Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000463.1 Hibiscus syriacus cultivar Beakdansim tig00000859_pilon, 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: 74275
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:440 original size:38 final size:39
Alignment explanation
Indices: 397--476 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
387 TTTTTTCATC
397 AAACGAGTTGTATCATGA-ATTTTTTTAAAAATAGAGTT
1 AAACGAGTTGTATCATGATATTTTTTTAAAAATAGAGTT
* **
435 AAACGAGTTGTATCATGATTTTTTTTTTTAAATAGAGTT
1 AAACGAGTTGTATCATGATATTTTTTTAAAAATAGAGTT
474 AAA
1 AAA
477 ACAGAATTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 18 0.47
39 20 0.53
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (39 bp):
AAACGAGTTGTATCATGATATTTTTTTAAAAATAGAGTT
Found at i:10439 original size:9 final size:9
Alignment explanation
Indices: 10408--10449 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
10398 TTCCTAATTT
*
10408 TTTAATTCA
1 TTTAATTCC
10417 TATTAA-TCC
1 T-TTAATTCC
*
10426 TTTAATTTC
1 TTTAATTCC
10435 TTTAATTCC
1 TTTAATTCC
10444 TTTAAT
1 TTTAAT
10450 GATGTGGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 4 0.14
9 20 0.71
10 4 0.14
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTAATTCC
Found at i:11170 original size:2 final size:2
Alignment explanation
Indices: 11163--11190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11153 ATTAATACGA
11163 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
11191 GAATAGTTTA
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:11372 original size:17 final size:19
Alignment explanation
Indices: 11337--11378 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
11327 CAACATATAT
11337 TCAAAATTATATCATAATA
1 TCAAAATTATATCATAATA
11356 TCAAAATT-TAT-ATAATA
1 TCAAAATTATATCATAATA
11373 T-AAAAT
1 TCAAAAT
11379 ATTTCGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 7 0.30
18 3 0.13
19 8 0.35
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
TCAAAATTATATCATAATA
Found at i:11766 original size:26 final size:26
Alignment explanation
Indices: 11712--11766 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
11702 TTAAGGAATG
* * *
11712 AATTTATAAATTTTTAGAGAGGAACA
1 AATTTATAAAATTTTAGAGAGAAAAA
11738 AATTTATAAAATTTTAG-GAGAATAAA
1 AATTTATAAAATTTTAGAGAGAA-AAA
11764 AAT
1 AAT
11767 AGATTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.35
Consensus pattern (26 bp):
AATTTATAAAATTTTAGAGAGAAAAA
Found at i:11820 original size:16 final size:15
Alignment explanation
Indices: 11775--11822 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
11765 ATAGATTATT
*
11775 AATAAAAAAA-TACA
1 AATAAAAAAATTAAA
*
11789 CATAAAAAAATTAAA
1 AATAAAAAAATTAAA
*
11804 AATAAAAGAATTTAAA
1 AATAAAA-AAATTAAA
11820 AAT
1 AAT
11823 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 9 0.32
15 9 0.32
16 10 0.36
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (15 bp):
AATAAAAAAATTAAA
Found at i:11831 original size:16 final size:15
Alignment explanation
Indices: 11790--11832 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
11780 AAAAATACAC
*
11790 ATAAAAAAATTAAAA
1 ATAAAAAATTTAAAA
11805 ATAAAAGAATTTAAAA
1 ATAAAA-AATTTAAAA
*
11821 ATTTAAAAATTT
1 A-TAAAAAATTT
11833 CAGAAGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 14 0.58
17 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
ATAAAAAATTTAAAA
Found at i:12526 original size:3 final size:3
Alignment explanation
Indices: 12518--12572 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
12508 GACATACAAA
* *
12518 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12566 TAT TAT T
1 TAT TAT T
12573 CAATTATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18966 original size:54 final size:54
Alignment explanation
Indices: 18899--19017 Score: 213
Period size: 54 Copynumber: 2.2 Consensus size: 54
18889 CGAATTTCAG
*
18899 AAATGA-CTGAATTACTCTGGAAACTCCGAAGTGACTGGGATAGACTTGACTACT
1 AAATGACCT-AATTACTCTGGAAACTCCGAAGTGACCGGGATAGACTTGACTACT
