Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 259 of 259
Found at i:81574497 original size:32 final size:31
Alignment explanation
Indices: 81574461--81574562 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 31
81574451 ACTTGAGGTG
*
81574461 TACATTCCTTTCCAAATGATACACAAAAAGTA
1 TACATTCCTTTCCAAATG-TACACACAAAGTA
* * *
81574493 TACATTTCCTTTTCATATGGTATACACAAAGTA
1 TACA-TTCCTTTCCAAAT-GTACACACAAAGTA
* * * *
81574526 TACCTAACCTTTCCAAGTGTACACACAAAGTG
1 TACAT-TCCTTTCCAAATGTACACACAAAGTA
81574558 TACAT
1 TACAT
81574563 AACTTTTTCA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
32 21 0.38
33 33 0.60
34 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (31 bp):
TACATTCCTTTCCAAATGTACACACAAAGTA
Found at i:81574575 original size:32 final size:33
Alignment explanation
Indices: 81574467--81574580 Score: 90
Period size: 33 Copynumber: 3.5 Consensus size: 33
81574457 GGTGTACATT
* * **
81574467 CCTTTCCAA-ATGATACACAAAAAGTATACATTT
1 CCTTTCCAAGTTG-TACACACAAAGTATACATAA
* * * *
81574500 CCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTCCA-AGTTGTACACACAAAGTATACATAA
*
81574533 CCTTTCCAAG-TGTACACACAAAGTGTACATAA
1 CCTTTCCAAGTTGTACACACAAAGTATACATAA
* *
81574565 CTTTTTCAAGTTGTAC
1 CCTTTCCAAGTTGTAC
81574581 CATTTGCGTA
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
32 27 0.43
33 34 0.54
34 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (33 bp):
CCTTTCCAAGTTGTACACACAAAGTATACATAA
Found at i:81576598 original size:29 final size:29
Alignment explanation
Indices: 81576563--81576636 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
81576553 GTTGTGAGAT
* *
81576563 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
81576592 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
81576621 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
81576637 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:81585918 original size:25 final size:26
Alignment explanation
Indices: 81585890--81585938 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
81585880 CTTATTTCAT
81585890 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAATATAA
* *
81585915 TAAATCAAATATATTTAAAAATAT
1 TAAATAAAAAATATTTAAAAATAT
81585939 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAATATAA
Found at i:81585947 original size:24 final size:25
Alignment explanation
Indices: 81585902--81585950 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
81585892 AATAAAAAAT
*
81585902 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAATAT-ATAAAACAAATATA
81585928 TTTAAAAATAT-TAAAACAAATAT
1 TTTAAAAATATATAAAACAAATAT
81585951 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
26 11 0.50
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTAAAAATATATAAAACAAATATA
Found at i:81585948 original size:12 final size:12
Alignment explanation
Indices: 81585933--81585991 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
81585923 ATATATTTAA
81585933 AAATATTAAAAC
1 AAATATTAAAAC
81585945 AAATATTAAAAC
1 AAATATTAAAAC
81585957 AAATA--AAAA-
1 AAATATTAAAAC
* *
81585966 TAATACTAAAAC
1 AAATATTAAAAC
* *
81585978 AATTCTTAAAAC
1 AAATATTAAAAC
81585990 AA
1 AA
81585992 TACATAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 4 0.10
11 4 0.10
12 27 0.69
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:81588565 original size:350 final size:347
Alignment explanation
Indices: 81587927--81588625 Score: 1371
Period size: 350 Copynumber: 2.0 Consensus size: 347
81587917 AAGCCTCTAA
81587927 AACACCATCGGTCCAGGAAGAAACCTCCACAACGTCGATTGTACAAGGAGACACCTCCAAAAGGA
1 AACACCATCGGTCCAGGAAGAAACCTCCACAACGTCGATTGTACAAGGAGACACCTCCAAAAGGA
81587992 AGACTGCAAAAAAAAAAAAAAAAGAAGCAAACTAAGAAGAAAAAGAATCAAACGGAAGTCCAAAT
66 AGACTGCAAAAAAAAAAAAAAAAGAAGCAAACTAAGAAGAAAAAGAATCAAACGGAAGTCCAAAT
81588057 GTCGTTTGAGATGTGAGTTATAGCGTTACGTTTTAACTCTTTTTTTTTGTATCAAGGTGATCTGA
131 GTCGTTTGAGATGTGAGTTATAGCGTTACGTTTTAACTCTTTTTTTTTGTATCAAGGTGATCTGA
81588122 TTGATAATCTTAATGAAGGATGGAATCTGCTGAGAAAACCTTGTATCATATTTTGAAGGAAGCCG
196 TTGATAATCTTAATGAAGGATGGAATCTGCTGAGAAAACCTTGTATCATATTTTGAAGGAAGCCG
81588187 GCGGTAAGGTTAAGATCAGAGCTGACTTGGTAAAAGCACTAAAAAATAAACGTTTTGAGCCAAAT
261 GCGGTAAGGTTAAGATCAGAGCTGACTTGGTAAAAGCACTAAAAAATAAACGTTTTGAGCCAAAT
81588252 GTGGTGACAAATGTGCTTGGCG
326 GTGGTGACAAATGTGCTTGGCG
81588274 AACACCATCGGTCCAGGAAGAAACCTCCACAACGTCGATTGTACAAGGAGACACCTCCAAAAGGA
1 AACACCATCGGTCCAGGAAGAAACCTCCACAACGTCGATTGTACAAGGAGACACCTCCAAAAGGA
81588339 AGACTGCAAAAAAAAAAAAAAAAAAGAAGCAAACTAAGAAGAAAAAGAATCAAACGGAAGTCCAA
