Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011731.1 Kokia drynarioides strain JFW-HI SEQ_126725, whole genome shotgun sequence
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: 3190
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Found at i:384 original size:221 final size:221
Alignment explanation
Indices: 1--2014 Score: 2546
Period size: 221 Copynumber: 9.0 Consensus size: 221
*
1 TCCCTGTTTTATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
* * * * * *
66 GTCATTTGTGTCCCTTTTCAAATAGTTTTACACCATATCCGTATTTTCATTCTTAATTTCAACGT
66 GTCATTTGTGTCCCTTTTCTAATTGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACAT
* * * * *
131 TTTCATCCTGAAAAATTAAAATTAAAATTAAAATCCTGAAATTGAAAATGAAATTGTTGATGTGG
131 TTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAAGATGAAATTGTTGGTGTGG
196 CATAAAACTATTGGAAAGGGATAATA
196 CATAAAACTATTGGAAAGGGATAATA
*
222 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAATGATTGAATGAAACAGTGACACCAC
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
287 GTCATTTGTGTCCCTTTTCT-ATTGTTTTTACGCCACATCAGTATTTTCATTCTTAATGTT-AAC
66 GTCATTTGTGTCCCTTTTCTAATTG-TTTTACGCCACATCAGTATTTTCATTCTTAAT-TTCAAC
* * *
350 ATTTTCATCCTGAGAAAATCAAATTAAAATTAAAATCCTGAAATTTAGGATGAAATTGTTGGTGT
129 ATTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAAGATGAAATTGTTGGTGT
415 GGCATAAAACTATTGGAAAGGGATAATA
194 GGCATAAAACTATTGGAAAGGGATAATA
* * *
443 TCCTTGTTTCATACAATTCTTTCTCTTCTTCAATGGAAAATGATTTAATAAAATGGAAAAGGATT
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAA-G----GAT----T-G---A--A-T
* ** *
508 GCATAAAACAGTGAAACCACGTCATTTGTGTCCCTTTT-TCAATAATTTTACGCTACATCAGTAT
50 G----AAACAGTGACACCACGTCATTTGTGTCCCTTTTCT-AATTGTTTTACGCCACATCAGTAT
** * * *
572 TTTCATTCTTAATTAAAAACATTTACATCCTGAAAAGAAACAAATTAAAATAAAAATCCTGAAAT
110 TTTCATTCTTAATT-TCAACATTTTCATCCTGAAAA-AATCAAATTAAAATTAAAATCCTGAAAT
* *
637 TCAAGATGAAATTGTTGGTGTGGCAAAAAACTATCGGAAAGGGATAATA
173 TCAAGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATA
** * * * *
686 TCCCTACTTCATACCACCCTTTCTTTTCTTTAATGGAAAAGGATTGAATGAAACAGTGACACCAC
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
* * * * *
751 GTCATTTCTGTCCCTTTTCTAATAGTTTTACACCATATCAGTATTTTCAATCTTAATTTCAACAT
66 GTCATTTGTGTCCCTTTTCTAATTGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACAT
* *
816 TTTCATCCTGTAAAAATCAAATTAAAATTAAAATCCTGAAATAC-AGAATGAAATTGTTGGTGTG
131 TTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAAG-ATGAAATTGTTGGTGTG
*
880 GCATAAAACTATTAGAAAGGGATAATA
195 GCATAAAACTATTGGAAAGGGATAATA
* *
907 TCCCTGTTTTATACAATCCTTTCTCCTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
* * *
972 GTCAATTGTGTCCCTTTTC-CATTAGTTTTACGCCACATCAGTATTTTCATTCATAATTTCAACA
66 GTCATTTGTGTCCCTTTTCTAATT-GTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACA
* * * *
1036 TTTTCATCCTG----AA--AAATTAAAATTAAAATCCTGAAATTGAAAATGAAATTTTTGATGTG
130 TTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAAGATGAAATTGTTGGTGTG
1095 GCATAAAACTATTGGAAAGGGATAATA
195 GCATAAAACTATTGGAAAGGGATAATA
* * * * * *
