Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold307
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: 622582
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 1 of 5
Found at i:1155 original size:19 final size:20
Alignment explanation
Indices: 1118--1160 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1108 AAATGGTTTA
* * *
1118 GAAATTTTTTTTGATAATT-
1 GAAATTTTATTTCAAAATTC
1137 GAAATTTTATTTCAAAATTC
1 GAAATTTTATTTCAAAATTC
1157 GAAA
1 GAAA
1161 GAAGCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (20 bp):
GAAATTTTATTTCAAAATTC
Found at i:4015 original size:108 final size:111
Alignment explanation
Indices: 3829--4054 Score: 359
Period size: 108 Copynumber: 2.1 Consensus size: 111
3819 ATGTCAACTA
** *
3829 TTTAACCTTTTTATTGAAAAAAAAATCCAACCCAATTCCCTTTTTTTTGTGTTGATTTCACAAGT
1 TTTAACCTTTTTATTGAAAAAAAAATCCAA-CCAATTCCCTTTGCTTTGGGTTGATTTCACAAGT
* * * *
3894 GTATATAAGCACCAGTTAAATATTATCTAATTACTCTTTT-AATTTT
65 ATATATAAACACCAGCTAAATATTATCCAATTACTCTTTTAAATTTT
3940 TTTAACCTTTTTATTGAAAAAAAAATCCAA-CAATTCCC-TTGCTTTGGGTTGATTTCACAAGTA
1 TTTAACCTTTTTATTGAAAAAAAAATCCAACCAATTCCCTTTGCTTTGGGTTGATTTCACAAGTA
4003 TATATAAACACCAGCTAAATATTATCCAATTACTCTTTTAAATTTT
66 TATATAAACACCAGCTAAATATTATCCAATTACTCTTTTAAATTTT
4049 TTTAAC
1 TTTAAC
4055 ATAAATATTT
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
108 57 0.53
109 20 0.19
111 30 0.28
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (111 bp):
TTTAACCTTTTTATTGAAAAAAAAATCCAACCAATTCCCTTTGCTTTGGGTTGATTTCACAAGTA
TATATAAACACCAGCTAAATATTATCCAATTACTCTTTTAAATTTT
Found at i:4284 original size:2 final size:2
Alignment explanation
Indices: 4272--4309 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4262 ATGAAGGAGC
*
4272 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4310 CTCTGACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4446 original size:2 final size:2
Alignment explanation
Indices: 4441--4471 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4431 AATATCCTTT
*
4441 TA TA TA TA TA TA CA 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 T
4472 CCTTTCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5951 original size:2 final size:2
Alignment explanation
Indices: 5944--5968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5934 TGTTATCTTC
5944 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 A
5969 CACATATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10531 original size:90 final size:90
Alignment explanation
Indices: 10364--10533 Score: 218
Period size: 90 Copynumber: 1.9 Consensus size: 90
10354 TTTTGGAAAG
* * * *
10364 CTATGGAGAAAGACTATGAAGTTCTTCCATTACCTCCAAATCCAACTATGGCACATCAAGAATCA
1 CTATGGAGAAAGACTATGAAGTTCCTCCATTACCTCCAAATCCAACTAGGGCAAATCAAAAATCA
*
10429 CAAAGAGAAAAAATTAAGTGGGCAA
66 CAAAAAGAAAAAATTAAGTGGGCAA
* * * *
10454 CTATGGAGGAGGACTACT-AAGTTCCTCCATTCCCTCCAAAT-CTACTACGGCGCAAATCAAAAA
1 CTATGGAGAAAGACTA-TGAAGTTCCTCCATTACCTCCAAATCCAACTA-GG-GCAAATCAAAAA
10517 TCACAAAAAGAAAAAAT
63 TCACAAAAAGAAAAAAT
10534 CAAGAAAGTC
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
89 5 0.07
90 36 0.53
91 27 0.40
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (90 bp):
CTATGGAGAAAGACTATGAAGTTCCTCCATTACCTCCAAATCCAACTAGGGCAAATCAAAAATCA
CAAAAAGAAAAAATTAAGTGGGCAA
Found at i:15949 original size:3 final size:3
Alignment explanation
Indices: 15941--16000 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
15931 TAAAATGGAA
15941 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15988 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
16001 CTCCATGCTG
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17086 original size:13 final size:13
Alignment explanation
Indices: 17068--17092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17058 ATCAGTTGCC
17068 TATATATATATAA
1 TATATATATATAA
17081 TATATATATATA
1 TATATATATATA
17093 TATCAAGCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:17223 original size:3 final size:3
Alignment explanation
Indices: 17210--17247 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
17200 AGATCAAGCC
*
17210 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
17248 GTACTTATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:18151 original size:21 final size:21
Alignment explanation
Indices: 18125--18172 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
18115 ATATATATTT
18125 TTATATGTACGTATATTTATA
1 TTATATGTACGTATATTTATA
** *
18146 TTATATGTATTTATTTTTATA
1 TTATATGTACGTATATTTATA
18167 TTATAT
1 TTATAT
18173 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATATGTACGTATATTTATA
Found at i:19640 original size:8 final size:8
Alignment explanation
Indices: 19627--19684 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 8
19617 TTATATTTAA
19627 AATATTAT
1 AATATTAT
*
19635 AATATTTAA
1 AATA-TTAT
19644 AATATTAT
1 AATATTAT
*
19652 AATATTTAA
1 AATA-TTAT
19661 AATATTAT
1 AATATTAT
*
19669 TATATTTAT
1 AATA-TTAT
19678 ATATATT
1 A-ATATT
19685 TTTATATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
8 17 0.43
9 20 0.50
10 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
AATATTAT
Found at i:19641 original size:17 final size:17
Alignment explanation
Indices: 19619--19676 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
19609 AATTATAATT
19619 ATATTTAAAATATTATA
1 ATATTTAAAATATTATA
19636 ATATTTAAAATATTATA
1 ATATTTAAAATATTATA
*
19653 ATATTTAAAATATTATT
1 ATATTTAAAATATTATA
19670 ATATTTA
1 ATATTTA
19677 TATATATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTAAAATATTATA
Found at i:19647 original size:9 final size:9
Alignment explanation
Indices: 19619--19666 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
19609 AATTATAATT
19619 ATATTTAAA
1 ATATTTAAA
*
19628 ATA-TTATA
1 ATATTTAAA
19636 ATATTTAAA
1 ATATTTAAA
*
19645 ATA-TTATA
1 ATATTTAAA
19653 ATATTTAAA
1 ATATTTAAA
19662 ATATT
1 ATATT
19667 ATTATATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 14 0.42
9 19 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATATTTAAA
Found at i:19709 original size:20 final size:20
Alignment explanation
Indices: 19661--19712 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
19651 TAATATTTAA
19661 AATATTATTATATTTATATAT
1 AATATTA-TATATTTATATAT
* *
19682 ATTTTTATATATTTATA-ATT
1 AATATTATATATTTATATA-T
19702 AATATTATATA
1 AATATTATATA
19713 AATTTTAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTATATATTTATATAT
Found at i:19755 original size:11 final size:11
Alignment explanation
Indices: 19741--19774 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19731 ATTATATTTT
19741 TATTTTTATTA
1 TATTTTTATTA
*
19752 TATTTTAATTA
1 TATTTTTATTA
19763 T-TTTTTATTA
1 TATTTTTATTA
19773 TA
1 TA
19775 ATGATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:19763 original size:20 final size:20
Alignment explanation
Indices: 19665--19774 Score: 77
Period size: 21 Copynumber: 5.4 Consensus size: 20
19655 ATTTAAAATA
19665 TTATTATA-TTTATATATATTT
1 TTATTATATTTTA-AT-TATTT
* *
19686 TTA-TATATTTATAATTAATA
1 TTATTATATTT-TAATTATTT
* *
19706 TTATATAAATTTTAAAGTATTT
1 TTAT-TATATTTT-AATTATTT
*
19728 AATATTATA-TTT--TTATTT
1 -TTATTATATTTTAATTATTT
19746 TTATTATATTTTAATTATTTT
1 TTATTATATTTTAATTA-TTT
19767 TTATTATA
1 TTATTATA
19775 ATGATAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
17 7 0.10
18 8 0.12
20 13 0.19
21 22 0.32
22 16 0.23
23 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
TTATTATATTTTAATTATTT
