Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold215
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: 59586
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4508 original size:40 final size:40
Alignment explanation
Indices: 4417--4639 Score: 218
Period size: 40 Copynumber: 5.6 Consensus size: 40
4407 TCCTCGTTCA
** * * * *
4417 AATGCCTTCGGGACACAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
4456 AATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
4496 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
4536 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
4576 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
4616 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
4640 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
39 35 0.22
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:4648 original size:41 final size:41
Alignment explanation
Indices: 4571--4648 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
4561 TTAGTATCTC
* * *
4571 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
4612 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
4649 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:8986 original size:15 final size:13
Alignment explanation
Indices: 8977--9032 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 13
8967 AATATTATTA
8977 AATTATATATTTT
1 AATTATATATTTT
8990 AATTATAATATATTT
1 AATTAT-ATAT-TTT
* *
9005 AATAATAATTATGTT
1 AATTAT-A-TATTTT
9020 AATT-TATATTTT
1 AATTATATATTTT
9032 A
1 A
9033 TAGTATCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
12 6 0.17
13 7 0.19
14 5 0.14
15 15 0.42
16 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
AATTATATATTTT
Found at i:9002 original size:16 final size:16
Alignment explanation
Indices: 8981--9023 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
8971 TTATTAAATT
8981 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
8997 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
9012 AT-TATGTTAATT
1 ATATATTTTAATT
9024 TATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:9063 original size:120 final size:120
Alignment explanation
Indices: 8918--9139 Score: 426
Period size: 120 Copynumber: 1.9 Consensus size: 120
8908 GCAATAACAG
*
8918 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAATAATATTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATATTATTAAATTAT
8983 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
66 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
*
9038 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATATTATTAAATTAT
9103 ATATTTTAATTATAATATATTTAATAATAATTATGTT
66 ATATTTTAATTATAATATATTTAATAATAATTATGTT
9140 TAAATATGAT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATATTATTAAATTAT
ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
Found at i:9105 original size:61 final size:60
Alignment explanation
Indices: 8920--9107 Score: 188
Period size: 61 Copynumber: 3.1 Consensus size: 60
8910 AATAACAGTC
*
8920 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAATAATATTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAA-AATTTTATTAAATT
* * * * * * * * * *
8981 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTATATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAAATTTTATTA-AATT
9040 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAA-AATTTTATTAAATT
9101 ATATATT
1 ATATATT
9108 TTAATTATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 28 0.29
60 26 0.27
61 36 0.38
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (60 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAAATTTTATTAAATT
Found at i:9122 original size:16 final size:16
Alignment explanation
Indices: 9101--9142 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
9091 TTATTAAATT
*
9101 ATATATTTTAATTATA
1 ATATATTTTAATAATA
9117 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
9132 AT-TATGTTTAA
1 ATATAT-TTTAA
9143 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:9127 original size:15 final size:15
Alignment explanation
Indices: 9092--9133 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9082 TTAAGAATTT
*
9092 TATTAAATTAT-ATA
1 TATTTAATTATAATA
9106 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
9120 TATTTAATAATAAT
