Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1501
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: 68474
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:6474 original size:1 final size:1
Alignment explanation
Indices: 6468--6495 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
6458 TTTGCTTCCT
6468 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
6496 CTTTGGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7928 original size:86 final size:88
Alignment explanation
Indices: 7733--7987 Score: 313
Period size: 86 Copynumber: 2.9 Consensus size: 88
7723 CAGATCAATG
* * *
7733 AAGACAAAGGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAAGCCTTGCCTC
** * * * *
7797 TTTCGGTTG-TGATAGAGCTGGTTG
65 CATCGGTTGCAG-TGGAGCTAGTTA
* *
7821 AAGACAAAAGATCTTGCCTTCCTTCATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
*
7885 ATCGATTGCAGTGGAGCTAGTTA
66 ATCGGTTGCAGTGGAGCTAGTTA
** *
7908 AAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCC
1 AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
*
7971 ATCGGTTGCATTGGAGC
66 ATCGGTTGCAGTGGAGC
7988 AGATTGAAGC
Statistics
Matches: 146, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
85 3 0.02
86 71 0.49
87 28 0.19
88 44 0.30
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (88 bp):
AAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCTAGTTA
Found at i:8005 original size:86 final size:84
Alignment explanation
Indices: 7742--8041 Score: 300
Period size: 86 Copynumber: 3.5 Consensus size: 84
7732 GAAGACAAAG
* * * * **
7742 GATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGT
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACA-AAGCCTTGCCTCCATCGGTTG-
* * * *
7807 GATAGAGCTGGTTGAAGACAAAA
64 CATGGAGC-AGTTGAAG-CAAGA
* * *
7830 GATCTTGCCTTCCTTCATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATTGC
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCCATCGGTTGC
*
7894 AGTGGAGCTAGTTAAAG-AAGCA
65 A-TGGAGC-AGTTGAAGCAAG-A
7916 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
*
7981 TTGGAGCAGATTGAAGCCAGA
66 -TGGAGCAG-TTGAAGCAAGA
** * * *
8002 GATCTTATCTCCCTGAGATT-ACAGCGGAGCAGATCAAAGA
1 GATCTTGCCTTCCTG-CATTAACAGCGAAGCAGATCAAAGA
8042 TAGTAATCCT
Statistics
Matches: 180, Mismatches: 25, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
85 7 0.04
86 103 0.57
87 33 0.18
88 35 0.19
89 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (84 bp):
GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
TGGAGCAGTTGAAGCAAGA
Found at i:8245 original size:44 final size:43
Alignment explanation
Indices: 7982--8287 Score: 186
Period size: 44 Copynumber: 7.1 Consensus size: 43
7972 TCGGTTGCAT
7982 TGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAG
1 TGGAGCAGATTGAAG-CAGAGATCTTATCTCCCTGAGATTACAG
* ** * * * *
8026 CGGAGCAGATCAAAG-ATAGTAATCCTATCTCCTTGAGATTACAA
1 TGGAGCAGATTGAAGCAGAG--ATCTTATCTCCCTGAGATTACAG
* *
8070 TGGAGCGGATT-AA--AG-GATCTTATCTCTCTGA-AGTTACAG
1 TGGAGCAGATTGAAGCAGAGATCTTATCTCCCTGAGA-TTACAG
* * * * *
8109 TAGAGAAGA-TCACATCAG-G-TCTTATCTTCCTGAGATTACAG
1 TGGAGCAGATTGA-AGCAGAGATCTTATCTCCCTGAGATTACAG
* ** * * *
8150 TGGAGTAGACCGAAGAATTGCAGATCTTATCCCCCTGA-AGTTATAG
1 TGGAGCAGATTGAAGCA--G-AGATCTTATCTCCCTGAGA-TTACAG
*
8196 TGGAGCAGATTGAAGCCAGAGATCTTATCTCCCCGAGATTACAG
1 TGGAGCAGATTGAAG-CAGAGATCTTATCTCCCTGAGATTACAG
* * ** *
8240 CGGAGCAGATCGAAGACA-CTATCCTATCTCCCTGA-AGTTACAG
1 TGGAGCAGATTGAAG-CAGAGATCTTATCTCCCTGAGA-TTACAG
8283 TGGAG
1 TGGAG
8288 TGGGTTAAAA
Statistics
Matches: 200, Mismatches: 44, Indels: 37
0.71 0.16 0.13
Matches are distributed among these distances:
38 2 0.01
39 24 0.12
40 1 0.00
41 28 0.14
42 10 0.05
43 26 0.13
44 75 0.38
45 4 0.02
46 29 0.14
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (43 bp):
TGGAGCAGATTGAAGCAGAGATCTTATCTCCCTGAGATTACAG
Found at i:9609 original size:19 final size:17
Alignment explanation
Indices: 9587--9649 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 17
9577 ATTATCTTCT
9587 TCATTATTTTAATGTATTA
1 TCATTATTTT-AT-TATTA
9606 TCATTTATTATTATTATTA
