Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012280.1 Kokia drynarioides strain JFW-HI SEQ_127281, 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: 4232
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Found at i:695 original size:221 final size:221
Alignment explanation
Indices: 1--4232 Score: 6051
Period size: 221 Copynumber: 19.0 Consensus size: 221
* * * *
1 GCGTAAAACTATTGGAAAAGGGACACAAATGACGTTGTGTCACTGTTTCATTCAGTCATTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* *
66 TTGAAGAAGAGAAAGGATTTTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACGT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
** *
131 CAACAATTTCATTTTGAATTTCAGGATTTTAATTTTAATTTTATTTTTTCAGGATGAAAATGTTG
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTG
196 AAATTAAGAATGAAAATACTGATGTG
196 AAATTAAGAATGAAAATACTGATGTG
* * *
222 GTGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* * * *
287 TTGAAAAAGAGAAAGGATTGTATAAAACAAGGATATTATCCCTTTCCAATAGTTTTATGCCACAC
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * * *
352 CAACAAATTTCATCCTGTA-TTCTAGGATTTTGATTTTAAGTTGTTTTTTTCAGGATGAAAATGT
131 CAAC-AATTTCATCCTGAATTTC-AGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGT
*
416 TGAAATTAAGAATGAAAATACTGATATG
194 TGAAATTAAGAATGAAAATACTGATGTG
* *
444 GCGTAAAACTATTGGAAAAGGGAAACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* * * * ** *
509 TTGAAGAGGAGAAAGGATTCTATGAAACTGGGATATTATCCCTTTGCTCTAGTTTTATGCCGCAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * * *
574 CGACAATTTCATCCAGAATTTCAGGATTTTAATTTTAATTTGATTTTTCCAGGATGAAAATGTTA
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTG
639 AAATTAAGAATGAAAATACTGATGTG
196 AAATTAAGAATGAAAATACTGATGTG
* * *
665 ACGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* * * *
730 TTGAAG-AGATAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAGTAGTTTTATGCCACAC
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * *
794 CAACAATTTAATCCTGTATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAAAGTTG
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTG
*
859 AAATTAAGAATGAAAATACTGATATG
196 AAATTAAGAATGAAAATACTGATGTG
* * *
885 GTGTAAAACTATTAGAAAAGGGACACAAATGACATGGTGTCACAGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
*
950 TTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
1015 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTG-TTTTTCTCAGGATGAAAATGTT
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTT-TCAGGATGAAAATGTT
* *
1079 GACATTAAGAATGAAAATACTGATGTA
195 GAAATTAAGAATGAAAATACTGATGTG
* * * *
1106 GCGTAAAACCAATAGAAAAGGGACACTAAATGACGTGGTGTCACTGTTTCATTCAATCATGTTCC
1 GCGTAAAACTATTAGAAAAGGGACAC-AAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCC
1171 ATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACA
65 ATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACA
*
1236 TCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTTAGGATGAAAATGAT
130 TCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATG-T
*
1301 T-AAATTAAGAATGAAAATACTGATCTG
194 TGAAATTAAGAATGAAAATACTGATGTG
* * * * * ** *
1328 GCATAAAACTATTAGAAAAGGGACATAGATGACGTCGTGACACTGTTTCATTCAATTATTTTCCG
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
*
1393 TTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACA-
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
*
1457 CTAACAATTTCATCCTGTATTTCAGGATTTTAATTTTAATTTGA-TTTTTCAGGATGAAAATGTT
131 C-AACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTT
*
1521 GAAATTAAGAATGAAAATACTGATATG
195 GAAATTAAGAATGAAAATACTGATGTG
* * *
1548 GCGTAAAACTATTAGAGAAGGGACACAACTGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCT
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* *
1613 TTGAAAAAGAGAAAGGATTGTAT-AATACAGGGATATTATTCCTGTT-CAATAGTTTTATGCCAC
66 TTGAAGAAGAGAAAGGATTGTATGAA-ACAGGGATATTATCCCT-TTCCAATAGTTTTATGCCAC
* * * *
1676 ATAAACAATTTCATCCTAAATTTCAGGATTTTAATTTTAATTTTATTTTTTAAGGATGAAAATGT
129 ATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGT
*
1741 TAAAATTAAGAATGAAAATACTGATGTG
194 TGAAATTAAGAATGAAAATACTGATGTG
* * *
1769 GCGTAAAACCAATAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
*
1834 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGAT-TTATCCCTTTCCAATAGTATTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
