Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1038
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: 31930
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:2784 original size:2 final size:2
Alignment explanation
Indices: 2777--2825 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
2767 TAAGAGTTCT
* *
2777 TA TA TA TA TA TA TA TA CA TA TA TA T- TA TA TA -A TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2817 TA TA TA TA T
1 TA TA TA TA T
2826 GAGGTTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4515 original size:34 final size:33
Alignment explanation
Indices: 4456--4521 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
4446 CACACCCAGA
*
4456 TGTATCGATACAAATTGCTAAGTATCGATACAT
1 TGTATCGATAAAAATTGCTAAGTATCGATACAT
**
4489 TGTATCGATAAAAAATTGCTTTGTATCGATACA
1 TGTATCGAT-AAAAATTGCTAAGTATCGATACA
4522 CCATGAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 9 0.31
34 20 0.69
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATAAAAATTGCTAAGTATCGATACAT
Found at i:5848 original size:19 final size:19
Alignment explanation
Indices: 5800--5850 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
5790 ATTGCCAGTT
5800 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATTG
* *
5819 TGTAAGTATCGATACAA-TG
1 T-CATGTATCGATACAATTG
5838 ATCATGTATCGAT
1 -TCATGTATCGAT
5851 GCAAGGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (19 bp):
TCATGTATCGATACAATTG
Found at i:14826 original size:13 final size:13
Alignment explanation
Indices: 14808--14832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14798 CATAAAGTGT
14808 TGTATCGATACAA
1 TGTATCGATACAA
14821 TGTATCGATACA
1 TGTATCGATACA
14833 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14848 original size:32 final size:33
Alignment explanation
Indices: 14788--14856 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
14778 TTCAACGATT
14788 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
14821 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
14853 TGTA
1 TGTA
14857 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:15021 original size:52 final size:52
Alignment explanation
Indices: 14872--15022 Score: 212
Period size: 52 Copynumber: 2.9 Consensus size: 52
14862 CTGCCAAAAA
* ** * * *
14872 ATGTATCGATACATTACTCTAATGTATCGATACATGCAGGTAAATCTGCCCAT
1 ATGTATCGATACACTA-TGAAATGTATCGATACATGCAGGCAAATTTGCCCAG
* * *
14925 ATGTATTGATACACTATGAAATGTATCGATACATACAAGCAAATTTGCCCAG
1 ATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAG
14977 ATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTT
15023 TCATATTTCA
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 72 0.84
53 14 0.16
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:21975 original size:12 final size:12
Alignment explanation
Indices: 21956--21993 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
21946 AGTCAAAAGT
21956 AAACACAAAAAA
1 AAACACAAAAAA
21968 CAAA-ACAAAAAA
1 -AAACACAAAAAA
21980 AAACACAGAAAAA
1 AAACACA-AAAAA
21993 A
1 A
21994 GGTGTAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 11 0.48
13 9 0.39
ACGTcount: A:0.82, C:0.16, G:0.03, T:0.00
Consensus pattern (12 bp):
AAACACAAAAAA
Found at i:23297 original size:32 final size:30
Alignment explanation
Indices: 23192--23310 Score: 141
Period size: 30 Copynumber: 3.9 Consensus size: 30
23182 TTCAAATACC
* * *
23192 TTCTTAAAGTCCACGACTTAGTGGCAATCTC
1 TTCTCAAAGTCCACGACTCAGTGGC-ATCTT
*
23223 TTCTCAAAGCCCACGACTCAGTGGCAT-TT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTT
23252 TGTCTCAAAGTCCACGACTCAGTGGCATCCTT
1 T-TCTCAAAGTCCACGACTCAGTGGCAT-CTT
* *
23284 TTCTTCAAAGTCCACAACTCTGTGGCA
1 TTC-TCAAAGTCCACGACTCAGTGGCA
23311 CCCTTTTAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
29 2 0.03
30 27 0.35
31 24 0.31
32 24 0.31
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (30 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCTT
Found at i:23329 original size:27 final size:27
Alignment explanation
Indices: 23291--23493 Score: 154
Period size: 27 Copynumber: 7.0 Consensus size: 27
23281 CTTTTCTTCA
23291 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTT
*
23318 AAGTTCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTT
* * * *
23345 CAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCTGTGGCA--C-----CCTTTT
23379 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTT
* ** *
23406 AAGCCCACAACTCCATGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCTGTGGCA--C-----CCTTTT
*
23440 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTT
* * * *
23467 AAGCCCATAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCTGTGGCACCCTTTT
23494 TCCTTCTAAG
Statistics
Matches: 142, Mismatches: 20, Indels: 28
0.75 0.11 0.15
Matches are distributed among these distances:
27 93 0.65
29 2 0.01
32 2 0.01
34 45 0.32
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.31
Consensus pattern (27 bp):
AAGTCCACAACTCTGTGGCACCCTTTT
Found at i:23387 original size:34 final size:33
Alignment explanation
Indices: 23349--23528 Score: 177
Period size: 34 Copynumber: 5.7 Consensus size: 33
23339 CCTTTTCAGC
23349 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCAC-CTTTTTCCTTCTAAGT
* * *
23383 CCACAACTCTGTGGCA-C-----CCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTCTAAGT
*
23410 CCACAACTCCATGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCAC-CTTTTTCCTTCTAAGT
* *
23444 CCACAACTCCGTGGCA-C-----CCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTCTAAGT
*
23471 CCATAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCAC-CTTTTTCCTTCTAAGT
*
23505 CCACAACTCTGTGGCACCTTTTTC
1 CCACAACTCCGTGGCACCTTTTTC
23529 TTTTCAAAGC
Statistics
Matches: 117, Mismatches: 15, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
27 45 0.38
29 2 0.02
32 2 0.02
33 7 0.06
34 61 0.52
ACGTcount: A:0.19, C:0.36, G:0.12, T:0.32
Consensus pattern (33 bp):
CCACAACTCCGTGGCACCTTTTTCCTTCTAAGT
Found at i:23391 original size:61 final size:61
Alignment explanation
Indices: 23312--23527 Score: 369
Period size: 61 Copynumber: 3.5 Consensus size: 61
23302 TCTGTGGCAC
* * *
23312 CCTTTTAAGTTCACAACTCTGTGGCACCCTTTTCAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTCTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
*
23373 CCTTCTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAACTCCATGGCACTCTTTTT
1 CCTTCTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
23434 CCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCATAACTCCGTGGCACTCTTTTT
1 CCTTCTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
*
23495 CCTTCTAAGTCCACAACTCTGTGGCACCTTTTT
1 CCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
23528 CTTTTCAAAG
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 146 1.00
ACGTcount: A:0.19, C:0.35, G:0.12, T:0.33
Consensus pattern (61 bp):
CCTTCTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
Found at i:23391 original size:88 final size:86
Alignment explanation
Indices: 23263--23432 Score: 241
Period size: 88 Copynumber: 2.0 Consensus size: 86
23253 GTCTCAAAGT
* **
23263 CCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACAACTCTGTGGCACCCTTTTAAGTTCACAA
1 CCACAACTCAGTGGCATCCTTTTCTTCAAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAA
**
23328 CTCTGTGGCACCCTTTTCAGC
66 CTCCATGGCACCCTTTTCAGC
* * *
23349 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
1 CCACAACTCAGTGGCA-TCCTTTT-CTTCAAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCAC
*
23414 AACTCCATGGCACTCTTTT
64 AACTCCATGGCACCCTTTT
23433 TCCTTCTAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 14 0.19
87 6 0.08
88 53 0.73
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.31
Consensus pattern (86 bp):
CCACAACTCAGTGGCATCCTTTTCTTCAAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAA
CTCCATGGCACCCTTTTCAGC
Found at i:23543 original size:34 final size:34
Alignment explanation
Indices: 23461--23543 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
23451 TCCGTGGCAC
* *
23461 CCTTTTAAGCCCATAACTCCGTGGCACTCTTTTT
1 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
23495 CCTTCTAAGTCCACAACTCTGTGGCAC-CTTTTT
1 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
23528 CTTTTCAAAGCCCACA
1 C-CTTCTAAGCCCACA
23544 CAAGTAGGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 7 0.17
