Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold406
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: 305902
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 17867 characters in sequence are not A, C, G, or T
Found at i:2501 original size:42 final size:43
Alignment explanation
Indices: 2404--2510 Score: 155
Period size: 42 Copynumber: 2.5 Consensus size: 43
2394 AAAAATGCTG
* *
2404 CTAAAGAACATGACCTTTAGCGGGACTTTTGACAAAAACGCCG
1 CTAAAGAACATGACCTTTAGCGGCACTTTTGACAAAAACGCCA
* *
2447 CTAAAGAGCATGACCTTTAGCGGCA-TTTT-ACCACAAACGCCA
1 CTAAAGAACATGACCTTTAGCGGCACTTTTGA-CAAAAACGCCA
2489 CTAAAGAACATGACCTTTAGCG
1 CTAAAGAACATGACCTTTAGCG
2511 ACGTTTTTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.02
42 34 0.59
43 23 0.40
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
CTAAAGAACATGACCTTTAGCGGCACTTTTGACAAAAACGCCA
Found at i:2985 original size:43 final size:43
Alignment explanation
Indices: 2911--3001 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
2901 ACATATGCAA
* * *
2911 GGTAATAAAACATACAAATGCATTTTCTAATCAAGTAAATCTT
1 GGTAATAAAACATACAAATACATTTACTAATCAAGGAAATCTT
* *
2954 GGTAATAAAAGATA-TAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAACATACAAATACATTTAC-TAATCAAGGAAATCTT
2997 -GTAAT
1 GGTAAT
3002 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 14 0.33
43 28 0.67
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (43 bp):
GGTAATAAAACATACAAATACATTTACTAATCAAGGAAATCTT
Found at i:4098 original size:19 final size:18
Alignment explanation
Indices: 4074--4110 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
4064 TCATTTCAAC
4074 TTATTTCAATATTGTTAAT
1 TTATTTCAATATT-TTAAT
*
4093 TTATTTTAATATTTTAAT
1 TTATTTCAATATTTTAAT
4111 ATATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTTCAATATTTTAAT
Found at i:5363 original size:40 final size:40
Alignment explanation
Indices: 5260--5353 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
5250 TTTATTGCGA
* *
5260 CGCTTTTTTAAAAACGCCGCTAAAAATAGAGCATTCACAG
1 CGCTTTTTCAAAAACGCCGCTAAAAATAGAGAATTCACAG
*
5300 CGCTTCTTCAAAAACGCCGCTAAAAATAGAGAATT-AGC-G
1 CGCTTTTTCAAAAACGCCGCTAAAAATAGAGAATTCA-CAG
5339 TCGCTTTTTCAAAAA
1 -CGCTTTTTCAAAAA
5354 TGTTGCTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 2 0.04
40 46 0.96
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (40 bp):
CGCTTTTTCAAAAACGCCGCTAAAAATAGAGAATTCACAG
Found at i:10421 original size:22 final size:21
Alignment explanation
Indices: 10395--10449 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
10385 TTTAAATCCA
10395 AAAAATAAAGAGACTAAATTCTT
1 AAAAATAAAGAGACTAAA-T-TT
*
10418 AAAAATAAATAGAGATTAAATTT
1 AAAAAT-AA-AGAGACTAAATTT
10441 AAAATATAA
1 AAAA-ATAA
10450 GAAGAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 14 0.50
24 5 0.18
25 9 0.32
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAAATAAAGAGACTAAATTT
Found at i:15359 original size:107 final size:107
Alignment explanation
Indices: 15173--15384 Score: 343
Period size: 107 Copynumber: 2.0 Consensus size: 107
15163 AAAGGAAGGT
* *
15173 TTTTCTAAATAAGGCAATATTTCATGTTTGGAAAATCGAGAAAATGTGCCCTAACGCGCTGGGTT
1 TTTTCTAAATAAGGCAATATTTCACGTTTGGAAAATCGAGAAAACGTGCCCTAACGCGCTGGGTT
*
15238 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAGA
66 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAAGA
* ** * *
15280 TTTTCTAAATAAGGCGATATTTTGCGTTTGGAAACTCGAGAAAACGTGCCCTAACGTGCTGGGTT
1 TTTTCTAAATAAGGCAATATTTCACGTTTGGAAAATCGAGAAAACGTGCCCTAACGCGCTGGGTT
*
15345 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTCTTAA
66 TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAA
15385 AACTTCGAAG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 96 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (107 bp):
TTTTCTAAATAAGGCAATATTTCACGTTTGGAAAATCGAGAAAACGTGCCCTAACGCGCTGGGTT
TCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTTAAGA
Found at i:18180 original size:22 final size:22
Alignment explanation
Indices: 18152--18196 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
18142 CAAAAAATCG
18152 TAATTTGTAAGTTTTTCGAGCA
1 TAATTTGTAAGTTTTTCGAGCA
18174 TAATTTGTAAGTTTTTCGAGCA
1 TAATTTGTAAGTTTTTCGAGCA
18196 T
1 T
18197 TCTAAGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.47
Consensus pattern (22 bp):
TAATTTGTAAGTTTTTCGAGCA
Found at i:19776 original size:18 final size:19
Alignment explanation
Indices: 19739--19777 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
19729 TTTTTTAGAA
*
19739 TTTTTTAAATATTTATATTT
1 TTTTTTAAATA-TTAAATTT
19759 TTTTTTAAATA-TAAATTT
1 TTTTTTAAATATTAAATTT
19777 T
1 T
19778 GAAATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTAAATATTAAATTT
Found at i:19809 original size:18 final size:20
Alignment explanation
Indices: 19773--19818 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
19763 TTAAATATAA
* *
19773 ATTTTGAAATTTTATAAA-T
1 ATTTTGAAAATTTAAAAATT
19792 ATTTT-AAAATTTAAAAATT
1 ATTTTGAAAATTTAAAAATT
19811 ATTTTGAA
1 ATTTTGAA
19819 TTTCTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.43
19 11 0.48
20 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
ATTTTGAAAATTTAAAAATT
Found at i:22569 original size:13 final size:15
Alignment explanation
Indices: 22551--22582 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22541 TATATGAAAT
22551 AATGATT-TT-ATGA
1 AATGATTATTGATGA
22564 AATGATTATTGATGA
1 AATGATTATTGATGA
22579 AATG
1 AATG
22583 CATGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
AATGATTATTGATGA
Found at i:23487 original size:38 final size:38
Alignment explanation
Indices: 23445--23522 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
23435 AAAATTTCAA
*
23445 TAAAACTTGCAGCGGACAGCATTATAGCAAATTGACCT
1 TAAAACTTGCAGCGGAAAGCATTATAGCAAATTGACCT
*
23483 TAAAACTTGTAGCGGAAAGCATTATAGCAAATTGACCT
1 TAAAACTTGCAGCGGAAAGCATTATAGCAAATTGACCT
23521 TA
1 TA
23523 TAATTGTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (38 bp):
TAAAACTTGCAGCGGAAAGCATTATAGCAAATTGACCT
Found at i:28291 original size:13 final size:13
Alignment explanation
Indices: 28255--28320 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
28245 AGTTCTTCAT
28255 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
28268 TGCTGTAGAAAAG
1 TGCTTTTGAAAAG
*
28281 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
28294 TGTTTTTGAGAAG
1 TGCTTTTGAAAAG
28307 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
28320 T
1 T
28321 TTGGTTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:29782 original size:30 final size:30
Alignment explanation
Indices: 29748--29807 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
29738 AATATATAAC
*
29748 TTATTTTTTAAAA-TTTAAAATTATTTATTA
1 TTATTTTTTAAAACTTTAAAA-TATTAATTA
29778 TTATTTTTTAAAACTTTAAAATATTAATTA
1 TTATTTTTTAAAACTTTAAAATATTAATTA
29808 AATGCTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATTTTTTAAAACTTTAAAATATTAATTA
Found at i:36304 original size:16 final size:16
Alignment explanation
Indices: 36272--36317 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
36262 AAATGAAAAT
*
36272 TTTAAAGAAACT-AAA
1 TTTAAAAAAACTGAAA
*
36287 ATTAAATAAAACTGAAA
1 TTTAAA-AAAACTGAAA
36304 TTTAAAAAAA-TGAA
1 TTTAAAAAAACTGAA
36318 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 9 0.35
16 9 0.35
17 8 0.31
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (16 bp):
TTTAAAAAAACTGAAA
Found at i:46112 original size:43 final size:43
Alignment explanation
Indices: 46044--46169 Score: 157
Period size: 43 Copynumber: 2.9 Consensus size: 43
46034 GGATTTTCGA
* *
46044 TATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAC
1 TATGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCATCG-C
* *
46088 T-TGTGTTTACATGTAAGACGACGTCTGGGACAGTT-GCATCGG
1 TATGTGTTTACATGTAAGACCACGTCTGGGAC-GTTGGCATCGC
* * *
46130 TATGTGATTACATGTAAGACCATGTCTAGGACGTTGGCAT
1 TATGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCAT
46170 TGTGCGAGCC
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
42 4 0.06
43 63 0.89
44 4 0.06
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (43 bp):
TATGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCATCGC
Found at i:48342 original size:18 final size:19
Alignment explanation
Indices: 48319--48362 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
48309 GATGCAATCT
48319 CATATACAAAAT-CAGATG
1 CATATACAAAATACAGATG
48337 CATATAC-AAATACAGATG
1 CATATACAAAATACAGATG
*
48355 CAAATACA
1 CATATACA
48363 GACATAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.20
Consensus pattern (19 bp):
CATATACAAAATACAGATG
Found at i:49743 original size:49 final size:50
Alignment explanation
Indices: 49659--49844 Score: 176
Period size: 50 Copynumber: 3.7 Consensus size: 50
49649 GGGAATGAGA
* *
49659 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCAAGATGAGAGG
* * * *
49709 TCCCATTTAAGACCTTG-ATGGGACATTGCATTGGCACTAAGATGAGAGG
1 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCAAGATGAGAGG
*** * * * * * * **
49758 TCCCCCATAAGACCATGTCTGGGAGATGTCAATGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCAAGATGAGAGG
* * * *
49808 TCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCA
49845 ATACAAGAAA
Statistics
Matches: 107, Mismatches: 28, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
49 41 0.38
50 66 0.62
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCAAGATGAGAGG
Found at i:52534 original size:2 final size:2
Alignment explanation
Indices: 52527--52560 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
52517 TGAGACGTAA
*
52527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52561 TAAGATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54548 original size:15 final size:15
Alignment explanation
Indices: 54525--54617 Score: 59
Period size: 15 Copynumber: 6.3 Consensus size: 15
54515 TAAAAACCCT
* * *
54525 AAATAAAAATTCCTA
1 AAATCAAAATCCCCA
54540 AAATCAAAATCCCCA
1 AAATCAAAATCCCCA
*
54555 AAATCAAAA--CCCT
1 AAATCAAAATCCCCA
* *
54568 TACTCAAAATCCCC-
1 AAATCAAAATCCCCA
* *
54582 AAAT-TAGATCACCCA
1 AAATCAAAATC-CCCA
*
54597 AAACCCAAAATCCCCA
1 AAA-TCAAAATCCCCA
54613 AAATC
1 AAATC
54618 CACAACCCTA
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
13 14 0.24
14 5 0.09
15 28 0.48
16 7 0.12
17 4 0.07
ACGTcount: A:0.51, C:0.31, G:0.01, T:0.17
Consensus pattern (15 bp):
AAATCAAAATCCCCA
Found at i:57003 original size:2 final size:2
Alignment explanation
Indices: 56996--57023 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56986 TACAATTGTG
56996 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
57024 GAGATGATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59773 original size:7 final size:7
Alignment explanation
Indices: 59762--59817 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
59752 ACATGAAATT
*
59762 TTAAAAT
1 TTAAAAA
59769 TTAAAAAA
1 TT-AAAAA
59777 TTAAAAA
1 TTAAAAA
59784 TTAAAAA
1 TTAAAAA
59791 -TAATCAAA
1 TTAA--AAA
59799 TT-AAAA
1 TTAAAAA
59805 TATAAAAA
1 T-TAAAAA
59813 TTAAA
1 TTAAA
59818 TACACAACGT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
6 7 0.17
7 19 0.45
8 15 0.36
9 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:59922 original size:14 final size:14
Alignment explanation
Indices: 59903--59932 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
59893 TTTTATTTAT
59903 TTTAACTGATTAAA
1 TTTAACTGATTAAA
59917 TTTAACTGATTAAA
1 TTTAACTGATTAAA
59931 TT
1 TT
59933 ATATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TTTAACTGATTAAA
Found at i:62909 original size:28 final size:28
Alignment explanation
Indices: 62861--62957 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 28
62851 AGAAATCCCC
* *
62861 AAAATCTCCAAAATTAAAAACCCTAAATA
1 AAAATCCCCAAAA-TCAAAACCCTAAATA
* * * * *
62890 AAAATTCCTAAAATCAAAACCCTTACTC
1 AAAATCCCCAAAATCAAAACCCTAAATA
* * *
62918 AAAATCCCCAAAATCAAAACCCTTACTC
1 AAAATCCCCAAAATCAAAACCCTAAATA
62946 AAAATCCCCAAA
1 AAAATCCCCAAA
62958 TTAGATCACC
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 49 0.83
29 10 0.17
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.20
Consensus pattern (28 bp):
AAAATCCCCAAAATCAAAACCCTAAATA
Found at i:63639 original size:37 final size:37
Alignment explanation
Indices: 63589--63662 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
63579 ATAGAGCGAT
63589 GGCAGTTGAAGACCCAAAGAATGCCTTGTGGCCAATA
1 GGCAGTTGAAGACCCAAAGAATGCCTTGTGGCCAATA
63626 GGCAGTTGAAGACCCAAAGAATGCCTTGTGGCCAATA
1 GGCAGTTGAAGACCCAAAGAATGCCTTGTGGCCAATA
63663 ACTATGTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (37 bp):
GGCAGTTGAAGACCCAAAGAATGCCTTGTGGCCAATA
Found at i:66957 original size:32 final size:32
Alignment explanation
Indices: 66921--66982 Score: 74
Period size: 32 Copynumber: 1.9 Consensus size: 32
66911 ATTATTTTGA
66921 ATATA-AT-TAATTTATCAATTGATATTTAAATT
1 ATATATATATAATTTATC--TTGATATTTAAATT
**
66953 ATATATATATTTTTTATCTTGATATTTAAA
1 ATATATATATAATTTATCTTGATATTTAAA
66983 GTTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 17 0.65
33 2 0.08
34 7 0.27
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (32 bp):
ATATATATATAATTTATCTTGATATTTAAATT
Found at i:68946 original size:2 final size:2
Alignment explanation
Indices: 68939--68969 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68929 TTTTGGGAAT
68939 TA TA TA 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 TA TA TA T
68970 TAGAGAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72949 original size:3 final size:3
Alignment explanation
Indices: 72941--72973 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
72931 ATTGGCATTA
72941 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
72974 TAGGTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:74424 original size:113 final size:112
Alignment explanation
Indices: 74216--74581 Score: 390
Period size: 113 Copynumber: 3.3 Consensus size: 112
74206 TATAGATCGA
*
74216 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTAATGG-CG--ATCTATAGCGGTGTTTTCCAAAAA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTAA-GGTCGCCAT-TA-A-CGGCGTTTTCCAAAAA
* * *
74278 TTGCCGCAAAAAATTAAGCACAACGTCGTCGTTTTATTTTGAGCTTTAGTG
62 GTGCCGCAAAAAATTAAGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTG
* * *
74329 GCATTAGTGGCGCTTTTTGAAAAACGCCGCTATAGGTCGCCATTAACGGCGTTTTCCAAGAAGCG
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTA-AGGTCGCCATTAACGGCGTTTTCCAAAAAGTG
* **
74394 CCGCAAAAAATTAAGCACAGCGCCACCGTTTTATGTTGAGCTTTAGTG
65 CCGCAAAAAATTAAGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTG
* * ** * * * * * * *
74442 GAATTAACGATGCTTTTTGAAAAAAGCCACTAA-TTCTCAATCTATTAGCGGCATTTTTCAAAAA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAGGTCGC---C-ATTAACGGCGTTTTCCAAAAA
*
74506 GTGCCGCAAAAAATTAAGCACAACGCCGTCGTTTTATGTTGAGC--TA-TA
62 GTGCCGCAAAAAATTAAGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTG
74554 G--TTAGCGGCGCTTTTTGAAAAACGCCGC
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGC
74582 AAAAAACATT
Statistics
Matches: 212, Mismatches: 33, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
110 22 0.10
111 3 0.01
112 3 0.01
113 118 0.56
114 5 0.02
115 59 0.28
116 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (112 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAGGTCGCCATTAACGGCGTTTTCCAAAAAGTGC
CGCAAAAAATTAAGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTG
Found at i:74878 original size:24 final size:24
Alignment explanation
Indices: 74848--74897 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
74838 TTTAAAAGAG
74848 ATAGTATTAATTTTCAAATATTGA
1 ATAGTATTAATTTTCAAATATTGA
74872 ATAGTATTAATTTTCAAATATTGA
1 ATAGTATTAATTTTCAAATATTGA
74896 AT
1 AT
74898 TAATTATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (24 bp):
ATAGTATTAATTTTCAAATATTGA
Found at i:74928 original size:7 final size:7
Alignment explanation
Indices: 74907--75066 Score: 72
Period size: 7 Copynumber: 22.4 Consensus size: 7
74897 TTAATTATCA
*
74907 TTATAGT
1 TTATGGT
*
74914 TTAGGGT
1 TTATGGT
74921 TTATGGT
1 TTATGGT
* *
74928 TGACGGT
1 TTATGGT
*
74935 TTAAGGT
1 TTATGGT
*
74942 TTAGGAGT
1 TTATG-GT
74950 TACTAT--T
1 T--TATGGT
*
74957 TTAAGGT
1 TTATGGT
*
74964 TTATGGA
1 TTATGGT
74971 TTATGGGT
1 TTAT-GGT
* *
74979 TTAGGGA
1 TTATGGT
*
74986 TTATGAT
1 TTATGGT
74993 TTATGGT
1 TTATGGT
75000 TTATGGT
1 TTATGGT
* *
75007 TTAAGGG
1 TTATGGT
*
75014 TTAGGGT
1 TTATGGT
*
75021 TTAAGGGT
1 TT-ATGGT
*
75029 TTAGGGT
1 TTATGGT
* *
75036 TTAGGGG
1 TTATGGT
*
75043 TTATGTT
1 TTATGGT
*
75050 TTATGAT
1 TTATGGT
*
75057 TTAAGGT
1 TTATGGT
75064 TTA
1 TTA
75067 AGGGATAGAA
Statistics
Matches: 116, Mismatches: 30, Indels: 14
0.73 0.19 0.09
Matches are distributed among these distances:
5 2 0.02
7 97 0.84
8 15 0.13
10 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (7 bp):
TTATGGT
Found at i:75005 original size:29 final size:29
Alignment explanation
Indices: 74975--75072 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
74965 TATGGATTAT
74975 GGGTTT-AGGGATTATGATTTATGGTTTA
1 GGGTTTAAGGGATTATGATTTATGGTTTA
* * * *
75003 TGGTTTAAGGG-TTAGGGTTTAAGGGTTTA
1 GGGTTTAAGGGATTATGATTT-ATGGTTTA
* * *
75032 GGGTTT-AGGGGTTATGTTTTATGATTTA
1 GGGTTTAAGGGATTATGATTTATGGTTTA
*
75060 AGGTTTAAGGGAT
1 GGGTTTAAGGGAT
75073 AGAAATTAAG
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 27 0.49
29 28 0.51
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (29 bp):
GGGTTTAAGGGATTATGATTTATGGTTTA
Found at i:75010 original size:50 final size:50
Alignment explanation
Indices: 74956--75072 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
74946 GAGTTACTAT
* * * * *
74956 TTTAAGGTTTATGGATTATGGGTTTAGGGATTATGATTTATGGTTTATGG
1 TTTAAGGTTTAGGGATTAAGGGTTTAGGGATTAGGAGTTATGGTTTATGA
* * * * *
75006 TTTAAGGGTTAGGGTTTAAGGGTTTAGGGTTTAGGGGTTATGTTTTATGA
1 TTTAAGGTTTAGGGATTAAGGGTTTAGGGATTAGGAGTTATGGTTTATGA
75056 TTTAAGGTTTAAGGGAT
1 TTTAAGGTTT-AGGGAT
