Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007174.1 Corchorus capsularis cultivar CVL-1 contig07195, 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: 66499
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1277 original size:33 final size:32
Alignment explanation
Indices: 1240--1346 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
1230 CGCCAAGCGA
* *
1240 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGATGGCCGGGCATCTCCA-GTCGCG
1273 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG
* * *
1306 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG
1339 TGGCCGGT
1 TGGCCGGT
1347 CACTCGCGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.03
33 63 0.95
34 1 0.02
ACGTcount: A:0.08, C:0.29, G:0.40, T:0.22
Consensus pattern (32 bp):
TGGCCGGTGATGGCCGGGCATCTCCAGTCGCG
Found at i:6366 original size:33 final size:32
Alignment explanation
Indices: 6329--6435 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 32
6319 CGCCAAGCGA
* *
6329 TGGCCGGTTATGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTTATGGCCGGGCATCTCCA-GTCGCG
*
6362 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTTATGGCCGGGCATCTCC-AGTCGCG
* *
6395 TGGCCGGTGT-TGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGT-TATGGCCGGGCATCTCC-AGTCGCG
6428 TGGCCGGT
1 TGGCCGGT
6436 CACTCGCGCC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
33 64 0.98
34 1 0.02
ACGTcount: A:0.09, C:0.29, G:0.39, T:0.22
Consensus pattern (32 bp):
TGGCCGGTTATGGCCGGGCATCTCCAGTCGCG
Found at i:6897 original size:30 final size:30
Alignment explanation
Indices: 6862--6921 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6852 AAAGGAGAGG
* *
6862 ATGGAATGGCAAAGTCTCATGGAGATGCCA
1 ATGGAATCGCAAAGCCTCATGGAGATGCCA
6892 ATGGAATCGCAAAGCCTCATGGAGATGCCA
1 ATGGAATCGCAAAGCCTCATGGAGATGCCA
6922 TTAAGATGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.18
Consensus pattern (30 bp):
ATGGAATCGCAAAGCCTCATGGAGATGCCA
Found at i:9308 original size:13 final size:14
Alignment explanation
Indices: 9285--9313 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9275 ACTTCTACTC
9285 AATGCATGAATGCA
1 AATGCATGAATGCA
9299 AATG-ATGAATGCA
1 AATGCATGAATGCA
9312 AA
1 AA
9314 GTCCGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (14 bp):
AATGCATGAATGCA
Found at i:13296 original size:30 final size:30
Alignment explanation
Indices: 13262--13320 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
13252 TAATGGGTCG
* *
13262 AATGGCCTGTTGTGGCCGGATGGCCCGTGC
1 AATGGCCGGTTGTGGCCAGATGGCCCGTGC
*
13292 AATGGCCGGTTGTGGCCAGATGGCTCGTG
1 AATGGCCGGTTGTGGCCAGATGGCCCGTG
13321 TGATGTCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.41, T:0.24
Consensus pattern (30 bp):
AATGGCCGGTTGTGGCCAGATGGCCCGTGC
Found at i:14976 original size:29 final size:29
Alignment explanation
Indices: 14942--15000 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
14932 TCTCTAATGG
14942 ATGGCAATCCTCTAGGAATTTTCTCACAA
1 ATGGCAATCCTCTAGGAATTTTCTCACAA
14971 ATGGCAATCCTCTAGGAATTTTCTCACAA
1 ATGGCAATCCTCTAGGAATTTTCTCACAA
15000 A
1 A
15001 AATAAGCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (29 bp):
ATGGCAATCCTCTAGGAATTTTCTCACAA
Found at i:15340 original size:33 final size:33
Alignment explanation
Indices: 15302--15398 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
15292 AATTAGCATC
*
15302 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * *
15335 TAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
** *
15368 CAAATTAGGTTTAGTATCATCGCAAACAACA
1 CAAAACAGATTTAGTATCATCGCAAACAACA
15399 TCTAAAAGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:16487 original size:20 final size:20
Alignment explanation
Indices: 16452--16489 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16442 GTAAACCCTA
*
16452 GTACCACTTATCTCCAATTT
1 GTACCACTTATATCCAATTT
*
16472 GTACCACTTGTATCCAAT