Found at i:19878 original size:4 final size:4
Alignment explanation
Indices: 19871--19905 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
19861 TATGTAGTGG
*
19871 GAAA GAAA GAAA GAAA AAAA GAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
19906 AAAAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:19893 original size:16 final size:17
Alignment explanation
Indices: 19872--19907 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
19862 ATGTAGTGGG
19872 AAAGAAAGAAAGAA-AA
1 AAAGAAAGAAAGAAGAA
19888 AAAGAAAGAAAGAAGAA
1 AAAGAAAGAAAGAAGAA
19905 AAA
1 AAA
19908 AAAATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAGAA
Found at i:19988 original size:26 final size:24
Alignment explanation
Indices: 19938--20007 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 24
19928 ATGTTTGTAT
19938 TTATATTTTTTTATTTTTAAAATA
1 TTATATTTTTTTATTTTTAAAATA
* *
19962 TTATATTTTTGTATATTTTTGACATA
1 TTATATTTTT-T-TATTTTTAAAATA
19988 TTAATAATTTATTTTATTTT
1 TT-AT-ATTT-TTTTATTTT
20008 ATGTATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 13 0.33
27 8 0.21
28 5 0.13
29 2 0.05
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (24 bp):
TTATATTTTTTTATTTTTAAAATA
Found at i:20116 original size:17 final size:17
Alignment explanation
Indices: 20081--20118 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20071 TATTATTTAA
20081 AATATTATAAATTTATGT
1 AATATTATAAA-TTATGT
20099 AATATTTATAAA-TATGT
1 AATA-TTATAAATTATGT
20116 AAT
1 AAT
20119 TATATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATATTATAAATTATGT
Found at i:25297 original size:26 final size:27
Alignment explanation
Indices: 25245--25300 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
25235 TGAAATTTTT
*
25245 TAAAAATATATATTATATATATAATTA
1 TAAAAATAAATATTATATATATAATTA
* *
25272 TAAAATATAAATATTTTATAATATTATTA
1 TAAAA-ATAAATATTATAT-ATATAATTA
25301 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 11 0.46
29 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TAAAAATAAATATTATATATATAATTA
Found at i:25966 original size:32 final size:33
Alignment explanation
Indices: 25902--25972 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
25892 TAATGTGTTA
*
25902 TTTAT-TTTTATAAATTTTGATACTGATAATAT
1 TTTATATTATATAAATTTTGATACTGATAATAT
* *
25934 TTTATATTATATAAATTTTGATAC-GTTTATAT
1 TTTATATTATATAAATTTTGATACTGATAATAT
25966 TTTATAT
1 TTTATAT
25973 CGTGTTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 18 0.51
33 17 0.49
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.58
Consensus pattern (33 bp):
TTTATATTATATAAATTTTGATACTGATAATAT
Found at i:26362 original size:62 final size:64
Alignment explanation
Indices: 26287--26410 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 64
26277 AAAATGGATG
* * * * *
26287 GTAAATAGCATTAATTAAACATAT-ATATATATGTG-ATGAAGAAATGGATGGTAAATAGCACT
1 GTAAATAGCATTAATAAAAAATATAACATATATGAGAAAGAAGAAATGGATGGTAAATAGCACT
*
26349 GTAAATAGCATTAATAAAAAATATAACATATATGAGAAAGAAGCAATGGATGGTAAATAGCA
1 GTAAATAGCATTAATAAAAAATATAACATATATGAGAAAGAAGAAATGGATGGTAAATAGCA
26411 TTAATTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 22 0.41
63 9 0.17
64 23 0.43
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (64 bp):
GTAAATAGCATTAATAAAAAATATAACATATATGAGAAAGAAGAAATGGATGGTAAATAGCACT
Found at i:31162 original size:93 final size:92
Alignment explanation
Indices: 31004--31192 Score: 274
Period size: 93 Copynumber: 2.1 Consensus size: 92
30994 AAAAGTACTA
* * *
31004 AAAG-TTGATTGATTGTAAATTTCAGACTACAAAGATTAGACTAATGCATATATTATATTTGAGA
1 AAAGATTGATTGATTGTAAATGTCAAACTACAAAGATTAGACTAATGCATATATTATATTTAAGA
31068 ATCAGATTATTTTTTATAGAAAAAAAAG
66 ATCAGATTATTTTTTATAG-AAAAAAAG
** *
31096 AAAGATTGATTGATTGTAAATGTCAAACTGTAAAGATTAGACTAATGTATGA-ATTATATTTAAG
1 AAAGATTGATTGATTGTAAATGTCAAACTACAAAGATTAGACTAATGCAT-ATATTATATTTAAG
* *
31160 AATCAGATTCTTTTTTATAGGAAAAAAG
65 AATCAGATTATTTTTTATAGAAAAAAAG
31188 AAAGA
1 AAAGA
31193 CTACAAGGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
92 16 0.18
93 70 0.80
94 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (92 bp):
AAAGATTGATTGATTGTAAATGTCAAACTACAAAGATTAGACTAATGCATATATTATATTTAAGA
ATCAGATTATTTTTTATAGAAAAAAAG
Found at i:32594 original size:46 final size:46
Alignment explanation
Indices: 32527--32619 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
32517 GAAAGAGGCC
32527 ATGGTTTCAGCTGTAAAGCACTATAACATCAAAAACTCTGTAGATT
1 ATGGTTTCAGCTGTAAAGCACTATAACATCAAAAACTCTGTAGATT
32573 ATGGTTTCAGCTGTAAAGCACTATAACATCAAAAACTCTGTAGATT
1 ATGGTTTCAGCTGTAAAGCACTATAACATCAAAAACTCTGTAGATT
32619 A
1 A
32620 CAAAATAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (46 bp):
ATGGTTTCAGCTGTAAAGCACTATAACATCAAAAACTCTGTAGATT
Found at i:36029 original size:21 final size:22
Alignment explanation
Indices: 36013--36062 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
36003 TTTAAATATG
36013 ATTTT-TTTATTTATAAAATTA
1 ATTTTATTTATTTATAAAATTA
*
36034 ATTTTATTTATTTTTATTAAATTA
1 ATTTTATTTA--TTTATAAAATTA
36058 ATTTT
1 ATTTT
36063 TACATGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 4 0.16
24 16 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTATTTATTTATAAAATTA
Found at i:36210 original size:11 final size:11
Alignment explanation
Indices: 36194--36230 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
36184 TTATTACTTT
36194 TTATTTATAAA
1 TTATTTATAAA
* *
36205 TTATTTTTAAT
1 TTATTTATAAA
36216 TTATTTATAAA
1 TTATTTATAAA
36227 TTAT
1 TTAT
36231 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:37332 original size:16 final size:17
Alignment explanation
Indices: 37304--37335 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
37294 AAAAAAATGT
37304 AGAAAAAGCAAATTGTC
1 AGAAAAAGCAAATTGTC
37321 AGAAAAAG-AAATTGT
1 AGAAAAAGCAAATTGT
37336 AAAGACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (17 bp):
AGAAAAAGCAAATTGTC
Found at i:37726 original size:13 final size:13
Alignment explanation
Indices: 37708--37743 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
37698 TAATCTCTTT
*
37708 AAAAAAATAACTA
1 AAAAAAATAACAA
*
37721 AAAAAAATTACAA
1 AAAAAAATAACAA
37734 AAAAAAATAA
1 AAAAAAATAA
37744 AAAGTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAAATAACAA
Found at i:39609 original size:18 final size:20
Alignment explanation
Indices: 39575--39612 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
39565 AATGTATATA
39575 TTTAAAATAATTAAATATTT
1 TTTAAAATAATTAAATATTT
39595 TTTAAAA-AA-TAAATATTT
1 TTTAAAATAATTAAATATTT
39613 ATATCATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAAATAATTAAATATTT
Found at i:40066 original size:13 final size:14
Alignment explanation
Indices: 40039--40069 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
40029 TATTAAATTT
40039 TATATAAATTATAA
1 TATATAAATTATAA
40053 TATATAAA-TATAA
1 TATATAAATTATAA
40066 TATA
1 TATA
40070 AATATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATAAATTATAA
Found at i:40073 original size:11 final size:11
Alignment explanation
Indices: 39974--40075 Score: 53
Period size: 11 Copynumber: 8.6 Consensus size: 11
39964 AAGATAATTC
*
39974 AAATATAGTAT
1 AAATATAATAT
*
39985 AAATATAAAAT
1 AAATATAATAT
*
39996 AAATA-AAAAT
1 AAATATAATAT
**
40006 TTATATAATAT
1 AAATATAATAT
*
40017 AAATTATTTACGTATT
1 AAA-TA--TA-ATA-T
* *
40033 AAATTTTATAT
1 AAATATAATAT
40044 AAATTATAATATAT
1 AAA-TAT-A-ATAT
40058 AAATATAATAT
1 AAATATAATAT
40069 AAATATA
1 AAATATA
40076 TGAATTACTT
