Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008729.1 Hibiscus syriacus cultivar Beakdansim tig00111798_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: 244119
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2354 original size:16 final size:16
Alignment explanation
Indices: 2330--2363 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2320 TATCGCCGAC
*
2330 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2346 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2362 CG
1 CG
2364 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2811 original size:21 final size:21
Alignment explanation
Indices: 2787--2853 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
2777 ATCTACCAAA
2787 ATTTACCAAACTTTGAAAAAC
1 ATTTACCAAACTTTGAAAAAC
**
2808 ATTTTTCAAA----G--AAAC
1 ATTTACCAAACTTTGAAAAAC
2823 ATTTACCAAACTTTGAAAAAC
1 ATTTACCAAACTTTGAAAAAC
*
2844 ATTTTCCAAA
1 ATTTACCAAA
2854 GTTGGTTGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
15 12 0.34
17 1 0.03
19 1 0.03
21 21 0.60
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.31
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAAAC
Found at i:4452 original size:21 final size:22
Alignment explanation
Indices: 4417--4459 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4407 TTATTTTATT
*
4417 TATTTTTTTTAATTAAAAATAA
1 TATTTTTATTAATTAAAAATAA
4439 TATTTTTATT-ATTAAAAATAA
1 TATTTTTATTAATTAAAAATAA
4460 AAATAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTATTAATTAAAAATAA
Found at i:4831 original size:60 final size:59
Alignment explanation
Indices: 4767--4880 Score: 129
Period size: 60 Copynumber: 1.9 Consensus size: 59
4757 ACTATGGTTA
* * * **
4767 TCATTATGAATTACTTCTCAAACTTTTGAATGTTTCAATTTCATTCCCAAACTATGACCT
1 TCATTATAAATTACTCCCCAAACTTTTGAACATTTCAATTTCA-TCCCAAACTATGACCT
* ** * *
4827 TCATTCTAAATTGGTCCCCAAATTTTTGAACATTTTAATTTCATCCCAAACTAT
1 TCATTATAAATTACTCCCCAAACTTTTGAACATTTCAATTTCATCCCAAACTAT
4881 ACATATATAC
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
59 11 0.25
60 33 0.75
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (59 bp):
TCATTATAAATTACTCCCCAAACTTTTGAACATTTCAATTTCATCCCAAACTATGACCT
Found at i:7852 original size:14 final size:13
Alignment explanation
Indices: 7833--7863 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
7823 TAAATTGAAT
7833 AAATATGAAATTAC
1 AAATATGAAATT-C
7847 AAATATGAAATTC
1 AAATATGAAATTC
7860 AAAT
1 AAAT
7864 CAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (13 bp):
AAATATGAAATTC
Found at i:8016 original size:26 final size:26
Alignment explanation
Indices: 7948--8019 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
7938 AATAATTATA
*
7948 ATAT-ATTAATATATATATAAAAACT
1 ATATAATTAATATATATATATAAACT
7973 ATATAA-TAATATAATATATATAAACT
1 ATATAATTAATAT-ATATATATAAACT
* *
7999 ATATAATTTATATTTATATAT
1 ATATAATTAATATATATATAT
8020 TATATATAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.24
26 26 0.63
27 5 0.12
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATAATTAATATATATATATAAACT
Found at i:8288 original size:13 final size:13
Alignment explanation
Indices: 8270--8294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8260 TTTTTATTTT
8270 TATATTATTTAAA
1 TATATTATTTAAA
8283 TATATTATTTAA
1 TATATTATTTAA
8295 TTACTAAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTATTTAAA
Found at i:8364 original size:14 final size:15
Alignment explanation
Indices: 8347--8378 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
8337 ATAATAAATA
8347 ATTAT-AAATATATT
1 ATTATAAAATATATT
8361 ATTATAAAATATATT
1 ATTATAAAATATATT
8376 ATT
1 ATT
8379 TTTAGCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:8428 original size:21 final size:21
Alignment explanation
Indices: 8404--8465 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
8394 TGTAAAAAAT
8404 ATTTATAAATATATTATTATA
1 ATTTATAAATATATTATTATA
*
8425 ATTTATAAAGTATATTATT-TT
1 ATTTATAAA-TATATTATTATA
* *
8446 ATTTTTAAA-ATATTAATATA
1 ATTTATAAATATATTATTATA
8466 TTTGATCGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 7 0.20
20 1 0.03
21 18 0.51
22 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTATAAATATATTATTATA
Found at i:9994 original size:31 final size:28
Alignment explanation
Indices: 9952--10015 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
9942 AATACGGTGG
* *
9952 AGTGACCATTTTGTTATAAATTAATAATATT
1 AGTGACCATTTTATTACAAA-T-A-AATATT
*
9983 AGTGACTATTTTATTACAAATAAATATT
1 AGTGACCATTTTATTACAAATAAATATT
10011 AGTGA
1 AGTGA
10016 TTAATTGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 1 0.03
30 1 0.03
31 17 0.57
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (28 bp):
AGTGACCATTTTATTACAAATAAATATT
Found at i:10979 original size:39 final size:39
Alignment explanation
Indices: 10936--11027 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 39
10926 TTTAAAAAAC
*
10936 AATTTAGAATGTTAAT-CTA-AAATAGTTTAAGAAATTAAG
1 AATTTAGAATGTTAATGATAGAAA-A-TTTAAGAAATTAAG
* *
10975 AATTTAGAAAGAT-ATGATAGTAAAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGATAG-AAAATTTAAGAAATTAAG
11014 AATTTAGAATGTTA
1 AATTTAGAATGTTA
11028 GAGTGAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
38 2 0.05
39 38 0.86
40 1 0.02
41 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.35
Consensus pattern (39 bp):
AATTTAGAATGTTAATGATAGAAAATTTAAGAAATTAAG
Found at i:12043 original size:16 final size:15
Alignment explanation
Indices: 12023--12064 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
12013 TATTTTTTTC
12023 AAATAATTATAATAA
1 AAATAATTATAATAA
*
12038 ACAATAAGTATAATAA
1 A-AATAATTATAATAA
12054 AAA-AATTATAA
1 AAATAATTATAA
12065 CGAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 3 0.12
16 14 0.58
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AAATAATTATAATAA
Found at i:14085 original size:2 final size:2
Alignment explanation
Indices: 14078--14103 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14068 TATCGTCCAC
14078 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
14104 GTTAAATCAA
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:14652 original size:16 final size:16
Alignment explanation