18953 AAATGACCTAATTACTCTGGAAACTCCGAAGTGACCGGGATAGACTTGACTACT
1 AAATGACCTAATTACTCTGGAAACTCCGAAGTGACCGGGATAGACTTGACTACT
19007 AAATGACCTAA
1 AAATGACCTAA
19018 GTATCCTCAA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
54 61 0.97
55 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (54 bp):
AAATGACCTAATTACTCTGGAAACTCCGAAGTGACCGGGATAGACTTGACTACT
Found at i:25499 original size:16 final size:16
Alignment explanation
Indices: 25478--25509 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25468 TTTTATTTTG
25478 AAATCAAGTTTGAAAT
1 AAATCAAGTTTGAAAT
25494 AAATCAAGTTTGAAAT
1 AAATCAAGTTTGAAAT
25510 TACTCCTCCT
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:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (16 bp):
AAATCAAGTTTGAAAT
Found at i:26189 original size:18 final size:18
Alignment explanation
Indices: 26166--26205 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
26156 AAGCATTTGA
* *
26166 TCCTCTGATTGTGCTTGT
1 TCCTCTGATCGTGCTTAT
*
26184 TCCTCTGCTCGTGCTTAT
1 TCCTCTGATCGTGCTTAT
26202 TCCT
1 TCCT
26206 TGTGCTGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.30, G:0.17, T:0.47
Consensus pattern (18 bp):
TCCTCTGATCGTGCTTAT
Found at i:27794 original size:21 final size:21
Alignment explanation
Indices: 27768--27826 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
27758 GAACCCTCAA
27768 GGGGTATCGATTCCCCTGTGG
1 GGGGTATCGATTCCCCTGTGG
27789 GGGGTATCGATTCCCCTGTGG
1 GGGGTATCGATTCCCCTGTGG
*
27810 GGGGAATCGATTCCCCT
1 GGGGTATCGATTCCCCT
27827 TCAAGGGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.12, C:0.25, G:0.36, T:0.27
Consensus pattern (21 bp):
GGGGTATCGATTCCCCTGTGG
Found at i:27834 original size:22 final size:21
Alignment explanation
Indices: 27768--27846 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
27758 GAACCCTCAA
*
27768 GGGGTATCGATTCCCCTGTGG
1 GGGGTATCGATTCCCCTGTAG
*
27789 GGGGTATCGATTCCCCTGTGG
1 GGGGTATCGATTCCCCTGTAG
*
27810 GGGGAATCGATTCCCCT-TCAAG
1 GGGGTATCGATTCCCCTGT--AG
*
27832 GGGGTATTGATTCCC
1 GGGGTATCGATTCCC
27847 TCTGCACCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 1 0.02
21 37 0.71
22 14 0.27
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (21 bp):
GGGGTATCGATTCCCCTGTAG
Found at i:31695 original size:22 final size:21
Alignment explanation
Indices: 31653--31692 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31643 TAGTTTATTT
*
31653 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
31674 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
31693 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:32972 original size:21 final size:20
Alignment explanation
Indices: 32927--32977 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
32917 GGAGCGTGGG
32927 GGGAATCGGTACCCCCTCAT
1 GGGAATCGGTACCCCCTCAT
32947 GGGAATCGGTACCCCCTCAT
1 GGGAATCGGTACCCCCTCAT
32967 GAGGAATCGGT
1 G-GGAATCGGT
32978 TCCCTAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.20
Consensus pattern (20 bp):
GGGAATCGGTACCCCCTCAT
Found at i:36321 original size:32 final size:31
Alignment explanation
Indices: 36280--36431 Score: 114
Period size: 31 Copynumber: 4.9 Consensus size: 31
36270 AGTCGAGGGT
36280 TTACCTATGTTCTACGGAACATATGGACATAA
1 TTACCTATGTTCTACGGAACATATGGACAT-A
* * * *
36312 TTACCTATG-TCTTTCGGGACATATGGATAGAA
1 TTACCTATGTTC-TACGGAACATATGGACA-TA
**
36344 TTACCTATG-TCT-TTGAGACATATGGACAGTA
1 TTACCTATGTTCTACGGA-ACATATGGACA-TA
** *
36375 -TACCTATGTTCTAAAGAACATATGGACATT
1 TTACCTATGTTCTACGGAACATATGGACATA
* * * *
36405 TTACCTAGGTTCTTCGGGACCTATGGA
1 TTACCTATGTTCTACGGAACATATGGA
36432 TAGTTGCCGA
Statistics
Matches: 96, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
30 10 0.10
31 49 0.51
32 37 0.39
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACATA
Found at i:36367 original size:31 final size:32
Alignment explanation
Indices: 36298--36383 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
36288 GTTCTACGGA
* *
36298 ACATATGGACATAATTACCTATGTCTTTCGGG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
