Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold615
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: 56758
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Found at i:5604 original size:13 final size:13
Alignment explanation
Indices: 5586--5616 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
5576 TCAATTCATC
5586 ATGTATCGATATA
1 ATGTATCGATATA
5599 ATGTATCGATATA
1 ATGTATCGATATA
5612 ATGTA
1 ATGTA
5617 CCATGTATCG
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:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:15837 original size:52 final size:52
Alignment explanation
Indices: 15776--16428 Score: 374
Period size: 52 Copynumber: 12.4 Consensus size: 52
15766 TCTCAGTTGT
*
15776 TCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTC
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTC
** *
15828 TTTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTT-
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTC
* * * * ** ** **
15880 TCACAATCGAGGATACTCCAACCTCGTTATTTTATCGGGGATACTCCAAC-CCCGTTACC
1 TCATAATCGGGGATACTCCAACCCCG--ATTTTAT------TTCTAAAACACCAATTTTC
** ** * * ***
15939 TC-CGA--GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTC
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTC
* * * *
15987 TCACAATCGGGAATACTCCAACCCCGTTTTTTATTTCTAAAACACTAAATTTTC
1 TCATAATCGGGGATACTCCAACCCCG-ATTTTATTTCTAAAACAC-CAATTTTC
* *
16041 -CACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTT-
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTC
* * *
16091 TCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTT-
1 TC-ATAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTC
* * * * ** * **
16144 TCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGTGATACTCCAAC-CCCATTACC
1 TCATAATCGGGGATACTCCAACCCCG--ATTTTAT---T--T-CTAAAACACCAATTTTC
** ** * * ***
16203 TC-CGA--GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTC
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTC
* * *
16251 TCATAATCGGGGATACTCTAACCCCGTTTTTATTTCTAAAACACTAAATTTT-
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC-CAATTTTC
* * *
16303 TCATAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACATCAAATTTC
1 TCATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTC
* * * *
16355 -CTTTAATTGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA-TTT-
1 TC-ATAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTC
* *
16406 TCACAATCGAGGATACTCCAACC
1 TCATAATCGGGGATACTCCAACC
16429 TCGTTATTTC
Statistics
Matches: 455, Mismatches: 104, Indels: 85
0.71 0.16 0.13
Matches are distributed among these distances:
48 15 0.03
49 5 0.01
51 79 0.17
52 203 0.45
53 66 0.15
54 26 0.06
56 32 0.07
57 1 0.00
58 13 0.03
59 12 0.03
60 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (52 bp):
TCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTC
Found at i:16250 original size:264 final size:262
Alignment explanation
Indices: 15780--16545 Score: 1295
Period size: 264 Copynumber: 2.9 Consensus size: 262
15770 AGTTGTTCAT
* *
15780 AATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAATACCAATTTTCTTTTAATCGGGGATAC
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTC-TTTAATCGGGGATAC
*
15844 TCCAACTCCGATTTTATTTCTAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTA
64 TCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTA
*
15909 TTTTATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCA
129 TTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCA
*
15974 AAATATTGATTTCTCACAATCGGGAATACTCCAACCCCGTTTTTTATTTCTAAAACACTAAATTT
194 AAATATTGATTTCTCATAATCGGG-ATACTCCAACCCCGTTTTTTATTTCTAAAACACTAAATTT
16039 TCCAC
258 TCCAC
16044 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAA-TTTTCTTTAATCGGGGATACT
16109 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
65 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
* *
16174 TTCATCGGTGATACTCCAACCCCATTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAA
130 TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAA
*
16239 AATATTGATTTCTCATAATCGGGGATACTCTAACCCCG-TTTTTATTTCTAAAACACTAAATTTT
195 AATATTGATTTCTCATAATC-GGGATACTCCAACCCCGTTTTTTATTTCTAAAACACTAAATTTT
* *
16303 TCAT
259 CCAC
* * *
16307 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAAATTTCCTTTAATTGGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACA-CCAATTTTCTTTAATCGGGGATACT
16372 CCAACTCCGATTTTATTTCCAAAAACACCAA-TTTTCACAATCGAGGATACTCCAACCTCGTTAT
65 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
*
16436 TTCGTCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAA
130 TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAA
* *
16501 AATATTGATTTCTCGTAATTTGGGATACTCCAACCCCGTTATTTT
195 AATATTGATTTCTCATAA-TCGGGATACTCCAACCCCGTT-TTTT
16546 CGAGGGGATA
Statistics
Matches: 476, Mismatches: 19, Indels: 14
0.94 0.04 0.03
Matches are distributed among these distances:
262 128 0.27
263 119 0.25
264 217 0.46
265 12 0.03
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (262 bp):
AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCTTTAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATT
TCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAA
ATATTGATTTCTCATAATCGGGATACTCCAACCCCGTTTTTTATTTCTAAAACACTAAATTTTCC
AC
Found at i:16456 original size:28 final size:28
Alignment explanation
Indices: 16416--16487 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
16406 TCACAATCGA
* * * *
16416 GGATACTCCAACCTCGTTA-TTTCGTCGG
1 GGATACTCCAACCCCGTTACCTCCG-AGG
16444 GGATACTCCAACCCCGTTACCTCCGAGG
1 GGATACTCCAACCCCGTTACCTCCGAGG
16472 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
16488 GCTTTATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 36 0.92
29 3 0.08
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.22
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACCTCCGAGG
Found at i:16526 original size:79 final size:79
Alignment explanation
Indices: 16440--16674 Score: 267
Period size: 79 Copynumber: 3.0 Consensus size: 79
16430 CGTTATTTCG
** * *
16440 TCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATA
1 TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATA
**
16505 TTGATTTCTCGTAA
66 TTGATTTCTCACAA
** * * * *
16519 TTTGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAATCCCGATTTTATTTCC-TAATC
1 TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAAT-
* *
16583 ATCGATTTTTCACAA
65 ATTGATTTCTCACAA
* * *
16598 TCGGGGATACTCCAACCCCATTATTTTCAAGGGGATACTCCAACCCC-GTTATTATCTCCAAAAT
1 TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT-TTATTTCCAAAAT
*
16662 ATTAAATTTCTCA
65 ATT-GATTTCTCA
16675 TCGGGACATA
Statistics
Matches: 126, Mismatches: 26, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
78 5 0.04
79 111 0.88
80 10 0.08
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATA
TTGATTTCTCACAA
Found at i:29076 original size:14 final size:14
Alignment explanation
Indices: 29054--29127 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 14
29044 TTCTTTTCTA
29054 AAAAAAAAAACAAAAGC
1 AAAAAAAAAAC--AA-C
29071 AAAAAAAAAACAAC
1 AAAAAAAAAACAAC
*
29085 AAAAAAAACGAACAAA
1 AAAAAAAA--AACAAC
*
29101 AAAAACAGAAAAAAAC
1 AAAAA-A-AAAACAAC
29117 AAAGAAAAAAA
1 AAA-AAAAAAA
29128 AAGAAAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
14 9 0.18
15 6 0.12
16 18 0.37
17 14 0.29
18 2 0.04
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAC
Found at i:29080 original size:12 final size:12
Alignment explanation
Indices: 29058--29129 Score: 60
Period size: 12 Copynumber: 5.8 Consensus size: 12
29048 TTTCTAAAAA
29058 AAAAAACAAAAGC
1 AAAAAA-AAAAGC
29071 AAAAAAAAAA-C
1 AAAAAAAAAAGC
29082 AACAAAAAAAACGAAC
1 AA-AAAAAAAA-G--C
*
29098 AAAAAAAACAG-
1 AAAAAAAAAAGC
29109 AAAAAAACAAAG-
1 AAAAAAA-AAAGC
29121 AAAAAAAAA
1 AAAAAAAAA
29130 GAAAAATCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
11 12 0.24
12 22 0.43
13 6 0.12
14 1 0.02
15 7 0.14
16 3 0.06
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:29090 original size:22 final size:20
Alignment explanation
Indices: 29053--29135 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 20
29043 CTTCTTTTCT
*
29053 AAAAAAAAAAAC-AAAAGCA
1 AAAAAAAAAAACAAAAAACA
29072 AAAAAAAAACAACAAAAAA-A
1 AAAAAAAAA-AACAAAAAACA
29092 ACGAACAAAAAAAACAGAAAAAAACA
1 A--AA-AAAAAAAAC---AAAAAACA
*
29118 AAGAAAAAAAAAGAAAAA
1 AA-AAAAAAAAACAAAAA
29136 TCTACTTAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
19 9 0.17
20 5 0.10
21 9 0.17
22 5 0.10
23 6 0.12
24 9 0.17
25 7 0.13
26 2 0.04
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAACAAAAAACA
Found at i:29098 original size:16 final size:15
Alignment explanation
Indices: 29056--29105 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
29046 CTTTTCTAAA
29056 AAAAAAAACAA-AAGC
1 AAAAAAAACAACAA-C
29071 AAAAAAAA-AACAAC
1 AAAAAAAACAACAAC
29085 AAAAAAAACGAACAA-
1 AAAAAAAAC-AACAAC
29100 AAAAAA
1 AAAAAA
29106 CAGAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.34
15 16 0.50
16 5 0.16
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (15 bp):
AAAAAAAACAACAAC
Found at i:29124 original size:10 final size:9
Alignment explanation
Indices: 29056--29134 Score: 58
Period size: 9 Copynumber: 8.9 Consensus size: 9
29046 CTTTTCTAAA
29056 AAAAAAAAC
1 AAAAAAAAC