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
10 8 0.12
11 34 0.49
12 7 0.10
13 4 0.06
14 9 0.13
15 3 0.04
16 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (11 bp):
AAATATAATAT
Found at i:40076 original size:13 final size:13
Alignment explanation
Indices: 40040--40076 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
40030 ATTAAATTTT
40040 ATATAAAT-TATA
1 ATATAAATATATA
40052 ATATATAA-ATATA
1 ATATA-AATATATA
40065 ATATAAATATAT
1 ATATAAATATAT
40077 GAATTACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAAATATATA
Found at i:41886 original size:24 final size:24
Alignment explanation
Indices: 41845--41891 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41835 CTGCTTCTGC
**
41845 CGATTTGCTTCTTGTTGCTGTTGT
1 CGATTTGCTTCTAATTGCTGTTGT
41869 CGATTTGCTTCTAATTGCTGTTG
1 CGATTTGCTTCTAATTGCTGTTG
41892 CCAATTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (24 bp):
CGATTTGCTTCTAATTGCTGTTGT
Found at i:41944 original size:57 final size:57
Alignment explanation
Indices: 41880--41990 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 57
41870 GATTTGCTTC
* * * *
41880 TAATTGCTGTTGCCAATTATTGC-CGTTGTTGTTAGGTTTAGTAGTTTAGTTGCTTTT
1 TAATTGCTATTGCCAATTATTGCAC-TAGCTATTAGGTTTAGTAGTTTAGTTGCTTTT
* *
41937 TAATTGCTATTGTCGATTATTGCACTAGCTATTAGGTTTAGTAGTTTAGTTGCT
1 TAATTGCTATTGCCAATTATTGCACTAGCTATTAGGTTTAGTAGTTTAGTTGCT
41991 GCTCATGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 46 0.98
58 1 0.02
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.49
Consensus pattern (57 bp):
TAATTGCTATTGCCAATTATTGCACTAGCTATTAGGTTTAGTAGTTTAGTTGCTTTT
Found at i:42978 original size:16 final size:17
Alignment explanation
Indices: 42936--42978 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
42926 AAACTTGATC
42936 TAAAATAA-TTAAACTT
1 TAAAATAATTTAAACTT
*
42952 TAAAATTATTTAAA-TT
1 TAAAATAATTTAAACTT
*
42968 TAAAGTAATTT
1 TAAAATAATTT
42979 CAATGCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAATAATTTAAACTT
Found at i:43097 original size:16 final size:15
Alignment explanation
Indices: 43058--43165 Score: 85
Period size: 16 Copynumber: 7.1 Consensus size: 15
43048 TTTTAAAGTT
*
43058 TAATT-AATTTAAGA
1 TAATTAAATTTAAAA
*
43072 TAAATAAATTTAAAA
1 TAATTAAATTTAAAA
43087 TCAATTAAATTTAAAA
1 T-AATTAAATTTAAAA
* * *
43103 TGATACAAATATAAAA
1 TAAT-TAAATTTAAAA
* *
43119 TAATTTAATTTATAA
1 TAATTAAATTTAAAA
* *
43134 TTATATAAATCTAAAA
1 TAAT-TAAATTTAAAA
43150 TTAATTAAA-TTAAAA
1 -TAATTAAATTTAAAA
43165 T
1 T
43166 TTTAATGTGA
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
14 5 0.07
15 26 0.36
16 38 0.53
17 3 0.04
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (15 bp):
TAATTAAATTTAAAA
Found at i:43098 original size:31 final size:29
Alignment explanation
Indices: 43058--43165 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 29
43048 TTTTAAAGTT
* *
43058 TAATT-AATTTAAGATAAATAAATTTAAAA
1 TAATTAAATTTAA-ATATATAAATATAAAA
*
43087 TCAATTAAATTTAAAATGATACAAATATAAAA
1 T-AATTAAATTT-AAAT-ATATAAATATAAAA
* *
43119 TAATTTAATTTATAATTATATAAATCTAAAA
1 TAATTAAATTTA-AA-TATATAAATATAAAA
*
43150 TTAATTAAATTAAAAT
1 -TAATTAAATTTAAAT
43166 TTTAATGTGA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
29 1 0.02
30 6 0.09
31 32 0.50
32 25 0.39
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (29 bp):
TAATTAAATTTAAATATATAAATATAAAA
Found at i:44761 original size:22 final size:20
Alignment explanation
Indices: 44716--44767 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
44706 AAGTTTGTAT
*
44716 ATTTATTTTA-TATTTATATT
1 ATTT-TTTTATTATTTATATA
44736 ATTTTTCTTATTATTTCATATA
1 ATTTTT-TTATTATTT-ATATA
44758 ATTTTTTTAT
1 ATTTTTTTAT
44768 ATAATATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 7 0.25
21 9 0.32
22 10 0.36
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTTTATTATTTATATA
Found at i:44777 original size:24 final size:23
Alignment explanation
Indices: 44723--44780 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
44713 TATATTTATT
* *
44723 TTATATTTATATTATTTTTCTTA
1 TTATATTCATATAATTTTTCTTA
44746 TTAT-TTCATATAATTTTT-TTA
1 TTATATTCATATAATTTTTCTTA
44767 TATAATATTCATAT
1 T-T-ATATTCATAT
44781 TATGTAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 13 0.43
23 6 0.20
24 7 0.23
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATATTCATATAATTTTTCTTA
Found at i:46149 original size:18 final size:17
Alignment explanation
Indices: 46100--46150 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
46090 AATGTATATA
*
46100 TTTAAAATAATTATCTT
1 TTTAAAATAATTATTTT
*
46117 TTTAAAATTATTATTTT
1 TTTAAAATAATTATTTT
*
46134 TTTAAAAATAAATATTT
1 TTT-AAAATAATTATTT
46151 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAAATAATTATTTT
Found at i:46530 original size:17 final size:20
Alignment explanation
Indices: 46501--46549 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 20
46491 TTGAAAAATT
*
46501 ATATTATAATATA-TT-TAA
1 ATATTAAAATATATTTATAA
46519 AT-TTAAAATATATTTATAA
1 ATATTAAAATATATTTATAA
46538 ATATTAAAATAT
1 ATATTAAAATAT
46550 TAATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 4 0.15
19 5 0.19
20 9 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTAAAATATATTTATAA
Found at i:46541 original size:27 final size:29
Alignment explanation
Indices: 46495--46552 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
46485 GTTATATTGA
*
46495 AAAATTATATTATAATATATTTAAAT-TT
1 AAAATTATATTATAATATATTAAAATATT
46523 AAAA-TATATTTATAA-ATATTAAAATATT
1 AAAATTATA-TTATAATATATTAAAATATT
46551 AA
1 AA
46553 TTTTTAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATTATATTATAATATATTAAAATATT
Found at i:47986 original size:19 final size:19
Alignment explanation
Indices: 47941--47995 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 19
47931 TGATATGAGC
* *
47941 TTTAGGTTTTAAAAAATTA
1 TTTAGATTTTAAAAATTTA
** *
47960 AATGGATTTTAAAAATTTA
1 TTTAGATTTTAAAAATTTA
*
47979 TTTAGATTATAAAAATT
1 TTTAGATTTTAAAAATT
47996 AAAAGCCCAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTAGATTTTAAAAATTTA
Found at i:48924 original size:17 final size:17
Alignment explanation
Indices: 48902--48992 Score: 73
Period size: 17 Copynumber: 5.4 Consensus size: 17
48892 AATAATAAAA
*
48902 ATATATATTAAATTAAT
1 ATATATATTAAATTTAT
*
48919 ATATATTTTAAAATTTAT
1 ATATATATT-AAATTTAT
48937 ATA-ATATT-AA-TTAT
1 ATATATATTAAATTTAT
*
48951 -TAATTTATTAAAATTTAT
1 AT-ATATATT-AAATTTAT
* *
48969 ATAAATATAAAATTTAT
1 ATATATATTAAATTTAT
*
48986 AAATATA
1 ATATATA
48993 ATTATAATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
13 1 0.02
14 5 0.09
15 6 0.10
17 27 0.47
18 18 0.31
19 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATTAAATTTAT
Found at i:48957 original size:29 final size:30
Alignment explanation
Indices: 48899--48974 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 30
48889 TAAAATAATA
*
48899 AAAATATATATTAAATTAATATAT-ATT-TT
1 AAAATTTATA-TAAATTAATATATAATTATT
48928 AAAATTTATATAATATTAAT-TATTAATTTATT
1 AAAATTTATATAA-ATTAATATA-TAA-TTATT
48960 AAAATTTATATAAAT
1 AAAATTTATATAAAT
48975 ATAAAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 5 0.12
29 16 0.39
30 1 0.02
31 4 0.10
32 15 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AAAATTTATATAAATTAATATATAATTATT
Found at i:49747 original size:29 final size:29
Alignment explanation
Indices: 49714--49771 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
49704 TTTGCCTTGA
49714 TTAGAATTGGATGGTTTAGAAACAAACAT
1 TTAGAATTGGATGGTTTAGAAACAAACAT
