Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000751.1 Kokia drynarioides strain JFW-HI SEQ_111795, 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: 2329
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Found at i:261 original size:85 final size:85
Alignment explanation
Indices: 116--279 Score: 204
Period size: 85 Copynumber: 1.9 Consensus size: 85
106 CATCATTGAC
* * * *
116 TTGGTCTACTTCTTTATATCTCATTAGGAAGATGACTGCTTCATTGATTTAATCCACTTCTCTGT
1 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGATTTAACCCACTTCTCTGT
* *
181 ACCTTATCAGGAAGGCGGAT
66 AACTCATCAGGAAGGCGGAT
* * * * * *
201 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCT-TTTTATTGCTTTGACCCTCTTCTCTG
1 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGA-CTGCTTCATTGATTTAACCCACTTCTCTG
265 TAACTCATCAGGAAG
65 TAACTCATCAGGAAG
280 ATGGGGCTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
85 64 0.97
86 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (85 bp):
TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGATTTAACCCACTTCTCTGT
AACTCATCAGGAAGGCGGAT
Found at i:366 original size:48 final size:48
Alignment explanation
Indices: 312--403 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
302 TATCGAGCTT
**
312 CGCTTCATTGATTT-CGTCTACTTCTCTGTATCTCATCAGGAAGATGAC
1 CGCTTCATTGATTTAATTC-ACTTCTCTGTATCTCATCAGGAAGATGAC
360 CGCTTCATTGATTTAATTCACTTCTCTGTATCTCATCAGGAAGA
1 CGCTTCATTGATTTAATTCACTTCTCTGTATCTCATCAGGAAGA
404 CGAATTTGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 39 0.95
49 2 0.05
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (48 bp):
CGCTTCATTGATTTAATTCACTTCTCTGTATCTCATCAGGAAGATGAC
Found at i:413 original size:208 final size:208
Alignment explanation
Indices: 46--1406 Score: 1355
Period size: 208 Copynumber: 6.5 Consensus size: 208
36 CAGATTTGGT
* * * * * * *
46 CCACTTCTCTGTATCTCATCAGGAATATTGGGTTTAAAGCCTCATTCGTATTAAGCTCCGCATCA
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
* * * * *
111 TTGACTTGGTCTACTTCTTTATATCTCATTAGGAAGATGACTGCTTCATTGATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * * * * **
176 TCTGTACCTTATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCTTT
131 TCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
241 TTATTGCTTTGAC
196 TTATTGCTTTGAC
* * * * * * *
254 CCTCTTCTCTGTAACTCATCAGGAAGATGGGGCTTAAAGCCTCATTTGTATCGAGCTTCGCTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
* *
319 TTGATTTCGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATTCACTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * * * * **
384 TCTGTATCTCATCAGGAAGACGAATTTGGTCCAGTACTCTGTGTCTTATCA-GAGAGATGGTCGC
131 TCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGA-AGATGACCGC
448 TTTATTGCTTTGAC
195 TTTATTGCTTTGAC
* * * * *
462 CCACTTCTCTATATCTTATTAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
* ** ** *
527 TTGATTTGGTCTACTTCTCTATGCCTCATCAGGAAGATGATAGCTTCATTAATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * * * *
592 TCTGTATCTCATCAGGAAGATGGATTTGATCCACTTCTCTGTATTTCATCAGGAAGATGACCGCT
131 TCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
*
657 TTATTGCTTTGAT
196 TTATTGCTTTGAC
* * * * *