**
29065 AAAAGCAA-
1 AAAAAAAAC
29073 AAAAAAAAC
1 AAAAAAAAC
*
29082 -AACAAAA-
1 AAAAAAAAC
**
29089 AAAACGAAC
1 AAAAAAAAC
29098 AAAAAAAAC
1 AAAAAAAAC
29107 AGAAAAAAAC
1 A-AAAAAAAC
29117 AAAGAAAAA-
1 AAA-AAAAAC
29126 AAAAGAAAA
1 AAAA-AAAA
29135 ATCTACTTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
8 17 0.31
9 23 0.43
10 14 0.26
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:30253 original size:55 final size:55
Alignment explanation
Indices: 30188--30552 Score: 448
Period size: 55 Copynumber: 6.4 Consensus size: 55
30178 CTCCTTTCGC
30188 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
30242 CCTTTCAGTCCTCAAAGAGCATGACACCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCA-G-GA----CGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
30303 TCTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAA-CCCTACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGC-----C-TTTCAAAGCCC-ACACAAGTTGGTGGCA
* *
30364 CCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
** *
30419 TTTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * *
30474 CCTTTTAGTCCTCAAAGAGCAGGACGTCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
30529 CTTTTTAGTCCTCAAAGAGCAGGA
1 CCTTTCAGTCCTCAAAGAGCAGGA
30553 TGCACCTTAT
Statistics
Matches: 272, Mismatches: 22, Indels: 33
0.83 0.07 0.10
Matches are distributed among these distances:
54 7 0.03
55 157 0.58
56 7 0.03
57 1 0.00
59 1 0.00
60 5 0.02
61 94 0.35
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:31420 original size:32 final size:32
Alignment explanation
Indices: 31375--31446 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
31365 ACAAACAGAA
* *
31375 AATGTATCGATACATAAGTGTTGTATTGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
* *
31407 ATTGTATCAATACATAAGTTTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
31439 AATGTATC
1 AATGTATC
31447 GCTACGAAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (32 bp):
AATGTATCAATACATAAGTGTTGTATCGATAC
Found at i:31476 original size:43 final size:43
Alignment explanation
Indices: 31428--31564 Score: 115
Period size: 43 Copynumber: 3.3 Consensus size: 43
31418 ACATAAGTTT
*
31428 TGTATCGATACAATGTATCGCTACGAAGCTACTGCCAAGGAAA
1 TGTATCGATACAATGTATCGCTACGAAGCTACTGCCAAAGAAA
** * * * * ***
31471 TGTATCGATAC-ATCG-AT--CTTTGTATCGA-T-ACATAAGTTT
1 TGTATCGATACAAT-GTATCGCTACGAAGCTACTGCCA-AAGAAA
*
31510 TGTATCGATACAATGTATCGCTACGAAGCTACTGCCAACGAAA
1 TGTATCGATACAATGTATCGCTACGAAGCTACTGCCAAAGAAA
31553 TGTATCGATACA
1 TGTATCGATACA
31565 TCGATCTTTG
Statistics
Matches: 66, Mismatches: 20, Indels: 16
0.65 0.20 0.16
Matches are distributed among these distances:
38 2 0.03
39 15 0.23
40 10 0.15
42 10 0.15
43 27 0.41
44 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (43 bp):
TGTATCGATACAATGTATCGCTACGAAGCTACTGCCAAAGAAA
Found at i:31508 original size:82 final size:82
Alignment explanation
Indices: 31408--31585 Score: 338
Period size: 82 Copynumber: 2.2 Consensus size: 82
31398 TATTGATACA
* *
31408 TTGTATCAATACATAAGTTTTGTATCGATACAATGTATCGCTACGAAGCTACTGCCAAGGAAATG
1 TTGTATCGATACATAAGTTTTGTATCGATACAATGTATCGCTACGAAGCTACTGCCAACGAAATG
31473 TATCGATACATCGATCT
66 TATCGATACATCGATCT
31490 TTGTATCGATACATAAGTTTTGTATCGATACAATGTATCGCTACGAAGCTACTGCCAACGAAATG
1 TTGTATCGATACATAAGTTTTGTATCGATACAATGTATCGCTACGAAGCTACTGCCAACGAAATG
31555 TATCGATACATCGATCT
66 TATCGATACATCGATCT
31572 TTGTATCGATACAT
1 TTGTATCGATACAT
31586 CTAGGAAGTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 94 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (82 bp):
TTGTATCGATACATAAGTTTTGTATCGATACAATGTATCGCTACGAAGCTACTGCCAACGAAATG
TATCGATACATCGATCT
Found at i:31513 original size:19 final size:20
Alignment explanation
Indices: 31471--31521 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
31461 GCCAAGGAAA
*
31471 TGTATCGATACATCGATCTT
1 TGTATCGATACATAGATCTT
31491 TGTATCGATACATA-AGT-TT
1 TGTATCGATACATAGA-TCTT
31510 TGTATCGATACA
1 TGTATCGATACA
31522 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATAGATCTT
Found at i:33974 original size:52 final size:51
Alignment explanation
Indices: 33915--34564 Score: 361
Period size: 52 Copynumber: 12.4 Consensus size: 51
33905 CTCAGTTGTT
* *
33915 CATAATCGGGGATACTCTAACCCCGGTTTTATTTCCAAAACACCAATTTTC
1 CATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTC
* * * * *
33966 CTTTAATC-GGGATACTCCAACTCTGATTTTATTTCTAAAAACACCAATTTTT
1 C-ATAATCGGGGATACTCCAACCCCGATTTTATTTC-CAAAACACCAATTTTC
* * * * * **
34018 CACAATCGAGGATACTCCAACCTC-A--TTATTTCATCAGGGATACTCCAA--CCC
1 CATAATCGGGGATACTCCAACCCCGATTTTATTTC--CA---AAACACCAATTTTC
* * ** * ***