Indices: 14608--14654 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
14598 AGCTAAAACT
14608 GCATGGTGTTTTGCTA
1 GCATGGTGTTTTGCTA
** *
14624 GTCA-CCTGCTTTGCTA
1 G-CATGGTGTTTTGCTA
14640 GCATGGTGTTTTGCT
1 GCATGGTGTTTTGCT
14655 CCTGTATTGC
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.11, C:0.19, G:0.28, T:0.43
Consensus pattern (16 bp):
GCATGGTGTTTTGCTA
Found at i:16708 original size:16 final size:16
Alignment explanation
Indices: 16687--16721 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16677 CTCAGAAAAC
*
16687 GAAGAAGATGAAGGAG
1 GAAGAAGAAGAAGGAG
*
16703 GAAGAAGAAGATGGAG
1 GAAGAAGAAGAAGGAG
16719 GAA
1 GAA
16722 ACTGATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.06
Consensus pattern (16 bp):
GAAGAAGAAGAAGGAG
Found at i:25318 original size:23 final size:23
Alignment explanation
Indices: 25258--25318 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
25248 ATAATTCAGT
* *
25258 CTTTGTGACAAGTTTATCTCTGC
1 CTTTGTGTCAAGTTTATCTATGC
* *
25281 CTTTATGGT-ATGTTTATCTATGC
1 CTTTGT-GTCAAGTTTATCTATGC
*
25304 CTTTGTGTCACGTTT
1 CTTTGTGTCAAGTTT
25319 TTCTCTGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.07
23 27 0.90
24 1 0.03
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.49
Consensus pattern (23 bp):
CTTTGTGTCAAGTTTATCTATGC
Found at i:35210 original size:26 final size:26
Alignment explanation
Indices: 35167--35217 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
35157 TTGTATTTAA
35167 ATTATTATTTAATTTTATTAATTACT
1 ATTATTATTTAATTTTATTAATTACT
*
35193 ATTA-TATTTATTTGTTATTAATTAC
1 ATTATTATTTAATT-TTATTAATTAC
35218 AATTTGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTATTATTTAATTTTATTAATTACT
Found at i:35474 original size:38 final size:37
Alignment explanation
Indices: 35383--35672 Score: 199
Period size: 36 Copynumber: 7.9 Consensus size: 37
35373 GCAAACGATC
* *
35383 TTTGAAAATACT-TATAATATACATAATTTTTGAAAACA-T
1 TTTGAAAATA-TATATAATAT--ATAGTTTTT-AAAATATT
* *
35422 TTTGAAAATGTATATAATATATAGTTTTAAAAATATTT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATA-TT
* *
35460 TTTGAAACTATATAT--TATATAGTTTTTAAAACATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATATT
*
35495 TTAGAAAATATATATAATATATAGTTTTTAAAATCATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAT-ATT
* * *
35533 TTTGAAAA-AGTATATAATATATTG-TTTT-GAATTTT
1 TTTGAAAATA-TATATAATATATAGTTTTTAAAATATT
* * * * * *
35568 TTTAAAACATTTAAATATTATATAATTTTTGAAAA-ACAT
1 TTTGAAA-ATATATATAATATATAGTTTTT-AAAATA-TT
* ***
35607 TTT--AAATATATATAATATATAATTTTTAAACCGTT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATATT
* * *
35642 TCTGAAAATATATAT--TATAAAATTTTTAAAA
1 TTTGAAAATATATATAATATATAGTTTTTAAAA
35673 CGATTTTAAA
Statistics
Matches: 202, Mismatches: 33, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
35 43 0.21
36 54 0.27
37 44 0.22
38 38 0.19
39 23 0.11
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAATATT
Found at i:35547 original size:73 final size:73
Alignment explanation
Indices: 35409--35563 Score: 208
Period size: 73 Copynumber: 2.1 Consensus size: 73
35399 ATATACATAA
* *
35409 TTTTTGAAAACATTTTGAAAATGTATATAATATATAGTTTTAAAAATATTTTTTGAAACTATATA
1 TTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTTTGAAACAATATA
*
35474 TTATATAG
66 TAATATAG
*
35482 TTTTT-AAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCA-TTTTTGAAA-AAGT
1 TTTTTGAAAACATTTT-GAAAATATATATAATATATAGTTTTAAAAAT-ATTTTTTGAAACAA-T
*
35544 ATATAATATAT
63 ATATAATATAG
35555 TGTTTTGAA
1 T-TTTTGAA
35564 TTTTTTTAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
72 11 0.15
73 54 0.75
74 5 0.07
75 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (73 bp):
TTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTTTGAAACAATATA
TAATATAG
Found at i:35595 original size:29 final size:29
Alignment explanation
Indices: 35562--35622 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
35552 TATTGTTTTG
**
35562 AATTTTTTTAAAACA-TTTAAATATTATAT
1 AATTTTTGAAAAACATTTTAAATA-TATAT
35591 AATTTTTGAAAAACATTTTAAATATATAT
1 AATTTTTGAAAAACATTTTAAATATATAT
35620 AAT
1 AAT
35623 ATATAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (29 bp):
AATTTTTGAAAAACATTTTAAATATATAT
Found at i:35768 original size:15 final size:16
Alignment explanation
Indices: 35748--35777 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35738 AGTATTATTA
35748 TTATTATT-TTATTTC
1 TTATTATTATTATTTC
35763 TTATTATTATTATTT
1 TTATTATTATTATTT
35778 ATGCTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTATTATTATTTC
Found at i:37004 original size:25 final size:25
Alignment explanation
Indices: 36940--37004 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
36930 TGATCCTAAG
* * *
36940 TTTTATCT-TTATTTTTCATTTTACT
1 TTTTAT-TATTATTTTTAATTTAACC
*
36965 TTTTAAATATT-TTTTTAATTTAACC
1 TTTT-ATTATTATTTTTAATTTAACC
36990 TTTTATTATTATTTT
1 TTTTATTATTATTTT
37005 ATTATTTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 5 0.16
25 24 0.75
26 3 0.09
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATTATTATTTTTAATTTAACC
Found at i:37019 original size:27 final size:28
Alignment explanation
Indices: 36989--37057 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
36979 TTAATTTAAC
*
36989 CTTTTATTATTATTTTATTATTTCT-TT
1 CTTTTATTATTATTTTATTATTTATATT
* *
37016 CTTTCATTATTATTATTATTTTTTATATT
1 CTTTTATTATTATT-TTATTATTTATATT
37045 -TTTT-TTATTATTT
1 CTTTTATTATTATTT
37058 AACATTTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 12 0.33
29 2 0.06
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (28 bp):
CTTTTATTATTATTTTATTATTTATATT
Found at i:37055 original size:30 final size:33
Alignment explanation
Indices: 36992--37056 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
36982 ATTTAACCTT
36992 TTATTATTATTTTATTATTTCTTTCTTTCATTA
1 TTATTATTATTTTATTATTTCTTTCTTTCATTA
37025 TTATTATTATTTT-TTATATT-TTT-TTT-ATTA
1 TTATTATTATTTTATTAT-TTCTTTCTTTCATTA
37055 TT
1 TT
37057 TAACATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 6 0.19
31 3 0.10
32 7 0.23
33 15 0.48
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.74
Consensus pattern (33 bp):
TTATTATTATTTTATTATTTCTTTCTTTCATTA
Found at i:38806 original size:19 final size:19
Alignment explanation
