Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003631.1 Hibiscus syriacus cultivar Beakdansim tig00007689_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: 125547
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3326 original size:21 final size:22
Alignment explanation
Indices: 3302--3351 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3292 TTTAGTATTG
* *
3302 AAAATAT-TCATTTTAGGTAAC
1 AAAATATAACATTTTAGGTAAA
*
3323 AAAAT-TAACATTTTCGGTAAA
1 AAAATATAACATTTTAGGTAAA
3344 AAAATATA
1 AAAATATA
3352 TTTTAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.88
22 2 0.08
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (22 bp):
AAAATATAACATTTTAGGTAAA
Found at i:20965 original size:15 final size:16
Alignment explanation
Indices: 20927--20965 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20917 ACAGAGCCTC
*
20927 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
20943 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
20959 T-AATCAT
1 TGAATCAT
20966 CTGAAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:31989 original size:58 final size:58
Alignment explanation
Indices: 31895--32092 Score: 218
Period size: 58 Copynumber: 3.4 Consensus size: 58
31885 TCATTTAGTT
* *
31895 ATTTGTGTTCGTTCATTTATTTGGTTAAAGTTAAACGAACAAACATGAACATACCCTC
1 ATTTGTGTTCATTCATTTATTTGGTTAAAGTTAAACGAACGAACATGAACATACCCTC
* * *
31953 ATTTGTGTTCATTCATTTATTCGGTTAAAGTAAAACGAACGAACATGAACATACTCTC
1 ATTTGTGTTCATTCATTTATTTGGTTAAAGTTAAACGAACGAACATGAACATACCCTC
* * * * * * ** * *
32011 A-TCGTGTTCGTTAATTTTTTTTTTGTTAAAATTAAACGAACGAACATGAACGCACGCTT
1 ATTTGTGTTCATTCA--TTTATTTGGTTAAAGTTAAACGAACGAACATGAACATACCCTC
*
32070 ATTTGTGTTCATTCGATTCATTT
1 ATTTGTGTTCATTC-ATTTATTT
32093 ACATGCCTAA
Statistics
Matches: 114, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
57 10 0.09
58 54 0.47
59 40 0.35
60 9 0.08
61 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (58 bp):
ATTTGTGTTCATTCATTTATTTGGTTAAAGTTAAACGAACGAACATGAACATACCCTC
Found at i:34867 original size:14 final size:14
Alignment explanation
Indices: 34848--34874 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34838 AATTTTATAT
34848 AAAAATTAAATTTA
1 AAAAATTAAATTTA
34862 AAAAATTAAATTT
1 AAAAATTAAATTT
34875 TGATGAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATTAAATTTA
Found at i:38239 original size:148 final size:148
Alignment explanation
Indices: 37971--38267 Score: 594
Period size: 148 Copynumber: 2.0 Consensus size: 148
37961 AATAAACTAG
37971 AAATTTTATCCTAAAAACTGAATCTTATTGCTCACGTCACCGGGAATAAAGTCATAAACCTAAAC
1 AAATTTTATCCTAAAAACTGAATCTTATTGCTCACGTCACCGGGAATAAAGTCATAAACCTAAAC
38036 AACTAGTCAGCATCCAAAGATTCTGCCATACCTGAGGTTTAGAAATATCACAAGAATGACTGCTC
66 AACTAGTCAGCATCCAAAGATTCTGCCATACCTGAGGTTTAGAAATATCACAAGAATGACTGCTC
38101 GGTGAGGCGGTATTGTAT
131 GGTGAGGCGGTATTGTAT
38119 AAATTTTATCCTAAAAACTGAATCTTATTGCTCACGTCACCGGGAATAAAGTCATAAACCTAAAC
1 AAATTTTATCCTAAAAACTGAATCTTATTGCTCACGTCACCGGGAATAAAGTCATAAACCTAAAC
38184 AACTAGTCAGCATCCAAAGATTCTGCCATACCTGAGGTTTAGAAATATCACAAGAATGACTGCTC
66 AACTAGTCAGCATCCAAAGATTCTGCCATACCTGAGGTTTAGAAATATCACAAGAATGACTGCTC
38249 GGTGAGGCGGTATTGTAT
131 GGTGAGGCGGTATTGTAT
38267 A
1 A
38268 TGAAAAGCAA
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 149 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (148 bp):
AAATTTTATCCTAAAAACTGAATCTTATTGCTCACGTCACCGGGAATAAAGTCATAAACCTAAAC
AACTAGTCAGCATCCAAAGATTCTGCCATACCTGAGGTTTAGAAATATCACAAGAATGACTGCTC
GGTGAGGCGGTATTGTAT
Found at i:43897 original size:27 final size:27
Alignment explanation
Indices: 43807--43889 Score: 157
Period size: 27 Copynumber: 3.1 Consensus size: 27
43797 TTTAAAGTTT
*
43807 TCAAGTTCGAGTTGAGTTCAGCAATAC
1 TCAAATTCGAGTTGAGTTCAGCAATAC
43834 TCAAATTCGAGTTGAGTTCAGCAATAC
1 TCAAATTCGAGTTGAGTTCAGCAATAC
43861 TCAAATTCGAGTTGAGTTCAGCAATAC
1 TCAAATTCGAGTTGAGTTCAGCAATAC
43888 TC
1 TC
43890 GAGTTCGACT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (27 bp):
TCAAATTCGAGTTGAGTTCAGCAATAC
Found at i:58463 original size:16 final size:16
Alignment explanation
Indices: 58442--58473 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58432 CCTCTTGACA
58442 AAAGATTCAAAATTTT
1 AAAGATTCAAAATTTT
58458 AAAGATTCAAAATTTT
1 AAAGATTCAAAATTTT
