Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold640
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: 76329
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:443 original size:3 final size:3
Alignment explanation
Indices: 435--464 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
425 ATGTAAATTT
435 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
465 GTTCCAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:454 original size:14 final size:14
Alignment explanation
Indices: 435--461 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
425 ATGTAAATTT
435 TTATTATTATTATA
1 TTATTATTATTATA
449 TTATTATTATTAT
1 TTATTATTATTAT
462 TATGTTCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:1269 original size:22 final size:22
Alignment explanation
Indices: 1243--1309 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 22
1233 TACATTTAAT
1243 TTATTAAAATAAAATAAAAAAA
1 TTATTAAAATAAAATAAAAAAA
**
1265 TTATT-TTATAAAA-ATAAAAAA
1 TTATTAAAATAAAATA-AAAAAA
*
1286 --ATTAAAATAAAATAAAATAA
1 TTATTAAAATAAAATAAAAAAA
1306 TTAT
1 TTAT
1310 AACAGTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
19 3 0.09
20 12 0.34
21 13 0.37
22 7 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TTATTAAAATAAAATAAAAAAA
Found at i:1297 original size:19 final size:19
Alignment explanation
Indices: 1245--1308 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
1235 CATTTAATTT
1245 ATTAAAATAAAATAAAAAA
1 ATTAAAATAAAATAAAAAA
**
1264 ATTATTTTATAAAAATAAAAAA
1 ATTA--AAAT-AAAATAAAAAA
*
1286 ATTAAAATAAAATAAAATA
1 ATTAAAATAAAATAAAAAA
1305 ATTA
1 ATTA
1309 TAACAGTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 18 0.49
20 2 0.05
21 2 0.05
22 15 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTAAAATAAAATAAAAAA
Found at i:2776 original size:15 final size:15
Alignment explanation
Indices: 2751--2809 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
2741 AATTAAATAT
2751 ATTAA-TAATTTAAA
1 ATTAATTAATTTAAA
* *
2765 GTTAATTAATTTAAC
1 ATTAATTAATTTAAA
* *
2780 TTTAAAATAA-TTAAA
1 ATT-AATTAATTTAAA
*
2795 ATTAATAAATTTAAA
1 ATTAATTAATTTAAA
2810 TGATAAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 8 0.24
15 21 0.62
16 5 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
ATTAATTAATTTAAA
Found at i:2869 original size:15 final size:15
Alignment explanation
Indices: 2849--2899 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
2839 AATTTAAATA
*
2849 TTAAATTTGATTAAT
1 TTAAATTTAATTAAT
*
2864 TTAAATTTAAAATAAT
1 TTAAATTT-AATTAAT
*
2880 TAAAATTTAATTAAT
1 TTAAATTTAATTAAT
2895 TTAAA
1 TTAAA
2900 CATTAAATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TTAAATTTAATTAAT
Found at i:2898 original size:16 final size:16
Alignment explanation
Indices: 2851--2899 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2841 TTTAAATATT
*
2851 AAATTTGATTAATTT-
1 AAATTTAATTAATTTA
*
2866 AAATTTAAAATAA-TTA
1 AAATTT-AATTAATTTA
2882 AAATTTAATTAATTTA
1 AAATTTAATTAATTTA
2898 AA
1 AA
2900 CATTAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATTTAATTAATTTA
Found at i:2942 original size:89 final size:87
Alignment explanation
Indices: 2757--2958 Score: 205
Period size: 89 Copynumber: 2.3 Consensus size: 87
2747 ATATATTAAT
* * * * *
2757 AATTTAAAGTTAATTAATTTAACTTTAAAATAATTAAAATTAATAAATTTAAATGATAAATTTAC
1 AATTTAAA-TTTATTAATTTAAATTTAAAATAATTAAAATTAATAAATTTAAATCATAAATTCAA
*
2822 TTGATCATAAATAGATTAATTTA
65 TTCATCATAAATAGATTAATTTA
*
2845 AATATTAAATTTGATTAATTTAAATTTAAAATAATTAAAATTTAATTAATTTAAA-CATTAAA-T
1 AAT-TTAAATTT-ATTAATTTAAATTTAAAATAATTAAAA-TTAATAAATTTAAATCA-TAAATT
* * *
2908 CAATTCAT-TTAAATCTGATATTATTTA
62 CAATTCATCATAAAT-AGAT-TAATTTA
2935 AATTTAAAATATT-TTAATTTAAAT
1 AATTT-AAAT-TTATTAATTTAAAT
2959 AAATTTTATT
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
88 10 0.10
89 54 0.56
90 30 0.31
91 2 0.02
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (87 bp):
AATTTAAATTTATTAATTTAAATTTAAAATAATTAAAATTAATAAATTTAAATCATAAATTCAAT
TCATCATAAATAGATTAATTTA
Found at i:2953 original size:15 final size:16
Alignment explanation
Indices: 2929--2970 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2919 AATCTGATAT
*
2929 TATTTAAATTTAAA-A
1 TATTTTAATTTAAATA
2944 TATTTTAATTTAAATA
1 TATTTTAATTTAAATA
*
2960 AATTTT-ATTTA
1 TATTTTAATTTA
2971 TCTAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTAATTTAAATA
Found at i:3510 original size:28 final size:28
Alignment explanation
Indices: 3459--3538 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 28
3449 TTAATATAAA
* * *
3459 AATATTTTTTTAATATTATAAAATTT-T
1 AATATTTTTTAAATATAATTAAATTTAT
3486 AATATTTTTTAAATATAATTTAAATTTAT
1 AATATTTTTTAAATATAA-TTAAATTTAT
** *
3515 AA-ATTAATTAAATTTAAATTAAAT
1 AATATTTTTTAAATAT-AATTAAAT
3539 AATAAATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 16 0.36
28 23 0.52
29 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AATATTTTTTAAATATAATTAAATTTAT
Found at i:3513 original size:17 final size:17
Alignment explanation