66 AGACTGC--AAAAAAAAAAAAAAAAGAAGCAAACTAAGAAGAAAAAGAATCAAACGGAAGTCCAA
81588404 ATGTCGTTTGAGATGTGAGTTATAGCGTTACGTTTTAACTCTTTTTTTTTTGTATCAAGGTGATC
129 ATGTCGTTTGAGATGTGAGTTATAGCGTTACGTTTTAACTC-TTTTTTTTTGTATCAAGGTGATC
81588469 TGATTGATAATCTTAATGAAGGATGGAATCTGCTGAGAAAACCTTGTATCATATTTTGAAGGAAG
193 TGATTGATAATCTTAATGAAGGATGGAATCTGCTGAGAAAACCTTGTATCATATTTTGAAGGAAG
81588534 CCGGCGGTAAGGTTAAGATCAGAGCTGACTTGGTAAAAGCACTAAAAAATAAACGTTTTGAGCCA
258 CCGGCGGTAAGGTTAAGATCAGAGCTGACTTGGTAAAAGCACTAAAAAATAAACGTTTTGAGCCA
81588599 AATGTGGTGACAAATGTGCTTGGCG
323 AATGTGGTGACAAATGTGCTTGGCG
81588624 AA
1 AA
81588626 AGGTTGGACC
Statistics
Matches: 349, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
347 72 0.21
349 97 0.28
350 180 0.52
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.24
Consensus pattern (347 bp):
AACACCATCGGTCCAGGAAGAAACCTCCACAACGTCGATTGTACAAGGAGACACCTCCAAAAGGA
AGACTGCAAAAAAAAAAAAAAAAGAAGCAAACTAAGAAGAAAAAGAATCAAACGGAAGTCCAAAT
GTCGTTTGAGATGTGAGTTATAGCGTTACGTTTTAACTCTTTTTTTTTGTATCAAGGTGATCTGA
TTGATAATCTTAATGAAGGATGGAATCTGCTGAGAAAACCTTGTATCATATTTTGAAGGAAGCCG
GCGGTAAGGTTAAGATCAGAGCTGACTTGGTAAAAGCACTAAAAAATAAACGTTTTGAGCCAAAT
GTGGTGACAAATGTGCTTGGCG
Found at i:81589061 original size:9 final size:9
Alignment explanation
Indices: 81589047--81589100 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
81589037 AAGACCAGGG
81589047 AAAGAAATA
1 AAAGAAATA
81589056 AAAGAAATA
1 AAAGAAATA
81589065 ACATA-AAATA
1 A-A-AGAAATA
81589075 AAAGAAATA
1 AAAGAAATA
* *
81589084 AAACAAAGAA
1 AAAGAAA-TA
81589094 AAAGAAA
1 AAAGAAA
81589101 AAGAAAGGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 1 0.03
9 22 0.58
10 14 0.37
11 1 0.03
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAGAAATA
Found at i:81589096 original size:19 final size:19
Alignment explanation
Indices: 81589051--81589100 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
81589041 CCAGGGAAAG
* *
81589051 AAATAAAAGAAATAACATA
1 AAATAAAAGAAATAAAACA
81589070 AAATAAAAGAAATAAAACA
1 AAATAAAAGAAATAAAACA
81589089 AAGA-AAAAGAAA
1 AA-ATAAAAGAAA
81589101 AAGAAAGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (19 bp):
AAATAAAAGAAATAAAACA
Found at i:81593064 original size:53 final size:53
Alignment explanation
Indices: 81592983--81593133 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
81592973 CTTACACGGT
* *
81592983 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
81593038 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** * *
81593091 TCACATTGCACTGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
81593134 GCGCACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:81594462 original size:26 final size:26
Alignment explanation
Indices: 81594427--81594479 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
81594417 TTTGAATAAC
81594427 AATCGAGAAGACCTTATGAAAATTGA
1 AATCGAGAAGACCTTATGAAAATTGA
81594453 AATCGAGAAGACCTTATGAAAATTGA
1 AATCGAGAAGACCTTATGAAAATTGA
81594479 A
1 A
81594480 CACTTTCGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (26 bp):
AATCGAGAAGACCTTATGAAAATTGA
Found at i:81595961 original size:51 final size:51
Alignment explanation
Indices: 81595906--81596041 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
81595896 TGGAAACATG
* *
81595906 ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATATGATATGTA
1 ATCTTAAAAGATATAATTTTATAATCTTAGAGATCTTAGATAAGATATGTA
* * * * *
81595957 ATCTTATAAGATATTATTTTATAGA-ATTACATATCTTAGATAAGATATGTA
1 ATCTTAAAAGATATAATTTTATA-ATCTTAGAGATCTTAGATAAGATATGTA
* *
81596008 ATCTTAGAAGATATAATTTTATATTCTTAGAGAT
1 ATCTTAAAAGATATAATTTTATAATCTTAGAGAT
81596042 TTAATTGTAG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
51 70 0.99
52 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.43
Consensus pattern (51 bp):
ATCTTAAAAGATATAATTTTATAATCTTAGAGATCTTAGATAAGATATGTA
Found at i:81601070 original size:25 final size:26
Alignment explanation
Indices: 81601025--81601073 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
81601015 TTTACAAGTG
*
81601025 AAAAAAATGTAAAATATATAATTATT
1 AAAAAAATGTAAAATAGATAATTATT
81601051 AAAAAATATGT-AAA-AGATAATTA
1 AAAAAA-ATGTAAAATAGATAATTA
81601074 AGGTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 9 0.43
27 4 0.19
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAAAAATGTAAAATAGATAATTATT
Found at i:81601548 original size:23 final size:22
Alignment explanation
Indices: 81601522--81601578 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
81601512 AAATGAAGGA
*
81601522 ATAAAAATTATTTAATTTTAATT
