Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1263
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: 23635
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Found at i:1233 original size:125 final size:124
Alignment explanation
Indices: 1011--1252 Score: 325
Period size: 125 Copynumber: 1.9 Consensus size: 124
1001 CTGAAAGGTG
*
1011 CCAACCACTTGTGTGGGCTTTGAGACGGTGGGTTGCTCTTGAGGGACTGGAGGATCGGCGCCACC
1 CCAACCACTTGTGTGGGCTTTGAGACGGGGGGTTGCTCTTGAGGGACTGGA-GA-CGGCGCCACC
1076 AACTTGTGTGGGCTTTCTTTAAGAGGTGGTCCTGCTCTTTGAGGACTGGAAAGGCGTGCCA
64 AACTTGTGTGGGCTTTCTTTAAGAGGTGGTCCTGCTCTTTGAGGACTGGAAAGGCGTGCCA
*
1137 CCAA-CACTTGTGTTGGGCTTTGAGAGGGGGGTGTCCTGCTCTTTGA-GGACTGGA-A-GGCGCC
1 CCAACCACTTGTG-TGGGCTTTGAGACGGGGG-GT--TGCTC-TTGAGGGACTGGAGACGGCGCC
* *
1198 ACCAACTTG-GTTGGCTTTCTTTTTAAGAGGT-GTCCTGCTCTTTGCGGACTGGAAA
61 ACCAACTTGTGTGGGCTTTC--TTTAAGAGGTGGTCCTGCTCTTTGAGGACTGGAAA
1253 ATGCACCACT
Statistics
Matches: 105, Mismatches: 4, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
124 9 0.09
125 46 0.44
126 30 0.29
127 3 0.03
129 13 0.12
130 4 0.04
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (124 bp):
CCAACCACTTGTGTGGGCTTTGAGACGGGGGGTTGCTCTTGAGGGACTGGAGACGGCGCCACCAA
CTTGTGTGGGCTTTCTTTAAGAGGTGGTCCTGCTCTTTGAGGACTGGAAAGGCGTGCCA
Found at i:1239 original size:60 final size:60
Alignment explanation
Indices: 1067--1392 Score: 211
Period size: 60 Copynumber: 5.4 Consensus size: 60
1057 CTGGAGGATC
*
1067 GGCGCCACCAACTTGTGTGGGCTTTC-TTTAAGAGGTGGTCCTGCTCTTTGAGGACTGGAAA
1 GGCGCCACCAACTTGTGTTGGCTTTCTTTTAAGAGGT-GTCCTGCTCTTTGAGGACTGG-AA
* * *
1128 GGCGTGCCACCAACACTTGTGTTGG---GCTTTGAGAGGGGGGTGTCCTGCTCTTTGAGGACTGG
1 GGC--GCCACC-A-ACTTGTGTTGGCTTTCTTTTA-A--GAGGTGTCCTGCTCTTTGAGGACTGG
1190 AA
59 AA
*
1192 GGCGCCACCAACTTG-GTTGGCTTTCTTTTTAAGAGGTGTCCTGCTCTTTGCGGACTGGAA
1 GGCGCCACCAACTTGTGTTGGCTTTC-TTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAA
*** * * * *
1252 AATG-CACC-ACTTGTG-TGG---TC-TTGAAAAGGTTGTCCTGCTCTTCG-GGACTGAAA
1 GGCGCCACCAACTTGTGTTGGCTTTCTTTTAAGAGG-TGTCCTGCTCTTTGAGGACTGGAA
* * *
1305 GGGCTTGCCACCAACTTGT-TGTGG---GC-TTGAGGAGGTGTCCTGCTCTTTTGAGGACTGGAA
1 -GGC--GCCACCAACTTGTGT-TGGCTTTCTTTTAAGAGGTGTCCTGCTC-TTTGAGGACTGGAA
*
1365 GGCTGCCACCAACTGTGTGATGGGCTTT
1 GGC-GCCACCAACT-TGTG-TTGGCTTT
1393 TCAGAGACGG
Statistics
Matches: 211, Mismatches: 25, Indels: 56
0.72 0.09 0.19
Matches are distributed among these distances:
53 15 0.07
54 13 0.06
55 2 0.01
56 1 0.00
57 4 0.02
58 35 0.17
59 30 0.14
60 42 0.20
61 5 0.02
62 9 0.04
63 13 0.06
64 7 0.03
65 31 0.15
66 4 0.02
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (60 bp):
GGCGCCACCAACTTGTGTTGGCTTTCTTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAA
Found at i:1737 original size:312 final size:294
Alignment explanation
Indices: 1070--1737 Score: 613
Period size: 312 Copynumber: 2.2 Consensus size: 294
1060 GAGGATCGGC
* *
1070 GCCACCAACTTGTGTGGGCTTTCTTTAAGAGGTGGTCCTGCTCTTTGAGGACTGGAAAGGCGTGC
1 GCCACCAATTTG-GTGGGCTTTCTTT-AGACGT-GTCCTGCTCTTTGAGGACTGGAAAGGCGTGC
** * * *
1135 CACCAACACTTGTGTTGGGCTTTGAGAGGGGGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCAC
63 CACCAACACTTGTGGGGGGCTTTGAGAGGGCGCTCTCCTGCTCTTTGAGGACTGGAAGGCGCCAC
* * * *
1200 CAACTTGGTTGGCTTTCTTTTTAAGAGGTGTCCTGCTCTTTGCGGACTGGAAAATGCACCACTTG
128 AAACTTGGTGGGCTTTCTTTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATCCACCACTTG
* **
1265 TGTGGTCTTGAAAAGGTTGTCCTGCTCTTCGGGACTGAAAGGGCTTGCCACCAACTTGTTGTGGG
193 TGTGGGCTTGAAAAGG-TGTCCTGCTCTTCGGGACTGAAAGAACTTGCCACCAACTTGTTGTGGG
* *
1330 CTTGAGGAGGTGTCCTGCTCTTTTGAGGACTGGAAGGCT
257 CTTGAAGAGGTGTCCTGC-CTTTTGAGGACTGAAAGGCT
* ** *
1369 GCCACCAACTGTGTGATGGGCTTT-TCAGAGACGGTTGTCCTGCT-TTTGAGGAGGACTGGACAG
1 GCCACCAA-T-T-TGGTGGGCTTTCT-TTAGAC-G-TGTCCTGCTCTTT---GAGGACTGGAAAG
** *
1432 GTTTTGCCCCCAAC-C-TGTGGGGGGCTTTGAGAGGTGTCCGCTCTCCCT-CTTCTTTGAGGACT