Indices: 3493--3533 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
3483 TTTAATATTT
3493 TTTAAATA-TAATTTAAA
1 TTTAAATATTAA-TTAAA
3510 TTTATAA-ATTAATTAAA
1 TTTA-AATATTAATTAAA
3527 TTTAAAT
1 TTTAAAT
3534 TAAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.10
17 14 0.67
18 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAATATTAATTAAA
Found at i:3546 original size:23 final size:23
Alignment explanation
Indices: 3502--3546 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3492 TTTTAAATAT
* *
3502 AATTTAAATTTATAAATTAATTA
1 AATTTAAATTAATAAATAAATTA
3525 AATTTAAATTAA-ATAATAAATT
1 AATTTAAATTAATA-AATAAATT
3547 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTAAATTAATAAATAAATTA
Found at i:3549 original size:19 final size:16
Alignment explanation
Indices: 3492--3551 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 16
3482 TTTTAATATT
3492 TTTTAAATATAATTTAAA
1 TTTTAAAT-TAA-TTAAA
3510 TTTATAAATTAATTAAA
1 TTT-TAAATTAATTAAA
3527 -TTTAAATTAAATAATAAA
1 TTTTAAATT-AAT--TAAA
3545 TTTTAAA
1 TTTTAAA
3552 AAATTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.16
16 5 0.14
17 5 0.14
18 10 0.27
19 11 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAATTAATTAAA
Found at i:4229 original size:40 final size:40
Alignment explanation
Indices: 4168--4244 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
4158 TTTGGTGATT
* *
4168 AAGATAAGTTATACTTAAAAAATTTAAAATTTTATAAACA
1 AAGATAAATAATACTTAAAAAATTTAAAATTTTATAAACA
*
4208 AAGATAAATAATACTCT-AAAAATTTAAATTTTTATAA
1 AAGATAAATAATACT-TAAAAAATTTAAAATTTTATAA
4245 TCAATCCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (40 bp):
AAGATAAATAATACTTAAAAAATTTAAAATTTTATAAACA
Found at i:4450 original size:73 final size:72
Alignment explanation
Indices: 4187--4866 Score: 575
Period size: 73 Copynumber: 9.5 Consensus size: 72
4177 TATACTTAAA
* * * * * * * * **
4187 AAATTTAAAATTTTATAAACAAAGATAAATAATACTC-TAAAAATTTAAATTTTTATAATCAATC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACACTTAAAAATTTAAACTCATATAATCAA-C
4251 CAAAAAAT
65 CAAAAAAT
* * * * ** *
4259 AAATTTAAATTTTTACAAATAAAAATAAATTATACAATTAAAAATTCAAACTTGTATATTCATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACACTTAAAAATTTAAACTCATATAATCA-A-
4324 CTCAAAAAAT
64 C-CAAAAAAT
* * * * * *
4334 ACATTTAAATTTCTATAAATAAAAATAAATTATACTA-TCAAAAATTTAAACTTACATAATCATA
1 AAATTTAAACTTCTACAAATAAAAATAAATTATAC-ACTTAAAAATTTAAACTCATATAATCA-A
4398 TCCAAAAAAT
64 -CCAAAAAAT
* * *
4408 ACATTTAAACTTCCAC-AATAAAAATAAATTATACACTAAAAAATTTAAACTCATATAATCATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACACTTAAAAATTTAAACTCATATAATCA-AC
* *
4472 CTAAAAAC
65 CAAAAAAT
* * *
4480 AAATTTAAACTTTTACAAATAAAAATAAATAATA-TCTTAAAAATTTAAACTCATATAATCAACC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACACTTAAAAATTTAAACTCATATAATCAACC
4544 -AAAAAT
66 AAAAAAT
* * * ** *
4550 AAGTTTTAAACTTCTACAAATAAAGATAAATAATA-TTTTAAAAATTTAAACTCGTATAATCAAA
1 AA-ATTTAAACTTCTACAAATAAAAATAAATTATACACTTAAAAATTTAAACTCATATAATC-AA
*
4614 ACAAAAAAT
64 CCAAAAAAT
* * * *
4623 AAATTTAAACTTTTACATATAAAAATAAATTACACTA-TTAAAAATTTAAACTCGTA-AAT--AC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATAC-ACTTAAAAATTTAAACTCATATAATCAAC
*
4684 CTAAAAAT
65 CAAAAAAT
* * * * * ** *
4692 ATACTTAAAATTCTACAAATCATAATAAATTATA-GTTTAAAAATTTAAACTCGA-ATAATTAA-
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACACTTAAAAATTTAAACTC-ATATAATCAAC
*
4754 -ATAAAAT
65 CAAAAAAT
* * *
4761 AAATTTAAACTTCTACAAAT-AAAA-AAATTATAC-TTTCAAAATTTAAACTTATATAATCATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACACTTAAAAATTTAAACTCATATAATCA-AC
* * *
4823 CTTACAAAC
65 C-AAAAAAT
* *
4832 AAATTTAAACTCCTACAAATAAAAATAAATAATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATAC
4867 TTTTAATAAA
Statistics
Matches: 508, Mismatches: 76, Indels: 47
0.81 0.12 0.07
Matches are distributed among these distances:
66 1 0.00
67 29 0.06
68 21 0.04
69 59 0.12
70 7 0.01
71 79 0.16
72 112 0.22
73 113 0.22
74 23 0.05
75 63 0.12
76 1 0.00
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (72 bp):
AAATTTAAACTTCTACAAATAAAAATAAATTATACACTTAAAAATTTAAACTCATATAATCAACC
AAAAAAT
Found at i:4922 original size:38 final size:39
Alignment explanation
Indices: 4845--4923 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 39
4835 TTTAAACTCC
* *
4845 TACAAATAAAAATAAATAATACTTTTAATAAAATTAATT
1 TACAAATAAAAATAAATAATACTTTAAATAAAATAAATT
*
4884 TACAAATAAAAA-AAATCATA-TATTAAATAAAATAAATT
1 TACAAATAAAAATAAATAATACT-TTAAATAAAATAAATT
4922 TA
1 TA
4924 AATTTTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 1 0.03
38 23 0.64
39 12 0.33
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (39 bp):
TACAAATAAAAATAAATAATACTTTAAATAAAATAAATT
Found at i:5005 original size:13 final size:13
Alignment explanation
Indices: 4987--5020 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
4977 AATAACTAAA
4987 AAAATTACTTAAT
1 AAAATTACTTAAT
5000 AAAATTACTTAAT
1 AAAATTACTTAAT
5013 AAATATTA
1 AAA-ATTA
5021 AAACTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTACTTAAT
Found at i:5064 original size:19 final size:19
Alignment explanation
Indices: 5037--5082 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
5027 AAACTTTCAT
* *
5037 AAAATTCTCTTTACTCAAG
1 AAAACTCTCTTTACTAAAG
5056 AAAACTCTCTTTACTAAAG
1 AAAACTCTCTTTACTAAAG
5075 AAAACTCT
1 AAAACTCT
5083 ACGAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAACTCTCTTTACTAAAG
Found at i:7515 original size:18 final size:18
Alignment explanation
Indices: 7475--7521 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
7465 ACATCCATAT
* *
7475 TTTAATTATTTTACTTATA
1 TTTAATTA-TATAATTATA
7494 -TTAATTATATAATTATA
1 TTTAATTATATAATTATA
*
7511 TTTAATAATAT
1 TTTAATTATAT
7522 CAAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAATTATATAATTATA
Found at i:7529 original size:27 final size:26
Alignment explanation
Indices: 7477--7529 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
7467 ATCCATATTT
* * * *
7477 TAATTATTTTACTTATATTAATTATA
1 TAATTATTTTAATAATATCAAATATA
7503 TAATTATATTTAATAATATCAAATATA
1 TAATTAT-TTTAATAATATCAAATATA
7530 ATTTTATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATTATTTTAATAATATCAAATATA
Found at i:8490 original size:16 final size:16
Alignment explanation
Indices: 8436--8517 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 16
8426 TCAGATTGAG
8436 TAAATTTAAATT-TTT
1 TAAATTTAAATTATTT
*
8451 AAAATTTTAAGAATT-TTT
1 TAAA-TTT-A-AATTATTT
*
8469 TTAATTTAAATTATTT
1 TAAATTTAAATTATTT
* *
8485 TAAATTTAAATCACTT
1 TAAATTTAAATTATTT
* *
8501 CAATTTTAAATTATTT
1 TAAATTTAAATTATTT
8517 T
1 T
8518 GAGTTGAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
15 7 0.13
16 32 0.62
17 4 0.08
18 9 0.17
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (16 bp):
TAAATTTAAATTATTT
Found at i:9789 original size:31 final size:31
Alignment explanation
Indices: 9753--9830 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
9743 TTATTTACAC
** *
9753 TTAAATAAGTTTTTTTTCATTAAAATTATAT
1 TTAAATAAAATTTTTATCATTAAAATTATAT
* *
9784 TTAAATAAAATTTTTATCATTTAATTTATAT
1 TTAAATAAAATTTTTATCATTAAAATTATAT
*
9815 CTAAATAAAATTTTTA
1 TTAAATAAAATTTTTA
9831 ATTTATATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (31 bp):
TTAAATAAAATTTTTATCATTAAAATTATAT
Found at i:9831 original size:24 final size:24
Alignment explanation
Indices: 9803--9848 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
9793 ATTTTTATCA
9803 TTTAATTTATATCTAAATAAAATT
1 TTTAATTTATATCTAAATAAAATT
*
9827 TTTAATTTATATTTAAATAAAA
1 TTTAATTTATATCTAAATAAAA
9849 CTTTAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAATTTATATCTAAATAAAATT
Found at i:9880 original size:55 final size:56
Alignment explanation
Indices: 9778--9886 Score: 134
Period size: 55 Copynumber: 2.0 Consensus size: 56
9768 TTCATTAAAA
* *
9778 TTATATTTAAATAAAATTTTTATCATTTAATTTATATCTAAATAAAATT-TTTAAT
1 TTATATTTAAATAAAATTTATATCAATTAATTTATATCTAAATAAAATTATTTAAT
* * *
9833 TTATATTTAAATAAAACTTTAATAT-AATTAATTTTTATTTGAA-AAAATTATTTA
1 TTATATTTAAATAAAA-TTT-ATATCAATTAATTTATATCTAAATAAAATTATTTA
9887 TTAGATAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 22 0.48
56 21 0.46
57 3 0.07
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (56 bp):
TTATATTTAAATAAAATTTATATCAATTAATTTATATCTAAATAAAATTATTTAAT
Found at i:10277 original size:28 final size:27
Alignment explanation
Indices: 10243--10315 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
10233 GATAATAATC
10243 TTTATTTAAATATAAAT-AAATGAATAAA
1 TTTATTTAAATATAAATAAAAT--ATAAA
* *
10271 TTTATTTTAATAT-AATAAAATATATA
1 TTTATTTAAATATAAATAAAATATAAA
* *
10297 TTTTTTTAAAAATAAATAA
1 TTTATTTAAATATAAATAA
10316 TTCTGTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 14 0.37
27 8 0.21
28 16 0.42
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
TTTATTTAAATATAAATAAAATATAAA
Found at i:10313 original size:22 final size:24
Alignment explanation
Indices: 10254--10314 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
10244 TTATTTAAAT
10254 ATAAATAAATGAATAAATTTATTTTA
1 ATAAATAAAT--ATAAATTTATTTTA
*
10280 ATATAATAAAATATATATTT-TTTTA
1 ATA-AAT-AAATATAAATTTATTTTA
10305 A-AAATAAATA
1 ATAAATAAATA
10315 ATTCTGTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 5 0.16
23 3 0.09
24 1 0.03
25 6 0.19
26 10 0.31
27 3 0.09
28 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAAATAAATATAAATTTATTTTA
Found at i:10556 original size:23 final size:24
Alignment explanation
Indices: 10528--10575 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
10518 TAAAGTTTAT
* *
10528 ATATATATATAATTTTTAAA-AAA
1 ATATATATAAAAATTTTAAATAAA
*
10551 ATATATTTAAAAATTTTAAATAAA
1 ATATATATAAAAATTTTAAATAAA
10575 A
1 A
10576 ATAAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATATATAAAAATTTTAAATAAA
Found at i:13203 original size:2 final size:2
Alignment explanation
Indices: 13198--13222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13188 TCTCTCTCTC
13198 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13223 TCTTCTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15322 original size:6 final size:6