1 GTACCACTTATATCCAAT
16490 AGGGTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.08, T:0.37
Consensus pattern (20 bp):
GTACCACTTATATCCAATTT
Found at i:17853 original size:18 final size:18
Alignment explanation
Indices: 17830--17882 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
17820 AATGGGTCGA
17830 ATGGCCGGTTGTGGCCGG
1 ATGGCCGGTTGTGGCCGG
*
17848 ATGGCC---CGT-G-C-G
1 ATGGCCGGTTGTGGCCGG
17860 ATGGCCGGTTGTGGCCGG
1 ATGGCCGGTTGTGGCCGG
17878 ATGGC
1 ATGGC
17883 TCGTGCGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 7 0.26
13 1 0.04
14 1 0.04
15 4 0.15
16 1 0.04
17 1 0.04
18 12 0.44
ACGTcount: A:0.08, C:0.25, G:0.47, T:0.21
Consensus pattern (18 bp):
ATGGCCGGTTGTGGCCGG
Found at i:17864 original size:30 final size:30
Alignment explanation
Indices: 17830--17892 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
17820 AATGGGTCGA
17830 ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
*
17860 ATGGCCGGTTGTGGCCGGATGGCTCGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
17890 ATG
1 ATG
17893 TCCCATGCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.08, C:0.24, G:0.46, T:0.22
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
Found at i:22528 original size:10 final size:10
Alignment explanation
Indices: 22513--22568 Score: 94
Period size: 10 Copynumber: 5.6 Consensus size: 10
22503 AATCCTCGAT
22513 ATATCCGTAA
1 ATATCCGTAA
22523 ATATCCGTAA
1 ATATCCGTAA
*
22533 ATATCCATAA
1 ATATCCGTAA
*
22543 GTATCCGTAA
1 ATATCCGTAA
22553 ATATCCGTAA
1 ATATCCGTAA
22563 ATATCC
1 ATATCC
22569 ATATTAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:22548 original size:30 final size:30
Alignment explanation
Indices: 22514--22571 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
22504 ATCCTCGATA
22514 TATCCGTAAATATCCGTAAATATCCATAAG
1 TATCCGTAAATATCCGTAAATATCCATAAG
22544 TATCCGTAAATATCCGTAAATATCCATA
1 TATCCGTAAATATCCGTAAATATCCATA
22572 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (30 bp):
TATCCGTAAATATCCGTAAATATCCATAAG
Found at i:22973 original size:16 final size:16
Alignment explanation
Indices: 22952--22991 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
22942 GGTTGATCAA
*
22952 GTTCGGGTCATTTTGG
1 GTTCGGGTCATTTCGG
*
22968 GTTCGGATCATTTCGG
1 GTTCGGGTCATTTCGG
22984 GTTCGGGT
1 GTTCGGGT
22992 ACCCAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.07, C:0.15, G:0.38, T:0.40
Consensus pattern (16 bp):
GTTCGGGTCATTTCGG
Found at i:25147 original size:23 final size:21
Alignment explanation
Indices: 25121--25162 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
25111 GTGTCAAAAC
*
25121 CTTTTATCTTTGTTTTTTGAAGT
1 CTTTTA-CTTT-TCTTTTGAAGT
25144 CTTTTACTTTTCTTTTGAA
1 CTTTTACTTTTCTTTTGAA
25163 AACTTCCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.14, C:0.12, G:0.10, T:0.64
Consensus pattern (21 bp):
CTTTTACTTTTCTTTTGAAGT
Found at i:39069 original size:6 final size:6
Alignment explanation
Indices: 39058--39085 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39048 AGTAAAAAGG
39058 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
39086 GTGAATTATG
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:41889 original size:28 final size:28
Alignment explanation
Indices: 41846--41901 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
41836 CAACAATCTT
*
41846 CATCAAGATATTTAAGGTATGGGCGTAG
1 CATCAAGATATGTAAGGTATGGGCGTAG
*
41874 CATCAAGATCTGTAAGGTATGGGCGTAG
1 CATCAAGATATGTAAGGTATGGGCGTAG
41902 AGCTGGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (28 bp):
CATCAAGATATGTAAGGTATGGGCGTAG
Found at i:44867 original size:31 final size:31
Alignment explanation
Indices: 44824--44882 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
44814 TTGAGCCGGT
44824 TTAAAATATTAAAAAAATAAAAAAATAAAAC
1 TTAAAATATTAAAAAAATAAAAAAATAAAAC
* *
44855 TTAAAATTTTAAAAAATTAAAAAAATAA
