Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold9
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: 3883850
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 144036 characters in sequence are not A, C, G, or T
File 19 of 24
Found at i:2821007 original size:28 final size:28
Alignment explanation
Indices: 2820554--2821001 Score: 412
Period size: 28 Copynumber: 15.5 Consensus size: 28
2820544 CACTAACTTG
* *
2820554 TGTGGGCTTTGAAAAGAGTTGCCACCGACTT
1 TGTGGGCTTTG-AAAG-GATGCCACTGAC-T
*
2820585 GTGTGGGCTTTAAAAGGGGATGCCACTGACT
1 -TGTGGGCTTTGAAA--GGATGCCACTGACT
* * * *
2820616 TGTAGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2820644 TGTGAGCTTTGGAAAGG-TGCCACTGATTT
1 TGTGGGCTTT-GAAAGGATGCCACTGA-CT
* *
2820673 GTGTGGGATTTGAAAGGGTATGCCACTAACT
1 -TGTGGGCTTTGAAA-GG-ATGCCACTGACT
* *
2820704 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
**
2820732 TGTGGGCTTTGAAAGGATGCCACAAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
2820760 TGTGGTCTTTTGAAAAGATGACACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* *
2820789 TGTGGGCTTTGGAAAGAGTTGCCACCGACTT
1 TGTGGGCTTT-GAAAG-GATGCCACTGAC-T
* * *
2820820 GTGTGGGCTTTGAAAGGGTGCCACCGAGT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2820849 TATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2820877 TGTGGGCTTTTAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
2820905 TATGGGCTTTGAAAGGATACCATTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
2820933 TGTGAGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
2820961 TGTGAGCTTTAAAAGGATGCCACTGACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
2820989 TGTGGGTTTTGAA
1 TGTGGGCTTTGAA
2821002 GAGATGAACG
Statistics
Matches: 349, Mismatches: 54, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
28 204 0.58
29 40 0.11
30 55 0.16
31 11 0.03
32 38 0.11
33 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:2836249 original size:20 final size:20
Alignment explanation
Indices: 2836224--2836261 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2836214 TTTTAACTAG
2836224 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
*
2836244 ATGTATCGATATATTATT
1 ATGTATCGATACATTATT
2836262 GATACATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTATTCA
Found at i:2836318 original size:20 final size:20
Alignment explanation
Indices: 2836289--2836399 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
2836279 AGACAAAATA
*
2836289 TATCGTTACATTAAAGAATG
1 TATCGATACATTAAAGAATG
* *
2836309 TATCGATACATTCATA-CATG
1 TATCGATACATT-AAAGAATG
* *
2836329 TATCGATACATTGAAGAATA
1 TATCGATACATTAAAGAATG
* *
2836349 TATCGATACATTCATA-CATG
1 TATCGATACATT-AAAGAATG
* *
2836369 TATCGATACATTGAAGAATA
1 TATCGATACATTAAAGAATG
*
2836389 TTTCGATACAT
1 TATCGATACAT
2836400 CTGGGTGAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.03
20 66 0.93
21 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (20 bp):
TATCGATACATTAAAGAATG
Found at i:2836333 original size:40 final size:40
Alignment explanation
Indices: 2836289--2836399 Score: 186
Period size: 40 Copynumber: 2.8 Consensus size: 40
2836279 AGACAAAATA
* * *
2836289 TATCGTTACATTAAAGAATGTATCGATACATTCATACATG
1 TATCGATACATTGAAGAATATATCGATACATTCATACATG
2836329 TATCGATACATTGAAGAATATATCGATACATTCATACATG
1 TATCGATACATTGAAGAATATATCGATACATTCATACATG
*
2836369 TATCGATACATTGAAGAATATTTCGATACAT
1 TATCGATACATTGAAGAATATATCGATACAT
2836400 CTGGGTGAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (40 bp):
TATCGATACATTGAAGAATATATCGATACATTCATACATG
Found at i:2845128 original size:19 final size:20
Alignment explanation
Indices: 2845086--2845129 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2845076 TTAACATATA
*
2845086 CAAAACAAATCAAACTTCTT
1 CAAAACAAATCAAAATTCTT
*
2845106 -AAAATAAATCAAAATT-TT
1 CAAAACAAATCAAAATTCTT
2845124 CAAAAC
1 CAAAAC
2845130 TGATTTAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (20 bp):
CAAAACAAATCAAAATTCTT
Found at i:2845502 original size:167 final size:163
Alignment explanation
Indices: 2845167--2845676 Score: 493
Period size: 167 Copynumber: 3.1 Consensus size: 163
2845157 TTAGATGAAA
* * ** * **
2845167 TTTAAAAATTTTAAACTAAGAAAAATCCCCCC-AAAAGCAATTATGGAAA--ATAAAACTGAAT-
1 TTTAAAAATTATAAACAAAGAAAAATCCCCCCGAAAA-C-ATT-TACAAAGTAGAAAACTCTATA
* * *
2845228 TTTTGAAAATAAGAGAATTTCAAAGAAAAATGAAAAATTATGAAAATAAA-TGAAATTTTTAAAA
63 TTTTGAAAACAAGAGAATTTCAAAAAAAAAAGAAAAATTATG-AAATAAAGT-AAATTTTTAAAA
* * * *
2845292 ATGATTTACTATGAATTAAATGATGATATTTGATAAAT
126 ATGAATTAATGTGAATTAAATAATGATATTTGATAAAT
* * * * *
2845330 TTTAAAAATTATAAACTAGGAAAAATCCCCCCGAAAACATTTACAGAGTAGAGAACTCTGTATTT
1 TTTAAAAATTATAAACAAAGAAAAATCCCCCCGAAAACATTTACAAAGTAGAAAACTCTATATTT
*
2845395 TGAAAACAAG-GAAATTTCAAGAAAAAAAAGAAAAGATTTATGAAATAAAGTTAATTTTTAAAAA
66 TGAAAACAAGAG-AATTTCAA-AAAAAAAAGAAAA-A-TTATGAAATAAAGTAAATTTTTAAAAA
* *
2845459 TTGAATTAATGTGAATTAAATAATGATATTTTATGAAT
127 -TGAATTAATGTGAATTAAATAATGATATTTGATAAAT
* * *
2845497 TTTAAAAATTATAAACAAAGAAAAATCCTCCTGAAACCATTTACAAAGTAGAAAACTCTATATTT
1 TTTAAAAATTATAAACAAAGAAAAATCCCCCCGAAAACATTTACAAAGTAGAAAACTCTATATTT
** * * * * *
2845562 CAAAAACATGAGAATTTTAAAAAAAATAA-AAAACTTATGAAATAAAAG-AAATTTTTCACAACT
66 TGAAAACAAGAGAATTTCAAAAAAAA-AAGAAAAATTATGAAAT-AAAGTAAATTTTT-AAAAAT
* *
2845625 G-ATTGAATGGTG-ATTAAGTAATAATATTTGATAAAT
128 GAATT-AAT-GTGAATTAAATAATGATATTTGATAAAT
2845661 TTTAAAAAATT-TAAAC
1 TTT-AAAAATTATAAAC
2845677 CAATGAAATT
Statistics
Matches: 290, Mismatches: 40, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
161 3 0.01
162 3 0.01
163 42 0.14
164 73 0.25
165 28 0.10
166 30 0.10
167 110 0.38
168 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (163 bp):
TTTAAAAATTATAAACAAAGAAAAATCCCCCCGAAAACATTTACAAAGTAGAAAACTCTATATTT
TGAAAACAAGAGAATTTCAAAAAAAAAAGAAAAATTATGAAATAAAGTAAATTTTTAAAAATGAA
TTAATGTGAATTAAATAATGATATTTGATAAAT
Found at i:2847660 original size:33 final size:32
Alignment explanation
Indices: 2847618--2847681 Score: 110
Period size: 33 Copynumber: 2.0 Consensus size: 32
2847608 CAAAAATCCT
2847618 AAGACTCAATCTAGACACCAAGATACTCATTCC
1 AAGACTCAATCTAGACACCAA-ATACTCATTCC
*
2847651 AAGACTCAATCTAGTCACCAAATACTCATTC
1 AAGACTCAATCTAGACACCAAATACTCATTC
2847682 GAATCTAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.39, C:0.30, G:0.08, T:0.23
Consensus pattern (32 bp):
AAGACTCAATCTAGACACCAAATACTCATTCC
Found at i:2848973 original size:25 final size:25
Alignment explanation
Indices: 2848912--2848966 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2848902 GAAAGAACAA
*
2848912 AAAAAATCAAAAAAATCAATGAATC
1 AAAAAATCAAAAAAATCAATAAATC
*
2848937 AAAAAATAAAAAAAATC-ATCAAATC
1 AAAAAATCAAAAAAATCAAT-AAATC
2848962 AAAAA
1 AAAAA
2848967 TCTAAAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.73, C:0.11, G:0.02, T:0.15
Consensus pattern (25 bp):
AAAAAATCAAAAAAATCAATAAATC
Found at i:2848999 original size:13 final size:15
Alignment explanation
Indices: 2848977--2849024 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
2848967 TCTAAAACCA
*
2848977 AAATAAAAAATAATG
1 AAATGAAAAATAATG
2848992 AAA-GAAAAA-AATG
1 AAATGAAAAATAATG
2849005 ATAATGAAAAATGAATG
1 A-AATGAAAAAT-AATG
2849022 AAA
1 AAA
2849025 CGACCAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 9 0.32
16 2 0.07
17 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (15 bp):
AAATGAAAAATAATG
Found at i:2849013 original size:15 final size:14
Alignment explanation
Indices: 2848982--2849024 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
2848972 AACCAAAATA
2848982 AAAAATAATGAAAG
1 AAAAATAATGAAAG
2848996 AAAAA-AATGATAATG
1 AAAAATAATGA-AA-G
2849011 AAAAATGAATGAAA
1 AAAAAT-AATGAAA
2849025 CGACCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 6 0.24
16 2 0.08
17 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (14 bp):
AAAAATAATGAAAG
Found at i:2849585 original size:21 final size:20
Alignment explanation
Indices: 2849542--2849598 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
2849532 AACCTAAAGC
* *
2849542 AGCAACCATCAGCAACCAGT
1 AGCAACCAACAGCAACAAGT
*
2849562 AGCAACCAACAGCATCGAAGT
1 AGCAACCAACAGCAAC-AAGT
*
2849583 AGCAACCAGCAGCAAC
1 AGCAACCAACAGCAAC
2849599 CAACAAACGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.07
Consensus pattern (20 bp):
AGCAACCAACAGCAACAAGT
Found at i:2849598 original size:10 final size:10
Alignment explanation
Indices: 2849539--2849600 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
2849529 AATAACCTAA
2849539 AGCAGCAACC
1 AGCAGCAACC
*
2849549 ATCAGCAACC
1 AGCAGCAACC
*
2849559 AGTAGCAACC
1 AGCAGCAACC
* * *
2849569 AACAGCATCGA
1 AGCAGCAAC-C
*
2849580 AGTAGCAACC
1 AGCAGCAACC
2849590 AGCAGCAACC
1 AGCAGCAACC
2849600 A
1 A
2849601 ACAAACGTAA
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
10 33 0.85
11 6 0.15
ACGTcount: A:0.42, C:0.34, G:0.18, T:0.06
Consensus pattern (10 bp):
AGCAGCAACC
Found at i:2852902 original size:11 final size:11
Alignment explanation
Indices: 2852879--2852927 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
2852869 ATCCTAACTA
*
2852879 TTTTTCT-TAT
1 TTTTTCTCTTT
2852889 TTTTTCTCTTT
1 TTTTTCTCTTT
*
2852900 TTTTCTTTCTTT
1 TTTT-TCTCTTT
*
2852912 TTTCTCTCTTT
1 TTTTTCTCTTT
2852923 TTTTT
1 TTTTT
2852928 TCTGAGTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
10 7 0.22
11 16 0.50
12 9 0.28