Alignment explanation
Indices: 15311--15336 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
15301 CTTCAATTTA
15311 TCTGAC TCTGAC TCTGAC TCTGAC TC
1 TCTGAC TCTGAC TCTGAC TCTGAC TC
15337 ATTGGATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.15, T:0.35
Consensus pattern (6 bp):
TCTGAC
Found at i:16819 original size:2 final size:2
Alignment explanation
Indices: 16814--16858 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16804 TAAAGAGAGA
16814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16856 AT A
1 AT A
16859 AACCCAGATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21656 original size:2 final size:2
Alignment explanation
Indices: 21651--21688 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
21641 GGGAAGTGTG
*
21651 TA TA TA TA TGA TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
21689 TTGATTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30872 original size:52 final size:52
Alignment explanation
Indices: 30787--30911 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
30777 ATATGAAAAG
* * *
30787 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
30839 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
30891 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
30912 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:30924 original size:52 final size:51
Alignment explanation
Indices: 30787--30931 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
30777 ATATGAAAAG
* *
30787 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
30839 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
30891 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
30932 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:30938 original size:13 final size:13
Alignment explanation
Indices: 30920--30944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30910 CAAAGATCAG
30920 TGTATCGATACAA
1 TGTATCGATACAA
30933 TGTATCGATACA
1 TGTATCGATACA
30945 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31026 original size:13 final size:13
Alignment explanation
Indices: 31008--31032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30998 ACAAAAAATA
31008 TGTATCGATACAT
1 TGTATCGATACAT
31021 TGTATCGATACA
1 TGTATCGATACA
31033 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:31028 original size:32 final size:33
Alignment explanation
Indices: 30987--31052 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
30977 AGTAGCTTAA
30987 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
31019 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
31052 A
1 A
31053 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:39667 original size:19 final size:19
Alignment explanation
Indices: 39625--39667 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39615 CAGTTAGATA
*
39625 CATTTAAATAATTTTCTAT
1 CATTTAAATAATTTTATAT
*
39644 GATTTAAA-AATTATTATAT
1 CATTTAAATAATT-TTATAT
39663 CATTT
1 CATTT
39668 CATGTATTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (19 bp):
CATTTAAATAATTTTATAT
Found at i:40601 original size:67 final size:68
Alignment explanation
Indices: 40475--40601 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 68
40465 ATTGGGTTTT
* * * *
40475 AAAGATGATGAAGGTGCCAATATGTTGATTCAAGGCCAGTAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGTTGATGCAAGGCCAATAATATTGGACTTAAAGATGAAGATG
40540 AGA
66 AGA
* * *
40543 AAAG-TGATAAAGATGCTAATATGTTGATGCACGGCCAATGATATTAGG-CTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGTTGATGCAAGGCCAATAATATT-GGACTTAAAGATGA
40602 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 45 0.88
68 6 0.12
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.26
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGTTGATGCAAGGCCAATAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:40822 original size:49 final size:49
Alignment explanation
Indices: 40614--41229 Score: 819
Period size: 49 Copynumber: 12.7 Consensus size: 49
40604 AAAAGGATGT
* *
40614 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
40666 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* ** *
40709 CAATGTGCTGATTCAAAGCCAGCTACGTTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
40757 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
40806 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
40855 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
40904 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
40953 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
41002 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
41054 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
41097 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
41145 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
41194 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA
41230 GAAGGGTTGC
Statistics
Matches: 495, Mismatches: 52, Indels: 37
0.85 0.09 0.06