1 TCA-TTATT-TTATTATTA
*
9625 TTATTATTTCTATTATTA
1 TCATTATTT-TATTATTA
*
9643 TTATTAT
1 TCATTAT
9650 GTACATTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 1 0.03
18 20 0.50
19 10 0.25
20 7 0.17
21 2 0.05
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
TCATTATTTTATTATTA
Found at i:9618 original size:3 final size:3
Alignment explanation
Indices: 9610--9680 Score: 65
Period size: 3 Copynumber: 23.3 Consensus size: 3
9600 GTATTATCAT
*
9610 TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TTA TTA TTA TGTA -CA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA
* * *
9655 TTA CTG TTA CTTA TCA TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA T
9681 GTGATAGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 2 0.04
3 47 0.85
4 6 0.11
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:21310 original size:92 final size:91
Alignment explanation
Indices: 21153--21361 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
21143 TTGATTTTAG
* * *
21153 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
21218 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
21245 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
21309 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * * *
21337 CAAATTTATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
21362 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 70 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:21324 original size:24 final size:25
Alignment explanation
Indices: 21289--21336 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
21279 TTATGAAATT
21289 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
21313 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
21337 CAAATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:21501 original size:66 final size:65
Alignment explanation
Indices: 21415--21622 Score: 185
Period size: 66 Copynumber: 3.3 Consensus size: 65
21405 AAATATATTT
*
21415 AATATTAATTATTTCA-AATTTTTATTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTA-TTAAGAATTTTTATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
21479 AG
64 AG
* * *
21481 AATATTAATTATTAAGAA-TTTTA-TTAA--AT--TATA-TAT--TTTAATTACAA-T-ATAT-T
1 AATATTAATTATTAAGAATTTTTATTTAAGTATCATATATTATGATTTGAGTA-AATTCATATAA
*
21534 T
65 G
* * *
21535 AATAATAATTATGT--TAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAT
1 AATATTAATTAT-TAAGAATTTTTA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATAT
21598 AAG
63 AAG
21601 AATATTAATTATTAAGAATTTT
1 AATATTAATTATTAAGAATTTT
21623 ATTAAATTAT
Statistics
Matches: 108, Mismatches: 15, Indels: 37
0.68 0.09 0.23
Matches are distributed among these distances:
53 2 0.02
54 15 0.14
55 5 0.05
56 10 0.09
57 3 0.03
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 3 0.03
64 10 0.09
65 13 0.12
66 24 0.22
67 5 0.05
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (65 bp):
AATATTAATTATTAAGAATTTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:21515 original size:120 final size:120
Alignment explanation
Indices: 21377--21669 Score: 491
Period size: 120 Copynumber: 2.4 Consensus size: 120
21367 AATTATTTTA
* * * *
21377 AATTTTATTAAATCATATATCTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTTTTA-T
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
21440 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
21497 AATTTTATTAAATTATATATTTTAATTACAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
21562 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
21617 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
21670 TAAATATGAT
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 7 0.04
120 155 0.95
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:21652 original size:16 final size:16
Alignment explanation
Indices: 21631--21672 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21621 TTATTAAATT
*
21631 ATATATTTTAATTATA
1 ATATATTTTAATAATA
21647 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
21662 AT-TATGTTTAA
1 ATATAT-TTTAA
