Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 7 of 198
Found at i:2487459 original size:7 final size:8
Alignment explanation
Indices: 2487442--2487479 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
2487432 CAGAGGAGTA
2487442 TTTTTATT
1 TTTTTATT
2487450 TTTTTATTT
1 TTTTTA-TT
2487459 TTTTTATT
1 TTTTTATT
*
2487467 TTTTTGTT
1 TTTTTATT
2487475 TTTTT
1 TTTTT
2487480 TGTTGAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:2487460 original size:9 final size:9
Alignment explanation
Indices: 2487442--2487480 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
2487432 CAGAGGAGTA
2487442 TTTTTA-TT
1 TTTTTATTT
2487450 TTTTTATTT
1 TTTTTATTT
2487459 TTTTTATTT
1 TTTTTATTT
2487468 TTTTGT-TTT
1 TTTT-TATTT
2487477 TTTT
1 TTTT
2487481 GTTGAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 6 0.21
9 22 0.76
10 1 0.03
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:2487464 original size:17 final size:17
Alignment explanation
Indices: 2487442--2487480 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2487432 CAGAGGAGTA
2487442 TTTTTATTTTTTTATTT
1 TTTTTATTTTTTTATTT
*
2487459 TTTTTATTTTTTTGTTT
1 TTTTTATTTTTTTATTT
2487476 TTTTT
1 TTTTT
2487481 GTTGAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.90
Consensus pattern (17 bp):
TTTTTATTTTTTTATTT
Found at i:2487929 original size:7 final size:6
Alignment explanation
Indices: 2487913--2487961 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
2487903 TGTTTCCTGC
*
2487913 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT --AAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAAAAT AAAAAT
2487960 AA
1 AA
2487962 TAGGAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 21 0.57
7 2 0.05
8 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:2487969 original size:22 final size:23
Alignment explanation
Indices: 2487927--2487974 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2487917 ATAAAAATGA
*
2487927 AAATAAAATAAAATAGTAAAAAT
1 AAATAAAATAAAATAGGAAAAAT
* *
2487950 AAATAAAA-ATAATAGGAAAATT
1 AAATAAAATAAAATAGGAAAAAT
2487972 AAA
1 AAA
2487975 ATGTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (23 bp):
AAATAAAATAAAATAGGAAAAAT
Found at i:2487976 original size:23 final size:24
Alignment explanation
Indices: 2487920--2487976 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
2487910 TGCAAAAATA
* *
2487920 AAAATGAAAATAAAATAAAATAGT
1 AAAATTAAAATAAAATAAAATAGG
* *
2487944 AAAAAT-AAATAAAA-ATAATAGG
1 AAAATTAAAATAAAATAAAATAGG
2487966 AAAATTAAAAT
1 AAAATTAAAAT
2487977 GTTTTTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 11 0.41
23 12 0.44
24 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (24 bp):
AAAATTAAAATAAAATAAAATAGG
Found at i:2496978 original size:42 final size:42
Alignment explanation
Indices: 2496886--2496981 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
2496876 TCGAAGGCTG
* *
2496886 AACAGAAGCTCATGAGAGCTAAACAGAAACACATAAGGGTTG
1 AACAGAAGCTCATGAGAGCTAAACAAAAACACATAAGGGTTA
** * *
2496928 AATGGAAGCTCGT-ATGAGC-ATAACAAAAACCCATAAGGGTTA
1 AACAGAAGCTCATGA-GAGCTA-AACAAAAACACATAAGGGTTA
2496970 AACAGAAGCTCA
1 AACAGAAGCTCA
2496982 AAATAGCGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCATGAGAGCTAAACAAAAACACATAAGGGTTA
Found at i:2501332 original size:102 final size:102
Alignment explanation
Indices: 2501214--2501624 Score: 339
Period size: 104 Copynumber: 4.0 Consensus size: 102
2501204 AAAATTATTT
*
2501214 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCA-ACAGTAAAAAAAAAGTT-TCCTTTTTT-TGT
1 TTTGGGTGCTGACCTGTCAATGGCCGGCACCCAGACAGTAAAAAAAAA-TTCT-CTTTTTTCTGT
2501276 CAGAATAAGATATAAATATACGAAAAAAATAATAAAAAAA
64 CAGAATAAGATATAAATATACGAAAAAAATAA-AAAAAAA
* ** *
2501316 TTTGGGTGCTGACCTGTCAATGGTCGGCACCCAGTACAGTTTAAAAAAATTCTTTTTTTTCGTGT
1 TTTGGGTGCTGACCTGTCAATGGCCGGCACCCAG-ACAGTAAAAAAAAATTCTCTTTTTTC-TGT
* *
2501381 CAGAATCAGATATAAATATACGAAAAAAATAAAAAAAAT
64 CAGAATAAGATATAAATATACGAAAAAAATAAAAAAAAA
* * ** * * * *
2501420 TTTGGGTGCCGGCCAATACAAT------TA--C--A-ATTAAAAAAAAGTTTTTACTTTTTTTTT
1 TTTGGGTGCTGACCTGT-CAATGGCCGGCACCCAGACAGTAAAAAAAA---ATT-C--TCTTTTT
* * * *
2501474 TCGTGTCAGAGTCAGATATAAATATATGAAAAAAAT-AAAAAAAT
59 TC-TGTCAGAATAAGATATAAATATACGAAAAAAATAAAAAAAAA
* * * *
2501518 TTTGGGTGCTGACCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAATTCTTTTTTTTGTGT
1 TTTGGGTGCTGACCTGTCAATGGCCGGCACCCAG-AC-AGTAAAAAAAAATTCTCTTTTTTCTGT
* * * *
2501583 CAAAATCATATATAAATATACGAAAAAAATTAAAAAAAA
64 CAGAATAAGATATAAATATACGAAAAAAATAAAAAAAAA
2501622 TTT
1 TTT
2501625 CGGAGTTGGC
Statistics
Matches: 251, Mismatches: 32, Indels: 50
0.75 0.10 0.15
Matches are distributed among these distances:
93 8 0.03
94 1 0.00
96 2 0.01
97 6 0.02
98 21 0.08
99 42 0.17
102 31 0.12
103 38 0.15
104 50 0.20
105 39 0.16
106 1 0.00
107 2 0.01
108 1 0.00
110 9 0.04
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (102 bp):
TTTGGGTGCTGACCTGTCAATGGCCGGCACCCAGACAGTAAAAAAAAATTCTCTTTTTTCTGTCA
GAATAAGATATAAATATACGAAAAAAATAAAAAAAAA
Found at i:2502385 original size:105 final size:107
Alignment explanation
Indices: 2502180--2502596 Score: 591
Period size: 108 Copynumber: 3.9 Consensus size: 107
2502170 TGAGTGTCAG
* * * *
2502180 CCATTAACAGGCCATCA-ACAAA-TTTTTTTTAATTTTTTTCGTATATTTATATCTGATTCTGAC
1 CCATTGACAGGCCAGCACCCAAATTTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGAC
2502243 ACGAAAAAAAAAGAA--TTTTTTTAATTTGTACTGGGTGCCGA
66 ACGAAAAAAAAA-AATTTTTTTTTAATTTGTACTGGGTGCCGA
*
2502284 CCATTGACAGGCCAGCACCCAAA-ATTTTTTT-A-TTTTTTCGTATATTTATATCTGACTCTGAC
1 CCATTGACAGGCCAGCACCCAAATTTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGAC
*
2502346 ACGAAAAAAAAAAATTTTTTTTTGAATTTGTACTAGGTGCCGA
66 ACGAAAAAAAAAAATTTTTTTTT-AATTTGTACTGGGTGCCGA
* *
2502389 CCATTGACAGGCCAGCACCCAAATTTTTTTTTAATTTTTTTCGCATATTTATATCTGATTCTGAC
1 CCATTGACAGGCCAGCACCCAAATTTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGAC
* *
2502454 ACG-AAAAAAAAGATTTTTTTTTAATTTGTACTGGGTGCCGG
66 ACGAAAAAAAAAAATTTTTTTTTAATTTGTACTGGGTGCCGA
* * *
2502495 CCATTGATAGGCCAGCACCCGAAATTTTTTTATTTATTTTTTTCGTACATTTATATCTGACTCTG
1 CCATTGACAGGCCAGCACCC-AAATTTTTTT-TTAATTTTTTTCGTATATTTATATCTGACTCTG
* *
2502560 ACACGAAAAAAAAGTAA-TTTTTTTTAAGTTGTACTGG
64 ACACGAAAAAAAA-AAATTTTTTTTTAATTTGTACTGG
2502597 CCAAAATTTT
Statistics
Matches: 282, Mismatches: 20, Indels: 17
0.88 0.06 0.05
Matches are distributed among these distances:
102 2 0.01
103 41 0.15
104 23 0.08
105 52 0.18
106 43 0.15
107 29 0.10
108 65 0.23
109 26 0.09
110 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (107 bp):
CCATTGACAGGCCAGCACCCAAATTTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGAC
ACGAAAAAAAAAAATTTTTTTTTAATTTGTACTGGGTGCCGA
Found at i:2502526 original size:211 final size:213
Alignment explanation
Indices: 2502180--2502584 Score: 640
Period size: 211 Copynumber: 1.9 Consensus size: 213
2502170 TGAGTGTCAG
* *
2502180 CCATTAACAGGCCATCAACAAATTTTTTTTAATTTTTTTCGTATATTTATATCTGATTCTGACAC
1 CCATTAACAGGCCAGCAACAAATTTTTTTTAATTTTTTTCGCATATTTATATCTGATTCTGACAC
2502245 GAAAAAAAAAGAATTTTTTTAATTTGTACTGGGTGCCGACCATTGACAGGCCAGCACCCAAAA-T
66 GAAAAAAAAAGAATTTTTTTAATTTGTACTGGGTGCCGACCATTGACAGGCCAGCACCCAAAATT
*
2502309 TTT-TTTA-TTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAA-AAATTTTTTTTTGA
131 TTTATTTATTTTTTTCGTACATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTTGA
2502371 ATTTGTACTAGGTGCCGA
196 ATTTGTACTAGGTGCCGA
* *
2502389 CCATTGACAGGCCAGCACCCAAATTTTTTTTTAATTTTTTTCGCATATTTATATCTGATTCTGAC
1 CCATTAACAGGCCAGCA-ACAAA-TTTTTTTTAATTTTTTTCGCATATTTATATCTGATTCTGAC
* * *
2502454 ACG-AAAAAAAAGATTTTTTTTTAATTTGTACTGGGTGCCGGCCATTGATAGGCCAGCACCCGAA
64 ACGAAAAAAAAAGA-ATTTTTTTAATTTGTACTGGGTGCCGACCATTGACAGGCCAGCACCC-AA
* *
2502518 ATTTTTTTATTTATTTTTTTCGTACATTTATATCTGACTCTGACACGAAAAAAAAGTAATTTTTT
127 A-ATTTTTATTTATTTTTTTCGTACATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTT
2502583 TT
191 TT
2502585 AAGTTGTACT
Statistics
Matches: 177, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
209 15 0.08
210 14 0.08
211 87 0.49
212 3 0.02
214 4 0.02
215 4 0.02
216 40 0.23
217 10 0.06
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (213 bp):
CCATTAACAGGCCAGCAACAAATTTTTTTTAATTTTTTTCGCATATTTATATCTGATTCTGACAC
GAAAAAAAAAGAATTTTTTTAATTTGTACTGGGTGCCGACCATTGACAGGCCAGCACCCAAAATT
TTTATTTATTTTTTTCGTACATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTTGA
ATTTGTACTAGGTGCCGA
Found at i:2502656 original size:73 final size:72
Alignment explanation
Indices: 2502530--2502669 Score: 235
Period size: 72 Copynumber: 1.9 Consensus size: 72
2502520 TTTTTTATTT
* *
2502530 ATTTTTTTCGTACATTTATATCTGACTCTGACACGAAAAAAAAGTAATTTTTTTTAAGTTGTACT
1 ATTTTTTTCGTACATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAAATTGTACT
2502595 GGCCAAA
66 GGCCAAA
* *
2502602 ATTTTTTTTGTATATTTATATCTGACTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTGTAC
1 ATTTTTTTCGTACATTTATATCTGACTCTGACACG-AAAAAAAAGAAATTTTTTTTAAATTGTAC
2502667 TGG
65 TGG
2502670 GTGCCGGCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 33 0.52
73 30 0.48
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (72 bp):
ATTTTTTTCGTACATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAAATTGTACT
GGCCAAA
Found at i:2502813 original size:106 final size:105