34 34 0.83
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.35
Consensus pattern (34 bp):
CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
Found at i:23565 original size:32 final size:33
Alignment explanation
Indices: 23529--23660 Score: 214
Period size: 33 Copynumber: 4.1 Consensus size: 33
23519 CACCTTTTTC
* *
23529 TTTTC-AAAGCCCACACAAGTAGGTGGTAACCT
1 TTTTCTAAAGCCCACACAAGTCGGTGGCAACCT
*
23561 TTTTCTAAAGCCCACACAAGTCGGTGGCAACCC
1 TTTTCTAAAGCCCACACAAGTCGGTGGCAACCT
23594 TTTTC-AAAGCCCACACAAGTCGGTGGCAACCT
1 TTTTCTAAAGCCCACACAAGTCGGTGGCAACCT
*
23626 TTTTCTAAAGCCCACACAAGTTGGTGGCAACCT
1 TTTTCTAAAGCCCACACAAGTCGGTGGCAACCT
23659 TT
1 TT
23661 CTAAGCCCAA
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
32 36 0.39
33 57 0.61
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (33 bp):
TTTTCTAAAGCCCACACAAGTCGGTGGCAACCT
Found at i:23604 original size:65 final size:64
Alignment explanation
Indices: 23528--23669 Score: 232
Period size: 65 Copynumber: 2.2 Consensus size: 64
23518 GCACCTTTTT
*
23528 CTTTTCAAAGCCCACACAAGTAGGTGGTAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAGCCCACACAAGTAGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAA-C
* *
23593 CTTTTCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGCAAC
1 CTTTTCAAAGCCCACACAAGTAGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
23657 C-TTTCTAAGCCCA
1 CTTTTCAAAGCCCA
23670 ATATCATTGG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 11 0.15
64 2 0.03
65 60 0.82
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (64 bp):
CTTTTCAAAGCCCACACAAGTAGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:23771 original size:43 final size:43
Alignment explanation
Indices: 23706--24854 Score: 930
Period size: 43 Copynumber: 25.0 Consensus size: 43
23696 TGGCACCTTT
* *
23706 ATCTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
23749 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * * *
23792 ACCTTTAAGTCCACTATAGCTGGCCTTGAATCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* *
23838 TTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGA
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
23884 ACCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* *
23930 TTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCATCACATTGGC
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
23976 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * * *
24019 ACCTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* * * *
24065 TTTATCTTTAAGACCAATGTAGCTGGCCTTTAATCAGCACATTAGC
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
*
24111 ATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * * * * *
24154 ACCTTTAAGTCCAATATAGATGGCCTTCATTCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* * *
24200 TTTATCTTTAAGACCAACGTCGTTGGCCTTGAATCAGCACATTGGC
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* ** * *
24246 ACCTTTAAGTCCAATACCGCTAGCCTTGAATCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* * *
24292 TTTATCTTTAAGACCAATGTCACTGGCCTTGAATCGGCACATTGGC
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * * *
24338 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG------C
*
24387 ATCTTTAAGTCCAATGTGGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
24430 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG------C
*
24479 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * * *
24522 ACCTTTAAGTCCAATATAGGTGGCCTTGAATCAGCATATTGGCACCTTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG------C
* *
24571 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACCTTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* ** * * * *
24614 ACCTCCAAGTCCAATATCGCTAGCCTTGAATCAACATATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
24657 ACCCTCGTCTTTTAAGCCCAATGTCGTTGGCCTTAAATCAGCACATTGAC
1 A------TC-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
24707 ACCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATAATGGCACCTTTGTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC---A---CA---TTGGC
* *
24759 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA-T--TG-----G-C
*