21673 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:21657 original size:15 final size:15
Alignment explanation
Indices: 21622--21663 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21612 TTAAGAATTT
*
21622 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21636 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21650 TATTTAATAATAAT
1 TATTTAATTATAAT
21664 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:21702 original size:76 final size:76
Alignment explanation
Indices: 21622--21850 Score: 184
Period size: 76 Copynumber: 3.0 Consensus size: 76
21612 TTAAGAATTT
*
21622 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAAATATGATTAAATTA
21687 TTTATTATTGA
66 TTTATTATTGA
* * ** ** *** * *
21698 TATT-AATAATCTTATTAAAATT-TAA-ATA-ACAATAATAATT-TACCAAAACAAAT-TTCTGC
1 TATTAAATTAT-ATATTTTAATTATAATATATTTAATAATAATTAT-GTTAAA-ATATGAT-T--
* * ** *
21757 TAATTATTAAGAATT-T
60 AAATTATTTATTATTGA
* *
21773 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAATATGATTAAAATA
1 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAAATATGATTAAATTA
21838 TTTATTATTGA
66 TTTATTATTGA
21849 TA
1 TA
21851 ATAATAATCT
Statistics
Matches: 105, Mismatches: 35, Indels: 26
0.63 0.21 0.16
Matches are distributed among these distances:
72 1 0.01
73 13 0.12
74 7 0.07
75 30 0.29
76 32 0.30
77 7 0.07
78 14 0.13
79 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (76 bp):
TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAAATATGATTAAATTA
TTTATTATTGA
Found at i:21761 original size:151 final size:151
Alignment explanation
Indices: 21606--21887 Score: 528
Period size: 151 Copynumber: 1.9 Consensus size: 151
21596 ATAAGAATAT
* *
21606 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
* *
21671 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAATAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAATAA
21736 TTTACCAAAACAAATTTCTGC
131 TTTACCAAAACAAATTTCTGC
21757 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
21822 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAATAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAATAA
21887 T
131 T
21888 AATCATTTAC
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 127 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (151 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAATAA
TTTACCAAAACAAATTTCTGC
Found at i:21797 original size:18 final size:17
Alignment explanation
Indices: 21769--21803 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21759 ATTATTAAGA
*
21769 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
21786 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
21804 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:21833 original size:26 final size:25
Alignment explanation
Indices: 21793--21842 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
21783 TATATTTTAA
21793 TTAAAATATATTTAATAATAATTATG
1 TTAAAATATATTTAA-AATAATTATG
*
21819 TTAAAATATGA-TTAAAATATTTAT
1 TTAAAATAT-ATTTAAAATAATTAT
21843 TATTGATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 13 0.59
27 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAAAATATATTTAAAATAATTATG
Found at i:22060 original size:16 final size:16
Alignment explanation
Indices: 22039--22074 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
22029 GATTTGCTAT
22039 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
22055 TACACCTCTAATTCAA
1 TACACCTCTAATCCAA
22071 TACA
1 TACA
22075 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:22215 original size:9 final size:9
Alignment explanation
Indices: 22188--22222 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
22178 CATCATTCTT
22188 ATCGTCCTC
1 ATCGTCCTC
* *
22197 ATTGTGCTC
1 ATCGTCCTC
22206 ATCGTCCTC
1 ATCGTCCTC
22215 ATCGTCCT
1 ATCGTCCT
22223 TTTTGCAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.11, C:0.37, G:0.14, T:0.37
Consensus pattern (9 bp):
ATCGTCCTC
Found at i:32343 original size:19 final size:19
Alignment explanation
Indices: 32300--32344 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