Indices: 38772--38816 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
38762 ATTTAGACAT
38772 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
38790 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
38809 TTTGCATT
1 TTTGCATT
38817 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:42434 original size:165 final size:164
Alignment explanation
Indices: 42164--43173 Score: 1190
Period size: 165 Copynumber: 6.1 Consensus size: 164
42154 TGCAGCTTAG
* * *
42164 CTCAAGGCCAGAAGGGCTATCTGCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGCGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
*
42228 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
66 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
42293 ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
131 ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
42327 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGCGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
42392 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
65 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
*
42457 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAA
130 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * * * * *
42492 CTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCTGAGG
1 CTCAAGGCTAGAAGGGTTATCTG-CGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC-CAAG
* * * ***
42557 GCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTC
64 GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTC
* * * * * * *
42622 GACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAG
125 GATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * * * * * *
42661 CTTAAGTCGATAAGGGCTATCT--G-CCAAAGACCTTTGAGTTCGACTACACTCGGCT-CAACGG
1 CTCAAGGCTAGAAGGGTTATCTGCGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GG
42722 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
65 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
*
42787 CACTCAGCTTCGAGGGCACATCATTTACAGCATAG
130 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
42822 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGCGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * * ***
42887 CATATCATTTGTAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACCTTTGAGTTCGATTA
65 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
* * * *
42952 CACTCAGCTTCGAGGACATATCATTTGCAGCACAA
130 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * * * * * *
42987 CTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGATTACGCTCAGCTTCGAGG
1 CTCAAGGCTAGAAGGGTTATCTG-CGACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAG
* * * * * * * **
43052 GCACATCATTTACAGCATAACTCAAGGCTACAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTC
64 GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCCCGAGTTC
* * *
43117 GATTACACTCAGC-TC-AGAGGCAAACCAGATTTACAGCATAG
125 GATTACACTCAGCTTCGAG-GGCACATC--ATTTACAGCATAA
* *
43158 CTCAATGCAAGAAGGG
1 CTCAAGGCTAGAAGGG
43174 CTATTCGTCA
Statistics
Matches: 728, Mismatches: 95, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
160 26 0.04
161 39 0.05
163 26 0.04
164 43 0.06
165 377 0.52
166 88 0.12
168 2 0.00
169 51 0.07
170 54 0.07
171 22 0.03
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (164 bp):
CTCAAGGCTAGAAGGGTTATCTGCGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
ACTCAGCTTCGAGGGCACATCATTTACAGCATAA
Found at i:42592 original size:250 final size:245
Alignment explanation
Indices: 42151--43131 Score: 1372
Period size: 250 Copynumber: 4.0 Consensus size: 245
42141 TAAACAAACT
* * * * *
42151 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AAGACCTTCGAGTTCGACTACACT
* * * *
42216 CAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
64 CAGCTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
42281 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
129 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
*
42346 TCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
194 TCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
** *
42398 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTCA
*
42463 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACC
66 GC-TCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACC
** * * * * * *
42528 TTCGAGTTCGACTACGCTCAGC-TCTGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGG
126 CCCGAGTTCGATTACACTCAGCTTC-GAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGG
** *
42592 GTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATC
190 GTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
* * *
42648 ATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACACTCG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTCA
* * *
42713 GCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGA
66 GCTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGA
*
42778 GTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAGCTCAAGGCTAGAAGGGTTATC
131 GTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC
42843 TGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
196 TGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
* * * *
42893 ATTTGTAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACCTTTGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTCA
* * * * * *
42958 GCTTCGAGGACATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACC
66 GC-TCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACC
*** * *
43023 TTTGAGTTCGATTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTACAAGGG
126 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
* * *
43088 TTATCTGTCACCAAAAGACCTTCGAGTTCGATTACACTCAGCTC
191 TTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
43132 AGAGGCAAAC
Statistics
Matches: 652, Mismatches: 68, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
244 3 0.00
245 196 0.30
246 87 0.13
247 36 0.06
248 1 0.00
249 48 0.07
250 278 0.43
251 3 0.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (245 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTCA
GCTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGA
GTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC
TGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
Found at i:43130 original size:495 final size:496
Alignment explanation
Indices: 42151--43177 Score: 1614
Period size: 495 Copynumber: 2.1 Consensus size: 496
42141 TAAACAAACT
* *
42151 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCT
1 ATTTGCAGCATAGCTCAAGGCCAGAAGGGCTATCTGCCA-CAAGACCTTCGAGTTCGACTACACT
42216 CAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
65 CAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
42281 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
130 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
42346 TCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAG
195 TCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAG
*
42411 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
260 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACAC
* *
42476 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACT
325 ATCATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * * *
42541 ACGCTCAGCTCTGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACC
390 ACGCTCAGCTCTGAGGGCACATCATTTACAGCATAACTCAAGGCAACAAGGGTTATCTGCCAACC
* *
42606 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATC
455 AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATC
* * * * *
42648 ATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCA-AAGACCTTTGAGTTCGACTACACTC
1 ATTTGCAGCATAGCTCAAGGCCAGAAGGGCTATCTGCCACAAGACCTTCGAGTTCGACTACACTC
* *
42712 GGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
66 AGCTCCAA-GGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
*
42776 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAGCTCAAGGCTAGAAGGGTTA
130 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
* *
42841 TCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAG
195 TCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAG
* *** *
42906 CTTAAGTCGATAAGGGCTATCTGCCAAAGACCTTTGAGTTCGATTACACTCAGCTTCGAGGACAT
260 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACAC
* * * *
42971 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGATT
325 ATCATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
43036 ACGCTCAGCT-TCGAGGGCACATCATTTACAGCATAACTCAAGGCTACAAGGGTTATCTGTC-AC
390 ACGCTCAGCTCT-GAGGGCACATCATTTACAGCATAACTCAAGGCAACAAGGGTTATCTGCCAAC
* * *
43099 CAAAAGACCTTCGAGTTCGATTACACTCAGCT-CAGAGGCAAACC
454 C-AAAGACCTTCGAGTTCGACTACACTCAGCTCCA-AGGCATATC
* * *
43143 AGATTTACAGCATAGCTCAATGCAAGAAGGGCTAT
1 --ATTTGCAGCATAGCTCAAGGCCAGAAGGGCTAT
43178 TCGTCAAAAC
Statistics
Matches: 483, Mismatches: 41, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
494 9 0.02
495 413 0.86
497 61 0.13
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (496 bp):
ATTTGCAGCATAGCTCAAGGCCAGAAGGGCTATCTGCCACAAGACCTTCGAGTTCGACTACACTC
AGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCG
AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
CTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGACACA
TCATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCTGAGGGCACATCATTTACAGCATAACTCAAGGCAACAAGGGTTATCTGCCAACCA
AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATC
Found at i:43874 original size:38 final size:37
Alignment explanation
Indices: 43783--44072 Score: 199
Period size: 36 Copynumber: 7.9 Consensus size: 37
43773 GCAAACGATC
* *
43783 TTTGAAAATACT-TATAATATACATAATTTTTGAAAACA-T
1 TTTGAAAATA-TATATAATAT--ATAGTTTTT-AAAATATT
* *
43822 TTTGAAAATGTATATAATATATAGTTTTAAAAATATTT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATA-TT
* *
43860 TTTGAAACTATATAT--TATATAGTTTTTAAAACATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATATT
*
43895 TTAGAAAATATATATAATATATAGTTTTTAAAATCATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAT-ATT
* * *
43933 TTTGAAAA-AGTATATAATATATTG-TTTT-GAATTTT
1 TTTGAAAATA-TATATAATATATAGTTTTTAAAATATT
* * * * * *
43968 TTTAAAACATTTAAATATTATATACTTTTTGAAAA-ACAT
1 TTTGAAA-ATATATATAATATATAGTTTTT-AAAATA-TT
* ***
44007 TTT--AAATATATATAATATATAATTTTTAAACCGTT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATATT
* * *
44042 TCTGAAAATATATAT--TATAAAATTTTTAAAA
1 TTTGAAAATATATATAATATATAGTTTTTAAAA
44073 CGTTTTTAAA
Statistics
Matches: 201, Mismatches: 34, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
35 43 0.21
36 53 0.26
37 44 0.22
38 38 0.19
39 23 0.11
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAATATT
Found at i:43947 original size:73 final size:73
Alignment explanation
Indices: 43809--43963 Score: 208
Period size: 73 Copynumber: 2.1 Consensus size: 73
43799 ATATACATAA
* *
43809 TTTTTGAAAACATTTTGAAAATGTATATAATATATAGTTTTAAAAATATTTTTTGAAACTATATA
1 TTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTTTGAAACAATATA
*
43874 TTATATAG
66 TAATATAG
*
43882 TTTTT-AAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCA-TTTTTGAAA-AAGT
1 TTTTTGAAAACATTTT-GAAAATATATATAATATATAGTTTTAAAAAT-ATTTTTTGAAACAA-T
*
43944 ATATAATATAT
63 ATATAATATAG
43955 TGTTTTGAA
1 T-TTTTGAA
43964 TTTTTTTAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
72 11 0.15
73 54 0.75
74 5 0.07
75 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (73 bp):
TTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTAAAAATATTTTTTGAAACAATATA
TAATATAG
Found at i:44033 original size:36 final size:35
Alignment explanation
Indices: 43795--44078 Score: 177
Period size: 35 Copynumber: 7.8 Consensus size: 35
43785 TGAAAATACT
*
43795 TATAATATACATAATTTTTGAAAACATTTTGAAAATGTA
1 TATAATAT--ATAATTTTT-AAAACATTTTG-AAATATA
* * *
43834 TATAATATATAGTTTTAAAAATATTTTTTGAAACTATA
1 TATAATATATAATTTTTAAAACA--TTTTGAAA-TATA
*
43872 TAT--TATATAGTTTTTAAAACATTTTAGAAAATATA
1 TATAATATATAATTTTTAAAACATTTT-G-AAATATA
* *
43907 TATAATATATAGTTTTTAAAATCATTTTTGAAAAAGTA
1 TATAATATATAATTTTTAAAA-CA-TTTTGAAATA-TA
* *** * * *
43945 TATAATATAT--TGTTTTGAATTTTTTTAAAACATT
1 TATAATATATAAT-TTTTAAAACATTTTGAAATATA
43979 TA-AATATTATATACTTTTTGAAAAACATTTT-AAATATA
1 TATAATA-TATA-A-TTTTT--AAAACATTTTGAAATATA
* *
44017 TATAATATATAATTTTTAAACCGTTTCTGAAA-ATA
1 TATAATATATAATTTTTAAAACATTT-TGAAATATA
* * *
44052 TATATTATAAAATTTTTAAAACGTTTT
1 TATAATATATAATTTTTAAAACATTTT
44079 TAAAAGCATT
Statistics
