Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 183 of 216
Found at i:57124924 original size:76 final size:75
Alignment explanation
Indices: 57124831--57124986 Score: 206
Period size: 76 Copynumber: 2.1 Consensus size: 75
57124821 CGTGTTTTCG
* * ** *
57124831 AAAATTCCCGTTTTTC-AAAAATTTTCTTGTTTTCAAAAAATATTTCCGTGTTTCATAAATTTCC
1 AAAATTCCCGTCTTTCAAAAAATTTTCGTGTTTTC-AAAAAT-TGACAGTGTTTCATAAATTTCC
*
57124895 GTGTTTGAAAAA
64 GTGTTTCAAAAA
* *
57124907 AAAATTCTCGTCTTTCAAAAAAATTTTCGTGTTTTCAAAAATTGACAGTGTTTCATAAATTTTCG
1 AAAATTCCCGTCTTTC-AAAAAATTTTCGTGTTTTCAAAAATTGACAGTGTTTCATAAATTTCCG
57124972 TGTTTCAAAAA
65 TGTTTCAAAAA
57124983 AAAA
1 AAAA
57124987 ATCTTCGTGT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
76 47 0.67
77 6 0.09
78 17 0.24
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (75 bp):
AAAATTCCCGTCTTTCAAAAAATTTTCGTGTTTTCAAAAATTGACAGTGTTTCATAAATTTCCGT
GTTTCAAAAA
Found at i:57125084 original size:20 final size:21
Alignment explanation
Indices: 57125056--57125098 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
57125046 AATTTTCATG
57125056 TTTCAAAAAGAAAAT-TCGTGT
1 TTTCAAAAA-AAAATCTCGTGT
57125077 TTTC-AAAAAAAATCTCGTGT
1 TTTCAAAAAAAAATCTCGTGT
57125097 TT
1 TT
57125099 CAGAATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 12 0.57
21 4 0.19
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (21 bp):
TTTCAAAAAAAAATCTCGTGT
Found at i:57125153 original size:35 final size:36
Alignment explanation
Indices: 57125064--57125162 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 36
57125054 TGTTTCAAAA
* **
57125064 AGAAAATTCGTGT-TTTCAAAAAAAATCTCGTGTTTC
1 AGAATATTCGTGTATTTTTAAAAAAAT-TCGTGTTTC
* *
57125100 AGAATTTTCGTGTTTTTTTAAAAAAATTCGTGTTTC
1 AGAATATTCGTGTATTTTTAAAAAAATTCGTGTTTC
*
57125136 TA-AA-ATTCTTGTATTTTTAAAAAAATT
1 -AGAATATTCGTGTATTTTTAAAAAAATT
57125163 TCGTCTTTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
35 20 0.37
36 22 0.41
37 12 0.22
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (36 bp):
AGAATATTCGTGTATTTTTAAAAAAATTCGTGTTTC
Found at i:57125153 original size:36 final size:35
Alignment explanation
Indices: 57125082--57125176 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 35
57125072 CGTGTTTTCA
* *
57125082 AAAAAAATCTCGTGTTTCAGAATTTTCGTGTTTTTTT
1 AAAAAAAT-TCGTGTTTCAAAATTTTCGTG-ATTTTT
57125119 AAAAAAATTCGTGTTTCTAAAATTCTT-GT-ATTTTT
1 AAAAAAATTCGTGTTTC-AAAATT-TTCGTGATTTTT
*
57125154 AAAAAAATTTCGTCTTTTCAAAA
1 AAAAAAA-TTCGT-GTTTCAAAA
57125177 AAAGCAAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
35 12 0.24
36 18 0.35
37 19 0.37
38 2 0.04
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (35 bp):
AAAAAAATTCGTGTTTCAAAATTTTCGTGATTTTT
Found at i:57129805 original size:23 final size:23
Alignment explanation
Indices: 57129774--57129824 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
57129764 ACCTACTTTC
* *
57129774 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
*
57129797 TTACAGTAGTGATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
57129820 TTACA
1 TTACA
57129825 TGAACATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:57133782 original size:93 final size:93
Alignment explanation
Indices: 57133669--57133854 Score: 336
Period size: 93 Copynumber: 2.0 Consensus size: 93
57133659 CACTCATGAC
*
57133669 TTTCAAAAGAAGGTATATATGCTTAGCAAATACATTAAAATGGTAATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGGTAATTTGAAAAGCTAGTATTCA
57133734 AGATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
* * *
57133762 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGGTAATTTGAAAAGCTAGTATTCA
57133827 AGATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
57133855 ATGTGATGTT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (93 bp):
TTTCAAAAGAAGGTATATATGCTTAGCAAATACAATAAAATGGTAATTTGAAAAGCTAGTATTCA
AGATTCAATACATAGAATATTAGATATT
Found at i:57141518 original size:6 final size:6
Alignment explanation
Indices: 57141507--57141534 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
57141497 AGTATCATAG
57141507 ATTTAT ATTTAT ATTTAT ATTTAT ATTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTT
57141535 TTAACGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:57142231 original size:40 final size:41
Alignment explanation
Indices: 57142187--57142280 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 41
57142177 GCGCCTACGA
*
57142187 GGACGCGATTTTCTGACACATCAGC-AAAACGCGCTGACGT
1 GGACGCGATTTTCTGACACATCACCGAAAACGCGCTGACGT
* ** * * *
57142227 GGACGCGATTTGCTGACATGTCCCCTGACATCGCGCTGACGT
1 GGACGCGATTTTCTGACACATCACC-GAAAACGCGCTGACGT
57142269 GGACGCGATTTT
1 GGACGCGATTTT
57142281 GGGGCAAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 20 0.45
42 24 0.55
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (41 bp):
GGACGCGATTTTCTGACACATCACCGAAAACGCGCTGACGT
Found at i:57148113 original size:21 final size:21
Alignment explanation
Indices: 57148089--57148132 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
57148079 GAATCTTTAG
*
57148089 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
57148110 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
57148131 TA
1 TA
57148133 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:57150958 original size:16 final size:16
Alignment explanation
Indices: 57150937--57151004 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
57150927 ATTTTTAACT
57150937 AATAATTGTAAATTAA
1 AATAATTGTAAATTAA
* *
57150953 AATAATTAT-AATTAT
1 AATAATTGTAAATTAA
* * * * *
57150968 CACAATTTTTAACT--
1 AATAATTGTAAATTAA
57150982 AATAATTGTAAATTAA
1 AATAATTGTAAATTAA
57150998 AATAATT
1 AATAATT
57151005 AAAATAACTA
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
14 9 0.24
15 11 0.29
16 18 0.47
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAATTGTAAATTAA
Found at i:57151919 original size:3 final size:3
Alignment explanation
Indices: 57151911--57151942 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
57151901 AAATCAATGT
57151911 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
57151943 TAAATCGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:57156385 original size:39 final size:37
Alignment explanation
Indices: 57156342--57156425 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
57156332 TAAGTGAAAG
* *
57156342 TTATAAAAATTATTAAATTTTATTAAAAATAAAAAAAAA
1 TTATAAAAATGATAAAATTTTA-T-AAAATAAAAAAAAA
* ***
57156381 TTATAAAAATGGTAAAATTTTATAAAATTCTAAAAAA
1 TTATAAAAATGATAAAATTTTATAAAATAAAAAAAAA
57156418 TTATAAAA
1 TTATAAAA
57156426 TTTTATAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 19 0.49
38 1 0.03
39 19 0.49
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (37 bp):
TTATAAAAATGATAAAATTTTATAAAATAAAAAAAAA
Found at i:57156388 original size:9 final size:9
Alignment explanation
Indices: 57156312--57156475 Score: 57
Period size: 10 Copynumber: 17.3 Consensus size: 9
57156302 ATGGACAAAT
*
57156312 AAAATGATA
1 AAAATTATA
57156321 AAAA--ATA
1 AAAATTATA
* *
57156328 AAAATAAGTG
1 AAAATTA-TA
*
57156338 AAAGTTATA
1 AAAATTATA
57156347 AAAATTATTA
1 AAAATTA-TA
**
57156357 AATTTTATTA
1 AAAATTA-TA
* *
57156367 AAAATAAAAA
1 AAAAT-TATA
57156377 AAAATTATA
1 AAAATTATA
**
57156386 AAAATGGT-
1 AAAATTATA
*
57156394 AAAATTTTA
1 AAAATTATA
*
57156403 TAAAATTCTAA
1 -AAAATTAT-A
57156414 AAAATTATA
1 AAAATTATA
*
57156423 AAATTTTATAAA
1 AAA-ATTAT--A
57156435 GAAAATTATA
1 -AAAATTATA
*
57156445 AAAAATATA
1 AAAATTATA
*
57156454 AAGAAATAT-
1 AA-AATTATA
57156463 AAAATTCATA
1 AAAATT-ATA
57156473 AAA
1 AAA
57156476 GAATTATCAT
Statistics
Matches: 117, Mismatches: 23, Indels: 29
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.06
8 9 0.08
9 38 0.32
10 53 0.45
11 2 0.02
12 5 0.04
13 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:57156388 original size:10 final size:10
Alignment explanation
Indices: 57156342--57156466 Score: 64
Period size: 10 Copynumber: 12.8 Consensus size: 10
57156332 TAAGTGAAAG
57156342 TTAT-AAAAA
1 TTATAAAAAA
* **
57156351 TTATTAAATT
1 TTATAAAAAA
*
57156361 TTATTAAAAA
1 TTATAAAAAA
* *
57156371 TAAAAAAAAA
1 TTATAAAAAA
57156381 TTAT-AAAAA
1 TTATAAAAAA
**
57156390 TGGT--AAAA
1 TTATAAAAAA
* *