32290 TCTAAAAAAA
32300 TTAAAAATAGAAAAATTCT
1 TTAAAAATAGAAAAATTCT
**
32319 AGAAAAATAGAAAAA-TCAT
1 TTAAAAATAGAAAAATTC-T
32338 TTAAAAA
1 TTAAAAA
32345 ATTAAATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.24
Consensus pattern (19 bp):
TTAAAAATAGAAAAATTCT
Found at i:35724 original size:30 final size:27
Alignment explanation
Indices: 35656--35724 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
35646 GTCTTTTTTC
* *
35656 TTTTTTGGTCACCCAAGTATCAATTTT
1 TTTTTTGGTCACCCAACTATCAATGTT
35683 TTTAATTTGGTCACCCAACTAATCGATATGTT
1 TTT--TTTGGTCACCCAACT-ATC-A-ATGTT
35715 TTTTTTGGTC
1 TTTTTTGGTC
35725 CCTTTCTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 3 0.09
29 14 0.40
30 10 0.29
31 1 0.03
32 7 0.20
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (27 bp):
TTTTTTGGTCACCCAACTATCAATGTT
Found at i:55856 original size:21 final size:21
Alignment explanation
Indices: 55831--55893 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
55821 ATTTTTGAGG
55831 ATATGTAATCTTAGATATGAT
1 ATATGTAATCTTAGATATGAT
*
55852 ATATGCAATCTTAGATATGAT
1 ATATGTAATCTTAGATATGAT
55873 ATA--TAATCTTAGATATGAT
1 ATATGTAATCTTAGATATGAT
55892 AT
1 AT
55894 GCAATCTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 17 0.43
21 23 0.57
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (21 bp):
ATATGTAATCTTAGATATGAT
Found at i:55899 original size:19 final size:19
Alignment explanation
Indices: 55830--55902 Score: 101
Period size: 19 Copynumber: 3.7 Consensus size: 19
55820 AATTTTTGAG
*
55830 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55849 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
**
55870 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55889 GATATGCAATCTTA
1 GATATGCAATCTTA
55903 AAATATATGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 29 0.62
21 18 0.38
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:56241 original size:13 final size:13
Alignment explanation
Indices: 56221--56250 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
56211 TGTAATTAAG
56221 TTTT-TTTTTATT
1 TTTTATTTTTATT
56233 TTTTATTTTTATT
1 TTTTATTTTTATT
56246 TTTTA
1 TTTTA
56251 CCCTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:56700 original size:24 final size:26
Alignment explanation
Indices: 56658--56706 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
56648 TATGTACATG
56658 TATATTTTTTTAAACGAATATTTTCC
1 TATATTTTTTTAAACGAATATTTTCC
*
56684 TATA-TTTTTT-AATGAATATTTTC
1 TATATTTTTTTAAACGAATATTTTC
56707 ATATTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 6 0.27
26 4 0.18
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (26 bp):
TATATTTTTTTAAACGAATATTTTCC
Found at i:57497 original size:98 final size:98
Alignment explanation
Indices: 57377--57573 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
57367 AAAAAAATAA
* *
57377 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
57442 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
57475 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
57540 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
57573 T
1 T
57574 TTTATTGTAC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:61683 original size:14 final size:13
Alignment explanation
Indices: 61662--61711 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
61652 AAAATATTTC
61662 AAAA-AAAAGAGGA
1 AAAAGAAAAGA-GA
61675 AAAAGAAAAGA-A
1 AAAAGAAAAGAGA
*
61687 AAAAGGAAAAAAGA
1 AAAA-GAAAAGAGA
61701 AAAAGTAAAAG
1 AAAAG-AAAAG
61712 GAGAGGCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 11 0.35
14 15 0.48
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAGAGA
Found at i:61693 original size:19 final size:21
Alignment explanation
Indices: 61665--61703 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
61655 ATATTTCAAA
61665 AAAAAGAGG-AAAAAGAAAAG
1 AAAAAGAGGAAAAAAGAAAAG
61685 AAAAA-AGGAAAAAAGAAAA
1 AAAAAGAGGAAAAAAGAAAA
61704 AGTAAAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAAGAGGAAAAAAGAAAAG
Found at i:63158 original size:132 final size:132