58474 CGGATCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
AAAGATTCAAAATTTT
Found at i:64362 original size:2 final size:2
Alignment explanation
Indices: 64355--64382 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64345 GCATTGTCTA
64355 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
64383 TAAAGCATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64922 original size:20 final size:20
Alignment explanation
Indices: 64897--65010 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
64887 CTATCGCAAA
64897 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
64917 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
64937 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
*
64958 ATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
64978 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
64998 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
65011 AGTCTACAGT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 68 0.82
21 15 0.18
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:64993 original size:61 final size:61
Alignment explanation
Indices: 64898--65013 Score: 232
Period size: 61 Copynumber: 1.9 Consensus size: 61
64888 TATCGCAAAT
64898 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
64959 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
65014 CTACAGTTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:65166 original size:6 final size:6
Alignment explanation
Indices: 65157--65189 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
65147 CATTACCATT
65157 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
65190 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:65832 original size:19 final size:19
Alignment explanation
Indices: 65808--65873 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
65798 TAAACTATCA
65808 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
65827 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
65849 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
*
65868 TAACGA
1 CAACGA
65874 CAACTGTAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 18 0.51
20 2 0.06
21 2 0.06
22 13 0.37
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:65850 original size:22 final size:22
Alignment explanation
Indices: 65823--65894 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
65813 AATTTGGAAA
65823 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
65845 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
65864 ATCGTAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
65886 ATCGCAACG
1 ATCGCAACG
65895 CGAAATGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:65858 original size:41 final size:41
Alignment explanation
Indices: 65801--65914 Score: 176
Period size: 41 Copynumber: 2.8 Consensus size: 41
65791 TTTTTTTTAA
*
65801 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
*
65842 ACTATCGCAACGAATTTGGAAAATCGTAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
*
65883 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG
1 ACTATCGCAA--CGAATTTGGAAAATCGCAACG
65915 CGATTTTCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
41 49 0.73
42 14 0.21
43 4 0.06
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:66609 original size:57 final size:56
Alignment explanation
Indices: 66499--66613 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 56
66489 TTAACAGTAA
* *
66499 TGTTTATCTTTCACCATAAAAAAATACCATGTCCAAGGACGAACATAAAAATTTATG
1 TGTTTATCTTTCACCATAAAAAAATAACATATCCAAGGACGAACA-AAAAATTTATG
*
66556 TGTTTA-CATTTCACCATAAAAAAATAACATATCCAAGGACCGATAC-AAGAATTTATG
1 TGTTTATC-TTTCACCATAAAAAAATAACATATCCAAGGA-CGA-ACAAAAAATTTATG
66613 T
1 T
66614 TAGAAGATGT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
56 1 0.02
57 46 0.88
58 3 0.06
59 2 0.04
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (56 bp):
TGTTTATCTTTCACCATAAAAAAATAACATATCCAAGGACGAACAAAAAATTTATG
Found at i:70581 original size:24 final size:22
Alignment explanation
Indices: 70541--70590 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
70531 TTGAATATTT
70541 TAATTTTTTTATATATT-TTAGA
1 TAATTTTTTTATATATTATT-GA
*
70563 TAATTTTTTTAAATGTATTATTGA
1 TAATTTTTTT--ATATATTATTGA
70587 TAAT
1 TAAT