670 CCACTTCTCTGTTTCTCATCAAGAAGATGGGCTTTGAAGTCTCATTCGTATTGAGCTTCACTTTA
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
* * **
735 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAAATGACTGAATCATTGATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * *
800 TCTGTATCTCATCAAGAAGGA-GAACTTGGTCAACTTCTCTGTATCTCATTAGGAAGATGACCGC
131 TCTGTATCTCATCAAGAA-GACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGC
*
864 TTTATT-ATATTGAC
195 TTTATTGCT-TTGAC
*** * * * *
878 CCACTTCTCTGTATCTCATCAGG-TTCTGAGCTTTG--CT-TCATT-G-ATTTG-GTCTACTTCT
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTA-TTGAG----CTTCG
* ** * * * ****** * *
936 CTAT-ATCTCATCAGGAACATGACCGCTTCAT-TG-ATTTAATCCACTTCTCTGTATC-TTATCA
61 CT-TCAT-TGATTTGG-TC-T-A---CTTC-TCTGTATCTCAT-CAGGAAGATG-ACCGCT-TC-
** ** * * *
997 GGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAAAAAGACGGATTTGGTCCACTTCTTTGT
113 ---A-TTG-ATTTAATCCACTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGT
** *
1062 ATCTCATCAGGAAGATGATTGCTTTATTTCTTTGAC
173 ATCTCATCAGGAAGATGACCGCTTTATTGCTTTGAC
* * * *
1098 ACACTGCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTTGTATTGAGCTTCGCTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
* * *
1163 TTGATTTGGTCTACTTCTCTGTATCTCATCATGAAGATTACCGCTTCATTGATTTAATTCACTTC
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * * * * *
1228 TCTATATCTTATCAAGAAGACGAATTTGGTCCACTTCTCTTTACCTCATCAGGAAGATAATCGCT
131 TCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
1293 TTATTGCTTTGAC
196 TTATTGCTTTGAC
* * *
1306 CCATTTCTCTGTATCTCATCAGGAAGATAGGATTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
* * *
1371 TTGATTTGGTTTACTTCTCTGCATCTCATCAAGAAG
66 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAG
1407 GTGATTTGGT
Statistics
Matches: 938, Mismatches: 175, Indels: 80
0.79 0.15 0.07
Matches are distributed among these distances:
202 2 0.00
203 4 0.00
204 5 0.01
205 1 0.00
206 8 0.01
207 17 0.02
208 717 0.76
209 6 0.01
210 2 0.00
212 5 0.01
213 10 0.01
214 9 0.01
215 10 0.01
216 5 0.01
218 2 0.00
219 4 0.00
220 97 0.10
221 14 0.01
222 8 0.01
223 1 0.00
224 5 0.01
225 4 0.00
226 2 0.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (208 bp):
CCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
TCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
TTATTGCTTTGAC
Found at i:574 original size:48 final size:48
Alignment explanation
Indices: 521--613 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
511 ATTGAGCTTT
* ** * *
521 GCTTCATTGATTTGGTCTACTTCTCTATGCCTCATCAGGAAGATGATA
1 GCTTCATTAATTTAATCCACTTCTCTATACCTCATCAGGAAGATGATA
* *
569 GCTTCATTAATTTAATCCACTTCTCTGTATCTCATCAGGAAGATG
1 GCTTCATTAATTTAATCCACTTCTCTATACCTCATCAGGAAGATG
614 GATTTGATCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (48 bp):
GCTTCATTAATTTAATCCACTTCTCTATACCTCATCAGGAAGATGATA
Found at i:633 original size:37 final size:37
Alignment explanation
Indices: 578--650 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
568 AGCTTCATTA
578 ATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGG
1 ATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGG
* *
615 ATTTGATCCACTTCTCTGTATTTCATCAGGAAGATG
