Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3430
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: 86312
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Found at i:13716 original size:14 final size:15
Alignment explanation
Indices: 13697--13733 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
13687 ATAATTAAAA
13697 ATATAATAATAAT-G
1 ATATAATAATAATAG
13711 ATATAAT-ATAATAG
1 ATATAATAATAATAG
*
13725 TTATAATAA
1 ATATAATAA
13734 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATAATAATAATAG
Found at i:13819 original size:45 final size:45
Alignment explanation
Indices: 13752--13860 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
13742 AATAAAACAT
*
13752 AAAG-AAAAGGGAAAAAGAAGGGCACGAACAGAATAAGGAAAAAAAG
1 AAAGAAAAAGGG--AAAGAAGGGCACGAACAGAACAAGGAAAAAAAG
* * * *
13798 AAAGAAAAAGGGAAAGAAGGGCAGGAACAGAACAGGGAAAGAATG
1 AAAGAAAAAGGGAAAGAAGGGCACGAACAGAACAAGGAAAAAAAG
*
13843 AAAGAAAAAAGGAAAGAA
1 AAAGAAAAAGGGAAAGAA
13861 AAAAAAAGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 45 0.80
46 4 0.07
47 7 0.12
ACGTcount: A:0.62, C:0.06, G:0.30, T:0.02
Consensus pattern (45 bp):
AAAGAAAAAGGGAAAGAAGGGCACGAACAGAACAAGGAAAAAAAG
Found at i:16013 original size:31 final size:31
Alignment explanation
Indices: 15942--16016 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
15932 TGTAACACAT
* *
15942 AAACTTTAA-TTTGGTGCAATTATACACGTG
1 AAACTTTAATTTTGGTGCAAATATACACGTA
* * * * *
15972 ATACTCTAATTTTGGTTCAAATATATACTTA
1 AAACTTTAATTTTGGTGCAAATATACACGTA
16003 AAACTTTAATTTTG
1 AAACTTTAATTTTG
16017 ATTTAATCAT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (31 bp):
AAACTTTAATTTTGGTGCAAATATACACGTA
Found at i:18367 original size:3 final size:3
Alignment explanation
Indices: 18359--18399 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
18349 AGAAGGAAAG
18359 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 AA
18400 GAGAATTGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18739 original size:18 final size:18
Alignment explanation
Indices: 18713--18774 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
18703 ATGCATTATA
*
18713 TATAATTAATTATATACT
1 TATACTTAATTATATACT
18731 TATACTTAA-TATAT--T
1 TATACTTAATTATATACT
18746 ATATA-TCTAATTATATACT
1 -TATACT-TAATTATATACT
18765 TATACTTAAT
1 TATACTTAAT
18775 ATTCTCGCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
15 2 0.05
16 7 0.19
17 10 0.27
18 16 0.43
19 2 0.05
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (18 bp):
TATACTTAATTATATACT
Found at i:18757 original size:34 final size:34
Alignment explanation
Indices: 18711--18776 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 34
18701 ATATGCATTA
18711 TATATAATTAATTATATACTTATACTTAATATAT
1 TATATAATTAATTATATACTTATACTTAATATAT
18745 TATAT-ATCTAATTATATACTTATACTTAATAT
1 TATATAAT-TAATTATATACTTATACTTAATAT
18777 TCTCGCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 2 0.06
34 29 0.94
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (34 bp):
TATATAATTAATTATATACTTATACTTAATATAT
Found at i:19130 original size:31 final size:29
Alignment explanation
Indices: 19053--19132 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
19043 GAATTAGATC
*
19053 AAATCAAAATTTCATGTATAAAATTGAACA
1 AAATC-AAAGTTCATGTATAAAATTGAACA
* *
19083 AAAACAAAGTTCATGTATAAAATTGCACA
1 AAATCAAAGTTCATGTATAAAATTGAACA
19112 TTAAATCATAA-TTCATGTATA
1 --AAATCA-AAGTTCATGTATA
19133 GTTTTAGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 22 0.51
30 4 0.09
31 15 0.35
32 2 0.05
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTGAACA
Found at i:19834 original size:3 final size:3
Alignment explanation
Indices: 19826--19869 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
19816 TGTCATTCTC
19826 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19870 GGATAACATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20281 original size:20 final size:19
