Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000075.1 Hibiscus syriacus cultivar Beakdansim tig00000139_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 141099
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2773 original size:22 final size:22
Alignment explanation
Indices: 2748--2791 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2738 ATTCACTGAC
2748 GGTGCTATTGATTTTGTTGAGA
1 GGTGCTATTGATTTTGTTGAGA
*
2770 GGTGCTATTGGTTTTGTTGAGA
1 GGTGCTATTGATTTTGTTGAGA
2792 TTAATTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.05, G:0.34, T:0.45
Consensus pattern (22 bp):
GGTGCTATTGATTTTGTTGAGA
Found at i:8535 original size:19 final size:19
Alignment explanation
Indices: 8506--8554 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
8496 CCTTTTATAT
*
8506 TGACAAGTGGCGATACGTTA
1 TGAC-AGTGGCGATACGTAA
8526 TGACAGTGGCGATACGTAA
1 TGACAGTGGCGATACGTAA
8545 TGACAGTGGC
1 TGACAGTGGC
8555 TTGAGTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (19 bp):
TGACAGTGGCGATACGTAA
Found at i:12607 original size:15 final size:16
Alignment explanation
Indices: 12587--12616 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12577 TATTGTTGAA
12587 TATGCTA-ATATGTGG
1 TATGCTAGATATGTGG
12602 TATGCTAGATATGTG
1 TATGCTAGATATGTG
12617 AATATTCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (16 bp):
TATGCTAGATATGTGG
Found at i:15826 original size:22 final size:21
Alignment explanation
Indices: 15775--15834 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
15765 CAAAAAATTG
*
15775 GTATCGATACCGTA--ATAGA
1 GTATCGATACCATAGTATAGA
15794 GTATC-AGTACCATAGTATAGTA
1 GTATCGA-TACCATAGTATAG-A
*
15816 GTATCGATACCATGGTATA
1 GTATCGATACCATAGTATA
15835 TGTATCAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 11 0.32
21 4 0.12
22 17 0.50
23 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (21 bp):
GTATCGATACCATAGTATAGA
Found at i:16256 original size:54 final size:54
Alignment explanation
Indices: 16174--17022 Score: 949
Period size: 54 Copynumber: 15.7 Consensus size: 54
16164 AAATAGGTAT
* * **
16174 TAAGTGTGCAATTCATGGAATTCATCATATTTTGATGAATAACCGTTTCAACAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* * *
16228 TAAGTGTGCAATTCACGGAATTCGTCATATGCTGATGAATAACCATTTCGGCAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
**
16282 TAAGTGTAAAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
*
16336 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGACAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* * * *
16390 TAAGTGTACAATTCACTGAATTCGTCATATGTTGATGAATAACCGTTTCGACAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* * *
16444 TAAGTGTGCAATTCACGGAATTCGTCATATGTTGATGAATAACCGTTTCGACGC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* * ** *
16498 TAAGTGTACAATTCATGGAATTTGTTATATGTTGATGAATAACCGTTTCGGCAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* *
16552 TAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAATCGTTTCGGCAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* * * *
16606 TAAGTGTGCAATTAATGGAATTCATCATATGTTGATAAATAACCGCTTCGGCAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* *
16660 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTCGACAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* * *
16714 TAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACTGTTTCAGCAC
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
* ** * * * * * *
16768 TATGTGTGCAACCCATGAAATTCATCACGA-GTTGATGAACAACCG-TACAGGTAC
1 TAAGTGTGCAATTCACGGAATTCATCA-TATGTTGATGAATAACCGTTTC-GGCAC
* ** * * * *
16822 TATGTGTGCAACCCACGAAATTCATCATGA-GTTGATGAACAATCG-TACAGGCAC
1 TAAGTGTGCAATTCACGGAATTCATCAT-ATGTTGATGAATAACCGTTTC-GGCAC
* ** * * * * *
16876 TATGTGTGCAACCCACGAAATTCATCATGA-GTTGATGAACAATCG-TACAAGCAC
1 TAAGTGTGCAATTCACGGAATTCATCAT-ATGTTGATGAATAACCGTTTC-GGCAC
* * * * * *
16930 TATGTGTGCAACTCACGGAATTTATCATGA-GTTAATGAACAACCG-TACAGGCAC
1 TAAGTGTGCAATTCACGGAATTCATCAT-ATGTTGATGAATAACCGTTTC-GGCAC
* * ** * *
16984 TATGTGTGAAACCCACAGAATTCATCATGTGTTGATGAA
1 TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAA
17023 CGACTGTATA
Statistics
Matches: 713, Mismatches: 78, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
53 2 0.00
54 710 1.00
55 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (54 bp):
TAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCAC
Found at i:19021 original size:2 final size:2
Alignment explanation
Indices: 19016--19092 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
19006 TACTTTTTTG
19016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19058 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19093 CTTACACAAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23021 original size:25 final size:27
Alignment explanation
Indices: 22966--23023 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 27
22956 ATTCTTATTT
*
22966 TTAATATTATAAATTTTAATAGTTTAA
1 TTAATATTATAAATTTTAATAGATTAA
*
22993 -TAATATTAT-TATTTTAATA-ATTAA
1 TTAATATTATAAATTTTAATAGATTAA
23017 TTAATAT
1 TTAATAT
23024 ACTTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.14
25 15 0.54
26 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TTAATATTATAAATTTTAATAGATTAA
Found at i:23080 original size:42 final size:42
Alignment explanation
Indices: 22990--23080 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
22980 TTTAATAGTT
* * *
22990 TAATAATATTATTATTTTAATAATTAATTAATATACTTAATA
1 TAATATTATTATTATATTAATAATAAATTAATATACTTAATA
* * *
23032 TTATATTATTTTTATATTAATAA-AAATTTAATATAATTTAATA
1 TAATATTATTATTATATTAATAATAAA-TTAATAT-ACTTAATA
23075 -AATATT
1 TAATATT