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:2852903 original size:12 final size:12
Alignment explanation
Indices: 2852879--2852930 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
2852869 ATCCTAACTA
*
2852879 TTTT-TCTTATT
1 TTTTCTCTTTTT
2852890 TTTTCTCTTTTT
1 TTTTCTCTTTTT
2852902 TTCTT-TC-TTTT
1 TT-TTCTCTTTTT
*
2852913 TTCTCTCTTTTT
1 TTTTCTCTTTTT
2852925 TTTTCT
1 TTTTCT
2852931 GAGTTTCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 12 0.35
12 19 0.56
13 2 0.06
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:2852912 original size:21 final size:22
Alignment explanation
Indices: 2852879--2852930 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2852869 ATCCTAACTA
*
2852879 TTTTTC-TTATTTTTTCTCT-T
1 TTTTTCTTTCTTTTTTCTCTCT
2852899 TTTTTCTTTCTTTTTTCTCTCT
1 TTTTTCTTTCTTTTTTCTCTCT
2852921 TTTTT-TTTCT
1 TTTTTCTTTCT
2852931 GAGTTTCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 6 0.21
21 17 0.59
22 6 0.21
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTCTTTTTTCTCTCT
Found at i:2853188 original size:12 final size:12
Alignment explanation
Indices: 2853173--2853197 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2853163 AGATAAGTTT
2853173 AAATGTTTTTCA
1 AAATGTTTTTCA
2853185 AAATGTTTTTCA
1 AAATGTTTTTCA
2853197 A
1 A
2853198 GTAAACTTTA
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:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
AAATGTTTTTCA
Found at i:2853334 original size:19 final size:20
Alignment explanation
Indices: 2853289--2853339 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2853279 GACACCCAGA
*
2853289 TGTATTGATACATATTGCTT
1 TGTATCGATACATATTGCTT
* *
2853309 GGTATCGATACATGTT-CTT
1 TGTATCGATACATATTGCTT
2853328 TGTATCGATACA
1 TGTATCGATACA
2853340 CCATAAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATATTGCTT
Found at i:2853424 original size:18 final size:17
Alignment explanation
Indices: 2853397--2853432 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
2853387 TGTTCATAAT
2853397 TGAATTGTATCGATATA
1 TGAATTGTATCGATATA
2853414 TGAAGTTGTATCGATATA
1 TGAA-TTGTATCGATATA
2853432 T
1 T
2853433 TGAGCCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (17 bp):
TGAATTGTATCGATATA
Found at i:2853489 original size:52 final size:50
Alignment explanation
Indices: 2853398--2853504 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 50
2853388 GTTCATAATT
*
2853398 GAATTGTATCGATATATGAAGTTGTATCGATATATTGAGCCCAACGGCTA
1 GAATTGTATCGATATATGAAGTTGTATCGATACATTGAGCCCAACGGCTA
* * *
2853448 TAATTGTATCGATACATTATGAA-TTGTTTCGATACATTGAGCCCAATGGCTA
1 GAATTGTATCGAT--A-TATGAAGTTGTATCGATACATTGAGCCCAACGGCTA
2853500 GAATT
1 GAATT
2853505 TTATATGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 12 0.24
52 31 0.63
53 6 0.12
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (50 bp):
GAATTGTATCGATATATGAAGTTGTATCGATACATTGAGCCCAACGGCTA
Found at i:2853984 original size:35 final size:34
Alignment explanation
Indices: 2853938--2854003 Score: 114
Period size: 35 Copynumber: 1.9 Consensus size: 34
2853928 TAAGTGATTG
*
2853938 AGAGGTTCTATCTTAGCCTTTGTAAAAGATAGGAA
1 AGAGGTTCTATCTTAGCCTTCG-AAAAGATAGGAA
2853973 AGAGGTTCTATCTTAGCCTTCGAAAAGATAG
1 AGAGGTTCTATCTTAGCCTTCGAAAAGATAG
2854004 TCTTGTAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCTTCGAAAAGATAGGAA
Found at i:2856738 original size:20 final size:20
Alignment explanation
Indices: 2856715--2856787 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2856705 ACAACTCAAA
2856715 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2856735 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2856756 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2856776 GTATCGATACAT
1 GTATCGATACAT
2856788 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2856766 original size:41 final size:42
Alignment explanation
Indices: 2856715--2856809 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
2856705 ACAACTCAAA
*
2856715 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2856756 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2856798 GTATCGATACAT
1 GTATCGATACAT
2856810 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:2856866 original size:13 final size:13
Alignment explanation
Indices: 2856848--2856873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2856838 TACAGCAAGT
2856848 ATGTATCGATACA
1 ATGTATCGATACA
2856861 ATGTATCGATACA
1 ATGTATCGATACA
2856874 CAAAATTGTA
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2856887 original size:31 final size:32
Alignment explanation
Indices: 2856830--2856891 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
2856820 TAGCCAAACT
*
2856830 TGTATCGATACAGCAAGTATGTATCGATACAA
1 TGTATCGATACAGCAAATATGTATCGATACAA
2856862 TGTATCGATACA-CAAA-ATTGTATCGATACA
1 TGTATCGATACAGCAAATA-TGTATCGATACA
2856892 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 1 0.04
31 15 0.54
32 12 0.43
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAGCAAATATGTATCGATACAA
Found at i:2860955 original size:15 final size:15
Alignment explanation
Indices: 2860935--2860973 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2860925 TAAAAATGTC
*
2860935 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2860950 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
2860965 CCAAATGAA
1 CAAAATGAA
2860974 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2863059 original size:20 final size:21
Alignment explanation
Indices: 2862981--2863058 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
2862971 ATGTCCAAAA
*
2862981 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
2863001 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
2863025 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
2863046 TGTATCGATACAT
1 TGTATCGATACAT
2863059 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:2863063 original size:13 final size:13
Alignment explanation
Indices: 2863045--2863083 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2863035 ACATTTTTTG
2863045 TTGTATCGATACA
1 TTGTATCGATACA
2863058 TTGTATCGATACA
1 TTGTATCGATACA
*
2863071 CTGTATCGATACA
1 TTGTATCGATACA
2863084 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2864930 original size:18 final size:16
Alignment explanation
Indices: 2864889--2864934 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
2864879 AATTACTTGA
2864889 TTAAGGGGGAGATTTT
1 TTAAGGGGGAGATTTT
2864905 TTAAGGGGGAGATTTT
1 TTAAGGGGGAGATTTT
2864921 TTAAACGGGGGAGA
1 TT-AA-GGGGGAGA
2864935 CAAAGGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 18 0.64
17 2 0.07
18 8 0.29
ACGTcount: A:0.28, C:0.02, G:0.39, T:0.30
Consensus pattern (16 bp):
TTAAGGGGGAGATTTT
Found at i:2865564 original size:20 final size:20
Alignment explanation
Indices: 2865541--2865613 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2865531 ACAACTCAAA
2865541 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2865561 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2865582 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2865602 GTATCGATACAT
1 GTATCGATACAT
2865614 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2865592 original size:41 final size:42
Alignment explanation
Indices: 2865541--2865635 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
2865531 ACAACTCAAA
*
2865541 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2865582 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2865624 GTATCGATACAT
1 GTATCGATACAT
2865636 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:2865692 original size:13 final size:13
Alignment explanation
Indices: 2865674--2865699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2865664 TACAGCAAGT
2865674 ATGTATCGATACA
1 ATGTATCGATACA
2865687 ATGTATCGATACA
1 ATGTATCGATACA
2865700 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2867437 original size:16 final size:16
Alignment explanation
Indices: 2867412--2867449 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2867402 TATCCATGTT
*
2867412 ATCTTTGATGAAACTA
1 ATCTTAGATGAAACTA
2867428 ATCTTAGATGAAACTA
1 ATCTTAGATGAAACTA
2867444 ACTCTT
1 A-TCTT
2867450 CCACGAGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (16 bp):
ATCTTAGATGAAACTA
Found at i:2876146 original size:18 final size:19
Alignment explanation
Indices: 2876109--2876146 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2876099 CATAATTGAA
2876109 TTGTATCGATATATGGTAAG
1 TTGTATCGATATAT-GTAAG
2876129 TTGTATCGATATAT-TAAG
1 TTGTATCGATATATGTAAG
2876147 CCCAATGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
20 14 0.78
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
TTGTATCGATATATGTAAG
Found at i:2878671 original size:166 final size:166
Alignment explanation
Indices: 2878334--2878928 Score: 426
Period size: 166 Copynumber: 3.6 Consensus size: 166
2878324 TTGGGGATGA
* * * * *
2878334 TTTTCTTAGTTTATAATTTTTAAAATTCATTAAACATTATTATTTAATCACCATTAAATTAGTTT
1 TTTTCTTAGTTTATAATTTTTTAAATTCATAAAATATTATTATTTAATCACCATTAAATCAATTT
* * *
2878399 TGAAAAATTCATTTGTTTTCATGAGTTTTCATTTTTTCTTAAAATTTCTCTGTTTTTTGAAATAT
66 TGAAAAATTCATTTATTTTCATGAGTTTTCATTTTTTCTTAAAATTTCCCTGTTTTTTGAAAAAT
2878464 AGAGTTTTTTCACTCCATAAATGTTTTCGAGAGTAT
131 AGAGTTTTTTCACTCCATAAATGTTTTCGAGAGTAT
* * * *
2878500 TTTTCTTGGTTTATAATTTTTTAAATTCATAAAATATCATAATTTAATTCA-TATTAAATCAATT