75073 AGAAATTAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 49 0.91
51 5 0.09
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.45
Consensus pattern (50 bp):
TTTAAGGTTTAGGGATTAAGGGTTTAGGGATTAGGAGTTATGGTTTATGA
Found at i:75021 original size:14 final size:14
Alignment explanation
Indices: 75004--75095 Score: 67
Period size: 14 Copynumber: 6.4 Consensus size: 14
74994 TATGGTTTAT
75004 GGTTTAAGGGTTAG
1 GGTTTAAGGGTTAG
75018 GGTTTAAGGGTTTAG
1 GGTTTAAGGG-TTAG
* *
75033 GGTTTAGGGGTTAT
1 GGTTTAAGGGTTAG
* * ** *
75047 GTTTTATGATTTAA
1 GGTTTAAGGGTTAG
*
75061 GGTTTAAGGGATAG
1 GGTTTAAGGGTTAG
***
75075 AAATTAAGGGTTTAG
1 GGTTTAAGGG-TTAG
75090 GGTTTA
1 GGTTTA
75096 GATTAATTAG
Statistics
Matches: 56, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
14 37 0.66
15 19 0.34
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (14 bp):
GGTTTAAGGGTTAG
Found at i:75032 original size:15 final size:15
Alignment explanation
Indices: 74997--75044 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
74987 TATGATTTAT
*
74997 GGTTTATGGTTTAAG
1 GGTTTAGGGTTTAAG
75012 GG-TTAGGGTTTAAG
1 GGTTTAGGGTTTAAG
*
75026 GGTTTAGGGTTTAGG
1 GGTTTAGGGTTTAAG
75041 GGTT
1 GGTT
75045 ATGTTTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GGTTTAGGGTTTAAG
Found at i:75038 original size:57 final size:57
Alignment explanation
Indices: 74975--75096 Score: 172
Period size: 57 Copynumber: 2.1 Consensus size: 57
74965 TATGGATTAT
* * * ***
74975 GGGTTTAGGGATTATGATTTATGGTTTATGGTTTAAGGGTTAGGGTTTAAGGGTTTA
1 GGGTTTAGGGATTATGATTTATGATTTAAGGTTTAAGGGATAGAAATTAAGGGTTTA
* *
75032 GGGTTTAGGGGTTATGTTTTATGATTTAAGGTTTAAGGGATAGAAATTAAGGGTTTA
1 GGGTTTAGGGATTATGATTTATGATTTAAGGTTTAAGGGATAGAAATTAAGGGTTTA
75089 GGGTTTAG
1 GGGTTTAG
75097 ATTAATTAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.42
Consensus pattern (57 bp):
GGGTTTAGGGATTATGATTTATGATTTAAGGTTTAAGGGATAGAAATTAAGGGTTTA
Found at i:76403 original size:43 final size:43
Alignment explanation
Indices: 76341--76526 Score: 225
Period size: 43 Copynumber: 4.3 Consensus size: 43
76331 AAGGCAATGA
* * *
76341 CTAAAGGTCATGTTCTTTAGCGGCGTTTGCAGGT-AAAGCGCCA
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTG-TGATAAAAGCGCCG
*
76384 CTAAAGGTCATGTTTTTTAGCGGCGTTTGTGATAAAAGCGCCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
** * **
76427 CTAAAAATCATGTTCTTTAGCGGCGTTTGTGGGT-AAAGCATCG
1 CTAAAGGTCATGTTCTTTAGCGGCGTTTGT-GATAAAAGCGCCG
**
76470 CTAAAGAG-CATGACCTTTAGCGGCGTTTGTGATAAAAGCGCCG
1 CTAAAG-GTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
76513 CTAAAGGTCATGTT
1 CTAAAGGTCATGTT
76527 TTATAGAGGC
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
42 5 0.04
43 112 0.94
44 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
CTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCG
Found at i:76489 original size:86 final size:86
Alignment explanation
Indices: 76348--76526 Score: 252
Period size: 86 Copynumber: 2.1 Consensus size: 86
76338 TGACTAAAGG
* ***
76348 TCATGTTCTTTAGCGGCGTTTGCAGGTAAAGCGCCACTAAAGGTCATGTTTTTTAGCGGCGTTTG
1 TCATGTTCTTTAGCGGCGTTTGCAGGTAAAGCACCACTAAAGGTCATGACCTTTAGCGGCGTTTG
76413 TGATAAAAGCGCCGCTAAAAA
66 TGATAAAAGCGCCGCTAAAAA
** * *
76434 TCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCATCGCTAAAGAG-CATGACCTTTAGCGGCGTTT
1 TCATGTTCTTTAGCGGCGTTTGCAGGTAAAGCACCACTAAAG-GTCATGACCTTTAGCGGCGTTT
**
76498 GTGATAAAAGCGCCGCTAAAGG
65 GTGATAAAAGCGCCGCTAAAAA
76520 TCATGTT
1 TCATGTT
76527 TTATAGAGGC
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 81 0.99
87 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (86 bp):
TCATGTTCTTTAGCGGCGTTTGCAGGTAAAGCACCACTAAAGGTCATGACCTTTAGCGGCGTTTG
TGATAAAAGCGCCGCTAAAAA
Found at i:79296 original size:5 final size:5
Alignment explanation
Indices: 79286--79313 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
79276 AAAATGTAAC
79286 TTTGT TTTGT TTTGT TTTGT TTTGT TTT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTT
79314 TAATTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTTGT
Found at i:81864 original size:26 final size:28
Alignment explanation
Indices: 81830--81882 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
81820 AACAATCATT
81830 GCATAGTCATGAACTAAGC-AATGAAAA
1 GCATAGTCATGAACTAAGCAAATGAAAA
* *
81857 GCAT-GTCATGGATTAAGCAAATGAAA
1 GCATAGTCATGAACTAAGCAAATGAAA
81883 CAAAATTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (28 bp):
GCATAGTCATGAACTAAGCAAATGAAAA
Found at i:82264 original size:3 final size:3
Alignment explanation
Indices: 82256--82288 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
82246 TCAATTGTAA
82256 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
82289 AATGGGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:83298 original size:3 final size:3
Alignment explanation
Indices: 83284--83318 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
83274 GAGGACTAAA
* *
83284 ATT ATC ATT ATT ATT ATT ATA ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
83319 ATCAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:83308 original size:15 final size:15
Alignment explanation
Indices: 83284--83319 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
83274 GAGGACTAAA
*
83284 ATTATCATTATTATT
1 ATTATAATTATTATT
83299 ATTATAATTATTATT
1 ATTATAATTATTATT
83314 ATTATA
1 ATTATA
83320 TCAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATAATTATTATT
Found at i:95097 original size:22 final size:22
Alignment explanation
Indices: 95072--95114 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
95062 AGATATGAGG
95072 TTAAACCACAAATTAAGTTATA
1 TTAAACCACAAATTAAGTTATA
95094 TTAAACCACAAATTAAGTTAT
1 TTAAACCACAAATTAAGTTAT
95115 CTCGAGTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (22 bp):
TTAAACCACAAATTAAGTTATA
Found at i:99288 original size:29 final size:28
Alignment explanation
Indices: 99248--99363 Score: 90
Period size: 29 Copynumber: 4.0 Consensus size: 28
99238 AGAAATCCCC
99248 AAAATCTCCAAAATTAAAAACCCTAAACA
1 AAAATC-CCAAAATTAAAAACCCTAAACA
* * * *
99277 AAAATTCCCAAAA-TCAAAACCCTTACCC
1 AAAA-TCCCAAAATTAAAAACCCTAAACA
* * * *
99305 AAAATCCCCAAATTAAACCACCCAAAACCC
1 AAAATCCCAAAATTAAA-AACCCTAAA-CA
** *
99335 AAAATCCCAAAATCGACAACCCTAAACA
1 AAAATCCCAAAATTAAAAACCCTAAACA
99363 A
1 A
99364 TTTATGGTGA
Statistics
Matches: 66, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
27 7 0.11
28 20 0.30
29 22 0.33
30 17 0.26
ACGTcount: A:0.53, C:0.33, G:0.01, T:0.14
Consensus pattern (28 bp):
AAAATCCCAAAATTAAAAACCCTAAACA
Found at i:99343 original size:57 final size:58
Alignment explanation
Indices: 99245--99357 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 58
99235 GTGAGAAATC
*
99245 CCCAAAATCTCCAAAATTAAAAACCCTAAACAAAAATTCCCAAAATC-AAAACCCTTA
1 CCCAAAATCTCCAAAATTAAAAACCCAAAACAAAAATTCCCAAAATCGAAAACCCTTA
* * * *
99302 CCCAAAATC-CCCAAATTAAACCACCCAAAACCCAAAA-TCCCAAAATCGACAACCCT
1 CCCAAAATCTCCAAAATTAAA-AACCCAAAA-CAAAAATTCCCAAAATCGAAAACCCT
99358 AAACAATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
56 10 0.21
57 26 0.54
58 12 0.25
ACGTcount: A:0.50, C:0.35, G:0.01, T:0.14
Consensus pattern (58 bp):
CCCAAAATCTCCAAAATTAAAAACCCAAAACAAAAATTCCCAAAATCGAAAACCCTTA
Found at i:100700 original size:14 final size:15
Alignment explanation
Indices: 100683--100712 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
100673 ATCATTTTGA
100683 TTAAT-ATAAATATT
1 TTAATAATAAATATT
100697 TTAATAATAAATATT
1 TTAATAATAAATATT
100712 T
1 T
100713 AGAAGGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATAATAAATATT
Found at i:106576 original size:19 final size:20
Alignment explanation
Indices: 106538--106576 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
106528 ACATGTGGAA
*
106538 TAATAATAAACATATGTATT
1 TAATAACAAACATATGTATT
*
106558 TAATAACAAA-ATATTTATT
1 TAATAACAAACATATGTATT
106577 GCTTATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (20 bp):
TAATAACAAACATATGTATT
Found at i:106622 original size:26 final size:29
Alignment explanation
Indices: 106557--106622 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 29
106547 ACATATGTAT
* * *
106557 TTAATAACAAAATATTTATTGCTTATTAA
1 TTAAGAACAAAATATATATTGATTATTAA
*
106586 TTAAGTA-AAAATATATATT-ATTA-TAA
1 TTAAGAACAAAATATATATTGATTATTAA
106612 TTAA-AACAAAA
1 TTAAGAACAAAA
106623 CAAATAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 1 0.03
26 11 0.35
27 3 0.10
28 11 0.35
29 5 0.16
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (29 bp):
TTAAGAACAAAATATATATTGATTATTAA
Found at i:111559 original size:21 final size:22
Alignment explanation
Indices: 111521--111564 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
111511 TTCAGTCAAT
111521 TTGATCTTGATAATGTATAAAA
1 TTGATCTTGATAATGTATAAAA
111543 TTGATCTTGAT-ATGTATAAAA
1 TTGATCTTGATAATGTATAAAA
111564 T
1 T
111565 GGTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
TTGATCTTGATAATGTATAAAA
Found at i:113141 original size:12 final size:12