*
36330 ACATATGGATAGAATTACCTATGTCTTT-GAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
*
36361 ACATATGGACAGTA-TACCTATGT
1 ACATATGGACAGAATTACCTATGT
36384 TCTAAAGAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 9 0.18
31 14 0.29
32 26 0.53
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAG
Found at i:37202 original size:21 final size:22
Alignment explanation
Indices: 37178--37222 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
37168 TATAACAGTA
*
37178 CTGTAGCA-GGGTATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
37199 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
37221 CT
1 CT
37223 AGCAGTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.16, C:0.24, G:0.33, T:0.27
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGTTCC
Found at i:37227 original size:20 final size:21
Alignment explanation
Indices: 37180--37227 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
37170 TAACAGTACT
*
37180 GTAGCA-GGGTATCGGTTCCC
1 GTAGCAGGGGAATCGGTTCCC
37200 TGTAGCAGGGGAATCGGTTCCC
1 -GTAGCAGGGGAATCGGTTCCC
37222 -TAGCAG
1 GTAGCAG
37228 TAATCTGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 6 0.24
22 13 0.52
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (21 bp):
GTAGCAGGGGAATCGGTTCCC
Found at i:38087 original size:29 final size:29
Alignment explanation
Indices: 38049--38122 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
38039 GCTGCTGGAA
* * * *
38049 AACCAGTTTGACCGTTTTCAACTGGTTTTG
1 AACCGGTTTGACCGGTTCCAACTGG-TTCG
* *
38079 -ACCGGTTTGATCGGTTCCGACTGGTTCG
1 AACCGGTTTGACCGGTTCCAACTGGTTCG
38107 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
38123 CTAAACCGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTCCAACTGGTTCG
Found at i:38168 original size:19 final size:19
Alignment explanation
Indices: 38144--38185 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
38134 TGGCCGGTCA
*
38144 GACCCGACCTGACTGACCC
1 GACCCGACCCGACTGACCC
38163 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
38182 GACC
1 GACC
38186 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (19 bp):
GACCCGACCCGACTGACCC
Found at i:38194 original size:7 final size:7
Alignment explanation
Indices: 38182--38218 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
38172 CGACTGACCC
38182 GACCGTT
1 GACCGTT
38189 GACCGTT
1 GACCGTT
38196 GACCG-T
1 GACCGTT
*
38202 GACCATT
1 GACCGTT
38209 GACCGTT
1 GACCGTT
38216 GAC
1 GAC
38219 TTCCTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:45497 original size:29 final size:30
Alignment explanation
Indices: 45430--45504 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
45420 GCTGCTGGAA
* * *
45430 AACCGGTTTGACCGCTTTTCAACCGGTTTTG
1 AACCGGTTTGACCG-GTTCCAACCGGTTTCG
* *
45461 -ACCAGTTTGACCGGTTCCGACCGG-TTCG
1 AACCGGTTTGACCGGTTCCAACCGGTTTCG
45489 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
45505 CTGAACTGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 3 0.08
29 22 0.59
30 12 0.32
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTCCAACCGGTTTCG
Found at i:45524 original size:19 final size:19
Alignment explanation
Indices: 45430--45524 Score: 68
Period size: 19 Copynumber: 4.9 Consensus size: 19
45420 GCTGCTGGAA
* * *
45430 AACCGGTTTGACCGCTTTTC
1 AACCGGTTTGACCG-GTCTG
* *
45450 AACCGGTTTTGACCAGTTTG
1 AACCGG-TTTGACCGGTCTG
*
45470 -ACCGGTTCCGACCGGT-TCG
1 AACCGGTT-TGACCGGTCT-G
45489 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
* *
45508 AACTGGTTTGGCCGGTC
1 AACCGGTTTGACCGGTC
45525 AGACCCGACC
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 17 0.27
21 7 0.11
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:45554 original size:19 final size:19
Alignment explanation
Indices: 45526--45567 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
45516 TGGCCGGTCA
*
45526 GACCCGACCCGACTGACCC
1 GACCCAACCCGACTGACCC
45545 GACCCAACCCGACTGACCC
1 GACCCAACCCGACTGACCC
45564 GACC
1 GACC
45568 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.52, G:0.19, T:0.05