57156398 TTTTATAAAA
1 TTATAAAAAA
*
57156408 TTCTAAAAAA
1 TTATAAAAAA
**
57156418 TTATAAAATT
1 TTATAAAAAA
57156428 TTATAAAGAAAA
1 TTAT-AA-AAAA
57156440 TTATAAAAAA
1 TTATAAAAAA
57156450 -TATAAAGAAA
1 TTATAAA-AAA
57156460 -TATAAAA
1 TTATAAAA
57156467 TTCATAAAAG
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
8 6 0.07
9 18 0.20
10 56 0.62
11 4 0.04
12 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:57156397 original size:18 final size:19
Alignment explanation
Indices: 57156375--57156425 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
57156365 TAAAAATAAA
*
57156375 AAAAAATTATAAAAATGGT
1 AAAAAATTATAAAAATGCT
** *
57156394 AAAATTTTAT-AAAATTCT
1 AAAAAATTATAAAAATGCT
57156412 AAAAAATTATAAAA
1 AAAAAATTATAAAA
57156426 TTTTATAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAAATTATAAAAATGCT
Found at i:57156407 original size:28 final size:29
Alignment explanation
Indices: 57156375--57156448 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
57156365 TAAAAATAAA
*
57156375 AAAAAATTATAAAAATGGTAAAATTTTAT
1 AAAAAATTATAAAAATGATAAAATTTTAT
* *
57156404 --AAAATTCTAAAAAATTATAAAATTTTAT
1 AAAAAATTAT-AAAAATGATAAAATTTTAT
57156432 AAAGAAAATTATAAAAA
1 -AA-AAAATTATAAAAA
57156449 ATATAAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.19
28 17 0.47
31 5 0.14
32 7 0.19
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAAAATTATAAAAATGATAAAATTTTAT
Found at i:57156455 original size:21 final size:22
Alignment explanation
Indices: 57156414--57156467 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
57156404 AAAATTCTAA
**
57156414 AAAATTATAAAATTTTATAAAG
1 AAAATTATAAAATAATATAAAG
57156436 AAAATTATAAAA-AATATAAAG
1 AAAATTATAAAATAATATAAAG
57156457 -AAA-TATAAAAT
1 AAAATTATAAAAT
57156468 TCATAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.24
20 3 0.10
21 7 0.24
22 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATTATAAAATAATATAAAG
Found at i:57156538 original size:18 final size:19
Alignment explanation
Indices: 57156495--57156539 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
57156485 TATAAAAAGA
57156495 ATCATTTTATAATTTTTCT
1 ATCATTTTATAATTTTTCT
* * *
57156514 ATAATTTT-TATTTTTTTT
1 ATCATTTTATAATTTTTCT
57156532 ATCATTTT
1 ATCATTTT
57156540 GCACCGCATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (19 bp):
ATCATTTTATAATTTTTCT
Found at i:57156705 original size:30 final size:31
Alignment explanation
Indices: 57156665--57156738 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
57156655 TTTATAATTA
* *
57156665 TTTATGATTTTTATA-AAATTTTACAATTTT
1 TTTATAATTTTTATATAAACTTTACAATTTT
*
57156695 TTTATAATTTTT-TATAAACTTTATAATTTT
1 TTTATAATTTTTATATAAACTTTACAATTTT
*
57156725 TTCATAATTTTTAT
1 TTTATAATTTTTAT
57156739 TATTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.92
31 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (31 bp):
TTTATAATTTTTATATAAACTTTACAATTTT
Found at i:57156717 original size:19 final size:18
Alignment explanation
Indices: 57156695--57156769 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 18
57156685 TTACAATTTT
*
57156695 TTTATAATTTTTTATAAAC
1 TTTATAA-TTTTTATAAAA
**
57156714 TTTATAATTTTTTCATAATT
1 TTTATAA-TTTTT-ATAAAA
*
57156734 TTTATTATTTTTATTAAAA
1 TTTATAATTTTTA-TAAAA
57156753 TTTAATAATTTTTATAA
1 TTT-ATAATTTTTATAA
57156770 TTTTTTTGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.02
19 27 0.57
20 19 0.40
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATAATTTTTATAAAA
Found at i:57156734 original size:11 final size:10
Alignment explanation
Indices: 57156654--57156775 Score: 83
Period size: 10 Copynumber: 12.4 Consensus size: 10
57156644 TTTTGATGCA
57156654 TTTTATAATT
1 TTTTATAATT
* *
57156664 ATTTATGA-T
1 TTTTATAATT
**
57156673 TTTTATAAAA
1 TTTTATAATT
*
57156683 TTTTACAATTT
1 TTTTATAA-TT
57156694 TTTTATAATT
1 TTTTATAATT
*
57156704 TTTTATAA-A
1 TTTTATAATT
*
57156713 CTTTATAATT
1 TTTTATAATT
57156723 TTTTCATAA-T
1 TTTT-ATAATT
*
57156733 TTTTATTA-T
1 TTTTATAATT
**
57156742 TTTTATTAAAA
1 TTTTA-TAATT
*
57156753 TTTAATAA-T
1 TTTTATAATT
57156762 TTTTATAATT
1 TTTTATAATT
57156772 TTTT
1 TTTT
57156776 TGCTACATGT
Statistics
Matches: 86, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
9 30 0.35
10 41 0.48
11 15 0.17
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:57156746 original size:29 final size:28
Alignment explanation
Indices: 57156653--57156774 Score: 102
Period size: 29 Copynumber: 4.2 Consensus size: 28
57156643 TTTTTGATGC
*
57156653 ATTTTATAATTATTTATGATTTTTATAAA
1 ATTTTATAATTATTTATAATTTTTAT-AA
* *
57156682 ATTTTACAATTTTTTTATAATTTTTTATAA
1 ATTTTATAA-TTATTTATAA-TTTTTATAA
* * *
57156712 ACTTTATAATTTTTTCATAATTTTTATTA
1 ATTTTATAATTATTT-ATAATTTTTATAA
* *
57156741 TTTTTATTAA-AATTTAATAATTTTTATAA
1 ATTTTA-TAATTATTT-ATAATTTTTATAA
*
57156770 TTTTT
1 ATTTT
57156775 TTGCTACATG
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
29 46 0.60
30 24 0.31
31 7 0.09
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (28 bp):
ATTTTATAATTATTTATAATTTTTATAA
Found at i:57157430 original size:20 final size:21
Alignment explanation
Indices: 57157397--57157436 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
57157387 AGTTTTAAAA
*
57157397 TCACCCTATATTTTTTGCCTT
1 TCACCCTATATTTTTCGCCTT
57157418 TCACCCTAT-TTTTTCGCCT
1 TCACCCTATATTTTTCGCCT
57157437 GAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.12, C:0.33, G:0.05, T:0.50
Consensus pattern (21 bp):
TCACCCTATATTTTTCGCCTT
Found at i:57164705 original size:2 final size:2
Alignment explanation
Indices: 57164700--57164725 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57164690 ATGAAAAAAC
57164700 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
57164726 TTTATTTTTA
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:57167489 original size:27 final size:28
Alignment explanation
Indices: 57167459--57167517 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
57167449 ACACACTCGG
**
57167459 AATAATAT-AAATCCTCCTTAACACACA
1 AATAATATCAAATCCTCCCAAACACACA
* *
57167486 AAT-ATATCATATCCTCCCAAACACACC
1 AATAATATCAAATCCTCCCAAACACACA
57167513 AATAA
1 AATAA
57167518 GGCATTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (28 bp):
AATAATATCAAATCCTCCCAAACACACA
Found at i:57167790 original size:29 final size:29
Alignment explanation
Indices: 57167753--57167809 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
57167743 CATATAATTC
57167753 AATATTCACACATATTCTTACTTAATTTT
1 AATATTCACACATATTCTTACTTAATTTT
57167782 AATATTCACACATATTCTTACTTAATTT
1 AATATTCACACATATTCTTACTTAATTT
57167810 CAAATGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATTCACACATATTCTTACTTAATTTT
Found at i:57167838 original size:24 final size:23
Alignment explanation
Indices: 57167794--57167840 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
57167784 TATTCACACA
57167794 TATTCTTACTTAATTTCAAATGT
1 TATTCTTACTTAATTTCAAATGT
*
57167817 TATTACTTACCTTACTTT-AAATGT
1 TATT-CTTA-CTTAATTTCAAATGT
57167841 CCCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACTTAATTTCAAATGT
Found at i:57168117 original size:22 final size:24
Alignment explanation
Indices: 57168076--57168119 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
57168066 TAACTAAGCT
*
57168076 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTATAACTTAATTCA
57168100 TACTTA-TTTTAT-ACTTAATT
1 TACTTACTTTTATAACTTAATT
57168120 TCTTGCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTATAACTTAATTCA
Found at i:57168739 original size:5 final size:5
Alignment explanation
Indices: 57168720--57168761 Score: 68
Period size: 5 Copynumber: 8.4 Consensus size: 5
57168710 TTAGTTTATT
57168720 TAATA T-ATAA TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TA
57168762 TAAAACATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 2 0.06
5 31 0.89
6 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:57171674 original size:5 final size:5
Alignment explanation
Indices: 57171664--57171732 Score: 138
Period size: 5 Copynumber: 13.8 Consensus size: 5
57171654 TCATTCATCA
57171664 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
57171714 CATAT CATAT CATAT CATA
1 CATAT CATAT CATAT CATA