1 TTTTCTTAGTTTATAATTTTTTAAATTCATAAAATATTATTATTTAA-TCACCATTAAATCAATT
* * *
2878564 TTGAAAAATTCATTTATTTTCATGAGTTTTTTATTTTTTTCTTTAAA-TTCCCTTTTTTTTGAAA
65 TTGAAAAATTCATTTATTTTCATGAG-TTTTCA-TTTTTTCTTAAAATTTCCCTGTTTTTTG-AA
** * * *
2878628 AAACTA-AGTTTTTT-GTTCTATAACA-G-TTTC-AGGGTGGT
127 AAA-TAGAGTTTTTTCACTCCATAA-ATGTTTTCGAGAGT-AT
* * * * * *
2878666 TTTTCTCAATTTATAA-TTTTTAATATTCATCAAATATTATTATTT-A--A--AGTAAATTAGTT
1 TTTTCTTAGTTTATAATTTTTTAA-ATTCATAAAATATTATTATTTAATCACCATTAAATCAATT
* * * * * * *
2878725 TTGAGAAATTTATTCATTTTCATGACTTTTTCATTTTTTCCTTGAAA-TGCCCT-TATTTTCGAG
65 TTGAAAAATTCATTTATTTTCATGA-GTTTTCATTTTTT-CTTAAAATTTCCCTGT-TTTTTGA-
* * * * * *
2878788 AAATTA-AATTTTCT-A-TCCCATAAATGTTCTC-AG-GGAA
126 AAAATAGAGTTTTTTCACT-CCATAAATGTTTTCGAGAGTAT
* * ** * * *
2878825 TTTTCTTAGGTTTA-AAATTTTTATAATGCATCTAATATTGTCATTGAACTC-CCATTAAATCAA
1 TTTTCTTA-GTTTATAATTTTTTA-AATTCATAAAATATTATTATTTAA-TCACCATTAAATCAA
* * *
2878888 TTTTGAAAAATTCAAATTA-TTTCATGAATTTTGAATTTTTT
63 TTTTGAAAAATTC-ATTTATTTTCATGAGTTTT-CATTTTTT
2878929 TGTATATATT
Statistics
Matches: 341, Mismatches: 62, Indels: 53
0.75 0.14 0.12
Matches are distributed among these distances:
159 11 0.03
160 49 0.14
161 62 0.18
162 1 0.00
164 4 0.01
165 45 0.13
166 115 0.34
167 27 0.08
168 25 0.07
169 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (166 bp):
TTTTCTTAGTTTATAATTTTTTAAATTCATAAAATATTATTATTTAATCACCATTAAATCAATTT
TGAAAAATTCATTTATTTTCATGAGTTTTCATTTTTTCTTAAAATTTCCCTGTTTTTTGAAAAAT
AGAGTTTTTTCACTCCATAAATGTTTTCGAGAGTAT
Found at i:2881140 original size:156 final size:154
Alignment explanation
Indices: 2880873--2881249 Score: 354
Period size: 156 Copynumber: 2.4 Consensus size: 154
2880863 CCAAGTCCGA
* * ** *
2880873 TTTTATGCCGAAGGTGGGTATTTAGGATAGGTTTATCCTGTCTATAATCCTTTTTAGGTCCTTTA
1 TTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCAATCTATAATCCTTTTTAAGTCCTTTA
* * * * ** *
2880938 GGAGTATCGAGTACTTTTACATCAAAGGTACCCTTTAAGGGTATTTTCATAATTTTTTCAGAATC
66 GGAGTATCGAGCACTTTTACATCAAAGGTACCCTATAAGGGCATTTTCAT-AGTTTCCCAAAATC
* *
2881003 GAGTCTTAAG-TTGTCATCGGGTTCGC
130 GAGTCCT-AGTTTGTCATCGGG-TCAC
** *
2881029 TTTTATGTTGAAGGTGGATATTTAGGATAGGTTCATCCAATCTATAATCCTTTTTAAGTTCTTTA
1 TTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCAATCTATAATCCTTTTTAAGTCCTTTA
* * ** *
2881094 GGGGTATC-AGGCA-TTTCTA-AGTCGAAGGTATTCTAT-AGGTGCATTTTCCTAGTTTCCCAAA
66 GGAGTATCGA-GCACTTT-TACA-TCAAAGGTACCCTATAAGG-GCATTTTCATAGTTTCCCAAA
*
2881155 ATTGAGTCCTAGTTTGTCATCGGGTCAC
127 ATCGAGTCCTAGTTTGTCATCGGGTCAC
* * * * * ** *
2881183 TTTTATACCGAAGATGGATATTTAGGATTA-G-TCATCCCATCTATGATTCTTTCCAAGTCCTCT
1 TTTTATGCCGAAGGTGGATATTTAGGA-TAGGTTCATCCAATCTATAATCCTTTTTAAGTCCTTT
2881246 AGGA
65 AGGA
2881250 TCTCCAAGCA
Statistics
Matches: 180, Mismatches: 35, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
153 28 0.16
154 29 0.16
155 36 0.20
156 87 0.48
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (154 bp):
TTTTATGCCGAAGGTGGATATTTAGGATAGGTTCATCCAATCTATAATCCTTTTTAAGTCCTTTA
GGAGTATCGAGCACTTTTACATCAAAGGTACCCTATAAGGGCATTTTCATAGTTTCCCAAAATCG
AGTCCTAGTTTGTCATCGGGTCAC
Found at i:2883851 original size:20 final size:20
Alignment explanation
Indices: 2883828--2883900 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2883818 ACAATTCAAA
2883828 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2883848 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2883869 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2883889 GTATCGATACAT
1 GTATCGATACAT
2883901 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2883872 original size:21 final size:21
Alignment explanation
Indices: 2883846--2883921 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2883836 ACATGTTGCA
2883846 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2883867 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2883887 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
2883908 TTGTATCGATACAT
1 ATGTATCGATACAT
2883922 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2883879 original size:41 final size:41
Alignment explanation
Indices: 2883828--2883921 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2883818 ACAATTCAAA
*
2883828 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
2883869 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2883910 GTATCGATACAT
1 GTATCGATACAT
2883922 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2883978 original size:13 final size:13
Alignment explanation
Indices: 2883960--2883985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2883950 TACAGCAAGT
2883960 ATGTATCGATACA
1 ATGTATCGATACA
2883973 ATGTATCGATACA
1 ATGTATCGATACA
2883986 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2890170 original size:20 final size:21
Alignment explanation
Indices: 2890091--2890169 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
2890081 AATGTCCAAA
*
2890091 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
2890111 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
2890136 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
2890156 TTGTATCGATACAT
1 ATGTATCGATACAT
2890170 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:2890174 original size:13 final size:13
Alignment explanation
Indices: 2890156--2890194 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2890146 ACATTTTTCT
2890156 TTGTATCGATACA
1 TTGTATCGATACA
2890169 TTGTATCGATACA
1 TTGTATCGATACA
*
2890182 CTGTATCGATACA
1 TTGTATCGATACA
2890195 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2892662 original size:20 final size:20
Alignment explanation
Indices: 2892639--2892711 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2892629 ACAATTCAAA
2892639 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2892659 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2892680 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2892700 GTATCGATACAT
1 GTATCGATACAT
2892712 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2892683 original size:21 final size:21
Alignment explanation
Indices: 2892657--2892732 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2892647 ACATGTTGCA
2892657 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2892678 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2892698 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
2892719 TTGTATCGATACAT
1 ATGTATCGATACAT
2892733 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2892690 original size:41 final size:41
Alignment explanation
Indices: 2892639--2892732 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2892629 ACAATTCAAA
*
2892639 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
2892680 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2892721 GTATCGATACAT
1 GTATCGATACAT
2892733 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2892789 original size:13 final size:13
Alignment explanation
Indices: 2892771--2892796 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2892761 TACAGCAAGT
2892771 ATGTATCGATACA
1 ATGTATCGATACA
2892784 ATGTATCGATACA
1 ATGTATCGATACA
2892797 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2894165 original size:7 final size:7
Alignment explanation
Indices: 2894153--2894178 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2894143 CTTTAACTCT
2894153 TTATCGA
1 TTATCGA
2894160 TTATCGA
1 TTATCGA
2894167 TTATCGA
1 TTATCGA
2894174 TTATC
1 TTATC
2894179 AAAAAAGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (7 bp):
TTATCGA
Found at i:2896544 original size:15 final size:15
Alignment explanation
Indices: 2896524--2896556 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2896514 AACCATTAAA
2896524 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
2896539 GATGATGATGATAAT
1 GATGATGAAGATAAT
2896554 GAT
1 GAT
2896557 AAAGTTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:2898426 original size:57 final size:57
Alignment explanation
Indices: 2898357--2898471 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
2898347 AGAAAAATTC
2898357 ATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGTTACTCCTTATCTAGCATAAGA
1 ATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGTTACTCCTTATCTAGCATAAGA
*
2898414 ATCACATTTTGTAAAATTGTTCAAAATGAAAAGGGTTACTCCTTATCTAGCATAAGA
1 ATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGTTACTCCTTATCTAGCATAAGA
2898471 A
1 A
2898472 GTGACCATGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (57 bp):
ATCACATTTTGTAAAATTGTTCAAAATGAAAAAGGTTACTCCTTATCTAGCATAAGA
Found at i:2899741 original size:16 final size:17
Alignment explanation
Indices: 2899717--2899752 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2899707 AAAGGCTTTC
*
2899717 AAAATTTTTAATAGA-A
1 AAAAGTTTTAATAGAGA
2899733 AAAAGTTTTAATAGAGA
1 AAAAGTTTTAATAGAGA
2899750 AAA
1 AAA
2899753 TGTTGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (17 bp):
AAAAGTTTTAATAGAGA
Found at i:2901121 original size:20 final size:21
Alignment explanation
Indices: 2901096--2901135 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2901086 ATTTTTCAGA
2901096 ATGTATCGATACAT-TGAAAG
1 ATGTATCGATACATCTGAAAG
2901116 ATGTATCGATACATCTGAAA
1 ATGTATCGATACATCTGAAA
2901136 ATTTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATCTGAAAG
Found at i:2901183 original size:30 final size:28
Alignment explanation
