Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: LOC111287627
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: 4150
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Found at i:1744 original size:66 final size:67
Alignment explanation
Indices: 1633--1764 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 67
1623 AGAAAGAGCA
* * * * * *
1633 AGAACTGGAGAATACAGTGAAGGAAAACGCATCTGGGGCAGATGATTTTGCTTGTATGGATTACC
1 AGAACTGGAGAATACACTCAAGGAAAACGCACCTGGGACAGATGATTTTACTTGGATGGATTACC
1698 TC
66 TC
* * *
1700 AGAA-TGGAGAATACACTCCAGGAAAATGCCCCTGGGACAGATGATTTTACTTGGATGGATTACC
1 AGAACTGGAGAATACACTCAAGGAAAACGCACCTGGGACAGATGATTTTACTTGGATGGATTACC
1764 T
66 T
1765 TCAACCAGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 52 0.93
67 4 0.07
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.25
Consensus pattern (67 bp):
AGAACTGGAGAATACACTCAAGGAAAACGCACCTGGGACAGATGATTTTACTTGGATGGATTACC
TC
Found at i:1968 original size:246 final size:245
Alignment explanation
Indices: 1534--2436 Score: 1409
Period size: 246 Copynumber: 3.7 Consensus size: 245
1524 CTTCTAGTGA
*
1534 TTATTC-ACTATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGTTCTGCTTCACAG
1 TTATTCAAC-ATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGTTCTGCTTCACTG
* * *
1598 AATCTCTTAGATATTGCGGAGTCTCAGAAA-GAGCAAG-AACTGGAGAATACAGTGAAGGAAAAC
65 AATCTCTTAGATATTGCAGAGTCTCA-AAATGAGCAAGTAA-TGGAGAATATAGTGAAGGAAAAT
* *
1661 GCATCTGGGGCAGATGATTTTGCTTGTATGGATTACCTCAGAATGGAGAATACACTCCAGGAAAA
128 GCATCT-GGGCAGATGATTTTGCTTGGATGGATTACCTCGGAATGGAGAATACACTCCAGGAAAA
*
1726 TGCCCCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCAT
192 TGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCAT
* *
1780 TTATTCAATATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAATT-TCGCTTCACTG
1 TTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGTTCT-GCTTCACTG
* * *
1844 AATCTCTCAGATGTCGCAGAGTCTCAAAATGAGCAAGTAATGGAGAATATAGTGAAGGAAAATGC
65 AATCTCTTAGATATTGCAGAGTCTCAAAATGAGCAAGTAATGGAGAATATAGTGAAGGAAAATGC
*
1909 ATCTGGGACAGATGATTTTGCTTGGATGGATTACCTCGGAATGGAGAATACAGTCCAGGAAAATG
130 ATCTGGG-CAGATGATTTTGCTTGGATGGATTACCTCGGAATGGAGAATACACTCCAGGAAAATG
* * *
1974 CCTCTGGGACTGATGATTTTACTTGGATGGATTACCTTCAACCAAGAACCAT
194 CCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCAT
* *
2026 TTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGTTCTGATTTACTGA
1 TTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGTTCTGCTTCACTGA
* *
2091 ATCTCTTAGATATTGCAGAGTCTCAGAACGAGCAAGTAATGGAGAATATAGTGAAGGAAAATGCA
66 ATCTCTTAGATATTGCAGAGTCTCAAAATGAGCAAGTAATGGAGAATATAGTGAAGGAAAATGCA
* * *
2156 CCTAGGGCAGATGATTTTGCTTGGATGGATTACCTAGGAATGGAGAATACACTCCAGGAAAATTC
131 TCT-GGGCAGATGATTTTGCTTGGATGGATTACCTCGGAATGGAGAATACACTCCAGGAAAATGC
* *
2221 CTCTGGAACAGATGATTTTACTTGGATGGATTGCCTTCAACCAGGAATCAT
195 CTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCAT
* * * *
2272 TTATTCAACATCAGGTGTTGTTGGCCCAAACACCAAGGCCACTGAAATCAGTTCTGCTTCACTGA
1 TTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGTTCTGCTTCACTGA
* * **
2337 ATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATATAGCAAAGGAAAATGCA
66 ATCTCTTAGATATTGCAGAGTCTCAAAATGAGCAAGTAATGGAGAATATAGTGAAGGAAAATGCA
2402 TCTGGGCCAGATGATTTTGCTTGGATGGATTACCT