1 ATTTAATCCACTTCTCTGTATCTCATCAGGAAGATG
651 ACCGCTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (37 bp):
ATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGG
Found at i:789 original size:48 final size:48
Alignment explanation
Indices: 734--1000 Score: 182
Period size: 48 Copynumber: 5.8 Consensus size: 48
724 GCTTCACTTT
* * * **
734 ATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAAATGACTGAATC
1 ATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTC
* * *
782 ATTGATTTAATCCACTTCTCTGTATCTCATCA--AGAAGGA--G----
1 ATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTC
* * * * * *
822 A---ACTTGGTCAACTTCTCTGTATCTCATTAGGAAGATGACCGCTTT
1 ATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTC
* *** *
867 ATT-ATATTGACCCACTTCTCTGTATCTCATCAGG-TTCTGAGCTTTGCTTC
1 ATTGAT-TTGATCCACTTCTCTGTATCTCATCAGGAAAATGA-C--CGCTTC
* * * *
917 ATTGATTTGGTCTACTTCTCTATATCTCATCAGGAACATGACCGCTTC
1 ATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTC
* *
965 ATTGATTTAATCCACTTCTCTGTATCTTATCAGGAA
1 ATTGATTTGATCCACTTCTCTGTATCTCATCAGGAA
1001 GGCGAATTTG
Statistics
Matches: 167, Mismatches: 36, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
37 23 0.14
39 4 0.02
40 1 0.01
41 1 0.01
44 1 0.01
45 1 0.01
46 5 0.03
47 4 0.02
48 90 0.54
50 32 0.19
51 5 0.03
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (48 bp):
ATTGATTTGATCCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTC
Found at i:867 original size:416 final size:415
Alignment explanation
Indices: 46--2325 Score: 1706
Period size: 416 Copynumber: 5.6 Consensus size: 415
36 CAGATTTGGT
* * * * * ** *
46 CCACTTCTCTGTATCTCATCAGGAATATTG-GGTTTAAAGCCTCATTCGTATTAAGCTCCGCATC
1 CCACTTCTCTATATCTCATCAGGAAGA-TGAGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTC
* * * *
110 ATTGACTTGGTCTACTTCTTTATATCTCATTAGGAAGATGACTGCTTCATTGATTTAATCCACTT
65 ATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTT
* * * **
175 CTCTGTACCTTATCAGGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCTT
130 CTCTGTATCTTATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGC
* * * * * *
240 TTTATTGCTTTGACCCTCTTCTCTGTAACTCATCAGGAAGATGGGGC-TTAAAGCCTCATTTGTA
195 TTTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGAT-GGGCTTTGAAGTCTCATTCGTA
* *
304 TCGAGCTTCGCTTCATTGATTTCGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATT
259 TTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATT
* * * * * *
369 GATTTAATTCACTTCTCTGTATCTCATCAGGAA-GACGAATTTGGTCCAGTACTCTGTGTCTTAT
324 GATTTAATCCACTTCTCTGTATCTCATCAAGAAGGA-GAATTTGGTCCACTTCTCTGTATCTCAT
* **
433 CA-GAGAGATGGTCGCTTTATTGCTTTGAC
388 TAGGA-AGATGACCGCTTTATT-CTTTGAC
* *
462 CCACTTCTCTATATCTTATTAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTCA
1 CCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTCA
** ** *
527 TTGATTTGGTCTACTTCTCTATGCCTCATCAGGAAGATGATAGCTTCATTAATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * * * *
592 TCTGTATCTCATCAGGAAGATGGATTTGATCCACTTCTCTGTATTTCATCAGGAAGATGACCGCT
131 TCTGTATCTTATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
* *
657 TTATTGCTTTGATCCACTTCTCTGTTTCTCATCAAGAAGATGGGCTTTGAAGTCTCATTCGTATT
