Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold998
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: 30126
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:9208 original size:2 final size:2
Alignment explanation
Indices: 9203--9238 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9193 TTTTAGTTAA
9203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9239 TCAATAAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13362 original size:19 final size:19
Alignment explanation
Indices: 13338--13377 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
13328 TTGATAATTT
13338 TATTACCCCTTTTGTCAAA
1 TATTACCCCTTTTGTCAAA
13357 TATTACCCCTTTTGTCAAA
1 TATTACCCCTTTTGTCAAA
13376 TA
1 TA
13378 CAATCGCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (19 bp):
TATTACCCCTTTTGTCAAA
Found at i:17258 original size:2 final size:2
Alignment explanation
Indices: 17240--17279 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
17230 CTAGTTTCAA
* *
17240 AT AT GT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17280 GAGTGCTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21204 original size:16 final size:18
Alignment explanation
Indices: 21185--21220 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
21175 ATAAATTTTG
21185 ATATTTTT-AT-ATATTT
1 ATATTTTTCATCATATTT
21201 ATATTTTTCATCATATTT
1 ATATTTTTCATCATATTT
21219 AT
1 AT
21221 TTTAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTTCATCATATTT
Found at i:21206 original size:24 final size:23
Alignment explanation
Indices: 21162--21208 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
21152 ATATTCATTT
21162 TATTTTTTTATTTATAAATTTTGA
1 TATTTTTTTATTTAT-AATTTTGA
*
21186 TATTTTTATATATTTATATTTTT
1 TATTTTT-T-TATTTATAATTTT
21209 CATCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 6 0.30
26 7 0.35
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TATTTTTTTATTTATAATTTTGA
Found at i:21612 original size:18 final size:19
Alignment explanation
Indices: 21561--21612 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
21551 TTAAAAATTT
*
21561 ATATAACACAAA--TTATTA
1 ATATAACA-AAATTTTATAA
21579 ATATAACAAAATTTTATAA
1 ATATAACAAAATTTTATAA
*
21598 ATATAA-AATATTTTA
1 ATATAACAAAATTTTA
21613 AGCACAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 16 0.53
19 11 0.37
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATAACAAAATTTTATAA
Found at i:25005 original size:52 final size:52
Alignment explanation
Indices: 24935--25063 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
24925 CGAAATATGA
*
24935 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATATGGGC
1 AAATTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATATGGGC
* *
24987 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATATGGGC
*
25039 AAATTTGCTTGCATGTATCAATACA
1 AAATTTGCTTGCATGTATCGATACA
25064 AAGATCAGTG
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:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATATGGGC
Found at i:25074 original size:52 final size:51
Alignment explanation
Indices: 24935--25081 Score: 206
Period size: 52 Copynumber: 2.8 Consensus size: 51
24925 CGAAATATGA
*
24935 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATATGGGC
1 AAATTTGCTTGCATGTATCGATACA-TTAATAGTGTATCGATACATATGGGC
* *
24987 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACA-TTAATAGTGTATCGATACATATGGGC
* *
25039 AAATTTGCTTGCATGTATCAATACA-AAGATCAGTGTATCGATA
1 AAATTTGCTTGCATGTATCGATACATTA-AT-AGTGTATCGATA
25082 TAATGTATCG
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (51 bp):
AAATTTGCTTGCATGTATCGATACATTAATAGTGTATCGATACATATGGGC
Found at i:25090 original size:13 final size:13
Alignment explanation
Indices: 25072--25096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25062 CAAAGATCAG
25072 TGTATCGATATAA
1 TGTATCGATATAA
25085 TGTATCGATATA
1 TGTATCGATATA
25097 TTTGAGTAAT