131 TCTGGG-CAGATGATTTTGCTTGGATGGATTACCT
2437 TCAACCAGGA
Statistics
Matches: 604, Mismatches: 45, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
245 10 0.02
246 587 0.97
247 7 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (245 bp):
TTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGTTCTGCTTCACTGA
ATCTCTTAGATATTGCAGAGTCTCAAAATGAGCAAGTAATGGAGAATATAGTGAAGGAAAATGCA
TCTGGGCAGATGATTTTGCTTGGATGGATTACCTCGGAATGGAGAATACACTCCAGGAAAATGCC
TCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCAT
Found at i:1969 original size:66 final size:66
Alignment explanation
Indices: 1882--2010 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 66
1872 ATGAGCAAGT
* * *
1882 AATGGAGAATATAGTGAAGGAAAATGCATCTGGGACAGATGATTTTGCTTGGATGGATTACCTCG
1 AATGGAGAATACAGTCAAGGAAAATGCATCTGGGACAGATGATTTTACTTGGATGGATTACCTCG
1947 G
66 G
* * *
1948 AATGGAGAATACAGTCCAGGAAAATGCCTCTGGGACTGATGATTTTACTTGGATGGATTACCT
1 AATGGAGAATACAGTCAAGGAAAATGCATCTGGGACAGATGATTTTACTTGGATGGATTACCT
2011 TCAACCAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (66 bp):
AATGGAGAATACAGTCAAGGAAAATGCATCTGGGACAGATGATTTTACTTGGATGGATTACCTCG
G
Found at i:2495 original size:426 final size:424
Alignment explanation
Indices: 1948--3284 Score: 2011
Period size: 426 Copynumber: 3.1 Consensus size: 424
1938 ATTACCTCGG
* * * *
1948 AATGGAGAATACAGTC-CAGGAAAATGCCTCTGGGACTGATGATTTTACTTGGATGGATTACCTT
1 AATGGAGAATACAG-CGAAGGAAAATGCATCTGGGACAGATGATTTTGCTTGGATGGATTACCTT
2012 CAACCAAGAACCATTTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAG
65 CAACCAAGAACCATTTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAG
* * * *
2077 TTCTGATTTACTGAATCTCTTAGATATTGCAGAGTCTCAGAACGAGCAAGTAATGGAGAATATAG
130 TTCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATATAG
* * *
2142 TGAAGGAAAATGCACCTAGGGCAGATGATTTTGCTTGGATGGATTACCTAGGAATGGAGAATACA
195 TGAAGGAAAATGCATCTGGGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGG-GAATA-A
* * *
2207 CTCCAGGAAAATTCCTCTGGAACAGATGATTTTACTTGGATGGATTGCCTTCAACCAGGAATCAT
258 CTCCAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCAT
* * * *
2272 TTATTCAACATCAGGTGTTGTTGGCCCAAACACCAAGGCCACTGAAATCAGTTCTGCTTCACTGA
323 TTATTCAATATCAGGTGCTGTTGGCCCAAACACCGAGGCCAATGAAATCAGTTCTGCTTCACTGA
*
2337 ATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGT
388 ATCTCTTAGATGTTGCAGAGTCTCAAAATGAGCAAGT
* * *
2374 AATGGAGAATATAGCAAAGGAAAATGCATCTGGGCCAGATGATTTTGCTTGGATGGATTACCTTC
1 AATGGAGAATACAGCGAAGGAAAATGCATCTGGGACAGATGATTTTGCTTGGATGGATTACCTTC
* ** * * * *
2439 AACCAGGAGTCATTTATTCTACATCAGATGCTGTTGGCGCAAGCACCAAGGCCAATGAAATCAGT
66 AACCAAGAACCATTTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGT
* *
2504 TCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGC
131 TCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATATAGT
*
2569 GAAGGAAAATGCATCTGGGGCAGATGATTTTGCTTGGATGGATTGCCTTGGAATGGGGAATATAC
196 GAAGGAAAATGCATCTGGGGCAGATGATTTTGCTTGGATGGATTACCTTGGAAT-GGGAATA-AC
*
2634 TCCAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGCATTACCTTCAACCAGGAATCATT
259 TCCAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATT
* * * * *
2699 TATTCAATACCAGGTGCTGTT-GACCAAAGCACCGAGGCCAATGGAATCAGGTCAGCTTCACTGA
324 TATTCAATATCAGGTGCTGTTGGCCCAAA-CACCGAGGCCAATGAAATCAGTTCTGCTTCACTGA