Consensus pattern (19 bp):
GACCCAACCCGACTGACCC
Found at i:45576 original size:7 final size:7
Alignment explanation
Indices: 45564--45594 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
45554 CGACTGACCC
45564 GACCGTT
1 GACCGTT
45571 GACCGTT
1 GACCGTT
45578 GACCGTT
1 GACCGTT
45585 GACCGTT
1 GACCGTT
45592 GAC
1 GAC
45595 TTCCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:51238 original size:24 final size:25
Alignment explanation
Indices: 51190--51238 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
51180 ATGGATGAAT
* *
51190 TTATACAATTTAAGAAGGGTTAAAA
1 TTATAAAATTTAAGAAGGGTAAAAA
*
51215 TTATAAAATTTTAG-AGGGTAAAAA
1 TTATAAAATTTAAGAAGGGTAAAAA
51239 CATATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (25 bp):
TTATAAAATTTAAGAAGGGTAAAAA
Found at i:54973 original size:72 final size:72
Alignment explanation
Indices: 54848--54987 Score: 219
Period size: 72 Copynumber: 1.9 Consensus size: 72
54838 CAAAATGAGA
* * * *
54848 TTCACTGGATTACCATGTTTTCGAATTTTTTAAATAAAAAATGATATTTAAAAATATTTTTTAAT
1 TTCACTGGATTACCATATTTTCGAATGTTTGAAATAAAAAAAGATATTTAAAAATATTTTTTAAT
54913 TATCGGG
66 TATCGGG
*
54920 TTCA-TGGAATTACCATATTTTCGAGTGTTTGAAATAAAAAAAGATATTTAAAAATATTTTTTAA
1 TTCACTGG-ATTACCATATTTTCGAATGTTTGAAATAAAAAAAGATATTTAAAAATATTTTTTAA
54984 TTAT
65 TTAT
54988 TAAACTTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 3 0.05
72 59 0.95
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (72 bp):
TTCACTGGATTACCATATTTTCGAATGTTTGAAATAAAAAAAGATATTTAAAAATATTTTTTAAT
TATCGGG
Found at i:55205 original size:31 final size:31
Alignment explanation
Indices: 55163--55272 Score: 116
Period size: 31 Copynumber: 3.5 Consensus size: 31
55153 ATTTTAATAA
*
55163 ATTTAAGGATCATTTTATAACAGTTATATAG
1 ATTTAATGATCATTTTATAACAGTTATATAG
*
55194 ATTTAATGATCATTTTATAATAGTT-TGATAG
1 ATTTAATGATCATTTTATAACAGTTAT-ATAG
* * * *
55225 AATTTAATGATCATCTTATAACTACTTACAAAG
1 -ATTTAATGATCATTTTATAAC-AGTTATATAG
*
55258 -TTTAATAATCATTTT
1 ATTTAATGATCATTTT
55273 TTAATTGTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.61
32 19 0.29
33 6 0.09
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (31 bp):
ATTTAATGATCATTTTATAACAGTTATATAG
Found at i:55235 original size:32 final size:32
Alignment explanation
Indices: 55162--55246 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 32
55152 AATTTTAATA
*
55162 AATTTAAGGATCATTTTATAACAGTTATATAG
1 AATTTAATGATCATTTTATAACAGTTATATAG
*
55194 -ATTTAATGATCATTTTATAATAGTT-TGATAG
1 AATTTAATGATCATTTTATAACAGTTAT-ATAG
*
55225 AATTTAATGATCATCTTATAAC
1 AATTTAATGATCATTTTATAAC
55247 TACTTACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 27 0.57
32 19 0.40
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (32 bp):
AATTTAATGATCATTTTATAACAGTTATATAG
Found at i:55628 original size:13 final size:12
Alignment explanation
Indices: 55610--55642 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
55600 ATTTAAGTTT
55610 TTTTAAATATATA
1 TTTTAAATAT-TA
55623 TTTTAAAT-TTA
1 TTTTAAATATTA
55634 TTTTAAATA
1 TTTTAAATA
55643 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAAATATTA
Found at i:55648 original size:23 final size:23
Alignment explanation
Indices: 55601--55648 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
55591 TTTAGAGAAA
* *
55601 TTTAAGTTTTTTTAAATATATAT
1 TTTAAATTTTTTTAAATATAAAT
55624 TTTAAATTTATTTTAAATA-AAAT
1 TTTAAATTT-TTTTAAATATAAAT
55647 TT
1 TT
55649 AAAAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTAAATTTTTTTAAATATAAAT
Found at i:61426 original size:31 final size:31
Alignment explanation
Indices: 61388--61512 Score: 153
Period size: 31 Copynumber: 4.0 Consensus size: 31
61378 CCCGAAGGAC
* * * *
61388 CAGTCCATAGGTTTCGAAGAACCTAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
61419 CAGTCCATATGTTCCGAAGAATATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
61450 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* * *