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:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:25163 original size:18 final size:18
Alignment explanation
Indices: 25140--25201 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
25130 TAGCTTAAAT
25140 TGTATCGATACAAACTTA
1 TGTATCGATACAAACTTA
25158 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
25171 TGTATCGATACAATACTTA
1 TGTATCGATACAA-ACTTA
25190 TGTATCGATACA
1 TGTATCGATACA
25202 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 12 0.32
19 12 0.32
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:25176 original size:13 final size:13
Alignment explanation
Indices: 25158--25214 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
25148 TACAAACTTA
25158 TGTATCGATACAT
1 TGTATCGATACAT
25171 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
25189 ATGTATCGATACAT
1 -TGTATCGATACAT
25203 TGTATCGATACA
1 TGTATCGATACA
25215 AAGATCAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25194 original size:32 final size:31
Alignment explanation
Indices: 25138--25245 Score: 153
Period size: 32 Copynumber: 3.4 Consensus size: 31
25128 AGTAGCTTAA
25138 ATTGTATCGATACAAACTTATGTATCGATAC
1 ATTGTATCGATACAAACTTATGTATCGATAC
25169 ATTGTATCGATACAATACTTATGTATCGATAC
1 ATTGTATCGATACAA-ACTTATGTATCGATAC
* * *
25201 ATTGTATCGATACAAAGATCAGTGTATCGATAT
1 ATTGTATCGATACAAA-CTTA-TGTATCGATAC
*
25234 AATGTATCGATA
1 ATTGTATCGATA
25246 TATTTGAGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
31 16 0.23
32 33 0.47
33 21 0.30
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (31 bp):
ATTGTATCGATACAAACTTATGTATCGATAC
Found at i:25228 original size:151 final size:152
Alignment explanation
Indices: 25052--25367 Score: 607
Period size: 151 Copynumber: 2.1 Consensus size: 152
25042 TTTGCTTGCA
*
25052 TGTATCAATACAAAGATCAGTGTATCGATATAATGTATCGATATATTTGAGTAATGTATCGATAA
1 TGTATCGATACAAAGATCAGTGTATCGATATAATGTATCGATATATTTGAGTAATGTATCGATAA
25117 ATTTTTTTGGCAGTAGCTTAAATTGTATCGATAC-AAACTTATGTATCGATACATTGTATCGATA
66 ATTTTTTTGGCAGTAGCTTAAATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATA
25181 CAATACTTATGTATCGATACAT
131 CAATACTTATGTATCGATACAT
*
25203 TGTATCGATACAAAGATCAGTGTATCGATATAATGTATCGATATATTTGAGTAATGTATCGATAT
1 TGTATCGATACAAAGATCAGTGTATCGATATAATGTATCGATATATTTGAGTAATGTATCGATAA
25268 ATTTTTTTGGCAGTAGCTTAAATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATA
66 ATTTTTTTGGCAGTAGCTTAAATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATA
25333 CAATACTTATGTATCGATACAT
131 CAATACTTATGTATCGATACAT
25355 TGTATCGATACAA
1 TGTATCGATACAA
25368 CACTTTATGT
Statistics
Matches: 162, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
151 97 0.60
152 65 0.40
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (152 bp):
TGTATCGATACAAAGATCAGTGTATCGATATAATGTATCGATATATTTGAGTAATGTATCGATAA
ATTTTTTTGGCAGTAGCTTAAATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATA
CAATACTTATGTATCGATACAT
Found at i:25241 original size:13 final size:13
Alignment explanation
Indices: 25223--25247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25213 CAAAGATCAG
25223 TGTATCGATATAA
1 TGTATCGATATAA
25236 TGTATCGATATA
1 TGTATCGATATA
25248 TTTGAGTAAT
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:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:25328 original size:13 final size:13
Alignment explanation
Indices: 25310--25399 Score: 63
Period size: 13 Copynumber: 5.9 Consensus size: 13
25300 ACAAAACTTA
25310 TGTATCGATACAT
1 TGTATCGATACAT
25323 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
25341 ATGTATCGATACAT
1 -TGTATCGATACAT
25355 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
25374 ATGTATCGATACAT
1 -TGTATCGATACAT
25388 TGTATCGATACA
1 TGTATCGATACA
25400 ACACTTTATG
Statistics
Matches: 64, Mismatches: 0, Indels: 26
0.71 0.00 0.29
Matches are distributed among these distances:
13 32 0.50
14 2 0.03
16 5 0.08
17 3 0.05