57171733 AATATTAGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 64 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:57182543 original size:27 final size:28
Alignment explanation
Indices: 57182504--57182568 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
57182494 ATATCATTTG
* *
57182504 ACAAGATTAAGTACT-AAATTAGATAAAA
1 ACAAGATTAAGTA-TGAAATAAGAAAAAA
57182532 ACAAG-TTAAGTATGAAATAAGAAAAAA
1 ACAAGATTAAGTATGAAATAAGAAAAAA
57182559 ACTAA-ATTAA
1 AC-AAGATTAA
57182569 ACAAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 20 0.62
28 11 0.34
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (28 bp):
ACAAGATTAAGTATGAAATAAGAAAAAA
Found at i:57200549 original size:27 final size:27
Alignment explanation
Indices: 57200508--57200652 Score: 136
Period size: 27 Copynumber: 5.4 Consensus size: 27
57200498 AACACGTTAG
* *
57200508 GAAATGAATGCCTTTGTGGCAATTTAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
57200535 GAAAGGAATGACTTTGTGACAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
57200562 GGAAGGAATGTCTTTGTGGCAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* * *
57200589 G-AATGAATGCCTTCGTGGCAGACTCTA-
1 GAAAGGAATGCCTTTGTGGCA-A-TATAT
* *
57200616 -AAGGGAATGCCTTTGTGGCAA-ACTCT
1 GAAAGGAATGCCTTTGTGGCAATA-TAT
57200642 GAAAGGAATGC
1 GAAAGGAATGC
57200653 ATTAACAGTG
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 17 0.18
27 74 0.78
28 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (27 bp):
GAAAGGAATGCCTTTGTGGCAATATAT
Found at i:57203006 original size:14 final size:14
Alignment explanation
Indices: 57202987--57203014 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57202977 CGCATACATA
57202987 TCAAAATATCAATC
1 TCAAAATATCAATC
57203001 TCAAAATATCAATC
1 TCAAAATATCAATC
57203015 ATCATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TCAAAATATCAATC
Found at i:57203273 original size:47 final size:48
Alignment explanation
Indices: 57203154--57203279 Score: 164
Period size: 47 Copynumber: 2.6 Consensus size: 48
57203144 CTCGTCCATT
* *
57203154 TGAAACACAATTTGTGGACAAACCACCACTGATTTGCAGATAAACTGCAAC
1 TGAAACAC--TTTGTGGACAAGCCACCAC-GATATGCAGATAAACTGCAAC
* * *
57203205 TGATAACACTTTGTGGACAAGCCACCAC-ATATGTAGATATACTGCCAC
1 TGA-AACACTTTGTGGACAAGCCACCACGATATGCAGATAAACTGCAAC
57203253 TGAAACACTTTGTGGACAAGCCACCAC
1 TGAAACACTTTGTGGACAAGCCACCAC
57203280 TGATTTATAG
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
47 24 0.35
48 19 0.28
50 18 0.26
51 3 0.04
52 5 0.07
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (48 bp):
TGAAACACTTTGTGGACAAGCCACCACGATATGCAGATAAACTGCAAC
Found at i:57205430 original size:23 final size:21
Alignment explanation
Indices: 57205357--57205421 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
57205347 CCTGATCAGT
* *
57205357 ATACGACACA-TAAGTGCCTG
1 ATACGACACACGAGGTGCCTG
*
57205377 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
57205398 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
57205419 ATA
1 ATA
57205422 TATGACACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 9 0.22
21 31 0.77
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:57206758 original size:11 final size:11
Alignment explanation
Indices: 57206742--57206783 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 11
57206732 ATTTAAAATA
57206742 TAATAATAATT
1 TAATAATAATT
57206753 TAATAATACTAATT
1 TAAT-A-A-TAATT
57206767 TAATAATAATT
1 TAATAATAATT
57206778 TAATAA
1 TAATAA
57206784 CATTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 15 0.54
12 2 0.07
13 2 0.07
14 9 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATAATAATT
Found at i:57206760 original size:14 final size:14
Alignment explanation
Indices: 57206741--57206776 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
57206731 TATTTAAAAT
57206741 ATAATAATAATTTA
1 ATAATAATAATTTA
*
57206755 ATAATACTAATTTA
1 ATAATAATAATTTA
57206769 ATAATAAT
1 ATAATAAT
57206777 TTAATAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:57212867 original size:21 final size:21
Alignment explanation
Indices: 57212808--57212868 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 21
57212798 CGGCACATAA
57212808 GTGCCTGAA-ACGACACACGAG
1 GTGCCT-AATACGACACACGAG
*
57212829 GTGCCTGATACGACACACGAG
1 GTGCCTAATACGACACACGAG
57212850 GTGCCTAATATACGACACA
1 GTGCCT-A-ATACGACACA
57212869 TAAAGTGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 24 0.69
23 10 0.29
ACGTcount: A:0.33, C:0.28, G:0.25, T:0.15
Consensus pattern (21 bp):
GTGCCTAATACGACACACGAG
Found at i:57212868 original size:23 final size:21
Alignment explanation
Indices: 57212808--57212855 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
57212798 CGGCACATAA
*
57212808 GTGCCTGAAACGACACACGAG
1 GTGCCTGATACGACACACGAG
57212829 GTGCCTGATACGACACACGAG
1 GTGCCTGATACGACACACGAG
57212850 GTGCCT
1 GTGCCT
57212856 AATATACGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (21 bp):
GTGCCTGATACGACACACGAG
Found at i:57214057 original size:3 final size:3
Alignment explanation
Indices: 57214049--57214080 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
57214039 TTATTCCTAG
*
57214049 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
57214081 TATTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:57214231 original size:14 final size:14
Alignment explanation
Indices: 57214212--57214257 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
57214202 TATTTAAAAT
57214212 ATAATAATAATTTA
1 ATAATAATAATTTA
*
57214226 ATAATACTAATTTA
1 ATAATAATAATTTA
57214240 ATAATAATAATTTA
1 ATAATAATAATTTA
57214254 ATAA
1 ATAA
57214258 AATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:57215444 original size:32 final size:32
Alignment explanation
Indices: 57215408--57215471 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
57215398 GTTACAACAA
*
57215408 AGTAAGTACTCCGAGGA-TCGTACCTTAGGGAT
1 AGTAAGTACTCCGAGGAGT-GTACCTAAGGGAT
*
57215440 AGTAAGTACTCTGAGGAGTGTACCTAAGGGAT
1 AGTAAGTACTCCGAGGAGTGTACCTAAGGGAT
57215472 TGCAATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (32 bp):
AGTAAGTACTCCGAGGAGTGTACCTAAGGGAT
Found at i:57222991 original size:50 final size:50
Alignment explanation
Indices: 57222882--57223120 Score: 232
Period size: 50 Copynumber: 4.7 Consensus size: 50
57222872 CATGCCAAAC
* ** * * * *
57222882 CCATGTCCCAGACATGGTCTTACATGAGATGTTTCTTGTAC--TACCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAATG
* * ** *
57222931 CCATTTCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATG
* * *
57222981 CCATGTCCCAGAAATGGTCTTACGA-GGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATATCGGTGCCAATG
*
57223031 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAATG
*
57223087 CCATGTCCCAGACATGGTCTTACATAGGACCTCT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCT
57223121 TTACCCAAAT
Statistics
Matches: 158, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
48 1 0.01
49 32 0.20
50 81 0.51
51 1 0.01
53 2 0.01
56 41 0.26
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATG
Found at i:57233429 original size:56 final size:55
Alignment explanation
Indices: 57233277--57233429 Score: 131
Period size: 56 Copynumber: 2.8 Consensus size: 55
57233267 CGGGATAGAA
* *
57233277 ATAA-TTTTTTTCATATACTTGTTTATTGAATGATTA-ATTATCGAGGTGAGTAT
1 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
* * * * *
57233330 ATCATTTTCGTATGAATTGATTTGC-TG-TGATTGAA-G-TT-GAATATTGAGGTGAGTAT
1 ATAATTTT--T-T---TTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
57233386 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGTAATAT
1 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAG-AATAT
57233430 GATTTAATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 25
0.68 0.10 0.23
Matches are distributed among these distances:
50 7 0.09
51 2 0.03
52 7 0.09
53 5 0.07
54 6 0.08
55 1 0.01
56 30 0.40
57 2 0.03
58 7 0.09
59 2 0.03
60 6 0.08
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (55 bp):
ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
Found at i:57234808 original size:17 final size:15
Alignment explanation
Indices: 57234778--57234811 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
57234768 CTCCCAGACT