Matches: 199, Mismatches: 25, Indels: 47
0.73 0.09 0.17
Matches are distributed among these distances:
33 4 0.02
34 18 0.09
35 43 0.22
36 33 0.17
37 41 0.21
38 38 0.19
39 22 0.11
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (35 bp):
TATAATATATAATTTTTAAAACATTTTGAAATATA
Found at i:44079 original size:110 final size:109
Alignment explanation
Indices: 43871--44089 Score: 241
Period size: 110 Copynumber: 2.0 Consensus size: 109
43861 TTGAAACTAT
* * * *
43871 ATATTATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCATTTTT
1 ATATTATATACTTTTTAAAACATTTT--AAAATATATATAATATATAATTTTTAAAACCATTTCT
* * **
43936 GAAAAAGTATATAATATATTGTTTTGAATTTTTTTAAAA-CATTTAA
64 GAAAAAGTATATAATAAATTG-TTTAAAAGTTTTTAAAAGCATTTAA
*
43982 ATATTATATACTTTTTGAAAAACATTTT-AAATATATATAATATATAATTTTT-AAACCGTTTCT
1 ATATTATATACTTTTT--AAAACATTTTAAAATATATATAATATATAATTTTTAAAACCATTTCT
*
44045 GAAAATA-TATATTATAAAATT-TTTAAAACGTTTTTAAAAGCATTT
64 GAAAA-AGTATATAAT-AAATTGTTTAAAA-GTTTTTAAAAGCATTT
44090 TGGAAATTTA
Statistics
Matches: 92, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
108 5 0.05
109 29 0.32
110 33 0.36
111 15 0.16
113 10 0.11
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (109 bp):
ATATTATATACTTTTTAAAACATTTTAAAATATATATAATATATAATTTTTAAAACCATTTCTGA
AAAAGTATATAATAAATTGTTTAAAAGTTTTTAAAAGCATTTAA
Found at i:44166 original size:15 final size:16
Alignment explanation
Indices: 44146--44175 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
44136 AGTATTATTA
44146 TTATTATT-TTATTTC
1 TTATTATTATTATTTC
44161 TTATTATTATTATTT
1 TTATTATTATTATTT
44176 ATGCTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTATTATTATTTC
Found at i:45400 original size:25 final size:25
Alignment explanation
Indices: 45336--45400 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
45326 TGATCCTAAG
* * *
45336 TTTTATCT-TTATTTTTCATTTTACT
1 TTTTAT-TATTATTTTTAATTTAACC
*
45361 TTTTAAATATT-TTTTTAATTTAACC
1 TTTT-ATTATTATTTTTAATTTAACC
45386 TTTTATTATTATTTT
1 TTTTATTATTATTTT
45401 ATTATTTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 5 0.16
25 24 0.75
26 3 0.09
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATTATTATTTTTAATTTAACC
Found at i:45402 original size:11 final size:11
Alignment explanation
Indices: 45386--45454 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
45376 TAATTTAACC
45386 TTTTATTATTA
1 TTTTATTATTA
45397 TTTTATTATT-
1 TTTTATTATTA
* *
45407 TCTTTCTT-TCA
1 T-TTTATTATTA
45418 TTATTATTATTA
1 TT-TTATTATTA
45430 TTTT-TTA-TA
1 TTTTATTATTA
45439 TTTT-TT-TTA
1 TTTTATTATTA
*
45448 TATTATT
1 TTTTATT
45455 TAACATTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
9 13 0.28
10 8 0.17
11 22 0.47
12 4 0.09
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:46278 original size:12 final size:12
Alignment explanation
Indices: 46261--46320 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
46251 CAAATAAATA
*
46261 TATGTATATGTG
1 TATGTATATATG
46273 TATGTATATATG
1 TATGTATATATG
*
46285 TATG----GATG
1 TATGTATATATG
*
46293 TATGTATATGTG
1 TATGTATATATG
46305 TATGTATATATG
1 TATGTATATATG
46317 TATG
1 TATG
46321 GATGGATCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
8 7 0.18
12 32 0.82
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (12 bp):
TATGTATATATG
Found at i:46283 original size:20 final size:20
Alignment explanation
Indices: 46258--46319 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
46248 TTACAAATAA
46258 ATATATGTATATGTGTATGT
1 ATATATGTATATGTGTATGT
46278 ATATATG--TATG-G-ATG-
1 ATATATGTATATGTGTATGT
46293 ---TATGTATATGTGTATGT
1 ATATATGTATATGTGTATGT
46310 ATATATGTAT
1 ATATATGTAT
46320 GGATGGATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
12 4 0.12
14 4 0.12
15 1 0.03
16 6 0.18
17 1 0.03
18 4 0.12
20 14 0.41
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (20 bp):
ATATATGTATATGTGTATGT
Found at i:46298 original size:32 final size:32
Alignment explanation
Indices: 46261--46324 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
46251 CAAATAAATA
46261 TATGTATATGTGTATGTATATATGTATGGATG
1 TATGTATATGTGTATGTATATATGTATGGATG
46293 TATGTATATGTGTATGTATATATGTATGGATG
1 TATGTATATGTGTATGTATATATGTATGGATG
46325 GATCATGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (32 bp):
TATGTATATGTGTATGTATATATGTATGGATG
Found at i:46498 original size:2 final size:2
Alignment explanation
Indices: 46491--46590 Score: 193
Period size: 2 Copynumber: 50.5 Consensus size: 2
46481 TGAGTGCTTC
46491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46574 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
46591 GAGGTGATTT
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 96 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46959 original size:30 final size:31
Alignment explanation
Indices: 46925--46989 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
46915 ATAGTTATTA
*
46925 TATTTTATATTAATATAAT-TATATAAAAAT
1 TATTTTATATTAAAATAATATATATAAAAAT
* * *
46955 TATTTTTTATTAAAATAATATTTATATAAAT
1 TATTTTATATTAAAATAATATATATAAAAAT
46986 TATT
1 TATT
46990 ATTTATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TATTTTATATTAAAATAATATATATAAAAAT
Found at i:46989 original size:31 final size:31
Alignment explanation
Indices: 46925--47021 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 31
46915 ATAGTTATTA
* * * *
46925 TATTTTATATTAATATAAT-TATATAAAAAT
1 TATTTTTTATTAAAATAATATTTATATAAAT
46955 TATTTTTTATTAAAATAATATTTATATAAAT
1 TATTTTTTATTAAAATAATATTTATATAAAT
* * * *
46986 TATTATTTATTTAAAT-TTA-TTA-ATTAAT
1 TATTTTTTATTAAAATAATATTTATATAAAT
47014 TATTTTTT
1 TATTTTTT
47022 TGTGCTAATT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 12 0.21
29 3 0.05
30 19 0.33
31 23 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TATTTTTTATTAAAATAATATTTATATAAAT
Found at i:47002 original size:16 final size:16
Alignment explanation
Indices: 46951--47007 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
46941 AATTATATAA
*
46951 AAATTATTTTTTA-TT
1 AAATTATTATTTATTT
* * *
46966 AAAATAATATTTATAT
1 AAATTATTATTTATTT
46982 AAATTATTATTTATTT
1 AAATTATTATTTATTT
46998 AAATTTATTA
1 AAA-TTATTA
47008 ATTAATTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
15 10 0.30
16 17 0.52