Indices: 2901109--2901196 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 28
2901099 TATCGATACA
*
2901109 TTGAAAGATGTATCGATACATCTGAAAAT
1 TTGAAAGATATATCGATACAT-TGAAAAT
*** *
2901138 TTTTCAGAATTTATCGATACATTGAAAGAT
1 TTGAAAG-ATATATCGATACATTGAAA-AT
2901168 GTTGAAAGATATATCGATACATTTGAAAA
1 -TTGAAAGATATATCGATACA-TTGAAAA
2901197 AACCCAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
29 9 0.19
30 28 0.60
31 10 0.21
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (28 bp):
TTGAAAGATATATCGATACATTGAAAAT
Found at i:2903735 original size:20 final size:20
Alignment explanation
Indices: 2903712--2903785 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
2903702 CATATCTAGA
**
2903712 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGTAT-AAT
*
2903732 TGTATCAATACATGTATAAT
1 TGTATCGATACATGTATAAT
2903752 TGTATCGATACATGTATAAT
1 TGTATCGATACATGTATAAT
2903772 TGTATCGATACATG
1 TGTATCGATACATG
2903786 AAACTGGCAG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 46 0.94
21 3 0.06
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATGTATAAT
Found at i:2903775 original size:40 final size:40
Alignment explanation
Indices: 2903692--2903785 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
2903682 AACCCTTGTA
* * **
2903692 TGTATCAATACATATCTAGATGTATCGATACATTATGCTT
1 TGTATCAATACATGTATAGATGTATCGATACATTATGAAT
2903732 TGTATCAATACATGTATA-ATTGTATCGATACATGTAT-AAT
1 TGTATCAATACATGTATAGA-TGTATCGATACAT-TATGAAT
*
2903772 TGTATCGATACATG
1 TGTATCAATACATG
2903786 AAACTGGCAG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.02
40 43 0.91
41 3 0.06
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (40 bp):
TGTATCAATACATGTATAGATGTATCGATACATTATGAAT
Found at i:2905475 original size:6 final size:6
Alignment explanation
Indices: 2905450--2905524 Score: 69
Period size: 6 Copynumber: 12.0 Consensus size: 6
2905440 TTGATCATAA
* * * * *
2905450 AAATAT AAATTT AATTTTT ATATTT AATTTT AAATTT AATTATTT ATATTT
1 AAATTT AAATTT AA-ATTT AAATTT AAATTT AAATTT AA--ATTT AAATTT
*
2905501 AAATTT ACATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT
2905525 TTTTAATACT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
6 46 0.84
7 4 0.07
8 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (6 bp):
AAATTT
Found at i:2905502 original size:26 final size:25
Alignment explanation
Indices: 2905450--2905514 Score: 94
Period size: 26 Copynumber: 2.6 Consensus size: 25
2905440 TTGATCATAA
*
2905450 AAATATAAATTTAATTTTTATATTT
1 AAATTTAAATTTAATTTTTATATTT
*
2905475 AATTTTAAATTTAATTATTTATATTT
1 AAATTTAAATTTAATT-TTTATATTT
*
2905501 AAATTTACATTTAA
1 AAATTTAAATTTAA
2905515 ATTTAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 14 0.40
26 21 0.60
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATTTAAATTTAATTTTTATATTT
Found at i:2915617 original size:22 final size:22
Alignment explanation
Indices: 2915572--2915613 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
2915562 TTAACTAATT
2915572 TTTCTATTTTTTCTCTCTTTTC
1 TTTCTATTTTTTCTCTCTTTTC
2915594 TTTCT-TTTTTTCTCTCTTTT
1 TTTCTATTTTTTCTCTCTTTT
2915614 TCTTCAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTCTATTTTTTCTCTCTTTTC
Found at i:2915625 original size:22 final size:21
Alignment explanation
Indices: 2915579--2915628 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2915569 ATTTTTCTAT
**
2915579 TTTTTCTCTCTTTTCTTTCTT
1 TTTTTCTCTCTTTTCTTTCAG
2915600 TTTTTCTCTCTTTT-TCTTCAAG
1 TTTTTCTCTCTTTTCT-TTC-AG
2915622 TTTTTCT
1 TTTTTCT
2915629 AAAGCTCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.68
22 7 0.28
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTCTCTCTTTTCTTTCAG
Found at i:2918082 original size:18 final size:17
Alignment explanation
Indices: 2918059--2918111 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 17
2918049 CCTATTCATT
*
2918059 TTTATTTTATTTAAATTA
1 TTTATTTTATATAAA-TA
*
2918077 TTTATTTAATATAAATA
1 TTTATTTTATATAAATA
*
2918094 TTCATTTTA-AT-AATA
1 TTTATTTTATATAAATA
2918109 TTT
1 TTT
2918112 CAATCTAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 6 0.20
16 2 0.07
17 9 0.30
18 13 0.43
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATTTTATATAAATA
Found at i:2921955 original size:20 final size:19
Alignment explanation
Indices: 2921934--2921980 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
2921924 TAGTTTTTTA
2921934 TTTTCTTCTCTATTTTTCTAT
1 TTTTCTT-TCT-TTTTTCTAT
2921955 TTTTCTTTCTTTTTTCT-T
1 TTTTCTTTCTTTTTTCTAT
*
2921973 TTCTCTTT
1 TTTTCTTT
2921981 TCTCTCTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 7 0.28
20 3 0.12
21 7 0.28
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTTTTCTAT
Found at i:2921970 original size:11 final size:12
Alignment explanation
Indices: 2921948--2921997 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2921938 CTTCTCTATT
2921948 TTTCTATTTTTC
1 TTTCTATTTTTC
2921960 TTTCT-TTTTTC
1 TTTCTATTTTTC
*
2921971 TTTTCT-CTTTTC
1 -TTTCTATTTTTC
*
2921983 TCTCTAATTTTTC
1 TTTCT-ATTTTTC
2921996 TT
1 TT
2921998 ACCAGCTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 10 0.32
12 15 0.48
13 6 0.19
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCTATTTTTC
Found at i:2921979 original size:18 final size:18
Alignment explanation
Indices: 2921927--2921980 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2921917 CTCTAGCTAG
* *
2921927 TTTTTTATTTTCT-TCTC
1 TTTTTTCTTTTCTCTTTC
*
2921944 TATTTTTCTATTTTTCTTTC
1 T-TTTTTCT-TTTCTCTTTC
2921964 TTTTTTCTTTTCTCTTT
1 TTTTTTCTTTTCTCTTT
2921981 TCTCTCTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.03
18 14 0.47
19 11 0.37
20 4 0.13
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTCTTTTCTCTTTC
Found at i:2921983 original size:19 final size:19
Alignment explanation
Indices: 2921927--2921980 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2921917 CTCTAGCTAG
2921927 TTTTT-TATTT-TCTTCTCT
1 TTTTTCTATTTCTCTT-TCT
*
2921945 ATTTTTCTATTTTTCTTTCT
1 -TTTTTCTATTTCTCTTTCT
2921965 TTTTTCT-TTTCTCTTT
1 TTTTTCTATTTCTCTTT
2921981 TCTCTCTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.25
19 12 0.38
20 8 0.25
21 4 0.12
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCTATTTCTCTTTCT
Found at i:2924633 original size:33 final size:33
Alignment explanation
Indices: 2924590--2924654 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2924580 TACCATTGTT
2924590 TGTATCGATACAT-AACACATTGTATCGATACAA
1 TGTATCGATACATGAACA-ATTGTATCGATACAA
* **
2924623 TGTATTGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGAACAATTGTATCGATACA
2924655 TTGCTTCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGAACAATTGTATCGATACAA
Found at i:2930907 original size:21 final size:22
Alignment explanation
Indices: 2930883--2930932 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2930873 ATCAAATCTT
* *
2930883 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
2930904 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
2930926 --TCAAAAT
1 CTTCAAAAT
2930933 CATCAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:2932799 original size:20 final size:20
Alignment explanation
Indices: 2932750--2932805 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
2932740 TGTATCGATA
**
2932750 AATTGTATCGATACATGTTC
1 AATTGTATCGATACATGCAC
* *
2932770 -ACTATATCGATACATGCAC
1 AATTGTATCGATACATGCAC
2932789 AATTGTATCGATACATG
1 AATTGTATCGATACATG
2932806 AAACTGGTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
AATTGTATCGATACATGCAC
Found at i:2932873 original size:13 final size:13
Alignment explanation
Indices: 2932855--2932879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2932845 CAATGTGCCT
2932855 TGTATCGATACAA
1 TGTATCGATACAA
2932868 TGTATCGATACA
1 TGTATCGATACA
2932880 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2939439 original size:20 final size:21
Alignment explanation
Indices: 2939414--2939465 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
2939404 TTTAAGATCG
*
2939414 GTATCGATACATTCACTTA-T
1 GTATCGATACATTCACTAATT
2939434 GTATCGATACATTCACTAATT
1 GTATCGATACATTCACTAATT
2939455 GTATCGATACA
1 GTATCGATACA
2939466 AATCGTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
GTATCGATACATTCACTAATT
Found at i:2940216 original size:49 final size:49
Alignment explanation
Indices: 2940144--2940239 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
2940134 CATCTAACCG
2940144 ATCCTCGACGGTCACCACGAAGTGACCGAAGTTTTAGAGTCGCAATTCA
1 ATCCTCGACGGTCACCACGAAGTGACCGAAGTTTTAGAGTCGCAATTCA
2940193 ATCCTCGACGGTCACCACGAAGTGACCGAAGTTTTAGAGTCGCAATT
1 ATCCTCGACGGTCACCACGAAGTGACCGAAGTTTTAGAGTCGCAATT
2940240 GGATCATTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (49 bp):
ATCCTCGACGGTCACCACGAAGTGACCGAAGTTTTAGAGTCGCAATTCA
Found at i:2943568 original size:20 final size:20
Alignment explanation
Indices: 2943545--2943617 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2943535 ACAATTCAAA
2943545 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2943565 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2943586 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2943606 GTATCGATACAT
1 GTATCGATACAT
2943618 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2943589 original size:21 final size:21
Alignment explanation
Indices: 2943563--2943638 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2943553 ACATGTTGCA