70591 CTGTTTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 10 0.42
24 12 0.50
25 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (22 bp):
TAATTTTTTTATATATTATTGA
Found at i:71331 original size:2 final size:2
Alignment explanation
Indices: 71324--71349 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71314 AGAAATTAAG
71324 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
71350 CTTTGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72803 original size:25 final size:26
Alignment explanation
Indices: 72751--72813 Score: 119
Period size: 25 Copynumber: 2.5 Consensus size: 26
72741 ATGTTTTAAT
72751 TTCAAAGTAAATCTATTAAAAAAAAA
1 TTCAAAGTAAATCTATTAAAAAAAAA
72777 TTCAAAGTAAATCTATT-AAAAAAAA
1 TTCAAAGTAAATCTATTAAAAAAAAA
72802 TTCAAAGTAAAT
1 TTCAAAGTAAAT
72814 ACTGGTTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 20 0.54
26 17 0.46
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.29
Consensus pattern (26 bp):
TTCAAAGTAAATCTATTAAAAAAAAA
Found at i:83703 original size:15 final size:15
Alignment explanation
Indices: 83673--83724 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 15
83663 AAATAGAATG
83673 ATAAAATAAAACAAAA
1 ATAAAAT-AAACAAAA
*
83689 ATAAAATATACAAAA
1 ATAAAATAAACAAAA
83704 A-AATAATAAACAAAA
1 ATAA-AATAAACAAAA
83719 ATAAAA
1 ATAAAA
83725 AAAAACAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 2 0.06
15 21 0.66
16 9 0.28
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (15 bp):
ATAAAATAAACAAAA
Found at i:83730 original size:16 final size:16
Alignment explanation
Indices: 83673--83733 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 16
83663 AAATAGAATG
*
83673 ATAAAATAAAACAAAA
1 ATAAAAAAAAACAAAA
* *
83689 AT-AAAATATACAAAA
1 ATAAAAAAAAACAAAA
* *
83704 A-AATAATAAACAAAA
1 ATAAAAAAAAACAAAA
83719 ATAAAAAAAAACAAA
1 ATAAAAAAAAACAAA
83734 GGAAAAAGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 23 0.64
16 13 0.36
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (16 bp):
ATAAAAAAAAACAAAA
Found at i:83941 original size:37 final size:36
Alignment explanation
Indices: 83843--83941 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 36
83833 AAATGTATAT
*
83843 AAAAATA-TAAAAAAAACAAATAGAAAAACCAAAAAG
1 AAAAATAGTAAAAAAAACAAA-AAAAAAACCAAAAAG
* * *
83879 AAAAATAG-AAGAACAAATAATAAAAAAAACCAAAATG
1 AAAAATAGTAA-AAAAAACAA-AAAAAAAACCAAAAAG
83916 AAAAATAGTAAAATAAAACAAAAAAA
1 AAAAATAGTAAAA-AAAACAAAAAAA
83942 TAAAATATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
36 9 0.17
37 35 0.67
38 8 0.15
ACGTcount: A:0.77, C:0.07, G:0.06, T:0.10
Consensus pattern (36 bp):
AAAAATAGTAAAAAAAACAAAAAAAAAACCAAAAAG
Found at i:84049 original size:20 final size:20
Alignment explanation
Indices: 84008--84051 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
83998 ACATAACATT
*
84008 AATAAAACAAACAAAAGTAA
1 AATAAAACAAACAAAAGCAA
84028 AATAAAACAAAACAAAA-CAA
1 AATAAAAC-AAACAAAAGCAA
84048 AATA
1 AATA
84052 TATAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.77, C:0.11, G:0.02, T:0.09
Consensus pattern (20 bp):
AATAAAACAAACAAAAGCAA
Found at i:85183 original size:3 final size:3
Alignment explanation
Indices: 85175--85217 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
85165 AAAAAGCATA
*
85175 AAT AAT AAT AAGA AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
85218 CTATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:85313 original size:37 final size:37
Alignment explanation
Indices: 85265--85574 Score: 240
Period size: 36 Copynumber: 8.4 Consensus size: 37
85255 ATAAATTTCC
*
85265 AAAATGCTTTTAAAAACTATATATTATACATGTTTTTA
1 AAAATG-TTTTAAAAACTATATATTATATATGTTTTTA
* * * *
85303 AAAACGTTTTAAAAACT-T-TATAATATATATTTTCA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* * * * *
85338 GAAACGGTTTAAAAATTATATATTATATATATTTTT-
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* * *
85374 AAAATGTTTTTCAAAAATTATATAATATTTAAATG-TTTTA
1 AAAATG-TTTT-AAAAACTATAT-AT-TATATATGTTTTTA
*** * * * *
85414 AAAA-AAATTCAAAACAATATATTATATAAGTTTTCA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
*
85450 AAAATGATTTTAAAAACTATATATTATATATATTTTCT-
1 AAAATG-TTTTAAAAACTATATATTATATATGTTTT-TA
* **
85488 AAAATGTTTTAAAAACTATATACTATATA-GTTTCAA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* * ** *