Alignment explanation
Indices: 2502602--2502801 Score: 282
Period size: 106 Copynumber: 1.9 Consensus size: 105
2502592 ACTGGCCAAA
* * * * *
2502602 ATTTTTTTTGTATATTTATATCTGACTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTGTAC
1 ATTTTTTTCGTATATTTATATATGACTCTAACACAAAAAAAAAAGAAATTTTTTTT-AACTGTAC
2502667 TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAT-TTTTTTT
65 -GGGTGCCGGCCATTGACAGGCCAGCACCCAAATATTTTTTT
* *
2502708 ATTTTTTTCGTATATTTATATATTATTCTAAC-CAAAAAAAAAAGGAAATTTTTTTT-ACTGTA-
1 ATTTTTTTCGTATATTTATATATGACTCTAACACAAAAAAAAAA-GAAATTTTTTTTAACTGTAC
2502770 GGGTGCCGGCCATTGACAGGCCAGCACCCAAA
65 GGGTGCCGGCCATTGACAGGCCAGCACCCAAA
2502802 AAATAATTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
102 32 0.37
104 5 0.06
105 10 0.12
106 39 0.45
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (105 bp):
ATTTTTTTCGTATATTTATATATGACTCTAACACAAAAAAAAAAGAAATTTTTTTTAACTGTACG
GGTGCCGGCCATTGACAGGCCAGCACCCAAATATTTTTTT
Found at i:2513725 original size:6 final size:6
Alignment explanation
Indices: 2513714--2513743 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2513704 GGTTCGGTCG
*
2513714 CCAACC CCAACC CCAACC CCAACC TCAACC
1 CCAACC CCAACC CCAACC CCAACC CCAACC
2513744 GCGTAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.63, G:0.00, T:0.03
Consensus pattern (6 bp):
CCAACC
Found at i:2513931 original size:3 final size:3
Alignment explanation
Indices: 2513923--2513954 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2513913 ATTAGTAATG
2513923 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2513955 GGACCATTTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2517467 original size:15 final size:15
Alignment explanation
Indices: 2517443--2517477 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2517433 TAAAATGAGA
2517443 AAATTATAAATTAT-
1 AAATTATAAATTATC
2517457 AAATTAGTAAATTATC
1 AAATTA-TAAATTATC
2517473 AAATT
1 AAATT
2517478 GTACTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 8 0.42
16 5 0.26
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (15 bp):
AAATTATAAATTATC
Found at i:2517469 original size:8 final size:7
Alignment explanation
Indices: 2517443--2517477 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
2517433 TAAAATGAGA
2517443 AAATTAT
1 AAATTAT
2517450 AAATTAT
1 AAATTAT
2517457 AAATTAGT
1 AAATTA-T
2517465 AAATTAT
1 AAATTAT
2517472 CAAATT
1 -AAATT
2517478 GTACTTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.54
8 12 0.46
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (7 bp):
AAATTAT
Found at i:2523425 original size:16 final size:17
Alignment explanation
Indices: 2523399--2523430 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2523389 TTTAATTAAC
2523399 TAAATTAATTTCTCAAT
1 TAAATTAATTTCTCAAT
2523416 TAAA-TAATTTCTCAA
1 TAAATTAATTTCTCAA
2523431 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTAATTTCTCAAT
Found at i:2528398 original size:30 final size:30
Alignment explanation
Indices: 2528362--2528419 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2528352 TTTACATATT
*
2528362 TGGAAAGCTAATTGCCTAACAACCTAGTAG
1 TGGAAAGCTAATAGCCTAACAACCTAGTAG
**
2528392 TGGAAAGCTTGTAGCCTAACAACCTAGT
1 TGGAAAGCTAATAGCCTAACAACCTAGT
2528420 TTCCACAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (30 bp):
TGGAAAGCTAATAGCCTAACAACCTAGTAG
Found at i:2529871 original size:18 final size:18
Alignment explanation
Indices: 2529823--2529872 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 18
2529813 TATCCAAAAT
2529823 TATTAAAATAATATTAAA
1 TATTAAAATAATATTAAA
2529841 TATTATATTAATAATATTAAA
1 TATTA-A--AATAATATTAAA
2529862 T-TTAAGAATAA
1 TATTAA-AATAA
2529873 ATAATGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.36
19 2 0.07
20 3 0.11
21 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
TATTAAAATAATATTAAA
Found at i:2530264 original size:20 final size:21
Alignment explanation
Indices: 2530241--2530281 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2530231 AACCCTTTAA
2530241 AATTGATTAAATTTTA-ATTT
1 AATTGATTAAATTTTATATTT
**
2530261 AATTTTTTAAATTTTATATTT
1 AATTGATTAAATTTTATATTT
2530282 TTACTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
AATTGATTAAATTTTATATTT
Found at i:2531115 original size:21 final size:22
Alignment explanation
Indices: 2531091--2531145 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
2531081 TCCGAATATT
*
2531091 TTTTATTTTAAATTTATTTT-A
1 TTTTATTTTAAATTAATTTTAA
**
2531112 TTTTATAATAAATTAATTTTAA
1 TTTTATTTTAAATTAATTTTAA
2531134 TTTTAATTTTAA
1 TTTT-ATTTTAA
2531146 TCGATAAGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.63
22 5 0.19
23 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATTTTAAATTAATTTTAA
Found at i:2531826 original size:19 final size:19
Alignment explanation
Indices: 2531804--2531841 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2531794 AACAAAATAG
2531804 TAGCAAAAAAACAAGAAAA
1 TAGCAAAAAAACAAGAAAA
* *
2531823 TAGCAACAAAACAATAAAA
1 TAGCAAAAAAACAAGAAAA
2531842 GAAAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.71, C:0.13, G:0.08, T:0.08
Consensus pattern (19 bp):
TAGCAAAAAAACAAGAAAA
Found at i:2531832 original size:22 final size:22
Alignment explanation
Indices: 2531791--2531833 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2531781 GTTATACAAG
* *
2531791 AACAACAAAATAGTAGCAAAAA
1 AACAACAAAATAGCAACAAAAA
*
2531813 AACAAGAAAATAGCAACAAAA
1 AACAACAAAATAGCAACAAAA
2531834 CAATAAAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.70, C:0.14, G:0.09, T:0.07
Consensus pattern (22 bp):
AACAACAAAATAGCAACAAAAA
Found at i:2532840 original size:28 final size:28
Alignment explanation
Indices: 2532805--2532870 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
2532795 ATAAAAAATA
**
2532805 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTTATTT
2532833 ACCAAAATATTATAAAATTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTTATTT
2532861 ACCAAAATAT
1 ACCAAAATAT
2532871 ACCAAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (28 bp):
ACCAAAATATTATAAAATTTTTTTATTT
Found at i:2533921 original size:18 final size:19
Alignment explanation
Indices: 2533887--2533937 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
2533877 NNNNNNNNNN
* *
2533887 GTTATTAAATGAGAATAG-
1 GTTATTAAATTAAAATAGA
* *
2533905 TTTATTACATTAAAATAGA
1 GTTATTAAATTAAAATAGA
2533924 GTTATTAAATTAAA
1 GTTATTAAATTAAA
2533938 CTATTTTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (19 bp):
GTTATTAAATTAAAATAGA
Found at i:2540968 original size:21 final size:22
Alignment explanation
Indices: 2540924--2540972 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2540914 GTACAGTTTT
*
2540924 GAGACAATTGATCTTAGATCTC
1 GAGACAAGTGATCTTAGATCTC
* *
2540946 GAGACAAGTGGTCTTTG-TCTC
1 GAGACAAGTGATCTTAGATCTC
2540967 GAGACA
1 GAGACA
2540973 GAGGTACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (22 bp):
GAGACAAGTGATCTTAGATCTC
Found at i:2544467 original size:2 final size:2
Alignment explanation
Indices: 2544460--2544489 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2544450 AAATCTGCAA
2544460 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
2544490 CTGCATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2547484 original size:9 final size:9
Alignment explanation
Indices: 2547470--2547499 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2547460 AATATTATAC
2547470 AATTCGATT
1 AATTCGATT
*
2547479 AATTCGACT
1 AATTCGATT
2547488 AATTCGATT
1 AATTCGATT
2547497 AAT
1 AAT
2547500 AATCGAGCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (9 bp):
AATTCGATT
Found at i:2549567 original size:31 final size:30
Alignment explanation
Indices: 2549532--2549591 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2549522 GGAGGTGGGA
*
2549532 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
2549563 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
2549592 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:2549820 original size:9 final size:9
Alignment explanation
Indices: 2549806--2549851 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
2549796 TATAGTTTGA
2549806 TATTCGAAT
1 TATTCGAAT
2549815 TATTCGAAT
1 TATTCGAAT
2549824 TATTCGAAT
1 TATTCGAAT
*
2549833 TATTCGAGT
1 TATTCGAAT
2549842 TATTCGAAT
1 TATTCGAAT
2549851 T
1 T
2549852 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:2549921 original size:9 final size:9
Alignment explanation
Indices: 2549904--2549934 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2549894 TCGAGTTGAT
2549904 TCGAATAAC
1 TCGAATAAC
*
2549913 TCGATTAAC
1 TCGAATAAC
2549922 TCGAATAAC
1 TCGAATAAC
2549931 TCGA
1 TCGA
2549935 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:2550170 original size:23 final size:23
Alignment explanation
Indices: 2550125--2550189 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
2550115 GTTTAAGTTC
**
2550125 ACAAACATGTTCATTTAAC-TTAA
1 ACAAACATGTTCA-CGAACATTAA
* *
2550148 TCGAACATGTTCACGAACATTAA
1 ACAAACATGTTCACGAACATTAA
2550171 ACAAACATGTTCACGAACA
1 ACAAACATGTTCACGAACA
2550190 ATGTTAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (23 bp):
ACAAACATGTTCACGAACATTAA
Found at i:2550373 original size:46 final size:46
Alignment explanation
Indices: 2550320--2550484 Score: 303