2943563 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2943584 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2943604 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2943625 ATGTATCGATACAT
1 ATGTATCGATACAT
2943639 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2943596 original size:41 final size:41
Alignment explanation
Indices: 2943545--2943638 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2943535 ACAATTCAAA
*
2943545 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2943586 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2943627 GTATCGATACAT
1 GTATCGATACAT
2943639 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2943695 original size:13 final size:13
Alignment explanation
Indices: 2943677--2943702 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2943667 TACAGCAAGT
2943677 ATGTATCGATACA
1 ATGTATCGATACA
2943690 ATGTATCGATACA
1 ATGTATCGATACA
2943703 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2947783 original size:15 final size:15
Alignment explanation
Indices: 2947763--2947793 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2947753 TAAAAATGTC
*
2947763 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2947778 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2947793 C
1 C
2947794 TAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2949886 original size:20 final size:21
Alignment explanation
Indices: 2949807--2949885 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
2949797 AATGTCCAAA
*
2949807 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
2949827 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
2949852 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
2949872 TTGTATCGATACAT
1 ATGTATCGATACAT
2949886 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:2949890 original size:13 final size:13
Alignment explanation
Indices: 2949872--2949910 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2949862 ACATTTTTCT
2949872 TTGTATCGATACA
1 TTGTATCGATACA
2949885 TTGTATCGATACA
1 TTGTATCGATACA
*
2949898 CTGTATCGATACA
1 TTGTATCGATACA
2949911 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2952384 original size:20 final size:20
Alignment explanation
Indices: 2952361--2952433 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2952351 ACAATTCAAA
2952361 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2952381 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2952402 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2952422 GTATCGATACAT
1 GTATCGATACAT
2952434 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2952405 original size:21 final size:21
Alignment explanation
Indices: 2952379--2952454 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2952369 ACATGTTGCA
2952379 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2952400 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2952420 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2952441 ATGTATCGATACAT
1 ATGTATCGATACAT
2952455 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2952412 original size:41 final size:41
Alignment explanation
Indices: 2952361--2952454 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2952351 ACAATTCAAA
*
2952361 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2952402 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2952443 GTATCGATACAT
1 GTATCGATACAT
2952455 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2952511 original size:13 final size:13
Alignment explanation
Indices: 2952493--2952518 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2952483 TACAGCAAGT
2952493 ATGTATCGATACA
1 ATGTATCGATACA
2952506 ATGTATCGATACA
1 ATGTATCGATACA
2952519 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2953498 original size:20 final size:21
Alignment explanation
Indices: 2953475--2953526 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2953465 TATTTCAGGC
2953475 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
2953495 ATGTCTCGATACATTTACTAT
1 ATGTATCGATACATTCACTAT
*
2953516 TTGTATCGATA
1 ATGTATCGATA
2953527 AAAATTGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:2956197 original size:51 final size:52
Alignment explanation
Indices: 2956079--2956199 Score: 147
Period size: 52 Copynumber: 2.3 Consensus size: 52
2956069 ATTTAACTGG
* * ** *
2956079 ATGTATCGATATATTGAAGAATGTATCGATACATTTGGGTCAAAAACCCACA
1 ATGTATCGATACAATGAAGAACATATCGATACAATTGGGTCAAAAACCCACA
* * *
2956131 ATATATCGATACAATGAAGAACATGTCGATACAATTGGGTC-AAAACCTGA-A
1 ATGTATCGATACAATGAAGAACATATCGATACAATTGGGTCAAAAACC-CACA
2956182 ATGTATCGATACAATGAA
1 ATGTATCGATACAATGAA
2956200 AAATTTTGCC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 24 0.41
52 35 0.59
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (52 bp):
ATGTATCGATACAATGAAGAACATATCGATACAATTGGGTCAAAAACCCACA
Found at i:2956287 original size:21 final size:20
Alignment explanation
Indices: 2956220--2956293 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
2956210 TGCATGGTCC
***
2956220 TGTATCGATACATTTCAAGCA
1 TGTATCGATACA-TTCACTTA
2956241 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
*
2956261 TGTATCGATACATTCACTTGT
1 TGTATCGATACATTCACTT-A
2956282 TGTATCGATACA
1 TGTATCGATACA
2956294 AATTGTAGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 24 0.50
21 24 0.50
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:2964373 original size:34 final size:35
Alignment explanation
Indices: 2964324--2964449 Score: 114
Period size: 34 Copynumber: 3.6 Consensus size: 35
2964314 CCACACCCAT
*
2964324 ACAATCCTTTTCAAAGTCCACACAAATCAATGGTA
1 ACAATCCTTTCCAAAGTCCACACAAATCAATGGTA
* * *
2964359 GA-AA-CCTTTCCAAAGTCTACACAAGTCAGTGGTA
1 -ACAATCCTTTCCAAAGTCCACACAAATCAATGGTA
* * * **
2964393 ACCAATCTTTTCCAAAGTCCACACAAGTTAGGGGT-
1 A-CAATCCTTTCCAAAGTCCACACAAATCAATGGTA
* *
2964428 ACAATCCTTTTCAAATTCCACA
1 ACAATCCTTTCCAAAGTCCACA
2964450 TGAGTTAGTG
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
33 1 0.01
34 44 0.58
35 5 0.07
36 26 0.34
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (35 bp):
ACAATCCTTTCCAAAGTCCACACAAATCAATGGTA
Found at i:2964529 original size:67 final size:67
Alignment explanation
Indices: 2964405--2964563 Score: 180
Period size: 67 Copynumber: 2.4 Consensus size: 67
2964395 CAATCTTTTC
* * * *
2964405 CAAAGTCCACACAAGTTAGG-GGT-A-CAATCCTTTTCAAATTCCACATGAGTTAGTGGCACCCC
1 CAAAGTCCACACAAGTT-GGTGGTAACCAAACCTTTTCAAAGTCCACACGAGGTAGTGGCACCCC
*
2964467 ATT
65 AGT
* * * *
2964470 TAAAGTCCACACAAGTTGGTGGTAACCAAACCTTTTCAAAGTCTACACGAGGTGGTGGCACCCTA
1 CAAAGTCCACACAAGTTGGTGGTAACCAAACCTTTTCAAAGTCCACACGAGGTAGTGGCACCCCA
2964535 GT
66 GT
** *
2964537 CAAAGTCCACATGAGTTGGTGGCAACC
1 CAAAGTCCACACAAGTTGGTGGTAACC
2964564 TTTTCAATGC
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 2 0.03
65 19 0.24
66 1 0.01
67 56 0.72
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (67 bp):
CAAAGTCCACACAAGTTGGTGGTAACCAAACCTTTTCAAAGTCCACACGAGGTAGTGGCACCCCA
GT
Found at i:2964578 original size:31 final size:31
Alignment explanation
Indices: 2964498--2964570 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
2964488 GTGGTAACCA
*
2964498 AACCTTTTCAAAGTCTACACGAGGTGGTGGC
1 AACCTTTTCAAAGTCCACACGAGGTGGTGGC
* ** * *
2964529 ACCCTAGTCAAAGTCCACATGAGTTGGTGGC
1 AACCTTTTCAAAGTCCACACGAGGTGGTGGC
2964560 AACCTTTTCAA
1 AACCTTTTCAA
2964571 TGCCCACAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (31 bp):
AACCTTTTCAAAGTCCACACGAGGTGGTGGC
Found at i:2964625 original size:29 final size:29
Alignment explanation
Indices: 2964562--2964633 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
2964552 TTGGTGGCAA
* *
2964562 CCTTTTCAATGCCCACAAGTCAATGGAAC
1 CCTTTTCAAAGCCCACAAGTCAATAGAAC
* * *
2964591 CCTTTTCAAAGCCCACAAGTTAGTAGCA-
1 CCTTTTCAAAGCCCACAAGTCAATAGAAC
*
2964619 CCTTTTTAAAGCCCA
1 CCTTTTCAAAGCCCA
2964634 TGAGTTAGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (29 bp):
CCTTTTCAAAGCCCACAAGTCAATAGAAC
Found at i:2964631 original size:28 final size:28
Alignment explanation
Indices: 2964591--2964663 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
2964581 TCAATGGAAC
* *
2964591 CCTTTTCAAAGCCCACAAGTTAGTAGCA
1 CCTTTTTAAAGCCCACAAGTTAGCAGCA
** *
2964619 CCTTTTTAAAGCCCATGAGTTAGCGGCA
1 CCTTTTTAAAGCCCACAAGTTAGCAGCA
* *
2964647 CCTCTTTAAAGACCACA
1 CCTTTTTAAAGCCCACA
2964664 TTAGCTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (28 bp):
CCTTTTTAAAGCCCACAAGTTAGCAGCA
Found at i:2964939 original size:32 final size:32
Alignment explanation
Indices: 2964903--2965091 Score: 114
Period size: 32 Copynumber: 6.2 Consensus size: 32
2964893 TGAGGTAACT
* *
2964903 CAAAAGCCTACATGAGTTTGTAGCAACCTTTC
1 CAAAAGCCCACATGAGTTGGTAGCAACCTTTC
* * *
2964935 CAAAAG-CCATATGAGCTGTTAGC-A-C---C
1 CAAAAGCCCACATGAGTTGGTAGCAACCTTTC
** *
2964961 CAAAAGTTCACATGAGTTGGT-GACATCCTTTC
1 CAAAAGCCCACATGAGTTGGTAG-CAACCTTTC
* * *
2964993 CTAAAAGCCCACATGAGTTGGTGGCAATCTTGC
1 C-AAAAGCCCACATGAGTTGGTAGCAACCTTTC
* *
2965026 CAAAAGCCCGCATGAGTTCGTAGC-A-C---C
1 CAAAAGCCCACATGAGTTGGTAGCAACCTTTC
* * * *
2965053 CAAAAGCCCATACGAGTTGGTGGCATCCTTTC
1 CAAAAGCCCACATGAGTTGGTAGCAACCTTTC
*
2965085 TAAAAGC
1 CAAAAGC
2965092 TAGCATGAGC
Statistics
Matches: 118, Mismatches: 25, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
26 8 0.07
27 31 0.26
29 3 0.03
30 2 0.02
31 13 0.11
32 35 0.30
33 25 0.21