61481 CAATCCATAT-ATCCTGAAGAACATAAGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
61512 C
1 C
61513 CCTCGACCCT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 2 0.02
31 80 0.98
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:63294 original size:24 final size:23
Alignment explanation
Indices: 63247--63317 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
63237 AATTAATAAT
*
63247 AAACAT-AATTAAAATAATTAAAAA
1 AAACATAAAATAAAA-AA-TAAAAA
* *
63271 CAACAAATAAATAAAAAAGTAAAAA
1 AAACATA-AAATAAAAAA-TAAAAA
63296 AAACATAAAATAAAAAATAAAA
1 AAACATAAAATAAAAAATAAAA
63318 TAAGTACAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 5 0.13
24 14 0.36
25 13 0.33
26 7 0.18
ACGTcount: A:0.76, C:0.06, G:0.01, T:0.17
Consensus pattern (23 bp):
AAACATAAAATAAAAAATAAAAA
Found at i:63298 original size:12 final size:11
Alignment explanation
Indices: 63265--63317 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
63255 TTAAAATAAT
63265 TAAAAACAACAAA
1 TAAAAA-AA-AAA
*
63278 TAAATAAAAAAG
1 TAAA-AAAAAAA
*
63290 TAAAAAAAACA
1 TAAAAAAAAAA
63301 TAAAATAAAAAA
1 TAAAA-AAAAAA
63313 TAAAA
1 TAAAA
63318 TAAGTACAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
11 10 0.29
12 16 0.47
13 6 0.18
14 2 0.06
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (11 bp):
TAAAAAAAAAA
Found at i:63318 original size:12 final size:12
Alignment explanation
Indices: 63275--63320 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
63265 TAAAAACAAC
63275 AAAT-AAATAAA
1 AAATAAAATAAA
63286 AAAGTAAAA-AAA
1 AAA-TAAAATAAA
*
63298 ACATAAAATAAA
1 AAATAAAATAAA
63310 AAATAAAATAA
1 AAATAAAATAA
63321 GTACAAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 8 0.27
12 19 0.63
13 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:64119 original size:18 final size:18
Alignment explanation
Indices: 64077--64120 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
64067 GACACAAAGT
64077 AATAAAAAAAATAATGTA
1 AATAAAAAAAATAATGTA
*
64095 AA-GAAAAAAATCAAT-TA
1 AATAAAAAAAAT-AATGTA
64112 AATAAAAAA
1 AATAAAAAA
64121 TAAAAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (18 bp):
AATAAAAAAAATAATGTA
Found at i:65424 original size:15 final size:15
Alignment explanation
Indices: 65404--65456 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
65394 TAAAAAAGAA
65404 AATAAATAATAATAT
1 AATAAATAATAATAT
*
65419 AATAAATAATAAAAT
1 AATAAATAATAATAT
65434 -AT-AATACATAAATAT
1 AATAAATA-AT-AATAT
65449 AATAAATA
1 AATAAATA
65457 TTTTCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 18 0.56
16 2 0.06
17 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAATAATAATAT
Found at i:65432 original size:27 final size:30
Alignment explanation
Indices: 65392--65456 Score: 91
Period size: 27 Copynumber: 2.3 Consensus size: 30
65382 TTTGGACCAA
*
65392 AATAAAAAAGAAAATA-AATA-AT-AATAT
1 AATAAATAAGAAAATATAATACATAAATAT
*
65419 AATAAATAATAAAATATAATACATAAATAT
1 AATAAATAAGAAAATATAATACATAAATAT
65449 AATAAATA
1 AATAAATA
65457 TTTTCAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 14 0.42
28 4 0.12
29 2 0.06
30 13 0.39
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (30 bp):
AATAAATAAGAAAATATAATACATAAATAT
Found at i:65471 original size:11 final size:11
Alignment explanation
Indices: 65452--65717 Score: 67
Period size: 11 Copynumber: 21.3 Consensus size: 11
65442 TAAATATAAT
65452 AAATATTTTCA
1 AAATATTTTCA
* *
65463 AAATGTTTTAA
1 AAATATTTTCA
65474 AAATATTTTCAA
1 AAATATTTTC-A
65486 AAATTATATATT-A
1 AAA-TAT-T-TTCA
65499 TATATATATTTTTTCA
1 -A-A-ATA--TTTTCA
65515 AAATATTTTCAA
1 AAATATTTTC-A
65527 AAACTATATATT-A
1 AAA-TAT-T-TTCA
* *
65540 TATATATTTTTA
1 -AAATATTTTCA
65552 AAATATTTTCAA
1 AAATATTTTC-A
65564 AAACTATATATT-A
1 AAA-TAT-T-TTCA
*
65577 TATATATGCTTTCA
1 -AAATAT--TTTCA
65591 AAATATTTTCAA
1 AAATATTTTC-A
65603 AAACTATATATT-A
1 AAA-TAT-T-TTCA
*
65616 TATATATGCTTTCA
1 -AAATAT--TTTCA
*
65630 AAATGTTTTCGA
1 AAATATTTTC-A
65642 AAACTATATATT-A
1 AAA-TAT-T-TTCA
*
65655 TATATATTTTCA
1 -AAATATTTTCA
65667 AAATATTTTCGA
1 AAATATTTTC-A
