Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013393.1 Kokia drynarioides strain JFW-HI SEQ_128417, 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: 20438
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:881 original size:297 final size:292
Alignment explanation
Indices: 435--2626 Score: 2032
Period size: 297 Copynumber: 7.6 Consensus size: 292
425 TGATTGGGCT
* * * *
435 TACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTG
1 TACCCCCTGAGTATTATAGTGTACTAAAGTTAGAAAATAAAAGGTTAACAGACTTCATAGAGTTG
* * * * * *
500 GTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGGGCTCGTCAAGTTTTCAA
66 GTGTAACATTACTTGTAGGTCCTA-GT--TCTGTAGT-GGTGCGTTGGACTCGTCGAGTTTCCAA
* * *
565 CAACCTTTATGTCGCTAGAGAATTATGCAAAACGAGAACACATATCAAAGATTCTATATGAGATA
127 CAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATTCCATATGAGATA
**
630 TATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATGTAAATTTTCTAAATGATATA
192 TATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCCAAATTTTCTAAATGATATA
* * * *
695 TAGTGGAATCTGCCACCTGAATAATACATGGTTGGTC
257 TAGTCGACTCTACCGCCTGAATAATACATGGTTGG-C
* * *
732 TTCCCCCTGAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTG
1 TACCCCCTGAGTATTATAGTGTACTAAAGTTAGAAAATAAAAGGTTAACAGACTTCATAGAGTTG
* *
797 GTGTAACATTACTTGTAGGTCCTAGGTCCTCTGTAGTTGGTGTGTT-GAGCTTGTCGAGTTTCCA
66 GTGTAACATTACTTGTAGGTCCTA-GT--TCTGTAG-TGGTGCGTTGGA-CTCGTCGAGTTTCCA
* *
861 ACAGCCTTTATGTTGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGAT
126 ACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATTCCATATGAGAT
* *
926 ATATGCAT-GTTTAAGAAATGAGCATTGACAAGCTGTGAAATGATCCAAATTTTCTAAATGATAT
191 ATATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCCAAATTTTCTAAATGATAT
* *
990 ATAGTTGACTTTACCGCCTGAATAATACATGGTTAGCGC
256 ATAGTCGACTCTACCGCCTGAATAATACATGGTT-G-GC
* **
1029 TACCGCCTGAGTATTATAGTGTACTAAAGTTAGAAAATAAAATATTAACAGACTTCATAGAG-T-
1 TACCCCCTGAGTATTATAGTGTACTAAAGTTAGAAAATAAAAGGTTAACAGACTTCATAGAGTTG
** *
1092 -TGTAACATTACTTGTAGGTCCTA---C-GTAGTGAGTGCGTTGGACTCGTCGAGTTTTTAATAG
66 GTGTAACATTACTTGTAGGTCCTAGTTCTGTAGTG-GTGCGTTGGACTCGTCGAGTTTCCAACAG
* *
1152 CCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAGATCCCATATGAGATATAT
130 CCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATTCCATATGAG--ATAT
* * *
1217 ATGCATGGTTCAAGAAATGAGCATTGACAAGCTATGAAATAATCCAAATTTTTTGAATGATATAT
193 ATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCCAAATTTTCTAAATGATATAT
* * **
1282 AGTCGACTCTACCGCCTGAGT-AT-TAT-AAT-GC
258 AGTCGACTCTACCGCCTGAATAATACATGGTTGGC
* * * ** * * * *
1313 -A----C----TA--A-AGT-TA-GAAA-ATA-AAAGGTTAACCGACTTCATAGA-GT--T-G-G
1 TACCCCCTGAGTATTATAGTGTACTAAAGTTAGAAA--ATAAAAG-GTTAACAGACTTCATAGAG