23081 TTACTTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.05
42 31 0.77
43 7 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (42 bp):
TAATATTATTATTATATTAATAATAAATTAATATACTTAATA
Found at i:23098 original size:32 final size:31
Alignment explanation
Indices: 23061--23121 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
23051 ATAAAAATTT
*
23061 AATATAATTTAATA-AATATTTTACTTTAATAA
1 AATATAA--TAATAGAATATTTTAATTTAATAA
23093 AATATAATAATATGAATATTTTAATTTAA
1 AATATAATAATA-GAATATTTTAATTTAA
23122 AATTGTAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 5 0.19
32 21 0.81
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (31 bp):
AATATAATAATAGAATATTTTAATTTAATAA
Found at i:28688 original size:21 final size:19
Alignment explanation
Indices: 28662--28700 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
28652 AACATTATTA
28662 TATATTCATTAATATTATAAG
1 TATATT-ATT-ATATTATAAG
28683 TATATTATTATATTATAA
1 TATATTATTATATTATAA
28701 ATAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTATTATATTATAAG
Found at i:28716 original size:20 final size:23
Alignment explanation
Indices: 28678--28718 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
28668 CATTAATATT
28678 ATAAGTATATTATTATATTATAA
1 ATAAGTATATTATTATATTATAA
28701 ATAA-TATATT-TT-TATTAT
1 ATAAGTATATTATTATATTAT
28719 TTTTAACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 6 0.33
23 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATAAGTATATTATTATATTATAA
Found at i:34358 original size:17 final size:17
Alignment explanation
Indices: 34338--34388 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
34328 ATATATATTC
*
34338 ATTAATATTATAAGTAT
1 ATTAATATAATAAGTAT
* *
34355 ATTATTATAATAATTAT
1 ATTAATATAATAAGTAT
34372 ATT-ATA-AATAA-TAT
1 ATTAATATAATAAGTAT
34386 ATT
1 ATT
34389 TTTATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 6 0.20
15 5 0.17
16 2 0.07
17 17 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTAATATAATAAGTAT
Found at i:34374 original size:14 final size:14
Alignment explanation
Indices: 34342--34388 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
34332 ATATTCATTA
*
34342 ATATTATAAGT-AT
1 ATATTATAAATAAT
34355 ATTATTAT-AATAATT
1 A-TATTATAAATAA-T
34370 ATATTATAAATAAT
1 ATATTATAAATAAT
34384 ATATT
1 ATATT
34389 TTTATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.10
14 19 0.66
15 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
ATATTATAAATAAT
Found at i:34393 original size:17 final size:16
Alignment explanation
Indices: 34347--34393 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
34337 CATTAATATT
34347 ATAAGTATATTATTATA
1 ATAA-TATATTATTATA
34364 ATAAT-TA-TATTATAA
1 ATAATATATTATTAT-A
*
34379 ATAATATATTTTTAT
1 ATAATATATTATTAT
34394 TATTTGCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
16 3 0.12
17 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATAATATATTATTATA
Found at i:35145 original size:131 final size:131
Alignment explanation
Indices: 34941--35395 Score: 595
Period size: 131 Copynumber: 3.5 Consensus size: 131
34931 TCTAACATAA
* * * *
34941 AATAAATGACCTCTCATACCTTAAAGCAGTCATTTATTACTCCAATCAAAATGAAGAAATATCAT
1 AATAAATGACCTCTCATACCTTAAAGCAGTCATTTATTGCTCCAATCGAAATGAAGAGATATCAC
* *
35006 TATTCCGTCTTAAAATTCAACATCGATTCGAGTGAAAACGATAATATCTAATGATTTCCACTCGA
66 TATTCCGTCTTAAAATTCAACATCGATTCGAGTGAAAACGATAATATCTAATGATTTTCAATCGA
35071 G
131 G
* * * *
35072 AATAAATGACCCCTAATACCTTAAAGCAGTCATTTATTGCTTCAATCGAAATGAACAGATATCAC
1 AATAAATGACCTCTCATACCTTAAAGCAGTCATTTATTGCTCCAATCGAAATGAAGAGATATCAC
* *
35137 TATCCCGTCTTAAAATTCAACATCGATTCGAGTGAAAACAATAATATCTAATGATTTTCAATCGA
66 TATTCCGTCTTAAAATTCAACATCGATTCGAGTGAAAACGATAATATCTAATGATTTTCAATCGA
35202 G
131 G
* *
35203 AATAAATAATCTCTCATACCTTAAAGCAGTCATTTATTGCTCCAATCGAAATGAAGAGATATCAC
1 AATAAATGACCTCTCATACCTTAAAGCAGTCATTTATTGCTCCAATCGAAATGAAGAGATATCAC
* * * * ** * * * * * *
35268 TATTCCATCATAAAAATCAATATTAATTCGAGAGAGAATGATATTATCAAATTATTTTCAATCGA
66 TATTCCGTCTTAAAATTCAACATCGATTCGAGTGAAAACGATAATATCTAATGATTTTCAATCGA
35333 G
131 G
* * * * ** * * *
35334 AATAAATGACCTCTCGTGCCTTAGAGCGGTCATTTATCACTCCAACCGAAATTAAAAGATAT
1 AATAAATGACCTCTCATACCTTAAAGCAGTCATTTATTGCTCCAATCGAAATGAAGAGATAT
35396 TATTATTCTC
Statistics
Matches: 281, Mismatches: 43, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
131 281 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30
Consensus pattern (131 bp):
AATAAATGACCTCTCATACCTTAAAGCAGTCATTTATTGCTCCAATCGAAATGAAGAGATATCAC
TATTCCGTCTTAAAATTCAACATCGATTCGAGTGAAAACGATAATATCTAATGATTTTCAATCGA
G
Found at i:37582 original size:3 final size:3
Alignment explanation
Indices: 37561--37609 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
37551 TAAAGCCTAA
* *
37561 AAT AAT AAA AATT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
37607 AAT
1 AAT
37610 GTCGGGACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 40 0.98
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:38076 original size:134 final size:135
Alignment explanation
Indices: 37780--38140 Score: 420
Period size: 134 Copynumber: 2.7 Consensus size: 135
37770 ATCGAGAAAT
* * * * * *
37780 GTTGACTCATTCCACTTTTCTTCAGGGAATATGGAATCGAGGTAGACTTATTCCACTTTTACTCA
1 GTTGATTCATTCCACTATTCTTCAGGGAATATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA
* * * * * * * *
37845 GGGAAGATTAAATCTTGAAAAATGAGGGATCTGTTCTGCTTCTTTTTTTTATGGAAAATCAAATT
66 GGGAATATCAAATCTTGAAAAA-GAAGGATCTGTTCTACTTC-TTTCTTGAGGGAAAATCAAATC
37910 TAGGGAC
129 TAGGGAC
* * * *
37917 ATTGATTCATTCCACTATTAC-TCAGGGAAGATTGAATTGAGGCATACTTGTTCCACTGTTACTC
1 GTTGATTCATTCCACTATT-CTTCAGGGAATATTGAATCGAGGCAGACTTGTTCCACTGTTACTC
