Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018179.1 Corchorus olitorius cultivar O-4 contig18212, 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: 88865
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:843 original size:337 final size:330
Alignment explanation
Indices: 1--1057 Score: 1100
Period size: 337 Copynumber: 3.2 Consensus size: 330
* * * * *
1 GTGGACAAAAAATTGTAGAAAATATTTTCGGCTTAGTTTTTGCAAAATTTTGGCTGAAATCATGT
1 GTGG-CAAAAAATTG-AGAAAAAATTTTCGGGTTAGTTTTTG-AAAATTTTAGCCGAAATCGTGT
* ** * *
66 ATTAACCATCACGATTTTTGGCTAAAAAT-GCTTTCGAGAGCCCCGGGTTAACTTTGCATGATTT
63 ACTAACCATCACGATTTTTGGCT-AAAATCGCTTTCG-GAGCCCCGACTCAATTTTGCATGATTT
* * * * *
130 TTGGCACAAAGACTCTTTGAAATATCTGTATTCATCGAACCAAATTTCAACCATAGTGGATATAC
126 TTGGCGCAAAGACTC-CTGAAATATCTGTATTCATCGTACCAAATTTCAGCCACAGTGGATATAC
195 AGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATG
190 AGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATG
* * * * * *
260 GAAAAACGATATTAGAAGCATTAAAGGCTCATGAATCTATTTGGCATT-CA-AT-TATATATTTT
255 GAAAAACGATATTAGAAGCATTAAAGGCCCATCAATTTTTTTGGCGTTGAATATATATATATTTT
322 TT-TGAGTATT
320 TTCTGAGTATT
* * * *
332 GTGGCGAAAAATTCAGAAGAAAATTTTCCGGGTAAG----T-----TTTTAGCCGAAATCTTGTA
1 GTGGCAAAAAATTGAGAA-AAAATTTT-CGGGTTAGTTTTTGAAAATTTTAGCCGAAATCGTGTA
* * ** *
388 CTAACCATCACGATTTTGGGGCTAAAATCGCGTTACGG-GTAACCGACTCAGTTTTGCATGATTT
64 CTAACCATCACGATTTT-TGGCTAAAATCGC-TTTCGGAG-CCCCGACTCAATTTTGCATGATTT
* * * ** * * * *
452 TTGGTAG-AAAGACTCCTTATAATATC-GATATTAATC-TAACTGAATGTCAGCCACATTGTAAA
126 TTGG-CGCAAAGACTCCTGA-AATATCTG-TATTCATCGT-ACCAAATTTCAGCCACAGTGGATA
* * * * *
514 TA-AGGTCTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAATT-GGAAA
187 TACAGAT-TTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTT-AAAAT-TAATTCGG-AA
* * * * ** *
577 AAAAATGGAAAAACGATATTATAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATA
248 TAAAATGGAAAAACGATATTAGAAGCATTAAAGGCCCATCAATTTTTTTGGCGTTGAA-TATATA
642 TATATTTTTTCTGAGTATT
312 TATATTTTTTCTGAGTATT
* *
661 GTGGCAAAAAATTGAGGAAAAAATCTTCGGGTTAGTTTTTGCAGAATTTTAGCCGAAATCGTGTA
1 GTGGCAAAAAATTGA-GAAAAAATTTTCGGGTTAGTTTTTG-AAAATTTTAGCCGAAATCGTGTA
* *
726 CTAACCATCACGGTTTTTGGCTAAAATCGCTTTCCGGAGCCCCGTCTCAATTTTGCATGATTTTT
64 CTAACCATCACGATTTTTGGCTAAAATCGCTTT-CGGAGCCCCGACTCAATTTTGCATGATTTTT
*
791 TGCGCAAAGACTCCTCGAAATATCTGTATTCATCGTACCAAATTTCAGCCACAGTGGATATACAG
128 GGCGCAAAGACTCCT-GAAATATCTGTATTCATCGTACCAAATTTCAGCCACAGTGGATATACAG
* * *
856 ATTTGCTTTTACGAGCATCTGAATTTTGTTTCAATTTAGGTAAAATTAATTCGGAATAAAATGGA
192 ATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGGA
* *
921 AAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTT-GCGTTGAAT-TAT-T-TATTTTT
257 AAAACGATATTAGAAGCATTAAAGGCCCATCAAT-TTTTTTGGCGTTGAATATATATATATTTTT
982 TCTGAGTATT
321 TCTGAGTATT
* ** * * *
992 GTGGCAAACAATTGAGGAAAAAAAATTCGTGTTAGTTTTCGATAAATTTTATCCGAAATCGTGTA
