Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold485
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: 155029
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 3650 characters in sequence are not A, C, G, or T
Found at i:7076 original size:19 final size:21
Alignment explanation
Indices: 7038--7076 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
7028 CCTTTTCTAA
*
7038 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
7059 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
7077 GAAAACAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:7301 original size:21 final size:21
Alignment explanation
Indices: 7275--7350 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
7265 AATCATATCT
7275 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
7296 TCTAAGATTGCATATATCATA
1 TCTAAGATTGTATATATCATA
7317 TCTAAGATTG--TATATCATA
1 TCTAAGATTGTATATATCATA
7336 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
7351 CCTCGAAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 19 0.37
21 33 0.63
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:8538 original size:1 final size:1
Alignment explanation
Indices: 8534--8563 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
8524 CCCCCCCCCC
*
8534 AAAAAAAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8564 GGAGGTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:21655 original size:15 final size:14
Alignment explanation
Indices: 21634--21669 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
21624 ATAATCCTTA
*
21634 ATAATTATCTTAAT
1 ATAATTATCCTAAT
21648 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
21663 ATAATTA
1 ATAATTA
21670 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:22244 original size:23 final size:23
Alignment explanation
Indices: 22218--22278 Score: 61
Period size: 27 Copynumber: 2.5 Consensus size: 23
22208 AGTCCCCAAA
*
22218 TTATATATTTTTTTATTTTTTAT
1 TTATATATTTTTTTATTTATTAT
*
22241 TTATTTTGATTTTGATTTATTTATTAT
1 TTA-TAT-ATTTT--TTTATTTATTAT
22268 TTATAT-TTTTT
1 TTATATATTTTT
22279 ATGCTTTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
22 1 0.03
23 3 0.10
24 6 0.19
25 5 0.16
26 2 0.06
27 14 0.45
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.75
Consensus pattern (23 bp):
TTATATATTTTTTTATTTATTAT
Found at i:22279 original size:16 final size:16
Alignment explanation
Indices: 22223--22280 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
22213 CCAAATTATA
*
22223 TATTTTTTTATT-TTT
1 TATTTATTTATTATTT
*
22238 TATTTATTT-TGATTT
1 TATTTATTTATTATTT
22253 TGATTTATTTATTATTT
1 T-ATTTATTTATTATTT
22270 ATATTT-TTTAT
1 -TATTTATTTAT
22281 GCTTTAGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.33
16 13 0.36
17 9 0.25
18 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TATTTATTTATTATTT
Found at i:23633 original size:5 final size:5
Alignment explanation
Indices: 23623--23701 Score: 58
Period size: 5 Copynumber: 15.4 Consensus size: 5
23613 AGTAATAAAT
* *
23623 AATAA AATAA AATAA ATTAATA AATAA AGT-A AA-AA AATAA AATAA AATAA
1 AATAA AATAA AATAA AAT-A-A AATAA AATAA AATAA AATAA AATAA AATAA
23673 TAA-ATA AATAA CAA-AA AATAAA AATAA AA
1 -AATA-A AATAA -AATAA AAT-AA AATAA AA
23702 ATTGGGTTGC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
4 7 0.12
5 37 0.62
6 13 0.22
7 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:23639 original size:4 final size:4
Alignment explanation
Indices: 23616--23683 Score: 59
Period size: 4 Copynumber: 16.2 Consensus size: 4
23606 AGTAATAAGT
* *
23616 AATA AAT- AATAA AATAA AATA AATT AATA AATA AAGTA AAAA AATAA
1 AATA AATA AAT-A AAT-A AATA AATA AATA AATA AA-TA AATA AAT-A
23663 AATA AA-A TAATA AATA AATA A
1 AATA AATA -AATA AATA AATA A
23684 CAAAAAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
3 4 0.07
4 33 0.61
5 17 0.31
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:23662 original size:30 final size:29
Alignment explanation
Indices: 23616--23701 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 29
23606 AGTAATAAGT
* *
23616 AATAAATAATAAAATAAAATAAATTAATA
1 AATAAATAAAAAAATAAAATAAAATAATA
23645 AATAAAGTAAAAAAATAAAATAAAATAATA
1 AATAAA-TAAAAAAATAAAATAAAATAATA