57 G-CGTGCCACCAACACTTGTGGGGGGCTTTGAGAGG-G--CGCTCT-CCTGC-TCTTTGAGGACT
*
1494 GGAAGGCGCCCCACAAAACTTGTGTGGGGCTTCTTTTTTTAAGAGGTGTCCTGCTCTTTGAGGAC
116 GGAAGGCG--CCAC-AAACTTG-GT-GGGCTT-TCTTTTTAAGAGGTGTCCTGCTCTTTGAGGAC
*
1559 -GGAAAATTCCACCCCAAC-TGTGTGGGCTTTG-AAAGG-GTCCTGCTCTTTGAGGACTGGAAA-
175 TGGAAAA-TCCA--CC-ACTTGTGTGGGC-TTGAAAAGGTGTCCTGCTCTTCG-GGACT-GAAAG
* * *
1619 AAC-TGCCACCAACTTGTGTGTGGTGTGGTGCTTTAAGCGGTTTTCCTG-CTTTTGAGGGACTGA
233 AACTTGCCACCAAC---T-TGT--TGTGG-GCTTGAAGAGG-TGTCCTGCCTTTTGA-GGACTGA
*
1682 AAGGTT
289 AAGGCT
1688 GCCACCAATTTGGTGGGCTTTCTTTAGACGTGTCCTGCTCTTTGAGGACT
1 GCCACCAATTTGGTGGGCTTTCTTTAGACGTGTCCTGCTCTTTGAGGACT
1738 CTAAAAGCGG
Statistics
Matches: 298, Mismatches: 32, Indels: 65
0.75 0.08 0.16
Matches are distributed among these distances:
299 8 0.03
300 7 0.02
301 18 0.06
302 20 0.07
303 15 0.05
304 9 0.03
305 4 0.01
306 23 0.08
308 4 0.01
309 6 0.02
310 2 0.01
311 11 0.04
312 62 0.21
313 6 0.02
314 28 0.09
315 10 0.03
316 17 0.06
317 2 0.01
318 13 0.04
319 27 0.09
320 6 0.02
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.31
Consensus pattern (294 bp):
GCCACCAATTTGGTGGGCTTTCTTTAGACGTGTCCTGCTCTTTGAGGACTGGAAAGGCGTGCCAC
CAACACTTGTGGGGGGCTTTGAGAGGGCGCTCTCCTGCTCTTTGAGGACTGGAAGGCGCCACAAA
CTTGGTGGGCTTTCTTTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATCCACCACTTGTGT
GGGCTTGAAAAGGTGTCCTGCTCTTCGGGACTGAAAGAACTTGCCACCAACTTGTTGTGGGCTTG
AAGAGGTGTCCTGCCTTTTGAGGACTGAAAGGCT
Found at i:2764 original size:19 final size:21
Alignment explanation
Indices: 2743--2786 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
2733 TTTGTTTTGT
2743 TTTTTTTTTTTTTTT-C-CTT
1 TTTTTTTTTTTTTTTGCTCTT
2762 TTTTTTTTTTTTTTTGCTCTT
1 TTTTTTTTTTTTTTTGCTCTT
2783 TTTT
1 TTTT
2787 GAAGAGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.65
20 1 0.04
21 7 0.30
ACGTcount: A:0.00, C:0.09, G:0.02, T:0.89
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTGCTCTT
Found at i:2786 original size:1 final size:1
Alignment explanation
Indices: 2727--2776 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
2717 TCTTTCTCTC
* * * **
2727 TTTTTCTTTGTTTTGTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2777 GCTCTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.06, G:0.04, T:0.90
Consensus pattern (1 bp):
T
Found at i:15222 original size:28 final size:27
Alignment explanation
Indices: 15183--15264 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 27
15173 TAATGTTTTG
*
15183 GAGATAATAACGAGGTTGGAGTGTTCCCT
1 GAGA-AATAACGAGGTTGGAGT-ATCCCT
* *
15212 CG-GAAGTAACGGGGTTGGAGTATCCCT
1 -GAGAAATAACGAGGTTGGAGTATCCCT
15239 GATGAAATAACGAGGTTGGAGTATCC
1 GA-GAAATAACGAGGTTGGAGTATCC
15265 TCGATTGTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 36 0.80
29 2 0.04
30 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (27 bp):
GAGAAATAACGAGGTTGGAGTATCCCT
Found at i:15412 original size:51 final size:51
Alignment explanation
Indices: 15252--15422 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
15242 GAAATAACGA
* * *
15252 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
15304 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
15357 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
15408 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
15423 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:15468 original size:27 final size:28
Alignment explanation
Indices: 15405--15480 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
15395 AAAATAAAGT
*
15405 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
15433 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
15460 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
15481 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:17808 original size:21 final size:21
Alignment explanation
Indices: 17782--17859 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