17 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTATTATTTATTT
Found at i:53788 original size:42 final size:42
Alignment explanation
Indices: 53723--53806 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
53713 AGAATTTGAA
* *
53723 TCATTTTGCACTAGCAAGTTATATATATATATATATATATAT
1 TCATTTTGCACTAACAAGATATATATATATATATATATATAT
**
53765 TCATTTTGCACTAACTTGATATATATATATATATATATATAT
1 TCATTTTGCACTAACAAGATATATATATATATATATATATAT
53807 ATAATGTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (42 bp):
TCATTTTGCACTAACAAGATATATATATATATATATATATAT
Found at i:53790 original size:2 final size:2
Alignment explanation
Indices: 53783--53809 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53773 CACTAACTTG
53783 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
53810 ATGTGTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55410 original size:2 final size:2
Alignment explanation
Indices: 55405--55465 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
55395 TTATATACAG
55405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55447 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
55466 CACACATACA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66862 original size:5 final size:6
Alignment explanation
Indices: 66847--66871 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
66837 TTCCAAATTC
66847 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
66872 ATATTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:69732 original size:31 final size:31
Alignment explanation
Indices: 69674--69732 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
69664 GCCCTGCGTG
* * *
69674 TTTAGTACCTAGACTATCAGTTTTGGTTCTT
1 TTTAATACCTAGACTATCAGGTATGGTTCTT
69705 TTTAATACCTAGACTATCAGGTATGGTT
1 TTTAATACCTAGACTATCAGGTATGGTT
69733 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (31 bp):
TTTAATACCTAGACTATCAGGTATGGTTCTT
Found at i:83229 original size:21 final size:21
Alignment explanation
Indices: 83185--83229 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
83175 AAACTACGTA
*
83185 TTTAGTACCCAAACAATCAGT
1 TTTAGTACCCAAACAATCAAT
* **
83206 TTTAGTACCTAAACTTTCAAT
1 TTTAGTACCCAAACAATCAAT
83227 TTT
1 TTT
83230 TCAAAACCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTAGTACCCAAACAATCAAT
Found at i:83841 original size:59 final size:59
Alignment explanation
Indices: 83738--83867 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 59
83728 AGTTTAGGGT
* *
83738 AAAGTATAC-AAATGGTTCCCGACTATAGGGTGTTACTTTGTTGAGT-CATTGACTATTA
1 AAAGT-TACAAAATGGTTCCCGACTATAGGATGTTACTTTGTTGAGTCCATCGACTATTA
* * * *
83796 AAAGTTACAAAATGGTTACTCGACTATAGGATGTTTCTTTTTTGAGTCCCTCGACTATTA
1 AAAGTTACAAAATGGTT-CCCGACTATAGGATGTTACTTTGTTGAGTCCATCGACTATTA
83856 AAAGTTACAAAA
1 AAAGTTACAAAA
83868 ATGTTCACCT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
57 3 0.05
58 13 0.21
59 25 0.40
60 22 0.35
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (59 bp):
AAAGTTACAAAATGGTTCCCGACTATAGGATGTTACTTTGTTGAGTCCATCGACTATTA
Found at i:92415 original size:6 final size:6
Alignment explanation
Indices: 92404--92438 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
92394 AAGTGAATGG
92404 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCTC TCTT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC-C TCTT
92439 TTACCATCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
TCTTCC
Found at i:95148 original size:39 final size:39
Alignment explanation
Indices: 95104--95205 Score: 177
Period size: 39 Copynumber: 2.6 Consensus size: 39
95094 TTAACGTTAG
*
95104 TACTAAAATGAAATAAAAACTAAAGATTTTAACAGCAGA
1 TACTAAAATGAAATAAAAACTAAAGATTTTAACAACAGA
*
95143 TACTAAAATGAAATAAAAACTAAAGATTTTAACAACATA
1 TACTAAAATGAAATAAAAACTAAAGATTTTAACAACAGA
*
95182 TACTAAAATGAAACAAAAACTAAA
1 TACTAAAATGAAATAAAAACTAAA
95206 TTTTAGATAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.23
Consensus pattern (39 bp):
TACTAAAATGAAATAAAAACTAAAGATTTTAACAACAGA
Found at i:95203 original size:17 final size:17
Alignment explanation
Indices: 95144--95205 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
95134 AACAGCAGAT
*
95144 ACTAAAATGAAATAAAA
1 ACTAAAATGAAACAAAA
**
95161 ACTAAAGATTTTAACAACATA
1 ACTAAA-A-TGAAACAA-A-A
95182 TACTAAAATGAAACAAAA
1 -ACTAAAATGAAACAAAA
95200 ACTAAA
1 ACTAAA
95206 TTTTAGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 12 0.34
18 2 0.06
19 6 0.17
20 7 0.20
21 2 0.06
22 6 0.17
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (17 bp):
ACTAAAATGAAACAAAA
Found at i:99300 original size:51 final size:51
Alignment explanation
Indices: 99225--99338 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
99215 GACCTGAAAA
* *
99225 ATATATAATTTTATCTTATATATTTAAGGATAATTACAACATTATCCCTCT
1 ATATATAATTTTACCCTATATATTTAAGGATAATTACAACATTATCCCTCT
* * *
99276 ATATATAATTTTACCCTATATATTTAGGGATAATTACAATATTATCTCTCT
1 ATATATAATTTTACCCTATATATTTAAGGATAATTACAACATTATCCCTCT
99327 ATATATAATTTT
1 ATATATAATTTT
99339 TTTCCAATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.46
Consensus pattern (51 bp):
ATATATAATTTTACCCTATATATTTAAGGATAATTACAACATTATCCCTCT
Found at i:102983 original size:2 final size:2
Alignment explanation
Indices: 102976--103019 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
102966 TAACGACATC
* * * *
102976 AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103018 AT
1 AT
103020 GTATGAGAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
AT
Found at i:103010 original size:20 final size:20
Alignment explanation
Indices: 102985--103024 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
102975 CATATATATA
*
102985 TATATATATATGTATGTATG
1 TATATATATATATATGTATG
*
103005 TATATATATTTATATGTATG
1 TATATATATATATATGTATG
103025 AGAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (20 bp):
TATATATATATATATGTATG
Found at i:103680 original size:2 final size:2
Alignment explanation
Indices: 103675--103699 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103665 TTTTTTTATT
103675 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 T
103700 TTTAAAATTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105842 original size:204 final size:207
Alignment explanation