23675 AATAAATAACAAAAAATAAAAATAAAA
1 AATAAAT-A-AAAAAAT-AAAATAAAA
23702 ATTGGGTTGC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.14
30 28 0.55
31 7 0.14
32 9 0.18
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.21
Consensus pattern (29 bp):
AATAAATAAAAAAATAAAATAAAATAATA
Found at i:23696 original size:8 final size:8
Alignment explanation
Indices: 23619--23702 Score: 55
Period size: 8 Copynumber: 10.1 Consensus size: 8
23609 AATAAGTAAT
*
23619 AAATAATA
1 AAATAAAA
23627 AAATAAAA
1 AAATAAAA
* *
23635 TAAATTAAT
1 -AAATAAAA
23644 AAATAAAGTA
1 AAATAAA--A
23654 AAA-AAATA
1 AAATAAA-A
23662 AAATAAAA
1 AAATAAAA
* *
23670 TAATAAAT
1 AAATAAAA
23678 AAATAACAA
1 AAATAA-AA
*
23687 AAA-ATAA
1 AAATAAAA
23694 AAATAAAA
1 AAATAAAA
23702 A
1 A
23703 TTGGGTTGCC
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
7 5 0.08
8 35 0.59
9 16 0.27
10 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (8 bp):
AAATAAAA
Found at i:23703 original size:38 final size:39
Alignment explanation
Indices: 23616--23703 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 39
23606 AGTAATAAGT
*
23616 AATAAATAATAAAATAAAATAAATTAATAAATAAAGTAAA
1 AATAAA-AATAAAATAAAATAAATTAACAAATAAAGTAAA
*
23656 AAAATAAAATAAAATAATAAATAAA-TAACAAA-AAA-TAAA
1 AATA-AAAATAAAAT-A-AAATAAATTAACAAATAAAGTAAA
23695 AATAAAAAT
1 AATAAAAAT
23704 TGGGTTGCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
38 5 0.12
39 7 0.17
40 14 0.33
41 9 0.21
42 7 0.17
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (39 bp):
AATAAAAATAAAATAAAATAAATTAACAAATAAAGTAAA
Found at i:27761 original size:12 final size:12
Alignment explanation
Indices: 27744--27772 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27734 AAGAGTTTGT
27744 TGTTGGATTCGC
1 TGTTGGATTCGC
27756 TGTTGGATTCGC
1 TGTTGGATTCGC
27768 TGTTG
1 TGTTG
27773 AAAATTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.14, G:0.34, T:0.45
Consensus pattern (12 bp):
TGTTGGATTCGC
Found at i:30152 original size:10 final size:10
Alignment explanation
Indices: 30103--30150 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
30093 TAAACTTCCA
30103 AAAGATAAAT
1 AAAGATAAAT
** *
30113 AAATTTAATT
1 AAAGATAAAT
*
30123 CAAGATAAAT
1 AAAGATAAAT
30133 AAAGATAAAT
1 AAAGATAAAT
30143 AAA-ATAAA
1 AAAGATAAA
30151 ATCCTAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:30194 original size:15 final size:14
Alignment explanation
Indices: 30173--30208 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
30163 ATAATCCTTA
*
30173 ATAATTATCTTAAT
1 ATAATTATCCTAAT
30187 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
30202 ATAATTA
1 ATAATTA
30209 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:34437 original size:17 final size:17
Alignment explanation
Indices: 34402--34438 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
34392 TTATTGGAAA
**
34402 CTCGTTTTGGTTAGCAG
1 CTCGTTTTGGTTAAAAG
34419 CTCGTTTTGGTTAAAAG
1 CTCGTTTTGGTTAAAAG
34436 CTC
1 CTC
34439 ATTGAAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (17 bp):
CTCGTTTTGGTTAAAAG
Found at i:47990 original size:50 final size:51
Alignment explanation
Indices: 47921--48055 Score: 191
Period size: 50 Copynumber: 2.7 Consensus size: 51
47911 NNNNAGGTCT
* * **
47921 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGA-GAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGATAACATCC
* * *
47971 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGATAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGATAACATCC
*
48022 CATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
48056 TGTTATGATC
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 39 0.53
51 35 0.47
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (51 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGATAACATCC
Found at i:49736 original size:43 final size:42
Alignment explanation
Indices: 49689--49801 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 42
49679 TTTCTCACAA
* *
49689 AAACGTCATTATAGAACATGACCTTTAACGGCACTTTTCCCAC
1 AAACGTCA-TAAAGAACATGACCTTTAACGGCACTTTCCCCAC
* * * *
49732 AAACGTCGCTAAAGAACATGATCTTTAGCGGCGCTTTCCCCAC
1 AAACGTC-ATAAAGAACATGACCTTTAACGGCACTTTCCCCAC
* *