65679 AAACTATATGTT-A
1 AAA-TAT-T-TTCA
*
65692 TATATATTTTCA
1 -AAATATTTTCA
65704 AAATATTTTCA
1 AAATATTTTCA
65715 AAA
1 AAA
65718 ACTATATACT
Statistics
Matches: 194, Mismatches: 19, Indels: 84
0.65 0.06 0.28
Matches are distributed among these distances:
11 66 0.34
12 30 0.15
13 54 0.28
14 22 0.11
15 18 0.09
16 3 0.02
17 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (11 bp):
AAATATTTTCA
Found at i:65555 original size:37 final size:37
Alignment explanation
Indices: 65468--65745 Score: 394
Period size: 37 Copynumber: 7.2 Consensus size: 37
65458 TTTCAAAATG
* *
65468 TTTTAAAAATATTTTCAAAAATTATATATTATATATATA
1 TTTTCAAAATATTTTCAAAAACTATATA-T-TATATATA
65507 TTTTTTCAAAATATTTTCAAAAACTATATATTATATATA
1 --TTTTCAAAATATTTTCAAAAACTATATATTATATATA
*
65546 TTTTTAAAATATTTTCAAAAACTATATATTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
65583 TGCTTTCAAAATATTTTCAAAAACTATATATTATATATA
1 T--TTTCAAAATATTTTCAAAAACTATATATTATATATA
* *
65622 TGCTTTCAAAATGTTTTCGAAAACTATATATTATATATA
1 T--TTTCAAAATATTTTCAAAAACTATATATTATATATA
* *
65661 TTTTCAAAATATTTTCGAAAACTATATGTTATATATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATA
65698 TTTTCAAAATATTTTCAAAAACTATATACTATATATATA
1 TTTTCAAAATATTTTCAAAAACTATATA-T-TATATATA
*
65737 TTTTTAAAA
1 TTTTCAAAA
65746 ACTATATATT
Statistics
Matches: 222, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
37 97 0.44
38 1 0.00
39 97 0.44
40 1 0.00
41 26 0.12
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (37 bp):
TTTTCAAAATATTTTCAAAAACTATATATTATATATA
Found at i:65603 original size:76 final size:74
Alignment explanation
Indices: 65468--65745 Score: 394
Period size: 76 Copynumber: 3.6 Consensus size: 74
65458 TTTCAAAATG
* *
65468 TTTTAAAAATATTTTCAAAAATTATATATTATATATATATTTTTTCAAAATATTTTCAAAAACTA
1 TTTTCAAAATATTTTCAAAAACTATATA-T-TATATATA--TTTTCAAAATATTTTCAAAAACTA
65533 TATATTATATATA
62 TATATTATATATA
*
65546 TTTTTAAAATATTTTCAAAAACTATATATTATATATATGCTTTCAAAATATTTTCAAAAACTATA
1 TTTTCAAAATATTTTCAAAAACTATATATTATATATAT--TTTCAAAATATTTTCAAAAACTATA
65611 TATTATATATA
64 TATTATATATA
* * *
65622 TGCTTTCAAAATGTTTTCGAAAACTATATATTATATATATTTTCAAAATATTTTCGAAAACTATA
1 T--TTTCAAAATATTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATA
*
65687 TGTTATATATA
64 TATTATATATA
*
65698 TTTTCAAAATATTTTCAAAAACTATATACTATATATATATTTTTAAAA
1 TTTTCAAAATATTTTCAAAAACTATATA-T-TATATATATTTTCAAAA
65746 ACTATATATT
Statistics
Matches: 184, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
74 26 0.14
75 1 0.01
76 96 0.52
77 1 0.01
78 60 0.33
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (74 bp):
TTTTCAAAATATTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATA
TTATATATA
Found at i:65732 original size:2 final size:2
Alignment explanation
Indices: 65720--65794 Score: 64
Period size: 2 Copynumber: 37.5 Consensus size: 2
65710 TTTCAAAAAC
* * * * *
65720 TA TA TA CTA TA TA TA TA TT TT TA AA AA CTA TA TA T- TA TA TG TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
65763 TA -A TA TA TA CA 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 TA T
65795 TAAATGAAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
1 2 0.03
2 56 0.92
3 3 0.05
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:65758 original size:26 final size:28
Alignment explanation
Indices: 65706--65764 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
65696 TATTTTCAAA
65706 ATATTTTCAAAAACTATATACTATATAT
1 ATATTTTCAAAAACTATATACTATATAT
* * *
65734 ATATTTTTAAAAACTATATATTATATGT
1 ATATTTTCAAAAACTATATACTATATAT
65762 ATA
1 ATA
65765 ATATATACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (28 bp):
ATATTTTCAAAAACTATATACTATATAT
Found at i:66275 original size:41 final size:41
Alignment explanation
Indices: 66173--66275 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
66163 ATCACAGTGC
* *
66173 ACAGGAGACGACGTCAGAAAAGATCAGAGGTGATAGCAGCA
1 ACAGGCGACGACGTCAGAAACGATCAGAGGTGATAGCAGCA
* * *
66214 ACAGGCGATGATGTCAGAAACGGTCAGAGGTGATAGCAGCA
1 ACAGGCGACGACGTCAGAAACGATCAGAGGTGATAGCAGCA