1122 TCACTGTTTTACACAATCCTTTCTCTTCTTTAATGGAAAATGATTGAATGAAATAGTGACACCAC
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
*
1187 GTCATTTGTGTCCCTTTTCT-ATTGTTTTTACGCCACATCAGTATTTTCATTCTTAATGTCAACA
66 GTCATTTGTGTCCCTTTTCTAATTG-TTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACA
* * *
1251 TTTTCATCCTGAGAAAATCAAATTAAAATTAAAATCCTGAAATTTATGATGAAATTGTTGGTGTG
130 TTTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAAGATGAAATTGTTGGTGTG
1316 GCATAAAACTATTGGAAAGGGATAATA
195 GCATAAAACTATTGGAAAGGGATAATA
* * *
1343 TCCTTGTTTCATACAATCCTTTCTCTTCTTCAGTGGAAAATGATTTAATAAAATGGAAAAGGATT
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAA-G----GAT----T-G---A--A-T
* ** * *
1408 GCCTAAAACAGTGAAACCACGTCATTTGTGTCCCTTTT-TCAATAATTTTACGCTAAATCAGTAT
50 G----AAACAGTGACACCACGTCATTTGTGTCCCTTTTCT-AATTGTTTTACGCCACATCAGTAT
* * *
1472 TTTCATTCTTAATTTCAACATTTACATCCTGAAAAGAAACAAATTAAAATAAAAATCCTGAAATT
110 TTTCATTCTTAATTTCAACATTTTCATCCTGAAAA-AATCAAATTAAAATTAAAATCCTGAAATT
* *
1537 CAAGATGAAATTGTTGGTGTGGCAAAAAACTATCGGAAAGGGATAATA
174 CAAGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATA
** * * * * *
1585 TCCCTACTTCATACCACCCTTTCTCTTCTTTAATGGAAAAGGATTAAATGAAACAGTGACTCCAC
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
* * * *
1650 GTCATTTGTGTCCCTTTTCTAATAGTTTTACACCATATCAATATTTTCATTCTTAATTTCAACAT
66 GTCATTTGTGTCCCTTTTCTAATTGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACAT
* * *
1715 TTTCATCCTGAAAAAAACAAATTAAAATTAAAATCCTGAAATACAGGATGAAATTGTTGGTGTGG
131 TTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAAGATGAAATTGTTGGTGTGG
*
1780 CATAAAACTACTGGAAAGGGATAATA
196 CATAAAACTATTGGAAAGGGATAATA
* * * **
1806 TCCCTGTTTTATACAATCCTTTCTCTTCTTCAGTGGAAAAGGATTG-A-GAAACAGTGAGAAGAC
1 TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
* * *
1869 GTCATCTGTGTCCCTTTTCTAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTTAACAT
66 GTCATTTGTGTCCCTTTTCTAATTGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACAT
* * *
1934 TTTCATCTTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGG
131 TTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAAGATGAAATTGTTGGTGTGG
*
1999 CATAAAACTAATGGAA
196 CATAAAACTATTGGAA
2015 CAGTGACACC
Statistics
Matches: 1568, Mismatches: 162, Indels: 128
0.84 0.09 0.07
Matches are distributed among these distances:
214 1 0.00
215 193 0.12
216 1 0.00
217 2 0.00
219 150 0.10
220 8 0.01
221 637 0.41
222 103 0.07
223 65 0.04
224 1 0.00
226 6 0.00
227 3 0.00
228 1 0.00
229 1 0.00
230 3 0.00
231 2 0.00
233 2 0.00
234 3 0.00
236 2 0.00
237 6 0.00
238 2 0.00
240 3 0.00
241 144 0.09
242 126 0.08
243 103 0.07
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (221 bp):
TCCCTGTTTCATACAATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACCAC
GTCATTTGTGTCCCTTTTCTAATTGTTTTACGCCACATCAGTATTTTCATTCTTAATTTCAACAT
TTTCATCCTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAAGATGAAATTGTTGGTGTGG
CATAAAACTATTGGAAAGGGATAATA
Found at i:513 original size:20 final size:20
Alignment explanation
Indices: 474--515 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
