Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_946 ID=scaffold_946-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: 3099
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.17
Warning! 919 characters in sequence are not A, C, G, or T
Found at i:188 original size:44 final size:44
Alignment explanation
Indices: 4--190 Score: 107
Period size: 44 Copynumber: 4.2 Consensus size: 44
1 TGT
* * *
4 AAATCTTATCGCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
1 AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAC
* ** *
48 AAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCAC
1 AAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGACGAC
* * * * * * * * * * *
91 AAAGCCTTGTCTCTCTGAGTAGCAGCGGAGAAGGAT-GAAGATTG-T
1 AAA-TCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGA-CGAC
*
136 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAC
1 AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAC
180 AAATCTTATCT
1 AAATCTTATCT
191 TTCCAAGATA
Statistics
Matches: 99, Mismatches: 32, Indels: 24
0.64 0.21 0.15
Matches are distributed among these distances:
42 4 0.04
43 13 0.13
44 70 0.71
45 10 0.10
46 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (44 bp):
AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGAC
Found at i:243 original size:132 final size:132
Alignment explanation
Indices: 1--699 Score: 1184
Period size: 132 Copynumber: 5.3 Consensus size: 132
* * * *
1 TGTAAATCTTATCGCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAG
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
* * *
66 ATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAGCAGCGGAGAAGGATGAAG
66 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
131 AT
131 AT
133 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
*
198 ATAGTGGGAAGCAGATTTATGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
66 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
263 AT
131 AT
* *
265 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGACTAATCTTATCTTTCCAAG
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
* *
330 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG-AG
66 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
394 AT
131 AT
* * * *
396 TGTAGATCTTATCACCGTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAG
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
* * * * *
461 ATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTTAGCAGCAGCGAAGAAGGTTGAAG
66 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
526 AT
131 AT
*
528 TGTAGATCTTATATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
593 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCATCCCTGAGTAGCAGCGGAGAAGGTTGAA
66 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTC-TCCCTGAGTAGCAGCGGAGAAGGTTGAA
658 GAT
130 GAT
661 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
700 NNNNNNNNNN
Statistics
Matches: 530, Mismatches: 35, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
131 120 0.23
132 345 0.65
133 65 0.12
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (132 bp):
TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
AT
Found at i:512 original size:263 final size:264
Alignment explanation
Indices: 1--699 Score: 1184
Period size: 263 Copynumber: 2.6 Consensus size: 264
* * * *
1 TGTAAATCTTATCGCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAG
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
* * *
66 ATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAGCAGCGGAGAAGGATGAAG
66 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
131 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCA
131 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCA
* * * *
196 AGATAGTGGGAAGCAGATTTATGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGA
196 AGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGAAGAAGGTTGA
261 AGAT
261 AGAT
* *
265 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGACTAATCTTATCTTTCCAAG
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
* *
330 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG-AG
66 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
* * * *
394 ATTGTAGATCTTATCACCGTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCA
131 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCA
* *
459 AGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTTAGCAGCAGCGAAGAAGGTTGA
196 AGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGAAGAAGGTTGA
524 AGAT
261 AGAT
*
528 TGTAGATCTTATATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
1 TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
593 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCATCCCTGAGTAGCAGCGGAGAAGGTTGAA
66 ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTC-TCCCTGAGTAGCAGCGGAGAAGGTTGAA
658 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
130 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
700 NNNNNNNNNN
Statistics
Matches: 405, Mismatches: 28, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
263 224 0.55
264 140 0.35
265 41 0.10
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (264 bp):
TGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAG
ATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAG
ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCA
AGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGAAGAAGGTTGA
AGAT
Found at i:1860 original size:132 final size:132
Alignment explanation
Indices: 1619--3099 Score: 2205
Period size: 132 Copynumber: 11.2 Consensus size: 132
1609 NNNNNNNNNN
* *
1619 GGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAAGCCACCAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* ** * *
1684 GCCTTGTCTCCCTGATCA-CTAGCAAAGTAGGTTGAAGATGGTAGATCTTATCTCCCTAAGCAGT
66 GCCTTGTCTCCCTGAGCAGC-AGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1748 AGT
130 AGT
* * * * *
1751 GGAGCAAATCAAAGATGACAAATCTTCTCATTCCAAGATAGTGGGAAGCATATTTAAGCCACAAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
*
1816 GCCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
1881 GT
131 GT
*
1883 GGAGCAGATCAAAGATAGGACGAAATCTTATC-TTCCAAGATAGTAGGAAGCAGATTTAAGCCAC
1 GGAGCAGATCAAAGAT--GAC-AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * * * * *
1947 AAAGCCTTGTCTCTCTGAGTAGCAGCAGAGAAGGATGAAGATTGTTGATCTTATCTCCCTAAGCA
63 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
2012 GTAGT
128 GTAGT
* *
2017 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTATGCCACCAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * *
2082 GCCTTGTATCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAATA
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
2147 GT
131 GT
*
2149 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * *
2214 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG-AGATTGTAGATCTTATCACCGTAAGCAGTA