Indices: 105472--105888 Score: 662
Period size: 204 Copynumber: 2.0 Consensus size: 207
105462 AGCAAAGGAG
105472 TTCAACAGAGGAAAATAAAGCACTTCAACGTACTTTCTGCAGCATTATCTATGGGGTTGGGGGGG
1 TTCAACAGAGGAAAATAAAGCACTTCAACGTACTTTCTGCAGCATTATCTA----G-TGGGGGGG
* * * * * *
105537 GTTGCAGGTTTCTTTGTTTTGTTTTTTATTTTATTTTATGTAGTTTCTTTTGGTTGAGGCTTTGA
61 ATTACAGGTTTCTTTGTTTTGATTTTTATTTGATTTTATGTAGTTTCTTTTGGTCGAGGATTTGA
105602 TAACATTGCTTCTAATTGTTGCTAAACTTGTTTGATGTTCCTAAATATCTGCTTAAATTGTTGCT
126 TAACATTGCTTCTAATTGTTGCTAAACTTGTTTGATGTTCCTAAATATCTGCTTAAATTGTTGCT
105667 AAATCATACCATTGTTA
191 AAATCATACCATTGTTA
* * *
105684 TTCAAGAGAGGAAAAATAAAGCACTTGAAGGTACTTTCTGCAGCATTATCTA-T-GGGGGGATTA
1 TTCAACAGAGG-AAAATAAAGCACTTCAACGTACTTTCTGCAGCATTATCTAGTGGGGGGGATTA
105747 CAGGTTTCTTTG-TTTGATTTTT-TTTGATTTTATGTAGTTTCTTTTGGTCGAGGATTTGATAAC
65 CAGGTTTCTTTGTTTTGATTTTTATTTGATTTTATGTAGTTTCTTTTGGTCGAGGATTTGATAAC
*
105810 ATTGCTTCTAATTGTTGCTGAACTTGTTTGATGTTCCTAAATATCTGCTTAAATTGTTGCTAAAT
130 ATTGCTTCTAATTGTTGCTAAACTTGTTTGATGTTCCTAAATATCTGCTTAAATTGTTGCTAAAT
105875 CATACCATTGTTA
195 CATACCATTGTTA
105888 T
1 T
105889 GAGGAATGTT
Statistics
Matches: 194, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
204 116 0.60
205 9 0.05
206 20 0.10
207 1 0.01
212 10 0.05
213 38 0.20
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (207 bp):
TTCAACAGAGGAAAATAAAGCACTTCAACGTACTTTCTGCAGCATTATCTAGTGGGGGGGATTAC
AGGTTTCTTTGTTTTGATTTTTATTTGATTTTATGTAGTTTCTTTTGGTCGAGGATTTGATAACA
TTGCTTCTAATTGTTGCTAAACTTGTTTGATGTTCCTAAATATCTGCTTAAATTGTTGCTAAATC
ATACCATTGTTA
Found at i:109917 original size:52 final size:52
Alignment explanation
Indices: 109829--109934 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
109819 TTGATCAAAC
* * *
109829 ACGGAATACGTCGAAGAGAAACTGAGCAGGACATTGGGACCTGTTAGAGTGA
1 ACGGAATACATCGAAGAGAAAATGAGCAGGAAATTGGGACCTGTTAGAGTGA
*
109881 ACGGAATACATCGAAGAGAAAATGAGTAGGAAATTGGGACCTGTTAGAGTGA
1 ACGGAATACATCGAAGAGAAAATGAGCAGGAAATTGGGACCTGTTAGAGTGA
109933 AC
1 AC
109935 AGGCTCGTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.38, C:0.13, G:0.31, T:0.18
Consensus pattern (52 bp):
ACGGAATACATCGAAGAGAAAATGAGCAGGAAATTGGGACCTGTTAGAGTGA
Found at i:116440 original size:30 final size:31
Alignment explanation
Indices: 116384--116443 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
116374 TTTATCAACC
*
116384 AAATCATTCAACTATTTAAGTACATTCAATT
1 AAATCATTCAACTATTTAAATACATTCAATT
116415 AAATCATTCAACTA-TTAAATACATTCAAT
1 AAATCATTCAACTATTTAAATACATTCAAT
116444 CAAGTCACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.37
Consensus pattern (31 bp):
AAATCATTCAACTATTTAAATACATTCAATT
Found at i:116645 original size:35 final size:35
Alignment explanation
Indices: 116595--116666 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
116585 TTTAAACCTC
116595 AAATCAAAAAAACTAATTTTAATATTATTAAGCTT
1 AAATCAAAAAAACTAATTTTAATATTATTAAGCTT
*
116630 AAATCAAAAATACTAATTTTAATATTATTAAGCTT
1 AAATCAAAAAAACTAATTTTAATATTATTAAGCTT
116665 AA
1 AA
116667 CTCGATTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (35 bp):
AAATCAAAAAAACTAATTTTAATATTATTAAGCTT
Found at i:117201 original size:19 final size:19
Alignment explanation
Indices: 117177--117216 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
117167 TAACACTCGA
117177 TCTCGGGCACCGACCCGGT
1 TCTCGGGCACCGACCCGGT
117196 TCTCGGGCACCGACCCGGT
1 TCTCGGGCACCGACCCGGT
117215 TC
1 TC
117217 CCAAGCCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.42, G:0.30, T:0.17
Consensus pattern (19 bp):
TCTCGGGCACCGACCCGGT
Found at i:128149 original size:36 final size:36
Alignment explanation
Indices: 128081--128150 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
128071 TTACTGATGT
**
128081 TTTGCTACTTTCTCTAATGAACCATGGTGTGGACGC
1 TTTGCTACTTTCTCTAATGAACCATGAAGTGGACGC
*
128117 TTTGTTACTTTCTCTAATGAACCATGAAGTGGAC
1 TTTGCTACTTTCTCTAATGAACCATGAAGTGGAC
128151 AGTTTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (36 bp):
TTTGCTACTTTCTCTAATGAACCATGAAGTGGACGC
Found at i:128973 original size:36 final size:34
Alignment explanation
Indices: 128884--128970 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 34
128874 TTGGTCATCG
*
128884 AAGTTTAATTTTTTTTAATTTAATTACTTAACTTTC
1 AAGTTT-ATTTTTTTT-ATTTAATCACTTAACTTTC
* * *
128920 AA-ATTA--CTTTTGATTTAATCACTCTAACTTTC
1 AAGTTTATTTTTTTTATTTAATCACT-TAACTTTC
128952 AAGTTTATTTTTTTTATTT
1 AAGTTTATTTTTTTTATTT
128971 TAATTATATA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
31 10 0.25
32 14 0.35
33 3 0.08
34 1 0.03
35 10 0.25
36 2 0.05
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.57
Consensus pattern (34 bp):
AAGTTTATTTTTTTTATTTAATCACTTAACTTTC
Found at i:135811 original size:31 final size:31
Alignment explanation
Indices: 135775--135833 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
135765 AACTTAAAAG
135775 AGTTTTACAATA-TTGAAATTTAAATAATTTT
1 AGTTTTACAATACTT-AAATTTAAATAATTTT
*
135806 AGTTTTATAATACTTAAATTTAAATAAT
1 AGTTTTACAATACTTAAATTTAAATAAT
135834 CAATACAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (31 bp):
AGTTTTACAATACTTAAATTTAAATAATTTT
Found at i:135883 original size:22 final size:22
Alignment explanation
Indices: 135858--136106 Score: 329
Period size: 22 Copynumber: 11.3 Consensus size: 22
135848 ATAATAAATT
*
135858 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
135880 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
*** *
135902 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
135924 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
135946 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
135968 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
135990 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* **
136012 TTTTAAATTAAAT-TTTCCCATA
1 TTTTAAAATAAATCAAT-CCATA
136034 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
136056 TTTTAAAATAAATTTTTCCATG
1 TTTTAAAATAAATCAATCCATA
* *
136078 TTTTAAAATAAATTAATCTATA
1 TTTTAAAATAAATCAATCCATA
136100 TTTTAAA
1 TTTTAAA
136107 TAATTTTAAT
Statistics
Matches: 197, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
21 1 0.01
22 195 0.99
23 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:136475 original size:3 final size:3