1 TATTTAATTATAAT
9134 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:9368 original size:45 final size:44
Alignment explanation
Indices: 9287--9377 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
9277 ACCTCTATTC
*
9287 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
9331 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
9376 CA
1 CA
9378 CCTCTAATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:9377 original size:16 final size:16
Alignment explanation
Indices: 9356--9425 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
9346 TTGATTTGCT
*
9356 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
9372 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
9388 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
* *
9404 AATACAGCTCTAATCC
1 ATTACACCTCTAATCC
*
9420 AATACA
1 ATTACA
9426 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.34, C:0.34, G:0.01, T:0.30
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:13664 original size:24 final size:24
Alignment explanation
Indices: 13632--13693 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
13622 CTATTAGTTC
13632 ATAGTGCATTAAATCTCTTCATCG
1 ATAGTGCATTAAATCTCTTCATCG
13656 ATAGTGCATTAAATCTCTTCATCG
1 ATAGTGCATTAAATCTCTTCATCG
*
13680 ATAGTGCATCAAAT
1 ATAGTGCATTAAAT
13694 ATTTTCCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (24 bp):
ATAGTGCATTAAATCTCTTCATCG
Found at i:14088 original size:24 final size:24
Alignment explanation
Indices: 14061--14112 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
14051 TTAGCAAGTC
*
14061 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
14085 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
14109 AAAT
1 AAAT
14113 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:14386 original size:24 final size:24
Alignment explanation
Indices: 14352--14404 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
14342 TTTCTAGAAG
* *
14352 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
14376 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
14400 ATTTA
1 ATTTA
14405 AATTTGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:14414 original size:24 final size:24
Alignment explanation
Indices: 14352--14415 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
14342 TTTCTAGAAG
* * *
14352 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGAATTTATTAGCATAATAT
*
14376 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGAATTTATTAGCATAATAT
14400 ATTTA-AATTTGATTAG
1 ATTTAGAATTT-ATTAG
14416 AATTAGGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCATAATAT
Found at i:15103 original size:17 final size:17
Alignment explanation
Indices: 15061--15108 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
15051 ATTTAATTCT
*
15061 TATATTT-TAATTTTTA
1 TATATTTATAATATTTA
*
15077 -ATATAATATAATATTTA
1 TATAT-TTATAATATTTA
15094 TATATTTATAATATT
1 TATATTTATAATATT
15109 ATTAATTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 4 0.15
16 1 0.04
17 17 0.65
18 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTATAATATTTA
Found at i:15687 original size:19 final size:18
Alignment explanation
Indices: 15650--15689 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
15640 CTCAAATGCC
15650 ATACAAATATATCATAAT
1 ATACAAATATATCATAAT
15668 ATACAAATAATAGT-ATAAT
1 ATACAAAT-ATA-TCATAAT
15687 ATA
1 ATA
15690 ATATAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 11 0.55
20 1 0.05
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (18 bp):
ATACAAATATATCATAAT
Found at i:18880 original size:5 final size:5
Alignment explanation
Indices: 18872--18912 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
18862 AATATTAAGC
* * *
18872 AAAAT AAAAT AAAAT AAAAT AAAAG AAAGT AAAAA AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
18913 CCTTTTGAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:19841 original size:25 final size:26
Alignment explanation
Indices: 19748--19906 Score: 128
Period size: 26 Copynumber: 6.5 Consensus size: 26
19738 TTTTTATATG
*
19748 TTATGTATATATTTTTAATATC-ATA
1 TTATGTATATATTTTTAATAACTATA
19773 TTA-GTCATATA--TTT-AT---TATA
1 TTATGT-ATATATTTTTAATAACTATA
19793 TTATGTATATATTTTTAATAACTATA
1 TTATGTATATATTTTTAATAACTATA
* *
19819 TTATGTATGTATTTTTAA-CACTATA