85524 AAAATATTTTTAAAACTATATATTATATA-CATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
85560 AAAATGTTTTAAAAA
1 AAAATGTTTTAAAAA
85575 ATTATGTATA
Statistics
Matches: 212, Mismatches: 48, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
35 32 0.15
36 60 0.28
37 58 0.27
38 47 0.22
39 6 0.03
40 9 0.04
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
Found at i:85350 original size:35 final size:36
Alignment explanation
Indices: 85273--85372 Score: 105
Period size: 35 Copynumber: 2.8 Consensus size: 36
85263 CCAAAATGCT
* * * * * *
85273 TTTAAAAACTATATATTATACATGTTTTTAAAAACGT
1 TTTAAAAATTATATA-TATATATATTTTCAGAAACGG
85310 TTTAAAAACTT-TATA-ATATATATTTTCAGAAACGG
1 TTTAAAAA-TTATATATATATATATTTTCAGAAACGG
85345 TTTAAAAATTATATATTATATATATTTT
1 TTTAAAAATTATATA-TATATATATTTT
85373 TAAAATGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
34 2 0.04
35 27 0.51
37 23 0.43
38 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTAAAAATTATATATATATATATTTTCAGAAACGG
Found at i:85418 original size:29 final size:31
Alignment explanation
Indices: 85359--85419 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
85349 AAAATTATAT
* **
85359 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
85390 ATTATATA-ATATTT-AAATGTTTTAAAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
85419 A
1 A
85420 ATTCAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 14 0.52
30 5 0.19
31 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTAAAAAA
Found at i:85542 original size:73 final size:72
Alignment explanation
Indices: 85230--85574 Score: 277
Period size: 75 Copynumber: 4.7 Consensus size: 72
85220 ATATATATAT
* * * * *
85230 AAATATTTTCAAAAA-TATGTAATATATAAATTTCCAAAATGCTTTTAAAAACTATATATTATAC
1 AAATATTTT-AAAAACTATATATTATATATATTTTCAAAATG-TTTTAAAAACTATATATTATAT
*
85294 ATGTTTTTAA
64 A-GTTTCTAA
** * * * *
85304 AAACGTTTTAAAAACT-T-TATAATATATATTTTCAGAAACGGTTTAAAAATTATATATTATATA
1 AAATATTTTAAAAACTATATATTATATATATTTTCA-AAATGTTTTAAAAACTATATATTATATA
* *
85367 -TATTTTTA
65 GT-TTCTAA
* * * * * * **** * *
85375 AAATGTTTTTCAAAAATTATATAATATTTAAATGTTTTAAAAAAAATTCAAAACAATATATTATA
1 AAAT-ATTTT-AAAAACTATATATTATATATAT-TTTCAAAATGTTTTAAAAACTATATATTATA
85440 TAAGTTT-TCAA
63 T-AGTTTCT-AA
*
85451 AAATGATTTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATACTATAT
1 AAAT-ATTTTAAAAACTATATATTATATATATTTTC-AAAATGTTTTAAAAACTATATATTATAT
*
85516 AGTTTCAAA
64 AGTTTCTAA
* *
85525 AAATATTTTTAAAACTATATATTATATACATTTTCAAAATGTTTTAAAAA
1 AAATATTTTAAAAACTATATATTATATATATTTTCAAAATGTTTTAAAAA
85575 ATTATGTATA
Statistics
Matches: 215, Mismatches: 43, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
70 1 0.00
71 8 0.04
72 52 0.24
73 45 0.21
74 23 0.11
75 68 0.32
76 17 0.08
77 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (72 bp):
AAATATTTTAAAAACTATATATTATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAG
TTTCTAA
Found at i:86308 original size:84 final size:81
Alignment explanation
Indices: 86233--87149 Score: 858
Period size: 84 Copynumber: 11.1 Consensus size: 81
86223 AGCTATGTTA
* * * *
86233 CAAATGATGTGCTGCT-GAGCTGAGTGTAGCCAAACTCGAAGGTCTTTTGGTCACAGATAACCCT
1 CAAATGATGTGC-CCTCGAGCTGAGTGTAGTCGAACTCAAAGGTC-TTTGGT--CAGATAACCCT
* * *
86297 TCTAGCCTTGAGTTATGATG
62 TCTAGACTTAAGTTATGCTG
* * * * * *
86317 TAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGACTTTTGGTCATAGATAACCCTT
1 CAAATGATGTGCCCTCGAGCTGAGTGTAGTCGAACTCAAAGGTC-TTTGGTC--AGATAACCCTT
** *
86382 CTATCCTTGAGTTATGCTG
63 CTAGACTTAAGTTATGCTG
* * * ***
86401 TAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGG-CAGATAACCCTTCT
1 CAAATGATGTGCCCTCG-AGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGTCAGATAACCCTTCT
* * *
86465 CGACTTAAGCTATACTG
65 AGACTTAAGTTATGCTG
* * ** *
86482 CAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTT
1 CAAATGATGTGCCCTCGAGCTGAGTGTAGTCGAACTCAAAGGTC-TTTGGT--CAGATAACCCTT
* *
86547 CTTGACTTAAGTTATACTG
63 CTAGACTTAAGTTATGCTG
*** *
86566 CAAATGATGTGCCCTCGAAGCTGAGTGT-GATCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTC
1 CAAATGATGTGCCCTCG-AGCTGAGTGTAG-TCGAACTCAAAGGTCTTTGGTCAGATAACCCTTC
* *
86629 TCGACTTAAGCTATGCTG
64 TAGACTTAAGTTATGCTG
* * * *