196 TTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGCTTTGAAGTCTCATTCGTATT
* * * * **
722 GAGCTTCACTTTATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAAATGACTGAATCATTGA
261 GAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGA
* *
787 TTTAATCCACTTCTCTGTATCTCATCAAGAAGGAGAACTTGGTCAACTTCTCTGTATCTCATTAG
326 TTTAATCCACTTCTCTGTATCTCATCAAGAAGGAGAATTTGGTCCACTTCTCTGTATCTCATTAG
*
852 GAAGATGACCGCTTTATTATATTGAC
391 GAAGATGACCGCTTTATTCT-TTGAC
*
878 CCACTTCTCTGTATCTCATC---------A-----G--G-----TTC----TGAGCTTTGCTTCA
1 CCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTCA
*
918 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAACATGACCGCTTCATTGATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
* * * *
983 TCTGTATCTTATCAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCA--AA-AAGA-CG--
131 TCTGTATCTTATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
* ** * * * * *
1042 -----GATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGATTGCTTT--A-TTTC-TTTG-A
196 TTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGATG--GGCTTTGAAGTCTCATTCGTA
*** * * * ** *** ** * * ** * *
1097 CACA-CTGCTCTAT-ATCTCATCAGGAAGA-TGGGGTTTGAAGTCTCAT-TTGTA-TTGAGCTTC
259 TTGAGCTTCGCT-TCAT-TGATTTGGTCTACT--TCTCTGTA-TCTCATCAGGAAGATGA-C--C
** * * * ** *
1157 GCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCATGAAGATTACCGCTTCATTGATTTAATT
316 GCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAAGAAG--GA--G----A---ATTTGGTC
* ** * * **
1222 CACTTCTC--TATATC-TTATCAAGAAGA-CG----A--ATTTGGT
370 CACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTCTTTGAC
* * * * * * *
1258 CCACTTCTCTTTACCTCATCAGGAAGAT-A--ATCG--CT-TTATT-GCT-TTGACCCATTT-CT
1 CCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCG-TATTGA-GC-TTTGCT
* * ** ** * * * *
1314 CTGTATCTCATCAGGAAGATAGGATT-T-GA-AGTCTCATTC--GTA-TTGAGCTTCGCTTCATT
63 -T-CAT-TGATTTGG--TCTA--CTTCTCTATA-TCTCA-TCAGGAAGATGA-C--CGCTTCATT
** ** * * ** *
1373 GATTTGGTTTACTTCTCTGCATCTCATCAAGAAG--GTGATTTGGTCTGCTTCTATGTATCTCAT
116 GATTTAATCCACTTCTCTGTATCTTATCAAGAAGACG-GATTTGGTCCACTTCTCTGTATCTCAT
* ** * *
1436 TAGGAAGAT-AGCCGCTTTATTATTTTGACCCACTTCTC--TATCTCATCAAGAACATGGGTTTT
180 CAGGAAGATGA-CCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGCTTT
* * * *
1498 GGAGTCTCATTCATATTGAGCTTCGCTTCATTGATTTGGTGTACTTCTCTATATCTCATCAGGAA
244 GAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAA
* * * * *
1563 GATGACCGCTTCATTAATTTAATCCATTTGTCTGTATCTCATC-AGAAAGGCGGATTTGGTCCAC
309 GATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAAG-AAGGAGAATTTGGTCCAC
* * *
1627 TTCTTTGTATCTCATTAGGAAGATGACTGCTTTATTGCTTTGTC
373 TTCTCTGTATCTCATTAGGAAGATGACCGCTTTATT-CTTTGAC
* * **
1671 ACACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCACTTCA
1 CCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTCA
* * * * * *
1736 TTGATTCGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTAATTTAA-CCTACTA
66 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCC-ACTT
* ** * * * * **
1800 CTCTATATCTTATCAAGAAGACAAATTTGATCCACTTCTTTTTACCTCATCAGGAAGACAACCGC
130 CTCTGTATCTTATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGC
* * ** *