1 TTATGTATATATTTTTAATAACTATA
* * ** *
19844 TTACGTACATGCTTTTAATATC-ATTA
1 TTATGTATATATTTTTAATAACTA-TA
19870 TTATGTATATATTTTTAAT-A-TATA
1 TTATGTATATATTTTTAATAACTATA
*
19894 -TATGTGTATATTT
1 TTATGTATATATTT
19907 ATGTAATACT
Statistics
Matches: 107, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
20 11 0.10
21 2 0.02
22 5 0.05
23 17 0.16
24 4 0.04
25 29 0.27
26 39 0.36
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (26 bp):
TTATGTATATATTTTTAATAACTATA
Found at i:19845 original size:71 final size:77
Alignment explanation
Indices: 19748--19906 Score: 187
Period size: 71 Copynumber: 2.2 Consensus size: 77
19738 TTTTTATATG
*
19748 TTATGTATATATTTTTAATATCATATTA-GT-CAT-ATATTT-AT-T-A-TATTATGTATATATT
1 TTATGTATATATTTTTAACATCATATTACGTACATGAT-TTTAATATCATTATTATGTATATATT
19806 TTTAATAACTATA
65 TTTAATAACTATA
* *
19819 TTATGTATGTATTTTTAACA-CTATATTACGTACATGCTTTTAATATCATTATTATGTATATATT
1 TTATGTATATATTTTTAACATC-ATATTACGTACATGATTTTAATATCATTATTATGTATATATT
19883 TTTAAT-A-TATA
65 TTTAATAACTATA
*
19894 -TATGTGTATATTT
1 TTATGTATATATTT
19907 ATGTAATACT
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
70 1 0.01
71 24 0.32
72 2 0.03
73 6 0.08
74 14 0.19
75 5 0.07
76 2 0.03
77 21 0.28
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (77 bp):
TTATGTATATATTTTTAACATCATATTACGTACATGATTTTAATATCATTATTATGTATATATTT
TTAATAACTATA
Found at i:19914 original size:51 final size:48
Alignment explanation
Indices: 19732--20027 Score: 199
Period size: 51 Copynumber: 6.2 Consensus size: 48
19722 TTTAAAATAT
* *
19732 TATAT-TTTTTTATATGTTATGTATATATTTTTAATATCA-TATTA-G
1 TATATATTTTTAATATATTATGTATATATTTTTAATATCATTATTATG
* *
19777 TCATATA--TTTATTATATTATGTATATATTTTTAATAAC-TATATTATG
1 T-ATATATTTTTAATATATTATGTATATATTTTTAATATCAT-TATTATG
* * * **
19824 TATGTATTTTTAACACTATATTACGTACATGCTTTTAATATCATTATTATG
1 TATATATTTTT-A-A-TATATTATGTATATATTTTTAATATCATTATTATG
* *
19875 TATATATTTTTAATATATATATGTGTATATTTATGTAATA-C--TATTA-A
1 TATATATTTTTAATATAT-TATGTATATATTT-T-TAATATCATTATTATG
* * * *
19922 TAGT-TGTTTTTAATATTATTAT-TAT-TATTTCTAATATGTATATATTATT
1 TA-TATATTTTTAATA-TATTATGTATATATTTTTAATAT-CAT-TATTATG
* * *
19971 TATATATTTTT-A-ATACTATGTATATACCTTTTAATATTATTATTATG
1 TATATATTTTTAATATATTATGTATATA-TTTTTAATATCATTATTATG
*
20018 TTTATATTTT
1 TATATATTTT
20028 AGTATATATA
Statistics
Matches: 196, Mismatches: 29, Indels: 50
0.71 0.11 0.18
Matches are distributed among these distances:
43 5 0.03
45 33 0.17
46 20 0.10
47 36 0.18
48 29 0.15
49 26 0.13
50 3 0.02
51 43 0.22
52 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (48 bp):
TATATATTTTTAATATATTATGTATATATTTTTAATATCATTATTATG
Found at i:20033 original size:70 final size:73
Alignment explanation
Indices: 19786--20036 Score: 189
Period size: 73 Copynumber: 3.4 Consensus size: 73
19776 GTCATATATT
* * * * *
19786 TATTA-TATTATGTATATATTTTTAATAACTATATTATGTATGTATTT-T-TAACACTA-TATTA
1 TATTATTATTATGTTTATA-TTTTAGT-A-TATATTATGTATATATTTATGTAATACTATTAATA
19847 CGTACATGCTTTTAA
63 -GTAC---CTTTTAA
* * * *
19862 TATCATTATTATGTATATATTTTTAATATATA-TATGTGTATATTTATGTAATACTATTAATAGT
1 TATTATTATTATGTTTATA-TTTTAGTATATATTATGTATATATTTATGTAATACTATTAATAGT
***
19926 TGTTTTTAA
65 ACCTTTTAA
* * * * *
19935 TATTATTATTATTATTTCTAATAT-GTATATATTATTTATATATTT-T-TAATACTATGT-ATA-
1 TATTATTATTA-TGTTTATATTTTAGTATATATTATGTATATATTTATGTAATACTAT-TAATAG
19995 TACCTTTTAA
64 TACCTTTTAA
20005 TATTATTATTATGTTTATATTTTAGTATATAT
1 TATTATTATTATGTTTATATTTTAGTATATAT
20037 ACGTATGTAT
Statistics
Matches: 143, Mismatches: 24, Indels: 22
0.76 0.13 0.12
Matches are distributed among these distances:
69 8 0.06
70 26 0.18
71 12 0.08
72 8 0.06
73 29 0.20
74 16 0.11
75 5 0.03
76 14 0.10
77 25 0.17
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (73 bp):
TATTATTATTATGTTTATATTTTAGTATATATTATGTATATATTTATGTAATACTATTAATAGTA
CCTTTTAA
Found at i:23946 original size:22 final size:22
Alignment explanation
Indices: 23921--23965 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
23911 ATTCATGACT
23921 AACATTTATTCGTCATTTATTC
1 AACATTTATTCGTCATTTATTC
* *
23943 AACATTTGTTTGTCATTTATTC
1 AACATTTATTCGTCATTTATTC
23965 A
1 A
23966 TTCATTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.51
Consensus pattern (22 bp):
AACATTTATTCGTCATTTATTC
Found at i:32390 original size:74 final size:74