Matches are distributed among these distances:
43 78 0.16
48 92 0.19
49 253 0.51
50 1 0.00
52 71 0.14
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:41271 original size:33 final size:33
Alignment explanation
Indices: 41229--41466 Score: 340
Period size: 33 Copynumber: 7.2 Consensus size: 33
41219 TATTGGGCTT
*
41229 AGAAGGGTTGCCACCGACTTGTGTGGCCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
41262 AGAATGGTTGCCACCAACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
41294 GGAAGGGTTGCCACCGACTTGTGTAGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
41326 GGAAGGGATTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
41360 AGGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 A-GAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
41393 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
* *
41427 AGAAGGTTTGCCACCGATTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
41460 A-AAGGGT
1 AGAAGGGT
41467 GAAAGATGCC
Statistics
Matches: 186, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
32 44 0.24
33 104 0.56
34 35 0.19
35 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.29
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:41306 original size:65 final size:67
Alignment explanation
Indices: 41230--41465 Score: 347
Period size: 67 Copynumber: 3.6 Consensus size: 67
41220 ATTGGGCTTA
* *
41230 GAAGGGTTGCCACCGACTTGTGTGGCCTTTAGAGAATGG-TTGCCACCAACTTGTGTGGGCTTT-
1 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGATTGCCACCAACTTGTGTGGGCTTTA
41293 GG
66 GG
* *
41295 GAAGGGTTGCCACCGACTTGTGTAGGCTTT-GGGAAGGGATTGCCACCAACTTGTGTGGGCTTTA
1 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGATTGCCACCAACTTGTGTGGGCTTTA
41359 GAG
66 G-G
* *
41362 GAA-GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTA
1 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGATTGCCACCAACTTGTGTGGGCTTTA
*
41426 GA
66 GG
* *
41428 GAAGGTTTGCCACCGATTTGTGTGGGCTTTAGA-AAGGG
1 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGG
41466 TGAAAGATGC
Statistics
Matches: 155, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
64 6 0.04
65 52 0.34
66 34 0.22
67 63 0.41
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.28
Consensus pattern (67 bp):
GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGATTGCCACCAACTTGTGTGGGCTTTA
GG
Found at i:41510 original size:71 final size:70
Alignment explanation
Indices: 41448--42073 Score: 689
Period size: 71 Copynumber: 9.2 Consensus size: 70
41438 CACCGATTTG
** * **
41448 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAGCAAGGTGCCAC
1 TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGGTGCCAC
41512 GGAGT
66 GGAGT
* * *
41517 TGTGGGCTTTA-AAAGGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCC
1 TGTGGGCTTTAGAAAGGG-AAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAG-GTGCC
41581 ACGGAGT
64 ACGGAGT
*
41588 TGTGGGC-TTAG-AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAAAAAGGTGCCA
1 TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCT-TAAAAAGAAAAAGGTGCCA
41650 CGGAGT
65 CGGAGT
*
41656 TGTGGGCTTT-GAAAAGGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAAAAGTGTGC
1 TGTGGGCTTTAG-AAAGGGAAAAAGAGTGCCACGAAGTTGTGGGC-TTAAAAAGAAAAAG-GTGC
*
41720 CACAGAGT
63 CACGGAGT
* * *
41728 TGTGGGC-TTAG-AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCA
1 TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAG-GTGCCA
41790 CGGAGT
65 CGGAGT
* * *
41796 TGTGGGC-TTAG-AA-GGAAAAA-AGTGCCACGTAGTTGTGGGCTT-TAAAGGAAAAGAGTGCCA
1 TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAG-GTGCCA
*
41856 CGTAGT
65 CGGAGT
* * * *
41862 CGTGGAC-TTA-AAA--G-----G-GTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCA
1 TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGC-TTAAAAAGAAAAAGGTGCCA
*
41914 CGAAGT
65 CGGAGT
*
41920 TGTGGGCTTTA-ACAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAAAAAGGTGCC
1 TGTGGGCTTTAGA-AAGGGAAAAAGAGTGCCACGAAGTTGTGGGCT-TAAAAAGAAAAAGGTGCC
41984 ACGGAGT
64 ACGGAGT
*
41991 TGTGGGCTTT-GAAAAGGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAAAAGTGTGC
1 TGTGGGCTTTAG-AAAGGGAAAAAGAGTGCCACGAAGTTGTGGGC-TTAAAAAGAAAAAG-GTGC
*
42055 CACAGAGT
63 CACGGAGT
42063 TGTGGGCTTTA
1 TGTGGGCTTTA
42074 AAGAAAAAAT
Statistics
Matches: 486, Mismatches: 36, Indels: 66
0.83 0.06 0.11
Matches are distributed among these distances:
58 16 0.03
59 7 0.01
60 20 0.04
61 2 0.00
62 5 0.01
65 1 0.00
66 30 0.06
67 23 0.05
68 121 0.25
69 57 0.12
70 35 0.07
71 126 0.26
72 43 0.09
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (70 bp):
TGTGGGCTTTAGAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGAAAAAGGTGCCAC
GGAGT
Found at i:41578 original size:34 final size:34
Alignment explanation
Indices: 41468--42088 Score: 677
Period size: 34 Copynumber: 18.4 Consensus size: 34
41458 AGAAAGGGTG
* * * *
41468 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAG
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