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
2278 GT
131 GT
** * *
2280 GGAGCAGATCAAAGATGGGAAATCTTATCTTTCCAAGATAGTGGGAAGGAGATTTAAGCCACAAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* ** * * * * * * * *
2345 GCCTTGGCTATCTTAACAGCAGCGGAAAAGGGTGAAGAATGAAGAACTTATCTCCCTAAGCAGGA
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
2410 GT
131 GT
*
2412 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * *
2477 GCCTTGTCTCCCTGAGTAGGAGCGGAGAAGGGTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
2542 GT
131 GT
* * * *
2544 AGAGCAGATCAGAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* *
2609 GCCTTGTCTCCCTGAGCAGCAACGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCCTAAGCAGT
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCT-CCCTAAGCAGT
2674 AGT
130 AGT
* * * * **
2677 GGAGCAGATCAAACATGGCAAATCTTATCTTTCCAAGATAGTGGAAAGTAGATTTAAGCCAAAAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * *
2742 GCCTTGTCTCTCTGAGCAGCGGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAACCAGTA
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
2807 GT
131 GT
* * *
2809 GGAGCAGATCAGAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * * * *
2874 GCCTTGTCTCCCTGAGCAGTAACGGAGTAGGTGGAAGATTGTAGATCTCATCTCCCTAAGCAGTA
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
2939 GT
131 GT
* *
2941 GGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCA-CAA
1 GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* *
3005 GCCTTGTCTCTCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
66 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
3070 GT
131 GT
*
3072 GGAGCAGATCAAAGATGGCAAATCTTAT
1 GGAGCAGATCAAAGATGACAAATCTTAT
Statistics
Matches: 1216, Mismatches: 126, Indels: 15
0.90 0.09 0.01
Matches are distributed among these distances:
131 216 0.18
132 758 0.62
133 119 0.10
134 114 0.09
135 9 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (132 bp):
GGAGCAGATCAAAGATGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
GT
Found at i:2493 original size:395 final size:396
Alignment explanation
Indices: 1619--3099 Score: 2306
Period size: 397 Copynumber: 3.7 Consensus size: 396
1609 NNNNNNNNNN
* * *
1619 GGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAAGCCACCAA
1 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
** * *
1684 GCCTTGTCTCCCTGA-TCA-CTAGCAAAGTAGGTTGAAGATGGTAGATCTTATCTCCCTAAGCAG
66 GCCTTGTCTCCCTGAGT-AGC-AGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * * * *
1747 TAGTGGAGCAAATCAAAGATGACAAATCTTCTCATTCCAAGATAGTGGGAAGCATATTTAAGCCA
129 TAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
* *
1812 CAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
194 CCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGC
*
1877 AGTAGTGGAGCAGATCAAAGATAGGACGAAATCTTATC-TTCCAAGATAGTAGGAAGCAGATTTA
259 AGTAGTGGAGCAGATCAAAGAT-GG-C-AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
* * *
1941 AGCCACAAAGCCTTGTCTCTCTGAGTAGCAGCAGAGAAGGATGAAGATTGTTGATCTTATCTCCC
321 AGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGAAGGATGAAGATTGTAGATCTTATCTCCC
2006 TAAGCAGTAGT
386 TAAGCAGTAGT
*
2017 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTATGCCACCAA
1 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* *
2082 GCCTTGTATCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAATA
66 GCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
2147 GTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
131 GTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
* * *
2212 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG-AGATTGTAGATCTTATCACCGTAAGCAG
196 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
2276 TAGTGGAGCAGATCAAAGATGGGAAATCTTATCTTTCCAAGATAGTGGGAAGGAGATTTAAGCCA
261 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
* * * * * * * * *
2341 CAAAGCCTTGGCTATCTTAACAGCAGCGGAAAAGGGTGAAGAATGAAGAACTTATCTCCCTAAGC
326 CAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGAAGGATGAAGATTGTAGATCTTATCTCCCTAAGC
*
2406 AGGAGT
391 AGTAGT
2412 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
1 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* *
2477 GCCTTGTCTCCCTGAGTAGGAGCGGAGAAGGGTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
66 GCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
* * *
2542 GTAGAGCAGATCAGAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACC
131 GTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
* *
2607 AAGCCTTGTCTCCCTGAGCAGCAACGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCCTAAGCA
196 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCT-CCCTAAGCA
* * *
2672 GTAGTGGAGCAGATCAAACATGGCAAATCTTATCTTTCCAAGATAGTGGAAAGTAGATTTAAGCC
260 GTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
* * * *
2737 AAAAAGCCTTGTCTCTCTGAGCAGCGGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAC
325 ACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGAAGGATGAAGATTGTAGATCTTATCTCCCTAAG
2802 CAGTAGT
390 CAGTAGT
* *
2809 GGAGCAGATCAGAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGTTTTAAGCCACCAA
1 GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * * * * *
2874 GCCTTGTCTCCCTGAGCAGTAACGGAGTAGGTGGAAGATTGTAGATCTCATCTCCCTAAGCAGTA
66 GCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
* * *
2939 GTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAAATTTAAGCCA-C
131 GTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
* *
3003 AAGCCTTGTCTCTCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
196 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
3068 TAGTGGAGCAGATCAAAGATGGCAAATCTTAT
261 TAGTGGAGCAGATCAAAGATGGCAAATCTTAT
Statistics
Matches: 994, Mismatches: 84, Indels: 13
0.91 0.08 0.01
Matches are distributed among these distances:
394 10 0.01
395 350 0.35
396 71 0.07
397 352 0.35
398 209 0.21
399 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (396 bp):
GGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
GCCTTGTCTCCCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
CAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGAAGGATGAAGATTGTAGATCTTATCTCCCTAAGC
AGTAGT
Found at i:3097 original size:44 final size:44
Alignment explanation
Indices: 2918--3099 Score: 102
Period size: 44 Copynumber: 4.2 Consensus size: 44
2908 AAGATTGTAG
*
2918 ATCTCATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* * ** ***
2962 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAG-CCACAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGCAA
** * * * * * * * * ** * * *
3005 GCCTTGTCTCTCTGAGTAGCAGCGGAGAAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
3049 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
3093 ATCTTAT
1 ATCTTAT
Statistics
Matches: 91, Mismatches: 40, Indels: 14
0.63 0.28 0.10
Matches are distributed among these distances:
42 6 0.07
43 21 0.23
44 59 0.65
45 5 0.05
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
Done.