Alignment explanation
Indices: 32264--32469 Score: 272
Period size: 74 Copynumber: 2.8 Consensus size: 74
32254 CTGATATTTT
* * * * * *
32264 TTTTTTATTTCAGTTATTCCAATAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
32329 GCTGAGGTA
66 GCTGAGGTA
* * *
32338 TTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGGGTTGAGCCTCAGGTCAC
1 TTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
*
32403 GTTGAGGTA
66 GCTGAGGTA
* *
32412 TTTTTAA-TTCT-ATTTTCAAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TTTTTAATTTCTGTTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
32470 GGGTCTCACG
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
72 5 0.04
73 4 0.03
74 108 0.92
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (74 bp):
TTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
GCTGAGGTA
Found at i:32595 original size:90 final size:94
Alignment explanation
Indices: 32432--32699 Score: 321
Period size: 101 Copynumber: 2.8 Consensus size: 94
32422 TATTTTCAAA
* * * * *
32432 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCTCACGTCGAGGTACTTTCAATT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGTTGAGGTATTTTCAATT
*
32497 TCT-GTTTTCAA-TTTTT-A-CGTTTTTC
66 TCTATTTTTCAATTTTTTAATCGTTTTTC
* *
32522 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTTCGGGTCACACGTTGAGGT-TTTTCAACT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGTTGAGGTATTTTCAATT
*
32586 TCTATTTTTCAAATTCTGTTTTTAATTTTTGTTTTTC
66 TCTATTTTTC-AA---T-TTTTTAA---TCGTTTTTC
* * *
32623 AAAAATCAACTTATACTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGTTGAGGTATTTTCAATT
32688 TCTATTTTTCAA
66 TCTATTTTTCAA
32700 AAAAATCAAT
Statistics
Matches: 151, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
89 10 0.07
90 55 0.36
91 2 0.01
96 5 0.03
97 1 0.01
101 60 0.40
102 18 0.12
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (94 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGTTGAGGTATTTTCAATT
TCTATTTTTCAATTTTTTAATCGTTTTTC
Found at i:32666 original size:101 final size:103
Alignment explanation
Indices: 32489--32700 Score: 338
Period size: 101 Copynumber: 2.1 Consensus size: 103
32479 GTCGAGGTAC
* *
32489 TTTCAATTTCTGTTTTCAATTTTTACGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTG
1 TTTCAAATTCTGTTTTCAATTTTTA-GTTTTTCAAAAATCAACTCATACTGCAAGAGGTGAGTTG
* *
32554 AGCTTCGGGTCACACGTTGAGGT-TTTTCAACTTCTATT
65 AGCCTCGGGTCACACGCTGAGGTATTTTCAACTTCTATT
* *
32592 TTTCAAATTCTGTTTTTAATTTTT-GTTTTTCAAAAATCAACTTATACTGCAAGAGGTGAGTTGA
1 TTTCAAATTCTGTTTTCAATTTTTAGTTTTTCAAAAATCAACTCATACTGCAAGAGGTGAGTTGA
*
32656 GCCTCGGGTCACACGCTGAGGTATTTTCAATTTCTATT
66 GCCTCGGGTCACACGCTGAGGTATTTTCAACTTCTATT
32694 TTTCAAA
1 TTTCAAA
32701 AAAATCAATC
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 58 0.57
102 21 0.21
103 22 0.22
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (103 bp):
TTTCAAATTCTGTTTTCAATTTTTAGTTTTTCAAAAATCAACTCATACTGCAAGAGGTGAGTTGA
GCCTCGGGTCACACGCTGAGGTATTTTCAACTTCTATT
Found at i:32816 original size:268 final size:264
Alignment explanation
Indices: 32338--32835 Score: 673
Period size: 268 Copynumber: 1.9 Consensus size: 264
32328 CGCTGAGGTA
* * *
32338 TTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGGGTTGAGCCTCAGGTCAC
1 TTTTTAATTTCTGTTTTTCAAAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGTCAC
* * * *
32403 GTTGAGGTATTTTTAATTCTATTTTCAAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCC
66 GCTGAGGTATTTTCAATTCTATTTTCAAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCC
* * *
32468 TCGGGTCTCACGTCGAGGTACTTTCAATTTCTGTTTTCAATTTTTACGTTTTTCAAAAATCAACT
131 TCGGG-CACACGTCGAGGTACTTTCAATTTCTGTTTTCAAATTCTA-GTTTTTCAAAAATCAACT
*
32533 CATATTGCAAGAGGTGAGTTGAGCTTCGGGTCACACGTTGAGGTTTTTCAACTTCTATTTTTCAA
194 CATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGTTGAGGTTTTTCAACTTCTATTTTTCAA
32598 ATTCTG
259 ATTCTG
* * *
32604 TTTTTAATTTTTGTTTTTC-AAAAATCAACTTATACTGCAAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTTTAATTTCTGTTTTTCAAAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGT--C
*
32668 ACGCTGAGGTATTTTCAATTTCTATTTTTC-AAAAAAATCAATCTCATATTGCGAAATGTGAGTT
64 ACGCTGAGGTATTTTCAA-TTCTA-TTTTCAAAAAAAATCAA-CTCATATTGCGAAAGGTGAGTT
* * *
32732 GAGCCTCGGG-ACACG-CTGAGGTATTTTCAGTTTTTGTTTTTCAAATTCT-GTTTTTATCAAAA