* *
2763 ATCTCTTAGCTGTTGAAGAGTCTCAAAATGAGCAAGT
388 ATCTCTTAGATGTTGCAGAGTCTCAAAATGAGCAAGT
* *
2800 AATGAAGAATACAGTGAAGGAAAATGCATCTGGGACAGATGA-TTTGACTTGGATGGATTACCTT
1 AATGGAGAATACAGCGAAGGAAAATGCATCTGGGACAGATGATTTTG-CTTGGATGGATTACCTT
*
2864 CAACCAAGAACCATTTATTCAACATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAG
65 CAACCAAGAACCATTTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAG
* * * *
2929 TTCTGCTTCACTGAATCTCTTAGATGTCGCAGAGTCTCAGAATGAACAAGTAATGGTGAACATAG
130 TTCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATATAG
2994 TGAAGGAAAATGCATCTGGGGCAGATGATTTTGCTTGGATGGATTACCTTGGAAT-GGAA-AACT
195 TGAAGGAAAATGCATCTGGGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGGGAATAACT
* *
3057 CCAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTATCTTCTACCAGGAATCATTT
260 CCAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTT
* * ** * *
3122 ATTCAATATCAGGTGCTGTTGGCCTAAGCATTGAGACCAATGAAATTAGTTCTGCTTCACTGAAT
325 ATTCAATATCAGGTGCTGTTGGCCCAAACACCGAGGCCAATGAAATCAGTTCTGCTTCACTGAAT
* *
3187 CTCTTAGATGTCGCTGAGTCTCAAAATGAGCAAGT
390 CTCTTAGATGTTGCAGAGTCTCAAAATGAGCAAGT
* * * *
3222 AATGGAGAATATAGTGAAGGAAAATGCATCTGAGG-CAGATGGTTTTGCTAGGATGGATTACCT
1 AATGGAGAATACAGCGAAGGAAAATGCATCTG-GGACAGATGATTTTGCTTGGATGGATTACCT
3285 CAGAATGGAG
Statistics
Matches: 822, Mismatches: 82, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
422 196 0.24
423 11 0.01
424 4 0.00
425 11 0.01
426 598 0.73
427 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (424 bp):
AATGGAGAATACAGCGAAGGAAAATGCATCTGGGACAGATGATTTTGCTTGGATGGATTACCTTC
AACCAAGAACCATTTATTCAACATCAGGTGCTGTTGGCCCAAGCACCGAGGCCAATGAAATCAGT
TCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATATAGT
GAAGGAAAATGCATCTGGGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGGGAATAACTC
CAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTA
TTCAATATCAGGTGCTGTTGGCCCAAACACCGAGGCCAATGAAATCAGTTCTGCTTCACTGAATC
TCTTAGATGTTGCAGAGTCTCAAAATGAGCAAGT
Found at i:2500 original size:180 final size:180
Alignment explanation
Indices: 2194--2617 Score: 670
Period size: 180 Copynumber: 2.4 Consensus size: 180
2184 ATTACCTAGG
** * * * *
2194 AATGGAGAATACA-CTCCAGGAAAATTCCTCTGGAACAGATGATTTTACTTGGATGGATTGCCTT
1 AATGGAGAATACAGC-AAAGGAAAATGCATCTGGGACAGATGATTTTGCTTGGATGGATTGCCTT
* * *
2258 CAACCAGGAATCATTTATTCAACATCAGGTGTTGTTGGCCCAAACACCAAGGCCACTGAAATCAG
65 CAACCAGGAATCATTTATTCAACATCAGATGCTGTTGGCCCAAACACCAAGGCCAATGAAATCAG
2323 TTCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGT
130 TTCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGT
* * *
2374 AATGGAGAATATAGCAAAGGAAAATGCATCTGGGCCAGATGATTTTGCTTGGATGGATTACCTTC
1 AATGGAGAATACAGCAAAGGAAAATGCATCTGGGACAGATGATTTTGCTTGGATGGATTGCCTTC
* * * *
2439 AACCAGGAGTCATTTATTCTACATCAGATGCTGTTGGCGCAAGCACCAAGGCCAATGAAATCAGT
66 AACCAGGAATCATTTATTCAACATCAGATGCTGTTGGCCCAAACACCAAGGCCAATGAAATCAGT
2504 TCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGT
131 TCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGT
* *
2554 AATGGAGAATACAGCGAAGGAAAATGCATCTGGGGCAGATGATTTTGCTTGGATGGATTGCCTT
1 AATGGAGAATACAGCAAAGGAAAATGCATCTGGGACAGATGATTTTGCTTGGATGGATTGCCTT
2618 GGAATGGGGA
Statistics
Matches: 223, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
180 222 1.00