Alignment explanation
Indices: 62916--63928 Score: 1729
Period size: 132 Copynumber: 7.7 Consensus size: 132
62906 AACAAATCAG
*
62916 TGAAAATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
* * *
62981 TTCCAAGATAGTGGGAAGCAGATTTAAGCCGCCAAGCCTCGTCTCCCTGAGCAGCAGTGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
63046 GT
131 GT
* *
63048 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCGAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
*
63113 TTCCAAGATAGTGAGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
63178 GT
131 GT
* *
63180 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
* * *
63245 TTCCAAGATAGTGGGAAGCAGATTTAAGCCGCCAAGTCTTGTCTCCCTGAACAGCAGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
63310 GT
131 GT
* * *
63312 TGAAAATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATAT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
* * *
63377 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCTTGAGCAACAGCGGAGAAT
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
63442 GT
131 GT
*
63444 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
* *
63509 TTCCAAGATAGTAGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGTAGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
63574 GT
131 GT
* *
63576 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATAT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
63641 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
63706 GT
131 GT
* * *
63708 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGACAAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
* *
63773 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
63838 GT
131 GT
* ** * *
63840 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAACAAATCATATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
63905 TTCCAAGATAGTGGGAAGCAGATT
66 TTCCAAGATAGTGGGAAGCAGATT
63929 AAAGTCGACA
Statistics
Matches: 832, Mismatches: 49, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 832 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (132 bp):
TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
GT
Found at i:63229 original size:44 final size:43
Alignment explanation
Indices: 62924--63890 Score: 227
Period size: 44 Copynumber: 22.0 Consensus size: 43
62914 AGTGAAAATT
* *
62924 GTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
** * * *
62967 GGCGAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCC
1 GTAG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGAC
* * ** * * * * *
63011 GCCA-AGCCTCGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
1 G-TAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
* *
63056 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
** * *
63099 GGCGAATCTTATCTTTCC-AAG-A-TAGTGAGAAGCAGATTTAAGCCAC
1 GTAG-ATCTTATC-TCCCTAAGCAGTAGTG-G-AGCAGATTGAAG--AC
** * * * * * * * *
63145 CAAG-CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
*
63188 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* * * *
63231 AG-CGAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCC
1 -GTAG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGAC
* * * * * * * *
63275 GCCA-AGTCTTGTCTCCCTGAA-CAGCAGCGGAGAAGGTTGAAAATT
1 G-TAGA-TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTGAAGA-C
* *
63320 ATAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* * * * *
63363 GGCAAATCTTATATTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCAC
1 -GTAGATCTTAT-CTCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--AC
** * * * * ** * * * *
63409 CAAG-CCTTGTCTCCTTGAGCAACAGCGGAGAATG-TTGAAAATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATTGAAGA-C
*
63452 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* *
63495 G-ACGAATCTTATCTTTCC-AAG-A-TAGTAGGAAGCAGATTTAAGCCAC
1 GTA-G-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--AC
** * * * * * * * *
63541 CAAG-CCTTGTCTCCCTGAGCAGTAGCGGAGAAGGTTGAAAATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
*
63584 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* * *