Alignment explanation
Indices: 20229--20283 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
20219 TTTAACCCCT
*
20229 AATATTT-ATAAATTTTAT
1 AATATTTAATAAATTTTAA
*
20247 TA-ATTTAATTCAAATTTTAAA
1 AATATTTAA-T-AAATTTT-AA
20268 AATATTTAATAAATTT
1 AATATTTAATAAATTT
20284 AACTTCAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
17 4 0.14
18 2 0.07
19 1 0.03
20 13 0.45
21 3 0.10
22 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATTTAATAAATTTTAA
Found at i:22046 original size:24 final size:24
Alignment explanation
Indices: 22019--22071 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
22009 CACATATCAA
22019 CACAATCTGTATAAACATGAAAAC
1 CACAATCTGTATAAACATGAAAAC
*
22043 CACAATCTGTATAACCATGAAAAC
1 CACAATCTGTATAAACATGAAAAC
22067 CACAA
1 CACAA
22072 CAGCTTCGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.25, G:0.08, T:0.19
Consensus pattern (24 bp):
CACAATCTGTATAAACATGAAAAC
Found at i:23755 original size:16 final size:15
Alignment explanation
Indices: 23729--23763 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
23719 TGATGTGAAT
23729 AATATAAAATATTAA
1 AATATAAAATATTAA
*
23744 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
23760 AATA
1 AATA
23764 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:23944 original size:25 final size:25
Alignment explanation
Indices: 23916--24060 Score: 102
Period size: 25 Copynumber: 5.8 Consensus size: 25
23906 TGATAATATT
*
23916 AAAAATATGTACATAATATAGTGTA
1 AAAAATATATACATAATATAGTGTA
* *
23941 AAAAATACATACATAATATAAT-T-
1 AAAAATATATACATAATATAGTGTA
* *
23964 -AAAATATATACATAAGATAACATGTA
1 AAAAATATATACATAATAT-A-GTGTA
* * *
23990 AAATATATATATAAATAATATAGTATT
1 AAA-A-ATATATACATAATATAGTGTA
* *
24017 AAAGATATATACATAAAATA--GTA
1 AAAAATATATACATAATATAGTGTA
* * *
24040 TAATATATATACGTAATATAG
1 AAAAATATATACATAATATAG
24061 AATTTAGAAT
Statistics
Matches: 93, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
22 16 0.17
23 18 0.19
24 3 0.03
25 34 0.37
27 7 0.08
28 2 0.02
29 13 0.14
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (25 bp):
AAAAATATATACATAATATAGTGTA
Found at i:23976 original size:47 final size:48
Alignment explanation
Indices: 23891--24038 Score: 138
Period size: 48 Copynumber: 3.0 Consensus size: 48
23881 TATGTACATA
* * * *
23891 TAAAAAATAAATACGTGATA-ATATTAAAAATATGTACATAATATAGTG
1 TAAAAAATAAATACATAATATATATT-AAAATATATACATAAAATAGTG
* * *
23939 TAAAAAATACATACATAATATA-ATTAAAATATATACATAAGATAACATG
1 TAAAAAATAAATACATAATATATATTAAAATATATACATAAAAT-A-GTG
* *
23988 TAAAATATATATATAAATAATATAGTATTAAAGATATATACATAAAATAGT
1 TAAAA-A-ATAAATACATAATATA-TATTAAA-ATATATACATAAAATAGT
24039 ATAATATATA
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
47 16 0.20
48 21 0.26
49 8 0.10
50 1 0.01
51 14 0.17
52 1 0.01
53 7 0.09
54 14 0.17
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (48 bp):
TAAAAAATAAATACATAATATATATTAAAATATATACATAAAATAGTG
Found at i:24007 original size:29 final size:29
Alignment explanation
Indices: 23967--24033 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
23957 TATAATTAAA
*
23967 ATATATACATAAGATAACATGTAAA-ATAT
1 ATATATAAATAAGATAACAT-TAAAGATAT
* **
23996 ATATATAAATAATATAGTATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAGATAT
*
24025 ATACATAAA
1 ATATATAAA
24034 ATAGTATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAGATAT
Found at i:24121 original size:23 final size:23
Alignment explanation
Indices: 23908--24123 Score: 79
Period size: 25 Copynumber: 9.0 Consensus size: 23
23898 TAAATACGTG
*
23908 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAAATA--TATATAAT
* * * *
23933 ATAGTGTAAAAAATACATACATAAT
1 ATAATATTAAAAAT--ATATATAAT
* *
23958 AT-A-ATTAAAATATATACATAAG
1 ATAATATTAAAA-ATATATATAAT
*
23980 ATAACATGTAAAATATATATATAAAT
1 ATAATAT-TAAAA-ATATATAT-AAT
* *
24006 AATATAGTATTAAAGATATATA-CAT