18 1 0.02
19 12 0.19
20 9 0.14
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25330 original size:32 final size:33
Alignment explanation
Indices: 25289--25419 Score: 221
Period size: 32 Copynumber: 4.0 Consensus size: 33
25279 AGTAGCTTAA
*
25289 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
*
25321 ATTGTATCGATACAATAC-TTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
25353 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
*
25386 ATTGTATCGATACAACACTTTATGTATCAATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
25419 A
1 A
25420 AATCATTGAA
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 48 0.51
33 47 0.49
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAACACTTTATGTATCGATAC
Found at i:25380 original size:20 final size:20
Alignment explanation
Indices: 25355--25420 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
25345 ATCGATACAT
25355 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
25375 TGTATCGAT---ACA---T-
1 TGTATCGATACAACACTTTA
25388 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
*
25408 TGTATCAATACAA
1 TGTATCGATACAA
25421 ATCATTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 21 0.55
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACACTTTA
Found at i:25386 original size:65 final size:65
Alignment explanation
Indices: 25289--25419 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
25279 AGTAGCTTAA
* *
25289 ATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAATAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCAATAC
*
25353 ATTGTATCGATACAACACTTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCAATA
1 ATTGTATCGATACAAAAC-TTATGTATCGATACATTGTATCGATACAACACTTTATGTATCAATA
25418 C
65 C
25419 A
1 A
25420 AATCATTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 17 0.27
65 31 0.50
66 14 0.23
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (65 bp):
ATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCAATAC
Found at i:26317 original size:58 final size:55
Alignment explanation
Indices: 26261--26411 Score: 215
Period size: 52 Copynumber: 2.9 Consensus size: 55
26251 TGTTAAAGAT
* *
26261 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAA
1 GAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAA
* *
26316 G-A--CGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGAC--A
1 GAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAA
*
26366 -AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
26412 GTGCCAATGT
Statistics
Matches: 88, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
50 2 0.02
52 84 0.95
54 1 0.01
55 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.22
Consensus pattern (55 bp):
GAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAA
Found at i:26428 original size:43 final size:44
Alignment explanation
Indices: 26365--27230 Score: 406
Period size: 43 Copynumber: 19.0 Consensus size: 44
26355 TAAAGATGAC
* *
26365 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* *
26408 AAAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGTG-CTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTG-GACTT--A
* *
26454 AGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTG
1 A-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* * * * * * *
26502 GAA-TTGCCAATGTGCTGATTCAAGGTCGGCTACATTAGACTTAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-A
*
26546 AGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
1 A-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* * * *
26593 AAAGGTGCCAATGTGCTTATTCAAGACCAGCTACATTGGACTTAAAGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT----A
* * *
26641 AGAAGGTGACAATATGCTGATTCAAGGCCAGCTACGTTGGACTTAAA
1 A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT--A
* * *
26688 GATGAAGGTGCTAATACGCTGATTCAAGGCCAGCGATATTGGACTTAA
1 -A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-A