* * * * * *
37981 ATGGAATATCAAATATTGAAAGAGAATGATTTGTTCTACTTC-TTCTTGAGGGAAAATCAGATCT
65 AGGGAATATCAAATCTTGAAAAAGAAGGATCTGTTCTACTTCTTTCTTGAGGGAAAATCAAATCT
*
38045 GGGGAC
130 AGGGAC
* * *
38051 GTTGATTCATTCAACTGTTCTTCAGGGAATATTGAATCGATGCAGACTTGTTCCACTGTTACTCA
1 GTTGATTCATTCCACTATTCTTCAGGGAATATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA
*
38116 GGGAATATCAAATCTTGAAATAGAA
66 GGGAATATCAAATCTTGAAAAAGAA
38141 AGTGTTGAGT
Statistics
Matches: 187, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
133 1 0.01
134 100 0.53
136 15 0.08
137 70 0.37
138 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (135 bp):
GTTGATTCATTCCACTATTCTTCAGGGAATATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA
GGGAATATCAAATCTTGAAAAAGAAGGATCTGTTCTACTTCTTTCTTGAGGGAAAATCAAATCTA
GGGAC
Found at i:41031 original size:20 final size:20
Alignment explanation
Indices: 40994--41032 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40984 AGATTGAGTG
* * *
40994 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
41014 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
41033 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:41235 original size:23 final size:21
Alignment explanation
Indices: 41209--41267 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
41199 TTACCCTGTG
41209 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
41232 GGGGGAATTGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
* *
41252 GGGGGGATCGATTCCC
1 GGGGGAATCGGTTCCC
41268 TCCACACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.39
21 4 0.13
22 3 0.10
23 12 0.39
ACGTcount: A:0.19, C:0.24, G:0.36, T:0.22
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:41256 original size:21 final size:23
Alignment explanation
Indices: 41208--41267 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
41198 ATTACCCTGT
41208 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
41231 AGGGGGAATTGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
41252 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
41268 TCCACACCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 5 0.16
21 11 0.35
22 3 0.10
23 12 0.39
ACGTcount: A:0.18, C:0.23, G:0.37, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:45273 original size:83 final size:83
Alignment explanation
Indices: 45134--45303 Score: 340
Period size: 83 Copynumber: 2.0 Consensus size: 83
45124 TAATCCGAAG
45134 CCAACCCATTATATTCCTTTAATAACTCATCATAGGATAAATCATCAAAATCGGATGAGTTAGAG
1 CCAACCCATTATATTCCTTTAATAACTCATCATAGGATAAATCATCAAAATCGGATGAGTTAGAG
45199 GTTACCTTAGAATCTTCC
66 GTTACCTTAGAATCTTCC
45217 CCAACCCATTATATTCCTTTAATAACTCATCATAGGATAAATCATCAAAATCGGATGAGTTAGAG
1 CCAACCCATTATATTCCTTTAATAACTCATCATAGGATAAATCATCAAAATCGGATGAGTTAGAG
45282 GTTACCTTAGAATCTTCC
66 GTTACCTTAGAATCTTCC
45300 CCAA
1 CCAA
45304 ATGCCATCAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (83 bp):
CCAACCCATTATATTCCTTTAATAACTCATCATAGGATAAATCATCAAAATCGGATGAGTTAGAG
GTTACCTTAGAATCTTCC
Found at i:48940 original size:10 final size:10
Alignment explanation
Indices: 48903--48948 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
48893 GAATCCCCTT
*
48903 TTTATTTAT-
1 TTTATTTTTC
48912 TTTATTTTTC
1 TTTATTTTTC
*
48922 -TT-CTTTTC
1 TTTATTTTTC
48930 TTTATTTTTC
1 TTTATTTTTC
48940 TTTATTTTT
1 TTTATTTTT
48949 TCTCCTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
8 5 0.16
9 12 0.39
10 14 0.45
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:48949 original size:29 final size:28
Alignment explanation
Indices: 48903--48977 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
48893 GAATCCCCTT
* *
48903 TTTATTTATTTTATTTTTCTTCTTTTC-
1 TTTATTTTTTTTATTTTTCTCCTTTTCA
48930 TTTATTTTTCTTTATTTTTTCTCCTTTTCA
1 TTTATTTTT-TTTA-TTTTTCTCCTTTTCA
* *
48960 TTTCTTTTGTTTCATTTT
1 TTTATTTT-TTTTATTTT
48978 CATTTTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 8 0.20
28 4 0.10
29 17 0.43
30 10 0.25
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.76
Consensus pattern (28 bp):
TTTATTTTTTTTATTTTTCTCCTTTTCA
Found at i:48967 original size:20 final size:20
Alignment explanation
Indices: 48935--48982 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
48925 TTTTCTTTAT
*
48935 TTTTC-TTTATTTT-TTCTCC
1 TTTTCATTTATTTTGTT-TCA
*
48954 TTTTCATTTCTTTTGTTTCA
1 TTTTCATTTATTTTGTTTCA
48974 TTTTCATTT
1 TTTTCATTT
48983 TAATTTTCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 18 0.72
21 2 0.08
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTCATTTATTTTGTTTCA
Found at i:59860 original size:131 final size:131
Alignment explanation
Indices: 59626--60117 Score: 662
Period size: 131 Copynumber: 3.8 Consensus size: 131
59616 ATAATTTTAA
* *
59626 GAGTGAAAACGATAATATCTAATTATTTCTAA-CCACGAATAAATGACCTCTCATACCTTAAAGC
1 GAGTGAAAACGATAATATCTAATTATTTCCAATCGA-GAATAAATGACCTCTCATACCTTAAAGC
* * * *
59690 AGTCATTTTTTACTCCAATCGGAATGAAGAAACATCACTATTCCGTCTTAAAATTCAACATCGAT
65 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAACATCGAT
59755 TC
130 TC
* * * *
59757 GAGTGAAAACGATAATATCTAATGATTTCCACTCGAGAATAAATGACCTCTCATACTTTAAAGTA
1 GAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * *
59822 GTCATTTATTGCTTCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAACGTCGATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAACATCGATT
59887 C
131 C
* * * * *
59888 GAGTGAAAACGATAATATCTAATAATTTTCAATCTAGAATAAATGATCTCTCATACCTTAAATCA
1 GAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * * * * **
59953 GTCATTTATTGCTCCAATCGAAATGAAGAGATATCATTATTCCATCTTAAAAATCAATATTAATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAACATCGATT
60018 C