Period size: 46 Copynumber: 3.6 Consensus size: 46
2550310 AATACAAACC
* *
2550320 AAGATAATTTTATTAATATATACTAATAGAAAAATAAACGAGTTTT
1 AAGATAATTTCATTAATATATACTAATAGAACAATAAACGAGTTTT
2550366 AAGATAATTTCATTAATATATACTAATAGAACAATAAACGAGTTTT
1 AAGATAATTTCATTAATATATACTAATAGAACAATAAACGAGTTTT
2550412 AAGATAATTTCATTAATATATACTAATAGAACAATAAACGAGTTTT
1 AAGATAATTTCATTAATATATACTAATAGAACAATAAACGAGTTTT
*
2550458 AAGATAATTTCGTTAATATATACTAAT
1 AAGATAATTTCATTAATATATACTAAT
2550485 GAATTTTTTA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 116 1.00
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.36
Consensus pattern (46 bp):
AAGATAATTTCATTAATATATACTAATAGAACAATAAACGAGTTTT
Found at i:2550936 original size:20 final size:20
Alignment explanation
Indices: 2550911--2550950 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2550901 TATAATCATA
*
2550911 AGATCAGGTCTAGTTTGCTC
1 AGATCAGGTCTAATTTGCTC
2550931 AGATCAGGTCTAATTTGCTC
1 AGATCAGGTCTAATTTGCTC
2550951 TATATGCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
AGATCAGGTCTAATTTGCTC
Found at i:2551256 original size:15 final size:16
Alignment explanation
Indices: 2551233--2551265 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2551223 GTTTACCACT
*
2551233 TACTTCCAC-AAACTC
1 TACTACCACAAAACTC
2551248 TACTACCACAAAACTC
1 TACTACCACAAAACTC
2551264 TA
1 TA
2551266 TTTCCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.24
Consensus pattern (16 bp):
TACTACCACAAAACTC
Found at i:2553207 original size:26 final size:26
Alignment explanation
Indices: 2553132--2553215 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 26
2553122 ATACATATTT
2553132 AATTATTT-ATA-TTTAATTATATAATA
1 AATTATTTAATATTTTAATT-T-TAATA
2553158 AATTA-TTAATATAATTTAATATTTTAATA
1 AATTATTTAATAT--TTT-A-ATTTTAATA
2553187 AATTATTTAATATTTTAA-TTTAATA
1 AATTATTTAATATTTTAATTTTAATA
2553212 AATT
1 AATT
2553216 TTAAAAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
25 13 0.25
26 9 0.18
27 1 0.02
28 3 0.06
29 13 0.25
30 9 0.18
31 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AATTATTTAATATTTTAATTTTAATA
Found at i:2553211 original size:33 final size:34
Alignment explanation
Indices: 2553127--2553211 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 34
2553117 TAAACATACA
2553127 TATTTAAT-TATTTATATTTAAT-TATATAATAAAT
1 TATTTAATAT-TTTA-ATTTAATATATATAATAAAT
*
2553161 TA-TTAATA---TAATTTAATAT-TTTAATAAAT
1 TATTTAATATTTTAATTTAATATATATAATAAAT
2553190 TATTTAATATTTTAATTTAATA
1 TATTTAATATTTTAATTTAATA
2553212 AATTTTAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
29 18 0.41
30 9 0.20
33 15 0.34
34 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TATTTAATATTTTAATTTAATATATATAATAAAT
Found at i:2553228 original size:16 final size:16
Alignment explanation
Indices: 2553207--2553240 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2553197 TATTTTAATT
2553207 TAATAAATTTTAAA-AA
1 TAAT-AATTTTAAATAA
2553223 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
2553239 TA
1 TA
2553241 TTCTTCGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:2553233 original size:25 final size:26
Alignment explanation
Indices: 2553153--2553234 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 26
2553143 TTTAATTATA
2553153 TAATAAATTATTAATATAATTTAAT-ATTT
1 TAATAAATTATTAA-A-AA--TAATAATTT
* * **
2553182 TAATAAATTATTTAATATTTTAA-TT
1 TAATAAATTATTAAAAATAATAATTT
2553207 TAATAAATT-TTAAAAATAATAATTT
1 TAATAAATTATTAAAAATAATAATTT
2553232 TAA
1 TAA
2553235 ATAATATTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
24 9 0.21
25 18 0.42
26 1 0.02
27 1 0.02
28 1 0.02
29 13 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAATAAATTATTAAAAATAATAATTT
Found at i:2558416 original size:21 final size:20
Alignment explanation
Indices: 2558391--2558446 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 20
2558381 GTACAGACTA
2558391 AAAAAACAAACAAAACAAAAAC
1 AAAAAA-AAACAAAAC-AAAAC
2558413 AAAAAAAAACAAAACAAAAC
1 AAAAAAAAACAAAACAAAAC
*
2558433 AAAAAAAAAGAAAA
1 AAAAAAAAACAAAA
2558447 GGGAGAGGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 18 0.55
21 9 0.27
22 6 0.18
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACAAAACAAAAC
Found at i:2558427 original size:26 final size:24
Alignment explanation
Indices: 2558390--2558446 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 24
2558380 AGTACAGACT
2558390 AAAAAAACAAACAAAACAAAAACAA
1 AAAAAAACAAACAAAACAAAAA-AA
2558415 AAAAAAACAAAACAAAACAAAAAAA
1 AAAAAAAC-AAACAAAACAAAAAAA
*
2558440 AAGAAAA
1 AAAAAAA
2558447 GGGAGAGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 16 0.53
26 14 0.47
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAAACAAACAAAACAAAAAAA
Found at i:2558447 original size:5 final size:5
Alignment explanation
Indices: 2558393--2558446 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
2558383 ACAGACTAAA
* * *
2558393 AAAAC -AAAC AAAAC AAAAAC AAAAA AAAAC AAAAC AAAAC AAAAA AAAAG
1 AAAAC AAAAC AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
2558443 AAAA
1 AAAA
2558447 GGGAGAGGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 4 0.09
5 34 0.79
6 5 0.12
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:2560858 original size:44 final size:44
Alignment explanation
Indices: 2560492--2561450 Score: 381
Period size: 44 Copynumber: 22.0 Consensus size: 44
2560482 GTGAATATTT
* * * * * **
2560492 CAGATCTTATCTCCCTGAGGTCACAGTGGAGTAAATTGAAGCCA
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * * * *
2560536 GAAATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGA-CA
1 CAGATCTTATCTCCCTGAAG-TTACAGTGGAGCAGAT-TAAAATCA
* * * **
2560580 C-TATCCTATCTCCCTGAAGTTATAGTGGAGTGGATTAAAAT-A
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * ** * ***
2560622 AAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGA-TCGCAT--
1 CA-GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * * * *** *
2560664 CAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGGCCGAAGAATTTA
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCA-GATTAA-AA-TCA
* * * * *
2560711 -AGATCTTGTCTCCCTGAGGTTACAATGGAGCAGATT-GAAGC-
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* *
2560752 CAGGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCAAAGA-CA
1 CA-GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAA-ATCA
* **
2560797 C-TATCTTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATCA
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * * ***
2560840 CAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCAT--
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * * **
2560881 CAGGTCTTATCTCCCTGAGGTTACAGCGGAGCAGACGAAAGA--A
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ATCA
* ** ** *
2560924 -AGTAATCCTATCTTTCTGAAGTTACAGTGGAGTGGATTAAAATAA
1 CAG--ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * * * **
2560969 AAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGGTTGAAGCCGA
1 CAGATCTTATCTCCCTGAAGTTACAGT-G-G-AG-------CAGATTAAAATC-A
* * *
2561024 CA-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCA
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * * *
2561067 CAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGA-TCACATC-
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* ** *
2561109 CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-AA
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ATCA
* * * * *
2561152 TTA-ATCCTATCTTCCTGAAGTTACAGTGGAGCGGATTAAAACCA
1 -CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * * ***
2561196 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATC-
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* ** *
2561238 CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-AA
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ATCA
* * *
2561281 TCA-ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA-CTA
1 -CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATC-A
* ** * ***
2561325 CAGATCTTATCTCTCTGAAGTGGCAGTAGAGCAGA-TCGCATC-
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
* * * * * *
2561367 CAG-TATTATCT-CCTAAAGTTGCAGTGGAGCAGACT-GAAGCTA
1 CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATC-A
* * * *
2561409 CTA-ATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAAT
1 C-AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAT
2561451 GATAAATCAT
Statistics
Matches: 678, Mismatches: 174, Indels: 125
0.69 0.18 0.13
Matches are distributed among these distances:
40 21 0.03
41 121 0.18
42 22 0.03
43 123 0.18
44 317 0.47
45 9 0.01
46 30 0.04
47 2 0.00
51 2 0.00
52 1 0.00
53 1 0.00
54 27 0.04
55 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
CAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCA
Found at i:2560873 original size:217 final size:216
Alignment explanation
Indices: 2560488--2561182 Score: 799
Period size: 217 Copynumber: 3.2 Consensus size: 216
2560478 ATCAGTGAAT
* * *
2560488 ATTTCAGATCTTATCTCCCTGAGGTCACAGTGGAGTAAATTGAAGCCAGAAATCTTATCTCCCTG
1 ATTT-AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAG-GATCTTATCTCCCTG
* *
2560553 AGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTATAGTGGAGTGGATTAA
64 AGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAA
* * *