Alignment explanation
Indices: 136469--136498 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
136459 ATTTTATTAT
136469 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
136499 AAAAGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:142232 original size:16 final size:18
Alignment explanation
Indices: 142213--142245 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
142203 TATCAACACT
142213 ATATTTT-TT-TATTTTC
1 ATATTTTGTTATATTTTC
142229 ATATTTTGTTATATTTT
1 ATATTTTGTTATATTTT
142246 TTAACTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (18 bp):
ATATTTTGTTATATTTTC
Found at i:148883 original size:37 final size:35
Alignment explanation
Indices: 148839--148926 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 35
148829 TCAAAATCAT
* *
148839 ATTTAAAATTTAACTTTTGTTTTATTTTAGTATTCGCC
1 ATTTAAAATTTAA-TTTTGTTTCATTTTAATA-TC-CC
*
148877 ATTAAAAATTCTAATTTTGTTTCATTTTAATATCCC
1 ATTTAAAATT-TAATTTTGTTTCATTTTAATATCCC
148913 ATTTAAAATTTAAT
1 ATTTAAAATTTAAT
148927 ATTAAGTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
35 4 0.09
36 11 0.24
37 2 0.04
38 25 0.56
39 3 0.07
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (35 bp):
ATTTAAAATTTAATTTTGTTTCATTTTAATATCCC
Found at i:149364 original size:2 final size:2
Alignment explanation
Indices: 149359--149395 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
149349 AAGATAAAAT
149359 TA 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 TA T
149396 TTGGGCCGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:165076 original size:2 final size:2
Alignment explanation
Indices: 165069--165094 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
165059 TCAAGTTTGG
165069 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
165095 CATACGAAGT
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:180326 original size:21 final size:21
Alignment explanation
Indices: 180302--180345 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
180292 TTTAAACTTA
*
180302 AGGGAGATGAACTAAAATTCT
1 AGGGAGACGAACTAAAATTCT
* *
180323 AGGGAGGCGGACTAAAATTCT
1 AGGGAGACGAACTAAAATTCT
180344 AG
1 AG
180346 AGGGCAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (21 bp):
AGGGAGACGAACTAAAATTCT
Found at i:180639 original size:5 final size:5
Alignment explanation
Indices: 180622--180653 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
180612 GGACGATTTA
180622 ATAAT ACTAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT A
180654 GAAACAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:191640 original size:4 final size:4
Alignment explanation
Indices: 191631--191655 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
191621 TGGGTTCAAT
191631 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
191656 AAGATGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:200061 original size:2 final size:2
Alignment explanation
Indices: 200054--200101 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
200044 AGATAAAGAT
200054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
200096 TA TA TA
1 TA TA TA
200102 GAGAGAGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:200264 original size:52 final size:52
Alignment explanation
Indices: 200203--200306 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
200193 TCTGCGTATG
*
200203 GGTGCACTCACGCGTACTTTCAGTTTGCAGGATGATAATCGTCGTAGGATTT
1 GGTGCACTCACGCGTACTTTCAGTTTGCAGGATGATAATCGTCGGAGGATTT
*
200255 GGTGCACTCACGCGTAGTTTCAGTTTGCAGGATGATAATCGTCGGAGGATTT
1 GGTGCACTCACGCGTACTTTCAGTTTGCAGGATGATAATCGTCGGAGGATTT
200307 TGTGGTGAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (52 bp):
GGTGCACTCACGCGTACTTTCAGTTTGCAGGATGATAATCGTCGGAGGATTT
Found at i:201309 original size:29 final size:31
Alignment explanation
Indices: 201235--201312 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
201225 AATTATATCA
*
201235 TTTCTCACTGAACTTTACTTTCTTTCTTATT
1 TTTCTCACTGAACTTTACGTTCTTTCTTATT
*
201266 TTTTTCACT-ATACTTT-CAGTT-TTTC-TATT
1 TTTCTCACTGA-ACTTTAC-GTTCTTTCTTATT
201295 TTTCTCACTGAACTTTAC
1 TTTCTCACTGAACTTTAC
201313 ATATTTAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 17 0.43
30 8 0.20
31 15 0.38
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (31 bp):
TTTCTCACTGAACTTTACGTTCTTTCTTATT
Found at i:214051 original size:15 final size:16
Alignment explanation
Indices: 214019--214051 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
214009 AAAATCTTTC
214019 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
214035 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
214050 TT
1 TT
214052 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:214825 original size:16 final size:16
Alignment explanation
Indices: 214801--214834 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
214791 TATCGCCGAC
*
214801 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
214817 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
214833 CG
1 CG
214835 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:218808 original size:27 final size:27
Alignment explanation
Indices: 218778--218835 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
218768 TTGAGTCTTG
* * *
218778 ATAT-TTGATATTATTTATAATTTTTTT
1 ATATATTGATAAT-TTTAAAATTATTTT
*
218805 ATATATTTATAATTTTAAAATTATTTT
1 ATATATTGATAATTTTAAAATTATTTT
218832 ATAT
1 ATAT
218836 GCCCGTTCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
ATATATTGATAATTTTAAAATTATTTT
Found at i:220557 original size:17 final size:17
Alignment explanation
Indices: 220524--220557 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
220514 TGTGCAAAAG
* *
220524 TATAGTAAGTTATAATT
1 TATAGTAAATTAAAATT
220541 TATAGTAAATTAAAATT
1 TATAGTAAATTAAAATT
220558 AATCATATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
TATAGTAAATTAAAATT
Found at i:236040 original size:23 final size:23
Alignment explanation
Indices: 235995--236040 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
235985 AACCTAACCT
*
235995 CTAAAAAAATAAAATTAAAAAAA
1 CTAAAAAAATAAAAATAAAAAAA
*
236018 CTAAAAAAATATAAAATATAAAA
1 CTAAAAAAATA-AAAATAAAAAA
236041 TGGTATTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (23 bp):
CTAAAAAAATAAAAATAAAAAAA
Done.