57234778 TAATAAAATAATAAA
1 TAATAAAATAATAAA
57234793 TAATAAAACTTAATAAA
1 TAATAAAA--TAATAAA
57234810 TA
1 TA
57234812 CAATATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATAAAATAATAAA
Found at i:57235168 original size:23 final size:23
Alignment explanation
Indices: 57235141--57235187 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
57235131 AATTTCGTCA
* *
57235141 TATTAGTTTATTATTATTATTAT
1 TATTAGTTTATCATAATTATTAT
* *
57235164 TATTATTTTCTCATAATTATTAT
1 TATTAGTTTATCATAATTATTAT
57235187 T
1 T
57235188 CGATTTTAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTAGTTTATCATAATTATTAT
Found at i:57245174 original size:17 final size:18
Alignment explanation
Indices: 57245152--57245187 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
57245142 ACTTTATGTC
57245152 TTAAAA-AATATAATATA
1 TTAAAATAATATAATATA
57245169 TTAAAATTAATATAATATA
1 TTAAAA-TAATATAATATA
57245188 AGCCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAATAATATAATATA
Found at i:57251714 original size:59 final size:59
Alignment explanation
Indices: 57251622--57251739 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
57251612 AAATACAGAC
57251622 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
1 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
*
57251681 TTGATTTTAATTGAAAACATGATCGATTGAGGCACAAACATTATAAGCATGAATCAAAT
1 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
57251740 AAATATTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (59 bp):
TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
Found at i:57255056 original size:19 final size:19
Alignment explanation
Indices: 57255031--57255076 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
57255021 AATGGTTAAA
57255031 AATAAAAA-TAAATAAAAGT
1 AATAAAAATTAAATAAAA-T
* *
57255050 TATAAAAATTTAATAAAAT
1 AATAAAAATTAAATAAAAT
57255069 AATAAAAA
1 AATAAAAA
57255077 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAAAAATTAAATAAAAT
Found at i:57255057 original size:20 final size:19
Alignment explanation
Indices: 57255034--57255079 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
57255024 GGTTAAAAAT
*
57255034 AAAAATAAATAAAAGTTATA
1 AAAAATAAATAAAA-TAATA
* *
57255054 AAAATTTAATAAAATAATA
1 AAAAATAAATAAAATAATA
57255073 AAAAATA
1 AAAAATA
57255080 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATAAATAAAATAATA
Found at i:57255090 original size:29 final size:29
Alignment explanation
Indices: 57255035--57255114 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
57255025 GTTAAAAATA
* * *
57255035 AAAATAA-ATAAAAGTTATAAAAATTTAAT
1 AAAATAAGAAAAAAATTAT-AAATTTTAAT
* *
57255064 AAAATAATAAAAAATATT-TAAATTTTATT
1 AAAATAAGAAAAAA-ATTATAAATTTTAAT
*
57255093 AAAATTAGAAAAAAATTATAAA
1 AAAATAAGAAAAAAATTATAAA
57255115 AATTGTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.07
29 31 0.74
30 6 0.14
31 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATAAGAAAAAAATTATAAATTTTAAT
Found at i:57255111 original size:20 final size:19
Alignment explanation
Indices: 57255092--57255158 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
57255082 TAAATTTTAT
57255092 TAAAATTAGAAAAAAATTA
1 TAAAATTAGAAAAAAATTA
57255111 TAAAAATT-GTAAAAATAA-TA
1 T-AAAATTAG-AAAAA-AATTA
57255131 TAGAAATATAGAAAAAAATTA
1 TA-AAAT-TAGAAAAAAATTA
57255152 TAAAATT
1 TAAAATT
57255159 TTATAAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
19 4 0.10
20 24 0.59
21 12 0.29
22 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (19 bp):
TAAAATTAGAAAAAAATTA
Found at i:57257453 original size:20 final size:20
Alignment explanation
Indices: 57257428--57257477 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
57257418 AGGAAGATGA
57257428 TACTTAATTCA-TCTTTTATT
1 TACTTAATT-ATTCTTTTATT
*
57257448 TACTTAGTTATTCTTTTATT
1 TACTTAATTATTCTTTTATT
*
57257468 TACTAAATTA
1 TACTTAATTA
57257478 CTACTTTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (20 bp):
TACTTAATTATTCTTTTATT
Found at i:57258054 original size:10 final size:10
Alignment explanation
Indices: 57258041--57258122 Score: 80
Period size: 10 Copynumber: 8.4 Consensus size: 10
57258031 TTTTGATACA
57258041 TTTTATAATT
1 TTTTATAATT
*
57258051 TTTTATGA-T
1 TTTTATAATT
**
57258060 TTTTATAAAA
1 TTTTATAATT
*
57258070 TTTTACAATT
1 TTTTATAATT
57258080 TTTTATATATT
1 TTTTATA-ATT
**
57258091 TTTTACGA-T
1 TTTTATAATT
57258100 TTTTATAA-T
1 TTTTATAATT
57258109 TTTTATAATT
1 TTTTATAATT
57258119 TTTT
1 TTTT
57258123 TCTGTTTTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 24 0.41
10 26 0.45
11 8 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:57258062 original size:29 final size:27
Alignment explanation
Indices: 57258030--57258121 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 27
57258020 TTAAAGTGCC
57258030 TTTTTGATACATTTTATAATTTTTTATGA
1 TTTTT-ATACATTTTATAATTTTTTAT-A
* *
57258059 TTTTTATAAAATTTTACAATTTTTTATA
1 TTTTTAT-ACATTTTATAATTTTTTATA
*
57258087 TATTTTTTACGATTTTTATAA-TTTTTATAA
1 T-TTTTATAC-A-TTTTATAATTTTTTAT-A
57258117 TTTTT
1 TTTTT
57258122 TTCTGTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
28 5 0.09
29 39 0.74
30 9 0.17
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTTTATACATTTTATAATTTTTTATA
Found at i:57258122 original size:29 final size:29
Alignment explanation
Indices: 57258041--57258140 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 29
57258031 TTTTGATACA
* * * *
57258041 TTTTATAATTTTTTATGATTTTTATA-AAA
1 TTTTATAA-TTTTTATAATTTTTTTACGAT
*
57258070 TTTTACAATTTTT-TATATATTTTTTACGAT
1 TTTTATAATTTTTATA-AT-TTTTTTACGAT
57258100 TTTTATAATTTTTATAATTTTTTT-CTG-T
1 TTTTATAATTTTTATAATTTTTTTAC-GAT
57258128 TTTTATATATTTT
1 TTTTATA-ATTTT
57258141 GAATTAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
27 1 0.02
28 16 0.27
29 25 0.42
30 15 0.25
31 2 0.03
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTATAATTTTTATAATTTTTTTACGAT
Found at i:57258479 original size:86 final size:86
Alignment explanation
Indices: 57258304--57258480 Score: 230
Period size: 86 Copynumber: 2.1 Consensus size: 86
57258294 CCTAATGGTC
* * ** *
57258304 TTTTTTATGTATTTTGACAGTTCAAGTACCCAATTAAGTGCAAAAAAAAAGGGGTTTAACTGCTT
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAAGGGGGCTAACTGCTG
* *
57258369 TTTTTGAAAAAGTTTGAGAAT
66 TTTTAGAAAAAATTTGAGAAT
* * * *
57258390 TTTTTTGATGCATTTTGAAAGTTTAAGTACCTAATTGAGTGC-AAAAAAAAGGGGGCTAATTGCT
1 TTTTTT-ATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAAGGGGGCTAACTGCT
*
57258454 GTTTTAGAAAAAATTTGAGAGT
65 GTTTTAGAAAAAATTTGAGAAT
57258476 TTTTT
1 TTTTT
57258481 ACGCCCTTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
86 48 0.62
87 30 0.38
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (86 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAAGGGGGCTAACTGCTG
TTTTAGAAAAAATTTGAGAAT
Found at i:57259456 original size:31 final size:30
Alignment explanation
Indices: 57259417--57259479 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
57259407 ACTGATTAAT
57259417 TGAATAAAA-TTCATACATAATAATACATGG
1 TGAATAAAACTT-ATACATAATAATACATGG
* *
57259447 TGAAGTAAAACTTATACGTAATAATATATGG
1 TGAA-TAAAACTTATACATAATAATACATGG
57259478 TG
1 TG
57259480 GAACTCAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 23 0.79
32 2 0.07
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (30 bp):
TGAATAAAACTTATACATAATAATACATGG
Found at i:57260981 original size:14 final size:14
Alignment explanation
Indices: 57260964--57260990 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57260954 GAGTATGGTA
57260964 AAATATTTAAAAAT
1 AAATATTTAAAAAT
57260978 AAATATTTAAAAA
1 AAATATTTAAAAA
57260991 GGTACTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTTAAAAAT
Found at i:57262788 original size:44 final size:43
Alignment explanation
Indices: 57262739--57262870 Score: 192
Period size: 44 Copynumber: 3.0 Consensus size: 43
57262729 ACTAATGTAA
** *
57262739 TATTTGATAGTACAAAATTAGTTGAAAATTTTAGAAGAGCTAAT
1 TATTTG-TAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
*
57262783 TATTTGCTAGTTCAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
1 TATTTG-TAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
*
57262827 TATTTTGTAGTATAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