49775 AAACGGCGATAAAGAACATGACTTTTA
1 AAACGTC-ATAAAGAACATGACCTTTA
49802 GCTTCATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (42 bp):
AAACGTCATAAAGAACATGACCTTTAACGGCACTTTCCCCAC
Found at i:49802 original size:43 final size:43
Alignment explanation
Indices: 49701--49803 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
49691 ACGTCATTAT
* * * * *
49701 AGAACATGACCTTTAACGGCACTTTTCCCACAAACGTCGCTAA
1 AGAACATGACTTTTAGCGGCACTTTCCCCACAAACGGCGATAA
*
49744 AGAACATGA-TCTTTAGCGGCGCTTTCCCCACAAACGGCGATAA
1 AGAACATGACT-TTTAGCGGCACTTTCCCCACAAACGGCGATAA
49787 AGAACATGACTTTTAGC
1 AGAACATGACTTTTAGC
49804 TTCATTTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 51 0.98
44 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
AGAACATGACTTTTAGCGGCACTTTCCCCACAAACGGCGATAA
Found at i:51847 original size:24 final size:24
Alignment explanation
Indices: 51815--51890 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 24
51805 TACTTGGGTA
* * *
51815 ATTTACCGTCAATTCATCTTTTAT
1 ATTTTCCGTCAATTCATCCTTTAC
51839 ATTTTCCGTCAATTCATCCTTTAC
1 ATTTTCCGTCAATTCATCCTTTAC
51863 A-TTTCCTGTCAATTCATCCTTTAC
1 ATTTTCC-GTCAATTCATCCTTTAC
51887 ATTT
1 ATTT
51891 GTAGTGCCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
23 5 0.11
24 40 0.85
25 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTTTCCGTCAATTCATCCTTTAC
Found at i:51940 original size:33 final size:32
Alignment explanation
Indices: 51895--52189 Score: 158
Period size: 33 Copynumber: 8.8 Consensus size: 32
51885 ACATTTGTAG
* *
51895 TGCCATAACCCAGTTATGGTCTTATCATTAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATTAGAA
*
51928 TGCCATAGCCCAGCTATGGTCTTACATATAAACA
1 TGCCATAGCCCAGCTATGGTCTTACAT-TAGA-A
* * * * * * * * *
51962 CTGTCATGGTCCAACCATAGTCTTACGTTCATAG
1 -TGCCATAGCCCAGCTATGGTCTTACATT-AGAA
* * * * *
51996 TGCCATAACCCAGTTATGGTCTTACGTTCATAG
1 TGCCATAGCCCAGCTATGGTCTTACATT-AGAA
* *
52029 TGCCATAACCCAGCTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATTAGAA
* * *
52062 TGCCATAGCCCAACTATGGTCTTCCATATAAACA
1 TGCCATAGCCCAGCTATGGTCTTACAT-TAGA-A
* * * * * * * *
52096 CTGCCATGGTCCAACCATGGTTTTACGTTCATAG
1 -TGCCATAGCCCAGCTATGGTCTTACATT-AGAA
* * * *
52130 TGTCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATTAGAA
* *
52163 TGCCATAGCTCAGCCATGGTCTTACAT
1 TGCCATAGCCCAGCTATGGTCTTACAT
52190 ATAAGCACTG
Statistics
Matches: 197, Mismatches: 55, Indels: 21
0.72 0.20 0.08
Matches are distributed among these distances:
32 9 0.05
33 135 0.69
34 8 0.04
35 45 0.23
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (32 bp):
TGCCATAGCCCAGCTATGGTCTTACATTAGAA
Found at i:52101 original size:101 final size:101
Alignment explanation
Indices: 52011--52255 Score: 409
Period size: 101 Copynumber: 2.4 Consensus size: 101
52001 TAACCCAGTT
* *
52011 ATGGTCTTACGTTCATAGTGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAAC
1 ATGGTCTTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAAC
* *
52076 TATGGTCTTCCATATAAACACTGCCATGGTCCAACC
66 CATGGTCTTACATATAAACACTGCCATGGTCCAACC
* * *
52112 ATGGTTTTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCTCAGC
1 ATGGTCTTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAAC
*
52177 CATGGTCTTACATATAAGCACTGCCATGGTCCAACC
66 CATGGTCTTACATATAAACACTGCCATGGTCCAACC
*
52213 ATGGTCTTACGTTCATAGTGTCATAACCTAGTTATGGTCTTAT
1 ATGGTCTTACGTTCATAGTGTCATAACCCAGTTATGGTCTTAT
52256 TCGTCAATTC
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 134 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (101 bp):
ATGGTCTTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAAC
CATGGTCTTACATATAAACACTGCCATGGTCCAACC
Found at i:52137 original size:134 final size:134
Alignment explanation
Indices: 51892--52153 Score: 452
Period size: 134 Copynumber: 2.0 Consensus size: 134
51882 TTTACATTTG
* * *
51892 TAGTGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGCTATGGTCTTACATAT
1 TAGTGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATAT
*
51957 AAACACTGTCATGGTCCAACCATAGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTACG
66 AAACACTGCCATGGTCCAACCATAGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTACG
52022 TTCA
131 TTCA
*
52026 TAGTGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTCCATAT
1 TAGTGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATAT
* * *
52091 AAACACTGCCATGGTCCAACCATGGTTTTACGTTCATAGTGTCATAACCCAGTTATGGTCTTA
66 AAACACTGCCATGGTCCAACCATAGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTA
52154 TCATCAGAAT
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 120 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (134 bp):
TAGTGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATAT
AAACACTGCCATGGTCCAACCATAGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTACG
TTCA
Found at i:52167 original size:134 final size:134
Alignment explanation
Indices: 51895--52186 Score: 442
Period size: 134 Copynumber: 2.2 Consensus size: 134
51885 ACATTTGTAG
* * *
51895 TGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGCTATGGTCTTACATATAAA
1 TGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAAA
* *
51960 CACTGTCATGGTCCAACCATAGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTACGTTC
66 CACTGCCATGGTCCAACCATAGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTACGATC
* *
52025 ATAG
131 AGAA
*
52029 TGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTCCATATAAA
1 TGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAAA
* * *
52094 CACTGCCATGGTCCAACCATGGTTTTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATC-AT
66 CACTGCCATGGTCCAACCATAGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTA-CGAT
52158 CAGAA
130 CAGAA
* * *
52163 TGCCATAGCTCAGCCATGGTCTTA
1 TGCCATAACCCAGCTATGGTCTTA
52187 CATATAAGCA
Statistics
Matches: 143, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
134 142 0.99
135 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (134 bp):
TGCCATAACCCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAAA
CACTGCCATGGTCCAACCATAGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTACGATC
AGAA
Found at i:58681 original size:11 final size:12
Alignment explanation
Indices: 58653--58686 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
58643 GCCCAAACGT
58653 CGAAATTTTTGAA
1 CGAAATTTTT-AA
58666 CGAAATTTTT-A
1 CGAAATTTTTAA
58677 CGAAATTTTT
1 CGAAATTTTT
58687 TCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:61707 original size:25 final size:25
Alignment explanation
Indices: 61673--61726 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
61663 ACAACACGAA
61673 GCAGCAGAGGGCTGCCGACGGAGAT
1 GCAGCAGAGGGCTGCCGACGGAGAT
* ** *
61698 GCAGTAGAGGGCTGTTGACGGCGAT
1 GCAGCAGAGGGCTGCCGACGGAGAT
61723 GCAG
1 GCAG
61727 AGGGTTGTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.44, T:0.13
Consensus pattern (25 bp):
GCAGCAGAGGGCTGCCGACGGAGAT
Found at i:62091 original size:41 final size:41
Alignment explanation
Indices: 62034--62146 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 41
62024 TACATATTCA
* * * *
62034 CGGCGTTTGGACCAAAATCGCCACTATTTCTCAACTTTTTG
1 CGGCGTTTGAACCAAAAACACCACTATTGCTCAACTTTTTG
62075 CGGCGTTTGAACCAAAAACACCACTATTGCTCAACTTTTTG
1 CGGCGTTTGAACCAAAAACACCACTATTGCTCAACTTTTTG
* *
62116 CGGCATTTGGAA-CAAAAACACCGCTATTGCT
1 CGGCGTTT-GAACCAAAAACACCACTATTGCT
62147 TACCTTTTGC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 62 0.95
42 3 0.05
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (41 bp):
CGGCGTTTGAACCAAAAACACCACTATTGCTCAACTTTTTG
Found at i:62266 original size:19 final size:18
Alignment explanation
Indices: 62242--62277 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
62232 CAATTTTAAA
*
62242 TAAATAATTTTTTAAAATT
1 TAAATAA-TATTTAAAATT
62261 TAAATAATATTTAAAAT
1 TAAATAATATTTAAAAT
62278 AATTAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATAATATTTAAAATT
Found at i:63958 original size:13 final size:12
Alignment explanation
Indices: 63931--63981 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
63921 GCTTGACCTG
*
63931 AAGAAAAAAATA
1 AAGAAAAAAAGA
63943 AAGAAAGAAAAGA
1 AAGAAA-AAAAGA
*
63956 AAGTGAAAAAAGA
1 AAG-AAAAAAAGA
63969 AAGAAAGAAAAGA
1 AAGAAA-AAAAGA
63982 GAATTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 8 0.24
13 23 0.70
14 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:64348 original size:19 final size:19
Alignment explanation
Indices: 64326--64379 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
