Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3031
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: 34034
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Found at i:277 original size:18 final size:19
Alignment explanation
Indices: 244--279 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
234 TTAAATTTAG
*
244 TAAATTAATTGAATTATGT
1 TAAATTAAATGAATTATGT
263 TAAATTAAATG-ATTATG
1 TAAATTAAATGAATTATG
280 GTTCCAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (19 bp):
TAAATTAAATGAATTATGT
Found at i:2483 original size:27 final size:27
Alignment explanation
Indices: 2445--2553 Score: 125
Period size: 27 Copynumber: 4.1 Consensus size: 27
2435 TTTGGAGGAA
*
2445 GGTGGCTATGCCACAATTATCTGATCT
1 GGTGGCTCTGCCACAATTATCTGATCT
*
2472 GGTGGCTCTGCCACATATT-TCTGTTCT
1 GGTGGCTCTGCCACA-ATTATCTGATCT
*
2499 GGTGGCTCTGCC-CGATTATCTGTATCT
1 GGTGGCTCTGCCACAATTATCTG-ATCT
* * *
2526 GGTGACTCTGTCAC-ATTATCTGTTCT
1 GGTGGCTCTGCCACAATTATCTGATCT
2552 GG
1 GG
2554 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
25 3 0.04
26 10 0.14
27 54 0.76
28 4 0.06
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (27 bp):
GGTGGCTCTGCCACAATTATCTGATCT
Found at i:2519 original size:53 final size:54
Alignment explanation
Indices: 2445--2553 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
2435 TTTGGAGGAA
* *
2445 GGTGGCTATGCCACAATTATCTG-ATCTGGTGGCTCTGCCACATATTTCTGTTCT
1 GGTGGCTATGCCACAATTATCTGTATCTGGTGACTCTGCCACAT-TATCTGTTCT
* * *
2499 GGTGGCTCTGCC-CGATTATCTGTATCTGGTGACTCTGTCACATTATCTGTTCT
1 GGTGGCTATGCCACAATTATCTGTATCTGGTGACTCTGCCACATTATCTGTTCT
2552 GG
1 GG
2554 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
53 20 0.41
54 29 0.59
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (54 bp):
GGTGGCTATGCCACAATTATCTGTATCTGGTGACTCTGCCACATTATCTGTTCT
Found at i:11389 original size:49 final size:49
Alignment explanation
Indices: 11320--11610 Score: 470
Period size: 47 Copynumber: 6.1 Consensus size: 49
11310 GAAATGATAG
11320 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
11369 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
11416 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
11465 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
11512 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
11560 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
11607 TAAG
1 TAAG
11611 TCCCGAAGGG
Statistics
Matches: 228, Mismatches: 9, Indels: 12
0.92 0.04 0.05
Matches are distributed among these distances:
46 5 0.02
47 96 0.42
48 35 0.15
49 92 0.40
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:11484 original size:96 final size:96
Alignment explanation
Indices: 11320--11610 Score: 503
Period size: 96 Copynumber: 3.0 Consensus size: 96
11310 GAAATGATAG
11320 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
11385 ATGTGATGAATGTGAAAGTGTATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATGTGA
11416 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
11481 ATGTGATGAATGTGAAAGTGTATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * *
11512 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATGTGACAGGGCCGAGTGGCCA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
* * *
11576 ACGTGATGGATGTGAAAGTGTATAAATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATGTGA
11607 TAAG
1 TAAG
11611 TCCCGAAGGG
Statistics
Matches: 187, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
95 61 0.33
96 126 0.67
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:13680 original size:43 final size:43
Alignment explanation
Indices: 13632--13820 Score: 351
Period size: 43 Copynumber: 4.4 Consensus size: 43
13622 TTGGTTTTCA
13632 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
*
13675 GCACTAAGTGTGCGGGAAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
* *
13718 ACACTAAGTGTGAGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
13761 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
13804 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
13821 TTGAAATGCA
Statistics
Matches: 140, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 140 1.00
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:13837 original size:29 final size:29
Alignment explanation
Indices: 13802--13875 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
13792 GTTGTGAGAT
* *
13802 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
13831 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