1 -ATA-A-TATTAAAAATATATATAAT
* * *
24031 AAAATAGTATAATATATATACGTAAT
1 ATAATATTA-AAAATATATA--TAAT
* * **
24057 ATAGA-ATTTAGAATATACCT-A-
1 ATA-ATATTAAAAATATATATAAT
24078 AT-ATATTAAAAATATATATAAT
1 ATAATATTAAAAATATATATAAT
24100 ATAATATTAAGAAATATA-ATAAT
1 ATAATATTAA-AAATATATATAAT
24123 A
1 A
24124 ACAAAAAAAG
Statistics
Matches: 144, Mismatches: 27, Indels: 42
0.68 0.13 0.20
Matches are distributed among these distances:
19 1 0.01
20 11 0.08
21 3 0.02
22 17 0.12
23 30 0.21
24 13 0.09
25 42 0.29
26 8 0.06
27 12 0.08
28 5 0.03
29 2 0.01
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (23 bp):
ATAATATTAAAAATATATATAAT
Found at i:24629 original size:18 final size:18
Alignment explanation
Indices: 24606--24659 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
24596 ACAAGTGGTG
24606 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
24624 GT-G-G--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
24636 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
24654 GTGGAG
1 GTGGAG
24660 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 4 0.14
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:24642 original size:30 final size:30
Alignment explanation
Indices: 24606--24669 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
24596 ACAAGTGGTG
24606 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
* *
24636 GTGGAGCAAGTGTGGCTAGTGGAGTTGGTG
1 GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
24666 GTGG
1 GTGG
24670 CAAAGGCTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.50, T:0.25
Consensus pattern (30 bp):
GTGGAGCAAGTGTGGCTAGTGGAGTAGGTA
Found at i:28696 original size:18 final size:19
Alignment explanation
Indices: 28673--28710 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28663 TATTTTATAG
*
28673 TTATTATAAATA-AAAAAA
1 TTATTATAAAAATAAAAAA
28691 TTATTATAAAAATAAAAAA
1 TTATTATAAAAATAAAAAA
28710 T
1 T
28711 CAATTCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TTATTATAAAAATAAAAAA
Found at i:29975 original size:48 final size:48
Alignment explanation
Indices: 29902--29999 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
29892 ACCAAAAAGT
*
29902 TATATATATATATAAAGTGTGTGTGTGAGAGGAAAATAGACTATCAAG
1 TATATATATATATAAAGTGTATGTGTGAGAGGAAAATAGACTATCAAG
29950 TATATATATATATAAAGTGTATGTGTGAGAGGAAAATAGACTATCAAG
1 TATATATATATATAAAGTGTATGTGTGAGAGGAAAATAGACTATCAAG
29998 TA
1 TA
30000 CCAAACTAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (48 bp):
TATATATATATATAAAGTGTATGTGTGAGAGGAAAATAGACTATCAAG
Found at i:31125 original size:26 final size:26
Alignment explanation
Indices: 31088--31171 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
31078 TGATACAAAT
* *
31088 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
31114 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
31140 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
31166 TGATAA
1 TGATAA
31172 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:32670 original size:25 final size:26
Alignment explanation
Indices: 32642--32693 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
32632 TTTACAGTTT
*
32642 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCACTAGAGATAAATTGACCGAAA
* * *
32667 TACCACTAGGGTTAAATTGACCTAAA
1 TACCACTAGAGATAAATTGACCGAAA
32693 T
1 T
32694 GCATGTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCACTAGAGATAAATTGACCGAAA
Found at i:34083 original size:19 final size:19
Alignment explanation
Indices: 34035--34084 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
34025 CTTTTCTTTG
34035 TTATAGATATAACAAATAAAA
1 TTATA-ATA-AACAAATAAAA
* *
34056 TTGTAATAAACAAATGAAA
1 TTATAATAAACAAATAAAA
*
34075 TTATTATAAA
1 TTATAATAAA
34085 GAAGGTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 3 0.12
21 4 0.16
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (19 bp):
TTATAATAAACAAATAAAA
Found at i:37435 original size:11 final size:12