181 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (180 bp):
AATGGAGAATACAGCAAAGGAAAATGCATCTGGGACAGATGATTTTGCTTGGATGGATTGCCTTC
AACCAGGAATCATTTATTCAACATCAGATGCTGTTGGCCCAAACACCAAGGCCAATGAAATCAGT
TCTGCTTCACTGAATCTCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGT
Found at i:2821 original size:246 final size:246
Alignment explanation
Indices: 2391--2863 Score: 725
Period size: 246 Copynumber: 1.9 Consensus size: 246
2381 AATATAGCAA
* * * *
2391 AGGAAAATGCATCTGGGCCAGATGATTTTGCTTGGATGGATTACCTTCAACCAGGAGTCATTTAT
1 AGGAAAATGCATCTGGGACAGATGATTTTACTTGGATGCATTACCTTCAACCAGGAATCATTTAT
* * * * *
2456 TCTACATCAGATGCTGTTGGCGCAAGCACCAAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
66 TCAACACCAGATGCTGTTGACGCAAGCACCAAGGCCAATGAAATCAGGTCAGCTTCACTGAATCT
* * *
2521 CTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGCGAAGGAAAATGCATCTG
131 CTTAGATGTTGAAGAGTCTCAAAATGAGCAAGTAATGAAGAATACAGCGAAGGAAAATGCATCTG
* *
2586 GGGCAGATGATTTTG-CTTGGATGGATTGCCTTGGAATGGGGAATATACTCC
196 GGACAGATGA-TTTGACTTGGATGGATTACCTTGGAATGGGGAATATACTCC
*
2637 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGCATTACCTTCAACCAGGAATCATTTAT
1 AGGAAAATGCATCTGGGACAGATGATTTTACTTGGATGCATTACCTTCAACCAGGAATCATTTAT
* * * *
2702 TCAATACCAGGTGCTGTTGAC-CAAAGCACCGAGGCCAATGGAATCAGGTCAGCTTCACTGAATC
66 TCAACACCAGATGCTGTTGACGC-AAGCACCAAGGCCAATGAAATCAGGTCAGCTTCACTGAATC
* *
2766 TCTTAGCTGTTGAAGAGTCTCAAAATGAGCAAGTAATGAAGAATACAGTGAAGGAAAATGCATCT
130 TCTTAGATGTTGAAGAGTCTCAAAATGAGCAAGTAATGAAGAATACAGCGAAGGAAAATGCATCT
2831 GGGACAGATGATTTGACTTGGATGGATTACCTT
195 GGGACAGATGATTTGACTTGGATGGATTACCTT
2864 CAACCAAGAA
Statistics
Matches: 204, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
245 5 0.02
246 199 0.98
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (246 bp):
AGGAAAATGCATCTGGGACAGATGATTTTACTTGGATGCATTACCTTCAACCAGGAATCATTTAT
TCAACACCAGATGCTGTTGACGCAAGCACCAAGGCCAATGAAATCAGGTCAGCTTCACTGAATCT
CTTAGATGTTGAAGAGTCTCAAAATGAGCAAGTAATGAAGAATACAGCGAAGGAAAATGCATCTG
GGACAGATGATTTGACTTGGATGGATTACCTTGGAATGGGGAATATACTCC
Found at i:2939 original size:180 final size:180
Alignment explanation
Indices: 2637--3043 Score: 591
Period size: 180 Copynumber: 2.3 Consensus size: 180
2627 AATATACTCC
* * * * *
2637 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGCATTACCTTCAACCAGGAATCATTTAT
1 AGGAAAATGCATCTGGGACAGATGATTTGACTTGGATGGATTACCTTCAACCAAGAACCATTTAT
* *
2702 TCAATACCAGGTGCTGTTGACCAAAGCACCGAGGCCAATGGAATCAGGTCAGCTTCACTGAATCT
66 TCAACACCAGGTGCTGTTGACCAAAGCACCGAGGCCAATGAAATCAGGTCAGCTTCACTGAATCT
* * * *
2767 CTTAGCTGTTGAAGAGTCTCAAAATGAGCAAGTAATGAAGAATACAGTGA
131 CTTAGATGTCGAAGAGTCTCAAAATGAACAAGTAATGAAGAACACAGTGA
2817 AGGAAAATGCATCTGGGACAGATGATTTGACTTGGATGGATTACCTTCAACCAAGAACCATTTAT
1 AGGAAAATGCATCTGGGACAGATGATTTGACTTGGATGGATTACCTTCAACCAAGAACCATTTAT
* * * * * *
2882 TCAACATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
66 TCAACACCAGGTGCTGTTGACCAAAGCACCGAGGCCAATGAAATCAGGTCAGCTTCACTGAATCT
* * ** *
2947 CTTAGATGTCGCAGAGTCTCAGAATGAACAAGTAATGGTGAACATAGTGA
131 CTTAGATGTCGAAGAGTCTCAAAATGAACAAGTAATGAAGAACACAGTGA
*
2997 AGGAAAATGCATCTGGGGCAGATGATTTTG-CTTGGATGGATTACCTT
1 AGGAAAATGCATCTGGGACAGATGA-TTTGACTTGGATGGATTACCTT
3044 GGAATGGAAA
Statistics
