Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020694.1 Corchorus olitorius cultivar O-4 contig20727, whole genome shotgun sequence
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: 169186
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:936 original size:14 final size:14
Alignment explanation
Indices: 917--950 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
907 TTTTATAATT
917 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
931 ATTTTATTTTTACT
1 ATTTTATTTTTACC
945 ATTTTA
1 ATTTTA
951 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:5870 original size:20 final size:22
Alignment explanation
Indices: 5827--5870 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5817 AGAACGATAC
*
5827 AAAGGGATGAGAAATTAGAGAA
1 AAAGGGATGAGAAATTACAGAA
5849 AAAGGGATGAGAAA-T-CAGAA
1 AAAGGGATGAGAAATTACAGAA
5869 AA
1 AA
5871 TCTTGGCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.57, C:0.02, G:0.30, T:0.11
Consensus pattern (22 bp):
AAAGGGATGAGAAATTACAGAA
Found at i:12106 original size:37 final size:37
Alignment explanation
Indices: 12033--12585 Score: 346
Period size: 37 Copynumber: 14.9 Consensus size: 37
12023 TATAAAAAAG
* * * * * *
12033 CTAAGCAGGGATCTTGAACAAGAATTCGATGAGACAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * * *
12070 CTAAACAGAGACCTTAAAAAAGGATTCGTTGAGACAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * *
12107 C-AATGCAGGGACCTTAAACAAGGATTTGATAAGACAC
1 CTAA-ACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * *
12144 CTAGACAGGGACCTTAAATAAGGATTTAATAAGACAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * * * *
12181 CTAAACAAGAATCTTGAATAAGAATTTGATGAGACAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * ** * ** *
12218 CTAAACAGGGACCATGAACCAGGTTTTGACAAGAAAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
** * * *
12255 CTAAACATAGATCTTGAACT-A-GATTTTGATAAGACAC
1 CTAAACAGGGACCTT-AAATAAGGA-TTTGATGAGACAC
* ** * ** *
12292 CTAAACATGGATTTTAAATAATGATTTGACAAGAAAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * * * **
12329 CTAAATAGCGATCTTGAACCA-GATTTAGATGAGACAC
1 CTAAACAGGGACCTTAAATAAGGATTT-GATGAGACAC
* * ** * *
12366 CTAAATAGGGATCC-TGAACCA-GATTTCGTTGAGACCC
1 CTAAACAGGGA-CCTTAAATAAGGATTT-GATGAGACAC
* *
12403 CTAAACAGGGACCTTAAATAAGGATTTAATAAGACAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * *
12440 CTAAACAGGGACCTTAAACAAGGATTTGATAAGAAAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * * * *
12477 CTAAACAGGAATCTTGAACAA-GATTTTGATGAAACAC
1 CTAAACAGGGACCTTAAATAAGGA-TTTGATGAGACAC
* *
12514 CTAAACATGGACCTTAAATAAGGATTTGATAAGACAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
* * * * * * *
12551 TTAAATAGGAATCTTGAACAAGGTTTTGATGAGAC
1 CTAAACAGGGACCTTAAATAAGGATTTGATGAGAC
12586 TGAATTTTGT
Statistics
Matches: 405, Mismatches: 99, Indels: 24
0.77 0.19 0.05
Matches are distributed among these distances:
36 15 0.04
37 378 0.93
38 12 0.03
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (37 bp):
CTAAACAGGGACCTTAAATAAGGATTTGATGAGACAC
Found at i:12179 original size:74 final size:74
Alignment explanation
Indices: 12033--12585 Score: 463
Period size: 74 Copynumber: 7.5 Consensus size: 74
12023 TATAAAAAAG
* * * * * * *
12033 CTAAGCAGGGATCTTGAACAAGAATTCGATGAGACACCTAAACAGAGACCTTAAAAAAGGATTCG
1 CTAAACAGGGATCTTGAACAAGGATTTGATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* *
12098 TTGAGACAC
66 ATAAGACAC
* * * * *
12107 C-AATGCAGGGACCTTAAACAAGGATTTGATAAGACACCTAGACAGGGACCTTAAATAAGGATTT
1 CTAA-ACAGGGATCTTGAACAAGGATTTGATAAGACACCTAAACAGGGACCTTAAACAAGGATTT
*
12171 AATAAGACAC
65 GATAAGACAC
* * * * * * * * *
12181 CTAAACAAGAATCTTGAATAAGAATTTGATGAGACACCTAAACAGGGACCATGAACCAGGTTTTG
1 CTAAACAGGGATCTTGAACAAGGATTTGATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* *
12246 ACAAGAAAC
66 ATAAGACAC
** * * ** * *
12255 CTAAACATAGATCTTGAACTA-GATTTTGATAAGACACCTAAACATGGATTTTAAATAATGATTT
1 CTAAACAGGGATCTTGAACAAGGA-TTTGATAAGACACCTAAACAGGGACCTTAAACAAGGATTT
* *
12319 GACAAGAAAC
65 GATAAGACAC
* * * * * * *
12329 CTAAATAGCGATCTTGAACCA-GATTTAGATGAGACACCTAAATAGGGATCC-TGAACCA-GATT
1 CTAAACAGGGATCTTGAACAAGGATTT-GATAAGACACCTAAACAGGGA-CCTTAAACAAGGATT
* * *
12391 TCGTTGAGACCC
64 T-GATAAGACAC
* * * *
12403 CTAAACAGGGACCTTAAATAAGGATTTAATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