126 GAGCCTCGGGCACACGTC-GAGGTACTTTCAATTTCTG-TTTTCAAATTCTAG-TTTT-TCAAAA
* * *
32794 GTCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
187 ATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACA
32836 TGCCGAGGAT
Statistics
Matches: 202, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
265 37 0.18
266 20 0.10
267 41 0.20
268 69 0.34
269 35 0.17
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (264 bp):
TTTTTAATTTCTGTTTTTCAAAAAATCAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGTCAC
GCTGAGGTATTTTCAATTCTATTTTCAAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCC
TCGGGCACACGTCGAGGTACTTTCAATTTCTGTTTTCAAATTCTAGTTTTTCAAAAATCAACTCA
TATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGTTGAGGTTTTTCAACTTCTATTTTTCAAAT
TCTG
Found at i:34501 original size:22 final size:20
Alignment explanation
Indices: 34476--34531 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
34466 TTAATTTTAA
34476 TATTATTTATACTATTATATTT
1 TATTATTTAT--TATTATATTT
34498 TATTACTGTTATTATTATATTT
1 TATTA-T-TTATTATTATATTT
*
34520 TTTTATTTATTA
1 TATTATTTATTA
34532 GCATTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 6 0.19
21 1 0.03
22 19 0.61
23 1 0.03
24 4 0.13
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTATTTATTATTATATTT
Found at i:34749 original size:21 final size:21
Alignment explanation
Indices: 34690--34965 Score: 97
Period size: 22 Copynumber: 12.3 Consensus size: 21
34680 ATATTAATAT
*
34690 TATATTATGTATATTATTTTTT
1 TATATTATGTATA-TATTTTTA
* *
34712 TA-AATAT-TATATTTTTTTA
1 TATATTATGTATATATTTTTA
*
34731 TATGTTATGTATATATTTTTA
1 TATATTATGTATATATTTTTA
34752 -ATATCATAT-TAGTCATATATTTTA
1 TATAT--TATGTA-T-ATAT-TTTTA
34776 TTATATTATGTATATATTTTTAATAA
1 -TATATTATGTATATA-TTTT--T-A
*
34802 CTATATTATGTATGTATTTTTAACA
1 -TATATTATGTATATATTTTT---A
* * *
34827 CTATATTACGTACATGCTTTTAATA
1 -TATATTATGTATAT-ATTTT--TA
*
34852 TCATTATTATGTATATATTTTAA
1 T-A-TATTATGTATATATTTTTA
*
34875 TATATATATGTGTATATTTATGTA
1 TATAT-TATGTATATATTT-T-TA
* *
34899 -ATACTAT-TA-ATAGTTGTTTT
1 TATATTATGTATATA-TT-TTTA
*
34919 TAATATTAT-TAT-TATTATTTC
1 T-ATATTATGTATATATT-TTTA
34940 TA-A-TATGTATATATTATTTA
1 TATATTATGTATATATT-TTTA
34960 TATATT
1 TATATT
34966 TTTAATACTA
Statistics
Matches: 194, Mismatches: 27, Indels: 66
0.68 0.09 0.23
Matches are distributed among these distances:
18 3 0.02
19 12 0.06
20 25 0.13
21 31 0.16
22 34 0.18
23 17 0.09
24 12 0.06
25 26 0.13
26 33 0.17
28 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.57
Consensus pattern (21 bp):
TATATTATGTATATATTTTTA
Found at i:34774 original size:25 final size:25
Alignment explanation
Indices: 34719--34972 Score: 150
Period size: 25 Copynumber: 10.5 Consensus size: 25
34709 TTTTAAATAT
* *
34719 TATATTTTT-TTAT-ATGTTATGTA
1 TATATTTTTAATATCATATTATGTA
34742 TATATTTTTAATATCATATTA-GTCA
1 TATATTTTTAATATCATATTATGT-A
34767 TATA-TTTT-AT-T-ATATTATGTA
1 TATATTTTTAATATCATATTATGTA
*
34788 TATATTTTTAATAACTATATTATGTA
1 TATATTTTTAATATC-ATATTATGTA
* * *
34814 TGTATTTTTAACA-CTATATTACGTA
1 TATATTTTTAATATC-ATATTATGTA
* **
34839 CATGCTTTTAATATCATTATTATGTA
1 TATATTTTTAATATCA-TATTATGTA
*
34865 TATA-TTTTAATAT-ATA-TATGTG
1 TATATTTTTAATATCATATTATGTA
*
34887 TATATTTATGTAATA-C-TATTA-ATA
1 TATATTT-T-TAATATCATATTATGTA
*
34911 GT-TGTTTTTAATAT--TATTAT-TA
1 -TATATTTTTAATATCATATTATGTA
* * *
34933 T-TATTTCTAATATGTATATATTATTTA
1 TATATTTTTAATA--T-CATATTATGTA
34960 TATATTTTTAATA
1 TATATTTTTAATA
34973 CTATGTATAT
Statistics
Matches: 184, Mismatches: 21, Indels: 47
0.73 0.08 0.19
Matches are distributed among these distances:
21 21 0.11
22 28 0.15
23 19 0.10
24 18 0.10
25 47 0.26
26 38 0.21
27 3 0.02
28 10 0.05
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (25 bp):
TATATTTTTAATATCATATTATGTA
Found at i:34883 original size:51 final size:48
Alignment explanation
Indices: 34719--35029 Score: 145
Period size: 46 Copynumber: 6.5 Consensus size: 48
34709 TTTTAAATAT
* * * *
34719 TATATTTTTTTATATGT-TATGTATATATTTTTAATATCA-TATTA-G
1 TATATATTTTAATATATATATGTATACATTTTTAATATCATTATTATG
* * *
34764 TCATATATTTTATTATAT-TATGTATATATTTTTAATAAC-TATATTATG
1 T-ATATATTTTAATATATATATGTATACATTTTTAATATCAT-TATTATG
* * *
34812 TATGTATTTTTAACA-CTATAT-TACGTACATGCTTTTAATATCATTATTATG
1 TATATA-TTTTAATATATATATGTA--TACAT--TTTTAATATCATTATTATG