49743 TTAGAATTGGATGGTTTAGAAACAAACAT
1 TTAGAATTGGATGGTTTAGAAACAAACAT
49772 AAAGACACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (29 bp):
TTAGAATTGGATGGTTTAGAAACAAACAT
Found at i:49821 original size:16 final size:16
Alignment explanation
Indices: 49800--49833 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
49790 AAACGCAATT
49800 GTTTAAGTGATGGCTG
1 GTTTAAGTGATGGCTG
49816 GTTTAAGTGATGGCTG
1 GTTTAAGTGATGGCTG
49832 GT
1 GT
49834 GTTTGATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.38, T:0.38
Consensus pattern (16 bp):
GTTTAAGTGATGGCTG
Found at i:57617 original size:58 final size:57
Alignment explanation
Indices: 57527--57851 Score: 180
Period size: 58 Copynumber: 5.6 Consensus size: 57
57517 TAAATATTTT
* * *
57527 TAAAATTCATGAAAGTTCCT-AGATCATAGAAAATGACTTAAATGATATTAAAATTAA
1 TAAAATTCATTAAAGTCCCTAAG-TCATTGAAAATGACTTAAATGATATTAAAATTAA
* * * * *
57584 TAAAATTACATTAAAGTCCCTAAGTCATTGAAAATAACCTAAATGCCT-CTAAAATTTA
1 TAAAATT-CATTAAAGTCCCTAAGTCATTGAAAATGACTTAAATG-ATATTAAAATTAA
* ** * * ** *
57642 TAAAATTCTATCCAAA-TCTTTAAGCCA-TGAAAAATGACTTACATGCCATTAAAATTCA
1 TAAAATTC-AT-TAAAGTCCCTAAGTCATTG-AAAATGACTTAAATGATATTAAAATTAA
* * * * *
57700 TAAAATTGCATCT-AAGTCCTTAAGT-AATGAAAAATGATTTAAATAATATTAAAATTAT
1 TAAAATT-CAT-TAAAGTCCCTAAGTCATTG-AAAATGACTTAAATGATATTAAAATTAA
* * * * ** * * *
57758 TAAAATT-ATAAAAAAATCCTTAAATCATAAAAAATGACTTAAATAATATCAAAATTCA
1 TAAAATTCAT--TAAAGTCCCTAAGTCATTGAAAATGACTTAAATGATATTAAAATTAA
* * *
57816 TTAAATTGCA-TACAAGTTCCTAAGTCATGGAAAATG
1 TAAAATT-CATTA-AAGTCCCTAAGTCATTGAAAATG
57852 TCCTACATGA
Statistics
Matches: 205, Mismatches: 47, Indels: 31
0.72 0.17 0.11
Matches are distributed among these distances:
56 2 0.01
57 15 0.07
58 179 0.87
59 8 0.04
60 1 0.00
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.32
Consensus pattern (57 bp):
TAAAATTCATTAAAGTCCCTAAGTCATTGAAAATGACTTAAATGATATTAAAATTAA
Found at i:57760 original size:19 final size:19
Alignment explanation
Indices: 57738--57821 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
57728 GAAAAATGAT
*
57738 TTAAATAATATTAAAATTA
1 TTAAATAATATAAAAATTA
* * **
57757 TTAAAATTATAAAAAAATCC
1 TT-AAATAATATAAAAATTA
* *
57777 TTAAATCATA-AAAAATGA
1 TTAAATAATATAAAAATTA
*
57795 CTTAAATAATATCAAAATTCA
1 -TTAAATAATATAAAAATT-A
57816 TTAAAT
1 TTAAAT
57822 TGCATACAAG
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
18 6 0.12
19 18 0.36
20 25 0.50
21 1 0.02
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (19 bp):
TTAAATAATATAAAAATTA
Found at i:57891 original size:58 final size:58
Alignment explanation
Indices: 57784--57951 Score: 153
Period size: 58 Copynumber: 2.9 Consensus size: 58
57774 TCCTTAAATC
* * * * *
57784 ATAAAAAATGACTTAAATAATATCAAAATTCATTAAATTGCA-TACAAGTTCCTAAG-T
1 ATAAAAAATGACCTAAATGACATCAAAATTCATAAAATTGCACCA-AAGTTCCTAAGCT
** * * * * *
57841 CATGGAAAATGTCCTACATGACATCAAACTTCATAAAATTGCACCAAAGTTCTTACGCT
1 -ATAAAAAATGACCTAAATGACATCAAAATTCATAAAATTGCACCAAAGTTCCTAAGCT
* * * *
57900 ATAAAAAATGACCTAAATGATATCAAATTTCATAAAATTACACCGAA-TTCCT
1 ATAAAAAATGACCTAAATGACATCAAAATTCATAAAATTGCACCAAAGTTCCT
57952 TTGGTCATTG
Statistics
Matches: 87, Mismatches: 21, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
57 4 0.05
58 81 0.93
59 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (58 bp):
ATAAAAAATGACCTAAATGACATCAAAATTCATAAAATTGCACCAAAGTTCCTAAGCT
Found at i:57959 original size:116 final size:117
Alignment explanation
Indices: 57784--58000 Score: 260
Period size: 116 Copynumber: 1.9 Consensus size: 117
57774 TCCTTAAATC
* * *
57784 ATAAAAAATGACTTAAATAATATCAAAATTCATTAAATTGCATACAAGTTCCTAAGTCA-TGGAA
1 ATAAAAAATGACCTAAATAATATCAAAATTCATAAAATTACATACAAGTTCCTAAGTCATTGGAA
** *
57848 AATGTCCTACATGACATCAAACTTCATAAAATTGCACCAAAGTTCTTACGCT
66 AATAACCTAAATGACATCAAACTTCATAAAATTGCACCAAAGTTCTTACGCT
* * * **
57900 ATAAAAAATGACCTAAATGATATCAAATTTCATAAAATTACA-CCGAA-TTCCTTTGGTCATTGG
1 ATAAAAAATGACCTAAATAATATCAAAATTCATAAAATTACATAC-AAGTTCC-TAAGTCATTGG
* * * *
57963 AAAATAACTTAAATGACATTAAATTTTATAAAATTGCA
64 AAAATAACCTAAATGACATCAAACTTCATAAAATTGCA
58001 TAAAAAATTC
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
115 5 0.06
116 44 0.53
117 34 0.41
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (117 bp):
ATAAAAAATGACCTAAATAATATCAAAATTCATAAAATTACATACAAGTTCCTAAGTCATTGGAA
AATAACCTAAATGACATCAAACTTCATAAAATTGCACCAAAGTTCTTACGCT
Found at i:58026 original size:59 final size:59
Alignment explanation
Indices: 57963--58102 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
57953 TGGTCATTGG
* * * *
57963 AAAATAACTTAAATGACATTAAA-T-TTTATAAAAT-TGCATAAAAAATTCTTAGATCATGA
1 AAAATAACTTAAATGACA-AAAAGTATGTATAAAATAT-CAT-AAAAATTCCTAAATCATGA
* *
58022 AAAATTACTTAAATGACAAAAAGTATGTATAAAATATCATAAAAATTCCTAAATCATGG
1 AAAATAACTTAAATGACAAAAAGTATGTATAAAATATCATAAAAATTCCTAAATCATGA
*
58081 AAAATGAC-TAAGATGACAAAAA
1 AAAATAACTTAA-ATGACAAAAA
58103 TGCATGAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
58 6 0.09
59 51 0.73
60 12 0.17
61 1 0.01
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (59 bp):
AAAATAACTTAAATGACAAAAAGTATGTATAAAATATCATAAAAATTCCTAAATCATGA
Found at i:60305 original size:56 final size:56
Alignment explanation
Indices: 60228--60347 Score: 141
Period size: 56 Copynumber: 2.1 Consensus size: 56
60218 ATTTTAAAAC
* * * *
60228 ATGTCTACTTTAGACATTGTCTTAATAAGATAAGCTTATCCATACTGTCTTAACAT
1 ATGTCTACTTTAAACATTGTCTTAATAAAATAACCTTATCCATAATGTCTTAACAT
* * ** * *
60284 ATGTTTACTTTAAATATTGTCTTGTTAAAATAACCTTATCCATAATGTTTTAACAC
1 ATGTCTACTTTAAACATTGTCTTAATAAAATAACCTTATCCATAATGTCTTAACAT
*
60340 ATATCTAC
1 ATGTCTAC
60348 CATAGACATT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (56 bp):
ATGTCTACTTTAAACATTGTCTTAATAAAATAACCTTATCCATAATGTCTTAACAT
Found at i:60688 original size:22 final size:23
Alignment explanation
Indices: 60645--60686 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
60635 AATGTTTTTG
60645 AAACATGATTATGATTTATTTAT
1 AAACATGATTATGATTTATTTAT
*
60668 AAACATTA-TATG-TTTATTT
1 AAACATGATTATGATTTATTT
60687 TAGCATTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (23 bp):
AAACATGATTATGATTTATTTAT
Found at i:60967 original size:18 final size:18
Alignment explanation
Indices: 60944--60981 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
60934 ATTTGACTCA
*
60944 GTGATAAATAGCCATGAT
1 GTGATAAATAACCATGAT
60962 GTGATAAATAACCATGAT
1 GTGATAAATAACCATGAT
60980 GT
1 GT
60982 TAAAGACGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (18 bp):
GTGATAAATAACCATGAT
Found at i:64332 original size:2 final size:2
Alignment explanation
Indices: 64325--64349 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64315 AATGTAAACA
64325 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 A
64350 AAAAAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64651 original size:24 final size:25
Alignment explanation
Indices: 64606--64652 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
64596 ATACTATTAG
64606 TTTATTTGCTTCTTAAGACTAACTA
1 TTTATTTGCTTCTTAAGACTAACTA
64631 TTTATTTGCTTC-TAAGACTAAC
1 TTTATTTGCTTCTTAAGACTAAC
64653 ATTGCCGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (25 bp):
TTTATTTGCTTCTTAAGACTAACTA
Found at i:66810 original size:8 final size:8
Alignment explanation
Indices: 66776--66856 Score: 62
Period size: 8 Copynumber: 9.9 Consensus size: 8
66766 GCATTCACGT
66776 TATATTTA
1 TATATTTA
66784 TATTATTT-
1 TA-TATTTA
66792 T-T-TTGTA
1 TATATT-TA
66799 TATATTTA