24811 ATCTTTAAGTCCAATGTCGCTGGCCTTTAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
24854 A
1 A
24855 CCTTCATCTT
Statistics
Matches: 895, Mismatches: 139, Indels: 144
0.76 0.12 0.12
Matches are distributed among these distances:
43 478 0.53
44 4 0.00
46 12 0.01
49 296 0.33
50 31 0.03
51 1 0.00
52 73 0.08
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
Found at i:23839 original size:21 final size:21
Alignment explanation
Indices: 23772--23839 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
23762 ATGTCGCTGG
*
23772 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCATATTGGCA
* *
23793 CCTTTAAGTCCA-CTATAGCTGG--
1 CCTTGAA-T-CAGC-ATA-TTGGCA
23815 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
23836 CCTT
1 CCTT
23840 TATCTTTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
19 3 0.09
20 5 0.14
21 12 0.34
22 8 0.23
23 4 0.11
24 3 0.09
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:23845 original size:92 final size:92
Alignment explanation
Indices: 23708--24800 Score: 1412
Period size: 92 Copynumber: 12.0 Consensus size: 92
23698 GCACCTTTAT
** *
23708 CTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGG---C---ATCTTTAAGTCCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
23767 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
23794 CTTTAAGTCCACTATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
*
23859 GCTGGCCTTGAATCAGCACATTGGAAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
23886 CTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
* *
23951 GCTGGCCTTGAATCATCACATTGGCAT
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
23978 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
* *
24037 GATGGCCTTGAATCAGCATATTGGCACC
66 GCTGGCCTTGAATCAGCACATTGGCA-C
* * * * * *
24065 TTTATCTTTAAGACCAATGTAGCTGGCCTTTAATCAGCACATT---AGC---ATCTTTAAATCCA
1 -----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCA
24124 ATGTCGCTGGCCTTGAATCAGCACATTGGCAC
61 ATGTCGCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
24156 CTTTAAGTCCAATATAGATGGCCTTCATTCAGCATATTGGCACCTTTATCTTTAAGACCAACGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
*
24221 GTTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
** * *
24248 CTTTAAGTCCAATACCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
* *
24313 ACTGGCCTTGAATCGGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
24340 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
24405 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
24432 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
24497 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
24524 CTTTAAGTCCAATATAGGTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
*
24589 GCTGGCCTTGAATCAGCACCTTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
** * * * * ** *
24616 CTCCAAGTCCAATATCGCTAGCCTTGAATCAACATATTGGCACCCTCGTCTTTTAAGCCCAATGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC-TTTAAGTCCAATGT
* * *
24681 CGTTGGCCTTAAATCAGCACATTGACAC
65 CGCTGGCCTTGAATCAGCACATTGGCAC
* * *
24709 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATAATGGCACCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGTCCAAT
* *
24774 ATCGCTGGCCTTGAATCAGCATATTGG
63 GTCGCTGGCCTTGAATCAGCACATTGG
24801 TGCCTTTGTC
Statistics
Matches: 889, Mismatches: 93, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
86 106 0.12
89 4 0.00
90 1 0.00
91 2 0.00
92 666 0.75
93 74 0.08
94 1 0.00
95 33 0.04
96 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:23919 original size:135 final size:135
Alignment explanation
Indices: 23677--24858 Score: 1150
Period size: 135 Copynumber: 8.6 Consensus size: 135
23667 CCAATATCAT
* *
23677 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACC--TATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * *
23742 CATTGGCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-CTTTAAGTCCA
64 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCA
*
23805 CTATAGC
129 ATATAGC
*
23812 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACC--TATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * * *
23877 CATTGGAACCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
64 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TCTTTAAG
*
23942 TCCAATGTAGC
125 TCCAATATAGC
* *
23953 TGGCCTTGAATCATCACATTGG---C-ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
1 TGGCCTTGAATCAGCATATTGGCACCTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
* * *
24014 TTGGCACCTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGAC
66 TTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TCTTTAAGTC
*
24079 CAATGTAGC
127 CAATATAGC
* * * *
24088 TGGCCTTTAATCAGCACATT---AGC-ATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACA
1 TGGCCTTGAATCAGCATATTGGCACCTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
* * * * *
24149 TTGGCACCTTTAAGTCCAATATAGATGGCCTTCATTCAGCATATTGGCACCTTTATCTTTAAGAC
66 TTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TCTTTAAGTC
** * *
24214 CAACGTCGT
127 CAATATAGC
* ** * *
24223 TGGCCTTGAATCAGCACATTGGCA-C---CTTTAAGTCCAATACCGCTAGCCTTGAATCAGCATA
1 TGGCCTTGAATCAGCATATTGGCACCTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
* * *
24284 TTGGCACCTTTATCTTTAAGACCAATGTCA-CTGGCCTTGAATCGGCACATTGGCA-C-CTTTAA
66 TTGGCA-C-----CTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAA
24346 GTCCAATATAGC
124 GTCCAATATAGC
* *
24358 TGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGTGGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACC-T-ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
*
24423 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAG
64 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C--C-TCTTTAAG
*
24488 TCCAATGTAGC
125 TCCAATATAGC
* * * * *
24499 TGGCCTTGAATCAGCACATTGGCA-C---CTTTAAGTCCAATATAGGTGGCCTTGAATCAGCATA
1 TGGCCTTGAATCAGCATATTGGCACCTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
* * *
24560 TTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACCTTGGCACCTC--CAAG
66 TTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAG
*
24623 TCCAATATCGC
125 TCCAATATAGC
* * * * * *
24634 TAGCCTTGAATCAACATATTGGCACCCTCGTCTTTTAAGCCCAATGTCGTTGGCCTTAAATCAGC
1 TGGCCTTGAATCAGCATATTGGCA-CCT-ATC-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
* * * * *
24699 ACATTGACACCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATAATGGCACCTTTGTCATCTT
63 ACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-----C-TCTT
*
24764 TAAGTCCAATATCGC
121 TAAGTCCAATATAGC
** *
24779 TGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTTAATCA
1 TGGCCTTGAATCAGCATATTGGCACC----T-ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCA
24844 GCACATTGGCACCTT
61 GCACATTGGCACCTT
24859 CATCTTTAAC
Statistics
Matches: 896, Mismatches: 94, Indels: 102
0.82 0.09 0.09
Matches are distributed among these distances:
134 1 0.00
135 537 0.60
136 39 0.04
137 5 0.01
138 4 0.00
139 2 0.00
140 4 0.00
141 185 0.21
142 36 0.04
143 2 0.00
144 2 0.00
145 34 0.04
147 41 0.05
148 4 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (135 bp):
TGGCCTTGAATCAGCATATTGGCACCTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA
TTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAAT
ATAGC
Found at i:24791 original size:52 final size:52
Alignment explanation
Indices: 24709--24858 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 52
24699 ACATTGACAC
*
24709 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATAATGGCACCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTGTCAT
* **
24761 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTGTCAT
* * *
24813 CTTTAAGTCCAATGTCGCTGGCCTTTAATCAGCACATTGGCACCTT
1 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTT
24859 CATCTTTAAC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTGTCAT
Found at i:25750 original size:13 final size:13
Alignment explanation
Indices: 25732--25756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25722 CATAAAGTGT
25732 TGTATCGATACAA
1 TGTATCGATACAA
25745 TGTATCGATACA
1 TGTATCGATACA
25757 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:25772 original size:32 final size:33
Alignment explanation
Indices: 25712--25780 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
25702 TTCAACGATT