1 TA-TTTGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
57262871 ATATCAATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 76 0.95
45 4 0.05
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (43 bp):
TATTTGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
Found at i:57265866 original size:27 final size:27
Alignment explanation
Indices: 57265818--57266113 Score: 235
Period size: 27 Copynumber: 11.0 Consensus size: 27
57265808 AAATCCGTAA
**
57265818 CAGTCATTTTATCTCCTA--GGGGTATAA
1 CAGTCATTTTA-C-CCTATGGGGGTATTT
57265845 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
57265872 TAGTCATTCTACCCCATTGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
*
57265899 CGGTCATTTTA-CCTCATGGGGGTATTT
1 CAGTCATTTTACCCT-ATGGGGGTATTT
* * * *
57265926 C-GATTATTTTACCTTAT-AGGGTGTTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* * *
57265952 CGGTCATTCTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
57265979 CAGTCATTCTATCTTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
57266006 C-GATCATTCTACCTTATGCGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* * *
57266033 CGGTCATTTTACCCTATGGAGGTGTTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
57266060 CAGTCATTCTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
57266087 CGGTTATTTTATCCTATGGAGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
57266114 TGGTCATAAC
Statistics
Matches: 218, Mismatches: 42, Indels: 18
0.78 0.15 0.06
Matches are distributed among these distances:
25 4 0.02
26 24 0.11
27 187 0.86
28 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:57265984 original size:107 final size:108
Alignment explanation
Indices: 57265845--57266087 Score: 335
Period size: 107 Copynumber: 2.3 Consensus size: 108
57265835 AGGGGTATAA
* * * * * *
57265845 CAGTCATTTTACCCTATGGGGGTATTTTAGTCATTCTACCCCATTGGGGTATTTCGGTCATTTTA
1 CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
* * *
57265910 CCTCATGGGGGTATTTCGATTATTTTACCTTATAG-GGTGTTT
66 CCTCATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
* * **
57265952 CGGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTATCTTATAGGGGTATTTCGATCATTCTA
1 CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
* * *
57266017 CCTTATGCGGGTATTTCGGTCATTTTACCCTATGGAGGTGTTT
66 CCTCATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
57266060 CAGTCATTCTACCCTATAGGGGTATTTC
1 CAGTCATTCTACCCTATAGGGGTATTTC
57266088 GGTTATTTTA
Statistics
Matches: 118, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
107 84 0.71
108 34 0.29
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (108 bp):
CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
CCTCATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
Found at i:57266111 original size:81 final size:78
Alignment explanation
Indices: 57265850--57266120 Score: 301
Period size: 81 Copynumber: 3.4 Consensus size: 78
57265840 TATAACAGTC
* ** * * *
57265850 ATTTTACCCTATGGGGGTATTTTAGTCATTCTACCCCATTGGGGTATTTCGGTCATTTTACCTCA
1 ATTTTACCTTAT-GGGGTATTTCGGTCATTCTACCCTA-TGGGGTATTTCAGTCATTCTACCT-A
*
57265915 TGGGGGTATTTCGATT
63 TAGGGGTATTTCGATT
* * *
57265931 ATTTTACCTTATAGGGTGTTTCGGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTATCTTAT
1 ATTTTACCTTATGGGGTATTTCGGTCATTCTACCCTAT-GGGGTATTTCAGTCATTCTA-CCTAT
*
57265996 AGGGGTATTTCGATC
64 AGGGGTATTTCGATT
* * *
57266011 ATTCTACCTTATGCGGGTATTTCGGTCATTTTACCCTATGGAGGTGTTTCAGTCATTCTACCCTA
1 ATTTTACCTTATG-GGGTATTTCGGTCATTCTACCCTATGG-GGTATTTCAGTCATTCTA-CCTA
*
57266076 TAGGGGTATTTCGGTT
63 TAGGGGTATTTCGATT
*
57266092 ATTTTATCC-TATGGAGGTATTTTGGTCAT
1 ATTTTA-CCTTATGG-GGTATTTCGGTCAT
57266121 AACAATGTAA
Statistics
Matches: 162, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 67 0.41
81 92 0.57
82 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (78 bp):
ATTTTACCTTATGGGGTATTTCGGTCATTCTACCCTATGGGGTATTTCAGTCATTCTACCTATAG
GGGTATTTCGATT
Found at i:57266120 original size:54 final size:53
Alignment explanation
Indices: 57265820--57266120 Score: 266
Period size: 54 Copynumber: 5.6 Consensus size: 53
57265810 ATCCGTAACA
** * * * **
57265820 GTCATTTTATCTCCTA-GGGGTATAACAGTCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTA-C-CCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * * *
57265874 GTCATTCTACCCCATTGGGGTATTTCGGTCATTTTA-CCTCATGGGGGTATTTCG
1 GTCATTTTACCCTA-TGGGGTATTTCGGTCATTCTACCCT-ATAGGGGTATTTCG
* * * * * *
57265928 ATTATTTTACCTTATAGGGTGTTTCGGTCATTCTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * * * *
57265981 GTCATTCTATCTTATAGGGGTATTTCGATCATTCTACCTTAT-GCGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTCTACCCTATAG-GGGTATTTCG
* *
57266035 GTCATTTTACCCTATGGAGGTGTTTCAGTCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGG-GGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * *
57266089 GTTATTTTATCCTATGGAGGTATTTTGGTCAT
1 GTCATTTTACCCTATGG-GGTATTTCGGTCAT
57266121 AACAATGTAA
Statistics
Matches: 201, Mismatches: 38, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
52 3 0.01
53 48 0.24
54 149 0.74
55 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
Found at i:57269796 original size:12 final size:12
Alignment explanation
Indices: 57269779--57269803 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57269769 CTCTCTGTGA
57269779 CCAGTTCAAACT
1 CCAGTTCAAACT
57269791 CCAGTTCAAACT
1 CCAGTTCAAACT
57269803 C
1 C
57269804 TATCACCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (12 bp):
CCAGTTCAAACT
Found at i:57270713 original size:15 final size:15
Alignment explanation
Indices: 57270693--57270800 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
57270683 TTTATGGAAA
57270693 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
57270708 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
57270722 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
57270738 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
57270752 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
57270768 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
57270782 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
57270798 ATC
1 ATC
57270801 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:57270722 original size:30 final size:30
Alignment explanation
Indices: 57270686--57270800 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
57270676 ATCCATATTT
*
57270686 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
57270716 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
57270746 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
57270776 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
57270801 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:57275402 original size:15 final size:15
Alignment explanation
Indices: 57275382--57275489 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
57275372 TTTATGGAAA
57275382 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
57275397 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
57275411 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
57275427 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
57275441 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
57275457 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
57275471 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
57275487 ATC
1 ATC
57275490 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:57275411 original size:30 final size:30
Alignment explanation
Indices: 57275375--57275489 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
57275365 ATCCATATTT
*
57275375 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
57275405 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
57275435 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
57275465 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
57275490 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:57280577 original size:42 final size:42
Alignment explanation
Indices: 57280490--57280588 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
57280480 TTCAGTATAG
* * * **
57280490 CTGATGATGCACTTATGTGCCAGTATATTTGCATCGATTTCT