*
66255 GCAGGCGACGACGTCAGAAAC
1 ACAGGCGACGACGTCAGAAAC
66276 TACCTAGGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.37, C:0.19, G:0.33, T:0.11
Consensus pattern (41 bp):
ACAGGCGACGACGTCAGAAACGATCAGAGGTGATAGCAGCA
Found at i:67038 original size:67 final size:63
Alignment explanation
Indices: 66805--67215 Score: 357
Period size: 65 Copynumber: 6.4 Consensus size: 63
66795 GAAACTAACA
* * * * * * *
66805 CAAAGGTTAGTGTTACAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATC
1 CAAA-GTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTTTTTCAAGAGAAA--ATT
66870 TT
62 TT
* * * * *
66872 -AAAGATTGGTGTGTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTATTTCAAGGGAAAA----
1 CAAAG-TTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTTTTTCAAGAGAAAATTTT
* * * * **
66932 -AGATTTTGTGTTTCAAGAGAAGCTGTCTCAAGGGAGACAAATTTTGTTTCAATAGAAACAAATT
1 CAAAGTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTT-TTTCAAGAGAAA-ATTTT
* * *
66996 CAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCTTTTCAAGGGAAAAGTT
1 CAAAG--TTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTTTTTCAAGAGAAAA-TT
67061 TT
62 TT
* * ** * *
67063 CAAAGTTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTTTTTCAAGAGAAA-ATTTT
* *
67128 CAAAGTTTGTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAATTTTTTTTCAAGAGAAATGTTTT
1 CAAAGTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA-TTTTTTTCAAGAGAAA-ATTTT
* *
67193 CAAAGTTTATATTTCAAGAGAAA
1 CAAAGTTTGTGTTTCAAGAGAAA
67216 TTGTAAATTC
Statistics
Matches: 292, Mismatches: 38, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
58 6 0.02
59 40 0.14
60 3 0.01
64 4 0.01
65 133 0.46
66 51 0.17
67 49 0.17
68 6 0.02
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (63 bp):
CAAAGTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTTTTCAAGAGAAAATTTT
Found at i:67192 original size:130 final size:129
Alignment explanation
Indices: 66805--67215 Score: 451
Period size: 130 Copynumber: 3.2 Consensus size: 129
66795 GAAACTAACA
* * *
66805 CAAAGGTTAGTGTTACAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACG-AT
1 CAAAGTTTA-TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAATTTGTTTCAAGGGAAACGTAT
* * * * *
66869 CTTAAAGATTGGTGTGTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTATTTCAAGGGAAA---
64 -TCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGGAAAGTT
66931 --
128 TT
* * * * ** **
66931 -AAGATTTTGTGTTTCAAGAGAAGCTGTCTCAAGGGAGACAAATTTTGTTTCAATAGAAACAAAT
1 CAA-AGTTTATGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTTGTTTCAAGGGAAACGTAT
* *
66995 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCTTTTCAAGGGAAAAGT
64 TCAAAGA-TTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGG-AAAGT
67060 TTT
127 TTT
** * *
67063 CAAAGTTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGTTTATGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTTGTTTCAAGGGAAACGTATT
* * *
67128 CAAAG-TTTGTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAATTTTTTTTCAAGAGAAATGTTT
65 CAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGGAAA-GTTT
67192 T
129 T
*
67193 CAAAGTTTATATTTCAAGAGAAA
1 CAAAGTTTATGTTTCAAGAGAAA
67216 TTGTAAATTC
Statistics
Matches: 237, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
125 51 0.22
126 51 0.22
127 3 0.01
129 3 0.01
130 73 0.31
132 54 0.23
133 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (129 bp):
CAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGAGACAAAATTTGTTTCAAGGGAAACGTATTC
AAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGGAAAGTTTT
Found at i:68034 original size:21 final size:22
Alignment explanation
Indices: 67991--68043 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
67981 GTATAAACAA
67991 TATCGATACCATATGGAAGGGG
1 TATCGATACCATATGGAAGGGG
68013 TATCGATACC-TATGTGAA-GGG
1 TATCGATACCATATG-GAAGGGG
68034 TATCGATACC
1 TATCGATACC
68044 CGGGGAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
TATCGATACCATATGGAAGGGG