41501 CAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAA-GG-AA
*
41537 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
41571 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
41605 AAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCT-TAAAAGGAA
41640 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
** *
41676 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
41711 AAAGTGTGCCACAGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
41745 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
41779 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
41813 AAA-AGTGCCACGTAGTTGTGGGCTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * *
41845 AAAGAGTGCCACGTAGTCGTGGACTTAAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
**
41876 ---G-GTGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
41904 GAAG-GTGCCACGAAGTTGTGGGCTTTAACAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAA-AA-GGAA
*
41940 AAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCT-TAAAAGGAA
41975 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
** *
42011 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
42046 AAAGTGTGCCACAGAGTTGTGGGCTTTAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
42079 AAA-A-TGCCAC
1 AAAGAGTGCCAC
42089 TAAGTCGTGG
Statistics
Matches: 517, Mismatches: 44, Indels: 56
0.84 0.07 0.09
Matches are distributed among these distances:
27 20 0.04
28 1 0.00
31 25 0.05
32 7 0.01
33 75 0.15
34 189 0.37
35 81 0.16
36 39 0.08
37 80 0.15
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.19
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:42114 original size:30 final size:30
Alignment explanation
Indices: 42079--42135 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
42069 CTTTAAAGAA
42079 AAAATGCCACTAAGTCGTGGACTTTGAGAC
1 AAAATGCCACTAAGTCGTGGACTTTGAGAC
*
42109 AAAATGCCACTGAGTCGTGGACTTTGA
1 AAAATGCCACTAAGTCGTGGACTTTGA
42136 AAAGGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (30 bp):
AAAATGCCACTAAGTCGTGGACTTTGAGAC
Found at i:50418 original size:52 final size:52
Alignment explanation
Indices: 50333--50457 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
50323 ATATGAAAAG
* * *
50333 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
50385 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
50437 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
50458 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:50470 original size:52 final size:51
Alignment explanation
Indices: 50333--50477 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
50323 ATATGAAAAG
* *
50333 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
50385 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
50437 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
50478 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:50484 original size:13 final size:13
Alignment explanation
Indices: 50466--50490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50456 CAAAGATCAG
50466 TGTATCGATACAA
1 TGTATCGATACAA
50479 TGTATCGATACA
1 TGTATCGATACA
50491 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:50572 original size:13 final size:13
Alignment explanation
Indices: 50554--50578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50544 ACAAAAAATA
50554 TGTATCGATACAT
1 TGTATCGATACAT
50567 TGTATCGATACA
1 TGTATCGATACA
50579 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50574 original size:32 final size:33
Alignment explanation
Indices: 50533--50598 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
50523 AGTAGCTTAA
50533 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
50565 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
50598 A
1 A
50599 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:59223 original size:19 final size:19
Alignment explanation
Indices: 59181--59223 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
59171 CAGTTAGATA
*
59181 CATTTAAATAATTTTCTAT
1 CATTTAAATAATTTTATAT
*
59200 GATTTAAA-AATTATTATAT
1 CATTTAAATAATT-TTATAT
59219 CATTT
1 CATTT
59224 CATGTATTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (19 bp):
CATTTAAATAATTTTATAT
Found at i:60155 original size:67 final size:68
Alignment explanation
Indices: 60029--60155 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 68
60019 ATTGGGTTTT
* * * *
60029 AAAGATGATGAAGGTGCCAATATGTTGATTCAAGGCCAGTAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGTTGATGCAAGGCCAATAATATTGGACTTAAAGATGAAGATG
60094 AGA
66 AGA
* * *
60097 AAAG-TGATAAAGATGCTAATATGTTGATGCACGGCCAATGATATTAGG-CTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGTTGATGCAAGGCCAATAATATT-GGACTTAAAGATGA
60156 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 45 0.88
68 6 0.12
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.26
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGTTGATGCAAGGCCAATAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:60376 original size:49 final size:49
Alignment explanation