2560618 AAT-AAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCTCTGA
129 AATCACA-GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGA
* *
2560682 GGTTACAGTGGAGTAGGCCG-AAGA
193 GGTTACAGTGGAGCA-GACGAAAGA
* * *
2560706 ATTTAAGATCTTGTCTCCCTGAGGTTACAATGGAGCAGATTGAAGCCAGGATCTTATCTCCCTGA
1 ATTT-AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAGGATCTTATCTCCCTGA
*
2560771 GATTACAGCGGAGCAGATCAAAGACACTATCTTATCTCCCTGAAGTTACAGTGGAGTGGATTAAA
65 GATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAA
2560836 ATCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGG
130 ATCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGG
*
2560901 TTACAGCGGAGCAGACGAAAGA
195 TTACAGTGGAGCAGACGAAAGA
** * ** * * * *** * *
2560923 AAGTA-ATCCTATCTTTCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGA
1 ATTTAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATT-GAAGCCAGGATCTTATCTCCCTGA
* * * *
2560987 -AGTTACAGTAGAGTAGATCACATCAGGTTGAAGCCGACAATCCTATCTCCCTGAAGTTACAGTG
65 GA-TTACAG-CG-G-AG--CAGATCA-----AAGAC-ACTATCCTATCTCCCTGAAGTTACAGTG
* * * *
2561051 GAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCACATCCA-GTCT
118 GAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT-CAGGTCT
* *
2561115 TATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA
182 TATCTCCCTGAGGTTACAGTGGAGCAGACGAAAGA
* * * *
2561150 AATTA-ATCCTATCTTCCTGAAGTTACAGTGGAG
1 ATTTAGATCTTATCTCCCTGAGGTTACAGTGGAG
2561183 CGGATTAAAA
Statistics
Matches: 415, Mismatches: 46, Indels: 23
0.86 0.10 0.05
Matches are distributed among these distances:
215 27 0.07
216 28 0.07
217 154 0.37
218 46 0.11
219 2 0.00
221 6 0.01
226 4 0.01
227 146 0.35
228 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (216 bp):
ATTTAGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAGGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAA
TCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGT
TACAGTGGAGCAGACGAAAGA
Found at i:2560974 original size:129 final size:128
Alignment explanation
Indices: 2560752--2561014 Score: 411
Period size: 129 Copynumber: 2.0 Consensus size: 128
2560742 AGATTGAAGC
* *
2560752 CAGGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTATCTTATCTCCCTGAAGT
1 CAGG-TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAACTATCCTATCTCCCTGAAGT
* * *
2560817 TACAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
65 TACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
* * **
2560881 CAGGTCTTATCTCCCTGAGGTTACAGCGGAGCAGA-CGAAAGAAAGTAATCCTATCTTTCTGAAG
1 CAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATC-AAAGAAACT-ATCCTATCTCCCTGAAG
2560945 TTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
64 TTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
2561010 CAGGT
1 CAGGT
2561015 TGAAGCCGAC
Statistics
Matches: 123, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
127 1 0.01
128 37 0.30
129 85 0.69
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (128 bp):
CAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAACTATCCTATCTCCCTGAAGTT
ACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACAT
Found at i:2561053 original size:98 final size:98
Alignment explanation
Indices: 2560927--2561108 Score: 301
Period size: 98 Copynumber: 1.9 Consensus size: 98
2560917 GAAAGAAAGT
** * *
2560927 AATCCTATCTTTCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAAGATCTTATCTCTCTGAAGTTA
*
2560992 CAGTAGAGTAGATCACATCAGGTTGAAGCCGAC
66 CAGTAGAGCAGATCACATCAGGTTGAAGCCGAC
* *
2561025 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAAGATCTTATCTCTCTGAAGTTA
2561090 CAGTAGAGCAGATCACATC
66 CAGTAGAGCAGATCACATC
2561109 CAGTCTTATC
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 77 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (98 bp):
AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACAAAAGATCTTATCTCTCTGAAGTTA
CAGTAGAGCAGATCACATCAGGTTGAAGCCGAC
Found at i:2561082 original size:227 final size:227
Alignment explanation
Indices: 2560803--2561237 Score: 710
Period size: 227 Copynumber: 1.9 Consensus size: 227
2560793 GACACTATCT
* *
2560803 TATCTCCCTGAAGTTACAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTA
* * *
2560868 GAGTAGATCGCAT-CAGGTCTTATCTCCCTGAGGTTACAGCGGAGCAGACGAAAGAAAGTAATCC
66 GAGCAGATCACATCCA-GTCTTATCTCCCTGAAGTTACAGCGGAGCAGACGAAAGAAAGTAATCC
* * *
2560932 TATCTTTCTGAAGTTACAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTA
130 TATCTTCCTGAAGTTACAGTGGAGCGGATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGTA
*
2560997 GAGTAGATCACATCAGGTTGAAGCCGACAATCC
195 GAGCAGATCACATCAGGTTGAAGCCGACAATCC
2561030 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTA
* * *
2561095 GAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAATTAATCCT
66 GAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTACAGCGGAGCAGACGAAAGAAAGTAATCCT
* * *
2561160 ATCTTCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAG
131 ATCTTCCTGAAGTTACAGTGGAGCGGATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGTAG
*
2561225 AGCAGATCGCATC
196 AGCAGATCACATC
2561238 CAGTCTTATC
Statistics
Matches: 191, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
227 189 0.99
228 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (227 bp):
TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTA
GAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTACAGCGGAGCAGACGAAAGAAAGTAATCCT
ATCTTCCTGAAGTTACAGTGGAGCGGATTAAAACAAAAGATCTTATCTCTCTGAAGTTACAGTAG
AGCAGATCACATCAGGTTGAAGCCGACAATCC
Found at i:2561362 original size:129 final size:129
Alignment explanation
Indices: 2561024--2561482 Score: 701
Period size: 129 Copynumber: 3.6 Consensus size: 129
2561014 TTGAAGCCGA
2561024 CAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
1 CAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
* *
2561089 ACAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAAT
66 GCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAAT
* *
2561153 TAATCCTATCTTCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
1 CAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
2561218 GCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAAT
66 GCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAAT
* * *
2561282 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTACAGATCTTATCTCTCTGAAGTG
1 CAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
* * **
2561347 GCAGTAGAGCAGATCGCATCCAGTATTATCT-CCTAAAGTTGCAGTGGAGCAGACTG-AAGCTA-
66 GCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-GAAAGAAAT
* * ** * * *
2561409 CTAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATGATAAATCATATAC-CTCTGAAG
1 C-AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTAT-CTCTCTGAAG
2561473 TTGCAGTAGA
64 TTGCAGTAGA
2561483 TTGAATTAGA
Statistics
Matches: 307, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
127 1 0.00
128 89 0.29
129 217 0.71
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (129 bp):
CAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
GCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAAT
Found at i:2563721 original size:109 final size:110
Alignment explanation
Indices: 2563430--2563960 Score: 826
Period size: 109 Copynumber: 4.9 Consensus size: 110
2563420 AATTTTCTTC
2563430 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* *
2563495 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAAATTTTTA
66 TTTCTCGTTCAACCAAATAGCTTAATATCCTTTT--AAAAATTTTCA
*
2563542 AAATAAGGCAATGTTTTGCGTTT-GAAA-TCGAGAAAATATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* *
2563605 TTTCTCGTTCAACCAAATAGCTAAATATCCTTCTAAAAA-TTTCA
66 TTTCTCGTTCAACCAAATAGCTTAATATCCTTTTAAAAATTTTCA
2563649 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
*
2563714 TTTCTCGTTCAACCAAAT-GACTTTATATCCTTTTAAAAATTTT-A
66 TTTCTCGTTCAACCAAATAG-CTTAATATCCTTTTAAAAATTTTCA
*
2563758 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGATAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* *
2563823 TTTCTCGTTCAACCAAATGGCTTAATATCATTTTAAAAATTTTCA
66 TTTCTCGTTCAACCAAATAGCTTAATATCCTTTTAAAAATTTTCA
* * * * *
2563868 AAATAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTACCCTAAGGTGCTGGGTTTCGA--
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
* **
2563930 TTTCTCGTTTAACCAAATAGCCAAATATCCT
66 TTTCTCGTTCAACCAAATAGCTTAATATCCT
2563961 CTCGAATTTC
Statistics
Matches: 390, Mismatches: 23, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
107 53 0.14
108 10 0.03
109 197 0.51
110 103 0.26
111 4 0.01
112 23 0.06
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (110 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
TTTCTCGTTCAACCAAATAGCTTAATATCCTTTTAAAAATTTTCA
Found at i:2563869 original size:219 final size:218
Alignment explanation
Indices: 2563430--2563947 Score: 839
Period size: 219 Copynumber: 2.4 Consensus size: 218
2563420 AATTTTCTTC
2563430 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
*
2563495 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAAATTTTTAAAATAAGGCAATGTTTTG
66 TTTCTCGTTCAACCAAATGACTTAATATCCTTTT-AAAAAATTTTTAAAATAAGGCAATGTTTTG
*
2563560 CGTTTGAAATCGAGAAAATATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAG
130 CGTTTGAAATCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAG
*