Alignment explanation
Indices: 37405--37445 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
37395 AATGTAAAAA
*
37405 ATAATATATAAT
1 ATAATAAATAAT
37417 ATATATAAATAAT
1 ATA-ATAAATAAT
37430 -TAATAAAT-AT
1 ATAATAAATAAT
37440 ATAATA
1 ATAATA
37446 CAAGTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 2 0.08
11 11 0.42
12 5 0.19
13 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATAAATAAT
Found at i:37472 original size:32 final size:31
Alignment explanation
Indices: 37424--37496 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 31
37414 AATATATATA
37424 AATAATTAATAAATATA-TAATACAAGTAAAA-
1 AATAA-TAATAAATATAGTAATA-AAGTAAAAT
*
37455 ACATAATAATAATATATAGTAATAATGTAAAAT
1 A-ATAATAATAA-ATATAGTAATAAAGTAAAAT
37488 AATAATAAT
1 AATAATAAT
37497 TTGTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
31 7 0.19
32 24 0.65
33 6 0.16
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (31 bp):
AATAATAATAAATATAGTAATAAAGTAAAAT
Found at i:37545 original size:19 final size:20
Alignment explanation
Indices: 37508--37566 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 20
37498 TGTGAAAAAC
37508 AATATACAATAGATA-ATAAT-
1 AATATA-AATA-ATATATAATG
37528 AATATAAATAATATATAATG
1 AATATAAATAATATATAATG
37548 AA-ATAATTATAATATATAA
1 AATATAA--ATAATATATAA
37567 AAAATAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.09
19 13 0.37
20 8 0.23
21 11 0.31
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (20 bp):
AATATAAATAATATATAATG
Found at i:37560 original size:14 final size:15
Alignment explanation
Indices: 37508--37560 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
37498 TGTGAAAAAC
*
37508 AATATACAATAGATAAT
1 AATATATAAT-GA-AAT
37525 AATA-AT-AT-AAAT
1 AATATATAATGAAAT
37537 AATATATAATGAAAT
1 AATATATAATGAAAT
37552 AAT-TATAAT
1 AATATATAAT
37561 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
12 7 0.22
13 3 0.09
14 8 0.25
15 9 0.28
16 1 0.03
17 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (15 bp):
AATATATAATGAAAT
Found at i:39314 original size:26 final size:26
Alignment explanation
Indices: 39277--39332 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
39267 TGATACAAAT
39277 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
39303 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
39329 TGAT
1 TGAT
39333 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:42308 original size:17 final size:18
Alignment explanation
Indices: 42286--42322 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
42276 TATTTTATAG
42286 TTATTAT-AAATAAAAAA
1 TTATTATAAAATAAAAAA
42303 TTATTATAAAAATAAAAAA
1 TTATTAT-AAAATAAAAAA
42322 T
1 T
42323 CAATTCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTATTATAAAATAAAAAA
Found at i:44411 original size:32 final size:30
Alignment explanation
Indices: 44345--44416 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 30
44335 ATTTTTTATT
* * *
44345 ATTTAATTATAAAAAAATTATGAAATAATT
1 ATTTAACTATAAAAAAATTATAAAATAATC
* *
44375 ATTTAACTATAAAATATATATATAAAATAGTC
1 ATTTAACTATAAAA-AAAT-TATAAAATAATC
44407 ATTTAACTAT
1 ATTTAACTAT
44417 TCACTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 13 0.37
31 3 0.09
32 19 0.54
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (30 bp):
ATTTAACTATAAAAAAATTATAAAATAATC
Found at i:47464 original size:54 final size:54
Alignment explanation
Indices: 47387--47489 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
47377 ATCAGTGACA
* *
47387 AGTGATAACTGGTAGCCTCAGCTACAGTTATCTGATCAGTGATAAGTGACAATT
1 AGTGATAACTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGACAATT
* * *
47441 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGA
1 AGTGATAACTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGA
47490 TAAATGTGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (54 bp):
AGTGATAACTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGACAATT
Found at i:48160 original size:26 final size:26
Alignment explanation
Indices: 48123--48180 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
48113 TGATACAAAT
48123 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
48149 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
48175 TGATAA
1 TGATAA
48181 GAATTTCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:49673 original size:25 final size:26
Alignment explanation
Indices: 49645--49696 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
49635 TTTACAGTTT
49645 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
49670 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
49696 T
1 T
49697 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:53856 original size:26 final size:26
Alignment explanation
Indices: 53819--53876 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
53809 TGATACAAAT
53819 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
53845 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
53871 TGATAA
1 TGATAA
53877 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:55377 original size:25 final size:26
Alignment explanation
Indices: 55349--55400 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
55339 TTTACAGTTT
55349 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
55374 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
55400 T
1 T
55401 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:61130 original size:25 final size:26
Alignment explanation
Indices: 61064--61130 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
61054 GGTTATGAAG
61064 TATA-TATATAA-ATTAAAGATAAAA
1 TATATTATATAATATTAAAGATAAAA
*
61088 TATATTATGTTAATTATT-AAG-TAAATA
1 TATATTAT-ATAA-TATTAAAGATAAA-A
61115 TATATTATATAATATT
1 TATATTATATAATATT
61131 GATAAAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
24 4 0.11
25 7 0.19
26 10 0.28
27 12 0.33
28 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (26 bp):
TATATTATATAATATTAAAGATAAAA
Found at i:61894 original size:20 final size:20
Alignment explanation
Indices: 61869--61917 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
61859 GCACTTTGGT
*
61869 ATTGAATTGAATTAAAATTG
1 ATTGAAATGAATTAAAATTG
*
61889 ATTGAAATGAATTAAAGTTG
1 ATTGAAATGAATTAAAATTG
61909 ATTGAAATG
1 ATTGAAATG
61918 GATTGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (20 bp):
ATTGAAATGAATTAAAATTG
Found at i:65157 original size:137 final size:137
Alignment explanation
Indices: 64924--65197 Score: 512
Period size: 137 Copynumber: 2.0 Consensus size: 137
64914 AGTCTAAGAA
64924 CATTTCTGAGATCCGTAGTTTTCTAGGTCTTACGGGTTATTATCGACGGTTTGTTGAGGGGTTCT
1 CATTTCTGAGATCCGTAGTTTTCTAGGTCTTACGGGTTATTATCGACGGTTTGTTGAGGGGTTCT
*
64989 CGTTGATTGCAGCTTCTTTGACTAAGCTTCTGTGTAAGAATGTTCCTTTTTTTTGGACTAATAGA
66 CGTTGATTGCAGCTTCTCTGACTAAGCTTCTGTGTAAGAATGTTCCTTTTTTTTGGACTAATAGA
65054 CAACCAT
131 CAACCAT
* *
65061 CATTTCTGAGATCCGTAGTTTTCTAGGTCTTGCGGGTTATTATTGACGGTTTGTTGAGGGGTTCT
1 CATTTCTGAGATCCGTAGTTTTCTAGGTCTTACGGGTTATTATCGACGGTTTGTTGAGGGGTTCT
*
65126 CGTTGATTGCAGCTTCTCTGACTAAGCTTCTGTGTAAGAATGTTCCTTTTTTTTGGACTAATGGA
66 CGTTGATTGCAGCTTCTCTGACTAAGCTTCTGTGTAAGAATGTTCCTTTTTTTTGGACTAATAGA
65191 CAACCAT
131 CAACCAT
65198 TGAGCTTTGA
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 133 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (137 bp):
CATTTCTGAGATCCGTAGTTTTCTAGGTCTTACGGGTTATTATCGACGGTTTGTTGAGGGGTTCT
CGTTGATTGCAGCTTCTCTGACTAAGCTTCTGTGTAAGAATGTTCCTTTTTTTTGGACTAATAGA
CAACCAT
Found at i:68392 original size:40 final size:39
Alignment explanation
Indices: 68308--68492 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
68298 TTGAATGATG
* * * *
68308 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
68348 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
68388 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