**** * * * * * * *
1357 TGTAACATTACTTCTAGGTTTTAGGTCC----TCTGTAGTGGGTGCATTGGACTCGTCAAGTTTT
63 T-TGGTGTAACAT-TA-CTTGTAGGTCCTAGTTCTGTAGT-GGTGCGTTGGACTCGTCGAGTTTC
* * *
1418 CAACAACCTTTATGTCGCTAGAGAATTATGCAAAACGAGAACACATATCAAAGATTCTATATGAG
124 CAACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATTCCATATGAG
* *
1483 ATATATGCATGGTTCAAGAAATGAGCATTGACAAACTGTGAAATAATCTAAATTTTCTAAATGAT
189 ATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCCAAATTTTCTAAATGAT
* * * *
1548 ATATAGTGGAATCTGCCACCTGAA-AATACATGGTTGGCC
254 ATATAGTCGACTCTACCGCCTGAATAATACATGGTTGG-C
* * *
1587 TTCCCCCCTGAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTT
1 -TACCCCCTGAGTATTATAGTGTACTAAAGTTAGAAAATAAAAGGTTAACAGACTTCATAGAGTT
* * *
1652 GGTGTAACATTACTTATAGGTCCTAGGTCTTCTGTAGTTGGTGTGTT-GAGCTTGTCGAGTTTCC
65 GGTGTAACATTACTTGTAGGTCCTA-G--TTCTGTAG-TGGTGCGTTGGA-CTCGTCGAGTTTCC
*
1716 AACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGA
125 AACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATTCCATATGAGA
* *
1781 TATATGCAT-GTTTAAGAAATGAGCATTGACAAGCTGTGAAATGATCCAAATTTTCTAAATGATA
190 TATATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCCAAATTTTCTAAATGATA
*
1845 TATAGTTGACTCTACCGCCTGAATAATACATGGTTAGCGC
255 TATAGTCGACTCTACCGCCTGAATAATACATGGTT-G-GC
* * * *
1885 TACCGCCTGAGTATTATAGTGTACTAAAGTTATAAAATAAAAGATTAATAGACTTCATAGAG-T-
1 TACCCCCTGAGTATTATAGTGTACTAAAGTTAGAAAATAAAAGGTTAACAGACTTCATAGAGTTG
* *
1948 -TGTAACATTACTTGTAGGTCCTA---C-GTAGTGAGTGCGTTGGACTCATCGAGTTTCCAATAG
66 GTGTAACATTACTTGTAGGTCCTAGTTCTGTAGTG-GTGCGTTGGACTCGTCGAGTTTCCAACAG
2008 CCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGA-TCTCATATGAGATATA
130 CCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATTC-CATATGAG--ATA
* * *
2072 TATGCATGGTTCAAGAAATGAGCATTGACAAGCTATGAAATAATCCAAATTTTTTGAATGATATA
192 TATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCCAAATTTTCTAAATGATATA
* * * **
2137 TAGTCGACTCTGCCGCCTGAGT-AT-TAT-AAT-GC
257 TAGTCGACTCTACCGCCTGAATAATACATGGTTGGC
* * * ** * * * *
2169 -A----C----TA--A-AGT-TA-GAAA-ATA-AAAGGTTAACCGACTTCATAGA-GT--T-G-G
1 TACCCCCTGAGTATTATAGTGTACTAAAGTTAGAAA--ATAAAAG-GTTAACAGACTTCATAGAG
**** * * * * *
2213 TGTAACATTAC-TT-C-T--AGGTCTTAGGTCCTCTATAGTGG-GTCTGTT-AAGCTCATCGAGT
63 T-TGGTGTAACATTACTTGTAGGTCCTA-GT--TCTGTAGTGGTG-C-GTTGGA-CTCGTCGAGT
* * * *
2271 TTCCAATAGCCTTTATGTCGCTAAAGAATTATGCAAAACGAGAATACATGTCAAAGATTTCATAT
121 TTCCAACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATTCCATAT
* * *
2336 GAGATATATGCATGGTTCAAGAAATGAGCATT-AGCAAGCTATGAAATAATCCAAATTTTATGAA
186 GAGATATATGCATGGTTCAAGAAATGAGCATTGA-CAAGCTGTGAAATAATCCAAATTTTCTAAA
* * *
2400 TGATATATAGTCCACTTTACCGCCTGAATAATAAATGG-TGGCCC
250 TGATATATAGTCGACTCTACCGCCTGAATAATACATGGTTGG--C