64316 TACAAGTAAG
64326 TATGATAATTGAATAT-ATT
1 TATGATAATTGAATATGA-T
**
64345 TATGA-AATAAAATATGAT
1 TATGATAATTGAATATGAT
*
64363 TATGATTATTGAATATG
1 TATGATAATTGAATATG
64380 TATAATGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (19 bp):
TATGATAATTGAATATGAT
Found at i:67733 original size:13 final size:13
Alignment explanation
Indices: 67715--67745 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
67705 GTCGACAATG
67715 GTGGCTAGTGGCA
1 GTGGCTAGTGGCA
67728 GTGGCTAGTGGCA
1 GTGGCTAGTGGCA
67741 GTGGC
1 GTGGC
67746 CAGTAGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.48, T:0.23
Consensus pattern (13 bp):
GTGGCTAGTGGCA
Found at i:69655 original size:13 final size:14
Alignment explanation
Indices: 69632--69661 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
69622 AGCCCGCCCA
69632 TATTAATTTTTTTG
1 TATTAATTTTTTTG
69646 TATT-ATTTTTTTG
1 TATTAATTTTTTTG
69659 TAT
1 TAT
69662 ATATATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TATTAATTTTTTTG
Found at i:70707 original size:19 final size:21
Alignment explanation
Indices: 70666--70731 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
70656 AGCTCATATT
70666 AAATATATATTTAATATATAA
1 AAATATATATTTAATATATAA
* *
70687 AAATATATATTTGATTAAAAATAA
1 AAATATATATTT-A--ATATATAA
*
70711 AAATATATATATAATATATAA
1 AAATATATATTTAATATATAA
70732 TTCAGGTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 18 0.49
22 1 0.03
23 1 0.03
24 17 0.46
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATATATATTTAATATATAA
Found at i:71298 original size:27 final size:28
Alignment explanation
Indices: 71254--71308 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
71244 TTAGCATTTG
* * *
71254 TTAATTTTATTGACATTTCAATATTTAA
1 TTAATTTTATTAAAATTTCAAAATTTAA
*
71282 TTAATTTT-TTAAAATTTTAAAATTTAA
1 TTAATTTTATTAAAATTTCAAAATTTAA
71309 ACAAAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (28 bp):
TTAATTTTATTAAAATTTCAAAATTTAA
Found at i:76326 original size:11 final size:11
Alignment explanation
Indices: 76312--76351 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
76302 ATATTTTTAG
76312 TTCTCTCTCAA
1 TTCTCTCTCAA
*
76323 TTCTCTCTTAA
1 TTCTCTCTCAA
76334 TTCTCTCTCAA
1 TTCTCTCTCAA
76345 TTCTCTC
1 TTCTCTC
76352 AACTTCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (11 bp):
TTCTCTCTCAA
Found at i:79101 original size:42 final size:42
Alignment explanation
Indices: 79041--79195 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 42
79031 CCGAAGGCTG
* * *
79041 AACAGAAGCTCATGAGAGCTAAAC-AGAAACCCATAAAGGTTG
1 AACAAAAGCTCATAAGAGCTAAACGA-AAACCCATAAAGGTTA
* * *
79083 AACGAAAGCTCGTAAGAGCTAAACGAAAACCCATAAGGGTTA
1 AACAAAAGCTCATAAGAGCTAAACGAAAACCCATAAAGGTTA
* * *
79125 AACAAAAGCTCA-ATAGAGCTGAACGGAAACTCC-T-ATGAGTTA
1 AACAAAAGCTCATA-AGAGCTAAACGAAAAC-CCATAAAG-GTTA
* * *
79167 AGCAGAAGCTCATAAGAGCTAAATGAAAA
1 AACAAAAGCTCATAAGAGCTAAACGAAAA
79196 GTAAACACGA
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.03
42 85 0.92
43 4 0.04
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (42 bp):
AACAAAAGCTCATAAGAGCTAAACGAAAACCCATAAAGGTTA
Found at i:79119 original size:21 final size:21
Alignment explanation
Indices: 79055--79119 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
79045 GAAGCTCATG
79055 AGAGCTAAAC-AGAAACCCATA
1 AGAGCTAAACGA-AAACCCATA
* * * * *
79076 A-AGGTTGAACGAAAGCTCGTA
1 AGA-GCTAAACGAAAACCCATA
79097 AGAGCTAAACGAAAACCCATA
1 AGAGCTAAACGAAAACCCATA
79118 AG
1 AG
79120 GGTTAAACAA
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
20 1 0.03
21 28 0.90
22 2 0.06
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (21 bp):
AGAGCTAAACGAAAACCCATA
Found at i:79126 original size:21 final size:21
Alignment explanation
Indices: 79067--79131 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
79057 AGCTAAACAG
* *
79067 AAACCCATAAAGGTTGAACGA
1 AAACCCATAAGGGTTAAACGA
* * * * *
79088 AAGCTCGTAAGAGCTAAACGA
1 AAACCCATAAGGGTTAAACGA
79109 AAACCCATAAGGGTTAAAC-A
1 AAACCCATAAGGGTTAAACGA
79129 AAA
1 AAA
79132 GCTCAATAGA
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.14
Consensus pattern (21 bp):
AAACCCATAAGGGTTAAACGA
Found at i:82681 original size:28 final size:29