Matches: 203, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 199 0.98
181 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (180 bp):
AGGAAAATGCATCTGGGACAGATGATTTGACTTGGATGGATTACCTTCAACCAAGAACCATTTAT
TCAACACCAGGTGCTGTTGACCAAAGCACCGAGGCCAATGAAATCAGGTCAGCTTCACTGAATCT
CTTAGATGTCGAAGAGTCTCAAAATGAACAAGTAATGAAGAACACAGTGA
Found at i:3310 original size:66 final size:66
Alignment explanation
Indices: 3222--3350 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 66
3212 ATGAGCAAGT
* * * *
3222 AATGGAGAATATAGTGAAGGAAAATGCATCTGAGG-CAGATGGTTTTGCTAGGATGGATTACCTC
1 AATGGAGAATACAGTCAAGGAAAATGCATCTG-GGACAGATGATTTTACTAGGATGGATTACCTC
3286 AG
65 AG
* * * *
3288 AATGGAGAATACAGTCCAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGTATTACCT
1 AATGGAGAATACAGTCAAGGAAAATGCATCTGGGACAGATGATTTTACTAGGATGGATTACCT
3351 TCAACGGGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
65 2 0.04
66 52 0.96
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (66 bp):
AATGGAGAATACAGTCAAGGAAAATGCATCTGGGACAGATGATTTTACTAGGATGGATTACCTCA
G
Found at i:3444 original size:246 final size:246
Alignment explanation
Indices: 2817--4031 Score: 1739
Period size: 242 Copynumber: 5.0 Consensus size: 246
2807 AATACAGTGA
* * * *
2817 AGGAAAATGCATCTGGGACAGATGATTTGACTTGGATGGATTACCTTCAACCAAGAACCATTTAT
1 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
*
2882 TCAACATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
66 TCAATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
* * * *
2947 CTTAGATGTCGCAGAGTCTCAGAATGAACAAGTAATGGTGAACATAGTGAAGGAAAATGCATCTG
131 CTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCTG
3012 GGGCAGATGATTTTGCTTGGATGGATTACCTTGGAAT-G-GAA-A-ACTCC
196 GGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGGAGAATACACTCC
* *
3059 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTATCTTCTACCAGGAATCATTTAT
1 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
* * * *
3124 TCAATATCAGGTGCTGTTGGCCTAAGCATTGAGACCAATGAAATTAGTTCTGCTTCACTGAATCT
66 TCAATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
* * *
3189 CTTAGATGTCGCTGAGTCTCAAAATGAGCAAGTAATGGAGAATATAGTGAAGGAAAATGCATCTG
131 CTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCTG
* * * ** *
3254 AGGCAGATGGTTTTGCTAGGATGGATTACCTCAGAATGGAGAATACAGTCC
196 GGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGGAGAATACACTCC
* **
3305 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGTATTACCTTCAACGGGGAATCATTTAT
1 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
* ** * *
3370 TCTATAGAAGGTGCTGTTGACCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCATTGAATCT
66 TCAATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
* * * ** * *
3435 CTCAGATGTCACTGAGAGTCAGAATGAGCTAGTAATGGAGAATACAGTGAAGGAAAATGCTTCTG
131 CTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCTG
*
3500 GGACAGATGATTTTGC-T---TGG---A---TGGAATGGAGAATACACTCC
196 GGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGGAGAATACACTCC
*
3541 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCTGGAATCATTTAT
1 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
* *
3606 TCAATATCA-G-GCTGTT-GCCTCAATCACTGAGGCCAATGAAATCAGTTCTGCTTCACAT-TAT
66 TCAATATCAGGTGCTGTTGGCC-CAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCAC-TGAAT
* ** *
