Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold351
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: 325634
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 3 of 3
Found at i:303311 original size:470 final size:470
Alignment explanation
Indices: 302431--303482 Score: 1748
Period size: 470 Copynumber: 2.2 Consensus size: 470
302421 GACGCCTTCT
* *
302431 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGATGCATTTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACGCCTTTCAAAG
* *
302496 CCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGTAAAACTCCTTTTAAAGCCCACACAAG
66 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAAACTCCTTTTAAAGCCCACACAAG
302561 TTGGTGGCGCTTCCTAGTCCTCAAAGAGCAGGACGCTCCCTCTTTTCGCCCTTTAGTCCTCAAAC
131 TTGGTGGCGCTTCCTAGTCCTCAAAGAGCAGGACGCTCCCTCTTTTCGCCCTTTAGTCCTCAAAC
* *
302626 AGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACG
196 AGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGAACG
302691 CCTTCGCCTTTCAAAGCCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAGGACGCCTT
261 CCTTCGCCTTTCAAAGCCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAGGACGCCTT
* *
302756 TCAAATCCCACACAAGTTGGTGGCACTATTCAGTCTTCAAAGAGCAGGACTCCTTTTAAAGCCCA
326 TCAAAGCCCACACAAGTTGGTGGCACTATTCAGTCCTCAAAGAGCAGGACTCCTTTTAAAGCCCA
*
302821 CACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCTCCCTTTAGTCC
391 CACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTTAGTCC
302886 TCAAAGAGCAGGACG
456 TCAAAGAGCAGGACG
* *
302901 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAATAGCAGGACACCTTTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACGCCTTTCAAAG
* *
302966 CACACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACTCCTTTTAAAGCCCACACAAG
66 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAAACTCCTTTTAAAGCCCACACAAG
* *
303031 TTGGTGGCGCTTCCTAGTCCTCAAAGAGCAGGACGCT-CCTTTCTTTCGCCCTTTATTCCTCAAA
131 TTGGTGGCGCTTCCTAGTCCTCAAAGAGCAGGACGCTCCCTCT-TTTCGCCCTTTAGTCCTCAAA
* *
303095 GAGCAGGACGCCTTTTAAAGTCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGAAC
195 CAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGAAC
* * * *
303160 GCCTTCGCCTTTCAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGATGCCT
260 GCCTTCGCCTTTCAAAGCCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAGGACGCCT
303225 TTCAAAGCCCACACAAGTTGGTGGCACCT-TTCAGTCCTCAAAGAGCAGGACTCCTTTTAAAGCC
325 TTCAAAGCCCACACAAGTTGGTGGCA-CTATTCAGTCCTCAAAGAGCAGGACTCCTTTTAAAGCC
*
303289 CACACAAGTTGGTGGTACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTTAGT
389 CACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTTAGT
303354 CCTCAAAGAGCAGGACG
454 CCTCAAAGAGCAGGACG
* * ** * *
303371 CCTTTTAAAGCCCACACAAGTCGGTGGCATTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTGCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCTTCAAAGAGCAGGA---C---GCCT
*
303436 TTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCA
59 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCA
303483 GGACGCTCTC
Statistics
Matches: 541, Mismatches: 32, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
469 4 0.01
470 471 0.87
471 17 0.03
474 1 0.00
477 48 0.09
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (470 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACGCCTTTCAAAG
CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAAACTCCTTTTAAAGCCCACACAAG
TTGGTGGCGCTTCCTAGTCCTCAAAGAGCAGGACGCTCCCTCTTTTCGCCCTTTAGTCCTCAAAC
AGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGAACG
CCTTCGCCTTTCAAAGCCCACACAAGTTGATGGCACCTTTCAGTCTTCAAAAAGCAGGACGCCTT
TCAAAGCCCACACAAGTTGGTGGCACTATTCAGTCCTCAAAGAGCAGGACTCCTTTTAAAGCCCA
CACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCCTTTAGTCC
TCAAAGAGCAGGACG
Found at i:303330 original size:55 final size:56
Alignment explanation
Indices: 303087--303330 Score: 307
Period size: 55 Copynumber: 4.3 Consensus size: 56
303077 CGCCCTTTAT
* * *
303087 TCCTCAAAGAGCAGGAC-GCCTTTTAAAGTCCACACAAGTTGGTGGCACTTTTCTAG
1 TCCTCAAAGAGCAGGACTGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AG
* * *
303143 TCCTCAAAAAGCAGAACGCCTTCGCCTTTCAAAGCCTACACAAGTTGGTGGCACCTTTCAG
1 TCCTCAAAGAGCAG---GAC-T-GCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAG
*
303204 TCTTCAAAGAGCAGGA-TGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAG
1 TCCTCAAAGAGCAGGACTGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAG
* * *
303259 TCCTCAAAGAGCAGGACT-CCTTTTAAAGCCCACACAAGTTGGTGGTA-CTTCCTAG
1 TCCTCAAAGAGCAGGACTGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AG