1 ATAAAAATTATTTAATATTAA-T
81601545 ATAAAAA-TA-TTAATATTAAT
1 ATAAAAATTATTTAATATTAAT
*
81601565 ATAATAATATATTT
1 ATAAAAAT-TATTT
81601579 TTAAAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 7 0.24
21 9 0.31
22 4 0.14
23 9 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAAATTATTTAATATTAAT
Found at i:81602298 original size:23 final size:23
Alignment explanation
Indices: 81602256--81602300 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
81602246 AAATTATATT
81602256 TTTAAAAAGAAATTTCAAAATCC
1 TTTAAAAAGAAATTTCAAAATCC
*
81602279 TTTAAAATATAAATTT-AAAATC
1 TTTAAAA-AGAAATTTCAAAATC
81602301 TGCATTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
TTTAAAAAGAAATTTCAAAATCC
Found at i:81603055 original size:14 final size:14
Alignment explanation
Indices: 81603036--81603066 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
81603026 TAGAATGGAT
81603036 TAGACGGGGTAATA
1 TAGACGGGGTAATA
81603050 TAGACGGGGTAATA
1 TAGACGGGGTAATA
81603064 TAG
1 TAG
81603067 TCTTTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.23
Consensus pattern (14 bp):
TAGACGGGGTAATA
Found at i:81615562 original size:22 final size:22
Alignment explanation
Indices: 81615537--81615579 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
81615527 AATAAACAAG
*
81615537 TTTACTTGTTTGATTAGTGGAC
1 TTTACTTATTTGATTAGTGGAC
81615559 TTTACTTATTTGATTAGTGGA
1 TTTACTTATTTGATTAGTGGA
81615580 ATCTGGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.51
Consensus pattern (22 bp):
TTTACTTATTTGATTAGTGGAC
Found at i:81617856 original size:23 final size:24
Alignment explanation
Indices: 81617820--81617867 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
81617810 TTCAAAATGG
*
81617820 TTAAAATCATTAATTAAAAAAAAT
1 TTAAAATCACTAATTAAAAAAAAT
* *
81617844 TTAAAAT-ACTAATTACAAATAAT
1 TTAAAATCACTAATTAAAAAAAAT
81617867 T
1 T
81617868 AATACTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAAAATCACTAATTAAAAAAAAT
Found at i:81618370 original size:30 final size:30
Alignment explanation
Indices: 81618247--81618378 Score: 113
Period size: 30 Copynumber: 4.4 Consensus size: 30
81618237 AAGGCCCACG
* * * *
81618247 GTCCATGCAGAAG-CTACAAAAGCGCCGACG
1 GTCCATGCAGAAGTC-GCAGAAGCGCCAACT
* * *
81618277 GACCATGCAGAAGTCGCTGAAGCGCCGACT
1 GTCCATGCAGAAGTCGCAGAAGCGCCAACT
* * * *
81618307 ATCTATGCAGAAGTCGTAGAAGCGTCAACT
1 GTCCATGCAGAAGTCGCAGAAGCGCCAACT
* * *
81618337 GTCCATGCAGAAGCCGCAGAAGCGGCAATT
1 GTCCATGCAGAAGTCGCAGAAGCGCCAACT
*
81618367 GTCCATGGAGAA
1 GTCCATGCAGAA
81618379 CTCTTAGAAG
Statistics
Matches: 82, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
30 81 0.99
31 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.28, T:0.15
Consensus pattern (30 bp):
GTCCATGCAGAAGTCGCAGAAGCGCCAACT
Found at i:81620571 original size:3 final size:3
Alignment explanation
Indices: 81620563--81620589 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
81620553 TCAATAAGTA
81620563 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
81620590 TAGATCTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:81621934 original size:21 final size:22
Alignment explanation
Indices: 81621910--81621951 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
81621900 GGTTCAATTA
81621910 AATATATA-ATTAAAAATTTAT
1 AATATATATATTAAAAATTTAT
81621931 AATATATATATTAAAAATTTA
1 AATATATATATTAAAAATTTA
81621952 GTTAAACCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATATATATTAAAAATTTAT
Found at i:81622853 original size:15 final size:15
Alignment explanation
Indices: 81622830--81622875 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
81622820 AAATTTAACT
81622830 TTAA-AAAAAATTAAA
1 TTAATAAAAAA-TAAA
81622845 TTAATAAAAAATAAA
1 TTAATAAAAAATAAA
* *
81622860 -TATTAAAAACTAAA
1 TTAATAAAAAATAAA
81622874 TT
1 TT
81622876 TATCATAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 12 0.44
15 9 0.33
16 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAATAAAAAATAAA
Found at i:81622864 original size:17 final size:15
Alignment explanation
Indices: 81622830--81622868 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
81622820 AAATTTAACT
*
81622830 TTAAAAAAAATTAAA
1 TTAAAAAAAATAAAA
81622845 TTAATAAAAAATAAATA
1 TTAA-AAAAAATAAA-A
81622862 TTAAAAA
1 TTAAAAA
81622869 CTAAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TTAAAAAAAATAAAA
Found at i:81647558 original size:21 final size:23
Alignment explanation
Indices: 81647524--81647577 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
81647514 ATTATAGAAA
*
81647524 AATACATAATTTTAAA-AA-ATAT