* ** ** * * *
26736 CGATGAAGATGAGAA-A-AATGA-TAAAGATGCCA---ATATGTTGA-TT-
1 --A--AAGGTGCCAATATGCTGATTCAAG--GCCAGCGACAT-TGGACTTA
* * * ** * * *
26779 CACGACTAACAATATTG-GGCTT-AA----A--G--A-TGAGA--AA
1 AAAG-GTGCCAATA-TGCTGATTCAAGGCCAGCGACATTG-GACTTA
* * * *
26813 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----T--A
** *
26866 AAAGGTGCCAATATGCTGATTCAAGGCCAGTTATATTGGACTT-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* * *
26909 AAAGGTGCCAATGTGCTGATTCAAGGCCATCTACATTGGACTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* *
26953 AAGATGAAGATGCCAATATGCTGATTCAAGGCCAACGATATTAGG-CTT-
1 AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGACATT-GGACTTA
** * * *
27001 GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT--A
*
27047 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
1 -A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
** * *
27093 GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT----A
* *
27141 CAAAGGTGCCAATATGCTGATTCCAGGCCAGCGATATTGGACTT-
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* *
27185 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
27229 AA
1 AA
27231 GGAATATGCC
Statistics
Matches: 638, Mismatches: 107, Indels: 155
0.71 0.12 0.17
Matches are distributed among these distances:
33 3 0.00
34 12 0.02
35 3 0.00
36 1 0.00
39 3 0.00
40 4 0.01
41 1 0.00
42 5 0.01
43 255 0.40
44 9 0.01
45 9 0.01
46 12 0.02
47 10 0.02
48 10 0.02
49 226 0.35
50 37 0.06
51 1 0.00
52 31 0.05
53 6 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (44 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
Found at i:26592 original size:49 final size:49
Alignment explanation
Indices: 26253--26743 Score: 498
Period size: 49 Copynumber: 10.2 Consensus size: 49
26243 CTTAGGAATG
*
26253 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
** * *
26302 TTAAAGATGACAAAGACGCCAATATGCTGATTTAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
26354 TTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
26406 TT----A--AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGTG-C
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTG-GAC
* *
26449 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * * *
26499 TT---G--GAA-TTGCCAATGTGCTGATTCAAGGTCGGCTACATTAGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
26542 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
26591 TT----A--AAGGTGCCAATGTGCTTATTCAAGACCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
26634 TTAAAGAAGAAGGTGACAATATGCTGATTCAAGGCCAGCTACGTTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
26683 TTAAAGATGAAGGTGCTAATACGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
*
26732 TTAACGATGAAG
1 TTAAAGATGAAG
26744 ATGAGAAAAA
Statistics
Matches: 368, Mismatches: 50, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
43 104 0.28
44 3 0.01
45 1 0.00
46 2 0.01
47 1 0.00
48 4 0.01
49 130 0.35
50 36 0.10
52 87 0.24
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:26602 original size:92 final size:91
Alignment explanation
Indices: 26319--26688 Score: 463
Period size: 92 Copynumber: 4.0 Consensus size: 91
26309 TGACAAAGAC
* * * * *
26319 GCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGA
1 GCCAATGTGCTGATTCAAGGCCAGCTACATT-GACTTAAAGATG---AAGGTGCCAATATGCTGA
26384 TTCAAGGCCAGCGATATTGGACTTAAAGGT
62 TTCAAGGCCAGCGATATTGGACTTAAAGGT
* * * *
26414 GCCAATGTGTTGATTCAAGGCCAGCGACATTGTGCTTAAAAGATGAGGGTGCCAATATGCTGATT
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTG-ACTT-AAAGATGAAGGTGCCAATATGCTGATT
* *
26479 CAAGGCCAGCGATATTGGACTTGGAA-TT
64 CAAGGCCAGCGATATTGGACTT-AAAGGT
* * *
26507 GCCAATGTGCTGATTCAAGGTCGGCTACATTAGACTTAAAGATGATGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATT-GACTTAAAGATGAAGGTGCCAATATGCTGATTC
26572 AAGGCCAGCGATATTGGACTTAAAGGT
65 AAGGCCAGCGATATTGGACTTAAAGGT
* * * *