* * *
34863 TATATATTTTAATATATATATGTGTATATTTATGTAATA-CTATTAATA-G
1 TATATATTTTAATATATATATGTATACATTT-T-TAATATC-ATTATTATG
* * * * *
34912 T-TGT-TTTTAATAT-TATTAT-TAT-TATTTCTAATATGTATATATTATT
1 TATATATTTTAATATATA-TATGTATACATTTTTAATAT-CAT-TATTATG
* *
34958 TATATATTTT--TA-ATACTATGTATATACCTTTTAATA-CTATTATTATG
1 TATATATTTTAATATATA-TATGTATACA-TTTTTAATATC-ATTATTATG
* * *
35005 TTTATATTTTAGTATATATACGTAT
1 TATATATTTTAATATATATATGTAT
35030 GTATATAGGT
Statistics
Matches: 204, Mismatches: 31, Indels: 58
0.70 0.11 0.20
Matches are distributed among these distances:
43 5 0.02
44 2 0.01
45 10 0.05
46 44 0.22
47 44 0.22
48 23 0.11
49 23 0.11
50 25 0.12
51 26 0.13
52 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.55
Consensus pattern (48 bp):
TATATATTTTAATATATATATGTATACATTTTTAATATCATTATTATG
Found at i:36990 original size:315 final size:315
Alignment explanation
Indices: 36418--37041 Score: 1106
Period size: 315 Copynumber: 2.0 Consensus size: 315
36408 ACTCTGAGGA
* * *
36418 TCGTACCCAATGGAGGCTAGTACTAAATTAATTCTAACCTAAATGCAAATAGATTTAATTAGTAC
1 TCGTACCCAATGGAGGCTAGCACTAAATTAATTCTAACCTAAACGCAAATAGATCTAATTAGTAC
*
36483 TTTAAATAAATCATATTACGATAAAATATAAATAGATTTTTTTAGGGTTTTATAAATAAAGGAAC
66 TTTAAATAAATCATATTACGATAAAATATAAATAGAATTTTTTAGGGTTTTATAAATAAAGGAAC
*
36548 AAAATAACATAAATGAAGAAAACTAACTTATAAACTCTATCAAATCTAGCTATGGGTGATTAGCT
131 AAAATAACATAAATGAAGAAAACTAACTTATAAACTCTATCAAATCTAGCTATAGGTGATTAGCT
36613 CGCTTTGGTGGTCATAACTAATTCCTATTTTTGAGTTTCTATTAAATTAACTAGTCATTAACTTA
196 CGCTTTGGTGGTCATAACTAATTCCTATTTTTGAGTTTCTATTAAATTAACTAGTCATTAACTTA
* *
36678 GTAGGATTTTTTGATCTTCCACTAAACTAATGAGTCGACAAGAACTATTGATCTC
261 GCAGGATTTTTCGATCTTCCACTAAACTAATGAGTCGACAAGAACTATTGATCTC
36733 TCGTACCCAATGGAGGCTAGCACTAAATTAATTCTAACCTAAACGCAAATAGATCTAATTAGTAC
1 TCGTACCCAATGGAGGCTAGCACTAAATTAATTCTAACCTAAACGCAAATAGATCTAATTAGTAC
* * *
36798 TTTAAATAAATCATATTACGATAAAATATAAATAGAATTTTTTGGGGTTTTATAAATAAATGATC
66 TTTAAATAAATCATATTACGATAAAATATAAATAGAATTTTTTAGGGTTTTATAAATAAAGGAAC
*
36863 AAAATAACATAAATGAAGAAAACTAACTTATAAATTCTATCAAATCTAGCTATAGGTGATTAGCT
131 AAAATAACATAAATGAAGAAAACTAACTTATAAACTCTATCAAATCTAGCTATAGGTGATTAGCT
*
36928 CGCTTTGGTGGTCATAACTAATTTCTATTTTTG-GCTTTCTATTAAATTAACTAGTCATTAACTT
196 CGCTTTGGTGGTCATAACTAATTCCTATTTTTGAG-TTTCTATTAAATTAACTAGTCATTAACTT
* *
36992 AGCAGGATTTTTCGATCTTCCACTAAACTAATGAGTCTATAAGAACTATT
260 AGCAGGATTTTTCGATCTTCCACTAAACTAATGAGTCGACAAGAACTATT
37042 TATTTCTTGA
Statistics
Matches: 294, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
314 1 0.00
315 293 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (315 bp):
TCGTACCCAATGGAGGCTAGCACTAAATTAATTCTAACCTAAACGCAAATAGATCTAATTAGTAC
TTTAAATAAATCATATTACGATAAAATATAAATAGAATTTTTTAGGGTTTTATAAATAAAGGAAC
AAAATAACATAAATGAAGAAAACTAACTTATAAACTCTATCAAATCTAGCTATAGGTGATTAGCT
CGCTTTGGTGGTCATAACTAATTCCTATTTTTGAGTTTCTATTAAATTAACTAGTCATTAACTTA
GCAGGATTTTTCGATCTTCCACTAAACTAATGAGTCGACAAGAACTATTGATCTC
Found at i:37847 original size:25 final size:25
Alignment explanation
Indices: 37811--37858 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
37801 GTTTTCTTTG
*
37811 TTTTATTATCCCAATTAAACTCTAT
1 TTTTATTATCCCAACTAAACTCTAT
*
37836 TTTTAGTT-TCCCACCTAAACTCT
1 TTTTA-TTATCCCAACTAAACTCT
37859 GATTAACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.46
Consensus pattern (25 bp):
TTTTATTATCCCAACTAAACTCTAT
Found at i:46955 original size:29 final size:31
Alignment explanation
Indices: 46884--46955 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 31
46874 TTTCACTAGT
* * * *
46884 TTTTAGTTATTTTATAATGTTTTCTTTATTA
1 TTTTATTTATTATATAATGTTATCTTTAATA
46915 TTTTATTT-TTATATAA-GTTATC-TTAATA
1 TTTTATTTATTATATAATGTTATCTTTAATA
*
46943 TTTTTTTTATTAT
1 TTTTATTTATTAT
46956 TTATGTAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 12 0.34
29 9 0.26
30 7 0.20
31 7 0.20
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (31 bp):
TTTTATTTATTATATAATGTTATCTTTAATA
Found at i:49159 original size:47 final size:47
Alignment explanation
Indices: 49081--49442 Score: 544
Period size: 47 Copynumber: 7.6 Consensus size: 47
49071 CCCTTCGGGA
* * * * * * *
49081 CTTATCACATTTATACACTTTCACATCCATCACGTTGACCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