2563625 CTAAATATCCTTCTAAAAATTTCA
195 CTAAATATCATTCTAAAAATTTCA
2563649 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
*
2563714 TTTCTCGTTCAACCAAATGACTTTATATCCTTTT-AAAAA-TTTTAAAATAAGGCAATGTTTTGC
66 TTTCTCGTTCAACCAAATGACTTAATATCCTTTTAAAAAATTTTTAAAATAAGGCAATGTTTTGC
* *
2563777 GTTTGGAAATTCGATAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATG
131 GTTT-GAAA-TCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATA
* *
2563842 GCTTAATATCATTTTAAAAATTTTCA
194 GCTAAATATCATTCTAAAAA-TTTCA
* * * * *
2563868 AAATAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTACCCTAAGGTGCTGGGTTTCGA--
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
*
2563930 TTTCTCGTTTAACCAAAT
66 TTTCTCGTTCAACCAAAT
2563948 AGCCAAATAT
Statistics
Matches: 282, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
216 45 0.16
217 9 0.03
218 93 0.33
219 135 0.48
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (218 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
TTTCTCGTTCAACCAAATGACTTAATATCCTTTTAAAAAATTTTTAAAATAAGGCAATGTTTTGC
GTTTGAAATCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGC
TAAATATCATTCTAAAAATTTCA
Found at i:2574447 original size:3 final size:3
Alignment explanation
Indices: 2574434--2574482 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
2574424 ATTTAAGAAA
2574434 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2574481 AA
1 AA
2574483 AGGTAAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2574563 original size:5 final size:5
Alignment explanation
Indices: 2574553--2574577 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2574543 CCTTTGTACG
2574553 TCTCT TCTCT TCTCT TCTCT TCTCT
1 TCTCT TCTCT TCTCT TCTCT TCTCT
2574578 GTCTGTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCTCT
Found at i:2575117 original size:16 final size:17
Alignment explanation
Indices: 2575086--2575118 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2575076 TTTCCTAATT
2575086 TTCATGCTGATATGTATG
1 TTCATGCT-ATATGTATG
2575104 TTCATGCT-TATGTAT
1 TTCATGCTATATGTAT
2575119 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (17 bp):
TTCATGCTATATGTATG
Found at i:2581258 original size:23 final size:24
Alignment explanation
Indices: 2581216--2581260 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2581206 TATAATGACA
* *
2581216 ATAATAAAATAAAGATATTTATTT
1 ATAAAAAAATAAAGACATTTATTT
2581240 ATAAAAAAATAAAG-CATTTAT
1 ATAAAAAAATAAAGACATTTAT
2581261 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
ATAAAAAAATAAAGACATTTATTT
Found at i:2582594 original size:11 final size:11
Alignment explanation
Indices: 2582580--2582604 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2582570 ATTTTAAAAA
2582580 ATTATTAAATT
1 ATTATTAAATT
2582591 ATTATTAAATT
1 ATTATTAAATT
2582602 ATT
1 ATT
2582605 TGAAAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:2590045 original size:50 final size:51
Alignment explanation
Indices: 2589947--2590047 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 51
2589937 AATAGCAGAA
* *
2589947 TTTAATTTTTTTATTATATTTTATATATATTAATTGTTTTTGATCATAAAAG
1 TTTAACTTTTTTATTATA-TTTATATATATTAATTGTTTTTGACCATAAAAG
*
2589999 TTTAACTTTTTTATTATA-TTATATATATTAATTGTTTTTTACCATAAAA
1 TTTAACTTTTTTATTATATTTATATATATTAATTGTTTTTGACCATAAAA
2590048 ATTATCGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 29 0.63
52 17 0.37
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (51 bp):
TTTAACTTTTTTATTATATTTATATATATTAATTGTTTTTGACCATAAAAG
Found at i:2591496 original size:7 final size:7
Alignment explanation
Indices: 2591484--2591508 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2591474 TCATTAATGG
2591484 TATAAAA
1 TATAAAA
2591491 TATAAAA
1 TATAAAA
2591498 TATAAAA
1 TATAAAA
2591505 TATA
1 TATA
2591509 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TATAAAA
Found at i:2592116 original size:3 final size:3
Alignment explanation
Indices: 2592108--2592145 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
2592098 CCACGTCTCG
2592108 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTAA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
2592146 GATTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2598494 original size:18 final size:18
Alignment explanation
Indices: 2598471--2598505 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2598461 ATAAATATTT
2598471 TTATATTTTTAATAATTC
1 TTATATTTTTAATAATTC
*
2598489 TTATATTTTTAGTAATT
1 TTATATTTTTAATAATT
2598506 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
TTATATTTTTAATAATTC
Found at i:2603194 original size:15 final size:15
Alignment explanation
Indices: 2603174--2603205 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2603164 ATACAAACGC
2603174 ACAACTAGAAACAGT
1 ACAACTAGAAACAGT
*
2603189 ACAACTGGAAACAGT
1 ACAACTAGAAACAGT
2603204 AC
1 AC
2603206 TTTCACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (15 bp):
ACAACTAGAAACAGT
Found at i:2605294 original size:18 final size:19
Alignment explanation
Indices: 2605271--2605307 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2605261 ACATAAGAAA
2605271 TGAATGT-TAGTTGAAAAG
1 TGAATGTATAGTTGAAAAG
2605289 TGAATGTGATAGTTGAAAA
1 TGAATGT-ATAGTTGAAAA
2605308 TAAACCACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (19 bp):
TGAATGTATAGTTGAAAAG
Found at i:2607206 original size:13 final size:12
Alignment explanation
Indices: 2607184--2607225 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
2607174 TTTCTAAATT
*
2607184 TATTTTTTTTAAA
1 TATTTATTTT-AA
2607197 TATTTATTTT-A
1 TATTTATTTTAA
*
2607208 TATTTATTTTAT
1 TATTTATTTTAA
2607220 TATTTA
1 TATTTA
2607226 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 11 0.42
12 6 0.23
13 9 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTTATTTTAA
Found at i:2607212 original size:11 final size:11
Alignment explanation
Indices: 2607196--2607225 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2607186 TTTTTTTTAA
2607196 ATATTTATTTT
1 ATATTTATTTT
2607207 ATATTTATTTT
1 ATATTTATTTT
2607218 ATTATTTA
1 A-TATTTA
2607226 ATAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATATTTATTTT
Found at i:2609109 original size:25 final size:25
Alignment explanation
Indices: 2609067--2609114 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
2609057 TTCCTTAATG
* *
2609067 ATTTTTAATGAATATTATTGTTTTTC
1 ATTTTAAATAAATATTATT-TTTTTC
2609093 ATTTTAAATAAAT-TTATTTTTT
1 ATTTTAAATAAATATTATTTTTT
2609115 ATAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 5 0.25
26 11 0.55
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (25 bp):
ATTTTAAATAAATATTATTTTTTTC
Found at i:2609132 original size:25 final size:25
Alignment explanation
Indices: 2609067--2609132 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
2609057 TTCCTTAATG
*
2609067 ATTTTTAATGAATATTATTGTTTTTC
1 ATTTTTAATGAAT-TTATTGTTTTTA
* *
2609093 ATTTTAAATAAATTTATT-TTTTATA
1 ATTTTTAATGAATTTATTGTTTT-TA
*
2609118 ATTTTTAATGGATTT
1 ATTTTTAATGAATTT
2609133 CATGAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 4 0.12
25 18 0.55
26 11 0.33
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
ATTTTTAATGAATTTATTGTTTTTA
Found at i:2614117 original size:3 final size:3
Alignment explanation
Indices: 2614109--2614136 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2614099 GGGAGGAAGT
2614109 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2614137 AAATTTACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2620171 original size:24 final size:24
Alignment explanation
Indices: 2620143--2620219 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
2620133 ATAAGATAAC
* * *
2620143 TTAAAATAATAATACCTAATAGCT
1 TTAAAACAATAATACATAATAGAT
* * *
2620167 TTAAAACAACAATACATAATAAAA
1 TTAAAACAATAATACATAATAGAT
*
2620191 TTAAAACAATTATACATAATAGAT
1 TTAAAACAATAATACATAATAGAT
2620215 TTAAA
1 TTAAA
2620220 TGAATGTACA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (24 bp):
TTAAAACAATAATACATAATAGAT
Found at i:2621216 original size:22 final size:25
Alignment explanation
Indices: 2621185--2621239 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
2621175 AAAAAGTGTA
2621185 TTTTCGTTTTT-CTCTTATTT-TCT
1 TTTTCGTTTTTGCTCTTATTTCTCT
*
2621208 TTTTC-TTTTTGCTGTTATTTCTCT
1 TTTTCGTTTTTGCTCTTATTTCTCT
2621232 TTTTCGTT
1 TTTTCGTT
2621240 CCTTTTTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 5 0.18
23 13 0.46
24 8 0.29
25 2 0.07
ACGTcount: A:0.04, C:0.16, G:0.07, T:0.73
Consensus pattern (25 bp):
TTTTCGTTTTTGCTCTTATTTCTCT
Found at i:2623358 original size:18 final size:17
Alignment explanation
Indices: 2623326--2623359 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2623316 GATTTCATGA
*
2623326 ATTTTTTTATTTTTTGT
1 ATTTTTTTATGTTTTGT
2623343 ATTTTTTTGATGTTTTG
1 ATTTTTTT-ATGTTTTG
2623360 AAAAAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (17 bp):
ATTTTTTTATGTTTTGT
Found at i:2625261 original size:42 final size:42
Alignment explanation
Indices: 2625202--2625296 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
2625192 AATTAAAGTT
*
2625202 AGCTGCTGTTTGAAGTCTTTTAGGTGACCATTCAGTCAAGGG
1 AGCTGCTGTTTGAAGTCTTTTAGGTGACCATTCAGCCAAGGG
*
2625244 AGCTGTTGTTTGAAGTCTTTTAGGTGACCATTCAGCCAAGGG
1 AGCTGCTGTTTGAAGTCTTTTAGGTGACCATTCAGCCAAGGG
2625286 AGCTGCTGTTT