26599 GCCAATGTGCTTATTCAAGACCAGCTACATTGGACTTAAAGAAGAAGGTGACAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATT-GACTTAAAGATGAAGGTGCCAATATGCTGATTC
* **
26664 AAGGCCAGCTACGTTGGACTTAAAG
65 AAGGCCAGCGATATTGGACTTAAAG
26689 ATGAAGGTGC
Statistics
Matches: 242, Mismatches: 28, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
91 2 0.01
92 128 0.53
93 71 0.29
94 4 0.02
95 30 0.12
96 7 0.03
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (91 bp):
GCCAATGTGCTGATTCAAGGCCAGCTACATTGACTTAAAGATGAAGGTGCCAATATGCTGATTCA
AGGCCAGCGATATTGGACTTAAAGGT
Found at i:27013 original size:92 final size:92
Alignment explanation
Indices: 26813--27231 Score: 651
Period size: 92 Copynumber: 4.5 Consensus size: 92
26803 AGATGAGAAA
* *
26813 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAAT
**
26878 ATGCTGATTCAAGGCCAGTTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
26909 AAAGGTGCCAATGTGCTGATTCAAGGCCATCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
26974 TGATTCAAGGCCAACGATATTAGG-CTT
66 TGATTCAAGGCCAGCGATATT-GGACTT
** *
27001 GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
27066 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
** **
27093 GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGACAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
27158 TGATTCCAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
27185 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
27232 GAATATGCCA
Statistics
Matches: 302, Mismatches: 19, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
91 2 0.01
92 251 0.83
93 2 0.01
94 1 0.00
95 41 0.14
96 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:27388 original size:32 final size:32
Alignment explanation
Indices: 27237--27390 Score: 222
Period size: 32 Copynumber: 4.8 Consensus size: 32
27227 TAAAGGAATA
* *
27237 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGC-TTTGAAAAAGGT
**
27270 TGCCACCGACTTGTGTGGGCTTT-AAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAAAGGT
*
27301 TGCCACCGACTTATGTGGGCTTT-AGAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTGA-AAAAGGT
*
27333 TGTCACCGACTTGTGTGGGCTTTGAAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAAAGGT
27365 TGCCACCGACTTGTGTGGGCTTTGAA
1 TGCCACCGACTTGTGTGGGCTTTGAA
27391 GGGGTGAAAG
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
31 28 0.26
32 61 0.56
33 20 0.18
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTGAAAAAGGT
Found at i:27447 original size:33 final size:34
Alignment explanation
Indices: 27397--27626 Score: 214
Period size: 33 Copynumber: 6.9 Consensus size: 34
27387 TGAAGGGGTG
*
27397 AAAGA-TGCCACGAAGTTGTGGAC-TTAAAAGGA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGA
* *
27429 ATAAG-GTGCCACGGAGTTGTGGGCTTTAAGAGGGGA
1 A-AAGAGTGCCACGGAGTTGTGGACTTTAA-A-AGGA
*
27465 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-G-
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGA
27497 ---G-GTGCCACGGAGTTGTGGAC-TTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGG-A
* * *
27527 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGA
* *
27561 AAA-AGGTGCCATGGAATTGTGGAC-TTAAAAGGA
1 AAAGA-GTGCCACGGAGTTGTGGACTTTAAAAGGA
* * *
27594 AAAGAGTGCCATGTAGTTGTGGGCTTTGAAAAG
1 AAAGAGTGCCACGGAGTTGTGGACTTT-AAAAG
27627 AAGATGCCAT
Statistics
Matches: 164, Mismatches: 16, Indels: 33
0.77 0.08 0.15
Matches are distributed among these distances:
27 6 0.04
28 19 0.12
29 1 0.01
32 1 0.01
33 49 0.30
34 43 0.26
35 17 0.10
36 28 0.17
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGA
Found at i:27496 original size:28 final size:28
Alignment explanation
Indices: 27464--27557 Score: 98
Period size: 28 Copynumber: 3.1 Consensus size: 28
27454 TTAAGAGGGG
27464 AAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT
* * *
27492 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTT------T
*
27526 AAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT
27554 AAAA