131 C
* * * * * * *
60019 GAGAGAGAACGATAATATCAAATTATTTTCAATCGAGAATAAATGACCTCTCGTGCCTTAAAGCG
1 GAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* *
60084 GTCATTTATTACTCCAACCGAAATGAAAAGATAT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATAT
60118 TATTATTCTC
Statistics
Matches: 318, Mismatches: 42, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
131 316 0.99
132 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (131 bp):
GAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATTCAACATCGATT
C
Found at i:62108 original size:26 final size:26
Alignment explanation
Indices: 62035--62100 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
62025 GATCTGGACA
*
62035 GTTATATCAACAAGCCGATCGAGACT
1 GTTATATCAACAAGCCGATCCAGACT
*
62061 GTTATATCAACAAGCCGATCCAGGCT
1 GTTATATCAACAAGCCGATCCAGACT
62087 GTTATATCAACAAG
1 GTTATATCAACAAG
62101 TCAATCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (26 bp):
GTTATATCAACAAGCCGATCCAGACT
Found at i:62300 original size:3 final size:3
Alignment explanation
Indices: 62292--62340 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
62282 TAAAGCCTAA
62292 AAT AAT 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
62340 A
1 A
62341 TTGGGACGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62920 original size:14 final size:14
Alignment explanation
Indices: 62902--62948 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
62892 ATATTCATTA
62902 ATATTATAAGTATAT
1 ATATTATAA-TATAT
*
62917 -TATTATAATATTT
1 ATATTATAATATAT
62930 ATATTATAA-ATAAT
1 ATATTATAATAT-AT
62944 ATATT
1 ATATT
62949 TATATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATTATAATATAT
Found at i:62927 original size:11 final size:10
Alignment explanation
Indices: 62884--62963 Score: 57
Period size: 9 Copynumber: 8.3 Consensus size: 10
62874 AAATTCAAAC
62884 ATTATTATAT
1 ATTATTATAT
62894 ATTCATTA-AT
1 ATT-ATTATAT
*
62904 ATTATAAGTAT
1 ATTATTA-TAT
62915 ATTATTATA-
1 ATTATTATAT
62924 A-TATT-TAT
1 ATTATTATAT
*
62932 ATTA-TAAAT
1 ATTATTATAT
62941 AATATATT-TAT
1 -AT-TATTATAT
62952 ATTATTAT-T
1 ATTATTATAT
62961 ATT
1 ATT
62964 TTTGAATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
7 2 0.04
8 6 0.11
9 16 0.29
10 15 0.27
11 16 0.29
12 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (10 bp):
ATTATTATAT
Found at i:62959 original size:28 final size:27
Alignment explanation
Indices: 62886--62959 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
62876 ATTCAAACAT
*
62886 TATTATATATTCATTAATATTATAAGTATA
1 TATT-TATATT-ATT-ATATTATAAATATA
*
62916 T-TATTATAATATTTATATTATAAATAATA
1 TAT-TTATATTA-TTATATTATAAAT-ATA
62945 TATTTATATTATTAT
1 TATTTATATTATTAT
62960 TATTTTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
28 15 0.41
29 19 0.51
30 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (27 bp):
TATTTATATTATTATATTATAAATATA
Found at i:65126 original size:2 final size:2
Alignment explanation
Indices: 65119--65157 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
65109 CTCTTGAGTC
65119 AT 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 AT A
65158 GCCTTATTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:74505 original size:21 final size:21
Alignment explanation
Indices: 74465--74505 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
74455 CCCGCTACAT
* *
74465 CCGCAATAGCGCCCGTGACGG
1 CCGCAATAGCACCCGCGACGG
*
74486 CCGCAATAGCACCTGCGACG
1 CCGCAATAGCACCCGCGACG
74506 ACCACAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.39, G:0.29, T:0.10
Consensus pattern (21 bp):
CCGCAATAGCACCCGCGACGG
Found at i:75286 original size:22 final size:22
Alignment explanation
Indices: 75229--75287 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
75219 ACGCGATTCT
75229 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
75251 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
75272 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
75288 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:75301 original size:20 final size:20
Alignment explanation
Indices: 75276--75447 Score: 161
Period size: 20 Copynumber: 8.6 Consensus size: 20
75266 TTTTCCGACT
75276 ATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAATATG-ACA
* *
75296 ATCGCAATGCGAGTATGACT
1 ATCGCAATGCGAATATGACA
75316 ATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAATATG-ACA
* *
75336 ATCGCAATGCGAGTATGACT
1 ATCGCAATGCGAATATGACA
75356 ATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAATATG-ACA
* * *
75376 ATCGCAATACGAGTATGACT
1 ATCGCAATGCGAATATGACA
* * *
75396 ATCGCAATGCGATTCTGACT
1 ATCGCAATGCGAATATGACA
* * * *
75416 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGAATATGACA
*
75436 ATCGCAACGCGA
1 ATCGCAATGCGA
75448 TTCTGACTGT
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.02
20 127 0.96
21 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATATGACA
Found at i:75324 original size:40 final size:40
Alignment explanation
Indices: 75272--75447 Score: 264
Period size: 40 Copynumber: 4.4 Consensus size: 40
75262 GCGATTTTCC
75272 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
75312 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
*
75352 GACTATCGCAATGCGAATATGTAAATCGCAATACGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
* * * * * *
75392 GACTATCGCAATGCGATTCTG-ACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGAGTAT
*
75432 GACTATCGCAACGCGA
1 GACTATCGCAATGCGA
75448 TTCTGACTGT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 1 0.01
40 125 0.99
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
Found at i:75448 original size:20 final size:20