13860 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
13876 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:14313 original size:40 final size:40
Alignment explanation
Indices: 14190--14450 Score: 278
Period size: 40 Copynumber: 6.5 Consensus size: 40
14180 TCGAATGATG
* *
14190 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TATA
* * * * *
14230 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGCTAGTGA-TATA
* *
14270 TCCGGGCTAAGTCCCGAAGAGCATTCATACTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* *
14310 TCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* *
14350 TCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* ** * * *
14390 TCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
14430 TCCGGGCTAGGTCCCGAAGAG
1 TCCGGGCTAAGTCCCGAAGAG
14451 TAATCATGAT
Statistics
Matches: 183, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 164 0.90
41 18 0.10
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:18083 original size:47 final size:47
Alignment explanation
Indices: 17976--18357 Score: 608
Period size: 47 Copynumber: 8.1 Consensus size: 47
17966 GAAATGATAG
17976 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
18025 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
18072 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
18119 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
18166 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATG-
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
18211 TGAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 T-AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
18259 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* * * * * * * *
18307 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
18354 TAAG
1 TAAG
18358 TCCCGAAGGG
Statistics
Matches: 313, Mismatches: 14, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
45 1 0.00
46 47 0.15
47 189 0.60
48 35 0.11
49 41 0.13
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:18244 original size:140 final size:142
Alignment explanation
Indices: 17976--18353 Score: 606
Period size: 140 Copynumber: 2.7 Consensus size: 142
17966 GAAATGATAG
17976 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCG
* *
18041 ATGTGATGAATGTGAAAGTGTATATATGTGAT-AAGGCCTAATGGCCGATGTGATGAATGTGAAA
65 ATGTGATGAATGTGAAAGTGTATATATATG-TGAAGGCCGAATGGCCGATGTGATGAATGTGAAA
18105 GTGTATATATGTGA
129 GTGTATATATGTGA
18119 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
18183 TGTGATGAATGTG-AAGTGTATATATATGTGAAGGCCGAATGGCCGATGTGATGAATGTGAAAGT
66 TGTGATGAATGTGAAAGTGTATATATATGTGAAGGCCGAATGGCCGATGTGATGAATGTGAAAGT
18247 GTATATATGTGA
131 GTATATATGTGA
* * * * *
18259 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATGTGACAGGGCCGAGTGGCCA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCG
* *
18323 ACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
65 ATGTGATGAATGTGAAAGTGTATATATATGTGA
18354 TAAGTCCCGA
Statistics
Matches: 222, Mismatches: 9, Indels: 11
0.92 0.04 0.05
Matches are distributed among these distances:
139 6 0.03
140 95 0.43
141 76 0.34
142 9 0.04
143 36 0.16
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (142 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGA
TGTGATGAATGTGAAAGTGTATATATATGTGAAGGCCGAATGGCCGATGTGATGAATGTGAAAGT
GTATATATGTGA
Found at i:18262 original size:93 final size:94
Alignment explanation
Indices: 17976--18357 Score: 626
Period size: 93 Copynumber: 4.0 Consensus size: 94
17966 GAAATGATAG
*
17976 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTG--AAGGCCGAATGGCCG
18041 ATGTGATGAATGTGAAAGTGTATATATGTGA
64 ATGTGATGAATGTGAAAGTGTATATATGTGA
* *
18072 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT-AAGGCCTAATGGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG-TGAAGGCCGAATGGCCGA
18136 TGTGATGAATGTGAAAGTGTATATATGTGA
65 TGTGATGAATGTGAAAGTGTATATATGTGA
18166 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATGTGAAGGCCGAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAAGGCCGAATGGCCGAT
18230 GTGATGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* *
18259 TAAGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATGTGACAGGGCCGAGTGGCCA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA-A-GGCCGAATGGCCG
* * *
18323 ACGTGATGGATGTGAAAGTGTATAAATGTGA
64 ATGTGATGAATGTGAAAGTGTATATATGTGA
18354 TAAG
1 TAAG
18358 TCCCGAAGGG
Statistics
Matches: 274, Mismatches: 8, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
92 1 0.00