1 CTGATGATGCACTTATGTGCCAATATAATTACATCGATCACT
*
57280532 CTGATGATGCACTTATGTGCCAATATAATTACTTCGA-CACAT
1 CTGATGATGCACTTATGTGCCAATATAATTACATCGATCAC-T
57280574 CTGATGATGCACTTA
1 CTGATGATGCACTTA
57280589 CGTGGAAGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (42 bp):
CTGATGATGCACTTATGTGCCAATATAATTACATCGATCACT
Found at i:57285964 original size:24 final size:23
Alignment explanation
Indices: 57285930--57285976 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
57285920 TTTACGTTCT
57285930 GGAAAGCTAAAAGAAAAAGAAAAA
1 GGAAAGCTAAAAG-AAAAGAAAAA
*
57285954 GGAAAGTTAAAAGAAAAGAAAAA
1 GGAAAGCTAAAAGAAAAGAAAAA
57285977 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.06
Consensus pattern (23 bp):
GGAAAGCTAAAAGAAAAGAAAAA
Found at i:57285971 original size:17 final size:18
Alignment explanation
Indices: 57285944--57285982 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
57285934 AGCTAAAAGA
* *
57285944 AAAAGAAAAAGGAAAGTT
1 AAAAGAAAAAGAAAAATT
57285962 AAAAG-AAAAGAAAAATT
1 AAAAGAAAAAGAAAAATT
57285979 AAAA
1 AAAA
57285983 TTATAGGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAATT
Found at i:57289272 original size:5 final size:5
Alignment explanation
Indices: 57289262--57289332 Score: 142
Period size: 5 Copynumber: 14.2 Consensus size: 5
57289252 GATTGTCTAT
57289262 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
57289312 ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA A
57289333 GCACGAGTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 66 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:57289491 original size:17 final size:16
Alignment explanation
Indices: 57289469--57289500 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
57289459 AATAGTTGTG
57289469 ATAATTATACATTTAAC
1 ATAATTATA-ATTTAAC
57289486 ATAATTATAATTTAA
1 ATAATTATAATTTAA
57289501 TAGAAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTATAATTTAAC
Found at i:57289522 original size:43 final size:44
Alignment explanation
Indices: 57289451--57289554 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
57289441 TTTAAAAAGT
* * * * *
57289451 TGAAATAAAATAGTTGTGATAATTATACATTTA-ACATAATTATAA
1 TGAAAT-AAA-AGTTATGGTAATAATACATTTACAAATAATTAGAA
** *
57289496 TTTAATAGAAGTTATGGTAATAATACATTTACAAATAATTAGAA
1 TGAAATAAAAGTTATGGTAATAATACATTTACAAATAATTAGAA
57289540 TGAAATAAAAGTTAT
1 TGAAATAAAAGTTAT
57289555 TCTAATTTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 19 0.40
44 24 0.51
45 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.37
Consensus pattern (44 bp):
TGAAATAAAAGTTATGGTAATAATACATTTACAAATAATTAGAA
Found at i:57291089 original size:11 final size:10
Alignment explanation
Indices: 57291061--57291085 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
57291051 TTTTTTAAAG
57291061 AAAAATAATA
1 AAAAATAATA
57291071 AAAAATAATA
1 AAAAATAATA
57291081 AAAAA
1 AAAAA
57291086 ATAAGATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATAATA
Found at i:57291231 original size:16 final size:17
Alignment explanation
Indices: 57291210--57291251 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
57291200 TTTAAAAAAA
57291210 TATAAAATTTAG-ATTT
1 TATAAAATTTAGAATTT
*
57291226 TATAAATATTTTGAATTT
1 TATAAA-ATTTAGAATTT
57291244 TA-AAAATT
1 TATAAAATT
57291252 ATTTTGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TATAAAATTTAGAATTT
Found at i:57291284 original size:20 final size:20
Alignment explanation
Indices: 57291223--57291277 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
57291213 AAAATTTAGA
*
57291223 TTTTATAAA-TATTTTGAA-
1 TTTTAAAAATTATTTTGAAC
57291241 TTTTAAAAATTATTTTGAAC
1 TTTTAAAAATTATTTTGAAC
*
57291261 TTTTGAAAATTATTTTG
1 TTTTAAAAATTATTTTG
57291278 TGTTTTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.24
19 9 0.27
20 16 0.48
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGAAC
Found at i:57299390 original size:29 final size:29
Alignment explanation
Indices: 57299344--57299403 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
57299334 CCTTAGTACC
57299344 TTAACATCATGTTACAAGATCTGGACAGG
1 TTAACATCATGTTACAAGATCTGGACAGG
* *
57299373 TTAACATCATGTTCCAAGATTTGGACAGG
1 TTAACATCATGTTACAAGATCTGGACAGG
57299402 TT
1 TT
57299404 CCTCTTCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (29 bp):
TTAACATCATGTTACAAGATCTGGACAGG
Found at i:57313125 original size:27 final size:27
Alignment explanation
Indices: 57313081--57313134 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
57313071 CCATAATCCT
*
57313081 CGTGTTTACTATCCTGTTAGAATATTC
1 CGTGTTTAATATCCTGTTAGAATATTC
* * *
57313108 CGTGTTTAATGTCTTGTTAGACTATTC
1 CGTGTTTAATATCCTGTTAGAATATTC
57313135 TACGATGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (27 bp):
CGTGTTTAATATCCTGTTAGAATATTC
Found at i:57323730 original size:6 final size:6
Alignment explanation
Indices: 57323719--57323759 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
57323709 AGGATTTCTA
*
57323719 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATT ATTAT
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTAT
57323760 ATTTACACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTATC
Found at i:57330154 original size:36 final size:36
Alignment explanation
Indices: 57330114--57330191 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
57330104 ACAAAGACTA
* * *
57330114 TCACATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAACAACACACCCACATATTCACTG
* *
57330150 TCACATGGCATGAACAACACACCCTCATATTCACTT
1 TCACATGGCATGAACAACACACCCACATATTCACTG
57330186 TCACAT
1 TCACAT
57330192 CATTCATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (36 bp):
TCACATGGCATGAACAACACACCCACATATTCACTG
Found at i:57330932 original size:20 final size:21
Alignment explanation
Indices: 57330895--57330934 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
57330885 TTTTGGGTTT
57330895 TAACTAAAACATTCAATTTTCA
1 TAACTAAAACA-TCAATTTTCA
57330917 TAACTAAAAC-TCAATTTT
1 TAACTAAAACATCAATTTT
57330935 AAAGTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (21 bp):
TAACTAAAACATCAATTTTCA
Found at i:57332650 original size:24 final size:24
Alignment explanation
Indices: 57332600--57332652 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
57332590 TTTCTAGAAG
* * *
57332600 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATTTATTAGCACAATAT
*
57332624 ATTTAGAATTTATTAGCACAATTT
1 ATTTAGAATTTATTAGCACAATAT
57332648 ATTTA
1 ATTTA
57332653 ACCTACTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCACAATAT
Found at i:57334602 original size:24 final size:24
Alignment explanation
Indices: 57334574--57334619 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
57334564 TTTTTAGAAG
*
57334574 ATTTAATATTTATTAGTATAATAT
1 ATTTAATATTTATTAGCATAATAT
57334598 ATTTAATATTTATTAGCATAAT
1 ATTTAATATTTATTAGCATAAT
57334620 TTAGTTGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTAATATTTATTAGCATAATAT
Found at i:57334660 original size:26 final size:26
Alignment explanation
Indices: 57334630--57334682 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
57334620 TTAGTTGACC
*
57334630 TACGAATTTAGCTTATAAATAATCTT
1 TACGAATTTAACTTATAAATAATCTT
*
57334656 TACGAATTTAACTTATAAATAGTCTT
1 TACGAATTTAACTTATAAATAATCTT
57334682 T
1 T
57334683 TTTTTATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (26 bp):
TACGAATTTAACTTATAAATAATCTT
Found at i:57339793 original size:93 final size:92
Alignment explanation
Indices: 57339661--57339855 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
57339651 TTGATTTTAG
* *
57339661 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
57339725 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
57339753 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
57339818 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
57339846 CAAATTCATA
1 TAAATTCATA
57339856 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:57339903 original size:48 final size:52
Alignment explanation
Indices: 57339833--57339931 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
57339823 AATAATTATT
57339833 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
57339881 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