Alignment explanation
Indices: 75391--75469 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
75381 AATACGAGTA
*
75391 TGACTATCGCAATGCGATTC
1 TGACTATCGCAACGCGATTC
75411 TGACTATCGCAACGCGATTC
1 TGACTATCGCAACGCGATTC
75431 TGACTATCGCAACGCGATTC
1 TGACTATCGCAACGCGATTC
* * *
75451 TGACTGTTGCAATGCGATT
1 TGACTATCGCAACGCGATT
75470 TTCAAAGCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (20 bp):
TGACTATCGCAACGCGATTC
Found at i:75455 original size:60 final size:60
Alignment explanation
Indices: 75272--75469 Score: 195
Period size: 60 Copynumber: 3.3 Consensus size: 60
75262 GCGATTTTCC
* * *
75272 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGAGTATGACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTATG-ACTATCGCAATGCGAATATGACTATCGCAATGCGAATAT
* * * * *
75332 GTA-AATCGCAATGCGAGTATGACTATCGCAATGCGAATATGTA-AATCGCAATACGAGTAT
1 G-ACTATCGCAATGCGATTATGACTATCGCAATGCGAATATG-ACTATCGCAATGCGAATAT
* * * * * * *
75392 GACTATCGCAATGCGATTCTGACTATCGCAACGCGATTCTGACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTATGACTATCGCAATGCGAATATGACTATCGCAATGCGAATAT
* *
75452 GACTGTTGCAATGCGATT
1 GACTATCGCAATGCGATT
75470 TTCAAAGCGC
Statistics
Matches: 113, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
59 3 0.03
60 108 0.96
61 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (60 bp):
GACTATCGCAATGCGATTATGACTATCGCAATGCGAATATGACTATCGCAATGCGAATAT
Found at i:75670 original size:22 final size:22
Alignment explanation
Indices: 75644--75686 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
75634 GGCGACATCC
*
75644 GTCCCCATCTCTGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
75666 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
75687 TGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:76177 original size:20 final size:20
Alignment explanation
Indices: 76073--76179 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
76063 AGAATCGCAA
*
76073 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
76092 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
76111 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
76131 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
76151 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
76171 TGCGATTTT
1 TGCGATTTT
76180 AAGTTTCAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
19 26 0.33
20 52 0.67
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:78456 original size:30 final size:30
Alignment explanation
Indices: 78422--78494 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
78412 CCCGAAGGAC
78422 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGTAA
*
78452 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGTAA
* *
78482 CTGTCCATAGGTC
1 CTATCCAGAGGTC
78495 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCATCGGTAA
Found at i:78518 original size:31 final size:31
Alignment explanation
Indices: 78480--78607 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
78470 GATCCTCGGT
* *
78480 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
78511 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
78542 TACCGTCCATATGTCTCGAA-AGACATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* *
78574 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
78605 AAC
1 AAC
78608 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 52 0.67
32 24 0.31
33 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:80932 original size:18 final size:18
Alignment explanation
Indices: 80909--80958 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
80899 TTTACTCGTA
80909 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
80927 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
80945 ATTTCACTTAGATT
1 ATTTCACTTAGATT
80959 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:81131 original size:20 final size:20
Alignment explanation
Indices: 81106--81173 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
81096 TAGTTTACTT
81106 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
81126 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* * *
81146 TTGCAACG-TGAATTTGACTA
1 TCGCAACGCGGAA-ATGACTA
81166 TCGCAACG
1 TCGCAACG
81174 AAAGAATAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.05
20 39 0.95
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:81242 original size:20 final size:19
Alignment explanation
Indices: 81217--81282 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
81207 CGATTCTCTC
*
81217 GTTGCGATAGTCAAATTCGA
1 GTTGCGATAGTC-AATTCGT
*
81237 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCA-ATTCGT
*
81257 GTTGCAATAGTC-ATTCGT
1 GTTGCGATAGTCAATTCGT
81275 GTTGCGAT
1 GTTGCGAT
81283 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 12 0.30
19 1 0.03
20 27 0.68
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (19 bp):
GTTGCGATAGTCAATTCGT
Found at i:83340 original size:36 final size:30
Alignment explanation
Indices: 83260--83325 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
83250 ATAAGAGTTG
83260 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
83290 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
83320 ATTTGT
1 ATTTGT
83326 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:83500 original size:20 final size:20
Alignment explanation
Indices: 83475--83792 Score: 269
Period size: 20 Copynumber: 16.9 Consensus size: 20
83465 GCGATTTTCT
*
83475 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
83495 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
83515 TGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
83534 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