86647 GAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTCGGCAGATAACCCTT
1 CAAATGATGTGCCCTCGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGT---CAGATAACCCTT
* *
86712 CTTGACTTGAGTTATGCTG
63 CTAGACTTAAGTTATGCTG
* * *** *
86731 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCT
1 CAAATGATGTGCCCTCG-AGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGTCAGATAACCCTTCT
* *
86795 CGACTTAAGCTATGCTG
65 AGACTTAAGTTATGCTG
* * * *
86812 CAAATGATGTGCCGTTGAGCCGAGTGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTT
1 CAAATGATGTGCCCTCGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGG-T--CAGATAACCCTT
*
86877 CTAGACTTAAGTTGTGCTG
63 CTAGACTTAAGTTATGCTG
* * * *
86896 CAAATGATATGCCCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-CAGATAGCCCTTCT
1 CAAATGATGTGCCCTC-GAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGTCAGATAACCCTTCT
* * *
86960 CGACGTAAGCTATGCTG
65 AGACTTAAGTTATGCTG
* * * *
86977 CAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTT
1 CAAATGATGTGCCCTCGAGCTGAGTGTAGTCGAACTCAAAGGTC-TTTGGT--CAGATAACCCTT
* *
87042 CTAGCCTTGAGTTATGCTG
63 CTAGACTTAAGTTATGCTG
* * *** *
87061 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCT
1 CAAATGATGTGCCCTCG-AGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGTCAGATAACCCTTCT
* *
87125 CGACTTAAGCTATGCTG
65 AGACTTAAGTTATGCTG
87142 CAAATGAT
1 CAAATGAT
87150 TGTTTAAAAA
Statistics
Matches: 681, Mismatches: 126, Indels: 55
0.79 0.15 0.06
Matches are distributed among these distances:
80 100 0.15
81 200 0.29
82 1 0.00
83 2 0.00
84 259 0.38
85 119 0.17
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (81 bp):
CAAATGATGTGCCCTCGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGGTCAGATAACCCTTCTA
GACTTAAGTTATGCTG
Found at i:86490 original size:165 final size:164
Alignment explanation
Indices: 86286--87149 Score: 1234
Period size: 165 Copynumber: 5.2 Consensus size: 164
86276 CTTTTGGTCA
* * * * * * *
86286 CAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CGTTGAGCTGAGCGTAGTCGAA
* * *
86351 CTCAAAGGACTTTTGGTCATAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATGTGCCCT
65 CTCAAAGGTCTTTTGGTCACAGATAACCCTTCTATACTTGAGTTATGCTGTAAATGATGTGCCCT
*
86416 CGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGG
130 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* * * *
86451 CAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCGTT-GAGCTGAGCGTAGTCGAA
* * * *
86516 CTCAAAGGTCTTTT-GTTAGCAGATAACCCTTCT-TGACTTAAGTTATACTGCAAATGATGTGCC
65 CTCAAAGGTCTTTTGGTCA-CAGATAACCCTTCTAT-ACTTGAGTTATGCTGTAAATGATGTGCC
*
86579 CTCGAAGCTGAGTGTGATCGAACTCGGGGGTCTTTGG
128 CTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* *
86616 CAGATAGCCCTTCTCGACTTAAGCTATGCTGGAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCGTT-GAGCTGAGCGTAGTCGAA
*
86681 CTCAAAGGTC-TTTGGTCGGCAGATAACCCTTCT-TGACTTGAGTTATGCTGTAAATGATGTGCC
65 CTCAAAGGTCTTTTGGTC-ACAGATAACCCTTCTAT-ACTTGAGTTATGCTGTAAATGATGTGCC
86744 CTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
128 CTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* *
86781 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCCGAGTGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CGTTGAGCTGAGCGTAGTCGAA
** * * * * * *
86846 CTCAAAGGTC-TTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCC
65 CTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTATACTTGAGTTATGCTGTAAATGATGTGCCC
* * * **
86910 TCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
129 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
*
86946 CAGATAGCCCTTCTCGACGTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CGTTGAGCTGAGCGTAGTCGAA
**
87011 CTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCT
65 CTCAAAGGTCTTTTGGTCACAGATAACCCTTCTATACTTGAGTTATGCTGTAAATGATGTGCCCT
87076 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
130 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
87111 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
87150 TGTTTAAAAA
Statistics
Matches: 628, Mismatches: 62, Indels: 18
0.89 0.09 0.03
Matches are distributed among these distances:
164 10 0.02
165 609 0.97
166 9 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (164 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCGTTGAGCTGAGCGTAGTCGAAC