1 CTAAACAGGGATCTTGAACAAGGATTTGATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
*
12468 ATAAGAAAC
66 ATAAGACAC
* * *
12477 CTAAACAGGAATCTTGAACAA-GATTTTGATGAA-ACACCTAAACATGGACCTTAAATAAGGATT
1 CTAAACAGGGATCTTGAACAAGGA-TTTGAT-AAGACACCTAAACAGGGACCTTAAACAAGGATT
12540 TGATAAGACAC
64 TGATAAGACAC
* * * * *
12551 TTAAATAGGAATCTTGAACAAGGTTTTGATGAGAC
1 CTAAACAGGGATCTTGAACAAGGATTTGATAAGAC
12586 TGAATTTTGT
Statistics
Matches: 377, Mismatches: 89, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
73 16 0.04
74 346 0.92
75 15 0.04
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (74 bp):
CTAAACAGGGATCTTGAACAAGGATTTGATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
ATAAGACAC
Found at i:12287 original size:111 final size:110
Alignment explanation
Indices: 12041--12580 Score: 485
Period size: 111 Copynumber: 4.9 Consensus size: 110
12031 AGCTAAGCAG
* * * * * * *
12041 GGATCTTGAACAAGAATTCGATGAGACACCTAAACA-GAGACCTTAAAAAAGGATTCGTTGAGAC
1 GGATCTTGAACAAGATTTTGATAAGACACCTAAACATG-GACCTTAAATAAGGATTTGATAAGAC
* * * * *
12105 ACC-AATGCAGGGACCTTAAACAAGGATTTGATAAGACACCTAGACA
65 ACCTAA-ACAGGGACCTTGAACAAGGTTTTGATAAGAAACCTAAACA
* * * * * * * * * *
12151 GGGACCTTAAATAAGGA-TTTAATAAGACACCTAAACAAGAATCTTGAATAAGAATTTGATGAGA
1 -GGATCTTGAACAA-GATTTTGATAAGACACCTAAACATGGACCTTAAATAAGGATTTGATAAGA
* * *
12215 CACCTAAACAGGGACCATGAACCAGGTTTTGACAAGAAACCTAAACA
64 CACCTAAACAGGGACCTTGAACAAGGTTTTGATAAGAAACCTAAACA
* * ** * * *
12262 TAGATCTTGAACTAGATTTTGATAAGACACCTAAACATGGATTTTAAATAATGATTTGACAAGAA
1 -GGATCTTGAACAAGATTTTGATAAGACACCTAAACATGGACCTTAAATAAGGATTTGATAAGAC
* * * * * * * * *
12327 ACCTAAATAGCGATCTTGAACCAGATTTAGATGAGACACCTAAATA
65 ACCTAAACAGGGACCTTGAACAAGGTTTTGATAAGAAACCTAAACA
* * * * * * * *
12373 GGGATCCTGAACCAGATTTCGTTGAGACCCCTAAACAGGGACCTTAAATAAGGATTTAATAAGAC
1 -GGATCTTGAACAAGATTTTGATAAGACACCTAAACATGGACCTTAAATAAGGATTTGATAAGAC
* *
12438 ACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACA
65 ACCTAAACAGGGACCTTGAACAAGGTTTTGATAAGAAACCTAAACA
12484 GGAATCTTGAACAAGATTTTGATGAA-ACACCTAAACATGGACCTTAAATAAGGATTTGATAAGA
1 GG-ATCTTGAACAAGATTTTGAT-AAGACACCTAAACATGGACCTTAAATAAGGATTTGATAAGA
* * * *
12548 CACTTAAATAGGAATCTTGAACAAGGTTTTGAT
64 CACCTAAACAGGGACCTTGAACAAGGTTTTGAT
12581 GAGACTGAAT
Statistics
Matches: 336, Mismatches: 87, Indels: 12
0.77 0.20 0.03
Matches are distributed among these distances:
110 4 0.01
111 326 0.97
112 6 0.02
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (110 bp):
GGATCTTGAACAAGATTTTGATAAGACACCTAAACATGGACCTTAAATAAGGATTTGATAAGACA
CCTAAACAGGGACCTTGAACAAGGTTTTGATAAGAAACCTAAACA
Found at i:13555 original size:17 final size:17
Alignment explanation
Indices: 13530--13574 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
13520 AATTTGAACC
*
13530 TTTTCCTTTTGAATTTT
1 TTTTTCTTTTGAATTTT
* *
13547 TTTTTCTTTTCACTTTT
1 TTTTTCTTTTGAATTTT
*
13564 TTTTTCCTTTG
1 TTTTTCTTTTG
13575 CTTTCTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (17 bp):
TTTTTCTTTTGAATTTT
Found at i:13596 original size:17 final size:17
Alignment explanation
Indices: 13543--13599 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
13533 TCCTTTTGAA
**
13543 TTTTTTTTTCTTTTCAC
1 TTTTTTTTTCTTTTTTC
13560 TTTTTTTTTCCTTTGCTTTC
1 TTTTTTTTT-CTTT--TTTC
13580 TTTTTTTTTCTTTTTTC
1 TTTTTTTTTCTTTTTTC
13597 TTT
1 TTT
13600 AGATTGCTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 16 0.46
18 4 0.11
19 4 0.11
20 11 0.31
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (17 bp):
TTTTTTTTTCTTTTTTC
Found at i:14328 original size:14 final size:14
Alignment explanation
Indices: 14305--14343 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
14295 TTGATAACCT
*
14305 TTTCTCGAAAATAG
1 TTTCTTGAAAATAG
*
14319 TTTCTTGAAAATAT
1 TTTCTTGAAAATAG
*
14333 TTTTTTGAAAA
1 TTTCTTGAAAA
14344 AACGTCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (14 bp):
TTTCTTGAAAATAG
Found at i:16978 original size:17 final size:17
Alignment explanation
Indices: 16956--16990 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16946 TTGCAATATG
16956 AGACAATCTTGAAACAA
1 AGACAATCTTGAAACAA
* *
16973 AGACAATTTTGAACCAA
1 AGACAATCTTGAAACAA
16990 A
1 A
16991 TAAAGAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.20
Consensus pattern (17 bp):
AGACAATCTTGAAACAA
Found at i:26432 original size:40 final size:40
Alignment explanation