1 TATATTTA
66807 TATAAATTTTGA
1 TAT--A-TTT-A
66819 TATATTTA
1 TATATTTA
66827 TATATTTA
1 TATATTTA
66835 TAT-TTTA
1 TATATTTA
* *
66842 TTTTTTTA
1 TATATTTA
66850 TATATTT
1 TATATTT
66857 TAATTATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 7 0.12
8 30 0.50
9 10 0.17
10 2 0.03
11 3 0.05
12 4 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (8 bp):
TATATTTA
Found at i:66823 original size:20 final size:21
Alignment explanation
Indices: 66792--66830 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
66782 TATATTATTT
66792 TTTTGTATATATTTATATAAA
1 TTTTGTATATATTTATATAAA
66813 TTTTG-ATATATTTATATA
1 TTTTGTATATATTTATATA
66831 TTTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTGTATATATTTATATAAA
Found at i:66855 original size:17 final size:19
Alignment explanation
Indices: 66833--66874 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
66823 TTTATATATT
66833 TATATTTT-ATT-TTTTTA
1 TATATTTTAATTATTTTTA
66850 TATATTTTAATTATTTTTA
1 TATATTTTAATTATTTTTA
66869 TCATAT
1 T-ATAT
66875 CGTGTTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 3 0.14
19 7 0.32
20 4 0.18
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TATATTTTAATTATTTTTA
Found at i:66867 original size:21 final size:23
Alignment explanation
Indices: 66776--66855 Score: 53
Period size: 23 Copynumber: 3.6 Consensus size: 23
66766 GCATTCACGT
*
66776 TATATTTATATTATT-TTTTTGTA
1 TATATTTATA-TATTATTTTTTTA
* *
66799 TATATTTATATA--A-ATTTTGA
1 TATATTTATATATTATTTTTTTA
*
66819 TATATTTATATATT-TATATTTTA
1 TATATTTATATATTAT-TTTTTTA
* *
66842 TTTTTTTATATATT
1 TATATTTATATATT
66856 TTAATTATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
20 16 0.36
22 2 0.05
23 26 0.59
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (23 bp):
TATATTTATATATTATTTTTTTA
Found at i:67375 original size:2 final size:2
Alignment explanation
Indices: 67368--67405 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
67358 AGATACAGAT
67368 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
67406 TGTACAGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:67934 original size:13 final size:12
Alignment explanation
Indices: 67887--67940 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
67877 ATAAATTTAA
67887 ATATTTATTATGT
1 ATATTTATTAT-T
*
67900 TTATTTA-TATT
1 ATATTTATTATT
*
67911 ATATGTAATTATT
1 ATAT-TTATTATT
67924 ATA-TTA-TATT
1 ATATTTATTATT
67934 ATATTTA
1 ATATTTA
67941 AAATTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 7 0.21
11 9 0.26
12 5 0.15
13 13 0.38
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (12 bp):
ATATTTATTATT
Found at i:77510 original size:2 final size:2
Alignment explanation
Indices: 77505--77530 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77495 CTTTAGTTTT
77505 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
77531 CACACACACA
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):
TA
Found at i:80355 original size:12 final size:12
Alignment explanation
Indices: 80340--80383 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
80330 TTAAAAATTT
80340 AAAAAAAATAAC
1 AAAAAAAATAAC
* *
80352 AAAATAAATGAC
1 AAAAAAAATAAC
*
80364 ACAAAAAAATAAT
1 A-AAAAAAATAAC
80377 AAAAAAA
1 AAAAAAA
80384 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (12 bp):
AAAAAAAATAAC
Found at i:80778 original size:19 final size:19
Alignment explanation
Indices: 80735--80779 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
80725 CTAACAAAAA
80735 TTGTAAAAATAAAAACTTT
1 TTGTAAAAATAAAAACTTT
*
80754 TCTGTAAAACTAATAAA-TTT
1 T-TGTAAAAATAA-AAACTTT
80774 TTGTAA
1 TTGTAA
80780 TGCACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 14 0.61
21 3 0.13
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (19 bp):
TTGTAAAAATAAAAACTTT
Found at i:81645 original size:37 final size:34
Alignment explanation
Indices: 81582--81650 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 34
81572 ATAATTATAT
81582 TTAAAATATTATATATTTATATAAATTTAATAGG
1 TTAAAATATTATATATTTATATAAATTTAATAGG
*
81616 TTAAAATTTTATATTATATTATATAAAATTTAATA
1 TTAAAATATTATA-TAT-TTATAT-AAATTTAATA
81651 TATTTATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 12 0.39
35 3 0.10
36 6 0.19
37 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (34 bp):
TTAAAATATTATATATTTATATAAATTTAATAGG
Found at i:81661 original size:22 final size:22
Alignment explanation
Indices: 81617--81660 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
81607 TTTAATAGGT
81617 TAAAATTTTATATTATATTATA
1 TAAAATTTTATATTATATTATA
*
81639 TAAAATTTAATA-TAT-TTATA
1 TAAAATTTTATATTATATTATA
81659 TA
1 TA
81661 TTTACTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAATTTTATATTATATTATA
Found at i:81682 original size:56 final size:57
Alignment explanation
Indices: 81529--81684 Score: 137
Period size: 56 Copynumber: 2.7 Consensus size: 57
81519 CTCAAATAAT
*
81529 TTTAATA-ATTTATATATTTATATTATATATGTT-TTTATATATTATAATTATATTTAAAA
1 TTTAATATATTTATATATTTAT-TTATAT-T-TTATTTTTATATTATAATTATA-TTAAAA
* ** *
81588 TATT-ATATATTTATATA--AATTTAATAGGTTAAAATTTTATATTAT-ATTATA-TAAAA
1 T-TTAATATATTTATATATTTATTT-ATA--TTTTATTTTTATATTATAATTATATTAAAA
81644 TTTAATATATTTATATATTTACTTTATATTTTATTTTTATA
1 TTTAATATATTTATATATTTA-TTTATATTTTATTTTTATA
81685 ATATTTTAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
55 2 0.03
56 29 0.37
57 2 0.03
58 15 0.19
59 18 0.23
60 12 0.15
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (57 bp):
TTTAATATATTTATATATTTATTTATATTTTATTTTTATATTATAATTATATTAAAA
Found at i:81930 original size:3 final size:3
Alignment explanation
Indices: 81922--81947 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
81912 GACGCTTAGA
81922 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
81948 CAACTATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:83178 original size:6 final size:6
Alignment explanation
Indices: 83169--83301 Score: 72
Period size: 6 Copynumber: 21.2 Consensus size: 6
83159 TTTATTTTTA
** * **
83169 AAATTT AAATTT AAATAA ATAATTT AAATTT ATTTATTT AAGATTAT TTATTT
1 AAATTT AAATTT AAATTT A-AATTT AAATTT A--AATTT AA-ATT-T AAATTT
* * * * *
83222 -AATAT AAA-AT AAATTT AATTTTT ATATTT AATTTT AAATTT AATTATTT
1 AAATTT AAATTT AAATTT AA-ATTT AAATTT AAATTT AAATTT AA--ATTT
* *
83271 ATATTT AAATTT TAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT A
83302 TTTTAATACA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
5 8 0.08
6 63 0.66
7 14 0.15
8 11 0.11
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:83181 original size:19 final size:20
Alignment explanation
Indices: 83153--83203 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
83143 TTGAGGTTAA
*
83153 TTAAATTTTATTTTTAA-AAT
1 TTAAA-TTTATTTTAAATAAT
**
83173 TTAAATTTA-AATAAATAAT
1 TTAAATTTATTTTAAATAAT
83192 TTAAATTTATTT
1 TTAAATTTATTT
83204 ATTTAAGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
18 3 0.12
19 16 0.67
20 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATTTATTTTAAATAAT
Found at i:83317 original size:38 final size:39
Alignment explanation
Indices: 83151--83317 Score: 92
Period size: 38 Copynumber: 4.2 Consensus size: 39
83141 ATTTGAGGTT
* * **
83151 AATTAAATTTTATTTTTAAAATTTAAATTTAAATAAATA-
1 AATTAAATTTTATATTT-AAATTTAAATTTAATTATTTAC
* * ** **
83190 ATTTAAATTTATTTATTTAAGATTATTTATTTAATATAAAATA-
1 AATTAAATTT-TATATTTAA-ATT-TAAATTTAAT-T-ATTTAC
* * *
83233 AATTTAATTTTTATATTTAATTTTAAATTTAATTATTTAT
1 AA-TTAAATTTTATATTTAAATTTAAATTTAATTATTTAC
*