34069 CGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTC
1 C-ATA-AT-CG-G-GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTC
* * * *
34124 TCACAATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAACACTAAATTTTC
1 -CATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC-CAATTTTC
* * *
34177 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAACAATTTTC
1 CATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTC
* * *
34228 CTTTAATC-GGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
1 C-ATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTC
* * * * ***** * * *
34280 CACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCTGTTAC
1 CATAATCGGGGATACTCCAACCCCG--ATTTTATTTCCAAAACACCAA---T-TTTC
* ** * ***
34337 C-T--CCGAGAGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTC
1 CATAATCG-G-GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTC
* * ** *
34386 TCATAATCGGGGATACTCCAACCCTGTTTTTATTTTTAAAACACTAAATTTTC
1 -CATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACAC-CAATTTTC
* * * *
34439 CACAATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTC
1 CATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTC
* * * * *
34490 CTCTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCATTTTTT
1 C-ATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTC
* *
34543 CACAATCGAGGATACTCCAACC
1 CATAATCGGGGATACTCCAACC
34565 TCGTTATTTC
Statistics
Matches: 444, Mismatches: 117, Indels: 75
0.70 0.18 0.12
Matches are distributed among these distances:
49 10 0.02
50 3 0.01
51 133 0.30
52 192 0.43
53 40 0.09
54 21 0.05
55 2 0.00
56 31 0.07
57 5 0.01
59 7 0.02
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
CATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTC
Found at i:34592 original size:28 final size:28
Alignment explanation
Indices: 34552--34623 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
34542 TCACAATCGA
* * * *
34552 GGATACTCCAACCTCGTTA-TTTCGTCGG
1 GGATACTCCAACCCCGTTACCTCCG-AGG
34580 GGATACTCCAACCCCGTTACCTCCGAGG
1 GGATACTCCAACCCCGTTACCTCCGAGG
34608 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
34624 ACTTTATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 36 0.92
29 3 0.08
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.22
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACCTCCGAGG
Found at i:34650 original size:263 final size:262
Alignment explanation
Indices: 33918--34676 Score: 1320
Period size: 262 Copynumber: 2.9 Consensus size: 262
33908 AGTTGTTCAT
* *
33918 AATCGGGGATACTCTAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTTTAATCGGGATACTC
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGATACTC
* * *
33983 CAACTCTGATTTTATTTCTAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCATTATT
66 CAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATT
*
34048 TCATCAGGGATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTTCCAAA
131 TCATCGGGGATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTTCCAAA
*
34113 ATATTGATTTCTCACAATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAACACTAAATTTTCC
196 ATATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAACACTAAATTTTCC
34178 AC
261 AC
* *
34180 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAACAATTTTCCTTTAATCGGGATACTC
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGATACTC
34245 CAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATT
66 CAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATT
*
34310 TCATCGGGGATACTCCAACCCTGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTTCCAAA
131 TCATCGGGGATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTTCCAAA
* *
34375 ATATTGATTTCTCATAATCGGGGATACTCCAACCCTGTTTTTATTTTTAAAACACTAAATTTTCC
196 ATATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAACACTAAATTTTCC
34440 AC
261 AC
* *
34442 AATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTCCTCTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC-GGGATACT
* *
34507 CCAACTCCGATTTTATTTCCAAAAATACCATTTTTTCACAATCGAGGATACTCCAACCTCGTTAT
65 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
* * *
34572 TTCGTCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAA
130 TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTTCCAA
* *
34637 AATATTGATTTCTCGTAATTGGGGATACTCCAACCCCGTT
195 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGTT
34677 ATTTTCGAGG
Statistics
Matches: 471, Mismatches: 25, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
262 302 0.64
263 169 0.36
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (262 bp):
AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGATACTC
CAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATT
TCATCGGGGATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTTCCAAA
ATATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAACACTAAATTTTCC
AC
Found at i:34686 original size:79 final size:79
Alignment explanation
Indices: 34576--34810 Score: 267
Period size: 79 Copynumber: 3.0 Consensus size: 79
34566 CGTTATTTCG
** * *
34576 TCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATA
1 TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAATA
**
34641 TTGATTTCTCGTAA
66 TTGATTTCTCACAA
* * * *
34655 TTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAATCCCGATTTTATTTCC-TAATC
1 TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAAT-
* *
34719 ATCGATTTTTCACAA
65 ATTGATTTCTCACAA
* * * * *
34734 TCGGAGATACTTCAACCCCGTTCTTTTCAAGGGGATACTCCAACCCCG-TTATTATCTCCAAAAT
1 TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATT-TTATTTCCAAAAT
*
34798 ATTAAATTTCTCA
65 ATT-GATTTCTCA
34811 TCGGGACATA
Statistics
Matches: 128, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
78 5 0.04
79 113 0.88
80 10 0.08
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
TCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAATA
TTGATTTCTCACAA
Found at i:34689 original size:107 final size:108
Alignment explanation
Indices: 34498--34694 Score: 256
Period size: 107 Copynumber: 1.8 Consensus size: 108
34488 TCCTCTAATC
* * *
34498 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCATTTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCATTTTCTCACAATCGAGGATACTCCAA
* *
34563 CCTCGTTATTTCGTCGGGGATACTCCAACCCCGTTACCTCCGA
66 CCCCGTTATTTCGTAGGGGATACTCCAACCCCGTTACCTCCGA
** ** * *
34606 GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGA-TTTCTCGTAATTGGGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATA-CCATTTTCTCACAATCGAGGATACTCCA
34669 ACCCCGTTATTTTCG-AGGGGATACTC
65 ACCCCGTTA-TTTCGTAGGGGATACTC
34695 TAATCCCGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 43 0.57
108 33 0.43
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (108 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCATTTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCGTAGGGGATACTCCAACCCCGTTACCTCCGA
Found at i:41333 original size:51 final size:51
Alignment explanation
Indices: 41173--41344 Score: 191
Period size: 51 Copynumber: 3.3 Consensus size: 51
41163 GAAATAACGA
* * *
41173 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
41225 AATTGGAGTATCCCCGATTTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGA-TT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
41279 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
41330 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
41345 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
51 39 0.40
52 14 0.14
53 4 0.04
54 30 0.31
55 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:41390 original size:27 final size:28
Alignment explanation
Indices: 41327--41402 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
41317 AAAATAAAGT
*
41327 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
41355 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
41382 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
41403 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:43887 original size:13 final size:13
Alignment explanation
Indices: 43869--43894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43859 ACAAAGATCC
43869 ATGTATCGATACA
1 ATGTATCGATACA
43882 ATGTATCGATACA
1 ATGTATCGATACA
43895 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:43891 original size:33 final size:33
Alignment explanation
Indices: 43849--43914 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
43839 AAATTTCCAG
***
43849 ATGTATCGATACAAAGATCCATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
*
43882 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
43915 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:43958 original size:19 final size:18
Alignment explanation
Indices: 43934--44001 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
43924 CAGTAGCTAA
43934 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
43953 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
43968 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
43985 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
44002 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:43974 original size:13 final size:13
Alignment explanation
Indices: 43956--43980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43946 ACAATACTTA
43956 TGTATCGATACAT
1 TGTATCGATACAT
43969 TGTATCGATACA