3667 CTCTTAGATGTCACAGAGAGTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATA
129 CTCTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATC
* * *
3732 TGGGGCAGATGATTTTGCTTGGATGGATTAGCTTAGTATGGAGAATACACTCC
194 TGGGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGGAGAATACACTCC
* *
3785 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCTGGACTCATTTAT
1 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
* * *
3850 TCAAATATCAGGTGCTGTTGGCCCAAGCTCTGAGGCCAATGAAAGCAGTTCTGCTTCACAGAATC
66 TC-AATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATC
*
3915 TCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCT
130 TCTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCT
* *
3980 GGGGCAGATGGTTTTGCTTGGAT-GATTTACCTTGGAATGGAGAGTACACTCC
195 GGGGCAGATGATTTTGCTTGGATGGA-TTACCTTGGAATGGAGAATACACTCC
4032 TTCAACCAGG
Statistics
Matches: 866, Mismatches: 85, Indels: 39
0.87 0.09 0.04
Matches are distributed among these distances:
233 2 0.00
234 119 0.14
235 3 0.00
236 85 0.10
238 3 0.00
239 1 0.00
241 1 0.00
242 214 0.25
243 1 0.00
244 87 0.10
245 8 0.01
246 193 0.22
247 146 0.17
248 3 0.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (246 bp):
AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
TCAATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
CTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCTG
GGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGGAGAATACACTCC
Found at i:3550 original size:56 final size:56
Alignment explanation
Indices: 3468--3580 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
3458 ATGAGCTAGT
* * * *
3468 AATGGAGAATACAGTGAAGGAAAATGCTTCTGGGACAGATGATTTTGCTTGGATGG
1 AATGGAGAATACACTCAAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGG
*
3524 AATGGAGAATACACTCCAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGG
1 AATGGAGAATACACTCAAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGG
3580 A
1 A
3581 TTACCTTCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (56 bp):
AATGGAGAATACACTCAAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGG
Found at i:3789 original size:66 final size:66
Alignment explanation
Indices: 3703--3827 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
3693 TGAGCAAGTA
* * * *
3703 ATGGAGAATACAGTGAAGGAAAATGCATATGGGGCAGATGATTTTGCTTGGATGGATTAGCTTAG
1 ATGGAGAATACACTCAAGGAAAATGCATATGGGACAGATGATTTTACTTGGATGGATTAGCTTAG
3768 T
66 T
* * *
3769 ATGGAGAATACACTCCAGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTA
1 ATGGAGAATACACTCAAGGAAAATGCATATGGGACAGATGATTTTACTTGGATGGATTA
3828 CCTTCAACCT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (66 bp):
ATGGAGAATACACTCAAGGAAAATGCATATGGGACAGATGATTTTACTTGGATGGATTAGCTTAG
T
Found at i:3820 original size:480 final size:484
Alignment explanation
Indices: 2817--4003 Score: 1751
Period size: 480 Copynumber: 2.5 Consensus size: 484
2807 AATACAGTGA
* * * *
2817 AGGAAAATGCATCTGGGACAGATGATTTGACTTGGATGGATTACCTTCAACCAAGAACCATTTAT
1 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
*
2882 TCAACATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
66 TCAATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
* * * *
2947 CTTAGATGTCGCAGAGTCTCAGAATGAACAAGTAATGGTGAACATAGTGAAGGAAAATGCATCTG