1 AAAA
27558 AGAAAAAGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
28 29 0.55
34 24 0.45
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (28 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTT
Found at i:27536 original size:34 final size:35
Alignment explanation
Indices: 27492--27626 Score: 152
Period size: 34 Copynumber: 3.9 Consensus size: 35
27482 TGTGGGCTTT
*
27492 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGA
* * *
27526 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGA
* *
27561 AAAAG-GTGCCATGGAATTGTGGAC-TTAAAAGG-
1 AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGA
* * *
27593 AAAAGAGTGCCATGTAGTTGTGGGCTTTGAAAAG
1 AAAAGAGTGCCACGGAGTTGTGGACTTT-AAAAG
27627 AAGATGCCAT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
32 5 0.06
33 23 0.27
34 39 0.46
35 18 0.21
ACGTcount: A:0.36, C:0.10, G:0.32, T:0.21
Consensus pattern (35 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGA
Found at i:27565 original size:97 final size:95
Alignment explanation
Indices: 27402--27592 Score: 267
Period size: 97 Copynumber: 2.0 Consensus size: 95
27392 GGGTGAAAGA
* * ** *
27402 TGCCACGAAGTTGTGGACTTAAAAGGAATAAGGTGCCACGGAGTTGTGGGCTTTAAGAGGGGAAA
1 TGCCACGAAGTTGTGGACTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAGAAAGAAAA
* *
27467 AGAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
66 AG-GTGCCACGGAATTGTGGAC-TTAAAAGGG
*
27499 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA-AAAGAAA
1 TGCCACGAAGTTGTGGACTTAAAAGGAAAAAG-GTGCCACAGAGTTGTGGGCTTTAAGAAAGAAA
*
27563 AAGGTGCCATGGAATTGTGGACTTAAAAGG
65 AAGGTGCCACGGAATTGTGGACTTAAAAGG
27593 AAAAGAGTGC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 8 0.10
96 16 0.19
97 37 0.44
98 23 0.27
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.21
Consensus pattern (95 bp):
TGCCACGAAGTTGTGGACTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAGAAAGAAAA
AGGTGCCACGGAATTGTGGACTTAAAAGGG
Found at i:27626 original size:67 final size:68
Alignment explanation
Indices: 27492--27628 Score: 206
Period size: 67 Copynumber: 2.0 Consensus size: 68
27482 TGTGGGCTTT
* *
27492 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA
27557 AAG
66 AAG
* * *
27560 AAAAAGGTGCCATGGAATTGTGGACTTAAAAGG-AAAAGAGTGCCA-TGTAGTTGTGGGCTTTGA
1 AAAAAGGTGCCACGGAATTGTGGACTTAAAAGGAAAAAGAGTGCCACAG-AGTTGTGGGCTTTAA
27623 AAAG
65 AAAG
27627 AA
1 AA
27629 GATGCCATAG
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
66 1 0.02
67 32 0.51
68 30 0.48
ACGTcount: A:0.37, C:0.10, G:0.31, T:0.21
Consensus pattern (68 bp):
AAAAAGGTGCCACGGAATTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA
AAG
Found at i:27635 original size:132 final size:130
Alignment explanation
Indices: 27397--27653 Score: 315
Period size: 132 Copynumber: 2.0 Consensus size: 130
27387 TGAAGGGGTG
* * * * *
27397 AAAGATGCCACGAAGTTGTGGACTTAAAAGGAATAAGGTGCCACGGAGTTGTGGGCTTTAAGAGG
1 AAAGATGCCACGAAGTTGTGGACTTAAAAAGAAAAAGGTGCCACGGAATTGTGGACTTTAAGAGA
* * *
27462 GGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
66 GGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGATGCCACAGAGTCGTGGACTTAAAAGGAA
* *
27527 AAAGAGTGCCAC-AGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCATGGAATTGTGGAC-TTAA-
1 AAAGA-TGCCACGA-AGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGGAATTGTGGACTTTAAG
* * *
27589 A-AGGAAAAGAGTGCCATGTAGTTGTGGGCTTTGAAAAGAAGATGCCATAGAGTCGTGGACTTAA
63 AGAGGAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG--GATGCCACAGAGTCGTGGACTTAA
27653 A
125 A
27654 GAAGGTATTT
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
129 28 0.26
130 12 0.11
131 19 0.18
132 49 0.45
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.22
Consensus pattern (130 bp):
AAAGATGCCACGAAGTTGTGGACTTAAAAAGAAAAAGGTGCCACGGAATTGTGGACTTTAAGAGA
GGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGATGCCACAGAGTCGTGGACTTAAAAGGAA
Done.