1 TTAAAATATTAAAAAAATAAAAAAATAA
44883 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (31 bp):
TTAAAATATTAAAAAAATAAAAAAATAAAAC
Found at i:44895 original size:31 final size:30
Alignment explanation
Indices: 44826--44900 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
44816 GAGCCGGTTT
* *
44826 AAAATATTAAAAAAATAAAAAAATAAAACTT
1 AAAATTTTAAAAAAATAAAAAAATAAAAC-A
*
44857 AAAATTTTAAAAAATTAAAAAAATAATAA-A
1 AAAATTTTAAAAAAATAAAAAAATAA-AACA
*
44887 AAATATTTTTAAAA
1 AAA-ATTTTAAAAA
44901 GCCACGTAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 33 0.87
32 2 0.05
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (30 bp):
AAAATTTTAAAAAAATAAAAAAATAAAACA
Found at i:45752 original size:27 final size:28
Alignment explanation
Indices: 45699--45753 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
45689 GAGAAAACCA
* **
45699 AAATATATTATTATATATTTAAAATTTC
1 AAATATAATATTATATAAATAAAATTTC
*
45727 AAATATAATATT-TATAAATAATATTTC
1 AAATATAATATTATATAAATAAAATTTC
45754 CATTTCCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
AAATATAATATTATATAAATAAAATTTC
Found at i:50875 original size:86 final size:86
Alignment explanation
Indices: 50730--50896 Score: 307
Period size: 86 Copynumber: 1.9 Consensus size: 86
50720 ATGATAATCA
*
50730 GTAATCAAAGTAAAAAGAGTAAAAGGAAGAGTAATAGCATATTAGTTTAATTCAGAGTAATTAGA
1 GTAATCAAAGTAAAAAGAGTAAAAGGAAGAGTAATAACATATTAGTTTAATTCAGAGTAATTAGA
50795 CTAAAAAGAGTAAAAGAAAGG
66 CTAAAAAGAGTAAAAGAAAGG
* *
50816 GTAATCAAAGTAAAAAGAGTAAAATGAGGAGTAATAACATATTAGTTTAATTCAGAGTAATTAGA
1 GTAATCAAAGTAAAAAGAGTAAAAGGAAGAGTAATAACATATTAGTTTAATTCAGAGTAATTAGA
50881 CTAAAAAGAGTAAAAG
66 CTAAAAAGAGTAAAAG
50897 GAGGAGCAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (86 bp):
GTAATCAAAGTAAAAAGAGTAAAAGGAAGAGTAATAACATATTAGTTTAATTCAGAGTAATTAGA
CTAAAAAGAGTAAAAGAAAGG
Found at i:50932 original size:55 final size:56
Alignment explanation
Indices: 50816--50949 Score: 198
Period size: 55 Copynumber: 2.4 Consensus size: 56
50806 AAAAGAAAGG
* * * *
50816 GTAATCAAAGTAAAAAGAGTAAAATGAGGAGTAATAACATATTAGTTTAATTCAGA
1 GTAATTAAACTAAAAAGAGTAAAAGGAGGAGCAATAACATATTAGTTTAATTCAGA
* **
50872 GTAATTAGACTAAAAAGAGTAAAAGGAGGAGCAATCGCA-ATTAGTTTAATTCAGA
1 GTAATTAAACTAAAAAGAGTAAAAGGAGGAGCAATAACATATTAGTTTAATTCAGA
50927 GTAATTAAACTAAAAAGAGTAAA
1 GTAATTAAACTAAAAAGAGTAAA
50950 GAAAAGGTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 38 0.54
56 32 0.46
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.25
Consensus pattern (56 bp):
GTAATTAAACTAAAAAGAGTAAAAGGAGGAGCAATAACATATTAGTTTAATTCAGA
Found at i:51121 original size:16 final size:15
Alignment explanation
Indices: 51083--51125 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
51073 TTAAGCTAAA
51083 AAGAGTAAAAGAAGT
1 AAGAGTAAAAGAAGT
* *
51098 AATTAGTAAAAGTAATT
1 AA-GAGTAAAAG-AAGT
51115 AAGAGTAAAAG
1 AAGAGTAAAAG
51126 CAAAAGAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 2 0.09
16 16 0.70
17 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (15 bp):
AAGAGTAAAAGAAGT
Found at i:51125 original size:40 final size:41
Alignment explanation
Indices: 51089--51163 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 41
51079 TAAAAAGAGT
* *
51089 AAAAGAAGTAATTAG-TAAA-AGTAATTAAGAGT-AAAAGC
1 AAAAGAAGTAATCAGAGAAATAGTAATTAAGAGTAAAAAGC
51127 AAAAGAAGTAATCAGAGAAATAGTAATTAAGAGTAAA
1 AAAAGAAGTAATCAGAGAAATAGTAATTAAGAGTAAA
51164 GTAAAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
38 14 0.44
39 3 0.09
40 13 0.41
41 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.19, T:0.20
Consensus pattern (41 bp):
AAAAGAAGTAATCAGAGAAATAGTAATTAAGAGTAAAAAGC
Found at i:51255 original size:32 final size:32
Alignment explanation
Indices: 51219--51436 Score: 136
Period size: 32 Copynumber: 6.7 Consensus size: 32
51209 CAGCAGAATG
*
51219 AAGTAAAAGTAAAAGAAGTAATCAGCAGAGTA
1 AAGTAAAAGTAAAAGAAGTAATCAGTAGAGTA
