Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_844 ID=scaffold_844-JGI_221_v2.0
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: 7349
ACGTcount: A:0.14, C:0.08, G:0.11, T:0.11
Warning! 4132 characters in sequence are not A, C, G, or T
Found at i:247 original size:132 final size:132
Alignment explanation
Indices: 5--1145 Score: 1739
Period size: 132 Copynumber: 8.6 Consensus size: 132
1 CAGT
* *
5 GGAGAAGGTTGAAGGTTGTAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAA
1 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* * * *
70 ATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAGTA
66 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAGCA
135 GC
131 GC
* *
137 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTAA
1 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* * *
202 ATCTTATCTTTCCATGATAGTGGAAAGCAGATTTAAGCCAAAAAGCCTTGTCTATCTGAGCAGCA
66 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAGCA
267 GC
131 GC
* *
269 GGAGATGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGTCAA
1 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* * * * *
334 ATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGTCACAAAGGCTTGTCTCTCTGAGTAGCA
66 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAGCA
399 GC
131 GC
* * *
401 GGAGAAGGTTGAAGATTGTCGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
1 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
** * * *
466 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGTA
66 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAGCA
531 GC
131 GC
* * *
533 GGAGTAGGTTGAAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCACATCAAAGATGGCAA
1 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* *
598 ATCTTATCTTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCAGAGCAGCA
66 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAGCA
663 GC
131 GC
665 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* * *
730 ATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCC-ACAAGCCTTGTCTCTCTGAGTAGCA
66 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAGCA
794 GC
131 GC
* * * *
796 GGAGAAGGTTGAAGATTGTTGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGACGACAA
1 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
** *
861 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGTA
66 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAGCA
926 GC
131 GC
* *
928 GGAGTAGGTTGAAGATTGTAGATCTCATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGACA
1 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG-CA
*
993 AATCTTATCTTTCCAAGATAGTGGGAAGCAAGATTTAAGCC-ACAAGCCTTGTGCTCTCTTGAGT
65 AATCTTATCTTTCCAAGATAGTGGGAAGC-AGATTTAAGCCAAAAAGCCTTGT-CTCTC-TGAG-
*
1057 AAGCAGCC
126 CAGCAG-C
*
1065 GGAAGAA-GTGTGAAGATTGTTGATCTTATCTCCCTTAAGCCAGTAGTGGAGCAGATCAAAGATG
1 GG-AGAAGGT-TGAAGATTGTAGATCTTATCTCCC-TAAG-CAGTAGTGGAGCAGATCAAAGATG
1129 GACAAATCTTAATCTTT
62 G-CAAATCTT-ATCTTT
1146 NNNNNNNNNN
Statistics
Matches: 921, Mismatches: 76, Indels: 15
0.91 0.08 0.01
Matches are distributed among these distances:
131 123 0.13
132 659 0.72
133 41 0.04
134 16 0.02
135 4 0.00
136 4 0.00
137 5 0.01
138 25 0.03
139 4 0.00
140 34 0.04
141 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (132 bp):
GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTGAGCAGCA
GC
Found at i:328 original size:44 final size:44
Alignment explanation
Indices: 280--738 Score: 124
Period size: 44 Copynumber: 10.4 Consensus size: 44
270 GAGATGGTTG
*
280 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA
* * * *
324 AAGA-TGTCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTT
1 AAGATTGT-AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTA
*** * * * * * * * * * * *
368 AAG-TCACAAAGGCTTGTCTCTCTGAGTAGCAGCGGAGAAGGTTG
1 AAGATTGTAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA
* *
412 AAGATTGTCGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA
* * * * *
456 AAGA-CGACAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTT
1 AAGATTG-TAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTA
*** * * * * * *
500 AAGCCA-CCAAG-CCTTGTCTCCCTAAGCAGTAGCGGAGTAGGTTG
1 AAG--ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA
* * *
544 AAGATTTTAGATCTTATCTCCCTAAGCAGTAGTGGAGCACATCA
1 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA
* * * * *
588 AAGATGGCAAATCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTT
1 AAGATTGTAGATCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATTA
*** * * * * * * * *
632 AAGCCA-AAAAG-CCTTGTCTCTC-AGAGCAGCAGCGGAGAAGGTTG
1 AAG--ATTGTAGATCTTATCTCCCTA-AGCAGTAGTGGAGCAGATTA
*
676 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA
* * *
720 AAGATGGCAAATCTTATCT
1 AAGATTGTAGATCTTATCT
739 TTCCAAGATA
Statistics
Matches: 284, Mismatches: 99, Indels: 64
0.64 0.22 0.14
Matches are distributed among these distances:
42 16 0.06
43 26 0.09
44 209 0.74
45 21 0.07
46 12 0.04
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA
Found at i:2066 original size:44 final size:44
Alignment explanation
Indices: 2018--2212 Score: 110
Period size: 44 Copynumber: 4.4 Consensus size: 44
2008 GAGAAGGTTG
*
2018 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
* * * * * **
2062 AAGATGGCAAATCTTATC-CTTCAAAG-A-TAGTGGGAAGCAAATTT
1 AAGATTGCAGATCTTATCTC-CCTAAGCAGTAGT-GG-AGCAGATCA
*** * * * * * * * * **
2106 AAG-CCACAAAGCCTTGTCTCTCTGAGCAGCAGTGGAGAAGGTTG
1 AAGATTGCAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
* *
2150 AAGGTTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
*
2194 AAGATTGCAAATCTTATCT
1 AAGATTGCAGATCTTATCT
2213 TTCCAAGATA
Statistics
Matches: 106, Mismatches: 37, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
42 4 0.04
43 8 0.08
44 85 0.80
45 6 0.06
46 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
AAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
Found at i:2195 original size:132 final size:132
Alignment explanation
Indices: 1958--2263 Score: 522
Period size: 132 Copynumber: 2.3 Consensus size: 132
1948 NNNNNNNNNN
* * * *
1958 AGTGGAAAGCAGATTTAAGCCAAAAAGCCTTGTCTCACTGAGCAGCAGCAGAGAAGGTTGAAGAT
1 AGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCAGAGAAGGTTGAAGAT
2023 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCCTTCAAAG
66 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCCTTCAAAG
2088 AT
131 AT
** *
2090 AGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGTGGAGAAGGTTGAAGGT
1 AGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCAGAGAAGGTTGAAGAT
* * *
2155 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATTGCAAATCTTATCTTTCCAAG
66 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCCTTCAAAG
2220 AT
131 AT
2222 AGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTGAG
1 AGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTGAG
2264 TAGTANNNNN
Statistics
Matches: 164, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 164 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (132 bp):
AGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCAGAGAAGGTTGAAGAT
TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCCTTCAAAG
AT
Found at i:5921 original size:44 final size:44
Alignment explanation
Indices: 5873--6052 Score: 98
Period size: 44 Copynumber: 4.1 Consensus size: 44
5863 GAGTAGGTTG
*
5873 AAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGTAAATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCA
* * * * **
5917 AAGATGGCAAATCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTT
1 AAGATTGTAAATCCTATC-TCCCTAAGCAGTAGTGG--AGCAGATCA
**** * * * * * * * **
5961 AAG-CCAAAAAGCCTTGTCTCTCTAAGCAGCAGCGGAGAAGGTTG
1 AAGATTGTAAATCC-TATCTCCCTAAGCAGTAGTGGAGCAGATCA
* *
6005 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATTGTAAATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCA
6049 AAGA
1 AAGA
6053 CGACAAATCT
Statistics
Matches: 92, Mismatches: 36, Indels: 16
0.64 0.25 0.11
Matches are distributed among these distances:
42 6 0.07
43 7 0.08
44 68 0.74
45 7 0.08
46 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (44 bp):
AAGATTGTAAATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCA
Found at i:6049 original size:132 final size:132
Alignment explanation
Indices: 5597--7349 Score: 2742
Period size: 132 Copynumber: 13.2 Consensus size: 132
5587 NNAGCGAGAA
* *
5597 AAGGTGGAAGATTGTAGATTCTTATCTCCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAAT
1 AAGGTTGAAGATTGTAGA-TCTTATCT-CCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
* * * *
5662 CTTATCTTTTCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCCTGGTCACTCTGAGTAGCAG
64 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAG-CCTTGTCTCTCTGAGCAGCAG
5727 CGGAG
128 CGGAG
*
5732 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAAGCAGTAGTGGAGCAGATCAGAGACGACAAATC
1 AAGGTTGAAGATTGTAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAGACGACAAATC
* * *
5797 TTATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAAGCCTTTGTCTAC-CTGAGCAGTAA