464 TCTCTTCTTC
* *
474 AATGGAAAATGATTTAATAA
1 AATGGAAAAGGATTGAATAA
*
494 AATGGAAAAGGATTGCATAA
1 AATGGAAAAGGATTGAATAA
514 AA
1 AA
516 CAGTGAAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.19, T:0.24
Consensus pattern (20 bp):
AATGGAAAAGGATTGAATAA
Found at i:2143 original size:158 final size:158
Alignment explanation
Indices: 1867--2172 Score: 497
Period size: 158 Copynumber: 1.9 Consensus size: 158
1857 CAGTGAGAAG
* *
1867 ACGTCATCTGTGTCCCTTTTCTAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTTAAC
1 ACGTCATCTGTGTCCCTTTTCTAATAGTTTTACGCCACATCAATATTTTCATTCTTAATTTAAAC
* * * * *
1932 ATTTTCATCTTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGT
66 ATTTTCATCCTGAAAAAAACAAATTAAAATCAAAATCCTAAAATACAGGATGAAATTGTTGATGT
1997 GGCATAAAACTAATGGAACAGTGACACC
131 GGCATAAAACTAATGGAACAGTGACACC
* *
2025 ACGTCATTTGTGTCCCTTTTAC-AATAGTTTTACGCCATATCAATATTTTCATTCTTAATTTAAA
1 ACGTCATCTGTGTCCCTTTT-CTAATAGTTTTACGCCACATCAATATTTTCATTCTTAATTTAAA
*
2089 CATTTTCATCCTGAAAAAAACAAATTAAAATCAAAATCCTAAAATACAGGATGAAATTGTTGGTG
65 CATTTTCATCCTGAAAAAAACAAATTAAAATCAAAATCCTAAAATACAGGATGAAATTGTTGATG
*
2154 TGGCATAAAACTATTGGAA
130 TGGCATAAAACTAATGGAA
2173 AGGGATAATA
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
158 135 0.99
159 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (158 bp):
ACGTCATCTGTGTCCCTTTTCTAATAGTTTTACGCCACATCAATATTTTCATTCTTAATTTAAAC
ATTTTCATCCTGAAAAAAACAAATTAAAATCAAAATCCTAAAATACAGGATGAAATTGTTGATGT
GGCATAAAACTAATGGAACAGTGACACC
Found at i:2401 original size:221 final size:220
Alignment explanation
Indices: 2008--2605 Score: 903
Period size: 221 Copynumber: 2.7 Consensus size: 220
1998 GCATAAAACT
* * * * *
2008 AATGGAACAGTGACACCACGTCATTTGTGTCCCTTTTACAATAGTTTTACGCCATATCAATATTT
1 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTAAGCCACATCAGTATTT
* * * * *
2073 TCATTCTTAATTTAAACATTTTCATCCTGAAAAAAACAAATTAAAATCAAAATCCTAAAATACAG
66 TCATTCTTAATTTCAACATTTTCATCCTGAAAAATA-AAATTAAAATTAAAATCCTGAAATTCAG
* *
2138 GATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTATTTTATACAATCCT
130 GATGAAATTGTTGGTGTGGCATAAAACAATTGGAAAGGGATAATATCCCTATTTCATACAATCCT
2203 TTCTCCTCTTCAATGGAAAA-GAATTG
195 TTCTCCTCTTCAATGGAAAATG-ATTG
*
2229 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTTAAGCCACATCAGTATTT
1 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTAAGCCACATCAGTATTT
*
2294 TCATTCTTAATTTCAACATTTTCATCCTGAAAAATTAAAATTAAAATTAAAATCCTGAAATTCAA
66 TCATTCTTAATTTCAACATTTTCATCCTGAAAAA-TAAAATTAAAATTAAAATCCTGAAATTCAG
* * * *
2359 AATGAAATTGTTGATGTGGCATAAAACAATTGGAAGGGGATAATATCCCTGTTTCATACAATCCT
130 GATGAAATTGTTGGTGTGGCATAAAACAATTGGAAAGGGATAATATCCCTATTTCATACAATCCT
* *
2424 TTCTCTTCTTTAATGGAAAATGATTG
195 TTCTCCTCTTCAATGGAAAATGATTG
* *
2450 AATGAAACAGTGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTATGCCACATCAGTATTT
1 AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTAAGCCACATCAGTATTT
* * *
2515 TCATTCTTAATTTCAACATTTTCACCCTGGGAAAATCAAATTAAAATTAAAAAT-CTGAAATTCA
66 TCATTCTTAATTTCAACATTTTCATCCT-GAAAAATAAAATTAAAATT-AAAATCCTGAAATTCA
*