17772 GTTGGGACCC
17782 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
17803 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
17823 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
17844 TGTATCGATACATTTG
1 TGTATCGATACATTTG
17860 GAAATTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:17846 original size:41 final size:41
Alignment explanation
Indices: 17782--17859 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
17772 GTTGGGACCC
* *
17782 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTGTGAA
17823 TGTATCGATACA-TTCTACAAATGTATCGATACATTTG
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTG
17860 GAAATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (41 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGTGAA
Found at i:18670 original size:55 final size:55
Alignment explanation
Indices: 18575--19535 Score: 1332
Period size: 55 Copynumber: 17.3 Consensus size: 55
18565 ATAAAGTGTA
* * * * * * *
18575 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
18630 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
18685 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTGAAA-ATAAAAAG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGT-----G
** * *
18744 CATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 --TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
18801 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
18856 TCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
18911 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
18966 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
19022 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
19077 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
19132 TCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * *
19187 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTCAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
19242 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
19298 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
19353 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
19408 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
19463 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGACGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
19518 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
19536 AAAAAGCGGA
Statistics
Matches: 824, Mismatches: 57, Indels: 50
0.89 0.06 0.05
Matches are distributed among these distances:
54 20 0.02
55 637 0.77
56 118 0.14
57 2 0.00
59 1 0.00
61 45 0.05
62 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:18709 original size:26 final size:26
Alignment explanation
Indices: 18621--18710 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
18611 GTGTGGGCTT
* *
18621 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
18647 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
18674 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
18702 TGAAAGGTG
1 TGAAAGGTG
18711 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:19116 original size:276 final size:276
Alignment explanation
Indices: 18598--19535 Score: 1567
Period size: 276 Copynumber: 3.4 Consensus size: 276
18588 GGAGTAAAAA
* * * *
18598 GTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAA
1 GTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGCGCCACCAA
* *
18663 CTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTAG
66 CTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGG
** * *** *
18727 GCTTTGA-AAATAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCT
131 GCTTTGAGAGGT-----G--TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCT
* *
18791 TTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
189 TTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
18856 TCCTGCTCTTCGGGGACTGAAAG
254 TCCTGCTCTTCGGGGACTGAAAG
*