Indices: 26386--26462 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
26376 GAAAGTGAAG
26386 ACTAGTTATATATAAAACACATTCTTATACACATATCCTC
1 ACTAGTTATATATAAAACACATTCTTATACACATATCCTC
*
26426 ACTAGTTATATATAAAACACATTCTTATACATATATC
1 ACTAGTTATATATAAAACACATTCTTATACACATATC
26463 TCTTTATTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (40 bp):
ACTAGTTATATATAAAACACATTCTTATACACATATCCTC
Found at i:27967 original size:1 final size:1
Alignment explanation
Indices: 27963--27992 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
27953 CCTTCTTCTG
27963 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27993 GGGTAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:31984 original size:31 final size:31
Alignment explanation
Indices: 31949--32012 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
31939 AGAGTTTGTC
31949 TTTATTTTCTTA-TTTAGGTTAGTATTAGGCT
1 TTTATTTTCTTATTTTA-GTTAGTATTAGGCT
*
31980 TTTATTTTCTTATTTTAGTTAGTATTGGGCT
1 TTTATTTTCTTATTTTAGTTAGTATTAGGCT
32011 TT
1 TT
32013 ATGGGCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.17, C:0.06, G:0.16, T:0.61
Consensus pattern (31 bp):
TTTATTTTCTTATTTTAGTTAGTATTAGGCT
Found at i:32674 original size:21 final size:21
Alignment explanation
Indices: 32650--32689 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
32640 TGATGAAGAG
32650 GAAGATTCTGATCTCTTTGGA
1 GAAGATTCTGATCTCTTTGGA
32671 GAAGATTCTGATCTCTTTG
1 GAAGATTCTGATCTCTTTG
32690 TTTGTGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (21 bp):
GAAGATTCTGATCTCTTTGGA
Found at i:33214 original size:31 final size:31
Alignment explanation
Indices: 33177--33241 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
33167 TAGAGTTTGT
33177 TTTTATTTTCTTA-TTTAGGTTAGTATTAGGC
1 TTTTATTTTCTTATTTTA-GTTAGTATTAGGC
*
33208 TTTTATTTTCTTATTTTAGTTAGTATTGGGC
1 TTTTATTTTCTTATTTTAGTTAGTATTAGGC
33239 TTT
1 TTT
33242 ATGGGCTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.17, C:0.06, G:0.15, T:0.62
Consensus pattern (31 bp):
TTTTATTTTCTTATTTTAGTTAGTATTAGGC
Found at i:36048 original size:1 final size:1
Alignment explanation
Indices: 36044--36068 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
36034 TTGTTCTTCC
36044 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
36069 GGATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:37441 original size:2 final size:2
Alignment explanation
Indices: 37428--37482 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
37418 CCAAAGGAAA
*
37428 AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37470 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
37483 AGGAATGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:38914 original size:17 final size:17
Alignment explanation
Indices: 38892--38927 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
38882 ATACAGAAGC
38892 TTCTTTTAC-TTCTTTTT
1 TTCTTTT-CTTTCTTTTT
38909 TTCTTTTCTTTCTTTTT
1 TTCTTTTCTTTCTTTTT
38926 TT
1 TT
38928 TTTAAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTCTTTTCTTTCTTTTT
Found at i:40816 original size:21 final size:21
Alignment explanation
Indices: 40783--40823 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40773 TTATTGATAC
* *
40783 TAAATACATTTTTTAATTTTT
1 TAAAAACAATTTTTAATTTTT
*
40804 TAAAAACAATTTTTCATTTT
1 TAAAAACAATTTTTAATTTT
40824 AAAAAAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAAAACAATTTTTAATTTTT
Found at i:50048 original size:30 final size:30
Alignment explanation
Indices: 49972--50050 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
49962 AAGTAACACG
*
49972 TAAACTT-TAAAA-TTGTCACTGTGCCCCC
1 TAAACTTCTAAAATTTGTCACTGTACCCCC
* *
50000 TAAAC-TCATAAAATTTTGTCACTTTACCCCT
1 TAAACTTC-TAAAA-TTTGTCACTGTACCCCC
50031 TAAACTTCTAAAATTTGTCA
1 TAAACTTCTAAAATTTGTCA
50051 TTTTGTCTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
27 1 0.02
28 5 0.12
29 5 0.12
30 7 0.16
31 23 0.53
32 2 0.05
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (30 bp):
TAAACTTCTAAAATTTGTCACTGTACCCCC
Found at i:53025 original size:31 final size:31
Alignment explanation
Indices: 52960--53026 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
52950 AATGACTTTG
* * *
52960 TTAAAAGTTTAGGGGGCAAAATGATAAAAAT
1 TTAAAAGTTTAGGGGCCAAAATAACAAAAAT
* *
52991 TTAAAAGTTTAGGGGCCAAAGTAACAAAATT
1 TTAAAAGTTTAGGGGCCAAAATAACAAAAAT
53022 TTAAA
1 TTAAA