** * * * * * *
2444 TGTCGCTTAAGTATTATAGT-TCACTAAAGTTAGAAAATAAAATGTTAACCGACTTCATAAAGTT
1 TACCCCCTGAGTATTATAGTGT-ACTAAAGTTAGAAAATAAAAGGTTAACAGACTTCATAGAGTT
* * * *
2508 AGTGTAACATTACTTGTAGGTCCTAGGTTCTCTGTAGTGGGTGTGTTGGCCTCGTCGAGTTTTCA
65 GGTGTAACATTACTTGTAGGTCCTA-G-T-TCTGTAGT-GGTGCGTTGGACTCGTCGAGTTTCCA
* * * * *
2573 ACAACCTTTATGTCACTAAAGAATTATGCAAAACAAGAATACATGTCAAAGATT
126 ACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATT
2627 TATAAAATAT
Statistics
Matches: 1572, Mismatches: 202, Indels: 242
0.78 0.10 0.12
Matches are distributed among these distances:
265 7 0.00
266 2 0.00
267 3 0.00
268 11 0.01
269 7 0.00
270 187 0.12
271 28 0.02
272 184 0.12
273 6 0.00
274 1 0.00
275 5 0.00
279 2 0.00
280 1 0.00
283 2 0.00
284 8 0.01
286 8 0.01
287 172 0.11
288 23 0.01
289 39 0.02
290 155 0.10
291 10 0.01
292 11 0.01
293 6 0.00
294 46 0.03
295 1 0.00
296 156 0.10
297 481 0.31
298 8 0.01
299 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (292 bp):
TACCCCCTGAGTATTATAGTGTACTAAAGTTAGAAAATAAAAGGTTAACAGACTTCATAGAGTTG
GTGTAACATTACTTGTAGGTCCTAGTTCTGTAGTGGTGCGTTGGACTCGTCGAGTTTCCAACAGC
CTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATTCCATATGAGATATATG
CATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCCAAATTTTCTAAATGATATATAGT
CGACTCTACCGCCTGAATAATACATGGTTGGC
Found at i:2087 original size:856 final size:856
Alignment explanation
Indices: 1--2626 Score: 3975
Period size: 856 Copynumber: 3.0 Consensus size: 856
* * * * *
1 AATTATGAAAAATGAGAATACATGTGAAAGATTTCATATGAGATATATGCATGATTCAAGAAATG
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATG-TTTAAGAAATG
* * * * * * *
66 ATCATTGACAAGCTGTGAAATGATCCAAATTTTTTGAATGATATATAGTCGAATATGCAGCCTGA
65 AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTAAATGATATATAGTTGACTATACCGCCTGA
* * * * * *
131 ATAATACATGATTGACCG-TACCGCTTGAGTATTATAGTGCATTAAAGTTAAAAAATAAAAGGTT
130 ATAATACATGGTT-AGCGCTACCGCCTGAGTATTATAGTGTACTAAAGTTAAAAAATAAAAGATT
* ** * *
195 AACCGACTTCATAGAGTTGGTGTAACATTACTTATAGGTCTTAGGTCCTTTGTAGTGGGTGCATT
194 AACAGACTTCATAGAG-T--TGTAACATTAC-T-T--G---TAGGTCCTACGTAGTGAGTGCGTT
** * *
260 GGGTTCGTCGAATTTCTAATAGCCTTTATATCGCTAGAGAATTATGCAAAACGAGAATACATGTC
249 GGACTCGTCGAGTTTCTAATAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTC
* * * ** *
325 AAAAAT-TCCATAT-A-AGATATATGCATGATTCAAGAAATGAGCATTGACAAGCCGTGAAATGA
314 AAAGATCT-CATATGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTATGAAATAA
*
387 TCCAAATTTTCTGAATGATATATAGTCGAATCTAACAATGATTGGGCTTACCGCCTGAGTATTAT
378 TCCAAATTTTTTGAATGATATATAGTCG------AC------T---C-TACCGCCTGAGTATTAT
* *
452 AGTGCACTAAACTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTACTTCTA
427 AATGCACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTACTTCTA
*
517 GGTCTTAGGTCCTCTGTAGTGGGTGCATTGGGCTCGTCAAGTTTTCAACAACCTTTATGTCGCTA
492 GGTCTTAGGTCCTCTGTAGTGGGTGCATTGGACTCGTCAAGTTTTCAACAACCTTTATGTCGCTA
582 GAGAATTATGCAAAACGAGAACACATATCAAAGATTCTATATGAGATATATGCATGGTTCAAGAA
557 GAGAATTATGCAAAACGAGAACACATATCAAAGATTCTATATGAGATATATGCATGGTTCAAGAA
*
647 ATGAGCATTGACAAGCTGTGAAATAATGTAAATTTTCTAAATGATATATAGTGGAATCTGCCACC
622 ATGAGCATTGACAAGCTGTGAAATAATCTAAATTTTCTAAATGATATATAGTGGAATCTGCCACC
*
712 TGAATAATACATGGTTGGTCTTCCCCCTGAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGT
687 TGAATAATACATGGTTGGCCTTCCCCCTGAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGT
*
777 TAACCGACTTCATAGAGTTGGTGTAACATTACTTGTAGGTCCTAGGTCCTCTGTAGTTGGTGTGT
752 TAACCGACTTCATAGAGTTGGTGTAACATTACTTGTAGGTCCTAGGTCTTCTGTAGTTGGTGTGT
*
842 TGAGCTTGTCGAGTTTCCAACAGCCTTTATGTTGCTAGAG
817 TGAGCTTGTCGAGTTTCCAACAGCCTTTATGTCGCTAGAG
882 AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGTTTAAGAAATGA
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGTTTAAGAAATGA
*
947 GCATTGACAAGCTGTGAAATGATCCAAATTTTCTAAATGATATATAGTTGACTTTACCGCCTGAA
66 GCATTGACAAGCTGTGAAATGATCCAAATTTTCTAAATGATATATAGTTGACTATACCGCCTGAA
* *
1012 TAATACATGGTTAGCGCTACCGCCTGAGTATTATAGTGTACTAAAGTTAGAAAATAAAATATTAA
131 TAATACATGGTTAGCGCTACCGCCTGAGTATTATAGTGTACTAAAGTTAAAAAATAAAAGATTAA
1077 CAGACTTCATAGAGTTGTAACATTACTTGTAGGTCCTACGTAGTGAGTGCGTTGGACTCGTCGAG
196 CAGACTTCATAGAGTTGTAACATTACTTGTAGGTCCTACGTAGTGAGTGCGTTGGACTCGTCGAG
* *
1142 TTTTTAATAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAGATCCCATA
261 TTTCTAATAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAGATCTCATA
1207 TGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTATGAAATAATCCAAATTTTTTG
326 TGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTATGAAATAATCCAAATTTTTTG
1272 AATGATATATAGTCGACTCTACCGCCTGAGTATTATAATGCACTAAAGTTAGAAAATAAAAGGTT
391 AATGATATATAGTCGACTCTACCGCCTGAGTATTATAATGCACTAAAGTTAGAAAATAAAAGGTT
*
1337 AACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTTTTAGGTCCTCTGTAGTGGGTGCATT
456 AACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATT
1402 GGACTCGTCAAGTTTTCAACAACCTTTATGTCGCTAGAGAATTATGCAAAACGAGAACACATATC
521 GGACTCGTCAAGTTTTCAACAACCTTTATGTCGCTAGAGAATTATGCAAAACGAGAACACATATC
*
1467 AAAGATTCTATATGAGATATATGCATGGTTCAAGAAATGAGCATTGACAAACTGTGAAATAATCT
586 AAAGATTCTATATGAGATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCT
1532 AAATTTTCTAAATGATATATAGTGGAATCTGCCACCTGAA-AATACATGGTTGGCCTTCCCCCCT
651 AAATTTTCTAAATGATATATAGTGGAATCTGCCACCTGAATAATACATGGTTGGCCTT-CCCCCT
1596 GAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACA
715 GAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACA
*
1661 TTACTTATAGGTCCTAGGTCTTCTGTAGTTGGTGTGTTGAGCTTGTCGAGTTTCCAACAGCCTTT