63627 GGT-GAATCTTATATTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCAC
1 -GTAG-ATCTTAT-CTCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--AC
** * * * * * * * * *
63673 CAAG-CCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAAATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
* *
63716 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* * * *
63759 GACAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCAC
1 G-TAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--AC
** * * * * * * * * *
63805 CAAG-CCTTGTTTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
*
63848 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
63891 AACAAATCAT
Statistics
Matches: 629, Mismatches: 208, Indels: 174
0.62 0.21 0.17
Matches are distributed among these distances:
42 35 0.06
43 65 0.10
44 449 0.71
45 49 0.08
46 30 0.05
47 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (43 bp):
GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
Found at i:63973 original size:44 final size:44
Alignment explanation
Indices: 63921--64579 Score: 259
Period size: 44 Copynumber: 15.2 Consensus size: 44
63911 GATAGTGGGA
*
63921 AGCAGATTAAAGTCGACAATCCTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
63965 AGCGGATTAAAATC-ACAGATCTTGTC-CCTCTGAAGTTGTAG-AG
1 AGCAGATTAAAGTCGACA-ATCTTATCTCC-CTGAAGTTGCAGTGG
*** * * *
64008 AGCAGATCGCA-TC--TAGTCTTGTCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
64049 AGCAGACT-AAGT-AAGCAAGTCTTATC-CTTCTAAAGTTACAGT-G
1 AGCAGATTAAAGTCGA-CAA-TCTTATCTC-CCTGAAGTTGCAGTGG
* * * *
64092 AGGCAGACTGAAGAT-GACAAATCTTATCTTCCTGAAGTTGCAGTGT
1 A-GCAGATTAAAG-TCGAC-AATCTTATCTCCCTGAAGTTGCAGTGG
* *
64138 AGCAGATTAAAG-CTGACAATCCTATCTCCTTGAAGTTGCAGTGG
1 AGCAGATTAAAGTC-GACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * * * *
64182 AGCGGATTAAAAT-TACAGATATTATCTCTCTGAACTTACAGAT--
1 AGCAGATTAAAGTCGACA-ATCTTATCTCCCTGAAGTTGCAG-TGG
*** * * *
64225 AGCAGATCGCA-TC--TAGTCTTATCTCCCTGAAGTTGCGGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
64266 A-CAAGACT-AAGT-AAGCAAGTCTTATC-CTTCTGAAGTTACAGT-G
1 AGC-AGATTAAAGTCGA-CAA-TCTTATCTC-CCTGAAGTTGCAGTGG
* *
64309 AGGCAGACTGAAGAT-GACAAATCTTATCTCCCTGAAGTTGCAGTGG
1 A-GCAGATTAAAG-TCGAC-AATCTTATCTCCCTGAAGTTGCAGTGG
* * * * * *
64355 AGCAGATTAAAGCCGATAATCCTATCTCCTTGACGTTGCAGTAG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
64399 AGCGGATTAAAATC-ACAGATCTTATCTCTCTGAAGTTGTAG-AG
1 AGCAGATTAAAGTCGACA-ATCTTATCTCCCTGAAGTTGCAGTGG
*** * *
64442 AGCAGATCGCA-TC--TAGTCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * ** *
64483 AGCAGACTAAGGAAG-CAAGTCTTATC-CTCCTGAAGTTGTAGT-G
1 AGCAGATTAAAGTCGACAA-TCTTATCTC-CCTGAAGTTGCAGTGG
* * * *
64526 AGGCAGACTGAAGAT-GGCAAGTCTTATCTCCCTAAAGTTGCAGTGG
1 A-GCAGATTAAAG-TCGACAA-TCTTATCTCCCTGAAGTTGCAGTGG
*
64572 AGTAGATT
1 AGCAGATT
64580 GAAGCACTAA
Statistics
Matches: 456, Mismatches: 109, Indels: 99
0.69 0.16 0.15
Matches are distributed among these distances:
39 1 0.00
40 58 0.13
41 25 0.05
42 5 0.01
43 46 0.10
44 208 0.46
45 98 0.21
46 15 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
Found at i:64158 original size:217 final size:217
Alignment explanation
Indices: 63921--64584 Score: 1053
Period size: 217 Copynumber: 3.1 Consensus size: 217
63911 GATAGTGGGA
*
63921 AGCAGATTAAAG-TCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGAT
1 AGCAGATTAAAGCT-GACAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGAT
* * *
63985 CTTGTCCCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTGTCTCCCTGAAGTTGCAGTGGA
65 CTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA
*
64050 GCAGACTAAGTAAGCAAGTCTTATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGACAAATC
130 GCAGACTAAGTAAGCAAGTCTTATCCTTCTGAAGTTACAGTGAGGCAGACTGAAGATGACAAATC
* *
64115 TTATCTTCCTGAAGTTGCAGTGT
195 TTATCTCCCTGAAGTTGCAGTGG
* *
64138 AGCAGATTAAAGCTGACAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATA
1 AGCAGATTAAAGCTGACAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
* ** * *