1 AATA-ATAAATTTAAATAATATAT
81647546 AATAATAAATTTAAATAATATAT
1 AATAATAAATTTAAATAATATAT
*
81647569 AAAAATAAA
1 AATAATAAA
81647578 AAATCATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.36
22 6 0.21
23 12 0.43
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAATAAATTTAAATAATATAT
Found at i:81651178 original size:18 final size:18
Alignment explanation
Indices: 81651152--81651186 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
81651142 ACCAATGATC
*
81651152 TTGAGAGGTACCTCTTTT
1 TTGACAGGTACCTCTTTT
*
81651170 TTGACAGGTTCCTCTTT
1 TTGACAGGTACCTCTTT
81651187 CTCAGACAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (18 bp):
TTGACAGGTACCTCTTTT
Found at i:81662251 original size:32 final size:34
Alignment explanation
Indices: 81662214--81662279 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
81662204 TTTAATTGTG
*
81662214 TTAATAATTAAA-C-AAATTTTAAAATCTGAAAA
1 TTAATAATTAAACCTAAATTTTAAAATCCGAAAA
* *
81662246 TTAATAGTTAAACCTAAATTTTAAGATCCGAAAA
1 TTAATAATTAAACCTAAATTTTAAAATCCGAAAA
81662280 ATAGGACTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 11 0.38
33 1 0.03
34 17 0.59
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (34 bp):
TTAATAATTAAACCTAAATTTTAAAATCCGAAAA
Found at i:81665264 original size:19 final size:18
Alignment explanation
Indices: 81665240--81665287 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
81665230 AATAAAATAA
*
81665240 ATAATTTAAAATTTTGAAT
1 ATAATTTAAAATATT-AAT
*
81665259 ATAA-TTAAAATATTATT
1 ATAATTTAAAATATTAAT
*
81665276 ATATTTTAAAAT
1 ATAATTTAAAAT
81665288 GATTGTATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 5 0.20
18 16 0.64
19 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAATTTAAAATATTAAT
Found at i:81667112 original size:16 final size:15
Alignment explanation
Indices: 81667087--81667134 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
81667077 CTATTTTAAG
81667087 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
81667102 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
81667119 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
81667134 T
1 T
81667135 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:81669465 original size:21 final size:22
Alignment explanation
Indices: 81669422--81669482 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
81669412 ATTAGAACAT
* * *
81669422 TATATTTATCATATATTATAAA
1 TATATTTATAATAAATTAAAAA
81669444 TATATTTA-AATAAATTAAAAA
1 TATATTTATAATAAATTAAAAA
* *
81669465 TATTATATATATTAAATT
1 TA-TATTTATAATAAATT
81669483 GGTTGGTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 12 0.38
22 13 0.41
23 7 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTTATAATAAATTAAAAA
Found at i:81669480 original size:18 final size:20
Alignment explanation
Indices: 81669422--81669480 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 20
81669412 ATTAGAACAT
81669422 TATATTTATCATATATTATAAA
1 TATATTTAT-ATATATTA-AAA
* *
81669444 TATATTTAAATAAATTAAAA
1 TATATTTATATATATTAAAA
81669464 -ATA-TTATATATATTAAA
1 TATATTTATATATATTAAA
81669481 TTGGTTGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 12 0.36
19 3 0.09
20 3 0.09
21 7 0.21
22 8 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATTTATATATATTAAAA
Found at i:81674145 original size:21 final size:21
Alignment explanation
Indices: 81674111--81674150 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
81674101 GAATTAAATA
*
81674111 AATTTTTATAATT-ATTTTGT
1 AATTTTTAAAATTAATTTTGT
81674131 AATTTGTTAAAATTAATTTT
1 AATTT-TTAAAATTAATTTT
81674151 TCTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
AATTTTTAAAATTAATTTTGT
Found at i:81722139 original size:25 final size:24
Alignment explanation
Indices: 81722103--81722155 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
81722093 TAAGTACGAA
81722103 TTTAATTATTTTTTTTATAAAAAG
1 TTTAATTATTTTTTTTATAAAAAG
81722127 TTTAATTATTTTTTTTATAAAAAG
1 TTTAATTATTTTTTTTATAAAAAG
81722151 TTTAA
1 TTTAA
81722156 AAACTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTAATTATTTTTTTTATAAAAAG
Found at i:81722163 original size:25 final size:24
Alignment explanation
Indices: 81722110--81722164 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
81722100 GAATTTAATT
**
81722110 ATTTTTTTTATAAAAAGTTTAATT
1 ATTTTTTTTATAAAAAGTTTAAAA
81722134 ATTTTTTTTATAAAAAGTTTAAAA
1 ATTTTTTTTATAAAAAGTTTAAAA
*
81722158 ACTTTTT
1 ATTTTTT
81722165 GGAAACTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTTTTTTATAAAAAGTTTAAAA
Found at i:81726952 original size:19 final size:20