780 TTACTTGTAGGTCCTAGGTCTTCTGTAGTTGGTGTGTTGAGCTTGTCGAGTTTCCAACAGCCTTT
1726 ATGTCGCTAGAG
845 ATGTCGCTAGAG
1738 AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGTTTAAGAAATGA
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGTTTAAGAAATGA
*
1803 GCATTGACAAGCTGTGAAATGATCCAAATTTTCTAAATGATATATAGTTGACTCTACCGCCTGAA
66 GCATTGACAAGCTGTGAAATGATCCAAATTTTCTAAATGATATATAGTTGACTATACCGCCTGAA
*
1868 TAATACATGGTTAGCGCTACCGCCTGAGTATTATAGTGTACTAAAGTTATAAAATAAAAGATTAA
131 TAATACATGGTTAGCGCTACCGCCTGAGTATTATAGTGTACTAAAGTTAAAAAATAAAAGATTAA
* *
1933 TAGACTTCATAGAGTTGTAACATTACTTGTAGGTCCTACGTAGTGAGTGCGTTGGACTCATCGAG
196 CAGACTTCATAGAGTTGTAACATTACTTGTAGGTCCTACGTAGTGAGTGCGTTGGACTCGTCGAG
* *
1998 TTTCCAATAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATATCAAAGATCTCATA
261 TTTCTAATAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAGATCTCATA
2063 TGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTATGAAATAATCCAAATTTTTTG
326 TGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTATGAAATAATCCAAATTTTTTG
*
2128 AATGATATATAGTCGACTCTGCCGCCTGAGTATTATAATGCACTAAAGTTAGAAAATAAAAGGTT
391 AATGATATATAGTCGACTCTACCGCCTGAGTATTATAATGCACTAAAGTTAGAAAATAAAAGGTT
*
2193 AACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTATAGTGGGT-C-TG
456 AACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCAT-
** * * * * * * * *
2256 TTAAGCTCATCGAGTTTCCAATAGCCTTTATGTCGCTAAAGAATTATGCAAAACGAGAATACATG
520 TGGA-CTCGTCAAGTTTTCAACAACCTTTATGTCGCTAGAGAATTATGCAAAACGAGAACACATA
*
2321 TCAAAGATT-TCATATGAGATATATGCATGGTTCAAGAAATGAGCATT-AGCAAGCTATGAAATA
584 TCAAAGATTCT-ATATGAGATATATGCATGGTTCAAGAAATGAGCATTGA-CAAGCTGTGAAATA
* * * ** * * * * *
2384 ATCCAAATTTTATGAATGATATATAGTCCACTTTACCGCCTGAATAATAAATGG-TGGCCCTGT-
647 ATCTAAATTTTCTAAATGATATATAGTGGAATCTGCCACCTGAATAATACATGGTTGG-CCT-TC
* * * * * * *
2447 CGCTTAAGTATTATAGT-TCACTAAAGTTAGAAAATAAAATGTTAACCGACTTCATAAAGTTAGT
710 CCCCTGAGTATTATAGTGT-ACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGT
* * *
2511 GTAACATTACTTGTAGGTCCTAGGT-TCTCTGTAGTGGGTGTGTTG-GCCTCGTCGAGTTTTCAA
774 GTAACATTACTTGTAGGTCCTAGGTCT-TCTGTAGTTGGTGTGTTGAG-CTTGTCGAGTTTCCAA
* * *
2574 CAACCTTTATGTCACTAAAG
837 CAGCCTTTATGTCGCTAGAG
*
2594 AATTATGCAAAACAAGAATACATGTCAAAGATT
1 AATTATGCAAAACGAGAATACATGTCAAAGATT
2627 TATAAAATAT
Statistics
Matches: 1632, Mismatches: 98, Indels: 55
0.91 0.05 0.03
Matches are distributed among these distances:
854 1 0.00
855 24 0.01
856 1229 0.75
857 12 0.01
858 1 0.00
860 1 0.00
866 2 0.00
870 90 0.06
871 1 0.00
872 70 0.04
873 1 0.00
875 1 0.00
876 1 0.00
877 11 0.01
879 4 0.00
880 134 0.08
881 49 0.03
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (856 bp):
AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGTTTAAGAAATGA
GCATTGACAAGCTGTGAAATGATCCAAATTTTCTAAATGATATATAGTTGACTATACCGCCTGAA
TAATACATGGTTAGCGCTACCGCCTGAGTATTATAGTGTACTAAAGTTAAAAAATAAAAGATTAA
CAGACTTCATAGAGTTGTAACATTACTTGTAGGTCCTACGTAGTGAGTGCGTTGGACTCGTCGAG
TTTCTAATAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAGATCTCATA
TGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTATGAAATAATCCAAATTTTTTG
AATGATATATAGTCGACTCTACCGCCTGAGTATTATAATGCACTAAAGTTAGAAAATAAAAGGTT
AACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATT
GGACTCGTCAAGTTTTCAACAACCTTTATGTCGCTAGAGAATTATGCAAAACGAGAACACATATC
AAAGATTCTATATGAGATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTGTGAAATAATCT
AAATTTTCTAAATGATATATAGTGGAATCTGCCACCTGAATAATACATGGTTGGCCTTCCCCCTG
AGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACAT
TACTTGTAGGTCCTAGGTCTTCTGTAGTTGGTGTGTTGAGCTTGTCGAGTTTCCAACAGCCTTTA
TGTCGCTAGAG
Found at i:2272 original size:559 final size:563
Alignment explanation
Indices: 1593--2625 Score: 1515
Period size: 559 Copynumber: 1.8 Consensus size: 563
1583 GGCCTTCCCC
* *
1593 CCTGAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTA
1 CCTGAGTATTATAATGCACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTA
* * * * * **
1658 ACATTACTTATAGGTCCTAGGTCTTCTGTAGTTGGTGTGTTGAGCTTGTCGAGTTTCCAACAGCC
66 ACATTACTTATAGGTCCTAGGTCCTCTATAGTGGGTCTGTTAAGCTCATCGAGTTTCCAACAGCC
*
1723 TTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGC
131 TTTATGTCGCTAAAGAATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGC
* * * *
1788 AT-GTTTAAGAAATGAGCATT-GACAAGCTGTGAAATGATCCAAATTTTCTAAATGATATATAGT
196 ATGGTTCAAGAAATGAGCATTAG-CAAGCTATGAAATAATCCAAATTTTATAAATGATATATAGT
** * * *
1851 TGACTCTACCGCCTGAATAATACATGGTTAGCGCTACCGCCTGAGTATTATAGTGT-ACTAAAGT
260 CCACTCTACCGCCTGAATAATAAATGG-TAGCCCTACCGCCTAAGTATTATAGT-TCACTAAAGT
* * *
1915 TATAAAATAAAA-GATTAATAGACTTCATAGAG-T-TGTAACATTACTTGTAGGTCCTA-C-GTA
323 TAGAAAATAAAATG-TTAACAGACTTCATAAAGTTATGTAACATTACTTGTAGGTCCTATCTGTA
* * * * *
1975 GTGAGTGCGTTGGACTCATCGAGTTTCCAATAGCCTTTATGTCGCTAGAGAATTATGCAAAACGA
387 GTGAGTGCGTTGGACTCATCGAGTTTCCAACAACCTTTATGTCACTAAAGAATTATGCAAAACAA
2040 GAATACATATCAAAGATCTCATATGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGC
452 GAATACATATCAAAGATCTCATATGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGC
2105 TATGAAATAATCCAAATTTTTTGAATGATATATAGTCGACTCTGCCG
517 TATGAAATAATCCAAATTTTTTGAATGATATATAGTCGACTCTGCCG
*
2152 CCTGAGTATTATAATGCACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTA
1 CCTGAGTATTATAATGCACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTA
* * *
2217 ACATTACTTCTAGGTCTTAGGTCCTCTATAGTGGGTCTGTTAAGCTCATCGAGTTTCCAATAGCC
66 ACATTACTTATAGGTCCTAGGTCCTCTATAGTGGGTCTGTTAAGCTCATCGAGTTTCCAACAGCC
*