49128 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49175 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
49222 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49271 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
49318 CTTATCACATATATATACACTTTCACATTCATCACATTGGCTATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49367 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49414 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
49443 TATTCAAATA
Statistics
Matches: 288, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
47 180 0.62
49 108 0.38
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:49275 original size:96 final size:96
Alignment explanation
Indices: 49081--49442 Score: 602
Period size: 96 Copynumber: 3.8 Consensus size: 96
49071 CCCTTCGGGA
* * * * * * * * *
49081 CTTATCACATTTATACACTTTCACATCCATCACGTTGACCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
49144 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
49175 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
49240 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
49271 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
49336 ACTTTCACATTCATCACATTGGCTATTCGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
49367 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
49432 ACTTTCACATT
66 ACTTTCACATT
49443 TATTCAAATA
Statistics
Matches: 254, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
94 46 0.18
96 208 0.82
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:49379 original size:143 final size:141
Alignment explanation
Indices: 49081--49442 Score: 562
Period size: 143 Copynumber: 2.5 Consensus size: 141
49071 CCCTTCGGGA
* * * * * * *
49081 CTTATCACATTTATACACTTTCACATCCATCACGTTGACCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
49146 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
49211 GGCCATTAGGC
131 GGCCATTAGGC
49222 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
49287 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
* * *
49352 CATTGGCTATTCGGC
127 CATCGGCCATTAGGC
* *
49367 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
49432 ACTTTCACATT
64 ACTTTCACATT
49443 TATTCAAATA
Statistics
Matches: 203, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
141 8 0.04
143 132 0.65
145 63 0.31
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:54152 original size:44 final size:46
Alignment explanation
Indices: 53947--54371 Score: 472
Period size: 46 Copynumber: 9.3 Consensus size: 46
53937 TTATACATTT
* * * * *
53947 TACACTTTCACAATCATCACGTTTGGCCACTCGGCCCTGTCACATATA
1 TACACTTTCACATTCATCAC-ATTGGCCA-TTGGCCTTATCACATATA
* *
53995 TACACTTTCACATTCATCACATCGGCCATTAGCCTTATCACATATA
1 TACACTTTCACATTCATCACATTGGCCATTGGCCTTATCACATATA
*
54041 TACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 TACACTTTCACATTCATCACATTGGCCATT-GGCCTTATCAC--ATATA
*
54090 TACACTTTCACATCCATCACATTGGCCATTCGGCCTT-T-ACATATA
1 TACACTTTCACATTCATCACATTGGCCATT-GGCCTTATCACATATA
* *
54135 T-CACTTTCACATTCATCACATCGGCCATTAGCCCTTATCACATATATA
1 TACACTTTCACATTCATCACATTGGCCATT-GGCCTTATCAC--ATATA
*
54183 TACACTTTCACATTCATCACATT-GCCATT-GCCTGATCAC--ATA
1 TACACTTTCACATTCATCACATTGGCCATTGGCCTTATCACATATA
54225 TACACTTTCACATTCATCACA-TGGCCATTAGG-CTTATCACATATAA
1 TACACTTTCACATTCATCACATTGGCCATT-GGCCTTATCACATAT-A
54271 TA-ACTTTCACATTCATCA-ATTGG-CATTCGG-CTTAT-ACATA-A
1 TACACTTTCACATTCATCACATTGGCCATT-GGCCTTATCACATATA
*
54312 TACAC-TTCACA-TCTATCACATCGG-CATTGGCCTTAATCACATAATA
1 TACACTTTCACATTC-ATCACATTGGCCATTGGCCTT-ATCACAT-ATA
54358 TACACTTTCACATT
1 TACACTTTCACATT
54372 TATTCAAATA
Statistics
Matches: 331, Mismatches: 21, Indels: 50
0.82 0.05 0.12
Matches are distributed among these distances:
40 2 0.01
41 16 0.05
42 43 0.13
43 14 0.04
44 48 0.15
45 29 0.09
46 63 0.19
47 24 0.07
48 33 0.10
49 59 0.18
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (46 bp):
TACACTTTCACATTCATCACATTGGCCATTGGCCTTATCACATATA
Found at i:54152 original size:93 final size:94
Alignment explanation
Indices: 53936--54371 Score: 545
Period size: 93 Copynumber: 4.8 Consensus size: 94
53926 CCCTTCGGGA
* * * * * * * *
53936 CTTATACAT-TTTACACTTTCACAATCATCACGTTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATACATATATACACTTTCACATTCATCAC-ATCGGCCATTAGGCCTTATCACATATATATAC