65 TTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCC-TTGTCT-CTCTGAGCAGCAG
5861 CGGAG
128 CGGAG
* * * *
5866 TAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* ** *
5931 TATCTTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTAAGCAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
5996 AG
131 AG
5998 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* * * **
6063 TATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGCAGTAG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
6128 AG
131 AG
* * * *
6130 TAGGTTG-AGATTGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGGCAAATC
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA-CGACAAATC
* *
6194 TTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCCTCTCTGAGTAGCAGC
65 TTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGT-CTCTCTGAGCAGCAGC
6259 GGAG
129 GGAG
* *
6263 AAGGATGCAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* * *
6328 TATCTTTCCAAGATAGTGGGAAGCAGATTTATGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
6393 AG
131 AG
*
6395 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGATAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* *
6460 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGACCAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
6525 AG
131 AG
* * * * *
6527 TAGGTTG-AGATTGTAGATCTTATCACCGTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
*
6591 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTTAGCAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
6656 AG
131 AG
* *
6658 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAGAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* * * *
6723 TATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAAGCCTTGTCACCCTGAGCTGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
6788 AG
131 AG
* * * *
6790 AAGGTTGAAGATTGTAGTTCTTATCTCCATAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* * * * *
6855 TATCTTTCCAAGATAGTGGGAAGCAAATTTAGGCCACAAAGCCTTGTCTCTCTGAGTAGCAGCGC
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
6920 AG
131 AG
* * * *
6922 AATGTTGAATATTGTAGATCTGATCTCCCTAAGCAGAAGTGGAGCAGATCAAAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
*
6987 TATCTGTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCT-TCCTGAGCAGCAGCG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCT-CTGAGCAGCAGCG
7051 GAG
130 GAG
* * * *
7054 TAGGTTG-AGATTGTAGATCTTATCTCCGTAAGCAGTAGTGGAGCAGATCAAAGATGACAAGTCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* *
7118 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTTAGCAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
7183 AG
131 AG
7185 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* * *
7250 TATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
7315 AG
131 AG
7317 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
Statistics
Matches: 1477, Mismatches: 130, Indels: 25
0.91 0.08 0.02
Matches are distributed among these distances:
131 289 0.20
132 848 0.57
133 151 0.10
134 171 0.12
135 18 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (132 bp):
AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGCGG
AG
Found at i:6629 original size:263 final size:264
Alignment explanation
Indices: 5597--7349 Score: 2747
Period size: 263 Copynumber: 6.6 Consensus size: 264
5587 NNAGCGAGAA
* *
5597 AAGGTGGAAGATTGTAGATTCTTATCTCCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAAT
1 AAGGTTGAAGATTGTAGA-TCTTATCT-CCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
* * * * *
5662 CTTATCTTTTCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCCTGGTCACTCTGAGTAGCAG
64 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAG-CCTTGTCTCCCTGAGCAGCAG
*
5727 CGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAAGCAGTAGTGGAGCAGATCAGAGACGAC
128 CGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAGACGAC
* *
5792 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAAGCCTTTGTCTACCTGAGCA
192 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCC-TTGTCTCCCTGAGCA
* *
5857 GTAACGGAG
256 GCAGCGGAG
* * * *
5866 TAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* ** * *
5931 TATCTTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTAAGCAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
5996 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
131 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
* * *
6061 CTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGCAGT
196 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGC
*
6126 AGAG
261 GGAG
* * * *
6130 TAGGTTG-AGATTGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGGCAAATC
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA-CGACAAATC
* * *
6194 TTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCCTCTCTGAGTAGCAGC
65 TTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGT-CTCCCTGAGCAGCAGC
* *
6259 GGAGAAGGATGCAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
129 GGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
* *
6324 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTATGCCACCAAGCCTTGTCTCCCTGAGTAGCA
194 ATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCA
6389 GCGGAG
259 GCGGAG
*
6395 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGATAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
*
6460 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGACCAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
* * * * *
6525 AGTAGGTTG-AGATTGTAGATCTTATCACCGTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAAT
131 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
* *
6589 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTTAGCAGCAGC
196 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGC
6654 GGAG
261 GGAG
* *
6658 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAGAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* * *
6723 TATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAAGCCTTGTCACCCTGAGCTGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
* * * *
6788 AGAAGGTTGAAGATTGTAGTTCTTATCTCCATAAGCAGTAGTGGAGCAGATCAAAGATGGCAAAT
131 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
* * * * *
6853 CTTATCTTTCCAAGATAGTGGGAAGCAAATTTAGGCCACAAAGCCTTGTCTCTCTGAGTAGCAGC
196 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGC
*
6918 GCAG
261 GGAG
* * * *
6922 AATGTTGAATATTGTAGATCTGATCTCCCTAAGCAGAAGTGGAGCAGATCAAAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* *
6987 TATCTGTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTTCCTGAGCAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
* * * *
7052 AGTAGGTTG-AGATTGTAGATCTTATCTCCGTAAGCAGTAGTGGAGCAGATCAAAGATGACAAGT
131 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
* * *
7116 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTTAGCAGCAGC
196 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGC
7181 GGAG
261 GGAG
7185 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* *
7250 TATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
7315 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
131 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
Statistics
Matches: 1376, Mismatches: 103, Indels: 15
0.92 0.07 0.01
Matches are distributed among these distances:
263 537 0.39
264 368 0.27
265 275 0.20
266 98 0.07
267 75 0.05
268 7 0.01
269 16 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (264 bp):
AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGC
GGAG
Found at i:6987 original size:527 final size:525
Alignment explanation
Indices: 5597--7349 Score: 2810
Period size: 527 Copynumber: 3.3 Consensus size: 525
5587 NNAGCGAGAA
* *
5597 AAGGTGGAAGATTGTAGATTCTTATCTCCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAAT
1 AAGGTTGAAGATTGTAGA-TCTTATCT-CCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
* * *
5662 CTTATCTTTTCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCCTGGTCACTCTGAGTAGCAG
64 CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAG-CCTTGTCACCCTGAGTAGCAG
*
5727 CGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAAGCAGTAGTGGAGCAGATCAGAGACGAC
128 CGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAGACGAC
* *
5792 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAAGCCTTTGTCTACCTGAGCA
192 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCC-TTGTCT-CCTGAGTA
* * * *
5857 GTAACGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
255 GCAGCGGAGAAGGTTGAAGATTGTAGAT-CTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * ** * *
5922 GGCAAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAAAGCCTTGTCTCTCTAAG
319 GACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAG
* *
5987 CAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAG
384 CAGCAGCGGAGTAGGTTG-AGATTGTAGATCTTATCTCCGTAAGCAGTAGTGGAGCAGATCAAAG
* * * * *
6052 ACGACAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCACCAGGCCTTGTCTCCCTG
448 ATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTT
**
6117 AGCAGCAGTAGAG