1865 TTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAACTTGGG-TTTTAGAGTCTCATTCGTA
195 TTTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGCTTTGA-AGTCTCATTCGTA
* * * * * * *
1929 TTCAGCTTTGCTTCGTTTATTTGGTCTACTTATCTGTATCTCATCAGGAAGATGACCACTTAATT
259 TTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATT
* * * *
1994 GATTTAATCCAGTTCTCTATATCTCATCAGGAAGGTAG-ATTTGATCCACTTCTCTGTATCTCAT
324 GATTTAATCCACTTCTCTGTATCTCATCAAGAAGG-AGAATTTGGTCCACTTCTCTGTATCTCAT
*
2058 AAGGAAGATGACCGCTTTATTACTTTGAC
388 TAGGAAGATGACCGCTTTATT-CTTTGAC
* * * * *
2087 ACACTTCTCTATATCTTATCAAGAAGATG-GAGTTTGAAGTCTCATTTGTATTGAGTTTTGCTTC
1 CCACTTCTCTATATCTCATCAGGAAGATGAG-GTTTGAAGTCTCATTCGTATTGAGCTTTGCTTC
* * **
2151 ATTGATTTGGTCAACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAATTTACTT
65 ATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTT
* * * * *
2216 CTCTATATTTTATCAAGAAGATGGATTTGGTCCACTTCTCTGTACCTCATTAGGAAGATGACCGC
130 CTCTGTATCTTATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGC
* *
2281 TTTATTGCTTTCACCCACTTCTCTATATCTCATCAAGAAGATGGG
195 TTTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGG
2326 GTTT
Statistics
Matches: 1450, Mismatches: 294, Indels: 240
0.73 0.15 0.12
Matches are distributed among these distances:
376 8 0.01
377 12 0.01
378 10 0.01
379 9 0.01
380 90 0.06
381 2 0.00
382 6 0.00
383 1 0.00
384 1 0.00
387 4 0.00
388 14 0.01
389 7 0.00
391 130 0.09
395 5 0.00
398 3 0.00
399 3 0.00
400 5 0.00
401 2 0.00
402 21 0.01
403 5 0.00
404 37 0.03
405 48 0.03
406 6 0.00
407 2 0.00
408 2 0.00
409 1 0.00
410 1 0.00
411 4 0.00
412 3 0.00
413 115 0.08
414 68 0.05
415 36 0.02
416 756 0.52
417 16 0.01
418 4 0.00
419 8 0.01
420 5 0.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (415 bp):
CCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTCA
TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC
TCTGTATCTTATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT
TTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGCTTTGAAGTCTCATTCGTATT
GAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGA
TTTAATCCACTTCTCTGTATCTCATCAAGAAGGAGAATTTGGTCCACTTCTCTGTATCTCATTAG
GAAGATGACCGCTTTATTCTTTGAC
Found at i:883 original size:85 final size:85
Alignment explanation
Indices: 740--898 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
730 CTTTATTGAT
* * *
740 TTGGTCTACTTCTCTGTATCTCATCAGGAAAATGACTGAATCATTGATTTAATCCACTTCTCTGT
1 TTGGTCAACTTCTCTGTATCTCATCAGGAAAATGACCGAATCATTGATTTAACCCACTTCTCTGT
805 ATCTCATCAAGAAGGAGAAC
66 ATCTCATCAAGAAGGAGAAC
* * ** * *
825 TTGGTCAACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATT-ATATTGACCCACTTCTCTG
1 TTGGTCAACTTCTCTGTATCTCATCAGGAAAATGACCGAATCATTGAT-TTAACCCACTTCTCTG
889 TATCTCATCA
65 TATCTCATCA
899 GGTTCTGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 2 0.03
85 62 0.97
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (85 bp):
TTGGTCAACTTCTCTGTATCTCATCAGGAAAATGACCGAATCATTGATTTAACCCACTTCTCTGT
ATCTCATCAAGAAGGAGAAC
Found at i:1025 original size:37 final size:37
Alignment explanation
Indices: 975--1076 Score: 150
Period size: 37 Copynumber: 2.8 Consensus size: 37
965 ATTGATTTAA
* *
975 TCCACTTCTCTGTATCTTATCAGGAAGGCGAATTTGG