Found at i:68948 original size:31 final size:31
Alignment explanation
Indices: 68908--68998 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 31
68898 AAGAGTCGTG
*
68908 GGTTACCTATGTCCTTTGAGATATATGGACA
1 GGTTACCTATGTCCTTTGAGACATATGGACA
* *
68939 GTTTACCTATGT-CTTTCGGGACATATGGACA
1 GGTTACCTATGTCCTTT-GAGACATATGGACA
* *
68970 GGTTACCTATGTCATTCGAGACATATGGA
1 GGTTACCTATGTCCTTTGAGACATATGGA
68999 TAGTGGTCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
30 4 0.08
31 45 0.88
32 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GGTTACCTATGTCCTTTGAGACATATGGACA
Found at i:69795 original size:36 final size:36
Alignment explanation
Indices: 69748--69960 Score: 187
Period size: 36 Copynumber: 6.1 Consensus size: 36
69738 GGGTGTTACA
*
69748 GAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTTTTCAAGG
* **
69784 GAAACTGTCTCAAGAGTGACAAAATTCGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTTTTCAAGG
* *
69820 GAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTTTTCAAGG
* *
69856 GAAACAT-TTTC-A-A-AG------TTTATGTTTCAAGA
1 GAAAC-TGTCTCAAGAGAGACAAAATTT-T-TTTCAAGG
* *
69885 GAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTTTTCAAGG
** * *
69921 GAAGTTGTCTTAAGAGAGACAAAATTCATTTT-AAGG
1 GAAACTGTCTCAAGAGAGACAAAATT-TTTTTCAAGG
69957 GAAA
1 GAAA
69961 TATTTTCAAA
Statistics
Matches: 141, Mismatches: 22, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
27 3 0.02
28 1 0.01
29 15 0.11
30 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 109 0.77
37 4 0.03
38 3 0.02
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTTTTTTCAAGG
Found at i:69957 original size:101 final size:102
Alignment explanation
Indices: 69776--70028 Score: 337
Period size: 101 Copynumber: 2.5 Consensus size: 102
69766 ACAAAATTTT
* * * *
69776 TTTCAAGGGAAACTGTCTCAAGAGTGACAAAATTCGTTTCAAGGGAAACTGTCTCAAGAGAAACA
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAAACA
**
69841 AAATTTGTTTCAAGGGAAACATTTTCAAAG-TTTATG
66 AAATTCATTTCAAGGGAAACATTTTCAAAGATTTATG
* ** * *
69877 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAGTTGTCTTAAGAGAGACA
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAAACA
* * *
69942 AAATTCATTTTAAGGGAAATATTTTCAAAGATTTTGTG
66 AAATTCATTTCAAGGGAAACATTTTCAAAGA-TTTATG
* * *
69980 TTTTAAGAGAAACTGTTTCAAGGGAGACAAAAGTTGTTTCAAGGGAAAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
70029 AGACTCAAAG
Statistics
Matches: 130, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
101 82 0.63
103 48 0.37
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (102 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAAACA
AAATTCATTTCAAGGGAAACATTTTCAAAGATTTATG
Found at i:70597 original size:24 final size:24
Alignment explanation
Indices: 70565--70612 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
70555 TCAATAAATT
70565 ATAGATATTTGACAAGTGTCAAGA
1 ATAGATATTTGACAAGTGTCAAGA
70589 ATAGATATTTGACAAGTGTCAAGA
1 ATAGATATTTGACAAGTGTCAAGA
70613 TCAATGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAGATATTTGACAAGTGTCAAGA
Found at i:71413 original size:15 final size:14
Alignment explanation
Indices: 71363--71424 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
71353 TCATATTTTT
*
71363 CTTTTTTTTCTTAG
1 CTTTTTTTTCTTTG
* *
71377 C-TCTTTTTCATTG
1 CTTTTTTTTCTTTG
71390 -TTTTGTTTTCTTTG
1 CTTTT-TTTTCTTTG
71404 CTCTTTTTTTCTTTG
1 CT-TTTTTTTCTTTG
71419 CTTTTT
1 CTTTTT
71425 CCTCGCTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 11 0.28
14 13 0.33
15 12 0.31
16 3 0.08
ACGTcount: A:0.03, C:0.16, G:0.08, T:0.73
Consensus pattern (14 bp):
CTTTTTTTTCTTTG
Found at i:73581 original size:13 final size:14
Alignment explanation
Indices: 73563--73591 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
73553 TAGGCAACTT
73563 AAGATACTTTA-CA
1 AAGATACTTTATCA
73576 AAGATACTTTATCA
1 AAGATACTTTATCA
73590 AA
1 AA
73592 CCCACACAAG
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:0.14, G:0.07, T:0.31
Consensus pattern (14 bp):
AAGATACTTTATCA
Done.