131 CTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCTG
3012 GGGCAGATGATTTTGCTTGGATGGATTACCTTGGAATGGAAAACTCCAGGAAAATGCCTCTGGGA
196 GGGCAGATGATTTTGCTTGGATGGA-TA-C-TGGAA-GGAAAACTCCAGGAAAATGCCTCTGGGA
* *
3077 CAGATGATTTTACTTGGATGGATTATCTTCTACCAGGAATCATTTATTCAATATCAGGTGCTGTT
257 CAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTATTCAATATCAGGTGCTGTT
* * * * *
3142 GGCCTAAGCATTGAGACCAATGAAATTAGTTCTGCTTCACTGAATCTCTTAGATGTCGCTGAGTC
322 GGCCTAAGCACTGAGACCAATGAAATCAGTTCTGCTTCACTGAATCTCTTAGATGTCACAGAGAC
* * *
3207 TCAAAATGAGCAAGTAATGGAGAATATAGTGAAGGAAAATGCATCTGAGGCAGATGGTTTTGCTA
387 TCAAAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATATGAGGCAGATGATTTTGCTA
*
3272 GGATGGATTACCTCAGAATGGAGAATACAGTCC
452 GGATGGATTACCTCAGAATGGAGAATACACTCC
* **
3305 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGTATTACCTTCAACGGGGAATCATTTAT
1 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
* ** * *
3370 TCTATAGAAGGTGCTGTTGACCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCATTGAATCT
66 TCAATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
* * * ** * *
3435 CTCAGATGTCACTGAGAGTCAGAATGAGCTAGTAATGGAGAATACAGTGAAGGAAAATGCTTCTG
131 CTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCTG
*
3500 GGACAGATGATTTTGCTTGGATGGA-A-TGG-A-GAATACACTCCAGGAAAATGCCTCTGGGACA
196 GGGCAGATGATTTTGCTTGGATGGATACTGGAAGGAA-A-ACTCCAGGAAAATGCCTCTGGGACA
*
3561 GATGATTTTACTTGGATGGATTACCTTCAACCTGGAATCATTTATTCAATATCA-G-GCTGTT-G
259 GATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTATTCAATATCAGGTGCTGTTGG
* * * *
3623 CCTCAATCACTGAGGCCAATGAAATCAGTTCTGCTTCACAT-TATCTCTTAGATGTCACAGAGAG
324 CCT-AAGCACTGAGACCAATGAAATCAGTTCTGCTTCAC-TGAATCTCTTAGATGTCACAGAGAC
* * *
3687 TCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATATGGGGCAGATGATTTTGCTT
387 TCAAAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATATGAGGCAGATGATTTTGCTA
* * *
3752 GGATGGATTAGCTTAGTATGGAGAATACACTCC
452 GGATGGATTACCTCAGAATGGAGAATACACTCC
* *
3785 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCTGGACTCATTTAT
1 AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
* * *
3850 TCAAATATCAGGTGCTGTTGGCCCAAGCTCTGAGGCCAATGAAAGCAGTTCTGCTTCACAGAATC
66 TC-AATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATC
*
3915 TCTTAGATGTTGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCT
130 TCTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCT
*
3980 GGGGCAGATGGTTTTGCTTGGATG
195 GGGGCAGATGATTTTGCTTGGATG
4004 ATTTACCTTG
Statistics
Matches: 625, Mismatches: 69, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
479 4 0.01
480 209 0.33
481 136 0.22
482 77 0.12
483 3 0.00
486 1 0.00
488 195 0.31
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (484 bp):
AGGAAAATGCCTCTGGGACAGATGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTAT
TCAATATCAGGTGCTGTTGGCCCAAGCACTGAGGCCAATGAAATCAGTTCTGCTTCACTGAATCT
CTTAGATGTCGCAGAGTCTCAGAATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATCTG
GGGCAGATGATTTTGCTTGGATGGATACTGGAAGGAAAACTCCAGGAAAATGCCTCTGGGACAGA
TGATTTTACTTGGATGGATTACCTTCAACCAGGAATCATTTATTCAATATCAGGTGCTGTTGGCC
TAAGCACTGAGACCAATGAAATCAGTTCTGCTTCACTGAATCTCTTAGATGTCACAGAGACTCAA
AATGAGCAAGTAATGGAGAATACAGTGAAGGAAAATGCATATGAGGCAGATGATTTTGCTAGGAT
GGATTACCTCAGAATGGAGAATACACTCC
Done.