2282 TTTATGTCGCTAAAGAATTATGCAAAACGAGAATACATGTCAAAGATTTCATATGAGATATATGC
131 TTTATGTCGCTAAAGAATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGC
*
2347 ATGGTTCAAGAAATGAGCATTAGCAAGCTATGAAATAATCCAAATTTTATGAATGATATATAGTC
196 ATGGTTCAAGAAATGAGCATTAGCAAGCTATGAAATAATCCAAATTTTATAAATGATATATAGTC
* * ** *
2412 CACTTTACCGCCTGAATAATAAATGGTGGCCCTGTCGCTTAAGTATTATAGTTCACTAAAGTTAG
261 CACTCTACCGCCTGAATAATAAATGGTAGCCCTACCGCCTAAGTATTATAGTTCACTAAAGTTAG
*
2477 AAAATAAAATGTTAACCGACTTCATAAAGTTAGTGTAACATTACTTGTAGGTCCTAGGTTCTCTG
326 AAAATAAAATGTTAACAGACTTCATAAAGTTA-TGTAACATTACTTGTAGGTCCTA-----TCTG
* * * * *
2542 TAGTGGGTGTGTTGGCCTCGTCGAGTTTTCAACAACCTTTATGTCACTAAAGAATTATGCAAAAC
385 TAGTGAGTGCGTTGGACTCATCGAGTTTCCAACAACCTTTATGTCACTAAAGAATTATGCAAAAC
*
2607 AAGAATACATGTCAAAGAT
450 AAGAATACATATCAAAGAT
2626 TTATAAAATA
Statistics
Matches: 415, Mismatches: 45, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
558 1 0.00
559 236 0.57
560 79 0.19
561 1 0.00
562 23 0.06
568 1 0.00
569 74 0.18
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (563 bp):
CCTGAGTATTATAATGCACCAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTA
ACATTACTTATAGGTCCTAGGTCCTCTATAGTGGGTCTGTTAAGCTCATCGAGTTTCCAACAGCC
TTTATGTCGCTAAAGAATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGC
ATGGTTCAAGAAATGAGCATTAGCAAGCTATGAAATAATCCAAATTTTATAAATGATATATAGTC
CACTCTACCGCCTGAATAATAAATGGTAGCCCTACCGCCTAAGTATTATAGTTCACTAAAGTTAG
AAAATAAAATGTTAACAGACTTCATAAAGTTATGTAACATTACTTGTAGGTCCTATCTGTAGTGA
GTGCGTTGGACTCATCGAGTTTCCAACAACCTTTATGTCACTAAAGAATTATGCAAAACAAGAAT
ACATATCAAAGATCTCATATGAGATATATATGCATGGTTCAAGAAATGAGCATTGACAAGCTATG
AAATAATCCAAATTTTTTGAATGATATATAGTCGACTCTGCCG
Found at i:2756 original size:179 final size:179
Alignment explanation
Indices: 2455--2805 Score: 542
Period size: 179 Copynumber: 2.0 Consensus size: 179
2445 GTCGCTTAAG
* * *
2455 TATTATAGTTCACTAAAGTTAGAAAATAAAATGTTAACCGACTTCATAAAGTTAGTGTAACATTA
1 TATTATAGTGCACTAAAGTTAGAAAATAAAAAGTTAACCAACTTCATAAAGTTAGTGTAACATTA
* * * * *
2520 CTTGTAGGTCCTAGGTTCTCTGTAGTGGGTGTGTTGGCCTCGTCGAGTTTTCAACAACCTTTATG
66 CTTGTAGGCCCTAAGTCCTCTGTAGTAGGTGTGTTGGCCTCGTCGAGTTTCCAACAACCTTTATG
* *
2585 TCACTAAAGAATTATGCAAAACAAGAATACATGTCAAAGATTTATAAAA
131 TCACTAAAGAATTATGCAAAACAAGAATACACGCCAAAGATTTATAAAA
* *
2634 TATTATAGTGCACTAAAGTTAGAAAATAAAAAGTTAACTAACTTCATAGAGTT-GATGTAACATT
1 TATTATAGTGCACTAAAGTTAGAAAATAAAAAGTTAACCAACTTCATAAAGTTAG-TGTAACATT
* * *
2698 ATTTGTAGGCCCTAAGTCCTCTGTAGTAGGTGTGTTGGGCTCGTTGAGTTTCCAACAACCTTTAT
65 ACTTGTAGGCCCTAAGTCCTCTGTAGTAGGTGTGTTGGCCTCGTCGAGTTTCCAACAACCTTTAT
*
2763 GTCGCTAAAGAATTATGCAAAACAAGAATACACGCCAAAGATT
130 GTCACTAAAGAATTATGCAAAACAAGAATACACGCCAAAGATT
2806 CCATATGAGA
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
178 1 0.01