* *
51251 AAGTAAAAGTAAAAGAAGCAATTAGTAAAAGGAAGAAGTTA
1 AAGTAAAAGTAAAAGAAGTAATCAGT-------AG-AG-TA
*
51292 TCAGTAAAAGTAAAAGAAGTAATCAGTAGAAGTGA
1 -AAGTAAAAGTAAAAGAAGTAATCAGTAG-AGT-A
* *
51327 GAGAGTAAAAG-AAGAAGAAGTAATTAGTAGA-AA
1 -A-AGTAAAAGTAA-AAGAAGTAATCAGTAGAGTA
51360 ATAGTAAAAGTAAAAGAAGTAAT---TA-AG--
1 A-AGTAAAAGTAAAAGAAGTAATCAGTAGAGTA
*
51387 -AGTAAAAGTAAGAGAAGTAATCAGTA-A--A
1 AAGTAAAAGTAAAAGAAGTAATCAGTAGAGTA
51415 AGAGTAAAAGTAAAAGAAGTAA
1 A-AGTAAAAGTAAAAGAAGTAA
51437 GCAGAAAATT
Statistics
Matches: 152, Mismatches: 13, Indels: 44
0.73 0.06 0.21
Matches are distributed among these distances:
25 20 0.13
28 4 0.03
29 2 0.01
30 19 0.12
32 42 0.28
33 3 0.02
34 1 0.01
35 9 0.06
36 23 0.15
39 2 0.01
40 2 0.01
41 2 0.01
42 23 0.15
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.17
Consensus pattern (32 bp):
AAGTAAAAGTAAAAGAAGTAATCAGTAGAGTA
Found at i:51334 original size:36 final size:32
Alignment explanation
Indices: 51294--51436 Score: 144
Period size: 36 Copynumber: 4.6 Consensus size: 32
51284 AGAAGTTATC
51294 AGTAAAAGTAAAAGAAGTAATCAGTAGAAGTGAGAG
1 AGTAAAAGTAAAAGAAGTAATCAGTAGAA---A-AG
* *
51330 AGTAAAAG-AAGAAGAAGTAATTAGTAGAAAAT
1 AGTAAAAGTAA-AAGAAGTAATCAGTAGAAAAG
51362 AGTAAAAGTAAAAGAAGTAAT---T----AAG
1 AGTAAAAGTAAAAGAAGTAATCAGTAGAAAAG
*
51387 AGTAAAAGTAAGAGAAGTAATCAGT--AAAAG
1 AGTAAAAGTAAAAGAAGTAATCAGTAGAAAAG
51417 AGTAAAAGTAAAAGAAGTAA
1 AGTAAAAGTAAAAGAAGTAA
51437 GCAGAAAATT
Statistics
Matches: 95, Mismatches: 5, Indels: 20
0.79 0.04 0.17
Matches are distributed among these distances:
25 22 0.23
28 1 0.01
29 1 0.01
30 22 0.23
32 19 0.20
33 3 0.03
35 2 0.02
36 25 0.26
ACGTcount: A:0.58, C:0.01, G:0.23, T:0.17
Consensus pattern (32 bp):
AGTAAAAGTAAAAGAAGTAATCAGTAGAAAAG
Found at i:51372 original size:74 final size:73
Alignment explanation
Indices: 51219--51375 Score: 178
Period size: 74 Copynumber: 2.1 Consensus size: 73
51209 CAGCAGAATG
51219 AAGTAAAAGTAAAAGAAGTAATCAGCAGAGTAAAGTAAAAGTAAAAGAAGCAATTAGTAAAAGGA
1 AAGTAAAAGTAAAAGAAGTAATCAGCAGAGTAAAGTAAAAGTAAAAGAAGCAATTAGTAAAA-GA
*
51284 AGAAGTTAT
65 AGAAGTTAA
* * * *
51293 CAGTAAAAGTAAAAGAAGTAATCAGTAGAAGTGAGAGAGTAAAAG-AAGAAGAAGTAATTAGTAG
1 AAGTAAAAGTAAAAGAAGTAATCAGCAG-AGT-A-A-AGTAAAAGTAA-AAGAAGCAATTAGTAA
*
51357 AA-AA-TAG-TAA
61 AAGAAGAAGTTAA
51367 AAGTAAAAG
1 AAGTAAAAG
51376 AAGTAATTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
74 36 0.51
75 5 0.07
76 3 0.04
77 3 0.04
78 24 0.34
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (73 bp):
AAGTAAAAGTAAAAGAAGTAATCAGCAGAGTAAAGTAAAAGTAAAAGAAGCAATTAGTAAAAGAA
GAAGTTAA
Found at i:51378 original size:55 final size:54
Alignment explanation
Indices: 51328--51436 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 54
51318 TAGAAGTGAG
* *
51328 AGAGTAAAAG-AAGAAGAAGTAATTAGTAGAAAATAGTAAAAGTAAAAGAAGTAATTA
1 AGAGTAAAAGTAAG-AGAAGTAATCAGT--AAAAGAGTAAAAGTAAAAGAAGTAA-TA
51385 AGAGTAAAAGTAAGAGAAGTAATCAGTAAAAGAGTAAAAGTAAAAGAAGTAA
1 AGAGTAAAAGTAAGAGAAGTAATCAGTAAAAGAGTAAAAGTAAAAGAAGTAA
51437 GCAGAAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
55 24 0.49
57 22 0.45
58 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.22, T:0.17
Consensus pattern (54 bp):
AGAGTAAAAGTAAGAGAAGTAATCAGTAAAAGAGTAAAAGTAAAAGAAGTAATA
Found at i:51416 original size:22 final size:22
Alignment explanation
Indices: 51252--51324 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
51242 AGCAGAGTAA
* *
51252 AGTAAAAGTAAAAGAAGCAATT
1 AGTAAAAGTAAAAGAAGTAATC
* *
51274 AGTAAAAG--GAAGAAGTTATC
1 AGTAAAAGTAAAAGAAGTAATC
51294 AGTAAAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATC
*
51316 AGTAGAAGT
1 AGTAAAAGT
51325 GAGAGAGTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 16 0.38
22 26 0.62
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.19
Consensus pattern (22 bp):
AGTAAAAGTAAAAGAAGTAATC