53027 GTTCATGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (31 bp):
TTAAAAGTTTAGGGGCCAAAATAACAAAAAT
Found at i:53211 original size:29 final size:29
Alignment explanation
Indices: 53151--53211 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
53141 ACAAAGCTTT
* * * * *
53151 AAAATTAAAGTTTAGGGGGTAAAATGTTC
1 AAAATAAAAGTTTAGGGAGCAAAACGTCC
53180 AAAATAAAAGTTTAGGGAGCAAAACGTCC
1 AAAATAAAAGTTTAGGGAGCAAAACGTCC
53209 AAA
1 AAA
53212 CGCTACAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (29 bp):
AAAATAAAAGTTTAGGGAGCAAAACGTCC
Found at i:53290 original size:13 final size:13
Alignment explanation
Indices: 53272--53296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53262 ACCGAAATCC
53272 AATTGAACAAATA
1 AATTGAACAAATA
53285 AATTGAACAAAT
1 AATTGAACAAAT
53297 TATATAGGCA
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (13 bp):
AATTGAACAAATA
Found at i:53534 original size:22 final size:26
Alignment explanation
Indices: 53484--53535 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
53474 ATTTATGAAG
53484 AGAGATAGTGAGTGGGAGGAGAAGAA
1 AGAGATAGTGAGTGGGAGGAGAAGAA
*
53510 AGAGTTAGT-AGTGGGAGAGAGAAGAA
1 AGAGATAGTGAGTGGGAG-GAGAAGAA
53536 GGGCAAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.13
Consensus pattern (26 bp):
AGAGATAGTGAGTGGGAGGAGAAGAA
Found at i:70170 original size:42 final size:43
Alignment explanation
Indices: 70120--70201 Score: 123
Period size: 45 Copynumber: 1.9 Consensus size: 43
70110 AGTGCATTAT
*
70120 CTAAATTCTA-T-TCCATCTCTAGATAATTCATTAAAATAAAA
1 CTAAATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAA
70161 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAAT
1 CTAA-ATTCTACT-CTCCATCTCTAGATAATTCATCAAAAT
70202 TAAGCAGGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
41 4 0.11
42 6 0.17
43 1 0.03
45 25 0.69
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (43 bp):
CTAAATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:70286 original size:17 final size:16
Alignment explanation
Indices: 70232--70282 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
70222 ATCACCCCCC
*
70232 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
70249 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
70266 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
70282 A
1 A
70283 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:72563 original size:45 final size:45
Alignment explanation
Indices: 72488--72584 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
72478 AGTGCATTAC
* * *
72488 CTAA-ATTCTACTCCTTCATTTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
* * *
72532 CTAATATTCTACTCCTCCATCTCTATATAATTCATCAAAGTAAAG
1 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
72577 CTAATATT
1 CTAATATT
72585 AACTGTTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 4 0.09
45 42 0.91
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (45 bp):
CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:79514 original size:2 final size:2
Alignment explanation
Indices: 79507--79543 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
79497 GCGATCACCC
79507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79544 AGGAAAGTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80032 original size:6 final size:6
Alignment explanation
Indices: 80021--80048 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
80011 TCCCGGCTTT
80021 GGTTCA GGTTCA GGTTCA GGTTCA GGTT
1 GGTTCA GGTTCA GGTTCA GGTTCA GGTT
80049 TGGGTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.36, T:0.36
Consensus pattern (6 bp):
GGTTCA
Found at i:84683 original size:32 final size:33
Alignment explanation
Indices: 84637--84708 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 33
84627 CAAATTGATA
* *
84637 GACAAAA-TAGCCCTCGAA-TTCTGACATAGA-AG
1 GACAAAATTAGCCCTCAAACTT-TGACA-AAATAG
84669 GACAAAATTA-CCCTCAAACTTTGACAAAATAG
1 GACAAAATTAGCCCTCAAACTTTGACAAAATAG
84701 GACAAAAT
1 GACAAAAT
84709 GTTCATTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 2 0.06
32 29 0.83
33 4 0.11
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.19
Consensus pattern (33 bp):
GACAAAATTAGCCCTCAAACTTTGACAAAATAG
Found at i:85839 original size:19 final size:19
Alignment explanation
Indices: 85821--85857 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