93 107 0.39
94 77 0.28
95 43 0.16
96 45 0.16
97 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (94 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAAGGCCGAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGA
Found at i:19882 original size:95 final size:95
Alignment explanation
Indices: 19721--19917 Score: 344
Period size: 95 Copynumber: 2.1 Consensus size: 95
19711 ATTTTCGAGT
19721 TGTGAAACTCAATATGATTTTTAAGGTGACAGTGTCGCAGTTAGCCAACTGCCTGGAAAATTTTA
1 TGTGAAACTCAATATGATTTTTAAGGTGACAGTGTCGCAGTTAGCCAACTGCCTGGAAAATTTTA
19786 AAA-AACTGCGAT-GTAAGCGAATTTAGTC
66 AAAGAACTGCGATAGTAAGCGAATTTAGTC
19814 TGTGAAACTCAATATATGATTTTTAAGGTGACAGTGTCGCAGTTAGCCAACTGCCTGGAAAATTT
1 TGTGAAACTC-A-ATATGATTTTTAAGGTGACAGTGTCGCAGTTAGCCAACTGCCTGGAAAATTT
*
19879 TAAAATGGACTGCGATAGTAAGCGAATTTAGTC
64 TAAAA-GAACTGCGATAGTAAGCGAATTTAGTC
19912 TGTGAA
1 TGTGAA
19918 CCCCTCGTGT
Statistics
Matches: 98, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
93 10 0.10
94 1 0.01
95 57 0.58
97 8 0.08
98 22 0.22
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (95 bp):
TGTGAAACTCAATATGATTTTTAAGGTGACAGTGTCGCAGTTAGCCAACTGCCTGGAAAATTTTA
AAAGAACTGCGATAGTAAGCGAATTTAGTC
Found at i:31463 original size:88 final size:87
Alignment explanation
Indices: 31335--31495 Score: 209
Period size: 88 Copynumber: 1.8 Consensus size: 87
31325 ATTCGACGGA
* * *
31335 GAGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTCAC-ATCGAAGTAGATCCAAGATG
1 GAGCAGATCGAAGACATAGCAGATCTAACCTTCCGATGTTT-ACGCT-GAAGCAGATCCAAGATG
31399 ATTTGGCATCCTTGCGTTGACAAG
64 ATTTGGCATCCTTGCGTTGACAAG
* ** * *
31423 GAGCAGATCGAAGACATAGCAGATTTGGCTTTCACG-TGTTTACGCTGAAGCAGATCTAAGATGA
1 GAGCAGATCGAAGACATAGCAGATCTAACCTTC-CGATGTTTACGCTGAAGCAGATCCAAGATGA
31487 TTTGGCATC
65 TTTGGCATC
31496 TCTGTACTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
87 27 0.43
88 35 0.56
89 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (87 bp):
GAGCAGATCGAAGACATAGCAGATCTAACCTTCCGATGTTTACGCTGAAGCAGATCCAAGATGAT
TTGGCATCCTTGCGTTGACAAG
Found at i:31656 original size:78 final size:79
Alignment explanation
Indices: 31528--31722 Score: 313
Period size: 81 Copynumber: 2.5 Consensus size: 79
31518 CGAAGAAACA
** * *
31528 GATTTGGCATCTCCATATTCGAC-GGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATT-GA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTAGA
31591 AGCAGATCCAAGAT
66 AGCAGATCCAAGAT
31605 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATT--A
31670 GAAGCAGATCCAAGAT
64 GAAGCAGATCCAAGAT
*
31686 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGA
31723 GATAACAGAT
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
77 20 0.18
78 37 0.34
81 52 0.48
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (79 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTAGA
AGCAGATCCAAGAT
Found at i:31749 original size:44 final size:43
Alignment explanation
Indices: 31686--31983 Score: 325
Period size: 44 Copynumber: 6.8 Consensus size: 43
31676 GATCCAAGAT
*
31686 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAGATAACA
1 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAGATAACA
* *
31730 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATC--GAGATAACA
* * * * * * * * *
31776 GATCTGACCT-TCATGTGTTTACATC-GAAGCAGATCCAAGATGATA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGAGCAGAT-CGAGATAACA
*
31821 GATTTGGCATCTCTGTATTAGACGGGAGCAAATCGAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGAGCAGATCGAGATAACA
* *
31864 GATTTGGCATCTCTGTATTAGACGGGAGCAGATTGA-A-AAGA
1 GATTTGGCATCTCTGTATTAGACGGGAGCAGATCGAGATAACA
*
31905 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCG-AGATAACA
*
31950 GATTTGGCGTCTCTGTATTAGACGGGAGCAGATC
1 GATTTGGCATCTCTGTATTAGACGGGAGCAGATC
31984 AAAGATAGCA
Statistics
Matches: 212, Mismatches: 30, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
41 25 0.12
42 12 0.06
43 43 0.20
44 57 0.27
45 42 0.20
46 27 0.13
47 5 0.02
48 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (43 bp):
GATTTGGCATCTCTGTATTAGACGGGAGCAGATCGAGATAACA
Found at i:31932 original size:219 final size:213
Alignment explanation
Indices: 31261--31996 Score: 700
Period size: 219 Copynumber: 3.5 Consensus size: 213
31251 AAGCGGATCC
** * * * *
31261 AAGATGATTTAACATCTCTGTATT-GTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCAT
1 AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGAAACAGATTTGGCATCTCCAT
* * * *
31325 ATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTCACATCGAAGTAGA
66 ATTAGACGG-GAGCAGATCGAAGACATAGCAGATCTGACCTTC--ATGTTTTACATCGAAGCAGA
** * *
31390 TCCAAGATGATTTGGCATC-CTTGCGTT-GACAAGGAGCAGATCGAAGACATAGCAGATTTGGCT
128 TCCAAGATGATTTGGCATCTC-TGTATTAGACAGGGAGCAGATCGAAG--ATAACAGATTTGGC-
* *
31453 TTCACGTGT-TTACG-CTGAAGCAGATCT
189 ATC-C-TGTATTA-GACAGAAGCAGAT-T
* * * * *
31480 AAGATGATTTGGCATCTCTGTACT-GTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCAT
1 AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGAAACAGATTTGGCATCTCCAT
*
31544 ATTCGACGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCA-----T---T-GAAGCAGATCC
66 ATTAGACGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATGTTTTACATCGAAGCAGATCC
* * *
31600 AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCT-G-A-CCT
131 AAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGATA-A-CAGATTTGGCATCCT
*
31662 -TCATT-GA-AGAAGCAGATCC
194 GT-ATTAGACAGAAGCAGAT-T
**
31681 AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCG-AGATAACAGATTTGGCATCTCTG
1 AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGA-AACAGATTTGGCATCTCCA
31745 TATTAGACGGGGAGCAGATC-AAGACATAGCAGATCTGACCTTCATGTGTTTACATCGAAGCAGA
65 TATTAGAC-GGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATGT-TTTACATCGAAGCAGA
*
31809 TCCAAGATGATAGATTTGGCATCTCTGTATTAGAC-GGGAGCAAATCG-AGATAACAGATTTGGC
128 TCC-A-A-GAT-GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGATAACAGATTTGGC
* *
31872 ATCTCTGTATTAGACGGGAGCAGATT
189 ATC-CTGTATTAGACAGAAGCAGATT
* * *
31898 GAAAAGA-GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTTGGCGTCT
1 ---AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGA-AACAGATTTGGCATCT
** *
31962 CTGTATTAGACGGGAGCAGATC-AA-AGATAGCAGAT
62 CCATATTAGACGGGAGCAGATCGAAGACATAGCAGAT
31997 ATCGCCTTCC
Statistics
Matches: 448, Mismatches: 34, Indels: 71
0.81 0.06 0.13
Matches are distributed among these distances:
201 38 0.08
202 61 0.14
203 14 0.03
204 1 0.00
206 2 0.00
207 31 0.07
208 26 0.06
211 1 0.00
212 17 0.04
213 3 0.01
214 6 0.01
215 15 0.03
216 29 0.06
217 3 0.01
218 50 0.11
219 117 0.26
220 34 0.08
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (213 bp):
AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGAAACAGATTTGGCATCTCCAT
ATTAGACGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATGTTTTACATCGAAGCAGATCC
AAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGATAACAGATTTGGCATCCTGT
ATTAGACAGAAGCAGATT
Found at i:32365 original size:19 final size:19
Alignment explanation
Indices: 32341--32414 Score: 141
Period size: 19 Copynumber: 3.9 Consensus size: 19
32331 ATAATCTTCA
32341 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32360 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32379 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32397 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
32415 AGATATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.33
19 36 0.67
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:32388 original size:37 final size:38
Alignment explanation
Indices: 32341--32421 Score: 141
Period size: 37 Copynumber: 2.2 Consensus size: 38
32331 ATAATCTTCA
32341 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
32379 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
32415 A-GATATG
1 ATGATATG
32422 ATTTTGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
35 3 0.07
36 3 0.07
37 31 0.74
38 5 0.12
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (38 bp):
ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:32440 original size:22 final size:22
Alignment explanation
Indices: 32341--32437 Score: 97
Period size: 19 Copynumber: 4.8 Consensus size: 22
32331 ATAATCTTCA
32341 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32360 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32379 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32397 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
32419 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
32438 GATTTAATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
18 18 0.25
19 33 0.46
22 8 0.11
23 12 0.17
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:32728 original size:17 final size:17
Alignment explanation
Indices: 32704--32738 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
32694 TGTTTCCCTG
*
32704 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
32722 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
32739 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Done.