344561 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
344520 TGTTCATAAC
*
344530 AAGGAGGAGGAGGAG
1 AAGGAGAAGGAGGAG
344545 AAGGAGAAGGAGGAG
1 AAGGAGAAGGAGGAG
344560 AA
1 AA
344562 ACTTGTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (15 bp):
AAGGAGAAGGAGGAG
Found at i:349088 original size:27 final size:27
Alignment explanation
Indices: 349025--349076 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
349015 TTTATCCAGT
* *
349025 ACCTCAAAACTTAAACTCTAAATCTTA
1 ACCTCAAACCATAAACTCTAAATCTTA
*
349052 ACCTCAAACCATAAACTTTAAATCT
1 ACCTCAAACCATAAACTCTAAATCT
349077 ACACCTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (27 bp):
ACCTCAAACCATAAACTCTAAATCTTA
Found at i:349124 original size:22 final size:22
Alignment explanation
Indices: 349094--349136 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
349084 GAACCCAAAT
*
349094 CTAAACCTTAAATCATAAACCC
1 CTAAACCTTAAACCATAAACCC
* *
349116 CTAATCCTTAAACCTTAAACC
1 CTAAACCTTAAACCATAAACC
349137 ATAAACTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.26
Consensus pattern (22 bp):
CTAAACCTTAAACCATAAACCC
Done.