85811 AATTAATTAT
85821 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
85839 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
85858 CTTAAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:87340 original size:31 final size:31
Alignment explanation
Indices: 87302--87372 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
87292 ACTACTTAAT
87302 GGAGCAGCCGCGATAAATAGAGGTGGCAAGG
1 GGAGCAGCCGCGATAAATAGAGGTGGCAAGG
87333 GGAGCAGCCGCGATAAATAGAGGTGGCAAGG
1 GGAGCAGCCGCGATAAATAGAGGTGGCAAGG
87364 GGAGCAGCC
1 GGAGCAGCC
87373 ACGCGGCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.31, C:0.18, G:0.42, T:0.08
Consensus pattern (31 bp):
GGAGCAGCCGCGATAAATAGAGGTGGCAAGG
Found at i:87648 original size:22 final size:22
Alignment explanation
Indices: 87623--87665 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
87613 ATTACTGAAC
87623 CTATGGTCAAG-CTATAGTTAAT
1 CTATGGT-AAGTCTATAGTTAAT
*
87645 CTATGGTTAGTCTATAGTTAA
1 CTATGGTAAGTCTATAGTTAA
87666 GTAATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.40
Consensus pattern (22 bp):
CTATGGTAAGTCTATAGTTAAT
Found at i:92182 original size:22 final size:22
Alignment explanation
Indices: 92157--92199 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
92147 ATTACTAAAC
92157 CTATGGTCAAG-CTATAGTTAAT
1 CTATGGT-AAGTCTATAGTTAAT
*
92179 CTATGGTTAGTCTATAGTTAA
1 CTATGGTAAGTCTATAGTTAA
92200 GTAATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.40
Consensus pattern (22 bp):
CTATGGTAAGTCTATAGTTAAT
Found at i:95941 original size:11 final size:11
Alignment explanation
Indices: 95927--95964 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
95917 ATTCATAACA
95927 AATTTATAATT
1 AATTTATAATT
95938 AATTTATAATT
1 AATTTATAATT
95949 -ATTTGATAATT
1 AATTT-ATAATT
*
95960 TATTT
1 AATTT
95965 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:100656 original size:19 final size:20
Alignment explanation
Indices: 100632--100669 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
100622 ATTTATCCTC
100632 TAATGGGTAG-TTTTATTTG
1 TAATGGGTAGTTTTTATTTG
100651 TAATGGGTAGTTTTTATTT
1 TAATGGGTAGTTTTTATTT
100670 TGTTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (20 bp):
TAATGGGTAGTTTTTATTTG
Found at i:104649 original size:15 final size:15
Alignment explanation
Indices: 104608--104643 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
104598 GTTTAATAAA
104608 ACTGAAAA-TTAAGT
1 ACTGAAAAGTTAAGT
*
104622 GCTGAAAAGTTAAGT
1 ACTGAAAAGTTAAGT
104637 ACTGAAA
1 ACTGAAA
104644 TTTTAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (15 bp):
ACTGAAAAGTTAAGT
Found at i:105356 original size:69 final size:68
Alignment explanation
Indices: 105246--105381 Score: 211
Period size: 69 Copynumber: 2.0 Consensus size: 68
105236 CAGATGATTT
* * *
105246 TGGATTTTTGTTTAGGCTAAAGAGTGGAAACCTAATCCCAATTTTT-TGAGATTAACGAGGAAGA
1 TGGATTTTTGTTTAGGCTAAAGAATGGAAACATAATCCCAATTTTTCT-AGATTAACAAGGAAGA
105310 AGAC
65 AGAC
*
105314 TGGATTTTTCGTTTAGGCTAAAGAATGGAAACATAATCCCAATTTTTCTAGATTAACAAGGAGGA
1 TGGATTTTT-GTTTAGGCTAAAGAATGGAAACATAATCCCAATTTTTCTAGATTAACAAGGAAGA
105379 AGA
65 AGA
105382 AGACGATAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
68 9 0.15
69 52 0.84
70 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (68 bp):
TGGATTTTTGTTTAGGCTAAAGAATGGAAACATAATCCCAATTTTTCTAGATTAACAAGGAAGAA
GAC
Found at i:112036 original size:14 final size:14
Alignment explanation
Indices: 112017--112043 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
112007 TAGTAAGATA
112017 AAAAAGAATTTATC
1 AAAAAGAATTTATC
112031 AAAAAGAATTTAT
1 AAAAAGAATTTAT
112044 ATATATTTAC
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:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAAAGAATTTATC
Found at i:113173 original size:17 final size:17
Alignment explanation
Indices: 113151--113183 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
113141 GTCTCCTTTA
113151 TTCTTGTACTTGAATTT
1 TTCTTGTACTTGAATTT
113168 TTCTTGTACTTGAATT
1 TTCTTGTACTTGAATT
113184 GTTTGATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (17 bp):
TTCTTGTACTTGAATTT
Found at i:115463 original size:107 final size:107
Alignment explanation
Indices: 115284--115498 Score: 367
Period size: 107 Copynumber: 2.0 Consensus size: 107
115274 TTCAAAAACC
* *
115284 TTGACCTGAAGTATCTAAAATACCCTTTTAAATTTTAAAATTTTAATTATATTTTAAAGGTTAAT