64203 TTATCTCTCTGAACTTACAGATAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGA-
66 TTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
64267 CAAGACTAAGTAAGCAAGTCTTATCCTTCTGAAGTTACAGTGAGGCAGACTGAAGATGACAAATC
131 C-AGACTAAGTAAGCAAGTCTTATCCTTCTGAAGTTACAGTGAGGCAGACTGAAGATGACAAATC
64332 TTATCTCCCTGAAGTTGCAGTGG
195 TTATCTCCCTGAAGTTGCAGTGG
* * * *
64355 AGCAGATTAAAGCCGATAATCCTATCTCCTTGACGTTGCAGTAGAGCGGATTAAAATCACAGATC
1 AGCAGATTAAAGCTGACAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
64420 TTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
66 TTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
* * ** * *
64485 CAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGATGGCAAGTCT
131 CAGACTAAGTAAGCAAGTCTTATCCTTCTGAAGTTACAGTGAGGCAGACTGAAGATGACAAATCT
*
64550 TATCTCCCTAAAGTTGCAGTGG
196 TATCTCCCTGAAGTTGCAGTGG
* *
64572 AGTAGATTGAAGC
1 AGCAGATTAAAGC
64585 ACTAATTCCT
Statistics
Matches: 410, Mismatches: 34, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
216 1 0.00
217 407 0.99
218 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
AGCAGATTAAAGCTGACAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
TTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
CAGACTAAGTAAGCAAGTCTTATCCTTCTGAAGTTACAGTGAGGCAGACTGAAGATGACAAATCT
TATCTCCCTGAAGTTGCAGTGG
Found at i:64811 original size:19 final size:19
Alignment explanation
Indices: 64787--64916 Score: 224
Period size: 19 Copynumber: 6.7 Consensus size: 19
64777 AATTTTTGAG
64787 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
64806 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
64825 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
64844 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
64865 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
64884 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
64903 GATATGCAATCTTA
1 GATATGCAATCTTA
64917 AAATATATGA
Statistics
Matches: 105, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
19 86 0.82
21 19 0.18
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:64854 original size:59 final size:57
Alignment explanation
Indices: 64787--64916 Score: 224
Period size: 59 Copynumber: 2.2 Consensus size: 57
64777 AATTTTTGAG
*
64787 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATACAATCTTAGATAT
*
64844 GATATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATACAATCTTAGATAT
64903 GATATGCAATCTTA
1 GATATGCAATCTTA
64917 AAATATATGA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
57 14 0.20
59 55 0.80
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATACAATCTTAGATAT
Found at i:65257 original size:13 final size:13
Alignment explanation
Indices: 65241--65266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
65231 TAATTAAGTT
65241 TTTTTATTTTTTA
1 TTTTTATTTTTTA
65254 TTTTTATTTTTTA
1 TTTTTATTTTTTA
65267 CCCTTTTATT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:65709 original size:25 final size:26
Alignment explanation
Indices: 65666--65715 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
65656 TATGTACATG
65666 TATATTTTTTTAAACGAATATTTTCC
1 TATATTTTTTTAAACGAATATTTTCC
*
65692 TATA-TTTTTTAAATGAATATTTTC
1 TATATTTTTTTAAACGAATATTTTC
65716 ATATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (26 bp):
TATATTTTTTTAAACGAATATTTTCC
Found at i:66499 original size:98 final size:98
Alignment explanation
Indices: 66374--66570 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
66364 TAAAAAATAA
* *
66374 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTATGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTTTAAAGGAATCATGCCCTAACGTATTGGGTGTGATTTC
66439 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* * *
66472 TAAATGAAATATTCCGAGTTTGAGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTTTAAAGGAATCATGCCCTAACGTATTGGGTGTGATTTC
*
66537 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66570 T
1 T
66571 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTTTAAAGGAATCATGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Done.