303314 TCCTCAAAGAGCAGGAC
1 TCCTCAAAGAGCAGGAC
303331 GCTCTCTCCT
Statistics
Matches: 166, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
54 4 0.02
55 98 0.59
56 15 0.09
58 1 0.01
59 2 0.01
61 14 0.08
62 32 0.19
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (56 bp):
TCCTCAAAGAGCAGGACTGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAG
Found at i:303481 original size:156 final size:152
Alignment explanation
Indices: 303196--303637 Score: 653
Period size: 156 Copynumber: 2.9 Consensus size: 152
303186 GTTGGTGGCA
* *
303196 CCTTTCAGTCTTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTC
* * *
303261 CTCAAAGAGCAGGA---C--TCCTTTTAAAGCCCACACAAGTTGGTGGTACTTCCTAGTCCTCAA
64 CTCAAAGAGTAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT-TTAGTCCTCAA
*
303321 AGAGCAGGACGCTCTCTCCTTTCGC
128 AGAGCAGGACGCTCTCTCCTTTCAC
* * *
303346 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTCGGTGGCATTTTTCTAGTC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTC-AGTC
*
303411 CTCAAAGAGTAGGACGCCTTTGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCA
64 CTCAAAGAGTAGGACGCCTTT-CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCTCA
303476 AAGAGCAGGACGCTCTCTCCTTTCAC
127 AAGAGCAGGACGCTCTCTCCTTTCAC
*
303502 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGAG-GGCACCTTCAGTCC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTG-GTGGCACTTTCAGTCC
303566 TCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAA
65 TCAAAGAGTAGGACGCCTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-AGTCCTCAA
303631 AGAGCAG
128 AGAGCAG
303638 AATGCTTTCT
Statistics
Matches: 265, Mismatches: 16, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
149 49 0.18
150 22 0.08
153 6 0.02
154 68 0.26
155 5 0.02
156 111 0.42
157 4 0.02
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (152 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCT
CAAAGAGTAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGA
GCAGGACGCTCTCTCCTTTCAC
Found at i:303499 original size:61 final size:60
Alignment explanation
Indices: 303348--303500 Score: 199
Period size: 61 Copynumber: 2.6 Consensus size: 60
303338 CCTTTCGCCC
**
303348 TTTAGTCCTCAAAGAGCAGGACG-C-CT--TTT-AAAGCCCACACAAGTCGGTGGCATTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTCTCCTTTCAAAGCCCACACAAGTCGGTGGCACCT
* * *
303403 TTCTAGTCCTCAAAGAGTAGGACGCCTTTGCCTTTCAAAGCCCACACAAGTTGGTGGCACCT
1 TT-TAGTCCTCAAAGAGCAGGACGCCTCT-CCTTTCAAAGCCCACACAAGTCGGTGGCACCT
303465 TTTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCA
1 TTTAGTCCTCAAAGAGCAGGACGC-CTCTCCTTTCA
303501 CCCTTTAGTC
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
55 2 0.02
56 20 0.24
57 1 0.01
58 1 0.01
61 31 0.37
62 28 0.34
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (60 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTCTCCTTTCAAAGCCCACACAAGTCGGTGGCACCT
Found at i:303662 original size:61 final size:61
Alignment explanation
Indices: 303507--303762 Score: 266
Period size: 61 Copynumber: 4.3 Consensus size: 61
303497 TTCACCCTTT
*
303507 AGTCCTCAAAGAGCAGGACG-C---C--TTTCAAAGCCCACACAAGTTGAG-GGCAC-CTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTTCAAAGCCCACACAAGTTG-GTGGCACTTTTC
* *
303561 AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * * *
303622 AGTCCTCAAAGAGCAGAATG-CTTTCTTTTTGCAAATCCCACACTAGTTGGTGGCA-TCTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTT-CAAAGCCCACACAAGTTGGTGGCACT-TTTC
** * *
303683 AGTCCTTGAAGAGCAGGACGCCTTT-TCTTTTCAAAGACCACACGAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCT-TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
*
303744 AGTCCTCAAAGAGCGGGAC
1 AGTCCTCAAAGAGCAGGAC
303763 ACACTTCTTT
Statistics
Matches: 167, Mismatches: 20, Indels: 23
0.80 0.10 0.11
Matches are distributed among these distances:
54 19 0.11
55 1 0.01
59 8 0.05
60 26 0.16
61 104 0.62
62 9 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:303724 original size:122 final size:121
Alignment explanation
Indices: 303532--303757 Score: 330
Period size: 122 Copynumber: 1.9 Consensus size: 121
303522 GGACGCCTTT
*
303532 CAAAGCCCACACAAGTTGAGGGCACCTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAG
1 CAAAGCCCACACAAGTTGAGGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAG
*
303597 CCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGAATGCTTTCTTTTTG
66 ACCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGAATGCTTTCTTTTTG
* * * ** *
303653 CAAATCCCACACTAGTTG-GTGGCATCTTCCAGTCCTTGAAGAGCAGGACGCCTT-TTCTTTTCA