34 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (32 bp):
CAAAAGCCCACATGAGTTGGTAGCAACCTTTC
Found at i:2965006 original size:33 final size:32
Alignment explanation
Indices: 2964960--2965043 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
2964950 CTGTTAGCAC
** *
2964960 CCAAAAGTTCACATGAGTTGGTGAC-ATCCTTT
1 CCAAAAGCCCACATGAGTTGGTGACAAT-CTTG
*
2964992 CCTAAAAGCCCACATGAGTTGGTGGCAATCTTG
1 CC-AAAAGCCCACATGAGTTGGTGACAATCTTG
*
2965025 CCAAAAGCCCGCATGAGTT
1 CCAAAAGCCCACATGAGTT
2965044 CGTAGCACCC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
32 18 0.40
33 25 0.56
34 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (32 bp):
CCAAAAGCCCACATGAGTTGGTGACAATCTTG
Found at i:2965072 original size:92 final size:90
Alignment explanation
Indices: 2964904--2965091 Score: 225
Period size: 92 Copynumber: 2.1 Consensus size: 90
2964894 GAGGTAACTC
* * * * **
2964904 AAAAGCCTACATGAGTTTGTAGCAACCTTTCCAAAAGCCATATGAGCTGTTAGCACCCAAAAGTT
1 AAAAGCCCACATGAGTTGGTAGCAACCTTGCCAAAAGCCACATGAGCTGTTAGCACCCAAAAGCC
*
2964969 CACATGAGTTGGTGACATCCTTTCCT
66 CACACGAGTTGGTGACATCCTTT-CT
* * * *
2964995 AAAAGCCCACATGAGTTGGTGGCAATCTTGCCAAAAGCCCGCATGAGTTCG-TAGCACCCAAAAG
1 AAAAGCCCACATGAGTTGGTAGCAACCTTGCCAAAAG-CCACATGAGCT-GTTAGCACCCAAAAG
* *
2965059 CCCATACGAGTTGGTGGCATCCTTTCT
64 CCCACACGAGTTGGTGACATCCTTTCT
2965086 AAAAGC
1 AAAAGC
2965092 TAGCATGAGC
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
91 40 0.49
92 41 0.50
93 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (90 bp):
AAAAGCCCACATGAGTTGGTAGCAACCTTGCCAAAAGCCACATGAGCTGTTAGCACCCAAAAGCC
CACACGAGTTGGTGACATCCTTTCT
Found at i:2965285 original size:91 final size:91
Alignment explanation
Indices: 2965098--2965285 Score: 268
Period size: 91 Copynumber: 2.1 Consensus size: 91
2965088 AAGCTAGCAT
* * * * * * *
2965098 GAGCTAATACACCCAAAAAAGCCCACGCAAGTTGGTGGCACTCAAATCTTTCCAAAAGTTGCACG
1 GAGCTGATACACCCAAAAAAGACCACGCAAATTGGTGGCAATCAAACCTTTCCAAAAGTCGCACA
2965163 AGTTCGTGACACCCAAAAGCCTACAC
66 AGTTCGTGACACCCAAAAGCCTACAC
* * * *
2965189 GAGCTGATGCACCCAAAAAAGAGCATGCAAATTGGTGGCAATCAAACCTTTTCAAAAGTCGCACA
1 GAGCTGATACACCCAAAAAAGACCACGCAAATTGGTGGCAATCAAACCTTTCCAAAAGTCGCACA
*
2965254 AGTTTGTGACACCCAAAAGCCTACAC
66 AGTTCGTGACACCCAAAAGCCTACAC
2965280 GAGCTG
1 GAGCTG
2965286 GTGGCGTCCT
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (91 bp):
GAGCTGATACACCCAAAAAAGACCACGCAAATTGGTGGCAATCAAACCTTTCCAAAAGTCGCACA
AGTTCGTGACACCCAAAAGCCTACAC
Found at i:2965373 original size:65 final size:64
Alignment explanation
Indices: 2965293--2965594 Score: 185
Period size: 65 Copynumber: 4.8 Consensus size: 64
2965283 CTGGTGGCGT
* * *
2965293 CCTTTCTTAAGGCTCACACGAGCTGGCAACACCCAAAAAGCCCACACAAGTTAGTGGCACTCAAA
1 CCTTTCTAAAAGCTCACACGAGTTGGCAACACCCAAAAAGCCCACACAAGTT-GTGGCACTCAAA
* ** * * * *
2965358 CCTTTCTAAAAGCTCATATAAGTTGTG--GCA-CCTAAAAGACCACACAAGCTGATGGC-CT---
1 CCTTTCTAAAAGCTCACACGAGTTG-GCAACACCCAAAAAGCCCACACAAGTTG-TGGCACTCAA
2965416 -
64 A
* * * * * * ** * * *
2965416 CTTTTCTCAAAGCCCACTCGAGCTGGCATCACCTTAAAAGCCCATACAAATTGATGGCACTTAAA
1 CCTTTCTAAAAGCTCACACGAGTTGGCAACACCCAAAAAGCCCACACAAGTTG-TGGCACTCAAA
* * * * * * *
2965481 CCTTTCTAAAAACTCGCATGAGTTGGTAGCTCCCAAAAAGCCTACACAAGTTGGTGGCACTCAAA
1 CCTTTCTAAAAGCTCACACGAGTTGGCAACACCCAAAAAGCCCACACAAGTT-GTGGCACTCAAA
* * *
2965546 CC-TTCTCAAAA-CCCTGCACGAGTTGGCGACACCCAAAAA-CCCACACAAG
1 CCTTTCT-AAAAGCTC-ACACGAGTTGGCAACACCCAAAAAGCCCACACAAG
2965595 CTAGTGCCAT
Statistics
Matches: 176, Mismatches: 48, Indels: 27
0.70 0.19 0.11
Matches are distributed among these distances:
57 1 0.01
58 17 0.10
59 2 0.01
60 21 0.12
61 2 0.01
62 3 0.02
63 21 0.12
64 17 0.10
65 90 0.51
66 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (64 bp):
CCTTTCTAAAAGCTCACACGAGTTGGCAACACCCAAAAAGCCCACACAAGTTGTGGCACTCAAA
Found at i:2965408 original size:123 final size:122
Alignment explanation
Indices: 2965216--2965593 Score: 298
Period size: 123 Copynumber: 3.0 Consensus size: 122
2965206 AAAGAGCATG
* *
2965216 CAAATTGGTGGCAATCAAACCTTT-TCAAAAGTCGCACAAGTTTGTGACACCCAAAAGCCTACAC
1 CAAATT-GTGGCACTCAAACCTTTCT-AAAAGTCACACAAGTTTGTGACACCCAAAAGCCTACAC
* * * * * *
2965280 GAGCTGGTGGCGTCCTTTCTTAAGGCTCACACGAGCTGGCAACACCCAAAAAGCCCACA
64 AAGCTGATGGCCTCCTTTCTCAAAGCCCACACGAGCTGGCAACACCCAAAAAGCCCACA
* * * * *
2965339 CAAGTTAGTGGCACTCAAACCTTTCTAAAAGCTCATATAAG-TTGTGGCACCTAAAAGACC-ACA
1 CAAATT-GTGGCACTCAAACCTTTCTAAAAG-TCACACAAGTTTGTGACACCCAAAAG-CCTACA
* * * ** *
2965402 CAAGCTGATGGCCTCTTTTCTCAAAGCCCACTCGAGCTGGCATCACCTTAAAAGCCCATA
63 CAAGCTGATGGCCTCCTTTCTCAAAGCCCACACGAGCTGGCAACACCCAAAAAGCCCACA
* * * ** * *
2965462 CAAATTGATGGCACTTAAACCTTTCTAAAAACTCGCATGAGTTGGT-AGCTCCCAAAAAGCCTAC
1 CAAATTG-TGGCACTCAAACCTTTCT-AAAAGTCACACAAGTTTGTGA-CACCC-AAAAGCCTAC
* * * * * * *
2965526 ACAAGTTGGTGGCACTCAAACCTTCTCAAAACCCTGCACGAGTTGGCGACACCCAAAAA-CCCAC
62 ACAAGCTGATGGC-CTC---CTTTCTCAAAGCCC-ACACGAGCTGGCAACACCCAAAAAGCCCAC
2965590 A
122 A
2965591 CAA
1 CAA
2965594 GCTAGTGCCA
Statistics
Matches: 198, Mismatches: 43, Indels: 22
0.75 0.16 0.08
Matches are distributed among these distances:
122 1 0.01
123 119 0.60
124 21 0.11
125 18 0.09
126 3 0.02
129 19 0.10
130 17 0.09
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (122 bp):
CAAATTGTGGCACTCAAACCTTTCTAAAAGTCACACAAGTTTGTGACACCCAAAAGCCTACACAA
GCTGATGGCCTCCTTTCTCAAAGCCCACACGAGCTGGCAACACCCAAAAAGCCCACA
Found at i:2969880 original size:13 final size:13
Alignment explanation
Indices: 2969862--2969886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2969852 CATAAAGTGT
2969862 TGTATCGATACAA
1 TGTATCGATACAA
2969875 TGTATCGATACA
1 TGTATCGATACA
2969887 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2969902 original size:32 final size:33
Alignment explanation
Indices: 2969842--2969907 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
2969832 TTGAACGATT
2969842 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
2969875 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2969907 T
1 T
2969908 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2975710 original size:22 final size:22
Alignment explanation
Indices: 2975680--2975721 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2975670 GCTTACTCAG
*
2975680 CTTTGATTAAAAGGGAGAAATT
1 CTTTAATTAAAAGGGAGAAATT
**
2975702 CTTTAATTAAGGGGGAGAAA
1 CTTTAATTAAAAGGGAGAAA
2975722 AATGAAAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.29
Consensus pattern (22 bp):
CTTTAATTAAAAGGGAGAAATT
Found at i:2976362 original size:13 final size:13
Alignment explanation
Indices: 2976341--2976371 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2976331 CGATACATGG
*
2976341 TACAATGTATCGA
1 TACATTGTATCGA
2976354 TACATTGTATCGA
1 TACATTGTATCGA
2976367 TACAT
1 TACAT
2976372 GATGAATTGT
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:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:2976367 original size:33 final size:33
Alignment explanation
Indices: 2976325--2976392 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
2976315 CTACCACTGT
*
2976325 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
2976358 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
2976391 TT
1 TT
2976393 TCCTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:2978740 original size:54 final size:57
Alignment explanation
Indices: 2978591--2978812 Score: 211
Period size: 58 Copynumber: 3.9 Consensus size: 57
2978581 AGGCACCTAT
* * * * *
2978591 TAAATCTTCTTTACTAAATCCCAATGTCGCTAGCCTTGAATTAACACATTGGCACTTG
1 TAAATCTTCTTT-CTCAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTG
* *
2978649 TCAAATCTTCTTTCTCAAGCCCAATGAT-GCTGACCTTGAATCAGTACATTGGCACTT-
1 T-AAATCTTCTTTCTCAAGCCCAATG-TCGCTGGCCTTGAATCAGCACATTGGCACTTG
* * * *
2978706 T-ATTGTT-TTTCTCAAGCCCAATGTCGCTGGCCTTGAATCAGCATATTAGCACTTG
1 TAAATCTTCTTTCTCAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTG
** * * * *
2978761 TCAAA-CATTCTTTCAAAAGCCTAATGTCACTGGCCTTGAATTAACACATTGG
1 T-AAATC-TTCTTTCTCAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGG
2978813 TACCCTACTT
Statistics
Matches: 133, Mismatches: 23, Indels: 16
0.77 0.13 0.09
Matches are distributed among these distances:
53 1 0.01
54 41 0.31
55 5 0.04
57 4 0.03
58 70 0.53
59 12 0.09
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.34
Consensus pattern (57 bp):
TAAATCTTCTTTCTCAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTG
Found at i:2978810 original size:112 final size:112
Alignment explanation
Indices: 2978610--2978812 Score: 257
Period size: 112 Copynumber: 1.8 Consensus size: 112
2978600 TTTACTAAAT
* * **
2978610 CCCAATGTCGCTAGCCTTGAATTAACACATTGGCACTTGTCAAATCTTCTTTCTCAAGCCCAATG
1 CCCAATGTCGCTAGCCTTGAATCAACACATTAGCACTTGTCAAATCTTCTTTCAAAAGCCCAATG
* **
2978675 ATGCTGACCTTGAATCAGTACATTGGCACTTTATTGTTTTTCTCAAG
66 ATACTGACCTTGAATCAACACATTGGCACTTTATTGTTTTTCTCAAG
* * * *
2978722 CCCAATGTCGCTGGCCTTGAATCAGCATATTAGCACTTGTCAAA-CATTCTTTCAAAAGCCTAAT
1 CCCAATGTCGCTAGCCTTGAATCAACACATTAGCACTTGTCAAATC-TTCTTTCAAAAGCCCAAT
* *
2978786 G-TCACTGGCCTTGAATTAACACATTGG
65 GAT-ACTGACCTTGAATCAACACATTGG
2978813 TACCCTACTT
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
111 2 0.03
112 74 0.97
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (112 bp):
CCCAATGTCGCTAGCCTTGAATCAACACATTAGCACTTGTCAAATCTTCTTTCAAAAGCCCAATG
ATACTGACCTTGAATCAACACATTGGCACTTTATTGTTTTTCTCAAG