Alignment explanation
Indices: 82624--82681 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
82614 TGGATTGTAA
**
82624 AAGATTTCTAGTTGAGCCACAAAAGTTAG
1 AAGATTTCTAGTTGAGCCACAAAAACTAG
82653 AAGATTT-TAGTTTGA-CCACAAAAACTAG
1 AAGATTTCTAG-TTGAGCCACAAAAACTAG
82681 A
1 A
82682 GGGGGAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (29 bp):
AAGATTTCTAGTTGAGCCACAAAAACTAG
Found at i:88104 original size:34 final size:34
Alignment explanation
Indices: 88021--88104 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 34
88011 TAAATTATTT
* *
88021 TTGTATTGGTTATTGTCTGTC-ATGTTGTATTAAA
1 TTGT-TTGGTTGTTGTCTGCCTATGTTGTATTAAA
*
88055 TTGTTT-G--G-TAT-TGCCTATGTTGTATTAAA
1 TTGTTTGGTTGTTGTCTGCCTATGTTGTATTAAA
88084 TTGTTTGGTTGTTGTCTGCCT
1 TTGTTTGGTTGTTGTCTGCCT
88105 TTATTGACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
28 3 0.08
29 21 0.52
30 1 0.03
32 2 0.05
33 4 0.10
34 9 0.22
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (34 bp):
TTGTTTGGTTGTTGTCTGCCTATGTTGTATTAAA
Found at i:92271 original size:16 final size:17
Alignment explanation
Indices: 92212--92270 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
92202 TAAAAGAAAT
92212 AAAGAAAGACAAAAGCA-
1 AAAGAAAGACAAAAG-AG
*
92229 AAACAAA-ACAAAA-AG
1 AAAGAAAGACAAAAGAG
92244 AAAGAAAAAGA-AAAAGAG
1 AAAG--AAAGACAAAAGAG
92262 AAAGAAAGA
1 AAAGAAAGA
92271 AGAACCTACG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 11 0.31
17 13 0.37
18 7 0.20
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAGACAAAAGAG
Found at i:96064 original size:3 final size:3
Alignment explanation
Indices: 96044--96103 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
96034 CTATTTTTTC
* * * * * *
96044 TCT TCT CCT TCG TCT TCT TCT TC- TCC TCC TCT TCT TTT TAT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
96091 TCT TCT TCT TCT T
1 TCT TCT TCT TCT T
96104 TTACTGCCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.02, C:0.35, G:0.02, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:96476 original size:12 final size:12
Alignment explanation
Indices: 96459--96484 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
96449 TGTAATTTTA
96459 TTTTTTATAATT
1 TTTTTTATAATT
96471 TTTTTTATAATT
1 TTTTTTATAATT
96483 TT
1 TT
96485 GCATATGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTATAATT
Found at i:96527 original size:10 final size:9
Alignment explanation
Indices: 96512--96578 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
96502 TGGATGTGCG
96512 TTTTTACTAA
1 TTTTTA-TAA
96522 TTTTTAAATAA
1 TTTTT--ATAA
*
96533 TATTTTAGAA
1 T-TTTTATAA
96543 TTTTTATTAA
1 TTTTTA-TAA
96553 -TTTT-TAA
1 TTTTTATAA
*
96560 TTTTTAAAA
1 TTTTTATAA
96569 TTTTT-TAA
1 TTTTTATAA
96577 TT
1 TT
96579 ATGTGACATG
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
7 3 0.06
8 8 0.17
9 16 0.34
10 11 0.23
11 4 0.09
12 5 0.11
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:97141 original size:14 final size:16
Alignment explanation
Indices: 97119--97150 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
97109 AATGGTTATA
97119 TTAATATTAT-TATTT
1 TTAATATTATCTATTT
97134 TTAA-ATTATCTATTT
1 TTAATATTATCTATTT
97149 TT
1 TT
97151 TATAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTAATATTATCTATTT
Found at i:101027 original size:140 final size:140
Alignment explanation
Indices: 100766--101046 Score: 463
Period size: 140 Copynumber: 2.0 Consensus size: 140
100756 AGGTTATGGT
*
100766 TTAGATTTGATCCTAGGTTGACTCCTTTCATCTAAACTTTTGGACTAGTAGAGAAGGCTATGAAA
1 TTAGATTTGATCCAAGGTTGACTCCTTTCATCTAAACTTTTGGACTAGTAGAGAAGGCTATGAAA
* *
100831 AGTCTGAGAGCTGAATAAGGATACATGGATACCATAATATGATAGGACTATACAAAATTGAAATT
66 AGTCTGAGAGCTGAATAAGGATACATAGATACCATAATATGATAGGACTACACAAAATTGAAATT
100896 TCAGAACTAA
131 TCAGAACTAA
* *
100906 TTAGATTTGATCCAAGGTTGACTCCTTTCATCTAAACTTTTGGACTAGTAGAGTAGGCTATGAAG
1 TTAGATTTGATCCAAGGTTGACTCCTTTCATCTAAACTTTTGGACTAGTAGAGAAGGCTATGAAA
* * * * * *
100971 AGTGTGAGAGCTGGATATGGATACATAGATACCATAATATTATAGGGCTACGCAAAATTGAAATT
66 AGTCTGAGAGCTGAATAAGGATACATAGATACCATAATATGATAGGACTACACAAAATTGAAATT
101036 TCAGAACTAA
131 TCAGAACTAA
101046 T
1 T
101047 GAAAATTCCA
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