1 TGTATCGATACA
43981 AAACTTATGT
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:43978 original size:32 final size:32
Alignment explanation
Indices: 43937--43999 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
43927 TAGCTAATTA
*
43937 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
43969 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
44000 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:44081 original size:21 final size:21
Alignment explanation
Indices: 44057--44113 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
44047 CATTTGTAGG
44057 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
44078 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
44099 ATGTATCGATACATT
1 ATGTATCGATACATT
44114 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:44123 original size:1 final size:1
Alignment explanation
Indices: 44117--44164 Score: 69
Period size: 1 Copynumber: 48.0 Consensus size: 1
44107 ATACATTTAA
***
44117 TTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44165 CAAACACTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:44152 original size:24 final size:24
Alignment explanation
Indices: 44120--44167 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
44110 CATTTAATTT
44120 TTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTCAA
44144 TTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTCAA
44168 ACACTTTATC
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:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTTTTTTTCAA
Found at i:44843 original size:55 final size:55
Alignment explanation
Indices: 44759--45875 Score: 1676
Period size: 55 Copynumber: 20.3 Consensus size: 55
44749 ATAAATTGTA
* * * * * *
44759 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
44814 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
44869 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
44924 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
44979 TCCTGTTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
45034 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
45089 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
45144 TCCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
45199 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
45254 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
45309 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
45364 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
45419 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
45474 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
45529 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGATG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
45584 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
45639 TCCTGCTC-TTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
45693 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGAGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
45748 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
45803 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGAG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
45858 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
45876 AAAAAGCGGA
Statistics
Matches: 998, Mismatches: 42, Indels: 44
0.92 0.04 0.04
Matches are distributed among these distances:
53 2 0.00
54 70 0.07
55 906 0.91
56 18 0.02
57 2 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:46861 original size:1 final size:1
Alignment explanation
Indices: 46857--46908 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
46847 CTTTTCTCTC
* * * * *
46857 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46909 GAAGAGAAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:46881 original size:13 final size:13
Alignment explanation
Indices: 46858--46909 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
46848 TTTTCTCTCT
46858 TTTTCTTTGTTTTG
1 TTTT-TTTGTTTTG
*
46872 TTTTTTTGTTTTT
1 TTTTTTTGTTTTG
*
46885 TTTTTTTTTTTTG
1 TTTTTTTGTTTTG
46898 TTTTTTT-TTTTG
1 TTTTTTTGTTTTG
46910 AAGAGAAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
12 5 0.14
13 26 0.74
14 4 0.11
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:46907 original size:18 final size:18
Alignment explanation
Indices: 46867--46908 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
46857 TTTTTCTTTG
*
46867 TTTTGTTTTTTTGTTTTT
1 TTTTTTTTTTTTGTTTTT
46885 TTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTGTTTTT
46903 TTTTTT
1 TTTTTT
46909 GAAGAGAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (18 bp):
TTTTTTTTTTTTGTTTTT
Done.