Found at i:51418 original size:30 final size:29
Alignment explanation
Indices: 51328--51444 Score: 100
Period size: 30 Copynumber: 4.0 Consensus size: 29
51318 TAGAAGTGAG
*
51328 AGAGTAAAAG-AAGAAGAAGTAATTAGTAGAAA
1 AGAGTAAAAGTAA-AAGAAGT-A--AGCAGAAA
* **
51360 ATAGTAAAAGTAAAAGAAGT-A--A-TTA
1 AGAGTAAAAGTAAAAGAAGTAAGCAGAAA
* *
51385 AGAGTAAAAGTAAGAGAAGTAATCAGTAAA
1 AGAGTAAAAGTAAAAGAAGTAAGCAG-AAA
51415 AGAGTAAAAGTAAAAGAAGTAAGCAGAAA
1 AGAGTAAAAGTAAAAGAAGTAAGCAGAAA
51444 A
1 A
51445 TTGGTAATCA
Statistics
Matches: 70, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
25 19 0.27
26 2 0.03
28 2 0.03
29 4 0.06
30 25 0.36
32 16 0.23
33 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.22, T:0.16
Consensus pattern (29 bp):
AGAGTAAAAGTAAAAGAAGTAAGCAGAAA
Found at i:51420 original size:15 final size:15
Alignment explanation
Indices: 51294--51436 Score: 86
Period size: 15 Copynumber: 9.3 Consensus size: 15
51284 AGAAGTTATC
51294 AGTAAAAGTAAAAGA
1 AGTAAAAGTAAAAGA
*
51309 AGTAATCAGTAGAAGTGAGA
1 AGTAA-AAGTA-AA---AGA
51329 GAGTAAAAG-AAGAAGA
1 -AGTAAAAGTAA-AAGA
*
51345 AGTAATTAGTAGAAA-A
1 AGTAA-AAGTA-AAAGA
51361 TAGTAAAAGTAAAAGA
1 -AGTAAAAGTAAAAGA
*
51377 AGT--AA-T-TAAG-
1 AGTAAAAGTAAAAGA
*
51387 AGTAAAAGTAAGAGA
1 AGTAAAAGTAAAAGA
*
51402 AGTAATCAGTAAAAG-
1 AGTAA-AAGTAAAAGA
51417 AGTAAAAGTAAAAGA
1 AGTAAAAGTAAAAGA
51432 AGTAA
1 AGTAA
51437 GCAGAAAATT
Statistics
Matches: 99, Mismatches: 10, Indels: 38
0.67 0.07 0.26
Matches are distributed among these distances:
10 3 0.03
11 3 0.03
12 3 0.03
13 3 0.03
14 10 0.10
15 31 0.31
16 22 0.22
17 10 0.10
18 2 0.02
19 2 0.02
20 5 0.05
21 5 0.05
ACGTcount: A:0.58, C:0.01, G:0.23, T:0.17
Consensus pattern (15 bp):
AGTAAAAGTAAAAGA
Found at i:51547 original size:54 final size:54
Alignment explanation
Indices: 51474--51714 Score: 407
Period size: 54 Copynumber: 4.5 Consensus size: 54
51464 GAAGAAGAAG
*
51474 TAAGCAGT-AAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTTACC
1 TAAGCAGTAAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACC
51527 TAAGCAGTAAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACC
1 TAAGCAGTAAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACC
*
51581 TAAGCAGTAAAAGGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACC
1 TAAGCAGTAAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACC
* *
51635 TAAGCAGT-AAAAGGAGAAAATCAGTAAATAGGATTAATTCCGAGTAATTAACC
1 TAAGCAGTAAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACC
*
51688 TAAGCAAGTAAAGAGG-GAAAATCAGTA
1 TAAGC-AGTAAAAAGGAGAAAATCAGTA
51715 GAAAAGAGTA
Statistics
Matches: 179, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
53 55 0.31
54 119 0.66
55 5 0.03
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (54 bp):
TAAGCAGTAAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACC
Found at i:51588 original size:107 final size:106
Alignment explanation
Indices: 51474--51714 Score: 412
Period size: 107 Copynumber: 2.2 Consensus size: 106
51464 GAAGAAGAAG
*
51474 TAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTTACCTAAGCAGTAAAA
1 TAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGT-AAA
*
51539 AGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACC
65 AGGAGAAAATCAGTAAATAGGATTAATTCAGAGTAATTAACC
51581 TAAGCAGTAAAAGGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAA
1 TAAGCAGTAAAA-GGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAA
*
51646 AGGAGAAAATCAGTAAATAGGATTAATTCCGAGTAATTAACC
65 AGGAGAAAATCAGTAAATAGGATTAATTCAGAGTAATTAACC
51688 TAAGCAAGTAAAGAGG-GAAAATCAGTA
1 TAAGC-AGTAAA-AGGAGAAAATCAGTA
51715 GAAAAGAGTA
Statistics
Matches: 128, Mismatches: 3, Indels: 6
0.93 0.02 0.04
Matches are distributed among these distances:
107 71 0.55
108 56 0.44
109 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (106 bp):
TAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAA
GGAGAAAATCAGTAAATAGGATTAATTCAGAGTAATTAACC
Found at i:51847 original size:16 final size:17
Alignment explanation
Indices: 51818--51850 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51808 GAAGAAGAAA
51818 AAATCAGTAGAAAGGAG
1 AAATCAGTAGAAAGGAG
51835 AAATCAGTA-AAAGGAG
1 AAATCAGTAGAAAGGAG
51851 TAAAAGGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.55, C:0.06, G:0.27, T:0.12
Consensus pattern (17 bp):
AAATCAGTAGAAAGGAG
Found at i:51957 original size:67 final size:67
Alignment explanation
Indices: 51849--52202 Score: 492
Period size: 67 Copynumber: 5.1 Consensus size: 67
51839 CAGTAAAAGG
* *
51849 AGTAAAAGGAGTAAATGAAGTAAACAGTAGTAATTAGCTTAATTCAAAGTAATTAAGTTAATCAA
1 AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAA
51914 GA
66 GA
51916 AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAA
1 AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAA
*
51981 GG
66 GA
* *
51983 AGTAAAAGGCGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAACTAAGTTAATCAA
1 AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAA
52048 GA
66 GA
* *
52050 AGTAAAAGGAGTAAAAGGAAGTAACCAGTAGTGATTAGCTTAATTCAGAGTAATTAAGTACTTAA
1 AGTAAAAGGAGTAAAA-GAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAG---TTAA
52115 TCAAGAAGTAAAA
62 TC---AAG----A
* *
52128 GGAGTAAAAGGAGTAAAAGGAAGTAACCAGTAGTAATTAGCTTAATTCAGAGCAATTAAGTTAAT
1 --AGTAAAAGGAGTAAAA-GAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAAT
*
52193 CAGGA
63 CAAGA
52198 AGTAA
1 AGTAA
52203 TAGTAAGACA
Statistics
Matches: 261, Mismatches: 13, Indels: 25
0.87 0.04 0.08
Matches are distributed among these distances:
67 143 0.55
68 43 0.16
70 1 0.00
71 6 0.02
74 5 0.02
77 6 0.02
78 1 0.00
80 56 0.21
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.25
Consensus pattern (67 bp):
AGTAAAAGGAGTAAAAGAAGTAAACAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAA
GA
Found at i:52135 original size:9 final size:9
Alignment explanation
Indices: 52121--52153 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
52111 TTAATCAAGA
52121 AGTAAAAGG
1 AGTAAAAGG
52130 AGTAAAAGG
1 AGTAAAAGG
52139 AGTAAAAGG
1 AGTAAAAGG
52148 AAGTAA
1 -AGTAA
52154 CCAGTAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (9 bp):
AGTAAAAGG
Found at i:54232 original size:75 final size:71
Alignment explanation
Indices: 54095--54386 Score: 458
Period size: 75 Copynumber: 4.0 Consensus size: 71
54085 GTGCCCCTGA
* *
54095 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAAATCATTAATTTATCAATTATACCCAAGTCA
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAAATCAGTAATTGATCAATTATACCCAAGTCA
54160 ATTTTT
66 ATTTTT
*
54166 AGTCTCGGTTCGTCTAATTTGAACATTCAAAAAAAAAAAATCAGTAATTGATCAATTATACCCAA
1 AGTCTCGGTTCGTCCAATTTGAACATT----AAAAAAAAATCAGTAATTGATCAATTATACCCAA
54231 GTCAATTTTT
62 GTCAATTTTT
*
54241 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACAACAGTAATTGATCAATTATACCCAAGTC
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAA-ATCAGTAATTGATCAATTATACCCAAGTC
54306 AATATTTTT
65 -A-ATTTTT
* *
54315 AGTCTCGGTTCGTCCAATTTGAACATTCAATAAAACATCAGTAATTGATCAATTATACCCAAGTC
1 AGTCTCGGTTCGTCCAATTTGAACATT-AAAAAAAAATCAGTAATTGATCAATTATACCCAAGTC
54380 AATTTTT
65 AATTTTT
54387 GCAGAGAGAA
Statistics
Matches: 205, Mismatches: 8, Indels: 15
0.90 0.04 0.07
Matches are distributed among these distances:
71 34 0.17
72 34 0.17
73 2 0.01
74 61 0.30
75 74 0.36
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (71 bp):
AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAAATCAGTAATTGATCAATTATACCCAAGTCA
ATTTTT
Found at i:54326 original size:74 final size:72
Alignment explanation
Indices: 54095--54386 Score: 460
Period size: 74 Copynumber: 4.0 Consensus size: 72
54085 GTGCCCCTGA
* * *
54095 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAA-ATCATTAATTTATCAATTATACCCAAGTC