140 130 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (140 bp):
TTAGATTTGATCCAAGGTTGACTCCTTTCATCTAAACTTTTGGACTAGTAGAGAAGGCTATGAAA
AGTCTGAGAGCTGAATAAGGATACATAGATACCATAATATGATAGGACTACACAAAATTGAAATT
TCAGAACTAA
Found at i:103364 original size:2 final size:2
Alignment explanation
Indices: 103357--103389 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
103347 GTGGCACCTG
103357 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
103390 TCCTTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:104134 original size:30 final size:30
Alignment explanation
Indices: 104098--104188 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
104088 GATAAACTAG
104098 ACAGCACTACAGAATTTATCATATGACTTA
1 ACAGCACTACAGAATTTATCATATGACTTA
104128 ACAGCACTACAGAATTTATCATATGACTTA
1 ACAGCACTACAGAATTTATCATATGACTTA
*
104158 ACAGCACTACAGAATTTATCATATCACTTA
1 ACAGCACTACAGAATTTATCATATGACTTA
104188 A
1 A
104189 GCTTTATATA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (30 bp):
ACAGCACTACAGAATTTATCATATGACTTA
Found at i:106748 original size:17 final size:17
Alignment explanation
Indices: 106722--106755 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
106712 AGCATATTTC
106722 TATTTCCTTAGTTTCTT
1 TATTTCCTTAGTTTCTT
* *
106739 TATTTGCTTATTTTCTT
1 TATTTCCTTAGTTTCTT
106756 ATACAAGGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.15, G:0.06, T:0.68
Consensus pattern (17 bp):
TATTTCCTTAGTTTCTT
Found at i:107725 original size:3 final size:3
Alignment explanation
Indices: 107717--107744 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
107707 ACCAATGTGA
107717 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
107745 CAGGCCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:109705 original size:2 final size:2
Alignment explanation
Indices: 109698--109734 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
109688 TCCTATCCAA
*
109698 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
109735 GAACTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:110222 original size:2 final size:2
Alignment explanation
Indices: 110215--110239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
110205 CAATGAACAA
110215 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
110240 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:112415 original size:31 final size:31
Alignment explanation
Indices: 112353--112415 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
112343 CAACCCAGTA
* ** *
112353 ACTTAAATAAAAACTTTTGAATTGTTCAGTG
1 ACTTAAATAAAAACTTTCGAATAATTAAGTG
112384 ACTTAAATAAAAACTTTCGAATAATTAAGTG
1 ACTTAAATAAAAACTTTCGAATAATTAAGTG
112415 A
1 A
112416 TCAAATTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCGAATAATTAAGTG
Found at i:114827 original size:18 final size:19
Alignment explanation
Indices: 114804--114876 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
114794 TTAGATATGA
*
114804 TTTTTAAT-ATTTTTATAC
1 TTTTTAATAAATTTTATAC
*
114822 TTTTTAATAAATTTTATGC
1 TTTTTAATAAATTTTATAC
** *
114841 TTTTTTTTTACATTTTAATA-
1 -TTTTTAATAAATTTT-ATAC
*
114861 TTTTTAATAATTTTTA
1 TTTTTAATAAATTTTA
114877 AACTGGTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
18 9 0.21
19 19 0.45
20 12 0.29
21 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTTTAATAAATTTTATAC
Found at i:120275 original size:22 final size:22
Alignment explanation
Indices: 120234--120275 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
120224 ACTGTTTTTC
*
120234 TCCTTCTCCTTCTCCTTCTTCT
1 TCCTTCTCCTTCTCCCTCTTCT
* *
120256 TCCTTCTCTTTTTCCCTCTT
1 TCCTTCTCCTTCTCCCTCTT
120276 TATAGCGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (22 bp):
TCCTTCTCCTTCTCCCTCTTCT
Found at i:130062 original size:23 final size:24
Alignment explanation
Indices: 130035--130079 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
130025 GAAAAATATT
*
130035 AAATAT-ATATTTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
130058 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
130080 AAGTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:130190 original size:9 final size:9
Alignment explanation
Indices: 130176--130203 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