83273 ATTTAAATTTTA-ATTTAAATTTAAATTT-ATT-TTAATAC
1 AATTAAATTTTATATTTAAATTTAAATTTAATTATT--TAC
83311 AATTAAA
1 AATTAAA
83318 ATAACACAAA
Statistics
Matches: 100, Mismatches: 19, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
36 2 0.02
37 3 0.03
38 23 0.23
39 23 0.23
40 10 0.10
41 15 0.15
42 3 0.03
43 14 0.14
44 7 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (39 bp):
AATTAAATTTTATATTTAAATTTAAATTTAATTATTTAC
Found at i:86782 original size:21 final size:23
Alignment explanation
Indices: 86747--86799 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
86737 AATATTAAGT
*
86747 AATATTTAA-ATATGTCATGAA-A
1 AATATTTAATATATGTAAT-AATA
86769 AA-ATTTAATA-ATGTAATAATA
1 AATATTTAATATATGTAATAATA
86790 AATATTTAAT
1 AATATTTAAT
86800 TGTTATACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 15 0.56
22 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.40
Consensus pattern (23 bp):
AATATTTAATATATGTAATAATA
Found at i:87540 original size:13 final size:13
Alignment explanation
Indices: 87522--87546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87512 TATTTTTATT
87522 TAATTAAATTTTA
1 TAATTAAATTTTA
87535 TAATTAAATTTT
1 TAATTAAATTTT
87547 GATTTTTTAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTAAATTTTA
Found at i:87558 original size:18 final size:17
Alignment explanation
Indices: 87537--87594 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 17
87527 AAATTTTATA
*
87537 ATTAAATTTTGATTTTTT
1 ATTAAATTTT-ATTGTTT
87555 ATTAAATTTTATTGTTT
1 ATTAAATTTTATTGTTT
*
87572 ATT---TTTTATT-TTA
1 ATTAAATTTTATTGTTT
87585 ATTAAATTTT
1 ATTAAATTTT
87595 GCCTGTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 5 0.14
14 7 0.20
16 4 0.11
17 9 0.26
18 10 0.29
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTAAATTTTATTGTTT
Found at i:87583 original size:31 final size:31
Alignment explanation
Indices: 87506--87594 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 31
87496 AGTAAATTTA
87506 TTATTTTATT-TTTATTTAATTAAATTTTATAAT
1 TTATTTT-TTATTT-TTT-ATTAAATTTTATAAT
* * * **
87539 TAAATTTTGATTTTTTATTAAATTTTATTGT
1 TTATTTTTTATTTTTTATTAAATTTTATAAT
*
87570 TTATTTTTTA-TTTTAATTAAATTTT
1 TTATTTTTTATTTTTTATTAAATTTT
87595 GCCTGTCAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
30 14 0.30
31 20 0.43
32 4 0.09
33 8 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (31 bp):
TTATTTTTTATTTTTTATTAAATTTTATAAT
Found at i:90686 original size:21 final size:21
Alignment explanation
Indices: 90657--90696 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
90647 ATATGATTAT
90657 ATATATAAACACAACATAAAA
1 ATATATAAACACAACATAAAA
* * *
90678 ATATTTAAATACAATATAA
1 ATATATAAACACAACATAA
90697 CATAAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATATAAACACAACATAAAA
Found at i:93696 original size:21 final size:22
Alignment explanation
Indices: 93667--93715 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
93657 AAGTTATATT
93667 TTTTCATCCAAAAAATGCATTC
1 TTTTCATCCAAAAAATGCATTC
**
93689 TTTT-ATCCAACCAATGCA-TC
1 TTTTCATCCAAAAAATGCATTC
*
93709 ATTTCAT
1 TTTTCAT
93716 TTAAAGATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTTCATCCAAAAAATGCATTC
Found at i:93916 original size:48 final size:48
Alignment explanation
Indices: 93840--93935 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
93830 TAGATTACAA
*
93840 ATTCTAAAATATAAAAAAGTATACAGTTATGTATAAAGAAAAGTTATC
1 ATTCCAAAATATAAAAAAGTATACAGTTATGTATAAAGAAAAGTTATC
*
93888 ATTCCAAAATATAATAAAA-TATACAGTTATGTATAAAGGAAAGTTATC
1 ATTCCAAAATATAA-AAAAGTATACAGTTATGTATAAAGAAAAGTTATC
93936 GTTAGATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 41 0.91
49 4 0.09
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (48 bp):
ATTCCAAAATATAAAAAAGTATACAGTTATGTATAAAGAAAAGTTATC
Found at i:97494 original size:15 final size:14
Alignment explanation
Indices: 97477--97516 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
97467 TTATAATATT
*
97477 TTTTGATATAAGTG
1 TTTTGATATAAGTA
*
97491 TTTTGACATAAGTA
1 TTTTGATATAAGTA
97505 CTTTTGATATAA
1 -TTTTGATATAA
97517 ATACTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (14 bp):
TTTTGATATAAGTA
Found at i:97521 original size:15 final size:15
Alignment explanation
Indices: 97477--97523 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
97467 TTATAATATT
*
97477 TTTTGATATAAGT-G
1 TTTTGATATAAGTAC
*
97491 TTTTGACATAAGTAC
1 TTTTGATATAAGTAC
*
97506 TTTTGATATAAATAC
1 TTTTGATATAAGTAC
97521 TTT
1 TTT
97524 AATACAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (15 bp):
TTTTGATATAAGTAC
Found at i:101547 original size:17 final size:18
Alignment explanation
Indices: 101510--101548 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
101500 ATATATTTTA
101510 TTTTATTTTATTAATTAT
1 TTTTATTTTATTAATTAT
101528 TTTTATTTT-TTAA-TAT
1 TTTTATTTTATTAATTAT
101544 TTTTA
1 TTTTA
101549 AATAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTTATTAATTAT
Found at i:101565 original size:19 final size:19
Alignment explanation
Indices: 101541--101577 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
101531 TATTTTTTAA
*
101541 TATTTTTAAATAATTTATT
1 TATTTTTAAATAACTTATT
*
101560 TATTTTTACATAACTTAT
1 TATTTTTAAATAACTTAT
101578 AAGTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTTAAATAACTTATT
Found at i:101778 original size:23 final size:24
Alignment explanation
Indices: 101743--101787 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
101733 AAATGTTAAG
101743 AATTAATTTTTATTTTATTTTATT
1 AATTAATTTTTATTTTATTTTATT
101767 AATT-ATTTTTATTTTATTTTA
1 AATTAATTTTTATTTTATTTTA
101788 AATATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
AATTAATTTTTATTTTATTTTATT
Found at i:101795 original size:23 final size:23
Alignment explanation
Indices: 101738--101788 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
101728 TTGGAAAATG
*
101738 TTAAGAATTAATTTTTATTTTATT
1 TTAATAATT-ATTTTTATTTTATT
*
101762 TTATTAATTATTTTTATTTTATT
1 TTAATAATTATTTTTATTTTATT
101785 TTAA
1 TTAA
101789 ATATTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTAATAATTATTTTTATTTTATT
Found at i:101800 original size:23 final size:23
Alignment explanation
Indices: 101751--101800 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
101741 AGAATTAATT
* *
101751 TTTATTTTATTTTATTAATTATT
1 TTTATTTTATTTTAATAATTATA
101774 TTTATTTTATTTTAA-ATATTATA
1 TTTATTTTATTTTAATA-ATTATA
101797 TTTA
1 TTTA
101801 AAAAAATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTATTTTATTTTAATAATTATA
Found at i:102390 original size:10 final size:9
Alignment explanation
Indices: 102353--102384 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
102343 TTGAAACTCG
102353 AAAAAA-AA
1 AAAAAAGAA
102361 AAAAAAGAA
1 AAAAAAGAA
102370 AAAAAAGAA
1 AAAAAAGAA
102379 AAAAAA
1 AAAAAA
102385 TCAAAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:112501 original size:21 final size:21
Alignment explanation
Indices: 112476--112521 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
112466 TCAATTTAGA
112476 ACTAATTGAACATTTAATTAT
1 ACTAATTGAACATTTAATTAT
112497 ACTAATTGAACATTTAATTAT
1 ACTAATTGAACATTTAATTAT
112518 ACTA
1 ACTA
112522 TAATCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (21 bp):
ACTAATTGAACATTTAATTAT
Found at i:112636 original size:21 final size:21
Alignment explanation
Indices: 112607--112651 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
112597 GTCTTAAATC
*
112607 AAATGACAACCATCTCTGTCT
1 AAATCACAACCATCTCTGTCT
*