1 TCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
** *
1012 TCCACTTCTCTGTATCTCATCAAAAAGACGGATTTGG
1 TCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
*
1049 TCCACTTCTTTGTATCTCATCAGGAAGA
1 TCCACTTCTCTGTATCTCATCAGGAAGA
1077 TGATTGCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (37 bp):
TCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGG
Found at i:1227 original size:48 final size:48
Alignment explanation
Indices: 1156--1247 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
1146 TATTGAGCTT
* * *
1156 CGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCATGAAGATTAC
1 CGCTTCATTGATTTAGTCTACTTCTCTATATCTCATCAAGAAGATTAC
* *
1204 CGCTTCATTGATTTAAT-TCACTTCTCTATATCTTATCAAGAAGA
1 CGCTTCATTGATTTAGTCT-ACTTCTCTATATCTCATCAAGAAGA
1248 CGAATTTGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 1 0.03
48 37 0.97
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (48 bp):
CGCTTCATTGATTTAGTCTACTTCTCTATATCTCATCAAGAAGATTAC
Found at i:1314 original size:85 final size:85
Alignment explanation
Indices: 1166--1332 Score: 199
Period size: 85 Copynumber: 2.0 Consensus size: 85
1156 CGCTTCATTG
* * * * **
1166 ATTTGGTCTACTTCTCTGTATCTCATCATGAAGATTACCGCTTCATTGATTTAATTCACTTCTCT
1 ATTTGGTCCACTTCTCTGTACCTCATCAGGAAGATAACCGCTTCATTGATTTAACCCACTTCTCT
*
1231 ATATCTTATCAAGAAGACGA
66 ATATCTCATCAAGAAGACGA
* * * * * *
1251 ATTTGGTCCACTTCTCTTTACCTCATCAGGAAGATAATCGCTTTATTGCTTTGACCCATTTCTCT
1 ATTTGGTCCACTTCTCTGTACCTCATCAGGAAGATAACCGCTTCATTGATTTAACCCACTTCTCT
* *
1316 GTATCTCATCAGGAAGA
66 ATATCTCATCAAGAAGA
1333 TAGGATTTGA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTGTACCTCATCAGGAAGATAACCGCTTCATTGATTTAACCCACTTCTCT
ATATCTCATCAAGAAGACGA
Found at i:1543 original size:157 final size:158
Alignment explanation
Indices: 1204--1564 Score: 447
Period size: 157 Copynumber: 2.3 Consensus size: 158
1194 TGAAGATTAC
** * * *
1204 CGCTTCATTGATTTAATTCACTTCTCTATATCTTATCAAGAAGACGAATTTGGTCCACTTCTCTT
1 CGCTTCATTGATTTGGTT-ACTTCTCTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTATG
* * * * *
1269 TACCTCATCAGGAAGATAATCGCTTTATTGCTTTGACCCATTTCTCTGTATCTCATCAGGAAGAT
65 TACCTCATCAGGAAGATAACCGCTTTATTACTTTGACCCACTTCTC-GTATCTCATCAAGAACAT
*
1334 AGGATTTGAAGTCTCATTCGTATTGAGCTT
129 AGGATTTGAAGTCTCATTCATATTGAGCTT
** ** **
1364 CGCTTCATTGATTTGGTTTACTTCTCTGCATCTCATCAAGAAGGTG-ATTTGGTCTGCTTCTATG
1 CGCTTCATTGATTTGG-TTACTTCTCTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTATG
* * * * *
1428 TATCTCATTAGGAAGATAGCCGCTTTATTATTTTGACCCACTTCTC-TATCTCATCAAGAACATG
65 TACCTCATCAGGAAGATAACCGCTTTATTACTTTGACCCACTTCTCGTATCTCATCAAGAACATA
* *
1492 GGTTTTGGAGTCTCATTCATATTGAGCTT
130 GGATTTGAAGTCTCATTCATATTGAGCTT
*
1521 CGCTTCATTGATTTGGTGTACTTCTCTATATCTCATCAGGAAGA
1 CGCTTCATTGATTTGGT-TACTTCTCTATATCTCATCAAGAAGA
1565 TGACCGCTTC
Statistics
Matches: 171, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
156 1 0.01
157 79 0.46
159 53 0.31
160 36 0.21
161 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (158 bp):
CGCTTCATTGATTTGGTTACTTCTCTATATCTCATCAAGAAGACGAATTTGGTCCACTTCTATGT
ACCTCATCAGGAAGATAACCGCTTTATTACTTTGACCCACTTCTCGTATCTCATCAAGAACATAG
GATTTGAAGTCTCATTCATATTGAGCTT