179 154 0.99
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (179 bp):
TATTATAGTGCACTAAAGTTAGAAAATAAAAAGTTAACCAACTTCATAAAGTTAGTGTAACATTA
CTTGTAGGCCCTAAGTCCTCTGTAGTAGGTGTGTTGGCCTCGTCGAGTTTCCAACAACCTTTATG
TCACTAAAGAATTATGCAAAACAAGAATACACGCCAAAGATTTATAAAA
Found at i:12571 original size:35 final size:35
Alignment explanation
Indices: 12532--12611 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
12522 TTGAAACTGC
*
12532 AAAAATCAAAGTCATTTTTGTTGAATCAAAACAAT
1 AAAAATCAAAGTCATCTTTGTTGAATCAAAACAAT
*
12567 AAAAATCAAAGTCATCTTTGTTGAATCGAAACAAT
1 AAAAATCAAAGTCATCTTTGTTGAATCAAAACAAT
*
12602 AGAAATCAAA
1 AAAAATCAAA
12612 TTGTGTGCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (35 bp):
AAAAATCAAAGTCATCTTTGTTGAATCAAAACAAT
Found at i:18603 original size:7 final size:7
Alignment explanation
Indices: 18593--18662 Score: 61
Period size: 7 Copynumber: 10.0 Consensus size: 7
18583 AAAAAAAAAT
*
18593 AATTGAG
1 AATTGAA
18600 AATTGAA
1 AATTGAA
18607 AATTGAA
1 AATTGAA
18614 AATTGAA
1 AATTGAA
* *
18621 TATTAAA
1 AATTGAA
18628 AATAT-AA
1 AAT-TGAA
**
18635 AATTGGG
1 AATTGAA
18642 AATTGAA
1 AATTGAA
*
18649 GATTGAA
1 AATTGAA
*
18656 GATTGAA
1 AATTGAA
18663 GATTTATGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
6 1 0.02
7 50 0.96
8 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (7 bp):
AATTGAA
Found at i:18617 original size:21 final size:21
Alignment explanation
Indices: 18593--18661 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
18583 AAAAAAAAAT
18593 AATTGAGAATTGAAAATTGAA
1 AATTGAGAATTGAAAATTGAA
*
18614 AATTGA-ATATTAAAAATAT-AA
1 AATTGAGA-ATTGAAAAT-TGAA
* *
18635 AATTGGGAATTGAAGATTGAA
1 AATTGAGAATTGAAAATTGAA
*
18656 GATTGA
1 AATTGA
18662 AGATTTATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (21 bp):
AATTGAGAATTGAAAATTGAA
Found at i:18626 original size:42 final size:42
Alignment explanation
Indices: 18580--18662 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
18570 AGAGAATAAA
18580 ATTAAAAA-AAAATAATTGAGAATTGAAAATTGAAAATTGAAT
1 ATTAAAAATAAAA-AATTGAGAATTGAAAATTGAAAATTGAAT
* * * *
18622 ATTAAAAATATAAAATTGGGAATTGAAGATTGAAGATTGAA
1 ATTAAAAATAAAAAATTGAGAATTGAAAATTGAAAATTGAA
18663 GATTTATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 33 0.92
43 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (42 bp):
ATTAAAAATAAAAAATTGAGAATTGAAAATTGAAAATTGAAT
Found at i:19459 original size:24 final size:26
Alignment explanation
Indices: 19421--19468 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
19411 TCTACATGGG
19421 CATAATCTCTCATAT-TCATCATTTTT
1 CATAATCTCTCATATATCA-CATTTTT
19447 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
19469 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTTT
Done.