83554 CGATGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
83574 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
83594 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
83608 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
83628 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
83648 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
*
83662 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
**
83682 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
83702 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
83716 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* * *
83736 CGTTGTGATAGTCATATTTG
1 CGTTGCGATAGTCAAATTCG
* *
83756 CGTTGTGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
83776 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
83793 GAATGTGTAA
Statistics
Matches: 237, Mismatches: 42, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
14 30 0.13
16 3 0.01
18 3 0.01
19 20 0.08
20 181 0.76
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:83632 original size:54 final size:54
Alignment explanation
Indices: 83492--83750 Score: 367
Period size: 54 Copynumber: 4.7 Consensus size: 54
83482 ATAGTCAAAT
* * *
83492 TCCCGTTGCGATAATCAAATTCGTGTTGCGATAGTCA-TTTCGCGTTGCGATAGTCAAA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT--T---A
* * *
83550 TTCGCGATGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
1 -TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
83605 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
*
83659 TCCCGTTGCGATAGTCAAATTTGCGTTGCGATAGTCATTTTCGCATTGCGATTA
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* * *
83713 TCCCGTTGCGATATTCAAATTCACGTTGTGATAGTCAT
1 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAT
83751 ATTTGCGTTG
Statistics
Matches: 185, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
54 138 0.75
55 1 0.01
58 1 0.01
59 32 0.17
60 13 0.07
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (54 bp):
TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
Found at i:83686 original size:74 final size:74
Alignment explanation
Indices: 83608--83789 Score: 199
Period size: 74 Copynumber: 2.5 Consensus size: 74
83598 GCGATTATCC
* * * * * *
83608 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA-TTTTCGCAT-TGCGATTATCCCGTTGCGAT
1 CGTTGCGATAGTCATATTCGCGTTGCGATAGTCACGTTGCG-ATATGCAAAT-TCACGTTGCGAT
83671 AGTCAAATTTG
64 AGTCAAATTTG
* * * * *
83682 CGTTGCGATAGTCATTTTCGCATTGCGATTA-TCCCGTTGCGATATTCAAATTCACGTTGTGATA
1 CGTTGCGATAGTCATATTCGCGTTGCGA-TAGTCACGTTGCGATATGCAAATTCACGTTGCGATA
*
83746 GTCATATTTG
65 GTCAAATTTG
*
83756 CGTTGTGATAGTCATATTCGCGTTGCGATAGTCA
1 CGTTGCGATAGTCATATTCGCGTTGCGATAGTCA
83790 AATGAATGTG
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
73 2 0.02
74 76 0.86
75 10 0.11
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (74 bp):
CGTTGCGATAGTCATATTCGCGTTGCGATAGTCACGTTGCGATATGCAAATTCACGTTGCGATAG
TCAAATTTG
Found at i:83709 original size:108 final size:111
Alignment explanation
Indices: 83492--83792 Score: 378
Period size: 108 Copynumber: 2.7 Consensus size: 111
83482 ATAGTCAAAT
* * *
83492 TCCCGTTGCGATAATCAAATTCGTGTTGCGATAGTCA-TTTCGCGTTGCGATAGTCAAATTCGCG
1 TCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATA-T--AATTCCCG
*
83556 ATGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
63 ATGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* *
83605 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT-T-A-TCCCGTTG
1 TCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATATAATTCCCGATG
*
83667 CGATAGTCAAATTTGCGTTGCGATAGTCATTTTCGCATTGCGATTA
66 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* * * * * *
83713 TCCCGTTGCGATATTCAAATTCACGTTGTGATAGTCATATTT-GCGTTGTGATAGTCATATTCGC
1 TCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAT-TTTCGCATTGCGATA-T-A-ATTCCC
*
83777 GTTGCGATAGTCAAAT
62 GATGCGATAGTCAAAT
83793 GAATGTGTAA
Statistics
Matches: 167, Mismatches: 13, Indels: 15
0.86 0.07 0.08
Matches are distributed among these distances:
108 93 0.56
109 4 0.02
110 1 0.01
112 1 0.01
113 36 0.22
114 32 0.19
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (111 bp):
TCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATATAATTCCCGATG
CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
Found at i:83990 original size:18 final size:18
Alignment explanation
Indices: 83967--84008 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
83957 AAGCCGGTTG
**
83967 TGATTGAGATTTTGATTT
1 TGATTGAGATTGCGATTT
*
83985 TGATTGCGATTGCGATTT
1 TGATTGAGATTGCGATTT
84003 TGATTG
1 TGATTG
84009 CCTTTTGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.26, T:0.50
Consensus pattern (18 bp):
TGATTGAGATTGCGATTT
Found at i:91248 original size:20 final size:21
Alignment explanation
Indices: 91210--91270 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
91200 TTTTGGTGCA
*
91210 GAGGGAATCGA-TCCTCCC-TT
1 GAGGGAACCGATTCC-CCCTTT
91230 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTTT
91251 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
91271 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 13 0.36
21 6 0.17
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:92926 original size:12 final size:12
Alignment explanation
Indices: 92905--92934 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
92895 AGATGAGCCT
92905 GAGCAACCCGAG
1 GAGCAACCCGAG
*
92917 GAGCAGCCCGAG
1 GAGCAACCCGAG
92929 GAGCAA
1 GAGCAA
92935 GCACAACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.30, G:0.37, T:0.00
Consensus pattern (12 bp):
GAGCAACCCGAG