Found at i:2979163 original size:52 final size:52
Alignment explanation
Indices: 2978945--2979165 Score: 175
Period size: 52 Copynumber: 4.3 Consensus size: 52
2978935 TATTTGCACT
* ** * * * *
2978945 CTTATCATCTTTAAGTCCAGTGTTGCTGGCCTAGAATCAGCACATTGGCA-A
1 CTTATCATCTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGACATC
* * ** * * *
2978996 C-T-T-GTCTTTAAG-CCAGTGTTGCTGGCCTTGAATCAGCAAATTGGCA-C
1 CTTATCATCTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGACATC
* * * * * *
2979043 CTTTATCATCTCTGAGACCAATGTCGCTAGCCTTGAATCAACACATTGACATT
1 C-TTATCATCTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGACATC
* * * *
2979096 CTTGTCATCTTTAAGTCTAATGTCACTAGCCTTGAATTAGCACATTGCCATC
1 CTTATCATCTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGACATC
2979148 CTTATCATCTTTAAGTCC
1 CTTATCATCTTTAAGTCC
2979166 TGTGTTAGAG
Statistics
Matches: 138, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
47 33 0.24
48 8 0.06
49 2 0.01
50 2 0.01
51 7 0.05
52 85 0.62
53 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (52 bp):
CTTATCATCTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGACATC
Found at i:2979864 original size:20 final size:20
Alignment explanation
Indices: 2979839--2979878 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2979829 ACAACAACTT
*
2979839 AATGTATCAATACGTAAGTG
1 AATGTATCAATACATAAGTG
2979859 AATGTATCAATACATAAGTG
1 AATGTATCAATACATAAGTG
2979879 CATGGATCGA
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:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (20 bp):
AATGTATCAATACATAAGTG
Found at i:2979891 original size:20 final size:20
Alignment explanation
Indices: 2979839--2979891 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2979829 ACAACAACTT
* *
2979839 AATGTATCAATACGTAAGTG
1 AATGGATCAATACATAAGTG
*
2979859 AATGTATCAATACATAAGTG
1 AATGGATCAATACATAAGTG
* *
2979879 CATGGATCGATAC
1 AATGGATCAATAC
2979892 TAGACCTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (20 bp):
AATGGATCAATACATAAGTG
Found at i:2981077 original size:51 final size:51
Alignment explanation
Indices: 2981008--2981114 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 51
2980998 ATGGGGTTAA
* * *
2981008 AGTATCCTCGATTATGGAAGATCGATATTTTGAAAATAAAATCCAAGTTGG
1 AGTATCCCCAATTATGGAAAATCGATATTTTGAAAATAAAATCCAAGTTGG
* * * * *
2981059 AGTATCCCCAATTGTGGAAAATCGATGTTTTGGAAATAAAATCGAGGTTGG
1 AGTATCCCCAATTATGGAAAATCGATATTTTGAAAATAAAATCCAAGTTGG
2981110 AGTAT
1 AGTAT
2981115 TCCCTCAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (51 bp):
AGTATCCCCAATTATGGAAAATCGATATTTTGAAAATAAAATCCAAGTTGG
Found at i:2981138 original size:79 final size:79
Alignment explanation
Indices: 2981054--2981274 Score: 268
Period size: 79 Copynumber: 2.8 Consensus size: 79
2981044 TAAAATCCAA
* * * *
2981054 GTTGGAGTATCCCCAATTGTGGAAAATCGATGTTTTGGAAATAAAATCG-AGGTTGGAGTATTCC
1 GTTGGAGTATCCCCAATTATGGAAAATTGATGTTTTGAAAATAAAATCGCA-GTTAGAGTA-TCC
2981118 -CTCAAAAATAACGAG
64 TCTCAAAAATAACGAG
** * **
2981133 GTTGGAGTATCCCTGATTTTAAAAAATTGATGTTTTGAAAATAAAATCGCAGTTAGAGTATCCTC
1 GTTGGAGTATCCCCAATTATGGAAAATTGATGTTTTGAAAATAAAATCGCAGTTAGAGTATCCTC
*
2981198 TCAAAAATAACGGG
66 TCAAAAATAACGAG
* * * *
2981212 GTTAGAGTATCCCCAATTATGGAAATTTGATGTTTTGAAAATAAAACTAG-GGTTAGAGTATCC
1 GTTGGAGTATCCCCAATTATGGAAAATTGATGTTTTGAAAATAAAA-TCGCAGTTAGAGTATCC
2981275 CCAATTATGA
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
78 3 0.02
79 115 0.95
80 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (79 bp):
GTTGGAGTATCCCCAATTATGGAAAATTGATGTTTTGAAAATAAAATCGCAGTTAGAGTATCCTC
TCAAAAATAACGAG
Found at i:2981142 original size:130 final size:130
Alignment explanation
Indices: 2980902--2981195 Score: 353
Period size: 130 Copynumber: 2.3 Consensus size: 130
2980892 AAAAAATTTA
* * *
2980902 ATATTTTGGAGATAAAA-ACAAGGTTGGAGTATCCCCAATAGTGAAAAATCGATGTTTTGGAAAT
1 ATATTTTGAAAATAAAATCCAA-GTTGGAGTATCCCCAATAGTGAAAAATCGATGTTTTGGAAAT
* * * ** *
2980966 AAAACCGAGGTTGGAGTACCCTCTCGAAAATAATGGGGTTAAAGTAT-CCTCGATTATGGAAGAT
65 AAAACCGAGGTTGGAGTACCCTCTCAAAAATAACGAGGTTAAAGTATCCCT-GATTATAAAAAAT
2981030 CG
129 CG
* *
2981032 ATATTTTGAAAATAAAATCCAAGTTGGAGTATCCCCAATTGTGGAAAATCGATGTTTTGGAAATA
1 ATATTTTGAAAATAAAATCCAAGTTGGAGTATCCCCAATAGTGAAAAATCGATGTTTTGGAAATA
* * ** * *
2981097 AAATCGAGGTTGGAGTATTCC-CTCAAAAATAACGAGGTTGGAGTATCCCTGATTTTAAAAAATT
66 AAACCGAGGTTGGAGTA-CCCTCTCAAAAATAACGAGGTTAAAGTATCCCTGATTATAAAAAATC
2981161 G
130 G
* *
2981162 ATGTTTTGAAAATAAAATCGC-AGTTAGAGTATCC
1 ATATTTTGAAAATAAAATC-CAAGTTGGAGTATCC
2981196 TCTCAAAAAT
Statistics
Matches: 141, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
130 132 0.94
131 9 0.06
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (130 bp):
ATATTTTGAAAATAAAATCCAAGTTGGAGTATCCCCAATAGTGAAAAATCGATGTTTTGGAAATA
AAACCGAGGTTGGAGTACCCTCTCAAAAATAACGAGGTTAAAGTATCCCTGATTATAAAAAATCG
Found at i:2981274 original size:51 final size:51
Alignment explanation
Indices: 2981210--2981327 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
2981200 AAAAATAACG
* *
2981210 GGGTTAGAGTATCCCCAATTATGGAAATTTGATGTTTTGAAAATAAAA-CTA
1 GGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTGAAAATAAAATC-A
* *
2981261 GGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAATCG
1 GGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTGAAAATAAAATCA
*
2981312 GGGTTGGAGTATCCCC
1 GGGTTAGAGTATCCCC
2981328 TTGAAAATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 60 0.98
52 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (51 bp):
GGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTGAAAATAAAATCA
Found at i:2981297 original size:209 final size:208
Alignment explanation
Indices: 2980922--2981415 Score: 575
Period size: 209 Copynumber: 2.4 Consensus size: 208
2980912 GATAAAAACA
* * *
2980922 AGGTTGGAGTATCCCCAATAGTGAAAAATCGATGTTTTGGAAATAAAACCGAGGTTGGAGTACCC
1 AGGTTGGAGTATCCCCAATAGTAAAAAATCGATGTTTTGAAAATAAAACCGAGGTTAGAGTACCC
* * * *
2980987 TCTCGAAAATAATGGGGTTAAAGTATCCTCGATTATGGAAGATCGATATTTTGAAAATAAAATCC
66 TCTCAAAAATAACGGGGTTAAAGTATCCCCAATTATGGAAGATCGATATTTTGAAAATAAAATCC
* * * *
2981052 AAGTTGGAGTATCCCCAATTGTGGAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGTATTC
131 AAGTTAGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
2981117 CCTCAAAAATAAC
196 CCTCAAAAATAAC
** ** * * *
2981130 GAGGTTGGAGTATCCCTGATTTTAAAAAATTGATGTTTTGAAAATAAAATCGCA-GTTAGAGTAT
1 -AGGTTGGAGTATCCCCAATAGTAAAAAATCGATGTTTTGAAAATAAAACCG-AGGTTAGAGTAC
* * *
2981194 CCTCTCAAAAATAACGGGGTTAGAGTATCCCCAATTATGGAA-ATTTGATGTTTTGAAAATAAAA
64 CCTCTCAAAAATAACGGGGTTAAAGTATCCCCAATTATGGAAGA-TCGATATTTTGAAAATAAAA
* * * *
2981258 -CTAGGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGT
128 TCCA-AGTTAGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGT
**
2981322 ATCCCCTTGAAAATAAC
192 ATCCCCTCAAAAATAAC
* * * * * * * *
2981339 AGGTTGGAGTATCTCCGATTGTGAAAAATC-AGTGCTTTGGAAATAAAACTGAGGTTGGAGTATC
1 AGGTTGGAGTATCCCCAATAGTAAAAAATCGA-TGTTTTGAAAATAAAACCGAGGTTAGAGTA-C
*
2981403 CC-CTCGAAAATAA
64 CCTCTCAAAAATAA
2981416 AAACATGAAT
Statistics
Matches: 240, Mismatches: 39, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
207 2 0.01
208 61 0.25
209 176 0.73
210 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (208 bp):
AGGTTGGAGTATCCCCAATAGTAAAAAATCGATGTTTTGAAAATAAAACCGAGGTTAGAGTACCC
TCTCAAAAATAACGGGGTTAAAGTATCCCCAATTATGGAAGATCGATATTTTGAAAATAAAATCC
AAGTTAGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
CCTCAAAAATAAC
Found at i:2981364 original size:78 final size:78
Alignment explanation
Indices: 2981262--2981415 Score: 204
Period size: 78 Copynumber: 2.0 Consensus size: 78
2981252 ATAAAACTAG
* * *
2981262 GGTTAGAGTATCCCCAATTATGAAAAAT-TGATGTTTTGGAAATAAAA-TCGGGGTTGGAGTATC
1 GGTTAGAGTATCCCCAATTATGAAAAATCAG-TGCTTTGGAAATAAAACT-GAGGTTGGAGTATC
*
2981325 CCCTTGAAAATAACA
64 CCCTCGAAAATAACA
* * * *
2981340 GGTTGGAGTATCTCCGATTGTGAAAAATCAGTGCTTTGGAAATAAAACTGAGGTTGGAGTATCCC
1 GGTTAGAGTATCCCCAATTATGAAAAATCAGTGCTTTGGAAATAAAACTGAGGTTGGAGTATCCC
2981405 CTCGAAAATAA
66 CTCGAAAATAA
2981416 AAACATGAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 64 0.97
79 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (78 bp):
GGTTAGAGTATCCCCAATTATGAAAAATCAGTGCTTTGGAAATAAAACTGAGGTTGGAGTATCCC
CTCGAAAATAACA
Found at i:2981418 original size:130 final size:130
Alignment explanation
Indices: 2981154--2981405 Score: 294
Period size: 130 Copynumber: 1.9 Consensus size: 130
2981144 CCTGATTTTA
* *
2981154 AAAAATTGATGTTTTGAAAATAAAATCGCAGTTAGAGTATCCTCTCAAAAATAACGGGGTTAGAG
1 AAAAATTGATGTTTTGAAAATAAAATCGCAGTTAGAGTATCCCCTCAAAAATAACGAGGTTAGAG
* ** * *
2981219 TATCCCCAATTATGGAAATTTGATGTTTTGAAAATAAAACTAGGGTTAGAGTATCCCCAATTATG
66 TATCCCCAATTATGAAAATCAGATGCTTTGAAAATAAAACTAGGGTTAGAGTATCCCCAATAATG
* ** * ** *
2981284 AAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTGAAAATAAC-AGGTTGGAG
1 AAAAATTGATGTTTTGAAAATAAAATCGCAGTTAGAGTATCCCCTCAAAAATAACGAGGTTAGAG
* * * * *
2981348 TATCTCCGATTGTGAAAAATCAG-TGCTTTGGAAATAAAACT-GAGGTTGGAGTATCCCC
66 TATCCCCAATTATG-AAAATCAGATGCTTTGAAAATAAAACTAG-GGTTAGAGTATCCCC
2981406 TCGAAAATAA
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
128 1 0.01
129 48 0.47
130 53 0.52
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (130 bp):
AAAAATTGATGTTTTGAAAATAAAATCGCAGTTAGAGTATCCCCTCAAAAATAACGAGGTTAGAG
TATCCCCAATTATGAAAATCAGATGCTTTGAAAATAAAACTAGGGTTAGAGTATCCCCAATAATG