112628 AAATCACAACTATCTCTGTCT
1 AAATCACAACCATCTCTGTCT
112649 AAA
1 AAA
112652 CTTACCTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.29
Consensus pattern (21 bp):
AAATCACAACCATCTCTGTCT
Found at i:113491 original size:17 final size:16
Alignment explanation
Indices: 113469--113506 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
113459 ATTAAGTAAA
113469 ATATATTATAAATTAAG
1 ATATATTATAAA-TAAG
*
113486 ATATATTATGAATAAG
1 ATATATTATAAATAAG
113502 ATATA
1 ATATA
113507 AATCTATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (16 bp):
ATATATTATAAATAAG
Found at i:113631 original size:22 final size:22
Alignment explanation
Indices: 113595--113655 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
113585 AAAATATATA
*
113595 AAAAATAAT-TAAAATGTAACAT
1 AAAAATAATAT-AAATATAACAT
*
113617 AAAAATAATATAAATATCACAT
1 AAAAATAATATAAATATAACAT
* *
113639 AAATA-AATATATATATA
1 AAAAATAATATAAATATA
113656 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 10 0.30
22 22 0.67
23 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAATAATATAAATATAACAT
Found at i:113718 original size:11 final size:11
Alignment explanation
Indices: 113586--113769 Score: 56
Period size: 11 Copynumber: 17.1 Consensus size: 11
113576 TATAAACACA
113586 AAATAT-ATA-
1 AAATATAATAT
*
113595 AAAAATAAT-T
1 AAATATAATAT
* *
113605 AAAATGTAACAT
1 -AAATATAATAT
*
113617 AAAAATAATAT
1 AAATATAATAT
* *
113628 AAATATCACAT
1 AAATATAATAT
113639 AAATA-AATAT
1 AAATATAATAT
* *
113649 ATATATATTA-
1 AAATATAATAT
*
113659 AAATTTACATA-
1 AAATATA-ATAT
113670 AACA-ACTAAT-T
1 AA-ATA-TAATAT
113681 AAAT-TAACTTAT
1 AAATATAA--TAT
*
113693 AAAATTTACATAT
1 -AAATATA-ATAT
113706 AAATATAATAT
1 AAATATAATAT
113717 AAAT-T-ATA-
1 AAATATAATAT
113725 AAATAT-ATA-
1 AAATATAATAT
*
113734 AAATAT-ATAAA
1 AAATATAAT-AT
*
113745 AAATATTATAT
1 AAATATAATAT
113756 AAATTTATAATAT
1 AAA--TATAATAT
113769 A
1 A
113770 TCAAACAATA
Statistics
Matches: 132, Mismatches: 21, Indels: 40
0.68 0.11 0.21
Matches are distributed among these distances:
8 4 0.03
9 23 0.17
10 17 0.13
11 57 0.43
12 13 0.10
13 15 0.11
14 2 0.02
15 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (11 bp):
AAATATAATAT
Found at i:113735 original size:9 final size:9
Alignment explanation
Indices: 113702--113750 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
113692 TAAAATTTAC
113702 ATAT-AAAT
1 ATATAAAAT
113710 ATAATATAAAT
1 AT-ATA-AAAT
113721 -TATAAAAT
1 ATATAAAAT
113729 ATATAAAAT
1 ATATAAAAT
*
113738 ATATAAAAA
1 ATATAAAAT
113747 ATAT
1 ATAT
113751 TATATAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 6 0.17
9 25 0.69
10 1 0.03
11 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATATAAAAT
Found at i:113742 original size:18 final size:19
Alignment explanation
Indices: 113702--113770 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
113692 TAAAATTTAC
113702 ATAT-AAATATAATATAAAT
1 ATATAAAATAT-ATATAAAT
113721 -TATAAAATATATA-AAAT
1 ATATAAAATATATATAAAT
113738 ATATAAAAAATATTATATAAAT
1 ATAT--AAAATA-TATATAAAT
* *
113760 TTATAATATAT
1 ATATAAAATAT
113771 CAAACAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
17 4 0.10
18 9 0.21
19 7 0.17
20 11 0.26
21 4 0.10
22 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAAATATATATAAAT
Found at i:113758 original size:39 final size:37
Alignment explanation
Indices: 113706--113789 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 37
113696 ATTTACATAT
*
113706 AAATATAATATAAATTATAAAATATATAAAATATATAAA
1 AAATATAATATAAATT-TAAAATATATAAAACA-ATAAA
* * *
113745 AAATATTATATAAATTTATAATATATCAAACAATAAA
1 AAATATAATATAAATTTAAAATATATAAAACAATAAA
113782 AAA-ATAAT
1 AAATATAAT
113790 CAACATAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 4 0.10
37 8 0.20
38 13 0.32
39 15 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (37 bp):
AAATATAATATAAATTTAAAATATATAAAACAATAAA
Found at i:113838 original size:17 final size:16
Alignment explanation
Indices: 113806--113864 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
113796 AAACACAATT
113806 TTTTTCTCTC-CTTCC
1 TTTTTCTCTCTCTTCC
113821 TTTCTTCTCTCTCTTCC
1 TTT-TTCTCTCTCTTCC
* *
113838 TTTTT-TTTCTCTTTTC
1 TTTTTCTCTCTC-TTCC
113854 TTTTTCTCTCT
1 TTTTTCTCTCT
113865 TCTTTTCTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 8 0.22
16 17 0.46
17 12 0.32
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTCTCTCTCTTCC
Found at i:113859 original size:13 final size:13
Alignment explanation
Indices: 113841--113870 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
113831 CTCTTCCTTT
*
113841 TTTTTCTCTTTTC
1 TTTTTCTCTCTTC
113854 TTTTTCTCTCTTC
1 TTTTTCTCTCTTC
113867 TTTT
1 TTTT
113871 CTTGACTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTCTCTTC
Found at i:114098 original size:19 final size:19
Alignment explanation
Indices: 114076--114114 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
114066 ATTTGTATTT
114076 ATATTAT-TTTTTATATAAA
1 ATATTATCTTTTTATA-AAA
114095 ATATTATCTTTTTATAAAA
1 ATATTATCTTTTTATAAAA
114114 A
1 A
114115 AAATTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTATCTTTTTATAAAA
Found at i:114115 original size:20 final size:19
Alignment explanation
Indices: 114076--114115 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
114066 ATTTGTATTT
*
114076 ATATTATTTTTTATATAAA
1 ATATTATTTTTTATAAAAA
114095 ATATTATCTTTTTATAAAAA
1 ATATTAT-TTTTTATAAAAA
114115 A
1 A
114116 AATTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTATTTTTTATAAAAA
Found at i:114413 original size:14 final size:15
Alignment explanation
Indices: 114386--114418 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
114376 TTATAAAATT
114386 TTTAATTAAATAAAA
1 TTTAATTAAATAAAA
114401 TTTAATT-AATAAAA
1 TTTAATTAAATAAAA
114415 TTTA
1 TTTA
114419 TTTTAACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:115567 original size:17 final size:17
Alignment explanation
Indices: 115529--115567 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
115519 ATAAAAAATT
* *
115529 ATAATATAATATAAAAT
1 ATAATATAATACAAAAA
*
115546 GTAATATAATACAAAAA
1 ATAATATAATACAAAAA
115563 ATAAT
1 ATAAT
115568 GTAAATATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAATATAATACAAAAA
Found at i:116399 original size:11 final size:11
Alignment explanation
Indices: 116385--116446 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
116375 TTATATAATT
116385 ATAATATAAAA
1 ATAATATAAAA
116396 ATAAT-TAAAA
1 ATAATATAAAA
**
116406 TATAAT-TAATT
1 -ATAATATAAAA
*
116417 TTAA-AT-AAA
1 ATAATATAAAA
*
116426 ATAAGATAAAA
1 ATAATATAAAA
116437 ATAATATAAA
1 ATAATATAAA
116447 TTTATTATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
9 4 0.10
10 11 0.28
11 25 0.62
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:116441 original size:30 final size:31
Alignment explanation
Indices: 116393--116491 Score: 75
Period size: 30 Copynumber: 3.3 Consensus size: 31
116383 TTATAATATA
* *
116393 AAAATAATTAAAATATAAT-TAATTTTAAAT
1 AAAATAAATAAAATATAATATAAATTTAAAT
*
116423 AAAATAAGATAAAA-ATAATATAAATTT-ATT
1 AAAATAA-ATAAAATATAATATAAATTTAAAT
* *
116453 ATAAATATAT-AAATA-AAT-TAAAATTTATAT
1 A-AAATAAATAAAATATAATAT-AAATTTAAAT
*
116483 AATATAAAT
1 AAAATAAAT
116492 TATTAATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
28 1 0.02
29 18 0.33
30 20 0.36
31 16 0.29
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (31 bp):
AAAATAAATAAAATATAATATAAATTTAAAT
Found at i:116474 original size:28 final size:27
Alignment explanation