1 TTGACCTGAAATATCTAAAATACCCTTTTAAATTTTAAAATTTTAATTATATTTTAAAGATTAAT
* *
115349 ATGTAATCTATCAAATCAGATTTTATTTCCATATTAAAAAAG
66 ATGTAATCTATCAAACCAAATTTTATTTCCATATTAAAAAAG
*
115391 TTGACCTGAAATATCTAAAATACCCTTTTAAATTTTTAAATTTTAATTATATTTTAAAGATTAAT
1 TTGACCTGAAATATCTAAAATACCCTTTTAAATTTTAAAATTTTAATTATATTTTAAAGATTAAT
* *
115456 ATGTAATCTATCCAGCCAAATTTTATTTCCATATTAAAAAAG
66 ATGTAATCTATCAAACCAAATTTTATTTCCATATTAAAAAAG
115498 T
1 T
115499 CTAAAATAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (107 bp):
TTGACCTGAAATATCTAAAATACCCTTTTAAATTTTAAAATTTTAATTATATTTTAAAGATTAAT
ATGTAATCTATCAAACCAAATTTTATTTCCATATTAAAAAAG
Found at i:118095 original size:276 final size:272
Alignment explanation
Indices: 117578--118100 Score: 805
Period size: 276 Copynumber: 1.9 Consensus size: 272
117568 CTAAAGTTTT
* **
117578 GCCATAATAATGTTACTTAAAACTTAAAAGTGTTTATGGTTATTACGAAAAGTAAAATTATCACA
1 GCCATAATAATGTTACTTAAAACCTAAAAGTGTTTATGGTTATTAAAAAAAGTAAAATTATCACA
*
117643 TCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACAGGGTTAAAAGTTTGACATGTGTCTTT
66 TCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACAGGGTTAAAAGATTGACATGTGTCTTT
* * *
117708 TTAGTGTATATTTTTTAAGGAAAAATATTTTATCCACCGTTAGTGAAGTTTAGCAGGCTGCACAT
131 TTAGTGTATATTTTTTAAGGAAAAATATCTTATCCACCATTAGTGAAGTTTAGCAGACTGCACAT
* * * *
117773 GCAGAGTTACGATTAAATGGTTGACATATGTACCCTTAGGGAATAGTTTTGATTTTTGAACATTA
196 GCAGAGCTACGATTAAAGGGTCGACACATGTACCCTTAGGGAATAGTTTTGATTTTTGAACATTA
117838 ATTAAGTAAAAA
261 ATTAAGTAAAAA
*
117850 GCCATAATACTGTTACTTAAATTAAACCTAAAAGTGTTTATGGTTATTAAAAAAAGTAAAATTAT
1 GCCATAATAATGTTACTT--A--AAACCTAAAAGTGTTTATGGTTATTAAAAAAAGTAAAATTAT
* * *
117915 CACATCCACTATTAGTGTAGTTTACTATTAGATTGTACAAACGGGGTTAAAGGATTGACATGTGT
62 CACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACAGGGTTAAAAGATTGACATGTGT
* *
117980 CTTTTTAGTGTATATTTTTTAAGGAAAATTATCTTATCCTCCATTAGTGAAGTTTAGCAGACTGC
127 CTTTTTAGTGTATATTTTTTAAGGAAAAATATCTTATCCACCATTAGTGAAGTTTAGCAGACTGC
* * * *
118045 ACATGCAGGGCTAGGGTTAAAGGGTCGACACGTGT-CTCCTTAGGGAATAGTTTTGA
192 ACATGCAGAGCTACGATTAAAGGGTCGACACATGTAC-CCTTAGGGAATAGTTTTGA
118101 ACATTAAATA
Statistics
Matches: 225, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
272 17 0.08
274 1 0.00
275 1 0.00
276 206 0.92
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (272 bp):
GCCATAATAATGTTACTTAAAACCTAAAAGTGTTTATGGTTATTAAAAAAAGTAAAATTATCACA
TCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACAGGGTTAAAAGATTGACATGTGTCTTT
TTAGTGTATATTTTTTAAGGAAAAATATCTTATCCACCATTAGTGAAGTTTAGCAGACTGCACAT
GCAGAGCTACGATTAAAGGGTCGACACATGTACCCTTAGGGAATAGTTTTGATTTTTGAACATTA
ATTAAGTAAAAA
Found at i:121525 original size:42 final size:42
Alignment explanation
Indices: 121446--121525 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
121436 GATTAGTTGT
* * *
121446 GTAAATCATGTCTTAGTGACAGTTAGGTGGGATTAAGTATGA
1 GTAAATCATGTCTTAATGACAGGTAGGTGGGAATAAGTATGA
121488 GTAAATCATGTC-TAATGACAGAGTA-GTCGGGAATAAGT
1 GTAAATCATGTCTTAATGACAG-GTAGGT-GGGAATAAGT
121526 GTAATTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 10 0.30
42 23 0.70
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (42 bp):
GTAAATCATGTCTTAATGACAGGTAGGTGGGAATAAGTATGA
Found at i:121819 original size:91 final size:92
Alignment explanation
Indices: 121711--121888 Score: 295
Period size: 91 Copynumber: 1.9 Consensus size: 92
121701 AATATATATA
* *
121711 TTTTTTCATAATGCTTGAAATTGATTTATTTATCAACTTGTTATCATGAGCAATCTTCATTTGAT
1 TTTTTTCATAATGCTTGAAATTGATTTATTTATCAACTTGTTAACATGAGCAAACTTCATTTGAT
121776 AAC-GTCTTTTACCTTAATCAATACAT
66 AACAGTCTTTTACCTTAATCAATACAT
* *
121802 TTTTTTTATAATGCTTGAAATTGATTTATTTATCAACTTGTTAACATGAGCAAACTTCATTTGGT
1 TTTTTTCATAATGCTTGAAATTGATTTATTTATCAACTTGTTAACATGAGCAAACTTCATTTGAT
* *
121867 AACATTTTTTTACCTTAATCAA
66 AACAGTCTTTTACCTTAATCAA
121889 AAATTGAATT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 64 0.80
92 16 0.20
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (92 bp):
TTTTTTCATAATGCTTGAAATTGATTTATTTATCAACTTGTTAACATGAGCAAACTTCATTTGAT
AACAGTCTTTTACCTTAATCAATACAT
Found at i:123053 original size:2 final size:2
Alignment explanation
Indices: 123042--123091 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
123032 TATTGTTTCT
123042 TA TA -A TA TA TA TA TA TA -A TA TA -A TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