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACAACAGTAATTGATCAATTATACCCAAGTC
54159 AATTTTT
66 AATTTTT
* *
54166 AGTCTCGGTTCGTCTAATTTGAACATTCAAAAAAAAAAAATCAGTAATTGATCAATTATACCCAA
1 AGTCTCGGTTCGTCCAATTTGAACATT--AAAAAAAACAA-CAGTAATTGATCAATTATACCCAA
54231 GTCAATTTTT
63 GTCAATTTTT
54241 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACAACAGTAATTGATCAATTATACCCAAGTC
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACAACAGTAATTGATCAATTATACCCAAGTC
54306 AATATTTTT
66 -A-ATTTTT
* * *
54315 AGTCTCGGTTCGTCCAATTTGAACATTCAATAAAACATCAGTAATTGATCAATTATACCCAAGTC
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACAACAGTAATTGATCAATTATACCCAAGTC
54380 AATTTTT
66 AATTTTT
54387 GCAGAGAGAA
Statistics
Matches: 206, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
71 26 0.13
72 33 0.16
73 20 0.10
74 69 0.33
75 58 0.28
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (72 bp):
AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACAACAGTAATTGATCAATTATACCCAAGTC
AATTTTT
Found at i:54359 original size:146 final size:144
Alignment explanation
Indices: 54095--54386 Score: 478
Period size: 146 Copynumber: 2.0 Consensus size: 144
54085 GTGCCCCTGA
* * *
54095 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAAATCATTAATTTATCAATTATACCCAAGTCA
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAAAACAGTAATTGATCAATTATACCCAAGTCA
*
54160 ATTTTTAGTCTCGGTTCGTCTAATTTGAACATTCAAAAAAAAAAAATCAGTAATTGATCAATTAT
66 ATTTTTAGTCTCGGTTCGTCCAATTTGAACATTC--AAAAAAAAAATCAGTAATTGATCAATTAT
54225 ACCCAAGTCAATTTTT
129 ACCCAAGTCAATTTTT
54241 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACAACAGTAATTGATCAATTATACCCAAGTC
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAA-AACAGTAATTGATCAATTATACCCAAGTC
* *
54306 AATATTTTTAGTCTCGGTTCGTCCAATTTGAACATTC-AATAAAACATCAGTAATTGATCAATTA
65 -A-ATTTTTAGTCTCGGTTCGTCCAATTTGAACATTCAAAAAAAAAATCAGTAATTGATCAATTA
54370 TACCCAAGTCAATTTTT
128 TACCCAAGTCAATTTTT
54387 GCAGAGAGAA
Statistics
Matches: 137, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
146 77 0.56
147 26 0.19
148 1 0.01
149 33 0.24
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (144 bp):
AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAAAACAGTAATTGATCAATTATACCCAAGTCA
ATTTTTAGTCTCGGTTCGTCCAATTTGAACATTCAAAAAAAAAATCAGTAATTGATCAATTATAC
CCAAGTCAATTTTT
Found at i:56094 original size:184 final size:184
Alignment explanation
Indices: 55785--56154 Score: 731
Period size: 184 Copynumber: 2.0 Consensus size: 184
55775 AAATAATAAT
55785 TATATATAAACAATATATAAATAAAATCTAATAATATTAATTGTAGAATGACAGTATAGAAATAT
1 TATATATAAACAATATATAAATAAAATCTAATAATATTAATTGTAGAATGACAGTATAGAAATAT
55850 ATCTGACAAATAAGGGTATAATAGACGATTCAAAAGTTTTACATGTGAACGTACTTTTTAATATA
66 ATCTGACAAATAAGGGTATAATAGACGATTCAAAAGTTTTACATGTGAACGTACTTTTTAATATA
55915 GTATAAATAGATATAGATTAGAGATCTAATTTCTTTTTATTTATGATGAGCAAA
131 GTATAAATAGATATAGATTAGAGATCTAATTTCTTTTTATTTATGATGAGCAAA
55969 TATATATAAACAATATATAAATAAAATCTAATAATATTAATTGTAGAATGACAGTATAGAAATAT
1 TATATATAAACAATATATAAATAAAATCTAATAATATTAATTGTAGAATGACAGTATAGAAATAT
*
56034 ATCTGACAAATAAGGGTATAATAGACGATTTAAAAGTTTTACATGTGAACGTACTTTTTAATATA
66 ATCTGACAAATAAGGGTATAATAGACGATTCAAAAGTTTTACATGTGAACGTACTTTTTAATATA
56099 GTATAAATAGATATAGATTAGAGATCTAATTTCTTTTTATTTATGATGAGCAAA
131 GTATAAATAGATATAGATTAGAGATCTAATTTCTTTTTATTTATGATGAGCAAA
56153 TA
1 TA
56155 CATACATACT
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 185 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (184 bp):
TATATATAAACAATATATAAATAAAATCTAATAATATTAATTGTAGAATGACAGTATAGAAATAT
ATCTGACAAATAAGGGTATAATAGACGATTCAAAAGTTTTACATGTGAACGTACTTTTTAATATA
GTATAAATAGATATAGATTAGAGATCTAATTTCTTTTTATTTATGATGAGCAAA
Found at i:59356 original size:63 final size:63
Alignment explanation
Indices: 59207--59496 Score: 266
Period size: 63 Copynumber: 4.5 Consensus size: 63
59197 AAATATGGCT
* * *