513 AGCAGCAGCGGAG
* * * *
6130 TAGGTTG-AGATTGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGGCAAATC
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA-CGACAAATC
*
6194 TTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTC-CTCTCTGAGTAGCAG
65 TTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCAC-C-CTGAGTAGCAG
* *
6258 CGGAGAAGGATGCAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACA
128 CGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACA
*
6323 AATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTATGCCACCAAGCCTTGTCTCCCTGAGTAGC
193 AATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCT-CCTGAGTAGC
6388 AGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGA
257 AGCGGAGAAGGTTGAAGATTGTAGATC-TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGA
* *
6453 TAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGACCA
321 CAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCA
*
6518 GCAGCGGAGTAGGTTGAGATTGTAGATCTTATCACCGTAAGCAGTAGTGGAGCAGATCAAAGATG
386 GCAGCGGAGTAGGTTGAGATTGTAGATCTTATCTCCGTAAGCAGTAGTGGAGCAGATCAAAGATG
*
6583 GCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTTAGC
451 ACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTTAGC
6648 AGCAGCGGAG
516 AGCAGCGGAG
* *
6658 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAGAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
*
6723 TATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAAGCCTTGTCACCCTGAGCT-GCAGCG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCACCCTGAG-TAGCAGCG
* * * *
6787 GAGAAGGTTGAAGATTGTAGTTCTTATCTCCATAAGCAGTAGTGGAGCAGATCAAAGATGGCAAA
130 GAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAA
* * *
6852 TCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAGGCCACAAAGCCTTGTCTCTCTGAGTAGCAG
195 TCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTC-CTGAGTAGCAG
* * * *
6917 CGCAGAATGTTGAATATTGTAGATCTGATCTCCCTAAGCAGAAGTGGAGCAGATCAAAGACGACA
259 CGGAGAAGGTTGAAGATTGTAGATCT-ATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACA
* *
6982 AATCTTATCTGTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTTCCTGAGCAGC
323 AATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGC
7047 AGCGGAGTAGGTTGAGATTGTAGATCTTATCTCCGTAAGCAGTAGTGGAGCAGATCAAAGATGAC
388 AGCGGAGTAGGTTGAGATTGTAGATCTTATCTCCGTAAGCAGTAGTGGAGCAGATCAAAGATGAC
* *
7112 AAGTCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTTAGCAG
453 AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTTAGCAG
7177 CAGCGGAG
518 CAGCGGAG
7185 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
1 AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
* *
7250 TATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGG
66 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCACCCTGAGTAGCAGCGG
7315 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
131 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
Statistics
Matches: 1136, Mismatches: 74, Indels: 26
0.92 0.06 0.02
Matches are distributed among these distances:
526 3 0.00
527 540 0.48
528 177 0.16
529 192 0.17
530 110 0.10
531 100 0.09
532 9 0.01
533 5 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (525 bp):
AAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCT
TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCACCCTGAGTAGCAGCGG
AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCTGAGTAGCAGCG
GAGAAGGTTGAAGATTGTAGATCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAAT
CTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGC
GGAGTAGGTTGAGATTGTAGATCTTATCTCCGTAAGCAGTAGTGGAGCAGATCAAAGATGACAAA
TCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTTAGCAGCAG
CGGAG
Found at i:7250 original size:44 final size:44
Alignment explanation
Indices: 7070--7254 Score: 110
Period size: 44 Copynumber: 4.2 Consensus size: 44
7060 GAGATTGTAG
* *
7070 ATCTTATCTCCGTAAGCAGTAGTGGAGCAGATCAAAGATGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
* * ** *
7114 GTCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGACGACAA
* * * * * * * * ** * * *
7157 AGCCTTGTCTCTCTTAGCAGCAGCGGAGAAGGTTGAAGATTG-TAG
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA-CGACAA
7202 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
7246 ATCTTATCT
1 ATCTTATCT
7255 TTCCAAGATA
Statistics
Matches: 96, Mismatches: 35, Indels: 20
0.64 0.23 0.13
Matches are distributed among these distances:
42 4 0.04
43 10 0.10
44 73 0.76
45 7 0.07
46 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
Done.