TCAAAGGTCTTTTGGTCACAGATAACCCTTCTATACTTGAGTTATGCTGTAAATGATGTGCCCTC
GAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
Found at i:86674 original size:330 final size:330
Alignment explanation
Indices: 86250--87149 Score: 1369
Period size: 330 Copynumber: 2.7 Consensus size: 330
86240 TGTGCTGCTG
* * * * * * * * *
86250 AGCTGAGTGTAGCCAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGA
1 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGC
* * *
86315 TGTAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGACTTTTGGTCATAGATAACCC
62 TGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCC
*
86380 TTCTATCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGGGGT
127 TTCTATCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGT
* * *
86445 CTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAACGT
192 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCCGAACGT
* * *
86509 AGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGAT
256 AGTCGAACTCAAAGGTCTTTGGTTAGCAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGAT
*
86574 GTGCCCTCGA
321 ATGCCCTCGA
* ** *
86584 AGCTGAGTGT-GATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGG
1 AGCTGAGCGTAG-TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
* *
86648 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTCGGCAGATAACCCT
65 AAATGATGTGTCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTC-ACAGATAACCCT
*
86711 TCT-TGACTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGT
128 TCTAT-CCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGT
**
86775 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCCGAGTGTA
192 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCCGAACGTA
* * *
86840 GTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATA
257 GTCGAACTCAAAGGTCTTTGGTTAGCAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATA
*
86905 TGCCCTCGG
322 TGCCCTCGA
*
86914 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACGTAAGCTATGCTGCA
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
86979 AATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCT
66 AATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCT
*
87044 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
131 ATCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
87109 GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
196 GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
87150 TGTTTAAAAA
Statistics
Matches: 518, Mismatches: 39, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
329 11 0.02
330 467 0.90
331 13 0.03
333 6 0.01
334 21 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (330 bp):
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
AATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCT
ATCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCCGAACGTAGTCG
AACTCAAAGGTCTTTGGTTAGCAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCC
CTCGA
Found at i:90236 original size:19 final size:19
Alignment explanation
Indices: 90209--90254 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
90199 AGTTAATGTG
*
90209 AATGTAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
90228 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
90247 AATGCAAA
1 AATGCAAA
90255 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:92225 original size:16 final size:15
Alignment explanation
Indices: 92199--92252 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
92189 AGAATGATAA
*
92199 AATAAAC-AAAAATT
1 AATAAACAAAAAAAT
*
92213 AAATATACAAAAAAAT
1 -AATAAACAAAAAAAT
92229 AATAAACAAAAATAA-
1 AATAAACAAAAA-AAT
92244 AA-AAACAAA
1 AATAAACAAA
92253 GGAAAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 7 0.21
15 19 0.56
16 8 0.24
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (15 bp):
AATAAACAAAAAAAT
Found at i:92459 original size:38 final size:37
Alignment explanation
Indices: 92361--92460 Score: 98
Period size: 38 Copynumber: 2.7 Consensus size: 37
92351 AAATGTATAT
* *
92361 AAAAATA-T-AAAAAAACAAATAGAAAAACCAAAAAG
1 AAAAATAGTAAAAAAAACAAAAAAAAAAACCAAAAAG
* * * *
92396 GAAAATAG-AAGAACAAATAATAAAAAAAAACCAAAATG
1 AAAAATAGTAA-AAAAAACAA-AAAAAAAAACCAAAAAG
92434 AAAAATAGTAAAATAAAACAAAAAAAA