1 CAAAGCCCACACAAGTTGAG-GGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT-A
*
303716 AAGACCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGC
63 AAGACCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGC
303758 GGGACACACT
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
120 1 0.01
121 29 0.31
122 63 0.68
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (121 bp):
CAAAGCCCACACAAGTTGAGGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAG
ACCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGAATGCTTTCTTTTTG
Found at i:303994 original size:40 final size:41
Alignment explanation
Indices: 303894--303997 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 41
303884 ACGAGACGTA
* *
303894 CTCTTTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTT
1 CTCTTTTT--CTTTGTCCTCAAGAAGCAGAACACTTTCCTATT
* * *
303937 CTTCTTTTCCTTTGTCCTCAAGGAGCAGAAC-CTATTTC-ATT
1 C-TCTTTTTCTTTGTCCTCAAGAAGCAGAACACT-TTCCTATT
303978 CTCTTTTTCTTTGTCCTCAA
1 CTCTTTTTCTTTGTCCTCAA
303998 AAAATGTGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 18 0.34
41 5 0.09
42 23 0.43
43 1 0.02
44 6 0.11
ACGTcount: A:0.17, C:0.28, G:0.11, T:0.44
Consensus pattern (41 bp):
CTCTTTTTCTTTGTCCTCAAGAAGCAGAACACTTTCCTATT
Found at i:304445 original size:12 final size:13
Alignment explanation
Indices: 304428--304456 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
304418 GTAAAAATCA
304428 AAAATTAAAATT-
1 AAAATTAAAATTC
304440 AAAATTAAAATTC
1 AAAATTAAAATTC
304453 AAAA
1 AAAA
304457 AAATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATTC
Found at i:304505 original size:35 final size:35
Alignment explanation
Indices: 304466--304735 Score: 477
Period size: 35 Copynumber: 7.7 Consensus size: 35
304456 AAAATAAATA
304466 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
* *
304501 ATAAAAATAAAGGCGTGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
304536 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
304571 ATAAAAATGAAGGCGTGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
304606 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
304641 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
304676 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
304711 ATAAAAATGAAGGCATGGAATGATG
1 ATAAAAATGAAGGCATGGAATGATG
304736 CGGATAAAAA
Statistics
Matches: 225, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 225 1.00
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20
Consensus pattern (35 bp):
ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
Found at i:306245 original size:79 final size:79
Alignment explanation
Indices: 306114--306861 Score: 1120
Period size: 79 Copynumber: 9.4 Consensus size: 79
306104 TTTAATTTTC
*
306114 TCAATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
306179 TTATTTCTAAAACA
66 TTATTTCTAAAACA
306193 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
306258 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* * *
306272 TCAATTTTTCATAATCGGGGATACTCCAACCCCTTTATTTTCGAAGGGATACTCTAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
306337 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * * *
306351 TTAATTTCTCATAATCTGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
306416 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* * *
306430 TCAATTTTTCATAATCGGAGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
306495 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* * *
306509 TCAATTTTTCATAATTGGGGATATTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
306574 TTATTTCTAAAACA
66 TTATTTCTAAAACA
*
306588 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
306653 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * *
306667 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAGCTCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
* *
306732 TTAATTCCAAAACA
66 TTATTTCTAAAACA
* * * * * *
306746 CCAATTTCTCACAATTGGGGATACTCCAACCCGGTTATTTTC-ATGGAGATACTCCAACCCCGGC
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGA-GGGGATACTCCAACCCCGG-
** *
306810 CCTTATTTCTAAAGCA
64 TTTTATTTCTAAAACA
* * * *
306826 TCAATTTTTTTTACAATCAGGGATACTCTAACCCCG
1 TCAA--TTTTTCATAATCGGGGATACTCCAACCCCG
306862 ATTTTATTTT
Statistics
Matches: 604, Mismatches: 61, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
78 1 0.00
79 565 0.94
80 14 0.02
82 24 0.04
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACA
Found at i:310932 original size:21 final size:22
Alignment explanation