*
1898 CAACAATTTCATCCTGAATTTCAGGA-TTTAATTTTAATTTGATATTTTCAGGATGAAAAT-TAT
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGT-T
*
1961 GAAATTAAGAATGAAAATACTGATTTG
195 GAAATTAAGAATGAAAATACTGATGTG
* * *
1988 GTGTAAAACTATTAGAAAAGGGACACAGATGACGTTGTGTCACTGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* *
2053 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATGGTTTTATGCCACAC
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
*
2118 CAACAATTTCATCCTAAATTTCAGGATTTTAATTTTAATTTG-TTTTTCTCAGGATGAAAATGTT
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTT-TCAGGATGAAAATGTT
*
2182 GACATTAAGAATGAAAATACTGATGTG
195 GAAATTAAGAATGAAAATACTGATGTG
* * * * * *
2209 GCATAAAACCAATAGAAAAGGTACACAAATGACGTGGTGGCACTGTTTCATTCAATCATTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* * *
2274 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCATTGGTTTTATGCCACAC
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
*
2339 CAACAATTTCATCCTAAATTTCAGGATTTTAATTTTAATTTG-TTTTTCTCAGGATGAAAATGTT
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTT-TCAGGATGAAAATGTT
*
2403 GACATTAAGAATGAAAATACTGATGTG
195 GAAATTAAGAATGAAAATACTGATGTG
* * ** *
2430 GCGTAAAACCAATAGAAAAGTTACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* * *
2495 TTGAAGAAGAGAAATGATTGTAAGAAACAGGGATATTATCCCTTCCCAATAGTTTTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* *
2560 CAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGATG
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTG
*
2625 AAATTAAGAATGAAAATAATGATGTG
196 AAATTAAGAATGAAAATACTGATGTG
* * * *
2651 GCGTAAAACTAATAGAAAAGGGACACAGATGACATCGTGTCACTGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* * * *
2716 TTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCGATAGTTTTTTGCCACAC
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * * *
2781 CAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGTTTATTTTCAGGATGTAAATTTT
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATT-TTTTCAGGATGAAAATGTT
* *
2846 AAAATTAAGAATGAAAATACTGATGTA
195 GAAATTAAGAATGAAAATACTGATGTG
* * *
2873 GCGTAAAATTATT-GAAAAAGGGACACAAATGTCGTGGTTTCACTGCTTTATTCAATCTTTTTCC
1 GCGTAAAACTATTAG-AAAAGGGACACAAATGACGTGGTGTCACTG---T-TTC-A-----TT-C
* * *
2937 ATTTTATTAAATCATTTTCCATTGAAGAAGAGAAAGGATTATATGAAACAAGGATATTATCCCTT
54 ---------AATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* * *
3002 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTAAATTTCAGGATTTTAATTTTTATTTGAT
110 TCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT
* *
3067 TTTCTCAGGATGAAAATGTTGACATTAAGAATGAAAATACTGATGTG
175 TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
* *
3114 GCGTAAAAAC-AATAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCC
1 GCGT-AAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCC
*
3178 ATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTACAATAGTTTTATGCCACA
65 ATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACA
* ** * * *
3243 TGAACAATTTCATTTTCAA-TTCAGGATTTTAATTTTAATTTTAATTTTTCAGGATGAAAATGTT
130 TCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTT
*
3307 GAAATTAAGAATGAAAATATTGATGTG
195 GAAATTAAGAATGAAAATACTGATGTG
* * *
3334 GCGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCTA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* * *
3399 TTGAAGAGGAGAAAGGATTGTATAAAACAGAGATATTATCCCTTTCCAATAGTTTTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * **
3464 CAACAATTTCATCCTGTATTTCATGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAACATTG
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTG
*
3529 AAATTAAGAATGAAAATACTGATATG
196 AAATTAAGAATGAAAATACTGATGTG
* * * * * *
3555 GTGTAAAACTATTTGAAAAGGGACACAAATGTCGTGTTGTCACTGTTTCATTCAATCATTTTACA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
*
3620 TTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * *
3685 CAACAATTTCATCCTAAATTTCAGGATTTTATTTTTAATTTGATTTTTTCAGGATGAAAATGTTA
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTG
*
3750 AAATTAAGAATCAAAATACTGATGTG
196 AAATTAAGAATGAAAATACTGATGTG
* ** * *
3776 GCGTAAAACTATTGGAAAAGAAACACAAATGACGTGGTGCCACTGTTTCATTCAATCCTTTTCCG
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
* **
3841 TTGAAGAAGAGAAAGGATTGTATGACACAAAGATATTATCCCTTTCCAATAGTTTTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