57339932 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:57339913 original size:17 final size:17
Alignment explanation
Indices: 57339888--57339921 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
57339878 ATAATTTTAA
*
57339888 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
57339905 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
57339922 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:57339938 original size:17 final size:16
Alignment explanation
Indices: 57339893--57339940 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
57339883 TTTAAATTTT
57339893 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
57339910 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
57339924 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
57339941 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:57339995 original size:54 final size:54
Alignment explanation
Indices: 57339937--57340115 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
57339927 ATAATCATAT
57339937 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
57339991 ATTATATATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
57340054 TA
54 -A
*
57340056 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
57340111 ATTAT
1 ATTAT
57340116 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:57339998 original size:61 final size:61
Alignment explanation
Indices: 57339933--57340120 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
57339923 AGTTATAATC
57339933 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * * *
57339994 ATATATTTTAATTAT-ATTATATTTA-ATAATAATTATGTTATT-TT-A-TATTTTA-CAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TAT-TAATTATTAAGAATTTTATTA-AATT
*
57340053 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
57340114 ATATATT
1 ATATATT
57340121 TTAATTAAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 30 0.32
60 14 0.15
61 38 0.40
62 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:57340012 original size:18 final size:17
Alignment explanation
Indices: 57339981--57340015 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57339971 ATTATTAAGA
57339981 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
57339998 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
57340016 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:57340054 original size:120 final size:120
Alignment explanation
Indices: 57339930--57340152 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
57339920 ATTAGTTATA
57339930 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
* *
57339995 TATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
*
57340050 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
57340115 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
57340153 TAAATATGAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
Found at i:57340129 original size:18 final size:17
Alignment explanation
Indices: 57340101--57340135 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57340091 ATTATTAAGA
*
57340101 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
57340118 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
57340136 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:57340147 original size:54 final size:54
Alignment explanation
Indices: 57339964--57340149 Score: 142
Period size: 54 Copynumber: 3.2 Consensus size: 54
57339954 TTCATATAAG
* *
57339964 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATATTATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
* * * *
57340018 AATAATAATTATGT--TATTTTATATTTTACAGTATCATATATTATGGTTTGAGTAAATTCATAT
1 AATAATAATTAT-TAAGAATTT-TA--TTA-A--AT--TATA-TAT--TTTAATTAAATT-ATAT
**
57340081 AAG
53 -TT
* *
57340084 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
57340138 AATAATAATTAT
1 AATAATAATTAT
57340150 GTTTAAATAT
Statistics
Matches: 99, Mismatches: 17, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
53 4 0.04
54 24 0.24
55 5 0.05
56 12 0.12
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 12 0.12
65 5 0.05
66 13 0.13
67 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (54 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
Found at i:57340256 original size:144 final size:147
Alignment explanation
Indices: 57340089--57340360 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
57340079 ATAAGAATAT
*
57340089 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
57340154 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
57340216 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
57340233 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
57340298 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
57340361 CAATAATCAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 91 0.75
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:57340273 original size:18 final size:17
Alignment explanation
Indices: 57340245--57340279 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57340235 ATTATTAAGA
*
57340245 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
57340262 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
57340280 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:57340490 original size:44 final size:45
Alignment explanation
Indices: 57340441--57340535 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
57340431 TTACACCTCT
* *
57340441 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
57340485 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
57340530 ATTACA
1 ATTACA
57340536 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:57340535 original size:16 final size:16
Alignment explanation
Indices: 57340514--57340546 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
57340504 TTGATTTGCT
*
57340514 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
57340530 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
57340546 A
1 A
57340547 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:57340556 original size:21 final size:21
Alignment explanation
Indices: 57340527--57340569 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
57340517 ACACCTCTAT
*
57340527 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
57340548 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
57340569 T
1 T
57340570 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:57346622 original size:13 final size:13
Alignment explanation
Indices: 57346604--57346629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57346594 TTTGATTCAT
57346604 ATTAGCCTTGGGC
1 ATTAGCCTTGGGC
57346617 ATTAGCCTTGGGC
1 ATTAGCCTTGGGC
57346630 TCTTCGGCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (13 bp):
ATTAGCCTTGGGC
Found at i:57353675 original size:33 final size:29
Alignment explanation
Indices: 57353637--57353711 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 29
57353627 CAACTATAAG
57353637 TGCCGAATGCACATATTCACTTATACCCACCTA
1 TGCCGAATGCACATA-T-A--TATACCCACCTA
*
57353670 TGCCGAATGCATACATATATATATCCACCTA
1 TGCCGAATGC--ACATATATATACCCACCTA
57353701 TGCCGAATGCA
1 TGCCGAATGCA
57353712 TACATATACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 1 0.03
31 21 0.54
33 11 0.28
34 1 0.03
35 5 0.13
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (29 bp):
TGCCGAATGCACATATATATACCCACCTA
Found at i:57353701 original size:31 final size:31
Alignment explanation
Indices: 57353658--57353719 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
57353648 CATATTCACT
57353658 TATACCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
*
57353689 TATATCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
57353720 CACACTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (31 bp):
TATACCCACCTATGCCGAATGCATACATATA
Found at i:57353972 original size:41 final size:41
Alignment explanation
Indices: 57353907--57354104 Score: 184
Period size: 41 Copynumber: 4.8 Consensus size: 41
57353897 TTTAAACAGA
* * * *
57353907 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTCTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCGTATAGTCTAATTCAG
* * * *
57353948 TTTACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTAATTCAG
** * * * * *
57353989 TTCAGTGGCAGTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTAATTCAG
* * * *
57354030 TTCACCGGCACTAAACCTGCT-GGACGTATAGTCCAATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CGTATAGTCTAATTCAG
*
57354071 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCT
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCT
57354105 GAACAATTTC
Statistics
Matches: 126, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
40 3 0.02
41 122 0.97
42 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCGTATAGTCTAATTCAG
Found at i:57356029 original size:21 final size:22
Alignment explanation
Indices: 57355987--57356029 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
57355977 GGGTTGTTAC
* **
57355987 ATTTCTTATTTTACTATTTTTG
1 ATTTCTTATATTACTAAATTTG
57356009 ATTTCTT-TATTACTAAATTTG
1 ATTTCTTATATTACTAAATTTG
57356030 TTCATTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.63
Consensus pattern (22 bp):
ATTTCTTATATTACTAAATTTG
Found at i:57356385 original size:19 final size:19
Alignment explanation
Indices: 57356361--57356432 Score: 117
Period size: 19 Copynumber: 3.8 Consensus size: 19
57356351 ATCTTCAGGA
57356361 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
57356380 ATATGCAATCTTAGATATA
1 ATATGCAATCTTAGATATG
**
57356399 ATATATAATCTTAGATATG
1 ATATGCAATCTTAGATATG
57356418 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
57356433 AGATATGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:57356458 original size:22 final size:21
Alignment explanation
Indices: 57356361--57356458 Score: 82
Period size: 19 Copynumber: 4.9 Consensus size: 21
57356351 ATCTTCAGGA
*
57356361 ATATGCAATCTT--AGATATG
1 ATATGTAATCTTAGAGATATG
* *
57356380 ATATGCAATCTT--AGATATA
1 ATATGTAATCTTAGAGATATG
*
57356399 ATATATAATCTT--AGATATG
1 ATATGTAATCTTAGAGATATG
*
57356418 ATATGCAATCTTAGAAGATATG
1 ATATGTAATCTTAG-AGATATG
*
57356440 ATTTTGTAATCTTAGAGAT
1 A-TATGTAATCTTAGAGAT
57356459 TTAATTTGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 44 0.66
22 12 0.18
23 11 0.16
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGTAATCTTAGAGATATG
Found at i:57360992 original size:16 final size:17
Alignment explanation
Indices: 57360971--57361003 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
57360961 AGGCCAAACA
57360971 AATCAAAT-CAAGATTC
1 AATCAAATACAAGATTC
57360987 AATCAAATACAAGATTC
1 AATCAAATACAAGATTC
57361004 GAGGACGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (17 bp):
AATCAAATACAAGATTC
Found at i:57367526 original size:27 final size:25
Alignment explanation
Indices: 57367485--57367550 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 25
57367475 ATGGCTCTTT
*
57367485 AGAGCTTCCCAATTAAAGGCTCATTC
1 AGAGCTTCCCGATTAAAGGCT-ATTC
* *
57367511 ATGAGCTTCCCGATTAATGGCTTTTC
1 A-GAGCTTCCCGATTAAAGGCTATTC
57367537 AGAGCTTCCCGATT
1 AGAGCTTCCCGATT
57367551 TTGGCTCGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.36
26 5 0.14
27 18 0.50
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (25 bp):
AGAGCTTCCCGATTAAAGGCTATTC
Found at i:57367550 original size:25 final size:26
Alignment explanation
Indices: 57367466--57367546 Score: 103
Period size: 25 Copynumber: 3.2 Consensus size: 26
57367456 CTTATGAGTG
*
57367466 TCCCAATTTATGGCTCTTT-AGAGCT
1 TCCCAATTAATGGCTCTTTCAGAGCT
* *
57367491 TCCCAATTAAAGGCTCATTCATGAGCT
1 TCCCAATTAATGGCTCTTTCA-GAGCT
*
57367518 TCCCGATTAATGGCT-TTTCAGAGCT
1 TCCCAATTAATGGCTCTTTCAGAGCT
57367543 TCCC
1 TCCC
57367547 GATTTTGGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
25 25 0.52
26 5 0.10
27 18 0.38
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (26 bp):
TCCCAATTAATGGCTCTTTCAGAGCT
Found at i:57367580 original size:49 final size:50
Alignment explanation
Indices: 57367510--57367608 Score: 125
Period size: 49 Copynumber: 2.0 Consensus size: 50
57367500 AAGGCTCATT
* *
57367510 CATGAGCTTCCCGATTAATGGCTTTTCA-GAGCTTCCCGATT-T-TGGCTCG
1 CATGAACTTCCCGATTAATGGC-TTACATGAGCTTCCC-ATTATATGGCTCG
57367559 CATGAACTTCCCG-TTACATGGCTTACATGAGCTTCCCATTATATGGCTCG
1 CATGAACTTCCCGATTA-ATGGCTTACATGAGCTTCCCATTATATGGCTCG
57367609 AGGGAGTGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
48 10 0.23
49 27 0.61
50 7 0.16
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.33
Consensus pattern (50 bp):
CATGAACTTCCCGATTAATGGCTTACATGAGCTTCCCATTATATGGCTCG
Found at i:57367587 original size:25 final size:25
Alignment explanation
Indices: 57367559--57367606 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
57367549 TTTTGGCTCG
*
57367559 CATGAACTTCCCGTTACATGGCTTA
1 CATGAACTTCCCATTACATGGCTTA
* *
57367584 CATGAGCTTCCCATTATATGGCT
1 CATGAACTTCCCATTACATGGCT
57367607 CGAGGGAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (25 bp):
CATGAACTTCCCATTACATGGCTTA
Found at i:57385806 original size:30 final size:30
Alignment explanation
Indices: 57385761--57385825 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
57385751 CACAAGAGAG
* * * * *
57385761 TGTGTCTAGCCCATGTGGCACACATGGGCT
1 TGTGTCCAGCCCATGTAGAACACATAGGCA
*
57385791 TGTGTCCAGCTCATGTAGAACACATAGGCA
1 TGTGTCCAGCCCATGTAGAACACATAGGCA
57385821 TGTGT
1 TGTGT
57385826 ACAAGCCGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (30 bp):
TGTGTCCAGCCCATGTAGAACACATAGGCA
Found at i:57387625 original size:31 final size:35
Alignment explanation
Indices: 57387590--57387660 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 35
57387580 AGAAACAACC
57387590 ATAAAAATAAA-AAAAT-AGT-TCAA-AAAATAA-A
1 ATAAAAATAAACAAAATAAGTCT-AAGAAAATAACA
57387621 AT-AAAATAAACAAAATAAGTCTAAGAAAATAACA
1 ATAAAAATAAACAAAATAAGTCTAAGAAAATAACA
57387655 ATAAAA
1 ATAAAA
57387661 CAACTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
30 8 0.24
31 7 0.21
32 5 0.15
33 8 0.24
34 3 0.09
35 3 0.09
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.18
Consensus pattern (35 bp):
ATAAAAATAAACAAAATAAGTCTAAGAAAATAACA
Found at i:57389139 original size:17 final size:17
Alignment explanation
Indices: 57389098--57389131 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
57389088 ATGATAATAA
*
57389098 AATAAAACT-AAGGAAT
1 AATAAAAATAAAGGAAT
57389114 AATAAAAATAAAGGAAT
1 AATAAAAATAAAGGAAT
57389131 A
1 A
57389132 TAATAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (17 bp):
AATAAAAATAAAGGAAT
Found at i:57389258 original size:23 final size:23
Alignment explanation
Indices: 57389230--57389273 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57389220 CATGAACAGA
*
57389230 ATAATAA-TAAACAAATGGAAAGC
1 ATAATAAGAAAACAAA-GGAAAGC
57389253 ATAATAAGAAAACAAAGGAAA
1 ATAATAAGAAAACAAAGGAAA
57389274 ATACATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (23 bp):
ATAATAAGAAAACAAAGGAAAGC
Found at i:57389300 original size:15 final size:13
Alignment explanation
Indices: 57389271--57389321 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 13
57389261 AAAACAAAGG
57389271 AAAATACATATAAT
1 AAAATA-ATATAAT
57389285 AGAAATAATATAAAT
1 A-AAATAATAT-AAT
57389300 AAGAATAATA-AAT
1 AA-AATAATATAAT
*
57389313 AAAAAAATA
1 AAAATAATA
57389322 CTAAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 6 0.18
13 5 0.15
14 6 0.18
15 16 0.48
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAATAATATAAT
Found at i:57389578 original size:13 final size:13
Alignment explanation
Indices: 57389560--57389590 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57389550 AAGAGGAGAG
57389560 GGTGTGGGGTGAC
1 GGTGTGGGGTGAC
*
57389573 GGTGTGGGGTGAG
1 GGTGTGGGGTGAC
57389586 GGTGT
1 GGTGT
57389591 TGGATTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.65, T:0.26
Consensus pattern (13 bp):
GGTGTGGGGTGAC
Found at i:57390328 original size:20 final size:21
Alignment explanation
Indices: 57390299--57390356 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
57390289 TTATTTTTTA
*
57390299 TAATTAAAAATTAAT-TGAAT
1 TAATTAAAAAATAATATGAAT
*
57390319 TAATTCAAAAATAATATGAAAT
1 TAATTAAAAAATAATATG-AAT
*
57390341 AAAGTTAAAAGAATAA
1 TAA-TTAAAA-AATAA
57390357 GTAGAATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.43
21 2 0.07
22 5 0.17
23 5 0.17
24 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (21 bp):
TAATTAAAAAATAATATGAAT
Done.