59207 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAA-A-TAGGA-TCTAAGTGCAGGAATGTGA-A
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAATACTA-AACT-TAAATGTAGGAATGTGACA
*
59268 GAAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAATACTAAACTTAAATGTAGGAATGTGACG
1 -AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAATACTAAACTTAAATGTAGGAATGTGACA
* * * *
59332 AAACTGACCCTTTGTTTGAAAGGGTTTTTTGGGAATACTAAACTTAAATG-CGAGAAGGTGACA
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAATACTAAACTTAAATGTAG-GAATGTGACA
** * * * *
59395 AAACCAACCCTTTGTCCGAAAGGGTGTTTTTGGGAATCAAAAGTACTTAACTTAAATGTGGGAAT
1 AAACTGACCCTTTGTCTGAAAGGGT-ATTTTGGG------AA-TACTAAACTTAAATGTAGGAAT
59460 GTGACA
58 GTGACA
* * * * *
59466 AAATTAACCCTCTGTTTGAAAGGGCATTTTG
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTG
59497 AGAAAAAGCG
Statistics
Matches: 191, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
62 36 0.19
63 94 0.49
64 11 0.06
70 7 0.04
71 42 0.22
72 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (63 bp):
AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAATACTAAACTTAAATGTAGGAATGTGACA
Found at i:59545 original size:49 final size:49
Alignment explanation
Indices: 59485--59613 Score: 136
Period size: 49 Copynumber: 2.6 Consensus size: 49
59475 CTCTGTTTGA
* * * *
59485 AAGGGCATTTTGAGAAAAAGCGAGTAAAAATCAA-TGCCTTCCGTCTGGG
1 AAGGGCGTTTTGAGAAAAAGCAAGTAAAAA-CAAGTGCCTTCCATCCGGG
* * * *
59534 AAGGGCGTTTTGGGAAATAGCAAGTAAAAAGAAGTGTCTTCCATCCGGG
1 AAGGGCGTTTTGAGAAAAAGCAAGTAAAAACAAGTGCCTTCCATCCGGG
* *
59583 AAGGGCGTTTTGGAGGAAAA-CAGGTAAAAAC
1 AAGGGCGTTTT-GAGAAAAAGCAAGTAAAAAC
59614 TGAAAATTGA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
48 2 0.03
49 58 0.89
50 5 0.08
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (49 bp):
AAGGGCGTTTTGAGAAAAAGCAAGTAAAAACAAGTGCCTTCCATCCGGG
Found at i:61017 original size:2 final size:2
Alignment explanation
Indices: 61010--61036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61000 TTTCTCTATT
61010 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 T
61037 TTTTGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61551 original size:24 final size:24
Alignment explanation
Indices: 61519--61567 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
61509 TGAGATCGTG
* *
61519 TTTGGTTTGCTTTGTTTTGTCTGA
1 TTTGGTTTGCTTTATCTTGTCTGA
61543 TTTGGTTTGCTTTATCTTGTCTGA
1 TTTGGTTTGCTTTATCTTGTCTGA
61567 T
1 T
61568 CTCATTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.10, G:0.22, T:0.61
Consensus pattern (24 bp):
TTTGGTTTGCTTTATCTTGTCTGA
Found at i:66238 original size:21 final size:21
Alignment explanation
Indices: 66214--66256 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
66204 GGCCTACCAA
66214 ACATGGCCTAAAATTGATTAG
1 ACATGGCCTAAAATTGATTAG
66235 ACATGGCCTAAAATTGATTAG
1 ACATGGCCTAAAATTGATTAG
66256 A
1 A
66257 TTTCTTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (21 bp):
ACATGGCCTAAAATTGATTAG
Found at i:66295 original size:40 final size:40
Alignment explanation
Indices: 66240--66320 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
66230 ATTAGACATG
66240 GCCTAAAATTGATTAGATTTCTTCTTGTTCAACAAACGTA
1 GCCTAAAATTGATTAGATTTCTTCTTGTTCAACAAACGTA
66280 GCCTAAAATTGATTAGATTTCTTCTTGTTCAACAAACGTA
1 GCCTAAAATTGATTAGATTTCTTCTTGTTCAACAAACGTA
66320 G
1 G
66321 GAGAACGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (40 bp):
GCCTAAAATTGATTAGATTTCTTCTTGTTCAACAAACGTA
Found at i:66367 original size:28 final size:28
Alignment explanation
Indices: 66327--66382 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
66317 GTAGGAGAAC
66327 GTTGGATCATAAGGATTTCATGTAACAA
1 GTTGGATCATAAGGATTTCATGTAACAA
*
66355 GTTGGATCATAAGTATTTCATGTAACAA
1 GTTGGATCATAAGGATTTCATGTAACAA
66383 ATTAATGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (28 bp):
GTTGGATCATAAGGATTTCATGTAACAA
Done.