2579 GGATGAAATTGTTGGTGCGGCATAAAA
129 GGATGAAATTGTTGGTGTGGCATAAAA
2606 AATGATTGAA
Statistics
Matches: 343, Mismatches: 30, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
221 331 0.97
222 12 0.03
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (220 bp):
AATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCAATAGTTTTAAGCCACATCAGTATTT
TCATTCTTAATTTCAACATTTTCATCCTGAAAAATAAAATTAAAATTAAAATCCTGAAATTCAGG
ATGAAATTGTTGGTGTGGCATAAAACAATTGGAAAGGGATAATATCCCTATTTCATACAATCCTT
TCTCCTCTTCAATGGAAAATGATTG
Found at i:2685 original size:385 final size:385
Alignment explanation
Indices: 2225--2990 Score: 1230
Period size: 385 Copynumber: 2.0 Consensus size: 385
2215 ATGGAAAAGA
** * * *
2225 ATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTTAAGCCACATCAGT
1 ATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTAAGCCACATCAGT
2290 ATTTTCATTCTTAATTTCAACATTTTCATCCTG-AAAAATTAAAATTAAAATTAAAATCCTGAAA
66 ATTTTCATTCTTAATTTCAACATTTTCATCCTGTAAAAA-TAAAATTAAAATTAAAATCCTGAAA
* *
2354 TTCAAAATGAAATTGTTGATGTGGCATAAAACAATTGGAAGGGGATAATATCCCTGTTTCATACA
130 TTCAAAATGAAATTGTTGATGTGGCATAAAACAATCGGAAAGGGATAATATCCCTGTTTCATACA
* *
2419 ATCCTTTCTCTTCTTTAATGGAAAATGATTGAATGAAACAGTGACACAACGTCATTTGTGTCCCT
195 ATCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACAACGTCATTTGTGTCCCT
* * * **
2484 TTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCACCCTGGGAAA
260 TTTCCAATAGTTTTACGCCACATCAATATTTTAATTCTTAATTTCAACATTTTCACCCTGAAAAA
*
2549 ATCAAATTAAAATTAAAAAT-CTGAAATTCAGGATGAAATTGTTGGTGCGGCATAAAAAATG
325 ATCAAATTAAAATT-AAAATCCTGAAATACAGGATGAAATTGTTGGTGCGGCATAAAAAATG
*
2610 ATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCACATCAGT
1 ATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTAAGCCACATCAGT
* * *
2675 ATTTTCATTCTTAATTTTAACTTTTTCATCCTGTAAAAATCAAATTAAAATTAAAATCCTGAAAT
66 ATTTTCATTCTTAATTTCAACATTTTCATCCTGTAAAAATAAAATTAAAATTAAAATCCTGAAAT
** * * *
2740 TCAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTGTTTTATACAA
131 TCAAAATGAAATTGTTGATGTGGCATAAAACAATCGGAAAGGGATAATATCCCTGTTTCATACAA
* *
2805 TCCTTTCTCTTCTTCAATGGGAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTT
196 TCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACAACGTCATTTGTGTCCCTT
* * *
2870 TTCTAATAGTTTTACGCCACATCAATATTTTAATTCTTAATTTCAACATTTTCATCCTTAAAAAA
261 TTCCAATAGTTTTACGCCACATCAATATTTTAATTCTTAATTTCAACATTTTCACCCTGAAAAAA
*
2935 TCAAATTAAAATTAAAATCCTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAA
326 TCAAATTAAAATTAAAATCCTGAAATACAGGATGAAATTGTTGGTGCGGCATAAAA
2991 CTATTGGAAA
Statistics
Matches: 349, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
384 5 0.01
385 339 0.97
386 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (385 bp):
ATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTAAGCCACATCAGT
ATTTTCATTCTTAATTTCAACATTTTCATCCTGTAAAAATAAAATTAAAATTAAAATCCTGAAAT
TCAAAATGAAATTGTTGATGTGGCATAAAACAATCGGAAAGGGATAATATCCCTGTTTCATACAA
TCCTTTCTCTTCTTCAATGGAAAAGGATTGAATGAAACAGTGACACAACGTCATTTGTGTCCCTT
TTCCAATAGTTTTACGCCACATCAATATTTTAATTCTTAATTTCAACATTTTCACCCTGAAAAAA