18879 GTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAA
1 GTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGCGCCACCAA
18944 CTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGG
66 CTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGG
19009 GCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAG
131 GCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAG
19074 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCT
196 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCT
19139 CTTCGGGGACTGAAAG
261 CTTCGGGGACTGAAAG
*
19155 GTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAA
1 GTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGCGCCACCAA
*
19220 CTTGTGTGGGCTTTCAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGG
66 CTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGG
19285 GCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAG
131 GCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAG
19350 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCT
196 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCT
* *
19415 CTTTGAGGACTGGAAA-
261 CTTCGGGGACT-GAAAG
* * *
19431 ATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAA
1 GTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGCGCCACCAA
*
19496 CTTGTGTGGGCTTTAAGACGTGTCCTGCTCTTTGAGGACT
66 CTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
19536 AAAAAGCGGA
Statistics
Matches: 629, Mismatches: 25, Indels: 11
0.95 0.04 0.02
Matches are distributed among these distances:
276 493 0.78
277 4 0.01
278 1 0.00
281 99 0.16
282 30 0.05
283 2 0.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (276 bp):
GTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGCGCCACCAA
CTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGG
GCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAG
GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCT
CTTCGGGGACTGAAAG
Found at i:20883 original size:303 final size:304
Alignment explanation
Indices: 20300--20913 Score: 1212
Period size: 303 Copynumber: 2.0 Consensus size: 304
20290 TTGATGAAGA
20300 AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
1 AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
20365 TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
66 TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
20430 GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
131 GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
20495 TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
196 TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
20560 TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
261 TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
20604 AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
1 AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
20669 TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
66 TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
20734 GTTTGATAA-CAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
131 GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
*
20798 TTCAGCTCCATTCCCTTACAAGGACAACAAAATCGTTCCTTGGAACTATGAAAACAAAACCTAGA
196 TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
20863 TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
261 TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
20907 AAGGTAG
1 AAGGTAG
20914 GTCACCTAAC
Statistics
Matches: 309, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
303 170 0.55
304 139 0.45
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (304 bp):
AAGGTAGTATTGAGTTTTATGATAAAAAGAAAATCACAGCTGTCTAGCCTATGGACTCACTACCA
TCAATCAATGCCACAGAGGGTGGTGACGATACTCTTCCTTACAGTGTTGGAAGGCCACTTATTTT
GTTTGATAACCAACCACAAGCTTAAGTGGCTCCTATTCAGATTGTGCCGAGTTGATTATCCAATC
TTCAGCTCCATTCCCTTACAAGGACAACAAAACCGTTCCTTGGAACTATGAAAACAAAACCTAGA
TTATTAGAGAACCATATCAGCAAACCGATAATGTTGACCTTTCT
Done.