68427 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
68468 -CCGGGCTATGTCTCGAAGGCATTTG
1 TCCGGGCTAAGTC-CGAAGGCATTTG
68493 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 36 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:68444 original size:79 final size:81
Alignment explanation
Indices: 68308--68492 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
68298 TTGAATGATG
* *
68308 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
68372 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
68387 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
68449 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* * *
68467 ACCGGGCTATGTCTCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
68493 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 32 0.36
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:68514 original size:79 final size:79
Alignment explanation
Indices: 68361--68515 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
68351 GGACTAAGAT
* * **
68361 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
68426 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
68440 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCTCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
68503 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
68516 ATTTCGAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.60
80 24 0.37
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:76570 original size:39 final size:41
Alignment explanation
Indices: 76469--76652 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
76459 TTGAATGATG
* *
76469 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
76509 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
76549 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
76588 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
76627 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
76653 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:76605 original size:79 final size:80
Alignment explanation
Indices: 76469--76652 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
76459 TTGAATGATG
*
76469 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
76533 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
76548 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
76610 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
76627 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
76653 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:76675 original size:78 final size:79
Alignment explanation
Indices: 76522--76685 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
76512 GGACTAAGAT
* **
76522 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
76587 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
76601 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
76663 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
76679 CCGAAGG
1 CCGAAGG
76686 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:84700 original size:39 final size:39
Alignment explanation
Indices: 84550--84728 Score: 163
Period size: 39 Copynumber: 4.6 Consensus size: 39
84540 TTGAATGATG
* * * * *
84550 TCCGGGCTAAGTCCCGAA-GCTTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
84589 TCCGGACTAAGAT-CCG-AGGCATTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTGTGCGAGTTACTAAA
*
84627 TCCGGGCTAAG-CCCGGA-GCATTTGTGCGAGGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCA-TTGTGCGA-GTTACTAAA
* *
84666 TCCGGGTTAAGTCCCAAAGGCATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTA-AA
*
84706 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
84729 TGAACGAGTA
Statistics
Matches: 114, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
37 6 0.05
38 25 0.22
39 65 0.57
40 15 0.13
41 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Done.