TCAAATTAAAATTAAAATCCTGAAATACAGGATGAAATTGTTGGTGCGGCATAAAAAATG
Found at i:2716 original size:164 final size:164
Alignment explanation
Indices: 2440--2769 Score: 554
Period size: 164 Copynumber: 2.0 Consensus size: 164
2430 TCTTTAATGG
** * *
2440 AAAATGATTGAATGAAACAGTGACACAACGTCATTTGTGTCCCTTTTCCAATAGTTTTATGCCAC
1 AAAATGATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
*
2505 ATCAGTATTTTCATTCTTAATTTCAACATTTTCACCCTGGGAAAATCAAATTAAAATTAAAAAT-
66 ATCAGTATTTTCATTCTTAATTTCAACATTTTCACCCTGGAAAAATCAAATTAAAATT-AAAATC
2569 CTGAAATTCAGGATGAAATTGTTGGTGCGGCATAA
130 CTGAAATTCAGGATGAAATTGTTGGTGCGGCATAA
2604 AAAATGATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
1 AAAATGATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
* * * *
2669 ATCAGTATTTTCATTCTTAATTTTAACTTTTTCATCCTGTAAAAATCAAATTAAAATTAAAATCC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTTCACCCTGGAAAAATCAAATTAAAATTAAAATCC
*
2734 TGAAATTCAGGATGAAATTGTTGGTGTGGCATAA
131 TGAAATTCAGGATGAAATTGTTGGTGCGGCATAA
2768 AA
1 AA
2770 CTATCGGAAA
Statistics
Matches: 155, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
163 5 0.03
164 150 0.97
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (164 bp):
AAAATGATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
ATCAGTATTTTCATTCTTAATTTCAACATTTTCACCCTGGAAAAATCAAATTAAAATTAAAATCC
TGAAATTCAGGATGAAATTGTTGGTGCGGCATAA
Found at i:2837 original size:606 final size:598
Alignment explanation
Indices: 1426--3182 Score: 2650
Period size: 606 Copynumber: 2.9 Consensus size: 598
1416 CAGTGAAACC
* * *
1426 ACGTCATTTGTGTCCCTTTTTC-AATAATTTTACGCTAAATCAGTATTTTCATTCTTAATTTCAA
1 ACGTCATTTGTGTCCC-TTTTCAAATAGTTTTACGCCAAATCAGTATTTTCATTCTTAATTTAAA
* *
1490 CATTTACATCCTGAAAAGAAACAAATTAAAATAAAAATCCTGAAATTCAAGATGAAATTGTTGGT
65 CATTTTCATCCTGAAAA-AAACAAATTAAAATAAAAATCCTGAAATTCAGGATGAAATTGTTGGT
* * * * * *
1555 GTGGCAAAAAACTATCGGAAAGGGATAATATCCCTACTTCATACCACCCTTTCTCTTCTTTAATG
129 GTGGCATAAAACTATCGGAAAGGGATAATATCCCTATTTTATACAATCCTTTCTCTTCTTCAATG
* *
1620 GAAAAGGATTAAATGAAACAGTGACTCCACGTCATTTGTGTCCCTTTTCTAATAGTTTTACA-CC
194 GAAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTAATAGTTTTA-AGCC
* *
1684 ATATCAATATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAAAACAAATTAAAATTAAAAT
258 ACATCAATATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAATA-AAATTAAAATTAAAAT
*
1749 CCTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTACTGGAAAGGGATAATATCCCTGTT
322 CCTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTT
* * *
1814 TTATACAATCCTTTCTCTTCTTCAGTGGAAAAGGATTG-A-GAAACAGTGAGA-AGACGTCATCT
387 TTATACAATCCTTTCTCTTCTTCAATGGAAAA-GATTGAATGAAACAGTGACACA-ACGTCATTT
* * *
1876 GTGTCCCTTTTCTAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTTAACATTTTCATC
450 GTGTCCCTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATC
* * *
1941 TTGAAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGTGGCATAAAA
515 CTGGAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGCGGCATAAAA
* ** *
2006 CTAATGGAACAGTGACACC
580 CTAATGAAACAACGACACA
* *