Indices: 60168--60783 Score: 819
Period size: 49 Copynumber: 12.7 Consensus size: 49
60158 AAAAGGATGT
* *
60168 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
60220 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* ** *
60263 CAATGTGCTGATTCAAAGCCAGCTACGTTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
60311 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
60360 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
60409 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
60458 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
60507 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
60556 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
60608 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
60651 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
60699 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
60748 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA
60784 GAAGGGTTGC
Statistics
Matches: 495, Mismatches: 52, Indels: 37
0.85 0.09 0.06
Matches are distributed among these distances:
43 78 0.16
48 92 0.19
49 253 0.51
50 1 0.00
52 71 0.14
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:60825 original size:33 final size:33
Alignment explanation
Indices: 60783--61017 Score: 338
Period size: 33 Copynumber: 7.2 Consensus size: 33
60773 TATTGGGCTT
*
60783 AGAAGGGTTGCCACCGACTTGTGTGGCCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
60816 AGAATGGTTGCCACCAACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
60848 -G-AGGGTTGCCACCGACTTGTGTAGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
60878 GGAAGGGATTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
60912 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
60944 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
* *
60978 AGAAGGTTTGCCACCGATTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
61011 A-AAGGGT
1 AGAAGGGT
61018 GAAAGATGCC
Statistics
Matches: 183, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.14
31 2 0.01
32 39 0.21
33 80 0.44
34 36 0.20
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:60890 original size:63 final size:65
Alignment explanation
Indices: 60776--61017 Score: 343
Period size: 63 Copynumber: 3.8 Consensus size: 65
60766 CCAGCTATAT
* *
60776 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTGTGGCCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTG
* *
60839 TGGGCTTT-G-GAGGGTTGCCACCGACTTGTGTAGGCTTT-GGGAAGGGATTGCCACCAACTTGT
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGG-TTGCCACCAACTTGT
60901 G
65 G
* *
60902 TGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGT
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGG-TTGCCACCAACTTGT
60967 G
65 G
* *
60968 TGGGCTTTAGAGAAGGTTTGCCACCGATTTGTGTGGGCTTTAGA-AAGGGT
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
61018 GAAAGATGCC
Statistics
Matches: 160, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
62 6 0.04
63 56 0.35
64 3 0.02
65 28 0.17
66 39 0.24
67 28 0.17
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (65 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTG
Found at i:61129 original size:34 final size:34
Alignment explanation
Indices: 61019--61635 Score: 625
Period size: 34 Copynumber: 18.4 Consensus size: 34
61009 AGAAAGGGTG
* * * *
61019 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAG
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
61052 CAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAA-GG-AA
*
61088 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
61122 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
61156 AAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCT-TAAAAGGAA
*
61191 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
** *
61226 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAG-A
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
61260 AAAGTGTGCCACAGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
61294 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
61328 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
61361 AAA-AGTGCCACGTAGTTGTGGGCTTTTAAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
61394 AAAGAGTG-CACGTAGTCGT-GACTTAAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
**
61423 ---G-GTGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
61451 GAAG-GTGCCCACGGAAGTTGTGGGCTTAACAAGGGAA
1 AAAGAGTG-CCACGG-AGTTGTGGGCTTAA-AA-GGAA
*
61488 AAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCT-TAAAAGGAA
61523 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
** *
61559 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
61594 AAAGTGTGCCACAGAGTTGT-GGCTTTAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
61626 AAA-A-TGCCAC
1 AAAGAGTGCCAC
61636 TAAGTCGTGG
Statistics
Matches: 510, Mismatches: 43, Indels: 65
0.83 0.07 0.11
Matches are distributed among these distances:
25 3 0.01
26 10 0.02
27 6 0.01
30 7 0.01
31 9 0.02
32 33 0.06
33 66 0.13