130166 TTTTGTTACA
130176 ACAATTAAT
1 ACAATTAAT
130185 ACAATTAAT
1 ACAATTAAT
130194 ACAATTAAT
1 ACAATTAAT
130203 A
1 A
130204 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:130225 original size:68 final size:66
Alignment explanation
Indices: 130146--130287 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
130136 TCAAGTTTGT
*
130146 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
130211 AAA
64 AAA
130214 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
130279 T
66 A
130280 TTTACTAA
1 TTTACTAA
130288 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:130297 original size:16 final size:16
Alignment explanation
Indices: 130276--130317 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
130266 AATAATTTGA
*
130276 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
130292 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
130308 TAGTTTTAAT
1 TAATTTTAAT
130318 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:130306 original size:59 final size:66
Alignment explanation
Indices: 130146--130309 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
130136 TCAAGTTTGT
*
130146 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
130211 AAA
64 AAA
130214 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
130277 AAT
64 AAA
*
130280 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
130310 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:132975 original size:20 final size:21
Alignment explanation
Indices: 132938--132976 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
132928 ATAAATATAT
**
132938 ATAAAACTATATTTTAAAAAA
1 ATAAAACTATATCCTAAAAAA
132959 ATAAAA-TATATCCTAAAA
1 ATAAAACTATATCCTAAAA
132977 CTAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAACTATATCCTAAAAAA
Found at i:134194 original size:16 final size:16
Alignment explanation
Indices: 134173--134205 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
134163 TTCGCTGTAT
*
134173 TGGAATAGAGGCGTAA
1 TGGAATAGAAGCGTAA
134189 TGGAATAGAAGCGTAA
1 TGGAATAGAAGCGTAA
134205 T
1 T
134206 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.21
Consensus pattern (16 bp):
TGGAATAGAAGCGTAA
Found at i:134456 original size:16 final size:16
Alignment explanation
Indices: 134419--134460 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
134409 TTAATCATAT
*
134419 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
134435 TT-AAATATATTATAA
1 TTAAAATATATTATAA
134450 TTAAAATATAT
1 TTAAAATATAT
134461 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:134467 original size:14 final size:15
Alignment explanation
Indices: 134428--134469 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
134418 TTTAAACATA
*
134428 ATTATTATTAAATAT
1 ATTATAATTAAATAT
134443 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
134457 A-TATAATTTAATA
1 ATTATAATTAAATA
134470 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:134681 original size:24 final size:25
Alignment explanation
Indices: 134635--134682 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
134625 TATGAATTTG
134635 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
134661 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
134683 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:134686 original size:92 final size:92
Alignment explanation
Indices: 134590--134818 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
134580 TGATTTAATA
* * *
134590 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
134652 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
134682 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
134747 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
134772 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
134819 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:149903 original size:22 final size:22
Alignment explanation
Indices: 149856--149900 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
149846 ATGCAATCTT
*
149856 AGATATGATATGCAATTTTAGA
1 AGATATGATATGCAATATTAGA
* *
149878 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
149901 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Done.