Found at i:1686 original size:85 final size:85
Alignment explanation
Indices: 1530--1692 Score: 193
Period size: 85 Copynumber: 1.9 Consensus size: 85
1520 TCGCTTCATT
** * *
1530 GATTTGGTGTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTAATTTAATCCATTTGTC
1 GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTAATTTAATCCACTTCTC
*
1595 TGTATCTCATCAGAAAGGCG
66 TATATCTCATCAGAAAGGCG
* * * * * ** *
1615 GATTTGGTCCACTTCTTTGTATCTCATTAGGAAGATGACTGCTTTATTGCTTT-GTCACACTTCT
1 GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTAATTTAATC-CACTTCT
1679 CTATATCTCATCAG
65 CTATATCTCATCAG
1693 GAAGATGGGG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
84 2 0.03
85 62 0.97
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTAATTTAATCCACTTCTC
TATATCTCATCAGAAAGGCG
Found at i:1753 original size:208 final size:208
Alignment explanation
Indices: 1383--2329 Score: 1134
Period size: 208 Copynumber: 4.6 Consensus size: 208
1373 GATTTGGTTT
** * ** *
1383 ACTTCTCTGCATCTCATCAAGAAGG-TGATTTGGTCTGCTTCTATGTATCTCATTAGGAAGAT-A
1 ACTTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGA
** * * *
1446 GCCGCTTTATTATTTTGACCCACTTCTC--TATCTCATCAAGAACATGGGTTTTGGAGTCTCATT
66 -CCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTCTCATT
* * * *
1509 CATATTGAGCTTCGCTTCATTGATTTGGTGTACTTCTCTATATCTCATCAGGAAGATGACCGCTT
130 CGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCACTT
1574 CATTAATTTAATCC
195 CATTAATTTAATCC
* * * * *
1588 ATTTGTCTGTATCTCATC-AGAAAGGCGGATTTGGTCCACTTCTTTGTATCTCATTAGGAAGATG
1 ACTTCTCTATATCTCATCAAG-AAGGCAGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGATG
* * * *
1652 ACTGCTTTATTGCTTTGTCACACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCATT
65 ACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTCTCATT
* * *
1717 CGTATTGAGCTTCACTTCATTGATTCGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCACTT
130 CGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCACTT
1782 CATTAATTTAA-CC
195 CATTAATTTAATCC
* * * * * * * * * **
1795 TACTACTCTATATCTTATCAAGAAGACAAATTTGATCCACTTCTTTTTACCTCATCAGGAAGACA
1 -ACTTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGATG
* * * *
1860 ACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAA-CTTGGGTTTTAGAGTCTCAT
65 ACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGA-AGTCTCAT
* * * * * * *
1924 TCGTATTCAGCTTTGCTTCGTTTATTTGGTCTACTTATCTGTATCTCATCAGGAAGATGACCACT
129 TCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCACT
* *
1989 TAATTGATTTAATCC
194 TCATTAATTTAATCC
* * * * *
2004 AGTTCTCTATATCTCATCAGGAAGGTAGATTTGATCCACTTCTCTGTATCTCATAAGGAAGATGA
1 ACTTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGA
* * * * *
2069 CCGCTTTATTACTTTGACACACTTCTCTATATCTTATCAAGAAGATGGAGTTTGAAGTCTCATTT
66 CCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTC
* * * *
2134 GTATTGAGTTTTGCTTCATTGATTTGGTCAACTTCTCTATATCTCATCAAGAAGATGACCGCTTC
131 GTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCACTTC
* **
2199 ATTGATTTAATTT
196 ATTAATTTAATCC
* * *** *
2212 ACTTCTCTATATTTTATCAAGAAGATGGATTTGGTCCACTTCTCTGTACCTCATTAGGAAGATGA
1 ACTTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGA
*
2277 CCGCTTTATTGCTTTCACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTT
66 CCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTT
Statistics
Matches: 631, Mismatches: 101, Indels: 17
0.84 0.13 0.02
Matches are distributed among these distances:
204 2 0.00
205 19 0.03
206 55 0.09
207 11 0.02
208 533 0.84
209 11 0.02
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (208 bp):
ACTTCTCTATATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGA
CCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTC
GTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCACTTC
ATTAATTTAATCC
Found at i:2047 original size:37 final size:37
Alignment explanation
Indices: 1994--2064 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
1984 CCACTTAATT
* *
1994 GATTTAATCCAGTTCTCTATATCTCATCAGGAAGGTA
1 GATTTAATCCACTTCTCTATATCTCATAAGGAAGGTA
* *
2031 GATTTGATCCACTTCTCTGTATCTCATAAGGAAG
1 GATTTAATCCACTTCTCTATATCTCATAAGGAAG
2065 ATGACCGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (37 bp):
GATTTAATCCACTTCTCTATATCTCATAAGGAAGGTA
Found at i:2095 original size:85 final size:85
Alignment explanation
Indices: 1947--2112 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 85
1937 TGCTTCGTTT
* * * *
1947 ATTTGGTCTACTTATCTGTATCTCATCAGGAAGATGACCACTTAATTGATTTAATCCAGTTCTCT
1 ATTTGATCCACTTATCTGTATCTCATAAGGAAGATGACCACTTAATTGATTTAATCCACTTCTCT
*
2012 ATATCTCATCAGGAAGGTAG
66 ATATCTCATCAAGAAGGTAG
* * * *
2032 ATTTGATCCACTTCTCTGTATCTCATAAGGAAGATGACCGCTTTATT-ACTTTGA-CACACTTCT
1 ATTTGATCCACTTATCTGTATCTCATAAGGAAGATGACCACTTAATTGA-TTTAATC-CACTTCT
*
2095 CTATATCTTATCAAGAAG
64 CTATATCTCATCAAGAAG
2113 ATGGAGTTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 67 0.97
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (85 bp):
ATTTGATCCACTTATCTGTATCTCATAAGGAAGATGACCACTTAATTGATTTAATCCACTTCTCT
ATATCTCATCAAGAAGGTAG
Found at i:2201 original size:48 final size:48
Alignment explanation
Indices: 2146--2238 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
2136 ATTGAGTTTT
**
2146 GCTTCATTGATTTGGTCAACTTCTCTATATCTCATCAAGAAGATGACC
1 GCTTCATTGATTTAATCAACTTCTCTATATCTCATCAAGAAGATGACC
** * *
2194 GCTTCATTGATTTAATTTACTTCTCTATATTTTATCAAGAAGATG
1 GCTTCATTGATTTAATCAACTTCTCTATATCTCATCAAGAAGATG
2239 GATTTGGTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (48 bp):
GCTTCATTGATTTAATCAACTTCTCTATATCTCATCAAGAAGATGACC
Found at i:2301 original size:85 final size:85
Alignment explanation
Indices: 2154--2324 Score: 225
Period size: 85 Copynumber: 2.0 Consensus size: 85
2144 TTGCTTCATT
* ***
2154 GATTTGGTCAACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAATTTACTTCTC
1 GATTTGGTCAACTTCTCTATACCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
* *
2219 TATATTTTATCAAGAAGATG
66 TATATCTCATCAAGAAGATG
* * * * * * *
2239 GATTTGGTCCACTTCTCTGTACCTCATTAGGAAGATGACCGCTTTATTGCTTTCACCCACTTCTC
1 GATTTGGTCAACTTCTCTATACCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
2304 TATATCTCATCAAGAAGATG
66 TATATCTCATCAAGAAGATG
2324 G
1 G
2325 GGTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (85 bp):
GATTTGGTCAACTTCTCTATACCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTC
TATATCTCATCAAGAAGATG
Done.