Alignment explanation
Indices: 113115--113147 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
113105 TTAAGATTTT
113115 ATTTTTCTA-GA
1 ATTTTTCTATGA
*
113126 ATTTTTCTATGC
1 ATTTTTCTATGA
113138 ATTTTTCTAT
1 ATTTTTCTAT
113148 TTTATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (12 bp):
ATTTTTCTATGA
Found at i:115760 original size:3 final size:3
Alignment explanation
Indices: 115752--116026 Score: 550
Period size: 3 Copynumber: 91.7 Consensus size: 3
115742 CCACTCATCT
115752 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
115800 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
115848 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
115896 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
115944 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
115992 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
116027 CTTACCTCAC
Statistics
Matches: 272, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 272 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:118947 original size:10 final size:10
Alignment explanation
Indices: 118922--118953 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
118912 ATAACTTATT
118922 TTTAAAATT-
1 TTTAAAATTA
118931 TTT-AAATTA
1 TTTAAAATTA
118940 TTTAAAATTA
1 TTTAAAATTA
118950 TTTA
1 TTTA
118954 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.24
9 6 0.29
10 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:118958 original size:17 final size:16
Alignment explanation
Indices: 118917--118959 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
118907 TATATATAAC
118917 TTATT-TTTAAAATTT
1 TTATTATTTAAAATTT
118932 TTAAATTATTTAAAATTAT
1 TT--ATTATTTAAAATT-T
118951 TTATTATTT
1 TTATTATTT
118960 TTTTAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.08
17 10 0.42
18 9 0.38
19 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATTTAAAATTT
Found at i:121242 original size:30 final size:30
Alignment explanation
Indices: 121201--121267 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
121191 GCTCAAGTTG
121201 AACATAATACCATAATAAAGAGGAAAAATTT
1 AACA-AATACCATAATAAAGAGGAAAAATTT
*
121232 AACAAATACCATAATAAATAGGAAAAATTT
1 AACAAATACCATAATAAAGAGGAAAAATTT
121262 AACAAA
1 AACAAA
121268 AAAAATTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.61, C:0.10, G:0.07, T:0.21
Consensus pattern (30 bp):
AACAAATACCATAATAAAGAGGAAAAATTT
Found at i:129348 original size:195 final size:196
Alignment explanation
Indices: 129009--129396 Score: 769
Period size: 195 Copynumber: 2.0 Consensus size: 196
128999 GATGAATGTA
129009 GGGGAATTAAACCCGGAAGCATTTATTTGAATGTTTGAAATTTATGTCCTTGAAACGTAATGACA
1 GGGGAATTAAACCCGGAAGCATTTATTTGAATGTTTGAAATTTATGTCCTTGAAACGTAATGACA
129074 CTTACAGATATGCTATTGGTATAATGATTCGTTATTGTTGTGTTTGCCTTCAGAATTTGAGAAAA
66 CTTACAGATATGCTATTGGTATAATGATTCGTTATTGTTGTGTTTGCCTTCAGAATTTGAGAAAA
129139 AATGTGAAAGAAGTAAAAAATAATGGCGCCGTCAGTTGGCTAAATTGTGATTATCTTTATGCTTA
131 AATGTGAAAGAAGTAAAAAATAATGGCGCCGTCAGTTGGCTAAATTGTGATTATCTTTATGCTTA
129204 G
196 G
129205 GGGGAA-TAAACCCGGAAGCATTTATTTGAATGTTTGAAATTTATGTCCTTGAAACGTAATGACA
1 GGGGAATTAAACCCGGAAGCATTTATTTGAATGTTTGAAATTTATGTCCTTGAAACGTAATGACA
129269 CTTACAGATATGCTATTGGTATAATGATTCGTTATTGTTGTGTTTGCCTTCAGAATTTGAGAAAA
66 CTTACAGATATGCTATTGGTATAATGATTCGTTATTGTTGTGTTTGCCTTCAGAATTTGAGAAAA
129334 AATGTGAAAGAAGTAAAAAATAATGGCGCCGTCAGTTGGCTAAATTGTGATTATCTTTATGCT
131 AATGTGAAAGAAGTAAAAAATAATGGCGCCGTCAGTTGGCTAAATTGTGATTATCTTTATGCT
129397 AATGCAGGCA
Statistics
Matches: 192, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
195 186 0.97
196 6 0.03
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (196 bp):
GGGGAATTAAACCCGGAAGCATTTATTTGAATGTTTGAAATTTATGTCCTTGAAACGTAATGACA
CTTACAGATATGCTATTGGTATAATGATTCGTTATTGTTGTGTTTGCCTTCAGAATTTGAGAAAA
AATGTGAAAGAAGTAAAAAATAATGGCGCCGTCAGTTGGCTAAATTGTGATTATCTTTATGCTTA
G
Found at i:132077 original size:17 final size:17
Alignment explanation
Indices: 132030--132097 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
132020 AGCTAATTTT
*
132030 AAAA-TGAAAATTTTAAA
1 AAAACTGAAAA-TTAAAA
* *
132047 GAAACT-AAAATTAAAT
1 AAAACTGAAAATTAAAA
*
132063 AAAACTGAAATTTAAAA
1 AAAACTGAAAATTAAAA
*
132080 AAAAATGAACAA-TAAAA
1 AAAACTGAA-AATTAAAA
132097 A
1 A
132098 TTTCGTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
16 9 0.22
17 29 0.73
18 2 0.05
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.22
Consensus pattern (17 bp):
AAAACTGAAAATTAAAA
Found at i:133356 original size:39 final size:39
Alignment explanation
Indices: 133243--133356 Score: 108
Period size: 40 Copynumber: 2.8 Consensus size: 39
133233 GCGTTTGGAT
* *
133243 AAAAAACGCCGCTAAAAATCAAACATTAGCGGCG-CTTCTG
1 AAAAAACG-CGCTAAAAAT-GAGCATTAGCGGCGTCTTCTG
* *
133283 AAAAAACGCGACTAAAGATTGAGCATTAGTGGCGTACTT-TG
1 AAAAAACGCG-CTAAA-AATGAGCATTAGCGGCGT-CTTCTG
*
133324 -GAAAACGCTGCTAAAAATGAGCATTAGCGGCGT
1 AAAAAACGC-GCTAAAAATGAGCATTAGCGGCGT
133357 TTTTCAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
39 18 0.29
40 36 0.58
41 5 0.08
42 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (39 bp):
AAAAAACGCGCTAAAAATGAGCATTAGCGGCGTCTTCTG
Found at i:133480 original size:113 final size:112
Alignment explanation
Indices: 133347--133596 Score: 383
Period size: 113 Copynumber: 2.2 Consensus size: 112
133337 AAAATGAGCA
*
133347 TTAGCGGCGTTTTTCAAAAAGCGCCACAAAAAACCTAAGCACAACGACGTCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTGAAAAAGCGCCACAAAAAACCTAAGCACAACGACGTCGTTTTCTGAGTTTT
* *
133412 TGGGGCTTTAGTGGCGTTTTATAAAAAGCGTCGCTAATGCATGGGGCT
66 AGGGGCTTTAGTGGCGTTTTATAAAAAGCGTCGCTAAAGCAT-GGGCT
* * * * * *
133460 TTAGCGGCGTTTTTGAAAAAGTGCCGCAAAAAACCTAAGCCCAACTACGTCTTTTTTTGAGTTTT
1 TTAGCGGCGTTTTTGAAAAAGCGCCACAAAAAACCTAAGCACAACGACGTCGTTTTCTGAGTTTT
* *
133525 AGGGGCTTTAGTGGCGTTTTTTAAAAAGCGTCGCTAAAGTATGGGCT
66 AGGGGCTTTAGTGGCGTTTTATAAAAAGCGTCGCTAAAGCATGGGCT
*
133572 TTAGCGGCGTTTTTGGAAAAGCGCC
1 TTAGCGGCGTTTTTGAAAAAGCGCC
133597 GCTAATGCTC
Statistics
Matches: 124, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
112 28 0.23
113 96 0.77
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (112 bp):
TTAGCGGCGTTTTTGAAAAAGCGCCACAAAAAACCTAAGCACAACGACGTCGTTTTCTGAGTTTT
AGGGGCTTTAGTGGCGTTTTATAAAAAGCGTCGCTAAAGCATGGGCT
Found at i:133784 original size:7 final size:7
Alignment explanation
Indices: 133761--133832 Score: 56
Period size: 7 Copynumber: 10.3 Consensus size: 7
133751 GATTTATAGA
*
133761 TTAAGGT
1 TTAAGGG
*
133768 TTAGGGG
1 TTAAGGG
133775 TTAAGGG
1 TTAAGGG
133782 TT-AGGAG
1 TTAAGG-G
*
133789 TTGAGGG
1 TTAAGGG
*
133796 TTAAGAG
1 TTAAGGG
133803 TTAAGGG
1 TTAAGGG
* *
133810 TTATGGT
1 TTAAGGG
* *
133817 TTATGGT
1 TTAAGGG
133824 TTAAGGG
1 TTAAGGG
133831 TT
1 TT
133833 GGGTGATACG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 3 0.06
7 47 0.89
8 3 0.06
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.38
Consensus pattern (7 bp):
TTAAGGG
Found at i:140081 original size:42 final size:42
Alignment explanation
Indices: 139995--140083 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
139985 ATAATTTTGT
* *** * *
139995 TAAAGGTTATGTTTTTAGTGGCGTTTTTGTGAGAAGTGCCGC
1 TAAAGGTTATGTTTTTAGCGGCGTTTGAATGAAAAGCGCCGC
*
140037 TAAAGGTT-TGTTCTTTAGCGGCGTTTGAATGAAAAGCGCTGC
1 TAAAGGTTATGTT-TTTAGCGGCGTTTGAATGAAAAGCGCCGC
140079 TAAAG
1 TAAAG
140084 ATATTATTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.36
Consensus pattern (42 bp):
TAAAGGTTATGTTTTTAGCGGCGTTTGAATGAAAAGCGCCGC
Found at i:142047 original size:207 final size:208
Alignment explanation
Indices: 141683--142097 Score: 823
Period size: 207 Copynumber: 2.0 Consensus size: 208
141673 GAAAATTAGG
141683 GATAATTATTTTTAAACCCTACAAAATTTCTCTATATTATCTATATTCAATACTCATTCTTTCAA
1 GATAATTATTTTTAAACCCTACAAAATTTCTCTATATTATCTATATTCAATACTCATTCTTTCAA
141748 AACAAACATAGAAAAAATATTAAGCAAATTTATATGTTTACAATGTGGAGCCTCTTAACCTCTTC
66 AACAAACATAGAAAAAATATTAAGCAAATTTATATGTTTACAATGTGGAGCCTCTTAACCTCTTC
141813 CTTCCATCATTCCTTTTCTCCTCTCTTTTGCACTATCCTTCTTTCCCACCTACACTTTCATCTTT
131 CTTCCATCATTCCTTTTCTCCTCTCTTTTGCACTATCCTTCTTTCCCACCTACACTTTCATCTTT
141878 CTCTACAACAACA
196 CTCTACAACAACA
141891 GATAATTA-TTTTAAACCCTACAAAATTTCTCTATATTATCTATATTCAATACTCATTCTTTCAA
1 GATAATTATTTTTAAACCCTACAAAATTTCTCTATATTATCTATATTCAATACTCATTCTTTCAA
141955 AACAAACATAGAAAAAATATTAAGCAAATTTATATGTTTACAATGTGGAGCCTCTTAACCTCTTC
66 AACAAACATAGAAAAAATATTAAGCAAATTTATATGTTTACAATGTGGAGCCTCTTAACCTCTTC
142020 CTTCCATCATTCCTTTTCTCCTCTCTTTTGCACTATCCTTCTTTCCCACCTACACTTTCATCTTT
131 CTTCCATCATTCCTTTTCTCCTCTCTTTTGCACTATCCTTCTTTCCCACCTACACTTTCATCTTT
142085 CTCTACAACAACA
196 CTCTACAACAACA
142098 TCACCAAGAA
Statistics
Matches: 207, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
207 199 0.96
208 8 0.04
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (208 bp):
GATAATTATTTTTAAACCCTACAAAATTTCTCTATATTATCTATATTCAATACTCATTCTTTCAA
AACAAACATAGAAAAAATATTAAGCAAATTTATATGTTTACAATGTGGAGCCTCTTAACCTCTTC