123080 TA TA TA TA TA TA
1 TA TA TA TA TA TA
123092 CACACTAGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:123060 original size:13 final size:13
Alignment explanation
Indices: 123042--123089 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
123032 TATTGTTTCT
123042 TATA-ATATAT-A
1 TATATATATATAA
123053 TATATA-ATATAA
1 TATATATATATAA
123065 TATATATATATAA
1 TATATATATATAA
123078 TATATATATATA
1 TATATATATATA
123090 TACACACTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.24
12 8 0.24
13 18 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATATATATAA
Found at i:124538 original size:22 final size:22
Alignment explanation
Indices: 124513--124637 Score: 89
Period size: 22 Copynumber: 5.7 Consensus size: 22
124503 CTCCAATGTA
124513 GAAATATTGATAACCACATT-T
1 GAAATATTGATAACCACATTAT
*
124534 CGAAA-ATTTGATAACCTCATTAT
1 -GAAATA-TTGATAACCACATTAT
* **
124557 GAAAT-TTCGATAACCTCCCTAT
1 GAAATATT-GATAACCACATTAT
* *
124579 GAAA-ATTTGATAACCACACTGT
1 GAAATA-TTGATAACCACATTAT
* * *
124601 GAAATTTTGTTAACCACACTAT
1 GAAATATTGATAACCACATTAT
124623 GAAAT-TTCGATAACC
1 GAAATATT-GATAACC
124638 TAAGTGTGTA
Statistics
Matches: 85, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.06
22 77 0.91
23 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (22 bp):
GAAATATTGATAACCACATTAT
Found at i:124561 original size:44 final size:42
Alignment explanation
Indices: 124513--124637 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 42
124503 CTCCAATGTA
* * *
124513 GAAATATTGATAACCACATTTCGAAAATTTGATAACCTCATTAT
1 GAAAT-TTGATAACCACATAT-GAAAATTTGATAACCACACTAT
* * *
124557 GAAATTTCGATAACCTCCCTATGAAAATTTGATAACCACACTGT
1 GAAATTT-GATAACC-ACATATGAAAATTTGATAACCACACTAT
*
124601 GAAATTTTGTTAACCACACTATG-AAATTTCGATAACC
1 GAAA-TTTGATAACCACA-TATGAAAATTT-GATAACC
124638 TAAGTGTGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
43 9 0.13
44 52 0.78
45 6 0.09
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (42 bp):
GAAATTTGATAACCACATATGAAAATTTGATAACCACACTAT
Found at i:124615 original size:66 final size:67
Alignment explanation
Indices: 124514--124638 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 67
124504 TCCAATGTAG
* * *
124514 AAATATTGATAACCACATTTCGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTCCCTAT
1 AAATATTGATAACCACATGTCGAAAATTTGATAACCACACTATGAAATTTCGATAACCTCCCTAT
124579 GA
66 GA
* *
124581 AAAT-TTGATAACCACACTGT-GAAATTTTGTTAACCACACTATGAAATTTCGATAACCT
1 AAATATTGATAACCACA-TGTCGAAAATTTGATAACCACACTATGAAATTTCGATAACCT
124639 AAGTGTGTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
66 46 0.88
67 6 0.12
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (67 bp):
AAATATTGATAACCACATGTCGAAAATTTGATAACCACACTATGAAATTTCGATAACCTCCCTAT
GA
Found at i:124775 original size:22 final size:22
Alignment explanation
Indices: 124535--125050 Score: 159
Period size: 22 Copynumber: 23.4 Consensus size: 22
124525 ACCACATTTC
*
124535 GAAAATTTGATAACCTCAT-TAT
1 GAAATTTTGATAACCTC-TCTAT
* *
124557 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCTCTCTAT
* * * *
124579 GAAAATTTGATAACCACACTGT
1 GAAATTTTGATAACCTCTCTAT
* * *
124601 GAAATTTTGTTAACCACACTAT
1 GAAATTTTGATAACCTCTCTAT
* *** *
124623 GAAATTTCGATAACCTAAGTGT
1 GAAATTTTGATAACCTCTCTAT
* **
124645 GTAATTTTGATAATATGC-CTAT
1 GAAATTTTGATAACCT-CTCTAT
* * * *
124667 -ACAATTTTAATAATCACACTAAT
1 GA-AATTTTGATAACCTCTCT-AT
* * *
124690 -AAA-ATTGGTAA-CTGCACTAT
1 GAAATTTTGATAACCT-CTCTAT
124710 GAAAATTTTGATAA--TCTC-AT
1 G-AAATTTTGATAACCTCTCTAT
* * * * *
124730 AAAATTTTGATAAGCACACCAT
1 GAAATTTTGATAACCTCTCTAT
124752 GAAATTTTGATAACCTCTCTAT
1 GAAATTTTGATAACCTCTCTAT
* *
124774 GAGAATGAAACTGTGATATCCTCTCTAT
1 GA-AAT-----TTTGATAACCTCTCTAT
* *
124802 G-TATTTTCGATAACCTCTCCAT
1 GAAATTTT-GATAACCTCTCTAT
* ** * *
124824 AAAATTTTCCTAACCTCCCTAG
1 GAAATTTTGATAACCTCTCTAT
* *
124846 GAAATTTTGATGA----GC-A-
1 GAAATTTTGATAACCTCTCTAT
* *
124862 CAAATTTTGGTAACCTCCCTCCCTAT
1 GAAATTTTGATAACCT--CT--CTAT
* * *
124888 GAAATTTT-ATTAACATCCCTAA
1 GAAATTTTGA-TAACCTCTCTAT
* * * *
124910 GAAATTTTGGTAACTTTTTTAT
1 GAAATTTTGATAACCTCTCTAT
* *
124932 GAAATTTTGGTAACCTCTGTAT
1 GAAATTTTGATAACCTCTCTAT
*
124954 GAAATTTTGATAA-CTACACTAT
1 GAAATTTTGATAACCT-CTCTAT
* * *
124976 GAAGTTTTGATTACCTCTATAT
1 GAAATTTTGATAACCTCTCTAT
* *** *