Indices: 116426--116488 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
116416 TTTAAATAAA
* *
116426 ATAAGATAAAAATAATAT-AAATTTATT
1 ATAATATATAAATAATATAAAATTTA-T
116453 ATAAATATATAAATAA-ATTAAAATTTAT
1 AT-AATATATAAATAATA-TAAAATTTAT
116481 ATAATATA
1 ATAATATA
116489 AATTATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 9 0.29
28 15 0.48
29 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
ATAATATATAAATAATATAAAATTTAT
Found at i:116499 original size:22 final size:22
Alignment explanation
Indices: 116437--116502 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
116427 TAAGATAAAA
**
116437 ATAATATAAATTTATTATAAATAT
1 ATAATATAAA-TTATTA-ATTTAT
*
116461 ATAA-ATAAATTA-AAATTTAT
1 ATAATATAAATTATTAATTTAT
116481 ATAATATAAATTATTAATTTAT
1 ATAATATAAATTATTAATTTAT
116503 TAAATTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 8 0.22
21 9 0.25
22 10 0.28
23 5 0.14
24 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATATAAATTATTAATTTAT
Found at i:118398 original size:2 final size:2
Alignment explanation
Indices: 118391--118416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
118381 TACCAACTAA
118391 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
118417 CGGAAGACAA
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:123583 original size:10 final size:10
Alignment explanation
Indices: 123568--123602 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
123558 ATTAGTATGC
123568 AAATTTATAT
1 AAATTTATAT
123578 AAATTTATAT
1 AAATTTATAT
123588 AAAAATTTATAT
1 --AAATTTATAT
123600 AAA
1 AAA
123603 AGAAACATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATTTATAT
Found at i:123593 original size:12 final size:12
Alignment explanation
Indices: 123568--123603 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
123558 ATTAGTATGC
123568 AAATTTATAT--
1 AAATTTATATAA
123578 AAATTTATATAA
1 AAATTTATATAA
123590 AAATTTATATAA
1 AAATTTATATAA
123602 AA
1 AA
123604 GAAACATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATTTATATAA
Found at i:123823 original size:27 final size:25
Alignment explanation
Indices: 123785--123878 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 25
123775 AAATTCACTA
*
123785 TTTATTTATCAAAAATAGTGATTATT
1 TTTATTTGTCAAAAATAGTGATT-TT
* *
123811 TTGTATTTGTCAAAAATGGTGGTTTCCT
1 TT-TATTTGTCAAAAATAGTGATTT--T
* * * *
123839 TTATATTTGTCAAATATAGAGACTTG
1 TT-TATTTGTCAAAAATAGTGATTTT
123865 TTTATTTGTCAAAA
1 TTTATTTGTCAAAA
123879 TTGGTGGCTT
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
25 11 0.20
26 5 0.09
27 18 0.33
28 20 0.37
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (25 bp):
TTTATTTGTCAAAAATAGTGATTTT
Found at i:123889 original size:25 final size:24
Alignment explanation
Indices: 123861--123907 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
123851 AATATAGAGA
123861 CTTGTTTATTTGTCAAAATTGGTGG
1 CTTG-TTATTTGTCAAAATTGGTGG
*
123886 CTTGTTGTTTGTCAAAATTGGT
1 CTTGTTATTTGTCAAAATTGGT
123908 AGCTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.19, C:0.09, G:0.23, T:0.49
Consensus pattern (24 bp):
CTTGTTATTTGTCAAAATTGGTGG
Found at i:128405 original size:24 final size:25
Alignment explanation
Indices: 128378--128510 Score: 108
Period size: 27 Copynumber: 5.2 Consensus size: 25
128368 AAAAGCCACC
128378 ATTTGTTTGTCAAAAATGGTGG-TT
1 ATTTGTTTGTCAAAAATGGTGGCTT
*
128402 ATTTTGTGTTTGTCAAAAATGGTGGTTT
1 A--TT-TGTTTGTCAAAAATGGTGGCTT
* * *
128430 CCTTTGTATTTGTCAAATATGGAGGCTT
1 -ATTTG--TTTGTCAAAAATGGTGGCTT
* * *
128458 GTTTATTTGTCAAAATTGGTGGCTT
1 ATTTGTTTGTCAAAAATGGTGGCTT
* * *
128483 -GTTGTTTGTCAAAATTGGTGGCTA
1 ATTTGTTTGTCAAAAATGGTGGCTT
128507 ATTT
1 ATTT
128511 TTATTAGAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
24 22 0.25
25 19 0.22
26 4 0.05
27 24 0.27
28 19 0.22
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.47
Consensus pattern (25 bp):
ATTTGTTTGTCAAAAATGGTGGCTT
Found at i:128470 original size:25 final size:24
Alignment explanation
Indices: 128436--128505 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
128426 GTTTCCTTTG
128436 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGAGGCTTG-T
*
128461 TATTTGTCAAAATTGGTGGCTTGT
1 TATTTGTCAAAATTGGAGGCTTGT
* *
128485 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGAGGCT
128506 AATTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 17 0.40
26 4 0.10
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (24 bp):
TATTTGTCAAAATTGGAGGCTTGT
Found at i:133472 original size:15 final size:14
Alignment explanation
Indices: 133448--133550 Score: 75
Period size: 14 Copynumber: 7.1 Consensus size: 14
133438 TGAAATTAAA
133448 TTAA-TTTTAAATTT
1 TTAATTTTTAAA-TT
133462 TTAATTTTTAAATT
1 TTAATTTTTAAATT
* * **
133476 TAAATTTTGATTTTT
1 TTAATTTTTA-AATT
**
133491 TTAATTTTTAAAAC
1 TTAATTTTTAAATT
133505 TTAATTTTATTAAATT
1 TTAA-TTT-TTAAATT
*
133521 TAAATTATTTAAA-T
1 TTAATT-TTTAAATT
133535 TTAATTATTTAAATT
1 TTAATT-TTTAAATT
133550 T
1 T
133551 GACACTTAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
14 31 0.45
15 29 0.42
16 9 0.13
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (14 bp):
TTAATTTTTAAATT
Found at i:133498 original size:7 final size:7
Alignment explanation
Indices: 133448--133501 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
133438 TGAAATTAAA
133448 TTAATTT
1 TTAATTT
*
133455 TAAATTT
1 TTAATTT
133462 TTAATTT
1 TTAATTT
*
133469 TTAAATT
1 TTAATTT
*
133476 TAAATTT
1 TTAATTT
* *
133483 TGATTTTT
1 TTA-ATTT
133491 TTAATTT
1 TTAATTT
133498 TTAA
1 TTAA
133502 AACTTAATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (7 bp):
TTAATTT
Found at i:135410 original size:20 final size:20
Alignment explanation
Indices: 135355--135426 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
135345 AAATATATCA
135355 AAATATATAATATTATT-T-T
1 AAATATATAATATT-TTATAT
** * *
135374 TTATATATAAAAATTTATAT
1 AAATATATAATATTTTATAT
*
135394 AAATATATAATATTTTAAAT
1 AAATATATAATATTTTATAT
135414 ATAAT-TATAATAT
1 A-AATATATAATAT
135427 ATAAATATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.05
19 11 0.27
20 25 0.61
21 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATATAATATTTTATAT
Found at i:135417 original size:14 final size:15
Alignment explanation
Indices: 135398--135452 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 15
135388 TTATATAAAT
135398 ATATAATATTT-TAA
1 ATATAATATTTATAA
135412 ATATAATTATAATATATAA
1 ATATAA-TAT--T-TATAA
135431 ATAT-ATATTTATAA
1 ATATAATATTTATAA
135445 ATATAATA
1 ATATAATA
135453 CAATTATGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 15 0.43
15 7 0.20
17 4 0.11
18 2 0.06
19 7 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAATATTTATAA
Found at i:135768 original size:2 final size:2
Alignment explanation
Indices: 135761--135789 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
135751 CCCCTTTTAT
135761 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 T
135790 GACTCTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:138495 original size:11 final size:12
Alignment explanation
Indices: 138480--138521 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
138470 AATATAATAA
138480 ATTTATATAATT
1 ATTTATATAATT
138492 -TTTATAT-ATT
1 ATTTATATAATT
* *
138502 ATTTATTTATTT
1 ATTTATATAATT
138514 ATTTATAT
1 ATTTATAT
138522 TTGATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 3 0.12
11 13 0.52
12 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTATATAATT
Done.