2025 ACGTCATTTGTGTCCCTTTT-ACAATAGTTTTACGCCATATCAATATTTTCATTCTTAATTTAAA
1 ACGTCATTTGTGTCCCTTTTCA-AATAGTTTTACGCCAAATCAGTATTTTCATTCTTAATTTAAA
* * *
2089 CATTTTCATCCTGAAAAAAACAAATTAAAATCAAAATCCTAAAATACAGGATGAAATTGTTGGTG
65 CATTTTCATCCTGAAAAAAACAAATTAAAATAAAAATCCTGAAATTCAGGATGAAATTGTTGGTG
* *
2154 TGGCATAAAACTATTGGAAAGGGATAATATCCCTATTTTATACAATCCTTTCTCCTCTTCAATGG
130 TGGCATAAAACTATCGGAAAGGGATAATATCCCTATTTTATACAATCCTTTCTCTTCTTCAATGG
* * *
2219 AAAAGAATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTTAAGCCAC
195 AAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTAATAGTTTTAAGCCAC
*
2284 ATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAATTAAAATTAAAATTAAAATCC
260 ATCAATATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAA-TAAAATTAAAATTAAAATCC
* ** * * * *
2349 TGAAATTCAAAATGAAATTGTTGATGTGGCATAAAACAATTGGAAGGGGATAATATCCCTGTTTC
324 TGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTT
*
2414 ATACAATCCTTTCTCTTCTTTAATGGAAAATGATTGAATGAAACAGTGACACAACGTCATTTGTG
389 ATACAATCCTTTCTCTTCTTCAATGGAAAA-GATTGAATGAAACAGTGACACAACGTCATTTGTG
*
2479 TCCCTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCACCCTG
453 TCCCTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTG
* *
2544 GGAAAATCAAATTAAAATTAAAAAT-CTGAAATTCAGGATGAAATTGTTGGTGCGGCATAAAAAA
518 GAAAAATCAAATTAAAATT-AAAATCCTGAAATTCAGGATGAAATTGTTGATGCGGCAT---AAA
*
2608 TGATTGAATGAAACAACGACACA
579 --ACT-AATGAAACAACGACACA
* *
2631 ACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCACATCAGTATTTTCATTCTTAATTTTAAC
1 ACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAAATCAGTATTTTCATTCTTAATTTAAAC
* * * *
2696 TTTTTCATCCTGTAAAAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGGTGT
66 ATTTTCATCCTGAAAAAAACAAATTAAAATAAAAATCCTGAAATTCAGGATGAAATTGTTGGTGT
* *
2761 GGCATAAAACTATCGGAAAGGGATAATATCCCTGTTTTATACAATCCTTTCTCTTCTTCAATGGG
131 GGCATAAAACTATCGGAAAGGGATAATATCCCTATTTTATACAATCCTTTCTCTTCTTCAATGGA
*
2826 AAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTAATAGTTTTACGCCACA
196 AAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTAATAGTTTTAAGCCACA
* * *
2891 TCAATATTTTAATTCTTAATTTCAACATTTTCATCCTTAAAAAATCAAATTAAAATTAAAATCCT
261 TCAATATTTTCATTCTTAATTTCAACATTTTCATCC-TGAAAAATAAAATTAAAATTAAAATCCT
2956 GAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTTA
325 GAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTTA
* *
3021 TACAATCCTTTCTCCTCTTCAATGGAAAAGAATTGAATGAAACAGTGACACCACGTCATTTGTGT
390 TACAATCCTTTCTCTTCTTCAATGGAAAAG-ATTGAATGAAACAGTGACACAACGTCATTTGTGT
*
3086 CCCTTTTCCATTAGTTTTACT-CCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCT-
454 CCCTTTTCCAATAGTTTTA-TGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTG
* *
3149 GAAAAATTAAAAGTAAAATTAAAATCCTGAAATT
518 GAAAAA-TCAAATTAAAATTAAAATCCTGAAATT
3183 GAAAATGA
Statistics
Matches: 1049, Mismatches: 89, Indels: 33
0.90 0.08 0.03
Matches are distributed among these distances:
597 1 0.00
598 313 0.30
599 71 0.07
600 130 0.12
601 6 0.01
603 3 0.00
605 13 0.01
606 504 0.48
607 8 0.01
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (598 bp):
ACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAAATCAGTATTTTCATTCTTAATTTAAAC
ATTTTCATCCTGAAAAAAACAAATTAAAATAAAAATCCTGAAATTCAGGATGAAATTGTTGGTGT
GGCATAAAACTATCGGAAAGGGATAATATCCCTATTTTATACAATCCTTTCTCTTCTTCAATGGA
AAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTAATAGTTTTAAGCCACA
TCAATATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAATAAAATTAAAATTAAAATCCTG
AAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTTAT
ACAATCCTTTCTCTTCTTCAATGGAAAAGATTGAATGAAACAGTGACACAACGTCATTTGTGTCC
CTTTTCCAATAGTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGGAA
AAATCAAATTAAAATTAAAATCCTGAAATTCAGGATGAAATTGTTGATGCGGCATAAAACTAATG
AAACAACGACACA
Found at i:2920 original size:21 final size:21
Alignment explanation
Indices: 2891--2930 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2881 TTACGCCACA
* *
2891 TCAATATTTTAATTCTTAATT
1 TCAACATTTTAATCCTTAATT
*
2912 TCAACATTTTCATCCTTAA
1 TCAACATTTTAATCCTTAA
2931 AAAATCAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (21 bp):
TCAACATTTTAATCCTTAATT
Found at i:2992 original size:221 final size:221
Alignment explanation
Indices: 2604--3181 Score: 951
Period size: 221 Copynumber: 2.6 Consensus size: 221
2594 TGCGGCATAA
* ** *
2604 AAAATGATTGAATGAAACAACGACACAACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
1 AAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
* *
2669 ATCAGTATTTTCATTCTTAATTTTAACTTTTTCATCCTGT-AAAAATCAAATTAAAATTAAAATC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCT-TAAAAAATCAAATTAAAATTAAAATC
*
2733 CTGAAATTCAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTGTTT
130 CTGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTGTTT
*
2798 TATACAATCCTTTCTCTTCTTCAATGG
195 TATACAATCCTTTCTCCTCTTCAATGG
* *
2825 GAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCTAATAGTTTTACGCCAC
1 AAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
* *
2890 ATCAATATTTTAATTCTTAATTTCAACATTTTCATCCTTAAAAAATCAAATTAAAATTAAAATCC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTTAAAAAATCAAATTAAAATTAAAATCC
*
2955 TGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATTGGAAAGGGATAATATCCCTGTTTT
131 TGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTGTTTT
3020 ATACAATCCTTTCTCCTCTTCAATGG
196 ATACAATCCTTTCTCCTCTTCAATGG
* * * *
3046 AAAAGAATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCCATTAGTTTTACTCCAC
1 AAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
* * * *
3111 ATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTGAAAAATTAAAAGTAAAATTAAAATCC
66 ATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTTAAAAAATCAAATTAAAATTAAAATCC
3176 TGAAAT
131 TGAAAT
3182 TGAAAATGA
Statistics
Matches: 332, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
220 1 0.00
221 331 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (221 bp):
AAAAGGATTGAATGAAACAGTGACACCACGTCATTTGTGTCCCTTTTCAAATAGTTTTACGCCAC
ATCAGTATTTTCATTCTTAATTTCAACATTTTCATCCTTAAAAAATCAAATTAAAATTAAAATCC
TGAAATACAGGATGAAATTGTTGGTGTGGCATAAAACTATCGGAAAGGGATAATATCCCTGTTTT
ATACAATCCTTTCTCCTCTTCAATGG
Done.