* *
53998 ACTTTCACATTCATCACATCGGCCATTAGC
65 ACTTTCACATTCATCACATTGGCCATTGGC
54028 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTAT-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
54093 ACTTTCACATCCATCACATTGGCCATTCGGC
65 ACTTTCACATTCATCACATTGGCCATT-GGC
*
54124 CTT-TACATATAT-CACTTTCACATTCATCACATCGGCCATTAGCCCTTATCACATATATATACA
1 CTTATACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
54187 CTTTCACATTCATCACATT-GCCATT-GC
66 CTTTCACATTCATCACATTGGCCATTGGC
* *
54214 CTGAT-CACATATACACTTTCACATTCATCACAT-GGCCATTAGG-CTTATCACATATA-ATA-A
1 CTTATACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
54274 CTTTCACATTCATCA-ATTGG-CATTCGG-
66 CTTTCACATTCATCACATTGGCCATT-GGC
54301 CTTATACATA-ATACAC-TTCACA-TCTATCACATCGG-CATT-GGCCTTAATCACATA-ATATA
1 CTTATACATATATACACTTTCACATTC-ATCACATCGGCCATTAGGCCTT-ATCACATATATATA
54360 CACTTTCACATT
64 CACTTTCACATT
54372 TATTCAAATA
Statistics
Matches: 309, Mismatches: 18, Indels: 38
0.85 0.05 0.10
Matches are distributed among these distances:
85 4 0.01
86 28 0.09
87 40 0.13
88 18 0.06
89 13 0.04
90 19 0.06
91 21 0.07
92 11 0.04
93 88 0.28
94 28 0.09
95 34 0.11
96 5 0.02
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
CTTTCACATTCATCACATTGGCCATTGGC
Found at i:57453 original size:47 final size:47
Alignment explanation
Indices: 57311--57714 Score: 518
Period size: 47 Copynumber: 8.6 Consensus size: 47
57301 CCCTTCGGGA
* * * * * * *
57311 CTTATCACATTTATACACTTTCACATCCATCACGTTGAACCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCG-GCCATTAGGC
*
57359 C-TGTCACATATATACACTTTCACA-T--TCACAT-GGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
57401 CTTATCACATACTATACACTTTCACATTCATCACATCGGCTATTA-GC
1 CTTATCACATA-TATACACTTTCACATTCATCACATCGGCCATTAGGC
57448 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
57495 CTTATCACATATATATACACTTTCATATTCATCACATTGGTCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
57544 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
57591 CTTATCACATATATATACCATTTCACATTCATCACATTGGCCATT-CGC
1 CTTATCACATATATACA-C-TTTCACATTCATCACATCGGCCATTAGGC
*
57639 CTTATCACATACTATACACTTTCACATTCATTACATCGGCCATTAGGC
1 CTTATCACATA-TATACACTTTCACATTCATCACATCGGCCATTAGGC
57687 CTTATCACATATATATACAC-TTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
57715 TATTCAAATA
Statistics
Matches: 316, Mismatches: 25, Indels: 30
0.85 0.07 0.08
Matches are distributed among these distances:
42 8 0.03
43 9 0.03
44 19 0.06
45 1 0.00
46 32 0.10
47 124 0.39
48 41 0.13
49 79 0.25
50 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:57568 original size:96 final size:96
Alignment explanation
Indices: 57311--57714 Score: 589
Period size: 96 Copynumber: 4.3 Consensus size: 96
57301 CCCTTCGGGA
* * * * *
57311 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGAACCACTCGGCC-TGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATTG-GCCATTCGGCCTTATCACATATATA
57373 CACTTTCACA-T--TCACAT-GGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
57401 CTTATCACATA-CTATACACTTTCACATTCATCACATCGGCTATT-AGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
57464 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
57495 CTTATCACATATATATACACTTTCATATTCATCACATTGGTCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
57560 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
57591 CTTATCACATATATATAC-CATTTCACATTCATCACATTGGCCATTC-GCCTTATCACATACTAT
1 CTTATCACATATATATACAC-TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATA-TAT
*
57654 ACACTTTCACATTCATTACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
57687 CTTATCACATATATATACAC-TTCACATT
1 CTTATCACATATATATACACTTTCACATT
57715 TATTCAAATA
Statistics
Matches: 285, Mismatches: 17, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
89 3 0.01
90 35 0.12
91 24 0.08
93 6 0.02
94 22 0.08
95 50 0.18
96 144 0.51
97 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:58283 original size:21 final size:21
Alignment explanation
Indices: 58257--58297 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58247 TAAATTTATC
*
58257 TTATAACCATTTTTGTAAAAT
1 TTATAACCATTTTTCTAAAAT
**
58278 TTATAATGATTTTTCTAAAA
1 TTATAACCATTTTTCTAAAA
58298 CAGAACAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (21 bp):
TTATAACCATTTTTCTAAAAT
Done.