Found at i:95712 original size:14 final size:14
Alignment explanation
Indices: 95693--95729 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
95683 TCCCGTGGCA
95693 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
95707 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
95721 TTCTTCTTC
1 TT-TTCTTC
95730 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:96841 original size:20 final size:20
Alignment explanation
Indices: 96792--96934 Score: 110
Period size: 20 Copynumber: 7.0 Consensus size: 20
96782 TTGAAATTCA
* * *
96792 GCATTGCGACAGCCAGAATC
1 GCATTGCGATAGTCATAATC
*
96812 GCGTTGCGATAGTCATAATC
1 GCATTGCGATAGTCATAATC
* *
96832 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CATAATC
* * *
96852 GCGTTGCAATAGTCATACTC
1 GCATTGCGATAGTCATAATC
* *
96872 GCATTGCGAT-TTACATATTC
1 GCATTGCGATAGT-CATAATC
*
96892 GCATTGCGATAGTCGGAAAATC
1 GCATTGCGATAGTC--ATAATC
* *
96914 GCAATGCGATAGTCAGAATC
1 GCATTGCGATAGTCATAATC
96934 G
1 G
96935 AGTTGCAAAT
Statistics
Matches: 97, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.02
20 76 0.78
21 2 0.02
22 17 0.18
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (20 bp):
GCATTGCGATAGTCATAATC
Found at i:96881 original size:40 final size:40
Alignment explanation
Indices: 96810--96923 Score: 165
Period size: 40 Copynumber: 2.8 Consensus size: 40
96800 ACAGCCAGAA
96810 TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
* *
96850 TCGCGTTGCAATAGTCATACTCGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
* * *
96890 TCGCATTGCGATAGTCGGAAAATCGCAATGCGAT
1 TCGCGTTGCGATAGTC--ATAATCGCATTGCGAT
96924 AGTCAGAATC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 52 0.80
42 13 0.20
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (40 bp):
TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:101859 original size:102 final size:102
Alignment explanation
Indices: 101683--101886 Score: 336
Period size: 102 Copynumber: 2.0 Consensus size: 102
101673 AATCATATAT
*
101683 ATATTCTATTTAATATCATAACTTTATTATTAGTTCTTAGATGCAAATCTTTTTAGCATAAAGAA
1 ATATTCTATTTAATATCATAACTTTATTATTAGTTCTTAGATGCAAATCTTTATAGCATAAAGAA
*
101748 ACATGAAATAGGTAAAATAGATATGATAGTAGTAGTA
66 ACATGAAATAGGTAAAATAGAGATGATAGTAGTAGTA
* * * * **
101785 ATATTCTATTTATTATCATAACTTTGTTATTTGTTCTTAGATGCAGATCTTTATAGTTTAAAGAA
1 ATATTCTATTTAATATCATAACTTTATTATTAGTTCTTAGATGCAAATCTTTATAGCATAAAGAA
101850 ACATGAAATAGGTAAAATAGAGATGATAGTAGTAGTA
66 ACATGAAATAGGTAAAATAGAGATGATAGTAGTAGTA
101887 CTGAAGTCAG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (102 bp):
ATATTCTATTTAATATCATAACTTTATTATTAGTTCTTAGATGCAAATCTTTATAGCATAAAGAA
ACATGAAATAGGTAAAATAGAGATGATAGTAGTAGTA
Found at i:103952 original size:59 final size:59
Alignment explanation
Indices: 103824--103959 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 59
103814 ATCAACATGT
* * *
103824 GACCATTTTGTAACTTTTAATAGCCGATGACTCAACAAAGCAATGTCCTATAGTCAAGG
1 GACCATTTTGTAACTTTTAACAGCCGAGGACTCAACAAAGCAATGTCCTATACTCAAGG
* ** * * * **
103883 GATCATTTTGTAACTTTTAACAGTTGAAGGACTTAACAAAGCAATTTCTTATACTTGAGG
1 GACCATTTTGTAACTTTTAACAGCCG-AGGACTCAACAAAGCAATGTCCTATACTCAAGG
103943 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
103960 ACCCTAATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 22 0.35
60 38 0.60
61 3 0.05
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (59 bp):
GACCATTTTGTAACTTTTAACAGCCGAGGACTCAACAAAGCAATGTCCTATACTCAAGG
Found at i:117177 original size:21 final size:20
Alignment explanation
Indices: 117148--117186 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
117138 TGCCATTATT
*
117148 TTAATATTTCTTCTTTTTAA
1 TTAATATTTCTTATTTTTAA
*
117168 TTAATTATTTGTTATTTTT
1 TTAA-TATTTCTTATTTTT
117187 TTTACAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (20 bp):
TTAATATTTCTTATTTTTAA
Found at i:118569 original size:7 final size:7
Alignment explanation
Indices: 118557--118589 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
118547 TTGTGTCGAC
118557 CCCTAAA
1 CCCTAAA
118564 CCCTAAA
1 CCCTAAA
118571 CCCTAAA
1 CCCTAAA
118578 CCCTAAA
1 CCCTAAA
118585 CCCTA
1 CCCTA
118590 GCCCGCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.15
Consensus pattern (7 bp):
CCCTAAA
Found at i:121521 original size:23 final size:23
Alignment explanation
Indices: 121494--121558 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
121484 CACAATTAAA
*
121494 TTTGCCACTACATTTCCATCCAC
1 TTTGCCACGACATTTCCATCCAC
121517 TTTGCCACGACATTTCCATCCAC
1 TTTGCCACGACATTTCCATCCAC
*
121540 TTTGCCACGACATATCCAT
1 TTTGCCACGACATTTCCAT
121559 TTGCTACCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.23, C:0.37, G:0.08, T:0.32
Consensus pattern (23 bp):
TTTGCCACGACATTTCCATCCAC
Found at i:125656 original size:10 final size:10
Alignment explanation
Indices: 125641--125669 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
125631 TTAATGTAAT
125641 TATATATATG
1 TATATATATG
125651 TATATATATG
1 TATATATATG
125661 TATATATAT
1 TATATATAT
125670 ACATAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:126454 original size:25 final size:25
Alignment explanation
Indices: 126386--126437 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
126376 TAAGGGGCAC
*
126386 CATTTTTCAAA-AT-CTTCATCAAA
1 CATTTTTCAAATCTCCTTCATCAAA
126409 CATTTTTCAAATCTCCTTCATCAAA
1 CATTTTTCAAATCTCCTTCATCAAA
126434 CATT
1 CATT
126438 ATTTAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 11 0.42
24 1 0.04
25 14 0.54
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (25 bp):
CATTTTTCAAATCTCCTTCATCAAA
Found at i:126457 original size:18 final size:18
Alignment explanation