1 AGCTGCTGTTT
2625297 CATGCTTCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (42 bp):
AGCTGCTGTTTGAAGTCTTTTAGGTGACCATTCAGCCAAGGG
Found at i:2635871 original size:41 final size:42
Alignment explanation
Indices: 2635784--2635870 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
2635774 CCATTTTTTC
2635784 TTTTCGTATTTTATGTTTTCTTAAATAAATTTTTTTGTCATT
1 TTTTCGTATTTTATGTTTTCTTAAATAAATTTTTTTGTCATT
*
2635826 TTTTCGTATTTTATGTTTTCTTAAATAATTTTTTTTGTCATT
1 TTTTCGTATTTTATGTTTTCTTAAATAAATTTTTTTGTCATT
2635868 TTT
1 TTT
2635871 CTTTTAATGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (42 bp):
TTTTCGTATTTTATGTTTTCTTAAATAAATTTTTTTGTCATT
Found at i:2636138 original size:28 final size:31
Alignment explanation
Indices: 2636093--2636154 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 31
2636083 AAAATACCCT
2636093 TTTTTTTTTCCTTCCTTC-CCTCTTCTTCTTC
1 TTTTTTTTTCCTTCCTTCTCCT-TTCTTCTTC
*
2636124 TTTTTTTTT-C-T-CTTCTCCTTTCTTTTTC
1 TTTTTTTTTCCTTCCTTCTCCTTTCTTCTTC
2636152 TTT
1 TTT
2636155 CCTTCTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 15 0.52
29 4 0.14
30 1 0.03
31 9 0.31
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (31 bp):
TTTTTTTTTCCTTCCTTCTCCTTTCTTCTTC
Found at i:2636143 original size:34 final size:34
Alignment explanation
Indices: 2636091--2636256 Score: 117
Period size: 39 Copynumber: 4.7 Consensus size: 34
2636081 AAAAAATACC
* * *
2636091 CTTTTTTTTT-TCCT-TCCTTCCCTCTTCTTCTT
1 CTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTCTT
*
2636123 CTTTTTTTTTCTCTTCTCCTTTCTTTTTCTTTCCTT
1 CTTTTTTTTTCTCTTCTCCTTTCCTTTTC-TT-CTT
*
2636159 CTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTT
1 C-TT-TTT-TTTTCTCTTCTCCTTTCCTTTTCTTCTT
* * *
2636196 CTTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTCTT
1 CTTT-TTT-TTTC-TCTTCTC-CTT-TCCTTTTCTTCTT
2636235 -TTTCTTTCTTTC-C-TCTCCTTTC
1 CTTT-TTT-TTTCTCTTCTCCTTTC
2636257 TTTCTTTCTT
Statistics
Matches: 110, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
32 10 0.09
33 5 0.05
34 13 0.12
35 7 0.06
36 11 0.10
37 11 0.10
38 20 0.18
39 33 0.30
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (34 bp):
CTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTCTT
Found at i:2636148 original size:4 final size:4
Alignment explanation
Indices: 2636121--2636280 Score: 108
Period size: 4 Copynumber: 40.8 Consensus size: 4
2636111 CCTCTTCTTC
* *
2636121 TTCT TT-T TT-T TTCT CTTC- TCCT TTC- TT-T TTCT TTCC TTCT TTCT
1 TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
2636165 TTCT TT-T TTCT TCTCCT TTCCT TT-T CTTC- TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT T-T-CT TT-CT TTCT -TTCT TTCT TTCT TTCT TTCT
* * * *
2636210 TTTT TTCT CTTC- TCCT TTCC TTC- TT-T TTCT TTCT TTCCT CTCCT TTCT
1 TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-CT -TTCT TTCT
*
2636258 TTCT TTCT TTCC TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTC
2636281 CCTCTCCTTC
Statistics
Matches: 126, Mismatches: 13, Indels: 34
0.73 0.08 0.20
Matches are distributed among these distances:
3 25 0.20
4 80 0.63
5 17 0.13
6 4 0.03
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:2636177 original size:39 final size:40
Alignment explanation
Indices: 2636117--2636280 Score: 170
Period size: 39 Copynumber: 4.3 Consensus size: 40
2636107 CTTCCCTCTT
*
2636117 CTTC-TTCTTT-TTTTTTCTCTTCTCCTTTCTTTTTCTTTC
1 CTTCTTTCTTTCTTTCTT-TCTTCTCCTTTCTTTTTCTTTC
*
2636156 CTTCTTTCTTTCTTT-TTTCTTCTCCTTTCCTTTTC-TT-
1 CTTCTTTCTTTCTTTCTTTCTTCTCCTTTCTTTTTCTTTC
* * *
2636193 CTTCTTTCTTTCTTTCTTT-TT-T--TCTCTTCTCCTTTC
1 CTTCTTTCTTTCTTTCTTTCTTCTCCTTTCTTTTTCTTTC
*
2636229 CTTC-TT-TTTCTTTCTTTCCTCTCCTTTCTTTCTTTCTTTC
1 CTTCTTTCTTTCTTTCTTTCTTCTCCTTTC-TT-TTTCTTTC
2636269 CTTCTTTCTTTC
1 CTTCTTTCTTTC
2636281 CCTCTCCTTC
Statistics
Matches: 103, Mismatches: 9, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
34 17 0.17
35 5 0.05
36 6 0.06
37 17 0.17
38 8 0.08
39 23 0.22
40 18 0.17
41 5 0.05
42 4 0.04
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (40 bp):
CTTCTTTCTTTCTTTCTTTCTTCTCCTTTCTTTTTCTTTC
Found at i:2636234 original size:42 final size:41
Alignment explanation
Indices: 2636126--2636280 Score: 162
Period size: 44 Copynumber: 3.8 Consensus size: 41
2636116 TCTTCTTCTT
*
2636126 TTTTTTTCTCTTCTCCTTT-C-T-TTTTCTTTCCTTCTTTC
1 TTTTTTTCTCTTCTCCTTTCCTTCTTTTCTTTCTTTCTTTC
*
2636164 TTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTTCTTTCTTTCTTTC
1 TTT-TTTTCTCTTCTCCTTTCC--TTCTT-TTCTTTCTTTCTTTC
*
2636209 TTTTTTTCTCTTCTCCTTTCCTTCTTTTTCTTTCTTTCCTCTC
1 TTTTTTTCTCTTCTCCTTTCCTTC-TTTTCTTTCTTT-CTTTC
* *
2636252 CTTTCTT-TCTT-T-CTTTCCTTC-TTTCTTTC
1 TTTTTTTCTCTTCTCCTTTCCTTCTTTTCTTTC
2636281 CCTCTCCTTC
Statistics
Matches: 102, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
38 11 0.11
39 15 0.15
40 10 0.10
41 1 0.01
42 17 0.17
43 12 0.12
44 19 0.19
45 17 0.17
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (41 bp):
TTTTTTTCTCTTCTCCTTTCCTTCTTTTCTTTCTTTCTTTC
Found at i:2636278 original size:83 final size:76
Alignment explanation
Indices: 2636090--2636278 Score: 200
Period size: 83 Copynumber: 2.4 Consensus size: 76
2636080 AAAAAAATAC
* * ** *
2636090 CCTTTTTTTTTTCCTTCCTTCCCTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCTTTTTCTTT
1 CCTTTTTTCTTTCTTTCCTTCTTTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCTTCTTCTTT
2636155 CCTTCTTTCTT
66 CCTTCTTTCTT
* *
2636166 TCTTTTTTCTTCTCCTTTCCTTTTCTTCTTCTTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCT
1 CCTTTTTTCTT-T-CTTTCCTTCT-TTCTTC-TTC-TTC-TT-TTTTTTTCTCTTCTCCTTT-CT
*
2636231 TCTT-TTTCTTTCTTTCCTCT
58 TCTTCTTTCCTTCTTT-CT-T
2636251 CCTTTCTTTCTTTCTTTCCTTCTTTCTT
1 CCTTT-TTTCTTTCTTTCCTTCTTTCTT
2636279 TCCCTCTCCT
Statistics
Matches: 92, Mismatches: 10, Indels: 15
0.79 0.09 0.13
Matches are distributed among these distances:
76 9 0.10
77 1 0.01
78 7 0.08
79 5 0.05
80 3 0.03
81 3 0.03
82 2 0.02
83 34 0.37
84 16 0.17
85 6 0.07
86 6 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (76 bp):
CCTTTTTTCTTTCTTTCCTTCTTTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCTTCTTCTTT
CCTTCTTTCTT
Found at i:2636361 original size:27 final size:27
Alignment explanation
Indices: 2636323--2636392 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
2636313 CCCTAATAAA
2636323 CATTGGTGCCGCCAATGG-TATTGGCAC
1 CATTGGTGCCGCCAATGGCT-TTGGCAC
2636350 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
2636377 CTTTGGTGCCGCCAAT
1 CATTGGTGCCGCCAAT
2636393 CCCATTGGCG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGCAC
Found at i:2636400 original size:27 final size:27
Alignment explanation
Indices: 2636323--2636401 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
2636313 CCCTAATAAA
*
2636323 CATTGGTGCCGCCAATGGTATTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
*
2636350 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
* **
2636377 CTTTGGTGCCGCCAATCCCATTGGC
1 CATTGGTGCCGCCAATGGCATTGGC
2636402 GTGACCAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCATTGGCAC
Found at i:2636480 original size:23 final size:23
Alignment explanation
Indices: 2636454--2636498 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2636444 GTTTTTTTTG
*
2636454 ATATATTTTGGTAAATAAAAAAT
1 ATATATTTTAGTAAATAAAAAAT
2636477 ATATATTTTAGTAAATAAAAAA
1 ATATATTTTAGTAAATAAAAAA
2636499 AAGTTATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATATTTTAGTAAATAAAAAAT
Found at i:2642882 original size:15 final size:16
Alignment explanation
Indices: 2642862--2642893 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2642852 ATGTAAACAG
2642862 ATTTGAAAAT-AATGA
1 ATTTGAAAATGAATGA
2642877 ATTTGAAAATGAATGA
1 ATTTGAAAATGAATGA
2642893 A
1 A
2642894 AAGGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (16 bp):
ATTTGAAAATGAATGA
Found at i:2643209 original size:19 final size:19
Alignment explanation
Indices: 2643185--2643238 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
2643175 AATCATATCT
*
2643185 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
2643204 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2643223 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
2643239 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2644899 original size:104 final size:105
Alignment explanation
Indices: 2644606--2645081 Score: 811
Period size: 105 Copynumber: 4.6 Consensus size: 105
2644596 TAGCCGTTAT
** *
2644606 TGGTGGATCCCGCACTTAGCACCACCACTG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
2644670 GAATCAGCACATAGCAA-CCCCCTTTTTATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
2644709 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
2644773 GAATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
2644813 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
2644878 GAATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
2644918 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
2644983 GAATCAGCACATAGCAA-CCCCCTTTCACATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCCCTTT-TCATTTCAAAGATA
* * **
2645023 TGGTGGATCA-CGCACATAGCACCACCCAT-AAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCT
2645082 TTTATATACA
Statistics
Matches: 360, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