1 AAAAATAGTAAAA-AAAACAAAAAAAA
92461 TAAAATATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
35 6 0.12
36 1 0.02
37 7 0.14
38 29 0.58
39 7 0.14
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.10
Consensus pattern (37 bp):
AAAAATAGTAAAAAAAACAAAAAAAAAAACCAAAAAG
Found at i:92568 original size:20 final size:20
Alignment explanation
Indices: 92527--92570 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
92517 ACATAACATT
*
92527 AATAAAACAAACAAAAGTAA
1 AATAAAACAAACAAAAGCAA
92547 AATAAAACAAAACAAAA-CAA
1 AATAAAAC-AAACAAAAGCAA
92567 AATA
1 AATA
92571 TATAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.77, C:0.11, G:0.02, T:0.09
Consensus pattern (20 bp):
AATAAAACAAACAAAAGCAA
Found at i:93816 original size:25 final size:24
Alignment explanation
Indices: 93788--93846 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
93778 TCCAAAATGC
*
93788 TTTTAAAAACTATATATTATACAT
1 TTTTAAAAACTATATAATATACAT
* *
93812 GTTTTAAAAACTTTATAATATATAT
1 -TTTTAAAAACTATATAATATACAT
*
93837 TTTCAAAAAC
1 TTTTAAAAAC
93847 GGTTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (24 bp):
TTTTAAAAACTATATAATATACAT
Found at i:93900 original size:38 final size:39
Alignment explanation
Indices: 93830--94076 Score: 161
Period size: 38 Copynumber: 6.7 Consensus size: 39
93820 AACTTTATAA
* * * *
93830 TATATATTTTCAAAAACG-GTTT-AAAAATTATATATTA
1 TATATATTTTCTAAAATGATTTTCAAAAACTATATATTA
* * *
93867 TATATATTTT-TAAAATGTTTTTCAAAAATTATATAATA
1 TATATATTTTCTAAAATGATTTTCAAAAACTATATATTA
* * * ** *
93905 TTTAAATGTTT-TAAAA-AAAATTC-AAAACAATATATTA
1 TATATAT-TTTCTAAAATGATTTTCAAAAACTATATATTA
*
93942 TATA-AGTTTTCAAAAATGATTTT-AAAAACTATATATTA
1 TATATA-TTTTCTAAAATGATTTTCAAAAACTATATATTA
* *
93980 TATATATTTTCTAAAATG-TTTTAAAAAACTATATA--C
1 TATATATTTTCTAAAATGATTTTCAAAAACTATATATTA
* * *
94016 TATATAGTTTCAAAAAAT-ATTTT--TAAACTATATA-T-
1 TATATATTTTC-TAAAATGATTTTCAAAAACTATATATTA
*
94051 TATACATTTTC-AAAATG-TTTTCAAAA
1 TATATATTTTCTAAAATGATTTTCAAAA
94077 TTATGTATAT
Statistics
Matches: 168, Mismatches: 27, Indels: 32
0.74 0.12 0.14
Matches are distributed among these distances:
33 9 0.05
35 21 0.12
36 19 0.11
37 45 0.27
38 65 0.39
39 9 0.05
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (39 bp):
TATATATTTTCTAAAATGATTTTCAAAAACTATATATTA
Found at i:93922 original size:29 final size:31
Alignment explanation
Indices: 93863--93923 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
93853 AAAATTATAT
* **
93863 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
93894 ATTATATA-ATATTT-AAATGTTTTAAAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
93923 A
1 A
93924 ATTCAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 14 0.52
30 5 0.19
31 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTAAAAAA
Found at i:93995 original size:75 final size:75
Alignment explanation
Indices: 93813--94054 Score: 180
Period size: 75 Copynumber: 3.3 Consensus size: 75
93803 ATTATACATG
* *** **
93813 TTTTAAAAACT-T-TATAATATATATTTTC-AAAAACGGTTTAAAAATTATATATTATATATA-T
1 TTTTAAAAACTATATATTATATATATTTTCTAAAAA-AAATTAAAAACAATATATTATATA-AGT
* *
93874 TTT-TAAAATGT
64 TTTCAAAAATGA
* * * * *
93885 TTTTCAAAAATTATATAATATTTAAATGTTT-TAAAAAAAATTCAAAACAATATATTATATAAGT
1 TTTT-AAAAACTATATATTATATATAT-TTTCTAAAAAAAATTAAAAACAATATATTATATAAGT
93949 TTTCAAAAATGA
64 TTTCAAAAATGA
**** * *
93961 TTTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAAACTATATACTATAT-AG-T
1 TTTTAAAAACTATATATTATATATATTTTCTAAAAAAAATT-AAAAACAATATATTATATAAGTT
94024 TTCAAAAAAT-A
65 TTC-AAAAATGA
*
94035 TTTT-TAAACTATATATTATA
1 TTTTAAAAACTATATATTATA
94055 CATTTTCAAA
Statistics
Matches: 135, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
72 4 0.03
73 21 0.16
74 14 0.10
75 63 0.47
76 33 0.24
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (75 bp):
TTTTAAAAACTATATATTATATATATTTTCTAAAAAAAATTAAAAACAATATATTATATAAGTTT
TCAAAAATGA
Found at i:94102 original size:73 final size:75
Alignment explanation
Indices: 93928--94076 Score: 184
Period size: 76 Copynumber: 2.0 Consensus size: 75
93918 AAAAAAATTC
* * *
93928 AAAACAATATATTATATAAGTTTTC-AAAAATGATTTTAAAAACTATATATTATATATATTTTCT
1 AAAACTATATACTATAT-A-TTTTCAAAAAATGATTTTAAAAACTATATATTATATACATTTTCT
93992 AAAATGTTTTAA