Alignment explanation
Indices: 81726930--81726974 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
81726920 ATAGTTTAAT
* *
81726930 AATAAAATAAA-GAAAATGA
1 AATAAAAGAAATGAAAAAGA
81726949 AATAAAAGAAATGAAAAAGA
1 AATAAAAGAAATGAAAAAGA
81726969 AA-AAAA
1 AATAAAA
81726975 AAGCAAACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (20 bp):
AATAAAAGAAATGAAAAAGA
Found at i:81726991 original size:22 final size:21
Alignment explanation
Indices: 81726952--81726992 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
81726942 AAAATGAAAT
*
81726952 AAAAGAAATGAAAAAGAAAAA
1 AAAAGAAACGAAAAAGAAAAA
*
81726973 AAAAGCAAACGAAACAGAAA
1 AAAAG-AAACGAAAAAGAAA
81726993 CAGAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAGAAACGAAAAAGAAAAA
Found at i:81727018 original size:4 final size:4
Alignment explanation
Indices: 81727009--81727042 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
81726999 AGAATAGGGG
*
81727009 AGAA AGAA AGGAA AGAA AGAA AGAA AGGA AGAA A
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A
81727043 AGGGAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:81727044 original size:17 final size:17
Alignment explanation
Indices: 81727009--81727042 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
81726999 AGAATAGGGG
81727009 AGAAAGAAAGGAAAGAA
1 AGAAAGAAAGGAAAGAA
81727026 AGAAAGAAAGG-AAGAA
1 AGAAAGAAAGGAAAGAA
81727042 A
1 A
81727043 AGGGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGGAAAGAA
Found at i:81728148 original size:25 final size:25
Alignment explanation
Indices: 81728056--81728135 Score: 160
Period size: 25 Copynumber: 3.2 Consensus size: 25
81728046 ATGTTAGACT
81728056 ACAAGATCACAATATCAAGCCTACA
1 ACAAGATCACAATATCAAGCCTACA
81728081 ACAAGATCACAATATCAAGCCTACA
1 ACAAGATCACAATATCAAGCCTACA
81728106 ACAAGATCACAATATCAAGCCTACA
1 ACAAGATCACAATATCAAGCCTACA
81728131 ACAAG
1 ACAAG
81728136 CATTCAACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.49, C:0.28, G:0.09, T:0.15
Consensus pattern (25 bp):
ACAAGATCACAATATCAAGCCTACA
Found at i:81729259 original size:10 final size:11
Alignment explanation
Indices: 81729243--81729272 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
81729233 TTCGAGTAAT
81729243 TATAAAATAAA
1 TATAAAATAAA
81729254 -ATAAAATAAA
1 TATAAAATAAA
81729264 TATAAAATA
1 TATAAAATA
81729273 TAAACGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TATAAAATAAA
Found at i:81737674 original size:58 final size:59
Alignment explanation
Indices: 81737563--81737674 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 59
81737553 GACTAATATT
*
81737563 TATCACAAAAATAGTATACATATTTCCTCCAAGTTTTTCAGTGTGAAAACTTAAAATGTA
1 TATCACAAAAACAGTATACATATTT-CTCCAAGTTTTTCAGTGTGAAAACTTAAAATGTA
* ** *
81737623 TATCACAAACACAGTATACATATTT-TCTGAGTTTTTCAGTGTGTAAACTTAA
1 TATCACAAAAACAGTATACATATTTCTCCAAGTTTTTCAGTGTGAAAACTTAA
81737675 CTATTTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 24 0.51
60 23 0.49
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (59 bp):
TATCACAAAAACAGTATACATATTTCTCCAAGTTTTTCAGTGTGAAAACTTAAAATGTA
Found at i:81740806 original size:13 final size:13
Alignment explanation
Indices: 81740788--81740813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
81740778 ATTCGATCTT
81740788 TAATCAGACACTC
1 TAATCAGACACTC
81740801 TAATCAGACACTC
1 TAATCAGACACTC
81740814 AACTCGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
TAATCAGACACTC
Found at i:81743824 original size:116 final size:116
Alignment explanation
Indices: 81743620--81743865 Score: 316
Period size: 116 Copynumber: 2.1 Consensus size: 116
81743610 CCAACACTTG
* ** * * * *
81743620 ATGAGTCGTGGGTGTTATGCTGCATTTTGCTATATCGATGCTAATACCTAACAATGGTTGATCGC
1 ATGAGTCATGGGTGTTATGCCACATTTTGCAATATCGATGCTAATACCTAACAATGGCTCATCAC
* * * *
81743685 CAAATTATATTCCTTTAAGTCATTGAACTAGGTCCTACAAGCCTATTTCCC
66 CAAATTACATTCCTTTAAGTCATTGAACCAAGTCCTACAAGACTATTTCCC
* * * *
81743736 ATGAGTCATGGGTTTTATGCCATATTTTGCAATGTTGATGCTAATACCTAACAATGGCTCATCAC
1 ATGAGTCATGGGTGTTATGCCACATTTTGCAATATCGATGCTAATACCTAACAATGGCTCATCAC
81743801 CAAATGT-CATT-CTTGTAAGTCATTGAACCAAGTCCTACAAGACTATTTCCC
66 CAAAT-TACATTCCTT-TAAGTCATTGAACCAAGTCCTACAAGACTATTTCCC
*
81743852 ATGAGCCATGGGTG
1 ATGAGTCATGGGTG
81743866 CTAAGCCATA
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
115 3 0.03
116 107 0.96
117 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (116 bp):
ATGAGTCATGGGTGTTATGCCACATTTTGCAATATCGATGCTAATACCTAACAATGGCTCATCAC
CAAATTACATTCCTTTAAGTCATTGAACCAAGTCCTACAAGACTATTTCCC