CTTCCATCATTCCTTTTCTCCTCTCTTTTGCACTATCCTTCTTTCCCACCTACACTTTCATCTTT
CTCTACAACAACA
Found at i:154865 original size:8 final size:8
Alignment explanation
Indices: 154845--154878 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
154835 GTAAGGGGAG
154845 ATAAAAAA
1 ATAAAAAA
154853 CATAAAAAA
1 -ATAAAAAA
154862 ATAAAAAA
1 ATAAAAAA
154870 ATAGAAAAA
1 ATA-AAAAA
154879 GAGGGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 11 0.46
9 13 0.54
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:154867 original size:17 final size:17
Alignment explanation
Indices: 154845--154878 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
154835 GTAAGGGGAG
154845 ATAAAAAACATA-AAAAA
1 ATAAAAAA-ATAGAAAAA
154862 ATAAAAAAATAGAAAAA
1 ATAAAAAAATAGAAAAA
154879 GAGGGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (17 bp):
ATAAAAAAATAGAAAAA
Found at i:155714 original size:72 final size:73
Alignment explanation
Indices: 155621--155762 Score: 277
Period size: 72 Copynumber: 2.0 Consensus size: 73
155611 TTATTCCCCG
155621 ATTAATTTCGTTTTAGTTGCAATCTAATCTTTTTTTTAATTAGTTTAATATTTTCATTAATATTA
1 ATTAATTTCGTTTTAGTTGCAATCTAATCTTTTTTTTAATTAGTTTAATATTTTCATTAATATTA
155686 GGATCCCA
66 GGATCCCA
155694 ATTAA-TTCGTTTTAGTTGCAATCTAATCTTTTTTTTAATTAGTTTAATATTTTCATTAATATTA
1 ATTAATTTCGTTTTAGTTGCAATCTAATCTTTTTTTTAATTAGTTTAATATTTTCATTAATATTA
155758 GGATC
66 GGATC
155763 ATTGTTGTTG
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 64 0.93
73 5 0.07
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (73 bp):
ATTAATTTCGTTTTAGTTGCAATCTAATCTTTTTTTTAATTAGTTTAATATTTTCATTAATATTA
GGATCCCA
Found at i:157494 original size:40 final size:40
Alignment explanation
Indices: 157391--157486 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
157381 TTTATTGCGA
* *
157391 CGCTTTTTCAAAAACGCCGCTAAAAATAGAGCATTCACAG
1 CGCTTTTTCAAAAATGCCGCTAAAAATAGAGAATTCACAG
* *
157431 CGCTTCTTCAAAAATGCCGCTAAAAATAGAGAATT-AGCGG
1 CGCTTTTTCAAAAATGCCGCTAAAAATAGAGAATTCA-CAG
157471 CGCTTTTTCAAAAATG
1 CGCTTTTTCAAAAATG
157487 TTGCTAAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 49 0.98
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (40 bp):
CGCTTTTTCAAAAATGCCGCTAAAAATAGAGAATTCACAG
Found at i:157683 original size:40 final size:40
Alignment explanation
Indices: 157639--157722 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
157629 AAATATGAGA
*
157639 TAAAAATAGAGCATTCA-CAGCGCTTCTTCAAAAATGCCGC
1 TAAAAATAGAGAATT-AGCAGCGCTTCTTCAAAAATGCCGC
* * *
157679 TAAAAATAGAGAATTAGCGGCGCTTTTTCAAAAATGTCGC
1 TAAAAATAGAGAATTAGCAGCGCTTCTTCAAAAATGCCGC
157719 TAAA
1 TAAA
157723 TCCCCAAGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.03
40 38 0.97
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (40 bp):
TAAAAATAGAGAATTAGCAGCGCTTCTTCAAAAATGCCGC
Found at i:177739 original size:23 final size:22
Alignment explanation
Indices: 177697--177759 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
177687 TTTTAAAAAA
*
177697 TAATTAAG-TTTATTTT--CTT
1 TAATTAAGATTTTTTTTCACTT
177716 TAAATTAAGATTTTTTTTCACTT
1 T-AATTAAGATTTTTTTTCACTT
**
177739 TAATGTATTATTTTTTTTCAC
1 TAAT-TAAGATTTTTTTTCAC
177760 AAGAATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.03
20 7 0.19
21 7 0.19
22 3 0.08
23 18 0.50
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.60
Consensus pattern (22 bp):
TAATTAAGATTTTTTTTCACTT
Found at i:178109 original size:16 final size:16
Alignment explanation
Indices: 178088--178119 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
178078 TATACAAGTC
178088 AATGAGTTGTATTAGG
1 AATGAGTTGTATTAGG
178104 AATGAGTTGTATTAGG
1 AATGAGTTGTATTAGG
178120 GTGTGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (16 bp):
AATGAGTTGTATTAGG
Found at i:178473 original size:16 final size:16
Alignment explanation
Indices: 178452--178483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
178442 ATATACAAGT
*
178452 CAATGAGTTGTATTAG
1 CAATGAGTTGAATTAG
178468 CAATGAGTTGAATTAG
1 CAATGAGTTGAATTAG
178484 GGTGTGACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
CAATGAGTTGAATTAG
Found at i:180383 original size:34 final size:34
Alignment explanation
Indices: 180331--180408 Score: 138
Period size: 34 Copynumber: 2.2 Consensus size: 34
180321 GAGAAGTTAG
180331 AAACACTGAGTGAGCTTATAGGCTCTGTAACACCCC
1 AAAC-CTG-GTGAGCTTATAGGCTCTGTAACACCCC
180367 AAACCTGGTGAGCTTATAGGCTCTGTAACACCCC
1 AAACCTGGTGAGCTTATAGGCTCTGTAACACCCC
180401 AAACCTGG
1 AAACCTGG
180409 CCTAGACGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 35 0.83
35 3 0.07
36 4 0.10
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (34 bp):
AAACCTGGTGAGCTTATAGGCTCTGTAACACCCC
Found at i:184828 original size:42 final size:42
Alignment explanation
Indices: 184781--184864 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
184771 AATCTCTCAA
*
184781 ACTATTAACTTTAAAGAAATTCTTGTAATGGCAGACAAACAT
1 ACTATTAACTTTAAAGAAATTCTTGTAATGCCAGACAAACAT
184823 ACTATTAACTTTAAAGAAATTCTTGTAATGCCAGACAAACAT
1 ACTATTAACTTTAAAGAAATTCTTGTAATGCCAGACAAACAT
184865 TTTTTCCAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (42 bp):
ACTATTAACTTTAAAGAAATTCTTGTAATGCCAGACAAACAT
Found at i:191420 original size:18 final size:19
Alignment explanation
Indices: 191397--191434 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
191387 TTTGAAATTC
*
191397 TTGTATTTTT-TTTCTTTT
1 TTGTATTTTTATTTATTTT
191415 TTGTATTTTTATTTATTTT
1 TTGTATTTTTATTTATTTT
191434 T
1 T
191435 AAAAAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.82
Consensus pattern (19 bp):
TTGTATTTTTATTTATTTT
Found at i:191931 original size:7 final size:7
Alignment explanation
Indices: 191920--191975 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
191910 ACATGAAATT
*
191920 TTAAAAT
1 TTAAAAA
191927 TTAAAAAA
1 TT-AAAAA
191935 TTAAAAA
1 TTAAAAA
191942 TTAAAAA
1 TTAAAAA
191949 -TAATCAAA
1 TTAA--AAA
191957 TT-AAAA
1 TTAAAAA
191963 TATAAAAA
1 T-TAAAAA
191971 TTAAA
1 TTAAA
191976 TACACAACGT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
6 7 0.17
7 19 0.45
8 15 0.36
9 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:192082 original size:14 final size:14
Alignment explanation
Indices: 192063--192092 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
192053 TTTTATTTAT
192063 TTTAACGGATTAAA
1 TTTAACGGATTAAA
*
192077 TTTAACTGATTAAA
1 TTTAACGGATTAAA
192091 TT
1 TT
192093 ATATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (14 bp):
TTTAACGGATTAAA
Found at i:192896 original size:9 final size:9
Alignment explanation
Indices: 192882--192914 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
192872 CTCCAGCATC
192882 TTGGATAAG
1 TTGGATAAG
*
192891 TTGGATAAC
1 TTGGATAAG
192900 TTGGATAAG
1 TTGGATAAG
192909 TTGGAT
1 TTGGAT
192915 TAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.36
Consensus pattern (9 bp):
TTGGATAAG
Found at i:193154 original size:297 final size:297
Alignment explanation
Indices: 192619--193173 Score: 950
Period size: 297 Copynumber: 1.9 Consensus size: 297
192609 AAAATATAAC
* *
192619 ATGAAATGGTATTAAAATGGAGGAATTAGATTTATAAAATAAATAAAATAAACTAAACTATAATG
1 ATGAAATGGTATTAAAATGGAGAAATTAGATTTATAAAATAAATAAAATAAACTAAAATATAATG
* * * *
192684 GTTCATATACCTTCAAAGCTTCCAAAGGGGTTGTAGAACATTTTTAAAGTTCGGATGGTCATCTC
66 GTT-AGATACCTTAAAAGCTTCCAAAGGGGTTGAAGAACATTTTTAAAGTTCGGATGGTCATCCC
192749 ACTCCAACCATTCCCACCATTCTGTCTCTGACCCGATGGTAAGAGAAGGTGGAGCATATGCAAAT
130 ACTCCAACCATTCCCACCATTCTGTCTCTGACCCGATGGTAAGAGAAGGTGGAGCATATGCAAAT
*
192814 GGCTGCCCATTGCCAACAAGGGGAACAAATGGAGGAATTCTCTTCAGTTTATAACAGTCTCCAGC
195 GGCTGCCCATTGCCAACAAGGGGAACAAATGGAGGAATTCTCTTCAGTTTATAACAATCTCCAGC
192879 ATCTTGGATAAGTTGGATAACTTGGATAAGTTGGATTA
260 ATCTTGGATAAGTTGGATAACTTGGATAAGTTGGATTA
**
192917 ATGAAATGGTATTAAAATGGAGAAATTAGATTTATAAAATAAATCGAATAAACTAAAATATAAAT
1 ATGAAATGGTATTAAAATGGAGAAATTAGATTTATAAAATAAATAAAATAAACTAAAATAT-AAT
*
192982 GGTT-GATACCTTAAAAGCTTCCAAAGGGGTTGAAGAACATTTTTAAAGTTTGGATGGTCATCCC
65 GGTTAGATACCTTAAAAGCTTCCAAAGGGGTTGAAGAACATTTTTAAAGTTCGGATGGTCATCCC
* * **
193046 ACTCCAACGATTCCCACCATTCTGTGTCTGACGTGATGGTAAGAGAAGGTGGAGCATATGCAAAT
130 ACTCCAACCATTCCCACCATTCTGTCTCTGACCCGATGGTAAGAGAAGGTGGAGCATATGCAAAT
*
193111 GGCTGCCCATTGCCAACAAGGGGAACAAATGGAGGAATTCTCTTCAGTTTATCACAATCTCCA
195 GGCTGCCCATTGCCAACAAGGGGAACAAATGGAGGAATTCTCTTCAGTTTATAACAATCTCCA
193174 AAAACTTTGA
Statistics
Matches: 241, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
297 177 0.73
298 57 0.24
299 7 0.03
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (297 bp):
ATGAAATGGTATTAAAATGGAGAAATTAGATTTATAAAATAAATAAAATAAACTAAAATATAATG
GTTAGATACCTTAAAAGCTTCCAAAGGGGTTGAAGAACATTTTTAAAGTTCGGATGGTCATCCCA
CTCCAACCATTCCCACCATTCTGTCTCTGACCCGATGGTAAGAGAAGGTGGAGCATATGCAAATG
GCTGCCCATTGCCAACAAGGGGAACAAATGGAGGAATTCTCTTCAGTTTATAACAATCTCCAGCA
TCTTGGATAAGTTGGATAACTTGGATAAGTTGGATTA
Found at i:197078 original size:18 final size:17
Alignment explanation