Indices: 126434--126472 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
126424 CTTCATCAAA
*
126434 CATTATTTAATATTCTTT
1 CATTATTTAAAATTCTTT
126452 CATTATTTAAAATTCTTT
1 CATTATTTAAAATTCTTT
126470 CAT
1 CAT
126473 AAAGCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (18 bp):
CATTATTTAAAATTCTTT
Found at i:127767 original size:164 final size:164
Alignment explanation
Indices: 127474--127779 Score: 380
Period size: 164 Copynumber: 1.9 Consensus size: 164
127464 AGGCGCTCAG
* * * * * * *
127474 ATTCTCTTCAACACGAATGAGAAGTTTCATTTCCAACATCAAATTATCTCTAGGCATTTAGATTT
1 ATTCTCTTCAACACGAATGAGAAGTGTCATTTCCAACACCAAATCATCTCTAGACAATCAAATTT
* * ** *
127539 CCTCAACAAGAAGGAACAATGTTATTTTCATATGCACAGTCACCTAAATATGACTAGATGTCCTC
66 CATCAACAAGAAAGAACAATACTATCTTCATATGCACAGTCACCTAAATATGACTAGATGTCCTC
127604 AACATGAAGGAATAATGTCGTCATAAACGACCAT
131 AACATGAAGGAATAATGTCGTCATAAACGACCAT
** * * *
127638 ATTCTCTTCAACTTGAATGAGCAGTGTCGTTTCCAACGCCAAATCATCTCTAGACAATCAAATTT
1 ATTCTCTTCAACACGAATGAGAAGTGTCATTTCCAACACCAAATCATCTCTAGACAATCAAATTT
* * * * * *
127703 CATCAACAAGAAAGAACAATACTGTCTTCATATGCATAGTCA-TTCAAATGTGGCTAGTTGTCCT
66 CATCAACAAGAAAGAACAATACTATCTTCATATGCACAGTCACCT-AAATATGACTAGATGTCCT
*
127767 CATCATGAAGGAA
130 CAACATGAAGGAA
127780 CAACACCATC
Statistics
Matches: 117, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
163 1 0.01
164 116 0.99
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (164 bp):
ATTCTCTTCAACACGAATGAGAAGTGTCATTTCCAACACCAAATCATCTCTAGACAATCAAATTT
CATCAACAAGAAAGAACAATACTATCTTCATATGCACAGTCACCTAAATATGACTAGATGTCCTC
AACATGAAGGAATAATGTCGTCATAAACGACCAT
Found at i:127922 original size:2 final size:2
Alignment explanation
Indices: 127915--127988 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
127905 CTCAAAAGCA
127915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127957 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
127989 GAGATAATTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128944 original size:17 final size:17
Alignment explanation
Indices: 128899--128945 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
128889 ATTTATTGAG
* *
128899 AGAGAACAAAAAGGAAA
1 AGAGATCAAAAAGAAAA
128916 AGAGATCCAAAAAGAAAA
1 AGAGAT-CAAAAAGAAAA
128934 AGAAGAT-AAAAA
1 AG-AGATCAAAAA
128946 TAAAGATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.70, C:0.06, G:0.19, T:0.04
Consensus pattern (17 bp):
AGAGATCAAAAAGAAAA
Found at i:131497 original size:21 final size:21
Alignment explanation
Indices: 131473--131552 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
131463 CCTTTATTTA
*
131473 GAGGGAGTGATCATTTTCCTC
1 GAGGGAGTGATCCTTTTCCTC
* *
131494 GAGGGA-TCGATCCTTTAT-TTA
1 GAGGGAGT-GATCCTTT-TCCTC
131515 GAGGGAGTGATCCTTTTCCTC
1 GAGGGAGTGATCCTTTTCCTC
131536 GAGGGA-TCGATCCTTTT
1 GAGGGAGT-GATCCTTTT
131553 GAAATGGGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 3 0.06
21 44 0.90
22 2 0.04
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (21 bp):
GAGGGAGTGATCCTTTTCCTC
Found at i:131514 original size:42 final size:42
Alignment explanation
Indices: 131455--131551 Score: 185
Period size: 42 Copynumber: 2.3 Consensus size: 42
131445 AATAATGAAC
131455 GGATCGATCCTTTATTTAGAGGGAGTGATCATTTTCCTCGAG
1 GGATCGATCCTTTATTTAGAGGGAGTGATCATTTTCCTCGAG
*
131497 GGATCGATCCTTTATTTAGAGGGAGTGATCCTTTTCCTCGAG
1 GGATCGATCCTTTATTTAGAGGGAGTGATCATTTTCCTCGAG
131539 GGATCGATCCTTT
1 GGATCGATCCTTT
131552 TGAAATGGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (42 bp):
GGATCGATCCTTTATTTAGAGGGAGTGATCATTTTCCTCGAG
Found at i:133837 original size:2 final size:2
Alignment explanation
Indices: 133830--133861 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
133820 ACATGAACTC
133830 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
133862 TTATGCCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134934 original size:58 final size:58
Alignment explanation
Indices: 134861--135030 Score: 207
Period size: 58 Copynumber: 2.9 Consensus size: 58
134851 AACTTGAGTG
* * ** *
134861 TGACACATAAGGTCATGCTCA-CATCTGCACTAGTTATACTTTAGTGCAGTCTTGAATA
1 TGACACATAAGGTCATGCCCACCATCTGCACTAGTTATACTTTAGTG-AATCCCGAAAA
* * *
134919 TGACACACAAGGTCATGCCCACCATATGCACCAGTTATACTTTAGTGAATCCCGAAAA
1 TGACACATAAGGTCATGCCCACCATCTGCACTAGTTATACTTTAGTGAATCCCGAAAA
* * * *
134977 TAACACATAAGGTCGTGCCCACCATCTACAATAGTTATACTTTAGTGTAATCCC
1 TGACACATAAGGTCATGCCCACCATCTGCACTAGTTATACTTTAGTG-AATCCC
135031 AAATATGCAA
Statistics
Matches: 95, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
58 66 0.69
59 29 0.31
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (58 bp):
TGACACATAAGGTCATGCCCACCATCTGCACTAGTTATACTTTAGTGAATCCCGAAAA
Found at i:137697 original size:31 final size:29
Alignment explanation
Indices: 137657--137725 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
137647 TTACCATTTA
* *
137657 GGTCCCTAAATATTTCTAAATTTTATACTTT
1 GGTCACTAAA-ATTTC-AAAATTTATACTTT
* *
137688 GGTCACTAAACTTTCAAAATTTATATTTT
1 GGTCACTAAAATTTCAAAATTTATACTTT
137717 GGTCACTAA
1 GGTCACTAA
137726 CCAAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 21 0.62
30 4 0.12
31 9 0.26
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (29 bp):
GGTCACTAAAATTTCAAAATTTATACTTT
Found at i:137712 original size:29 final size:30
Alignment explanation
Indices: 137669--137725 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
137659 TCCCTAAATA
*
137669 TTTCTAAATTTTATACTTTGGTCACTAAAC
1 TTTCTAAAATTTATACTTTGGTCACTAAAC
*
137699 TTTC-AAAATTTATATTTTGGTCACTAA
1 TTTCTAAAATTTATACTTTGGTCACTAA
137726 CCAAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (30 bp):
TTTCTAAAATTTATACTTTGGTCACTAAAC
Done.