Indices: 310918--310957 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
310908 CTTCAAATTT
310918 TTTATTTTTCACTTCAAAATAC
1 TTTATTTTTCACTTCAAAATAC
310940 TTTATTTTTCA--TCAAAAT
1 TTTATTTTTCACTTCAAAAT
310958 CATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATTTTTCACTTCAAAATAC
Found at i:312676 original size:23 final size:23
Alignment explanation
Indices: 312650--312725 Score: 109
Period size: 23 Copynumber: 3.2 Consensus size: 23
312640 ATATTGTTTT
312650 GAAAATAAATTTTTATCAAGGGA
1 GAAAATAAATTTTTATCAAGGGA
312673 GAAAATAAATTTTTATCAA-GGA
1 GAAAATAAATTTTTATCAAGGGA
*
312695 GGAAAATAAATTTTTATTAAGGAGGA
1 -GAAAATAAATTTTTATCAA-G-GGA
312721 GAAAA
1 GAAAA
312726 ACGAAACTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
22 3 0.06
23 37 0.77
25 5 0.10
26 3 0.06
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (23 bp):
GAAAATAAATTTTTATCAAGGGA
Found at i:313282 original size:13 final size:13
Alignment explanation
Indices: 313264--313290 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
313254 ACATTATGCT
313264 TTGTATCGATACA
1 TTGTATCGATACA
313277 TTGTATCGATACA
1 TTGTATCGATACA
313290 T
1 T
313291 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:313320 original size:20 final size:19
Alignment explanation
Indices: 313273--313330 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
313263 TTTGTATCGA
313273 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
*
313292 TTCATTGTATCGATACATAG
1 TACATTGTATCGATACAT-G
313312 -ACAATTGTATCGATACATG
1 TAC-ATTGTATCGATACATG
313331 AAACTGGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
TACATTGTATCGATACATG
Found at i:317514 original size:2 final size:2
Alignment explanation
Indices: 317495--317606 Score: 72
Period size: 2 Copynumber: 57.5 Consensus size: 2
317485 TTAGTAATTG
* * *
317495 TA TA TA TG TT TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
317537 TA T- TA CA TA GA TT TA TG TA TA TA TA TA -A CA TA TA T- TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* **
317577 -A CA TA TA T- TA GTA GC TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T
317607 CTATGAGCGT
Statistics
Matches: 84, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
1 5 0.06
2 76 0.90
3 3 0.04
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:317724 original size:31 final size:31
Alignment explanation
Indices: 317669--317751 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
317659 TGTATATATT
* * * *
317669 AAATTGCAACAAAAGTAAAGTGCATAAATT-T
1 AAATTACAA-AAAAATAAATTGCATAAATTAA
*
317700 AAATTACGAAAAAAATAAATTGCATATATTAA
1 AAATTAC-AAAAAAATAAATTGCATAAATTAA
*
317732 AAATTACAAGAAAATAAATT
1 AAATTACAAAAAAATAAATT
317752 AACTGCATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
31 35 0.80
32 9 0.20
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (31 bp):
AAATTACAAAAAAATAAATTGCATAAATTAA
Found at i:318839 original size:2 final size:2
Alignment explanation
Indices: 318834--318861 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
318824 AAAAGTGATA
318834 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
318862 TCATGGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321688 original size:16 final size:16
Alignment explanation
Indices: 321667--321707 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
321657 TAAATTTGTC
321667 AAAAAAATAAAAAAGA
1 AAAAAAATAAAAAAGA
* * *
321683 AAAAAAAGAAGAAATA
1 AAAAAAATAAAAAAGA
321699 AAAAAAATA
1 AAAAAAATA
321708 TGTAAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (16 bp):
AAAAAAATAAAAAAGA
Found at i:323181 original size:13 final size:13
Alignment explanation
Indices: 323163--323187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
323153 CATAAAGTAT
323163 TGTATCGATACAA
1 TGTATCGATACAA
323176 TGTATCGATACA
1 TGTATCGATACA
323188 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:323185 original size:33 final size:33
Alignment explanation
Indices: 323143--323209 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
323133 TTCAACGATT
323143 TGTATCGATACATAAAGTATTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
*** *
323176 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
323209 T
1 T
323210 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTATTGTATCGATACAA
Found at i:323268 original size:13 final size:13
Alignment explanation
Indices: 323250--323274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
323240 ATCACTTAAA
323250 TGTATCGATACAT
1 TGTATCGATACAT
323263 TGTATCGATACA
1 TGTATCGATACA
323275 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.