Indices: 197048--197081 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
197038 AATTACATTT
197048 ATTTTCTTTAATTTAAG
1 ATTTTCTTTAATTTAAG
*
197065 ATTTTTTTTCAATTTAA
1 ATTTTCTTT-AATTTAA
197082 TGTATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTTCTTTAATTTAAG
Found at i:200447 original size:13 final size:13
Alignment explanation
Indices: 200431--200460 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
200421 TAAAACTTGA
200431 AATTAAATCTAAT
1 AATTAAATCTAAT
200444 AATTAAATCTAAT
1 AATTAAATCTAAT
200457 AATT
1 AATT
200461 TTAATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAATCTAAT
Found at i:203219 original size:14 final size:15
Alignment explanation
Indices: 203202--203231 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
203192 ATAATTTTGA
203202 TTAATA-TAAATATT
1 TTAATAGTAAATATT
203216 TTAATAGTAAATATT
1 TTAATAGTAAATATT
203231 T
1 T
203232 AGAAGGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATAGTAAATATT
Found at i:209307 original size:13 final size:13
Alignment explanation
Indices: 209270--209308 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
209260 TAATCTTTGA
*
209270 TTTATTATTTTAT
1 TTTATTTTTTTAT
* *
209283 TTTAGTTATTTAT
1 TTTATTTTTTTAT
209296 TTTATTTTTTTAT
1 TTTATTTTTTTAT
209309 CTGACTTGGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTATTTTTTTAT
Found at i:217162 original size:43 final size:43
Alignment explanation
Indices: 217114--217448 Score: 420
Period size: 43 Copynumber: 7.8 Consensus size: 43
217104 CTGCTAAAAG
217114 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
1 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* *
217157 CCATGACCTTTAGTGGCGCTTTTCCCACAAACGCCGCTATAGA
1 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * * **
217200 TCAAGACCTTTAGCAGCCCTTTTTTCACAAACGCCGCTATAGA
1 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * * * *
217243 CCGTGACCTTTAGCGGTGTTTTTCCCACAAATGCCGCTATAGA
1 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * *
217286 TCAAGACCTTTAGCAGCGCTTTTTCCACAAACGCCGCTATAGA
1 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * *
217329 TCAGGACCTTTAGCGGCGCTTTTTCCACAAATGCCGCTATAGA
1 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * *
217372 TCAGGACCTTTAGCGGTGCTTTTCCCACAAACGCCGTTATAGA
1 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * * * * *
217415 ACA-AACCTTTAGCGACGCTTCTCGCAAAAACGCC
1 TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCC
217449 ACTAAAAACA
Statistics
Matches: 251, Mismatches: 41, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
42 25 0.10
43 226 0.90
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (43 bp):
TCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
Found at i:219361 original size:75 final size:77
Alignment explanation
Indices: 219227--219382 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 77
219217 TGATTTTATA
*
219227 AAACATTTATTATTATTTATAAATTATTAAGAAAAAAATGATTAAATGGCTGTAATTAATTATTA
1 AAACATTTATTATTATTTAT--ATTAATAAGAAAAAAATGATTAAATGGCTGTAATTAATTATTA
219292 AGTTAGAATTATCC
64 AGTTAGAATTATCC
219306 AAACATTTATTATTATTT-T-TTAATAAGAAAAAAATGATTAAAATGGCTGT-ATTAATTATTAA
1 AAACATTTATTATTATTTATATTAATAAGAAAAAAATGATT-AAATGGCTGTAATTAATTATTAA
219368 GTTAGAATTATCC
65 GTTAGAATTATCC
219381 AA
1 AA
219383 TGTAAGCAAT
Statistics
Matches: 75, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
75 46 0.61
76 10 0.13
78 1 0.01
79 18 0.24
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (77 bp):
AAACATTTATTATTATTTATATTAATAAGAAAAAAATGATTAAATGGCTGTAATTAATTATTAAG
TTAGAATTATCC
Found at i:219833 original size:7 final size:7
Alignment explanation
Indices: 219823--219940 Score: 62
Period size: 7 Copynumber: 16.6 Consensus size: 7
219813 TCATAAAACA
219823 TAAACCC
1 TAAACCC
219830 TAAACCCC
1 TAAA-CCC
219838 T-AACCTC
1 TAAACC-C
219845 T-AACCC
1 TAAACCC
*
219851 TTAACCCC
1 -TAAACCC
*
219859 TAACCCC
1 TAAACCC
*
219866 TAAACCT
1 TAAACCC
219873 TAAACCC
1 TAAACCC
219880 -AAACCC
1 TAAACCC
*
219886 TTAAACCA
1 -TAAACCC
* *
219894 TAATCCA
1 TAAACCC
* *
219901 TAATCCA
1 TAAACCC
*
219908 TAATCCC
1 TAAACCC
*
219915 TAAACACA
1 TAAAC-CC
*
219923 TAATCCC
1 TAAACCC
*
219930 TAAACCT
1 TAAACCC
219937 TAAA
1 TAAA
219941 ATCATTTAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
6 9 0.10
7 64 0.70
8 18 0.20
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:219849 original size:21 final size:22
Alignment explanation
Indices: 219823--219892 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 22
219813 TCATAAAACA
*
219823 TAAACCCTAAACCCCTAACCTC
1 TAAACCCTAAACCCCTAACCCC
*
219845 T-AACCCTTAACCCCTAACCCC
1 TAAACCCTAAACCCCTAACCCC
* * *
219866 TAAACCTTAAA-CCCAAACCCT
1 TAAACCCTAAACCCCTAACCCC
219887 TAAACC
1 TAAACC
219893 ATAATCCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 33 0.80
22 8 0.20
ACGTcount: A:0.37, C:0.44, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAACCCTAAACCCCTAACCCC
Found at i:219926 original size:15 final size:14
Alignment explanation
Indices: 219887--219935 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
219877 CCCAAACCCT
*
219887 TAAACCATAATCCA
1 TAAACCATAATCCC
*
219901 TAATCCATAATCCC
1 TAAACCATAATCCC
219915 TAAACACATAATCCC
1 TAAAC-CATAATCCC
219930 TAAACC
1 TAAACC
219936 TTAAAATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:220621 original size:7 final size:7
Alignment explanation
Indices: 220609--220652 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
220599 CCTTAAACCA
220609 CATAATC
1 CATAATC
220616 CATAATC
1 CATAATC
220623 CATAATC
1 CATAATC
*
220630 CCTAATC
1 CATAATC
* *
220637 CCTAAAC
1 CATAATC
220644 ACATAATC
1 -CATAATC
220652 C
1 C
220653 TTAAATTACC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (7 bp):
CATAATC
Found at i:220965 original size:40 final size:40
Alignment explanation
Indices: 220882--220957 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
220872 TTTTGCGGCA
* *
220882 TTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCCACG
1 TTTTTCAAAAAGCACCGCTAATGCGCGACCTATAGCCACG
* *
220922 TTTTTCAAGAAGCACCGCTAATGCGCGATCTATAGC
1 TTTTTCAAAAAGCACCGCTAATGCGCGACCTATAGC
220958 AGTGTTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (40 bp):
TTTTTCAAAAAGCACCGCTAATGCGCGACCTATAGCCACG
Found at i:225043 original size:29 final size:30
Alignment explanation
Indices: 224999--225058 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
224989 ATTTCTTTTA
*
224999 TTAAATTAAATATTGA-CAATTTTTTATAT
1 TTAAATTAAATATTGATCAATTTTGTATAT
*
225028 TTAAATTAAACT-TTGATTAATTTTGTATAT
1 TTAAATTAAA-TATTGATCAATTTTGTATAT
225058 T
1 T
225059 AATTTTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (30 bp):
TTAAATTAAATATTGATCAATTTTGTATAT
Found at i:237296 original size:59 final size:59
Alignment explanation
Indices: 237204--237480 Score: 363
Period size: 55 Copynumber: 4.8 Consensus size: 59
237194 AAATGCTGGG
* ** *
237204 TCATATTTCATAATAATTTTACGAATAATTAATTAATTTTTTATTAATTAAATAAATCA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATTAAATAAATAA
* *
237263 TCATATTTCATAATAATTTTATGAATAATTAA-T--TTTT-GATTAGTTAGATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATTAAATAAATAA
* * * * *
237318 TCATATTTCATAATAATTTTACGAATACTTAATTAATTTCCAATTAATTAATTAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATTAAATAAATAA
* * * *
237377 TCTTATTTCATAATAATTGTATG---AA-TAATTAGTTTTCGATTAATTAAATAAGTAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATTAAATAAATAA
237432 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATT
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATT
237481 TACATAAACA
Statistics
Matches: 186, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
55 90 0.48
56 6 0.03
58 6 0.03
59 84 0.45
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (59 bp):
TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATTAAATAAATAA
Found at i:237342 original size:114 final size:114
Alignment explanation
Indices: 237204--237480 Score: 419
Period size: 114 Copynumber: 2.4 Consensus size: 114
237194 AAATGCTGGG
** *
237204 TCATATTTCATAATAATTTTACGAATAATTAATTAATTTTTTATTAATTAAATAAATCATCATAT
1 TCATATTTCATAATAATTTTACGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATAT
* * * *
237269 TTCATAATAATTTTATGAATAATTAATTTTTGATTAGTTAGATAAATAA
66 TTCATAATAATTGTATGAATAATTAATTTTCGATTAATTAAATAAATAA
* * * *
237318 TCATATTTCATAATAATTTTACGAATACTTAATTAATTTCCAATTAATTAATTAAATAATCTTAT
1 TCATATTTCATAATAATTTTACGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATAT
* *
237383 TTCATAATAATTGTATGAATAATTAGTTTTCGATTAATTAAATAAGTAA
66 TTCATAATAATTGTATGAATAATTAATTTTCGATTAATTAAATAAATAA
* *
237432 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATT
1 TCATATTTCATAATAATTTTACGAATAATTAATTAATTTTCAATTAATT
237481 TACATAAACA
Statistics
Matches: 146, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 146 1.00
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (114 bp):
TCATATTTCATAATAATTTTACGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATAT
TTCATAATAATTGTATGAATAATTAATTTTCGATTAATTAAATAAATAA
Found at i:241048 original size:36 final size:36
Alignment explanation
Indices: 241002--241073 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
240992 ATTGCTATAA
* *
241002 ATATCACAAACTGAGTCAGTTTTCAAAATTTTAATT
1 ATATCACAAACCGAGTCAGTTTTCAAAACTTTAATT
* * *
241038 ATATTACAAACCGATTTAGTTTTCAAAACTTTAATT
1 ATATCACAAACCGAGTCAGTTTTCAAAACTTTAATT
241074 TTTGCTGTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (36 bp):
ATATCACAAACCGAGTCAGTTTTCAAAACTTTAATT
Found at i:242075 original size:22 final size:22
Alignment explanation
Indices: 242045--242095 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
242035 AAATGGTATT
*
242045 AAACTAAAGA-ATTAAAGTGCA
1 AAACAAAAGAGATTAAAGTGCA
* *
242066 AATACAAAAGAGTTTAAAGTGCT
1 AA-ACAAAAGAGATTAAAGTGCA
242089 AAACAAA
1 AAACAAA
242096 TAAATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 12 0.48
23 11 0.44
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.20
Consensus pattern (22 bp):
AAACAAAAGAGATTAAAGTGCA
Found at i:244308 original size:41 final size:41
Alignment explanation
Indices: 244260--244342 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
244250 AAAAATGAAA
*
244260 CAAAATGAAATTTATTTCAAAAGTAACAAGATAAAAACAAC
1 CAAAATGAAATTGATTTCAAAAGTAACAAGATAAAAACAAC
244301 CAAAATGAAATTGATTTCAAAAGTAACAAGATAAAAACAAC
1 CAAAATGAAATTGATTTCAAAAGTAACAAGATAAAAACAAC
244342 C
1 C
244343 TATTTTATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.20
Consensus pattern (41 bp):
CAAAATGAAATTGATTTCAAAAGTAACAAGATAAAAACAAC
Found at i:244864 original size:32 final size:33
Alignment explanation
Indices: 244821--244889 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 33
244811 TTGTCTCACT
*
244821 TCGATAGTGATATCACG-ACCCAGAGCCTGGTA
1 TCGATACTGATATCACGAACCCAGAGCCTGGTA
*
244853 TCGATACTGATATCACGATACCTAGAGCCTGGTA
1 TCGATACTGATATCACGA-ACCCAGAGCCTGGTA
244887 TCG
1 TCG
244890 TGATATCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 16 0.48
34 17 0.52
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (33 bp):
TCGATACTGATATCACGAACCCAGAGCCTGGTA
Found at i:245361 original size:3 final size:3
Alignment explanation
Indices: 245353--245390 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
245343 TGCGTGTTTT
* *
245353 TTG TTG TTG TTG CTA TTG TTG TTG TTG TTG TTG -TG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
245391 GTATGATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.03, C:0.03, G:0.32, T:0.63
Consensus pattern (3 bp):
TTG
Found at i:247452 original size:14 final size:15
Alignment explanation
Indices: 247428--247462 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
247418 TATACACATT
247428 ACCATATAAATACTA
1 ACCATATAAATACTA
247443 ACCATA-AAATACTA
1 ACCATATAAATACTA
247457 ATCCAT
1 A-CCAT
247463 GATTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:249622 original size:28 final size:28
Alignment explanation
Indices: 249568--249624 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
249558 TTTGTTTGTT
*
249568 TTTATTATAATAACTTTATAATTTATTA
1 TTTATTATAATAACTTTATAATATATTA
*
249596 TTTATTATTATAACCTTTATAA-ATATTA
1 TTTATTATAATAA-CTTTATAATATATTA
249624 T
1 T
249625 AAAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACTTTATAATATATTA
Found at i:253923 original size:544 final size:547
Alignment explanation
Indices: 253198--254288 Score: 2064
Period size: 544 Copynumber: 2.0 Consensus size: 547
253188 ACATATTGAT
253198 ATTTCCGTTTAGTTTGACAAATATTTTACCCCCTCTCTCCCACCCCCCCTTATTTTGTAGTGTCC
1 ATTTCCGTTTAGTTTGACAAATATTTTACCCCCTCTCTCCCACCCCCCCTTATTTTGTAGTGTCC
253263 CAATGTGCAAAAAAGTATAAGGTATATATATATGTTATATCATCATGCGGTTTAAAAGGTAAGTC
66 CAATGTGCAAAAAAGTATAAGGTATATATATATGTTATATCATCATGCGGTTTAAAAGGTAAGTC
253328 ACATTAATTTTTTTAATGGAACTAAACATGAGGGAAGTC-AAAAAAAAAAAAATTTGGGGTCAAA
131 ACATTAATTTTTTTAATGGAACTAAACATGAGGGAAGTCAAAAAAAAAAAAAATTT-GGGTCAAA
253392 ATGAAATTTTAATTTTTAATAGTTTATTATCTTTATAACTTTTAAAAGATTAAATTAAATTTTAA
195 ATGAAATTTTAATTTTTAATAGTTTATTATCTTTATAACTTTTAAAAGATTAAATTAAATTTTAA
*
253457 TAATTTTA-AGATGGCCAAAATGCAAGTTTAGATTTACTATTTTG-AAATTTTAAAATTTTCTAA
260 TAATTTTAGAGATGGCCAAAATGCAAGTTTACATTTACTATTTTGAAAATTTTAAAATTTTCTAA
* * * *
253520 AGAGTTAAAATAATAATTTTTTATTTTAAGGGG-CCGGGCCCCTACCATCCCTCCTACATTCACC
325 AGAGCTAAAACAATAATTTTCTATTTTAAGGGGACCAGGCCCCTACCATCCCTCCTACATTCACC
253584 TCTGGAGCTAAAGAAAATATTGGTCAAAATATTGAATATACACATTTCGAAAAATAAAGCTTAAA
390 TCTGGAGCTAAAGAAAATATTGGTCAAAATATTGAATATACACATTTCGAAAAATAAAGCTTAAA
*
253649 AACAATCAAATTATAATAGAAAAACTAAATCAACCATAAACAAATAGTATATGGAGCTTCTATAC
455 AACAATCAAATTATAAAAGAAAAACTAAATCAACCATAAACAAATAGTATATGGAGCTTCTATAC
253714 AAAGAGATATCTCGATGCTCCAAACTAA
520 AAAGAGATATCTCGATGCTCCAAACTAA
253742 ATTTCCGTTTAGTTTGACAAATATTTTACCCCCTCTCTCCCACCCCCCCTTATTTTGTAGTGTCC
1 ATTTCCGTTTAGTTTGACAAATATTTTACCCCCTCTCTCCCACCCCCCCTTATTTTGTAGTGTCC
253807 CAATGTGCAAAAAAGTATAAGGTATATATATATGTTATATCATCATGCGGTTTAAAAGGTAAGTC
66 CAATGTGCAAAAAAGTATAAGGTATATATATATGTTATATCATCATGCGGTTTAAAAGGTAAGTC
*
253872 ACATTAATTTTTTTAATGGAACTAAACATGAGGGAAGTCAAAAAAAAAAAAAATTTGGGTCGAAA
131 ACATTAATTTTTTTAATGGAACTAAACATGAGGGAAGTCAAAAAAAAAAAAAATTTGGGTCAAAA
*
253937 TGAAATTTTAATTTTTAATAGTTTATTATCTTTATAATTTTTAAAAGATTAAATTAAATTTTAAT
196 TGAAATTTTAATTTTTAATAGTTTATTATCTTTATAACTTTTAAAAGATTAAATTAAATTTTAAT
254002 AATTTTAGAGATGGCCAAAATGCAAGTTTACATTTACTATTTTGAAAATTTTAAAATTTTCTAAA
261 AATTTTAGAGATGGCCAAAATGCAAGTTTACATTTACTATTTTGAAAATTTTAAAATTTTCTAAA
*
254067 GAGCTAAAACAATAATTTTCTATTTTAAGGGGACTAGGCCCCTACCATCCCTCCTACATTCACCT
326 GAGCTAAAACAATAATTTTCTATTTTAAGGGGACCAGGCCCCTACCATCCCTCCTACATTCACCT
254132 CTGGAGCTAAAGAAAATATTGGTCAAAATATTGAATATACACATTTCGAAAAATAAAGCTTAAAA
391 CTGGAGCTAAAGAAAATATTGGTCAAAATATTGAATATACACATTTCGAAAAATAAAGCTTAAAA
254197 ACAATCAAATTATAAAAGAAAAACTAAATCAACCATAAACAAATAGTATATGGAGCTTCTATACA
456 ACAATCAAATTATAAAAGAAAAACTAAATCAACCATAAACAAATAGTATATGGAGCTTCTATACA
254262 AAGAGATATCTCGATGCTCCAAACTAA
521 AAGAGATATCTCGATGCTCCAAACTAA
254289 CATATGAAAT
Statistics
Matches: 534, Mismatches: 9, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
544 248 0.46
545 51 0.10
546 49 0.09
547 186 0.35
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (547 bp):
ATTTCCGTTTAGTTTGACAAATATTTTACCCCCTCTCTCCCACCCCCCCTTATTTTGTAGTGTCC
CAATGTGCAAAAAAGTATAAGGTATATATATATGTTATATCATCATGCGGTTTAAAAGGTAAGTC
ACATTAATTTTTTTAATGGAACTAAACATGAGGGAAGTCAAAAAAAAAAAAAATTTGGGTCAAAA
TGAAATTTTAATTTTTAATAGTTTATTATCTTTATAACTTTTAAAAGATTAAATTAAATTTTAAT
AATTTTAGAGATGGCCAAAATGCAAGTTTACATTTACTATTTTGAAAATTTTAAAATTTTCTAAA
GAGCTAAAACAATAATTTTCTATTTTAAGGGGACCAGGCCCCTACCATCCCTCCTACATTCACCT
CTGGAGCTAAAGAAAATATTGGTCAAAATATTGAATATACACATTTCGAAAAATAAAGCTTAAAA
ACAATCAAATTATAAAAGAAAAACTAAATCAACCATAAACAAATAGTATATGGAGCTTCTATACA
AAGAGATATCTCGATGCTCCAAACTAA
Found at i:256697 original size:21 final size:21
Alignment explanation
Indices: 256640--256700 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
256630 ATAATTACGC
256640 GTATAAAAAGACGAATGTTGT
1 GTATAAAAAGACGAATGTTGT
* * **
256661 GGAT--ATA-ATTAATGTTGT
1 GTATAAAAAGACGAATGTTGT
256679 GTATAAAAAGACGAATGTTGT
1 GTATAAAAAGACGAATGTTGT
256700 G
1 G
256701 GAAAGCATAA
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
18 12 0.41
19 2 0.07
20 2 0.07
21 13 0.45
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (21 bp):
GTATAAAAAGACGAATGTTGT
Found at i:257712 original size:39 final size:39
Alignment explanation
Indices: 257669--257752 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 39
257659 TTTTAAGGTT
257669 TTAAAAATATATGTA-ACTTATTTTTTAAAA-TTAAAATTA
1 TTAAAAATATATGTATA-TTATTTTTTAAAACTTAAAA-TA
* *
257708 TTAAAAATGTATTTATTATTATTTTTTAAAACTTTAAAATA
1 TTAAAAATATATGTA-TATTATTTTTTAAAAC-TTAAAATA
257749 TTAA
1 TTAA
257753 TTAAATGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
39 13 0.33
40 13 0.33
41 7 0.18
42 6 0.15
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (39 bp):
TTAAAAATATATGTATATTATTTTTTAAAACTTAAAATA
Found at i:259173 original size:15 final size:15
Alignment explanation
Indices: 259150--259192 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
259140 ATAGCATGTT
259150 TCATATCTTATCTTA
1 TCATATCTTATCTTA
* *
259165 TCTTATCTTATCATA
1 TCATATCTTATCTTA
259180 TCCCATATCTTAT
1 T--CATATCTTAT
259193 TATATCACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 14 0.61
17 9 0.39
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (15 bp):
TCATATCTTATCTTA
Found at i:260810 original size:2 final size:2
Alignment explanation
Indices: 260803--260833 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
260793 CCCATGCATT
260803 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
260834 AATTTATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:262344 original size:142 final size:142
Alignment explanation
Indices: 262082--262586 Score: 884
Period size: 142 Copynumber: 3.6 Consensus size: 142
262072 CAAGTGTAAG
*