Found at i:81743896 original size:116 final size:116
Alignment explanation
Indices: 81743660--81744160 Score: 325
Period size: 116 Copynumber: 4.3 Consensus size: 116
81743650 TATATCGATG
* * * * * *
81743660 CTAATACCTAACAATGGTTGATCGCCAAATTATATTCCTTTAAGTCATTGAACTAGGTCCTACAA
1 CTAATACCTAACAATGGCTCATCACCAAATTACATTCCTTTAAGTCATTGAACCAAGTCCTACAA
* * ** * ** * ** *
81743725 GCCTATTTCCCATGAGTCATGGGTTTTATGCCATATTTTGCAATGTTGATG
66 GACTATTTCCCATGAGCCATGGGTGCTAAGCCATATAGTGCAAGGTCAATA
81743776 CTAATACCTAACAATGGCTCATCACCAAATGT-CATT-CTTGTAAGTCATTGAACCAAGTCCTAC
1 CTAATACCTAACAATGGCTCATCACCAAAT-TACATTCCTT-TAAGTCATTGAACCAAGTCCTAC
**
81743839 AAGACTATTTCCCATGAGCCATGGGTGCTAAGCCATATAGTGTGAGGTCAATA
64 AAGACTATTTCCCATGAGCCATGGGTGCTAAGCCATATAGTGCAAGGTCAATA
* * ** * * ** * * * * *
81743892 CTAATGCCCATTAAT-GTTCGTTGCCAACATT-TATTCC-CTAACTCATTGAACTAAGTCCTATA
1 CTAATACCTAACAATGGCTCATCACCAA-ATTACATTCCTTTAAGTCATTGAACCAAGTCCTACA
* * * * * ** * *
81743954 AGCCCA-TTCCCAATGAGTCATGGGTGTTATGCCATACCGTTCAAGGTCAATG
65 AGACTATTTCCC-ATGAGCCATGGGTGCTAAGCCATATAGTGCAAGGTCAATA
* * * ** ** * * * *
81744006 CTAACAGCTATCAATGGCTCATTGCCAGAA-TACATTCCCAT-AGTTATTGTACGTAAGTCCTAT
1 CTAATACCTAACAATGGCTCATCACCA-AATTACATTCCTTTAAGTCATTGAAC-CAAGTCCTAC
* * * * * * * *
81744069 GAGCCTGTTTCCCATAAGCCATGGGTGTTATGCCATATTGTGCAAGGTCAATG
64 AAGACTATTTCCCATGAGCCATGGGTGCTAAGCCATATAGTGCAAGGTCAATA
* * *
81744122 CTAATACCTATCAATGCCTCATCACCAAATTATATTCCT
1 CTAATACCTAACAATGGCTCATCACCAAATTACATTCCT
81744161 ACGAGTTATT
Statistics
Matches: 303, Mismatches: 70, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
113 5 0.02
114 67 0.22
115 40 0.13
116 185 0.61
117 6 0.02
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (116 bp):
CTAATACCTAACAATGGCTCATCACCAAATTACATTCCTTTAAGTCATTGAACCAAGTCCTACAA
GACTATTTCCCATGAGCCATGGGTGCTAAGCCATATAGTGCAAGGTCAATA
Found at i:81746413 original size:10 final size:10
Alignment explanation
Indices: 81746378--81746420 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
81746368 TCTAAATTCT
81746378 AAAAATTAAA
1 AAAAATTAAA
* * *
81746388 AATAATGAAT
1 AAAAATTAAA
81746398 AAAAATTAAA
1 AAAAATTAAA
81746408 AAAAATATAAA
1 AAAAAT-TAAA
81746419 AA
1 AA
81746421 GTTTAACTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:81749436 original size:18 final size:18
Alignment explanation
Indices: 81749415--81749451 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
81749405 CTACTTTTCC
81749415 TTTTAAAATGACTTTACA
1 TTTTAAAATGACTTTACA
81749433 TTTTAAAATGACTTTACA
1 TTTTAAAATGACTTTACA
81749451 T
1 T
81749452 GTATTACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TTTTAAAATGACTTTACA
Found at i:81754889 original size:13 final size:13
Alignment explanation
Indices: 81754871--81754918 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
81754861 CTAGTTTAAC
81754871 AATACTTTTGAAA
1 AATACTTTTGAAA
81754884 AATACTTTTGAAA
1 AATACTTTTGAAA
* * *
81754897 AATGCTGTGGAAA
1 AATACTTTTGAAA
*
81754910 AGTACTTTT
1 AATACTTTT
81754919 CAGAAGTGCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AATACTTTTGAAA
Found at i:81756729 original size:19 final size:19
Alignment explanation
Indices: 81756705--81756742 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
81756695 CTGCCTTGGA
81756705 ATTTCATTGTGTTATTTAT
1 ATTTCATTGTGTTATTTAT
81756724 ATTTCATTGTGTTATTTAT
1 ATTTCATTGTGTTATTTAT
81756743 CCACCTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (19 bp):
ATTTCATTGTGTTATTTAT
Found at i:81766870 original size:4 final size:4
Alignment explanation
Indices: 81766861--81766907 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
81766851 CTGAATTTTT
81766861 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
81766908 TTCTCTAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:81775807 original size:43 final size:44
Alignment explanation
Indices: 81775746--81775838 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
81775736 TCCTAATTGG
81775746 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
81775789 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
81775833 -AAAATA
1 GAAAATA
81775839 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:81780536 original size:43 final size:44
Alignment explanation
Indices: 81780475--81780571 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 44
81780465 TCCTAATTGG
*
81780475 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
81780518 GAAAATAGTTTCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
81780562 -AAAATA-TTTC
1 GAAAATAGTTTC