103 78 0.22
104 87 0.24
105 194 0.54
106 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
GAATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
Found at i:2645443 original size:29 final size:29
Alignment explanation
Indices: 2645410--2645473 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
2645400 TAATCCACCA
2645410 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
2645439 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
2645469 CCCAA
1 CCCAA
2645474 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:2645447 original size:30 final size:30
Alignment explanation
Indices: 2645417--2645473 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2645407 CCACCCAACT
2645417 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
2645446 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
2645474 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:2646952 original size:88 final size:88
Alignment explanation
Indices: 2646841--2647191 Score: 542
Period size: 88 Copynumber: 4.0 Consensus size: 88
2646831 GATAAGACTG
* * * * * * *
2646841 GTGTCTTCGATCTACTTCGCTGTCGGTGCATGAAGGCAAAATCTGCTATCTTCAAACTGCTCCGC
1 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGC
2646906 TGCAACCCAGGGAGGCAAGGCTA
66 TGCAACCCAGGGAGGCAAGGCTA
* *
2646929 GTGTCTTCGATCTGCTTCACTGTCAGTATAGGAAGGCAAGATCTGCTATCTTCAGCCTGCTCCGC
1 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGC
2646994 TGCAACCCAGGGAGGCAAGGCTA
66 TGCAACCCAGGGAGGCAAGGCTA
* *
2647017 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGC
1 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGC
*
2647082 TGCAACCCAGGGAGGCAACGCTA
66 TGCAACCCAGGGAGGCAAGGCTA
* * *
2647105 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAATGG-AAGATCTGCTATTTTCAGCTTGCTCCG
1 GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAA-GGCAAGATCTGCTATCTTCAACCTGCTCCG
*
2647169 CTGCAACTCAGGGAGGCAAGGCT
65 CTGCAACCCAGGGAGGCAAGGCT
2647192 TTGTGATTTT
Statistics
Matches: 247, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
88 245 0.99
89 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.26
Consensus pattern (88 bp):
GTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCGC
TGCAACCCAGGGAGGCAAGGCTA
Found at i:2646966 original size:44 final size:44
Alignment explanation
Indices: 2646913--2647138 Score: 158
Period size: 44 Copynumber: 5.1 Consensus size: 44
2646903 CGCTGCAACC
*
2646913 CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
* * * * * * ***
2646957 TAGGAAGGCAAGATCT-GCTATCTTC-AGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTAG-TGTCTTCGA-TCTGCTTCACTGTCAGTA
*
2647001 CAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
* * * * * * ***
2647045 CAGGAAGGCAAGATCT-GCTATTTTC-AGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTAG-TGTCTTCGA-TCTGCTTCACTGTCAGTA
* *
2647089 CAGGGAGGCAACGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
2647133 CAGGAA
1 CAGGAA
2647139 TGGAAGATCT
Statistics
Matches: 128, Mismatches: 42, Indels: 24
0.66 0.22 0.12
Matches are distributed among these distances:
43 33 0.26
44 62 0.48
45 33 0.26
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTA
Found at i:2648012 original size:28 final size:28
Alignment explanation
Indices: 2647955--2648018 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
2647945 GATTTCGCGG
*
2647955 AAAATGGCCCATTCCGGTAAATAATCAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
* *
2647983 AAAATCGGCCCATTTCGGTAAAT-TTAAA
1 AAAAT-GGCCCATTCCGGTAAATAATAAA
2648011 AAAATGGC
1 AAAATGGC
2648019 TTTTTTTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 3 0.09
28 13 0.41
29 16 0.50
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:2651406 original size:15 final size:16
Alignment explanation
Indices: 2651374--2651414 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2651364 ATCTTTATAC
*
2651374 TTTA-ATTTTGTTATT
1 TTTAGATTTTGTTAAT
2651389 TTTAGATTTT-TTAAT
1 TTTAGATTTTGTTAAT
2651404 TTTAGAATTTT
1 TTTAG-ATTTT
2651415 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (16 bp):
TTTAGATTTTGTTAAT
Found at i:2655238 original size:103 final size:101
Alignment explanation
Indices: 2655120--2655450 Score: 461
Period size: 102 Copynumber: 3.2 Consensus size: 101
2655110 CCAGTGATTC
*
2655120 GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
2655185 ACCAATGATTCGGAGAATCAGCACTTAGCAACCCCTT
66 ACCAATGATTCGG-GAATCAGCACTTAGCAACCCCTT
* * * *
2655222 AGGGGAATCAGCACTTAGCAACCCCATTCACATTTAAA-ATACGGTGGGATCAGCACTTAGCAAC
1 -GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAAC
* *
2655286 CACCAATGAATCGGGGAATCAGCACTTAGCAATCCCTT
65 CACCAATGATTC-GGGAATCAGCACTTAGCAACCCCTT
* * * *
2655324 TGGGAATCAACACTTAGCAACCCCCTTT-ATATTCAAAGATACGGTGGAATCAGCATTTTGCAAC
1 GGGGAATCAACACTTAGCAA-CCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAAC
* *
2655388 CACCAATGAGTTAGGGAATCAGCACCTAGCAACCCCTT
65 CACCAATGA-TTCGGGAATCAGCACTTAGCAACCCCTT
2655426 GGGGGAATCAGA-ACTTAGCAACCCC
1 -GGGGAATCA-ACACTTAGCAACCCC
2655451 CTTTATATTC
Statistics
Matches: 202, Mismatches: 20, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
101 25 0.12
102 122 0.60
103 54 0.27
104 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (101 bp):
GGGGAATCAACACTTAGCAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGATTCGGGAATCAGCACTTAGCAACCCCTT
Found at i:2680288 original size:74 final size:74
Alignment explanation
Indices: 2680167--2680313 Score: 294
Period size: 74 Copynumber: 2.0 Consensus size: 74
2680157 ACAGGCTCCA
2680167 CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
1 CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
2680232 TTTATCTTG
66 TTTATCTTG
2680241 CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
1 CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
2680306 TTTATCTT
66 TTTATCTT
2680314 TCTTATGTAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (74 bp):
CCTAACACTGGTCATTACAGCAACGGTCTGTTGTTGGATGATGTAAGTTCATTTCTGCTTTACAT
TTTATCTTG
Found at i:2686203 original size:21 final size:22
Alignment explanation
Indices: 2686172--2686217 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2686162 TTGAATTCAA
* *
2686172 AACCTTAAAACCTCGAGCCTTG
1 AACCTTAAAACCTCGAACATTG
2686194 AACC-TAAAACCTCGAACATTG
1 AACCTTAAAACCTCGAACATTG
2686215 AAC
1 AAC
2686218 ACCGAACACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (22 bp):
AACCTTAAAACCTCGAACATTG
Found at i:2686768 original size:23 final size:25
Alignment explanation
Indices: 2686742--2686787 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2686732 TATTACCTAT
2686742 TAGATCAT-ATAT-ATTTTTAAAAA
1 TAGATCATAATATAATTTTTAAAAA
*
2686765 TAGATCATAATTTAATTTTTAAA
1 TAGATCATAATATAATTTTTAAA
2686788 TCATAGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 3 0.15
25 9 0.45
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (25 bp):
TAGATCATAATATAATTTTTAAAAA
Found at i:2691699 original size:2 final size:2
Alignment explanation
Indices: 2691694--2691729 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2691684 CTCTCTCCTC
2691694 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
2691730 TATGATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2692267 original size:18 final size:17
Alignment explanation
Indices: 2692235--2692273 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2692225 AATTTTTAAT
* *
2692235 TTATAAATTATAAAAGA
1 TTATAAATAATAAAAAA
2692252 TTATAAATAAATAAAAAA
1 TTATAAAT-AATAAAAAA
2692270 TTAT
1 TTAT
2692274 TTTAGGACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTATAAATAATAAAAAA
Found at i:2694047 original size:48 final size:48
Alignment explanation
Indices: 2693976--2694094 Score: 195
Period size: 48 Copynumber: 2.5 Consensus size: 48
2693966 TTATGGAAAA
*
2693976 TTATATGAGTGCTAGATAGGAGCAGTACAATATTGGTTTGAACTCGTG
1 TTATATAAGTGCTAGATAGGAGCAGTACAATATTGGTTTGAACTCGTG
*
2694024 TTATATAAGTGCTAGATAGGAGCATTACAATATTGGTTTGAACTCGTG
1 TTATATAAGTGCTAGATAGGAGCAGTACAATATTGGTTTGAACTCGTG
*
2694072 TTATTTAAGTGTCT-GATAGGAGC
1 TTATATAAGTG-CTAGATAGGAGC
2694095 TTTAATAATC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 65 0.97
49 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (48 bp):
TTATATAAGTGCTAGATAGGAGCAGTACAATATTGGTTTGAACTCGTG
Found at i:2705834 original size:16 final size:17
Alignment explanation
Indices: 2705795--2705844 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
2705785 AATCAAAATA
2705795 AAAAAAGAATAATAAGAGT
1 AAAAAA-AA-AATAAGAGT
*
2705814 AAAAACAAAATAAGA-T
1 AAAAAAAAAATAAGAGT
*
2705830 AAAAAAAAAACAAGA
1 AAAAAAAAAATAAGA
2705845 CAAACTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.50
17 7 0.25
18 2 0.07
19 5 0.18
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAATAAGAGT
Found at i:2708589 original size:2 final size:2
Alignment explanation
Indices: 2708582--2708618 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2708572 GGATGCAGTA
2708582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2708619 CATGATACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2715453 original size:20 final size:19
Alignment explanation
Indices: 2715399--2715456 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
2715389 TGTCAATTCA
2715399 AAAATAATTAAATAAATTATT
1 AAAAT-ATTAAA-AAATTATT