262082 GGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGA
1 GGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGA
* *
262147 TATTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAAAAATCTTATCTCCC
66 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCC
262212 TGAGATTACAAC
131 TGAGATTACAAC
*
262224 GGAGTAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGA
1 GGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGA
* *
262289 TCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCTAGAAATCTTATCTCCC
66 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCC
*
262354 TGAGATTGCAAC
131 TGAGATTACAAC
* *
262366 GGAGCAGATTGAAGCTAGTAATCCCATCTCCCTAAGATTACAGTGGAGTGGATTAAAATAAAGGA
1 GGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGA
*
262431 TCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCC
66 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCC
*
262496 TGAGATTACAGC
131 TGAGATTACAAC
* *
262508 GGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTACGGTGGAGCGGATTAAAATAAGGGA
1 GGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGA
*
262573 TCTTATCTTTCTGA
66 TCTTATCTCTCTGA
262587 GTCTAGTCCC
Statistics
Matches: 343, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 343 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (142 bp):
GGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGA
TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCC
TGAGATTACAAC
Found at i:269630 original size:142 final size:142
Alignment explanation
Indices: 269374--269900 Score: 856
Period size: 142 Copynumber: 3.7 Consensus size: 142
269364 AAGTGTAAGA
* * * * *
269374 GAGCAGATTGAAGCTTGTAATCCTATCTCCCTGAGATTATAGTGAAGCGGATTAAAATAAAGGAT
1 GAGCAGATTGAAGCTAGTAATCCCATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGAT
*
269439 CTTATCTATCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCCT
66 CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCCT
269504 GAGATTACAGCG
131 GAGATTACAGCG
* *
269516 GAGCAGATTGAAGCTGGTAATCCCATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAAAGGAT
1 GAGCAGATTGAAGCTAGTAATCCCATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGAT
* *
269581 CTTATCTCTCTGAAGTTACAGCATAGTAGATCGCATTATATTGGAGCCAGAAATCTTATCTCCCT
66 CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCCT
*
269646 GAGATTACAACG
131 GAGATTACAGCG
*
269658 GAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGAT
1 GAGCAGATTGAAGCTAGTAATCCCATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGAT
* * *
269723 CTTATCTCTATGAAGTTACAACAGAGTAGATCGCATTAGATTAGAGCCAGAAATCTTATCTCCCT
66 CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCCT
* * *
269788 GAGATCATAGCA
131 GAGATTACAGCG
* * *
269800 GAGCAGATTGAAGTTAGTAATCCCATCTCCCTAAGATTACGGTGGAGCGGATTAAAATAAGGGAT
1 GAGCAGATTGAAGCTAGTAATCCCATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGAT
*
269865 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
269901 CAGGTCTTAT
Statistics
Matches: 356, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 356 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (142 bp):
GAGCAGATTGAAGCTAGTAATCCCATCTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGAT
CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATTAGATTGGAGCCAGAAATCTTATCTCCCT
GAGATTACAGCG
Found at i:270632 original size:27 final size:25
Alignment explanation
Indices: 270593--270646 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
270583 AAAGCAGGCA
270593 AACAGCAGAAAAACGATACAAAAAGGG
1 AACAGCAGAAAAA--ATACAAAAAGGG
*
270620 AACAG-AGAGAAAAATAGAAAAAGGG
1 AACAGCAGA-AAAAATACAAAAAGGG
270645 AA
1 AA
270647 AAAGATGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 13 0.52
26 3 0.12
27 9 0.36
ACGTcount: A:0.63, C:0.09, G:0.24, T:0.04
Consensus pattern (25 bp):
AACAGCAGAAAAAATACAAAAAGGG
Found at i:275126 original size:2 final size:2
Alignment explanation
Indices: 275119--275159 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
275109 TCCAGTTTTG
275119 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
275160 CCCCTCTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:287929 original size:10 final size:10
Alignment explanation
Indices: 287882--287930 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
287872 ATAGCATGTT
287882 TCATATCTTA
1 TCATATCTTA
*
287892 TCTTATCTTA
1 TCATATCTTA
*
287902 TCTTATCTTA
1 TCATATCTTA
287912 TCTTATATCTTA
1 TC--ATATCTTA
287924 TCATATC
1 TCATATC
287931 ACACCCCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 26 0.74
12 9 0.26
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.55
Consensus pattern (10 bp):
TCATATCTTA
Found at i:287931 original size:5 final size:5
Alignment explanation
Indices: 287885--287917 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
287875 GCATGTTTCA
287885 TATCT TATCT TATCT TATCT TATCT TATCT TAT
1 TATCT TATCT TATCT TATCT TATCT TATCT TAT
287918 ATCTTATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (5 bp):
TATCT
Found at i:288723 original size:34 final size:32
Alignment explanation
Indices: 288664--288732 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
288654 TTGTTTCCCT
* * *
288664 TCGATAGTGATATCGCGACCTAGAGCCTGGTA
1 TCGACAGTGATATCACGACCTAGAGCCTAGTA
288696 TCGACAGTGATATCACGATACCTAGAGCCTAGTA
1 TCGACAGTGATATCACG--ACCTAGAGCCTAGTA
288730 TCG
1 TCG
288733 CGATATCCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 15 0.47
34 17 0.53
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (32 bp):
TCGACAGTGATATCACGACCTAGAGCCTAGTA
Found at i:289183 original size:2 final size:2
Alignment explanation
Indices: 289176--289226 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
289166 GTTAAACTTT
* * * *
289176 TG TG TG TG TG AG TG TG TG TG TG TG TG TT TT TT TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
289218 TG TG TG TG T
1 TG TG TG TG T
289227 TGGTGTGATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.02, C:0.00, G:0.43, T:0.55
Consensus pattern (2 bp):
TG
Found at i:292450 original size:10 final size:11
Alignment explanation
Indices: 292435--292463 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
292425 TCTTGTTCGA
292435 TTTATTTTA-T
1 TTTATTTTATT
292445 TTTATTTTATT
1 TTTATTTTATT
292456 TTTATTTT
1 TTTATTTT
292464 TAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:293415 original size:18 final size:20
Alignment explanation
Indices: 293392--293434 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
293382 CATATACATG
*
293392 CATACATTTT-A-TAATACA
1 CATACATTTTAATTAATAAA
293410 CATACATTTTAATTAATAAA
1 CATACATTTTAATTAATAAA
293430 CATAC
1 CATAC
293435 TTATACATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 11 0.50
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (20 bp):
CATACATTTTAATTAATAAA
Found at i:294851 original size:2 final size:2
Alignment explanation
Indices: 294844--294900 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
294834 ATGTTAAACT
294844 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
294886 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
294901 TTATTGTGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:295235 original size:2 final size:2
Alignment explanation
Indices: 295228--295262 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
295218 CCCATGCATG
295228 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
295263 AATTTATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:297224 original size:2 final size:2
Alignment explanation
Indices: 297217--297399 Score: 366
Period size: 2 Copynumber: 91.5 Consensus size: 2
297207 TCCAGTTTTG
297217 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
297259 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
297301 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
297343 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
297385 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
297400 AATACACTCA
Statistics
Matches: 181, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 181 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:301712 original size:4 final size:5
Alignment explanation
Indices: 301689--301717 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
301679 ATTAAATTAG
301689 TTATT TTATT TTATT TTA-T TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
301718 ATCTTAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:302870 original size:24 final size:26
Alignment explanation
Indices: 302825--302891 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 26
302815 AGCTTTCCAA
*
302825 ATAATATGCCACAAAGGCCTTT-TAG
1 ATAATTTGCCACAAAGGCCTTTATAG
*
302850 ATAATTTGCCAC-AAGGGCTTTATAG
1 ATAATTTGCCACAAAGGCCTTTATAG
**
302875 ATAATTCACCACAAAGG
1 ATAATTTGCCACAAAGG
302892 TTCGACTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 8 0.22
25 24 0.67
26 4 0.11
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (26 bp):
ATAATTTGCCACAAAGGCCTTTATAG
Done.