81780572 TAGAATATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 4 0.08
43 45 0.90
44 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (44 bp):
GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:81781573 original size:254 final size:254
Alignment explanation
Indices: 81781117--81781617 Score: 903
Period size: 254 Copynumber: 2.0 Consensus size: 254
81781107 ATTGAATTGC
81781117 CCTACCTCTTATCCATTGCTAAGTGGACCAATTTGAAAATATGTCACAAATTTAGACAAAAAAAC
1 CCTACCTCTTATCCATTGCTAAGTGGACCAATTTGAAAATATGTCACAAATTTAGACAAAAAAAC
*
81781182 AATAAACATTTAAAGGAATATGGTTAAAGTAAATAGCATGAAATATATATATTGATCAAGGGGAA
66 AATAAACATTTAAAGGAATATGGTTAAAGTAAATAGCATGAAATATAAATATTGATCAAGGGGAA
*
81781247 AAGAGAAAAGTTAAAAGATTTTATTTTTTGGGGTTTTTGGTTTAGTGAGGGTTATTTTAATTTTG
131 AAGAGAAAAGTTAAAAGATTTTATTTTTTGGGGTTTTCGGTTTAGTGAGGGTTATTTTAATTTTG
* **
81781312 TTTATTTATTTTAAATTGGGATTAATTTTTAAATATTTTTATTAATTTTTATAATATGT
196 GTTATTTATTTTAAATTAAGATTAATTTTTAAATATTTTTATTAATTTTTATAATATGT
*
81781371 CCTACCTCTTATCCATTGCTAAGTGGACCAATTTGAAAATATGTCACAAATTTGGACAAAAAAAC
1 CCTACCTCTTATCCATTGCTAAGTGGACCAATTTGAAAATATGTCACAAATTTAGACAAAAAAAC
* *
81781436 AATAAACATTTAAAGGAATATGGTTGAAGTAAATAGCATGAAATATAAATATTGATTAAGGGGAA
66 AATAAACATTTAAAGGAATATGGTTAAAGTAAATAGCATGAAATATAAATATTGATCAAGGGGAA
* *
81781501 AAGAGAAAAGTTAAAAGATTTTATTTTTTTGGGTTTTCGGTTTAGTGAGGGTTGTTTTAATTTTG
131 AAGAGAAAAGTTAAAAGATTTTATTTTTTGGGGTTTTCGGTTTAGTGAGGGTTATTTTAATTTTG
*
81781566 GTTATTTATTTTAGATTAAGATTAATTTTTAAATATTTTTATTAATTTTTAT
196 GTTATTTATTTTAAATTAAGATTAATTTTTAAATATTTTTATTAATTTTTAT
81781618 TATTGTGTCT
Statistics
Matches: 236, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
254 236 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (254 bp):
CCTACCTCTTATCCATTGCTAAGTGGACCAATTTGAAAATATGTCACAAATTTAGACAAAAAAAC
AATAAACATTTAAAGGAATATGGTTAAAGTAAATAGCATGAAATATAAATATTGATCAAGGGGAA
AAGAGAAAAGTTAAAAGATTTTATTTTTTGGGGTTTTCGGTTTAGTGAGGGTTATTTTAATTTTG
GTTATTTATTTTAAATTAAGATTAATTTTTAAATATTTTTATTAATTTTTATAATATGT
Found at i:81799058 original size:12 final size:12
Alignment explanation
Indices: 81799043--81799067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
81799033 GTCTCCATGC
81799043 TAGATCAAAGCA
1 TAGATCAAAGCA
81799055 TAGATCAAAGCA
1 TAGATCAAAGCA
81799067 T
1 T
81799068 GAGGAGTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (12 bp):
TAGATCAAAGCA
Found at i:81810897 original size:18 final size:18
Alignment explanation
Indices: 81810874--81810966 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
81810864 CCCAACTACT
*
81810874 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
81810892 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
81810910 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
81810928 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
81810946 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
81810964 GTA
1 GTA
81810967 AACGGTCGTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:81810926 original size:36 final size:36
Alignment explanation
Indices: 81810874--81810966 Score: 177
Period size: 36 Copynumber: 2.6 Consensus size: 36
81810864 CCCAACTACT
*
81810874 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
81810910 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
81810946 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
81810967 AACGGTCGTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:81818866 original size:21 final size:23
Alignment explanation
Indices: 81818841--81818883 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
81818831 AATTAAAAAA
*
81818841 AAGTTAATATAT-T-ATAATTAT
1 AAGTTAAAATATGTAATAATTAT
81818862 AAGTTAAAATATGTAATAATTA
1 AAGTTAAAATATGTAATAATTA
81818884 CTTAAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
AAGTTAAAATATGTAATAATTAT
Found at i:81820296 original size:20 final size:20
Alignment explanation
Indices: 81820247--81820303 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
81820237 AGATAAGGGC
*
81820247 ACATGCCCGTGTGGCCTGGG
1 ACATGCCCGTGTGGCCTGGA
**
81820267 ACACCCCCGTGTGGCCTGGA
1 ACATGCCCGTGTGGCCTGGA
*
81820287 ACATGTCCGTGTGGCCT
1 ACATGCCCGTGTGGCCT
81820304 ACCCGTAGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.33, G:0.33, T:0.21
Consensus pattern (20 bp):
ACATGCCCGTGTGGCCTGGA
Found at i:81820849 original size:13 final size:13
Alignment explanation
Indices: 81820831--81820866 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
81820821 GATAATTAGT
81820831 AAATCATACATAC
1 AAATCATACATAC
*
81820844 AAATCATACATAT