Found at i:2984453 original size:34 final size:33
Alignment explanation
Indices: 2984377--2984502 Score: 101
Period size: 34 Copynumber: 3.5 Consensus size: 33
2984367 CATCTTACTT
* * * *
2984377 TTTGAGGGCAAAGAAAAAAGAGTACGTCCTG-TT
1 TTTGAGGACAAAG-GAAAAGAGTATGTCCTGCTC
*
2984410 TTTCAAGGACAAAGGAAAATGAGTATGTCCTGCTC
1 TTT-GAGGACAAAGGAAAA-GAGTATGTCCTGCTC
2984445 TTTGAGGACAAAGGAAAAGAGAATGAAATGGGTCCTGCTC
1 TTTGAGGACAAAGGAAAAGAG--T---AT--GTCCTGCTC
*
2984485 CTTGAGGACAAAGGAAAA
1 TTTGAGGACAAAGGAAAA
2984503 AGGGAAATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
33 10 0.13
34 33 0.43
35 5 0.07
38 2 0.03
40 26 0.34
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.21
Consensus pattern (33 bp):
TTTGAGGACAAAGGAAAAGAGTATGTCCTGCTC
Found at i:2984571 original size:44 final size:43
Alignment explanation
Indices: 2984437--2984579 Score: 186
Period size: 42 Copynumber: 3.4 Consensus size: 43
2984427 AATGAGTATG
* **
2984437 TCCTGCTCTTTGAGGACAAAGGAAAAG-A-G-AATGAAATGGG
1 TCCTGCTCTTTGAGGACAAAGGAAAAGAAGGAAATAAAATGCA
* *
2984477 TCCTGCTCCTTGAGGACAAAGGAAAA-AGGGAAATAAAATGCA
1 TCCTGCTCTTTGAGGACAAAGGAAAAGAAGGAAATAAAATGCA
2984519 TCCTGCTCTTTGAGGACAAAGGAAAAGAAGGAAATTAAAATGCA
1 TCCTGCTCTTTGAGGACAAAGGAAAAGAAGGAAA-TAAAATGCA
* *
2984563 TCTTGCTCTTTGGGGAC
1 TCCTGCTCTTTGAGGAC
2984580 TAGAAGGTGC
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
40 25 0.28
41 1 0.01
42 33 0.37
43 6 0.07
44 24 0.27
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (43 bp):
TCCTGCTCTTTGAGGACAAAGGAAAAGAAGGAAATAAAATGCA
Found at i:2984766 original size:61 final size:61
Alignment explanation
Indices: 2984566--2985253 Score: 754
Period size: 61 Copynumber: 11.4 Consensus size: 61
2984556 AAATGCATCT
* * * *** *
2984566 TGCTCTTTGGGGACT-AGAAGGTGCCACCAACTTATGTGGGTTTTGCCAGGAGAAAGCG--TCT
1 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAG-GTATCC
* * * * *
2984627 TGCTATTTGAGGACT-AAATGGAGCCACCAGCTCGTGTGGGCTTTAAAA-GAAAAGGTGTCC
1 TGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* * *
2984687 TACTCTTTGAGGACTGAAAGATGCCACAAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* * * * * * *
2984748 TGTTCTTTGAGGATTGAAAGGTGCTACCAACTTATGTGGGCTTTACAAGGAAAAGGTGTCT
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* *
2984809 TGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-GAAAAGCT-TCC
1 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* * * * *
2984868 TACTCTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACG--TCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* * *
2984927 TACTCTTTGAGGACTGGAAA-GTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
1 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* * * *
2984988 TGCTCTTTGAGGACTGAAAGATGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAGGCATCT
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* * * *
2985049 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAATGAAAAGATGTCC
1 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* * * * ***
2985110 TGCTCTTTGAGGACT-AGAAGGTGCCAGCAACTTGTGCGAGCTTTAAAATGAAAAGACGTCC
1 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
* * **
2985171 TACTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACATCC
1 TGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
2985232 TGCTCTTTGAGGACTGAAAGGT
1 TGCTCTTTGAGGACTGAAAGGT
2985254 TAAAAGGTTT
Statistics
Matches: 541, Mismatches: 72, Indels: 28
0.84 0.11 0.04
Matches are distributed among these distances:
58 1 0.00
59 100 0.18
60 64 0.12
61 375 0.69
62 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (61 bp):
TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCC
Found at i:2985010 original size:301 final size:301
Alignment explanation
Indices: 2984568--2985251 Score: 933
Period size: 301 Copynumber: 2.3 Consensus size: 301
2984558 ATGCATCTTG
* * * ** * *
2984568 CTCTTTGGGGACTAGAAGGTGCCACCAACTTATGTGGGTTTTGCCAGGAGAAAGCGTCTTGCTAT
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AAA-CGTCCTGCTCT
* **
2984633 TTGAGGACT-AAATGGAGCCACCAGCTCGTGTGGGCTTTAAAAGAAAAGGTGTCCTACTCTTTGA
64 TTGAGGACTGAAA--GAGCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGCATCCTACTCTTTGA
* * *
2984697 GGACTGAAAGATGCCACAAACTTGTGTGGGCTTTAAAAGGAAAAGGTATCCTGTTCTTTGAGGAT
127 GGACTGAAAGATGCCACAAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGAC
* * * * *
2984762 TGAAAGGTGCTACCAACTTATGTGGGCTTTACAAGGAAAAGGTGTCTTGCTCTTTGAGGACTAGA
192 TGAAAGGTGCCACCAACTTATGTAGGCTTTAAAAGGAAAAGATGTCCTGCTCTTTGAGGACTAGA
* * * *
2984827 AGGTGCCACCAACTTGTGTGGGCTTTGAAA-GAAAAG-CTTCCTA
257 AGGTGCCACCAACTTGTGCGAGCTTTAAAATGAAAAGACGTCCTA
* * *
2984870 CTCTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACGTCCTACTCTTT
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACGTCCTGCTCTTT
* * * *
2984935 GAGGACTGGAAAGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
66 GAGGACT-GAAAGAGCCACCAACTCGTGTGGGCTTTAAAA-GAAAAGGCATCCTACTCTTTGAGG
* * *
2985000 ACTGAAAGATGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAGGCATCTTGCTCTTTGAGGACTG
129 ACTGAAAGATGCCACAAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTG
* *
2985065 AAAGGTGCCACCAACTTGTGTAGGCTTTAAAATGAAAAGATGTCCTGCTCTTTGAGGACTAGAAG
194 AAAGGTGCCACCAACTTATGTAGGCTTTAAAAGGAAAAGATGTCCTGCTCTTTGAGGACTAGAAG
*
2985130 GTGCCAGCAACTTGTGCGAGCTTTAAAATGAAAAGACGTCCTA
259 GTGCCACCAACTTGTGCGAGCTTTAAAATGAAAAGACGTCCTA
* * *
2985173 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACATCCTGCTCT
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-GAAAGGAAA-ACGTCCTGCTCT
2985238 TTGAGGACTGAAAG
64 TTGAGGACTGAAAG
2985252 GTTAAAAGGT
Statistics
Matches: 334, Mismatches: 41, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
300 41 0.12
301 165 0.49
302 51 0.15
303 46 0.14
304 12 0.04
305 19 0.06
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (301 bp):
CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACGTCCTGCTCTTT
GAGGACTGAAAGAGCCACCAACTCGTGTGGGCTTTAAAAGAAAAGGCATCCTACTCTTTGAGGAC
TGAAAGATGCCACAAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAA
AGGTGCCACCAACTTATGTAGGCTTTAAAAGGAAAAGATGTCCTGCTCTTTGAGGACTAGAAGGT
GCCACCAACTTGTGCGAGCTTTAAAATGAAAAGACGTCCTA
Found at i:2986227 original size:1 final size:1
Alignment explanation
Indices: 2986216--2986259 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
2986206 TTCTTTTCTC
* * * *
2986216 TTTTTTCTTTTTTTTCTTTTTTTCTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2986260 GGAAAAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (1 bp):
T
Found at i:2986227 original size:7 final size:7
Alignment explanation
Indices: 2986204--2986258 Score: 51
Period size: 7 Copynumber: 7.6 Consensus size: 7
2986194 AAGTAGGTTC
2986204 TTTTCTT
1 TTTTCTT
*
2986211 TTCTCTT
1 TTTTCTT
2986218 TTTTCTTTT
1 TTTTC--TT
2986227 TTTTCTTT
1 TTTTC-TT
2986235 TTTTCTT
1 TTTTCTT
2986242 TTTT-TT
1 TTTTCTT
2986248 TGTTT-TT
1 T-TTTCTT
2986255 TTTT
1 TTTT
2986259 TGGAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 6 0.14
7 22 0.51
8 8 0.19
9 7 0.16
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:2986227 original size:8 final size:8
Alignment explanation
Indices: 2986209--2986259 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
2986199 GGTTCTTTTC
2986209 TTTTCTCTT
1 TTTTCT-TT
2986218 TTTTCTTTT
1 TTTTC-TTT
2986227 TTTTCTTT
1 TTTTCTTT
2986235 TTTTCTTT
1 TTTTCTTT
*
2986243 TTTT-TTG
1 TTTTCTTT
2986250 TTTT-TTT
1 TTTTCTTT
2986257 TTT
1 TTT
2986260 GGAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 11 0.28
8 15 0.38
9 12 0.31
10 1 0.03
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (8 bp):
TTTTCTTT
Found at i:2986229 original size:10 final size:9
Alignment explanation
Indices: 2986201--2986256 Score: 71
Period size: 9 Copynumber: 6.2 Consensus size: 9
2986191 CTTAAGTAGG
2986201 TTCTTTTCTT
1 TTCTTTT-TT
*
2986211 TTCTCTTTT
1 TTCTTTTTT
2986220 TTCTTTTTT
1 TTCTTTTTT
2986229 TTC-TTTTT
1 TTCTTTTTT
2986237 TTCTTTTTT
1 TTCTTTTTT
2986246 TT-TGTTTTT
1 TTCT-TTTTT
2986255 TT
1 TT
2986257 TTTGGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
8 9 0.21
9 27 0.64
10 6 0.14
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:2986236 original size:17 final size:18
Alignment explanation
Indices: 2986201--2986259 Score: 79
Period size: 17 Copynumber: 3.4 Consensus size: 18
2986191 CTTAAGTAGG
2986201 TTCTTTTCTTTTCTCTTTT
1 TTCTTTT-TTTTCTCTTTT
2986220 TTCTTTTTTTTCT-TTTT
1 TTCTTTTTTTTCTCTTTT
*
2986237 TTCTTTTTTTT-TGTTTT
1 TTCTTTTTTTTCTCTTTT
2986254 TT-TTTT
1 TTCTTTT
2986260 GGAAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.13
17 21 0.54
18 6 0.15
19 7 0.18
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (18 bp):
TTCTTTTTTTTCTCTTTT
Found at i:2991244 original size:38 final size:40
Alignment explanation
Indices: 2991160--2991244 Score: 95
Period size: 38 Copynumber: 2.2 Consensus size: 40
2991150 TTTTCTTTTA
* *
2991160 TTTCTCCCTTAATCAAAATAAATTTAACAAATTTGTACAT
1 TTTCCCCCTTAATCAAAATAAATTTAACAAATTTATACAT
* * *
2991200 TCTCCCCCTTAAT-AAAAT-AATTGTAGC-AATTTATGCAT
1 TTTCCCCCTTAATCAAAATAAATT-TAACAAATTTATACAT
2991238 TTTCCCC
1 TTTCCCC
2991245 TTTATCTCCC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
38 19 0.50
39 8 0.21
40 11 0.29
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (40 bp):
TTTCCCCCTTAATCAAAATAAATTTAACAAATTTATACAT
Done.