34 204 0.40
35 63 0.12
36 53 0.10
37 53 0.10
38 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:61166 original size:138 final size:136
Alignment explanation
Indices: 61019--61622 Score: 681
Period size: 138 Copynumber: 4.5 Consensus size: 136
61009 AGAAAGGGTG
* * **
61019 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAGCAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
61083 GGAAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCT
66 GG--AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG-AAAAGAGTGCCACGGAGTTGTGGGCT
61147 TAGAAGGAA
128 TAGAAGGAA
61156 AAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCT-TAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAA
** * *
61221 AGGGAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAAAGTGTGCCACAGAGTTGTGGGCTT
64 AGGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGAGTGCCACGGAGTTGTGGGCTT
61286 AGAAGGAA
129 AGAAGGAA
* * *
61294 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
* * * * * *
61358 -GGAAAA-AGTGCCACGTAGTTGTGGGCTTTTAAAGGAAAAGAGTG-CACGTAGTCGT-GACTT-
65 GGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGAGTGCCACGGAGTTGTGGGCTTA
61418 ------A
130 GAAGGAA
* *
61419 AAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCCACGGAAGTTGTGGGC-TTAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAAGAAAAAGGTG-CCACGG-AGTTGTGGGCTTTAA
*
61480 CAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAAAA-AGGTGCCACGGAGTTGTGG
63 -AAGGG-AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGA-GTGCCACGGAGTTGTGG
*
61544 GCTTTGAAAAGGGAA
125 GC-TT-AGAA-GGAA
** *
61559 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGT-GGCTTTAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
61623 GAAAAAATGC
Statistics
Matches: 398, Mismatches: 39, Indels: 56
0.81 0.08 0.11
Matches are distributed among these distances:
122 3 0.01
123 9 0.02
124 13 0.03
125 26 0.07
126 7 0.02
127 5 0.01
128 32 0.08
129 9 0.02
130 2 0.01
131 2 0.01
132 4 0.01
133 8 0.02
134 33 0.08
135 6 0.02
136 3 0.01
137 18 0.05
138 117 0.29
139 39 0.10
140 37 0.09
141 4 0.01
142 10 0.03
143 8 0.02
144 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (136 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
GGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAGAGTGCCACGGAGTTGTGGGCTTAG
AAGGAA
Found at i:61577 original size:71 final size:71
Alignment explanation
Indices: 61418--61621 Score: 276
Period size: 71 Copynumber: 2.9 Consensus size: 71
61408 GTCGTGACTT
* *
61418 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCCACGGAAGTTGTGGGC-TTA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTG-CCACGG-AGTTGTGGGCTTTA
61479 ACAAGGGA
64 ACAAGGGA
*
61487 AAAAGAGTGCCACGGAGTTGTGGGCTGTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AA
61552 -AAGGGA
65 CAAGGGA
** *
61558 AAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGT-GGCTTTAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
61622 AGAAAAAATG
Statistics
Matches: 122, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
69 31 0.25
70 12 0.10
71 57 0.47
72 22 0.18
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (71 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAC
AAGGGA
Found at i:69957 original size:52 final size:52
Alignment explanation
Indices: 69872--69996 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
69862 ATATGAAAAG
* * *
69872 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
69924 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
69976 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
69997 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:70009 original size:52 final size:51
Alignment explanation
Indices: 69872--70016 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
69862 ATATGAAAAG
* *
69872 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
69924 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
69976 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
70017 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:70023 original size:13 final size:13
Alignment explanation
Indices: 70005--70029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69995 CAAAGATCAG
70005 TGTATCGATACAA
1 TGTATCGATACAA
70018 TGTATCGATACA
1 TGTATCGATACA
70030 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:70112 original size:13 final size:13
Alignment explanation
Indices: 70094--70118 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70084 ACAAAAAATA
70094 TGTATCGATACAT
1 TGTATCGATACAT
70107 TGTATCGATACA
1 TGTATCGATACA
70119 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:70114 original size:32 final size:33
Alignment explanation
Indices: 70073--70138 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
70063 GTAGCTTTAA
70073 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
70105 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
70138 A
1 A
70139 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Done.