25712 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
25745 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
25777 TGTA
1 TGTA
25781 AGCTACTGCG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:25836 original size:13 final size:13
Alignment explanation
Indices: 25818--25842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25808 ATTACTCTAA
25818 TGTATCGATACAT
1 TGTATCGATACAT
25831 TGTATCGATACA
1 TGTATCGATACA
25843 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25840 original size:34 final size:33
Alignment explanation
Indices: 25797--25863 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
25787 TGCGAAAAAA
*
25797 TGTATCGATACA-TTACTCTAATGTATCGATACAT
1 TGTATCGATACACTGA-TCT-ATGTATCGATACAT
*
25831 TGTATCGATACACTGATCTTTGTATCGATACAT
1 TGTATCGATACACTGATCTATGTATCGATACAT
25864 GCAGGCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 13 0.43
34 15 0.50
35 2 0.07
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (33 bp):
TGTATCGATACACTGATCTATGTATCGATACAT
Found at i:25978 original size:52 final size:52
Alignment explanation
Indices: 25851--25979 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
25841 CACTGATCTT
*
25851 TGTATCGATACATGCAGGCAAATCTGCCCAGATGCATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGCATCGATACACTATGAAA
* *
25903 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGCATCGATACACTATGAAA
25955 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
25980 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGCATCGATACACTATGAAA
Found at i:29178 original size:13 final size:13
Alignment explanation
Indices: 29160--29184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29150 CAATGATCAT
29160 GTATCGATACAAG
1 GTATCGATACAAG
29173 GTATCGATACAA
1 GTATCGATACAA
29185 AGCATAATGT
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:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAG
Found at i:29202 original size:33 final size:32
Alignment explanation
Indices: 29141--29203 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
29131 CCAGTTTCAT
* *
29141 GTATCGATACAATGATCATGTATCGATACAAG
1 GTATCGATACAAAGATAATGTATCGATACAAG
*
29173 GTATCGATACAAAGCATAATGTATTGATACA
1 GTATCGATACAAAG-ATAATGTATCGATACA
29204 TCTAGATGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (32 bp):
GTATCGATACAAAGATAATGTATCGATACAAG
Found at i:30515 original size:146 final size:147
Alignment explanation
Indices: 30054--30555 Score: 479
Period size: 146 Copynumber: 3.4 Consensus size: 147
30044 ACTTACTCAG
* * * *
30054 ATATCACTAAGACCTACCATCGACGTAGAAGTGCCCGAAGATCCT-AGTGGACTT-AAAAAGACA
1 ATATCCCTAAGGCCTACCATCGACTTAGAAGTGCCCGATGATCCTAAG-GGACTTGAAAAAG-C-
* * *
30117 AAAACAAACCTACTCCTAATTCT-TACCTTCGACATAGAAGCAGACCTAGTAATTTTATAGAACT
63 AAAA-AAACCTACTCCTAATT-TATACCTTCGACATAGAAACAGACCTAGTAATTTTATAGGATT
30181 AGGTTTTGGGAGAAA-TGCTAAA
126 AGGTTTTGGGA-AAAGTGCTAAA
** ** * * *
30203 AGGTCCCTAAGGCCTACCATCGACTTAGAAGTGCTTGGTGATCCTAAGGGACTTGAAAGA-TAAA
1 ATATCCCTAAGGCCTACCATCGACTTAGAAGTGCCCGATGATCCTAAGGGACTTGAAAAAGCAAA
* * * * *
30267 AAAGCCTACCCCTAATTTATACTTTCGACATAGAAAC-GAACCTAGTAATTTCATAGGGTTAGGT
66 AAAACCTACTCCTAATTTATACCTTCGACATAGAAACAG-ACCTAGTAATTTTATAGGATTAGGT
*
30331 TTCGGGAAAAAG-GCTAAA
130 TTTGGG-AAAAGTGCTAAA
** * *
30349 ATATCCCTAAGGTTTACCATCGACTTAGAAGTGCCTGATGATCTTAAGGGACTTGAAAAAGCAAA
1 ATATCCCTAAGGCCTACCATCGACTTAGAAGTGCCCGATGATCCTAAGGGACTTGAAAAAGCAAA
* ** * *
30414 AATGAACCTA-TTCTAATTTATACCTTC-AGTGTAGAAACAGATCC-GGTAGTTTTATAGGATTA
66 AA--AACCTACTCCTAATTTATACCTTCGA-CATAGAAACAGA-CCTAGTAATTTTATAGGATTA
* *
30476 GCTTTTAGGAAAAGTGCTAAA
127 GGTTTTGGGAAAAGTGCTAAA
* * * ***
30497 ATAT-CCTAAGG-CTCCCATCGACTTAGGAGTACCCGATGATCCTAAAAAACTTGAAAAAG
1 ATATCCCTAAGGCCTACCATCGACTTAGAAGTGCCCGATGATCCTAAGGGACTTGAAAAAG
30556 ATTGCAAAGA
Statistics
Matches: 289, Mismatches: 51, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
145 2 0.01
146 156 0.54
147 23 0.08
148 52 0.18
149 50 0.17
150 6 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (147 bp):
ATATCCCTAAGGCCTACCATCGACTTAGAAGTGCCCGATGATCCTAAGGGACTTGAAAAAGCAAA
AAAACCTACTCCTAATTTATACCTTCGACATAGAAACAGACCTAGTAATTTTATAGGATTAGGTT
TTGGGAAAAGTGCTAAA
Done.