124998 GAAATTTTGGTAACCAAGCGAT
1 GAAATTTTGATAACCTCTCTAT
* *
125020 GAAATTTTGATAATCTTTCTAT
1 GAAATTTTGATAACCTCTCTAT
*
125042 GTAATTTTG
1 GAAATTTTG
125051 GTTTGATTGT
Statistics
Matches: 359, Mismatches: 101, Indels: 68
0.68 0.19 0.13
Matches are distributed among these distances:
16 10 0.03
17 1 0.00
18 1 0.00
19 12 0.03
20 5 0.01
21 18 0.05
22 260 0.72
23 19 0.05
24 2 0.01
25 1 0.00
26 14 0.04
28 16 0.04
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTCTAT
Found at i:126673 original size:180 final size:180
Alignment explanation
Indices: 126358--126706 Score: 653
Period size: 180 Copynumber: 1.9 Consensus size: 180
126348 AGTCTAAATC
126358 AAATTTCCTTTGGAAAAACCAACAAAGATATCAACAGTCTCCAAGTGCAATATTTTTGACTTTGT
1 AAATTTCCTTTGGAAAAACCAACAAAGATATCAACAGTCTCCAAGTGCAATATTTTTGACTTTGT
* *
126423 TTAGATTCTCATTGGAATTCAAATTCATCATCTCCTCAAATTCTTTACATGGTAAATCTTCTTGG
66 TTAGATTCTCATTGGAATCCAAATTCATCATCTCCTCAAATTCTTTACATGGTAAATCTTCTTCG
126488 TATAAATTATCAATAAATCTATGAAGCTGTAAAGAAGAATATATACATAT
131 TATAAATTATCAATAAATCTATGAAGCTGTAAAGAAGAATATATACATAT
* *
126538 AAATTTTCTTTGGAAAAACCAACAAAGATATCAACAGTCTCCAAGTGCGATATTTTTGACTTTGT
1 AAATTTCCTTTGGAAAAACCAACAAAGATATCAACAGTCTCCAAGTGCAATATTTTTGACTTTGT
126603 TTAGATTCTCATTGGAATCCAAATTCATCATCTCCTCAAATTCTTTACATGGTAAATCTTCTTCG
66 TTAGATTCTCATTGGAATCCAAATTCATCATCTCCTCAAATTCTTTACATGGTAAATCTTCTTCG
*
126668 TATAAATTATCAATCAATCTATGAAGCTGTAAAGAAGAA
131 TATAAATTATCAATAAATCTATGAAGCTGTAAAGAAGAA
126707 ATCTATGAAG
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 164 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (180 bp):
AAATTTCCTTTGGAAAAACCAACAAAGATATCAACAGTCTCCAAGTGCAATATTTTTGACTTTGT
TTAGATTCTCATTGGAATCCAAATTCATCATCTCCTCAAATTCTTTACATGGTAAATCTTCTTCG
TATAAATTATCAATAAATCTATGAAGCTGTAAAGAAGAATATATACATAT
Found at i:126710 original size:23 final size:23
Alignment explanation
Indices: 126683--126729 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
126673 ATTATCAATC
126683 AATCTATGAAGCTGTAAAGAAGA
1 AATCTATGAAGCTGTAAAGAAGA
126706 AATCTATGAAGCTGTAAAGAAGA
1 AATCTATGAAGCTGTAAAGAAGA
126729 A
1 A
126730 TATATACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (23 bp):
AATCTATGAAGCTGTAAAGAAGA
Found at i:138231 original size:19 final size:18
Alignment explanation
Indices: 138198--138233 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
138188 TTGAAATTAT
138198 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
138216 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
138234 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:139116 original size:18 final size:18
Alignment explanation
Indices: 139081--139115 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
139071 CTCCTCTATC
*
139081 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
139099 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
139116 TTAATTACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:159287 original size:14 final size:15
Alignment explanation
Indices: 159266--159303 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
159256 CTAGAGAATA
159266 TCTAATGTATAA-TG
1 TCTAATGTATAATTG
* *
159280 TGTAATGTCTAATTG
1 TCTAATGTATAATTG
159295 TCTAATGTA
1 TCTAATGTA
159304 CTTAGGGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (15 bp):
TCTAATGTATAATTG
Found at i:161321 original size:31 final size:31
Alignment explanation
Indices: 161285--161389 Score: 183
Period size: 31 Copynumber: 3.4 Consensus size: 31
161275 TTTGGCGTCG
***
161285 TTGCCGGGGAAGGAAAACTTTCTTTTGGTTT
1 TTGCCGGGGAAGGAAAACTTTCTCCCGGTTT
161316 TTGCCGGGGAAGGAAAACTTTCTCCCGGTTT
1 TTGCCGGGGAAGGAAAACTTTCTCCCGGTTT
161347 TTGCCGGGGAAGGAAAACTTTCTCCCGGTTT
1 TTGCCGGGGAAGGAAAACTTTCTCCCGGTTT
161378 TTGCCGGGGAAG
1 TTGCCGGGGAAG
161390 TAAGGAATAG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.30
Consensus pattern (31 bp):
TTGCCGGGGAAGGAAAACTTTCTCCCGGTTT
Found at i:164392 original size:21 final size:21
Alignment explanation
Indices: 164366--164414 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
164356 CCAAGTCACT
164366 TGCCCGGCCACCCGAGCCACC
1 TGCCCGGCCACCCGAGCCACC
* * * *
164387 TGCCCGGCCATCTGCGCCACT
1 TGCCCGGCCACCCGAGCCACC
164408 TGCCCGG
1 TGCCCGG
164415 TCAAGCTTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.51, G:0.27, T:0.12
Consensus pattern (21 bp):
TGCCCGGCCACCCGAGCCACC
Done.