64 AAAATGTTTTAA
* *
94004 AAAACTATATACTATATAGTTTCAAAAAAT-ATTTT-TAAACTATATA-T-TATACATTTTC-AA
1 AAAACTATATACTATATATTTTCAAAAAATGATTTTAAAAACTATATATTATATACATTTTCTAA
*
94064 AATGTTTTCA
66 AATGTTTTAA
94074 AAA
1 AAA
94077 TTATGTATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
70 14 0.21
71 10 0.15
72 1 0.02
73 10 0.15
74 9 0.14
75 7 0.11
76 15 0.23
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (75 bp):
AAAACTATATACTATATATTTTCAAAAAATGATTTTAAAAACTATATATTATATACATTTTCTAA
AATGTTTTAA
Found at i:94168 original size:12 final size:13
Alignment explanation
Indices: 94145--94173 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
94135 ATGTATATAT
94145 AATAATAATAAAA
1 AATAATAATAAAA
94158 AATAA-AATAAAA
1 AATAATAATAAAA
94170 AATA
1 AATA
94174 GACGAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAATAATAAAA
Found at i:94806 original size:8 final size:8
Alignment explanation
Indices: 94763--94817 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
94753 CTAAATACTT
94763 TAATTTAA
1 TAATTTAA
**
94771 TAATAAAA
1 TAATTTAA
94779 TCAA-TTAA
1 T-AATTTAA
94787 TAATTTAA
1 TAATTTAA
94795 -AATTTAA
1 TAATTTAA
94802 TAA-TTAA
1 TAATTTAA
*
94809 TAATGTAA
1 TAATTTAA
94817 T
1 T
94818 CCATTTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
7 16 0.42
8 20 0.53
9 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (8 bp):
TAATTTAA
Found at i:98711 original size:30 final size:28
Alignment explanation
Indices: 98608--98750 Score: 155
Period size: 27 Copynumber: 5.0 Consensus size: 28
98598 ACTTCAATTT
*
98608 GAACAGCAGCGGCAGTTGGAACTTCAGC
1 GAACAGCAGCGGCAGTTGGAGCTTCAGC
*
98636 -AACAGCAGCGGCAGTTGGAACTTCAGC
1 GAACAGCAGCGGCAGTTGGAGCTTCAGC
* *
98663 -AACAACAGCGGAAGTTGGAGCTTCAGC
1 GAACAGCAGCGGCAGTTGGAGCTTCAGC
* *
98690 GACGGCAGCAGCAGCAGTTGGAGCTTCAGC
1 GA--ACAGCAGCGGCAGTTGGAGCTTCAGC
** *
98720 GGCGGCAGCAGCAGCAGTTGGAGCTTCAGC
1 -G-AACAGCAGCGGCAGTTGGAGCTTCAGC
98750 G
1 G
98751 GCAGCAGTTG
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
27 51 0.50
28 1 0.01
29 1 0.01
30 48 0.47
31 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.34, T:0.14
Consensus pattern (28 bp):
GAACAGCAGCGGCAGTTGGAGCTTCAGC
Found at i:98751 original size:30 final size:30
Alignment explanation
Indices: 98675--98757 Score: 148
Period size: 30 Copynumber: 2.8 Consensus size: 30
98665 CAACAGCGGA
*
98675 AGTTGGAGCTTCAGCGACGGCAGCAGCAGC
1 AGTTGGAGCTTCAGCGGCGGCAGCAGCAGC
98705 AGTTGGAGCTTCAGCGGCGGCAGCAGCAGC
1 AGTTGGAGCTTCAGCGGCGGCAGCAGCAGC
*
98735 AGTTGGAGCTTCAGCGGCAGCAG
1 AGTTGGAGCTTCAGCGGCGGCAG
98758 TTGCTGCTGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.22, C:0.25, G:0.39, T:0.14
Consensus pattern (30 bp):
AGTTGGAGCTTCAGCGGCGGCAGCAGCAGC
Found at i:100956 original size:14 final size:14
Alignment explanation
Indices: 100937--100970 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
100927 AATTACCATG
100937 TTCCTTATCCTATA
1 TTCCTTATCCTATA
100951 TTCCTTATCCTATA
1 TTCCTTATCCTATA
*
100965 ATCCTT
1 TTCCTT
100971 TCATGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (14 bp):
TTCCTTATCCTATA
Found at i:113411 original size:19 final size:18
Alignment explanation
Indices: 113374--113419 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
113364 TTTTTAAAAG
113374 ATAATACTTGAATATTATA
1 ATAATA-TTGAATATTATA
* *
113393 TTAATATTGTATATATATA
1 ATAATATTGAATAT-TATA
113412 ATAATATT
1 ATAATATT
113420 ACTTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (18 bp):
ATAATATTGAATATTATA
Found at i:113847 original size:16 final size:17
Alignment explanation
Indices: 113815--113847 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
113805 GGGTCAAGCT
*
113815 TCGGGAAAAAATCAAAA
1 TCGGCAAAAAATCAAAA
113832 TCGGCAAAAAAT-AAAA
1 TCGGCAAAAAATCAAAA
113848 GGAGTCCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.61, C:0.12, G:0.15, T:0.12
Consensus pattern (17 bp):
TCGGCAAAAAATCAAAA
Found at i:121570 original size:2 final size:2
Alignment explanation
Indices: 121565--121617 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
121555 ATGTGTTGGG
121565 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
121607 TC TC TC TC TC T
1 TC TC TC TC TC T
121618 TATCTGTCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.