*
3906 CAACAATTTCATCC-G-------GAATTTTAATTTT-A--T--TTTTTT-AGGATGAAAATGTTG
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTG
* *
3957 AAATTAAGAATTAAAATATTGATGTG
196 AAATTAAGAATGAAAATACTGATGTG
* * *
3983 GCGTAAAATTATTGGAAAAGGGGCACAAATGACGTGGTGTCACTGTTTTATTCAATCCTTCTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTG---T-TTC-A----T-T-CA
4048 TTTTATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTA-CCCTTT
55 ----A-TC---C-TTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
* * * *
4112 CCAATGGTTTTATGCCACACCAACAATTTCATCCTAAATTTCAGGATTTTGATTTTAATTTGATT
111 CCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATT
*
4177 TTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
176 TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
*
4223 GTGTAAAACT
1 GCGTAAAACT
Statistics
Matches: 3614, Mismatches: 315, Indels: 145
0.89 0.08 0.04
Matches are distributed among these distances:
207 78 0.02
208 6 0.00
210 2 0.00
211 3 0.00
212 2 0.00
213 11 0.00
216 1 0.00
217 1 0.00
218 3 0.00
219 161 0.04
220 695 0.19
221 1809 0.50
222 481 0.13
223 9 0.00
225 1 0.00
226 42 0.01
227 42 0.01
230 1 0.00
231 2 0.00
232 2 0.00
233 1 0.00
234 11 0.00
235 1 0.00
236 1 0.00
237 4 0.00
238 1 0.00
239 5 0.00
240 47 0.01
241 74 0.02
242 117 0.03
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (221 bp):
GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTG
AAATTAAGAATGAAAATACTGATGTG
Found at i:1005 original size:441 final size:442
Alignment explanation
Indices: 1--4232 Score: 6046
Period size: 441 Copynumber: 9.5 Consensus size: 442
* * *
1 GCGTAAAACTATTGGAAAAGGGACACAAATGACGTTGTGTCACTGTTTCATTCAGTCATTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
* *
66 TTGAAGAAGAGAAAGGATTTTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACGT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
** * *
131 CAACAATTTCATTTTGAATTTCAGGATTTTAATTTTAATTTTATTTTTTCAGGATGAAAATGTTG
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTCCAGGATGAAAATGTTG
*
196 AAATTAAGAATGAAAATACTGATGTGGTGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTG
196 AAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTG
* *
261 TCACTGTTTCATTCAATCCTTTTCCATTGAAAAAGAGAAAGGATTGTATAAAACAAGGATATTAT
261 TCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTAT
* * *
326 CCCTTTCCAATAGTTTTATGCCACACCAACAAATTTCATCCTGTA-TTCTAGGATTTTGATTTTA
326 CCCTTTCCAATAGTTTTATGCCACATCAAC-AATTTCATCCTGAATTTC-AGGATTTTAATTTTA
* * *
390 AGTTGTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATATG
389 ATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
* * *
444 GCGTAAAACTATTGGAAAAGGGAAACAAATGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
* * * * ** *
509 TTGAAGAGGAGAAAGGATTCTATGAAACTGGGATATTATCCCTTTGCTCTAGTTTTATGCCGCAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * *
574 CGACAATTTCATCCAGAATTTCAGGATTTTAATTTTAATTTGATTTTTCCAGGATGAAAATGTTA
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTCCAGGATGAAAATGTTG
*
639 AAATTAAGAATGAAAATACTGATGTGACGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTG
196 AAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTG
*
704 TCACTGTTTCATTCAATCCTTTTCCATTGAAG-AGATAAAGGATTGTATAAAACAGGGATATTAT
261 TCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTAT
* * * *
768 CCCTTTCCAGTAGTTTTATGCCACACCAACAATTTAATCCTGTATTTCAGGATTTTAATTTTAAT
326 CCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAAT
* *
833 TTGATTTTTTCAGGATGAAAAAGTTGAAATTAAGAATGAAAATACTGATATG
391 TTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
* * * *
885 GTGTAAAACTATTAGAAAAGGGACACAAATGACATGGTGTCACAGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
*
950 TTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
1015 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTG-TTTTTCTCAGGATGAAAATGTT
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTC-CAGGATGAAAATGTT
* * * *
1079 GACATTAAGAATGAAAATACTGATGTAGCGTAAAACCAATAGAAAAGGGACACTAAATGACGTGG
195 GAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACAC-AAATGACGTGG
* * *
1144 TGTCACTGTTTCATTCAATCATGTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATT
259 TGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATT
1209 ATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTA
324 ATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTA
* *
1274 ATTTGATTTTTTTAGGATGAAAATGATT-AAATTAAGAATGAAAATACTGATCTG
389 ATTTGATTTTTTCAGGATGAAAATG-TTGAAATTAAGAATGAAAATACTGATGTG
* * * * * * *
1328 GCATAAAACTATTAGAAAAGGGACATAGATGACGTCGTGACACTGTTTCATTCAATTATTTTCCG
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
*
1393 TTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACA-
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
*
1457 CTAACAATTTCATCCTGTATTTCAGGATTTTAATTTTAATTTGATTTTT-CAGGATGAAAATGTT
131 C-AACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTCCAGGATGAAAATGTT
* * * * *
1521 GAAATTAAGAATGAAAATACTGATATGGCGTAAAACTATTAGAGAAGGGACACAACTGACGTGGT
195 GAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGGT
* * *
1586 GTCACTGTTTCATTCAATCCTTTTCCTTTGAAAAAGAGAAAGGATTGTATAATACAGGGATATTA
260 GTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTA
* * *
1651 TTCCTGTT-CAATAGTTTTATGCCACATAAACAATTTCATCCTAAATTTCAGGATTTTAATTTTA
325 TCCCT-TTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTA
* * *
1715 ATTTTATTTTTTAAGGATGAAAATGTTAAAATTAAGAATGAAAATACTGATGTG
389 ATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
* *
1769 GCGTAAAACCAATAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
*
1834 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGAT-TTATCCCTTTCCAATAGTATTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
1898 CAACAATTTCATCCTGAATTTCAGGA-TTTAATTTTAATTTGATATTTT-CAGGATGAAAAT-TA
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGAT-TTTTCCAGGATGAAAATGT-
* * * * * *
1960 TGAAATTAAGAATGAAAATACTGATTTGGTGTAAAACTATTAGAAAAGGGACACAGATGACGTTG
194 TGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGG
*
2025 TGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATT
259 TGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATT
* * *
2090 ATCCCTTTCCAATGGTTTTATGCCACACCAACAATTTCATCCTAAATTTCAGGATTTTAATTTTA
324 ATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTA
*
2155 ATTTG-TTTTTCTCAGGATGAAAATGTTGACATTAAGAATGAAAATACTGATGTG
389 ATTTGATTTTT-TCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
* * * * *
2209 GCATAAAACCAATAGAAAAGGTACACAAATGACGTGGTGGCACTGTTTCATTCAATCATTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
* * *
2274 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCATTGGTTTTATGCCACAC
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
*
2339 CAACAATTTCATCCTAAATTTCAGGATTTTAATTTTAATTTG-TTTTTCTCAGGATGAAAATGTT
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTC-CAGGATGAAAATGTT
* * * **
2403 GACATTAAGAATGAAAATACTGATGTGGCGTAAAACCAATAGAAAAGTTACACAAATGACGTGGT
195 GAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGGT
* *
2468 GTCACTGTTTCATTCAATCATTTTCCATTGAAGAAGAGAAATGATTGTA-AGAAACAGGGATATT
260 GTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATA-AAACAGGGATATT
* *
2532 ATCCCTTCCCAATAGTTTTATGCCACATCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTA
324 ATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTA
* *
2597 ATTTGATTTTTTCAGGATGAAAATGATGAAATTAAGAATGAAAATAATGATGTG
389 ATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
* * * * *
2651 GCGTAAAACTAATAGAAAAGGGACACAGATGACATCGTGTCACTGTTTCATTCAATCCTTTTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
* * * *
2716 TTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCGATAGTTTTTTGCCACAC
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * * * *
2781 CAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGTTTATTTTCAGGATGTAAATTTT
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATT-TTTCCAGGATGAAAATGTT
* * * * * *
2846 AAAATTAAGAATGAAAATACTGATGTAGCGTAAAATTATTGAAAAAGGGACACAAATGTCGTGGT
195 GAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGGT
* *
2911 TTCACTGCTTTATTCAATCTTTTTCCATTTTATTAAATCATTTTCCATTGAAGAAGAGAAAGGAT
260 GTCACTG---T-TTC-A-----TT-C---------AATCCTTTTCCATTGAAGAAGAGAAAGGAT
* * * * *
2976 TATATGAAACAAGGATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCTAAA
305 TGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAA
* * *
3041 TTTCAGGATTTTAATTTTTATTTGATTTTCTCAGGATGAAAATGTTGACATTAAGAATGAAAATA
370 TTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATA
3106 CTGATGTG
435 CTGATGTG
*
3114 GCGTAAAAAC-AATAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCC
1 GCGT-AAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCC
*
3178 ATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTACAATAGTTTTATGCCACA
65 ATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACA
* ** * *
3243 TGAACAATTTCATTTTCAA-TTCAGGATTTTAATTTTAATTTTAATTTTT-CAGGATGAAAATGT
130 TCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAA-TTTGATTTTTCCAGGATGAAAATGT
*
3306 TGAAATTAAGAATGAAAATATTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGG
194 TGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGG
* * *
3371 TGTCACTGTTTCATTCAATCCTTTTCTATTGAAGAGGAGAAAGGATTGTATAAAACAGAGATATT
259 TGTCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATT
* *
3436 ATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGTATTTCATGATTTTAATTTTA
324 ATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTA
** *
3501 ATTTGATTTTTTCAGGATGAAAACATTGAAATTAAGAATGAAAATACTGATATG
389 ATTTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
* * * * *
3555 GTGTAAAACTATTTGAAAAGGGACACAAATGTCGTGTTGTCACTGTTTCATTCAATCATTTTACA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
*
3620 TTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
66 TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
* * * *
3685 CAACAATTTCATCCTAAATTTCAGGATTTTATTTTTAATTTGATTTTTTCAGGATGAAAATGTTA
131 CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTCCAGGATGAAAATGTTG
* * **
3750 AAATTAAGAATCAAAATACTGATGTGGCGTAAAACTATTGGAAAAGAAACACAAATGACGTGGTG
196 AAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTG
* * * * **
3815 CCACTGTTTCATTCAATCCTTTTCCGTTGAAGAAGAGAAAGGATTGTATGACACAAAGATATTAT
261 TCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTAT
*
3880 CCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCC-G-------GAATTTTAATTTT-A-
326 CCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAAT
* *
3935 -T--TTTTTT-AGGATGAAAATGTTGAAATTAAGAATTAAAATATTGATGTG
391 TTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
* * *
3983 GCGTAAAATTATTGGAAAAGGGGCACAAATGACGTGGTGTCACTGTTTTATTCAATCCTTCTCCA
1 GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTG-------------TT-T-C-
4048 TTTTATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTA-CCCTTT
50 ----ATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
* * * *
4112 CCAATGGTTTTATGCCACACCAACAATTTCATCCTAAATTTCAGGATTTTGATTTTAATTTGA-T
111 CCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATT
*
4176 TTTCTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGTGTAAAACT
176 TTTC-CAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACT
Statistics
Matches: 3434, Mismatches: 285, Indels: 136
0.89 0.07 0.04
Matches are distributed among these distances:
428 75 0.02
429 6 0.00
431 1 0.00
433 1 0.00
434 11 0.00
439 25 0.01
440 403 0.12
441 908 0.26
442 768 0.22
443 647 0.19
444 10 0.00
446 5 0.00
447 117 0.03
448 53 0.02
450 1 0.00
451 2 0.00
453 2 0.00
454 1 0.00
456 1 0.00
457 3 0.00
458 1 0.00
461 77 0.02
462 22 0.01
463 289 0.08
464 5 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (442 bp):
GCGTAAAACTATTAGAAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCATTTTCCA
TTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACAT
CAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGATTTTTCCAGGATGAAAATGTTG
AAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAAGGGACACAAATGACGTGGTG
TCACTGTTTCATTCAATCCTTTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTAT
CCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAAT
TTGATTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTG
Found at i:2944 original size:20 final size:20
Alignment explanation
Indices: 2919--2959 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2909 GTTTCACTGC
* *
2919 TTTATTCAATCTTTTTCCAT
1 TTTATTAAATCATTTTCCAT
2939 TTTATTAAATCATTTTCCAT
1 TTTATTAAATCATTTTCCAT
2959 T
1 T
2960 GAAGAAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTAAATCATTTTCCAT
Found at i:4053 original size:20 final size:20
Alignment explanation
Indices: 4028--4069 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4018 GGTGTCACTG
*
4028 TTTTATTCAATCCTTCTCCA
1 TTTTATTCAATCATTCTCCA
*
4048 TTTTATTCAATCATTTTCCA
1 TTTTATTCAATCATTCTCCA
4068 TT
1 TT
4070 GAAGAAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTATTCAATCATTCTCCA
Done.