1 AAATCATACATAC
81820857 AAATTCATAC
1 AAA-TCATAC
81820867 CAAACTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATCATACATAC
Found at i:81822271 original size:19 final size:18
Alignment explanation
Indices: 81822238--81822285 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
81822228 ATTTTCCCTT
* *
81822238 TTTCTTTTTCTTTTCTTC-
1 TTTCTTTCTCTTTTC-ACG
81822256 TTTCTTTCTCTCTTTCACG
1 TTTCTTTCTCT-TTTCACG
81822275 TTTCTTTCTCT
1 TTTCTTTCTCT
81822286 GTAACTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTCTTTCTCTTTTCACG
Found at i:81824340 original size:22 final size:22
Alignment explanation
Indices: 81824312--81824359 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
81824302 CGGACTCAAC
*
81824312 AATATGTTAATCAAAGGAAAAG
1 AATATGTTAATCAAAAGAAAAG
81824334 AATATGTTAATCAAAAGAAAAG
1 AATATGTTAATCAAAAGAAAAG
81824356 AATA
1 AATA
81824360 AACCCAGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.23
Consensus pattern (22 bp):
AATATGTTAATCAAAAGAAAAG
Found at i:81826454 original size:1 final size:1
Alignment explanation
Indices: 81826448--81826473 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
81826438 TTTAGTGAGT
81826448 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
81826474 TAATAAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:81828463 original size:50 final size:51
Alignment explanation
Indices: 81828386--81828514 Score: 206
Period size: 50 Copynumber: 2.5 Consensus size: 51
81828376 GACCATGGCA
* *
81828386 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
*
81828437 A-AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* *
81828487 ACAAGTGAAAAGTGGTAGCTTCGGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
81828515 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
50 47 0.66
51 24 0.34
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:81828528 original size:31 final size:31
Alignment explanation
Indices: 81828490--81828669 Score: 261
Period size: 31 Copynumber: 5.8 Consensus size: 31
81828480 ACAAATGACA
81828490 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
81828521 AGTGAAAAGTGGTAGATTCTGCTACCTGATA
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
81828552 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
81828583 AGTGAAAAATGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
81828614 AATGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
81828645 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
81828670 AAGTGACAAG
Statistics
Matches: 134, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 134 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:81828787 original size:46 final size:45
Alignment explanation
Indices: 81828691--81828858 Score: 158
Period size: 46 Copynumber: 3.6 Consensus size: 45
81828681 GATTTCCGTA
* * * * *
81828691 TAAGACCATATC-GGGATATGGCATCGGTGTGATATATGCTACTATA
1 TAAGACCATATCTGGGATATGGCATC-GTGTGATATGTGATTC-GTG
* *
81828737 TAAGACCATATCTAGGATATGGCATCAGTGAGATATGTGATTCGTG
1 TAAGACCATATCTGGGATATGGCATC-GTGTGATATGTGATTCGTG
* *
81828783 TAAGACCATAGCTGGGTTATGGCATCGATACGTGATATGTGATTACGTG
1 TAAGACCATATCTGGGATATGGCATCG-T--GTGATATGTGATT-CGTG
* * *
81828832 TAAGACCATAGCTGGGCTATGACATCG
1 TAAGACCATATCTGGGATATGGCATCG
81828859 ATATATGAAG
Statistics
Matches: 103, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
45 1 0.01
46 37 0.36
47 24 0.23
48 12 0.12
49 29 0.28
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (45 bp):
TAAGACCATATCTGGGATATGGCATCGTGTGATATGTGATTCGTG
Found at i:81828838 original size:49 final size:48
Alignment explanation
Indices: 81828768--81828861 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 48
81828758 GCATCAGTGA
* *
81828768 GATATGTGATTCGTGTAAGACCATAGCTGGGTTATGGCATCGATACGT
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGACATCGATACGT
81828816 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGACATCGATA
1 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGACATCGATA
81828862 TATGAAGATG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
48 11 0.26
49 32 0.74
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (48 bp):
GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGACATCGATACGT
Found at i:81830526 original size:5 final size:5
Alignment explanation
Indices: 81830510--81830545 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
81830500 TTGGGAAACA
*
81830510 AAAAT AACAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
81830546 TTTTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Done.