* *
2715420 AAAAAATAATAAAAATTAATT
1 AAAATATTA-AAAAATT-ATT
2715441 AAAATATTAAAAAATT
1 AAAATATTAAAAAATT
2715457 TATGAACTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATTAAAAAATTATT
Found at i:2717663 original size:30 final size:30
Alignment explanation
Indices: 2717619--2717681 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2717609 GCTTAACAAG
2717619 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
2717649 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
2717679 CAA
1 CAA
2717682 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:2724027 original size:31 final size:31
Alignment explanation
Indices: 2723970--2724029 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2723960 GGAGGTGGAA
*
2723970 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
2724001 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
2724030 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:2724257 original size:9 final size:9
Alignment explanation
Indices: 2724243--2724279 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2724233 TATAGTTTGA
2724243 TATTCGAAT
1 TATTCGAAT
2724252 TATTCGAAT
1 TATTCGAAT
*
2724261 TATTCGAGT
1 TATTCGAAT
2724270 TATTCGAAT
1 TATTCGAAT
2724279 T
1 T
2724280 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:2730078 original size:21 final size:21
Alignment explanation
Indices: 2730052--2730092 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2730042 GCCTAAAATT
* *
2730052 TGAATTTGATTGAATTGAATA
1 TGAATTTCATTAAATTGAATA
2730073 TGAATTTCATTAAATTGAAT
1 TGAATTTCATTAAATTGAAT
2730093 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (21 bp):
TGAATTTCATTAAATTGAATA
Found at i:2732837 original size:18 final size:17
Alignment explanation
Indices: 2732814--2732852 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2732804 TTTTATAAAT
2732814 TGTGAATT-ATATCTGATA
1 TGTGAATTAATAT-TGA-A
2732832 TGTGAATTAATATTGAA
1 TGTGAATTAATATTGAA
2732849 TGTG
1 TGTG
2732853 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.44
Consensus pattern (17 bp):
TGTGAATTAATATTGAA
Found at i:2733095 original size:23 final size:23
Alignment explanation
Indices: 2733064--2733139 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
2733054 AGTGTTATTG
2733064 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
2733087 TTCAGTGGTAGCTACGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2733110 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2733133 ATCAGTG
1 ATCAGTG
2733140 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2736264 original size:21 final size:23
Alignment explanation
Indices: 2736238--2736287 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2736228 TTTTTTGCTA
2736238 TATTAT-ATTA-T-TTGTTATTAT
1 TATTATGATTATTGTTGTTA-TAT
2736259 TATTATGATTATTGTTGTTATAT
1 TATTATGATTATTGTTGTTATAT
2736282 TATTAT
1 TATTAT
2736288 TATACTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.23
22 4 0.15
23 10 0.38
24 6 0.23
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (23 bp):
TATTATGATTATTGTTGTTATAT
Found at i:2736498 original size:21 final size:21
Alignment explanation
Indices: 2736474--2736514 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
2736464 ATATTTTACA
2736474 TTTTATACATATATATATATAT
1 TTTTATA-ATATATATATATAT
2736496 TTTTATAATATATATATAT
1 TTTTATAATATATATATAT
2736515 TCATACACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATAATATATATATATAT
Found at i:2738661 original size:25 final size:25
Alignment explanation
Indices: 2738627--2738676 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2738617 TACATATTGT
* *
2738627 ATATATAAAT-AATTATATTTATTTA
1 ATATAAAAATAAATTA-ATGTATTTA
2738652 ATATAAAAATAAATTAATGTATTTA
1 ATATAAAAATAAATTAATGTATTTA
2738677 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATATAAAAATAAATTAATGTATTTA
Found at i:2747564 original size:29 final size:27
Alignment explanation
Indices: 2747498--2747564 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
2747488 GAGTCTCACG
*
2747498 TGTATAATTGCATCAAATTAAGATTTA
1 TGTATAATTGCATCAAATTAAAATTTA
*
2747525 TGTATACAATTGTACATTAAATTAAAATTTA
1 TGTAT--AATTG--CATCAAATTAAAATTTA
2747556 TGTATAATT
1 TGTATAATT
2747565 TAGAACTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 9 0.26
31 20 0.59
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (27 bp):
TGTATAATTGCATCAAATTAAAATTTA
Found at i:2747953 original size:14 final size:14
Alignment explanation
Indices: 2747934--2747960 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2747924 GTGACTAAAT
2747934 TATAAATTTTAACA
1 TATAAATTTTAACA
2747948 TATAAATTTTAAC
1 TATAAATTTTAAC
2747961 TTGAGGATGT
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TATAAATTTTAACA
Found at i:2754338 original size:74 final size:74
Alignment explanation
Indices: 2754217--2754370 Score: 290
Period size: 74 Copynumber: 2.1 Consensus size: 74
2754207 TTCTTTATAC
2754217 GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
1 GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
*
2754282 CATTTAAGG
66 CATCTAAGG
2754291 GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
1 GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
2754356 CATCTAAGG
66 CATCTAAGG
*
2754365 GTGAGT
1 GAGAGT
2754371 AAACTTAAAC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (74 bp):
GAGAGTGGTCAATTGGATTCTCTTGTATTAATTTATTTTGTTCGGTACACTAAGTGGATATGTGT
CATCTAAGG
Found at i:2760306 original size:2 final size:2
Alignment explanation
Indices: 2760299--2760325 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2760289 TTTGTTTGTT
2760299 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 T
2760326 TTGTATATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2762837 original size:38 final size:38
Alignment explanation
Indices: 2762786--2762862 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
2762776 CTCAATTTCA
*
2762786 ACTTCAACTCAACCATGAGAGTCATGTTCATTTTTACT
1 ACTTCAACTCAACCATGAGAATCATGTTCATTTTTACT
*
2762824 ACTTCAGCTCAACCATGAGAATCATGTTCATTTTTACT
1 ACTTCAACTCAACCATGAGAATCATGTTCATTTTTACT
2762862 A
1 A
2762863 GGAAATAGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (38 bp):
ACTTCAACTCAACCATGAGAATCATGTTCATTTTTACT
Found at i:2770088 original size:31 final size:31
Alignment explanation
Indices: 2770053--2770112 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2770043 CTACTTTTGA
*
2770053 CAATTAATCTTCGAAGTATAATATAATAAAC
1 CAATTAATCTACGAAGTATAATATAATAAAC
*
2770084 CAATTCATCTACGAAGTATAATATAATAA
1 CAATTAATCTACGAAGTATAATATAATAA
2770113 TCTATCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (31 bp):
CAATTAATCTACGAAGTATAATATAATAAAC
Found at i:2776749 original size:15 final size:14
Alignment explanation
Indices: 2776729--2776769 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
2776719 TAGACTTTGC
2776729 TTTCTTTTTTTTCTT
1 TTTCTTTTTTTT-TT
2776744 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
*
2776758 TTGACTTTTTTT
1 TT-TCTTTTTTT
2776770 GTTATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.85
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:2781285 original size:15 final size:15
Alignment explanation
Indices: 2781265--2781298 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2781255 TTAATCATAA
2781265 TTAATTAATAAAAAC
1 TTAATTAATAAAAAC
* *
2781280 TTAATTAATTAAACC
1 TTAATTAATAAAAAC
2781295 TTAA
1 TTAA
2781299 GTGTAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAATTAATAAAAAC
Found at i:2783570 original size:32 final size:32
Alignment explanation
Indices: 2783514--2783574 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2783504 CTTAGGCAAC
* *
2783514 TTTGGCTAATGAAAAAGCGGCACATGGCATGT
1 TTTGGCCAATGAAAAAACGGCACATGGCATGT
* *
2783546 TTTGGCCAATGAAAAAATGTCACATGGCA
1 TTTGGCCAATGAAAAAACGGCACATGGCA
2783575 ATTAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (32 bp):
TTTGGCCAATGAAAAAACGGCACATGGCATGT
Found at i:2783799 original size:22 final size:21
Alignment explanation
Indices: 2783756--2783822 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
2783746 CATATATAAT
2783756 ATATATTTTTAAAAATTAAAA
1 ATATATTTTTAAAAATTAAAA
2783777 ATAT-TTTTTATAAAATTTTAAAA
1 ATATATTTTTA-AAAA--TTAAAA
* **
2783800 TATATAATTTTAAATTTTAAAA
1 -ATATATTTTTAAAAATTAAAA
2783822 A
1 A
2783823 GTCAAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 6 0.16
21 9 0.24
22 6 0.16
23 6 0.16
24 6 0.16
25 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATATTTTTAAAAATTAAAA
Found at i:2783850 original size:21 final size:19
Alignment explanation
Indices: 2783826--2783869 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2783816 TTAAAAAGTC
2783826 AAAATAATA-TATAAAAATT
1 AAAA-AATATTATAAAAATT
*
2783845 AAAAAATGTTATAAAAATT
1 AAAAAATATTATAAAAATT
2783864 AAAAAA
1 AAAAAA
2783870 AGGTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAATATTATAAAAATT
Found at i:2783882 original size:19 final size:19
Alignment explanation
Indices: 2783835--2783875 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2783825 CAAAATAATA
* *
2783835 TATAAAAATTAAAAAATGT
1 TATAAAAATTAAAAAAAGG
2783854 TATAAAAATTAAAAAAAGG
1 TATAAAAATTAAAAAAAGG
2783873 TAT
1 TAT
2783876 TTAAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
TATAAAAATTAAAAAAAGG
Done.