1 GTGGCAAAAAATTGA-GAAAAAATTTTCGGGTTAGTTTTTGA-AAATTTTAGCCGAAATCGTGTA
1057 C
64 C
1058 CATCACCGAT
Statistics
Matches: 591, Mismatches: 95, Indels: 80
0.77 0.12 0.10
Matches are distributed among these distances:
321 44 0.07
322 103 0.17
323 11 0.02
324 49 0.08
325 1 0.00
327 3 0.01
328 19 0.03
329 32 0.05
330 19 0.03
331 84 0.14
332 2 0.00
333 3 0.01
334 1 0.00
335 50 0.08
336 15 0.03
337 114 0.19
338 41 0.07
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (330 bp):
GTGGCAAAAAATTGAGAAAAAATTTTCGGGTTAGTTTTTGAAAATTTTAGCCGAAATCGTGTACT
AACCATCACGATTTTTGGCTAAAATCGCTTTCGGAGCCCCGACTCAATTTTGCATGATTTTTGGC
GCAAAGACTCCTGAAATATCTGTATTCATCGTACCAAATTTCAGCCACAGTGGATATACAGATTT
GTTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGGAAAAA
CGATATTAGAAGCATTAAAGGCCCATCAATTTTTTTGGCGTTGAATATATATATATTTTTTCTGA
GTATT
Found at i:3383 original size:323 final size:316
Alignment explanation
Indices: 2717--4578 Score: 1747
Period size: 323 Copynumber: 5.7 Consensus size: 316
2707 GACACCTTAT
* * * *
2717 AATATCGATATTCATCTAACCGAATCTCAGCCACATTGGA-ATAAGGTCTTGTTTTTACTAGCAT
1 AATATCGATATTCATCT-ACCAAATCTCAGCCACAGTGGATATAAGAT-TTGTTTTTACGAGCAT
*
2781 CTGAATCTTGTTTCGATTTAATTAAAAATAAAATT-GGAA-AAAATGGAAAAACGATATTAGAAG
64 CTGAATTTTGTTTCGATTTAATT-AAAAT-AAATTCGGAATAAAATGGAAAAACGATATTAGAAG
* * *
2844 CGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATCATATATTTTTTTCTGAGTATTGTGG-AAAA
127 CATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAA
* * *
2908 AATTGAGGAAAAAATCTTCGGGTTAGTTTTGCAGAATTTTAGCCGAAATCGTGTACTAACCATCA
191 AATT-AAGAAAATAT-TTCGGG-TA-------AG-TTTTTAGCCGAAATCGTGTACTAACCATCA
* * * * *
2973 CGGTTTTTGTCT-AAAATCGCTTTTCGGATCCCCGGCTCAATTTTGCATGATTTTTTGCGCAAAG
245 CGGGTTTTGGCTAAAAAT-GCTTTACGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCG-AAAG
*
3037 ACTCCTCGA
308 ACTCCTTGA
* * * *
3046 AATATCTATATTCATCGTACCAAATTTCAGCCACAGTGGATATATATATTTGCTTTTACGAGCAT
1 AATATCGATATTCATC-TACCAAATCTCAGCCACAGTGGATATA-AGATTTGTTTTTACGAGCAT
* * *
3111 CTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGGAAAAACGATTTTAGAAGCA
64 CTGAATTTTGTTTCGATTTAATTAAAATAAATTCGGAATAAAATGGAAAAACGATATTAGAAGCA
* * * *
3176 TGAAAAGCTCGTCAATATCTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAT
129 TGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAT
* *
3241 TCAAACGAAAATATTTCGGGTAAGTTTTTAGCCGAAATCATGTAATAACCATCACGGGTTTTGGT
194 T--AA-GAAAATATTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGG-
* * * * * *
3306 CTAAAAATGCGTTACGGGGCCCCGACT-ACGTTTTGCATGATTTCTGGCAGAAAAACTCCTTGA
255 CTAAAAATGCTTTACGGAGCCCCGGCTCA-ATTTTGCATGATTTTTGGC-GAAAGACTCCTTGA
* * *
3369 AATATCGATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTGTTTTTTACGAGCAT
1 AATATCGATATTCATCT-ACCAAATCTCAGCCACAGTGGATATAAGATTTG-TTTTTACGAGCAT
* * * * *
3434 TTGAATCTTGTTTCGATTTAATGTGAAATAAATTCGG-ATAACATGGACAAACGATATTAGAAGC
64 CTGAATTTTGTTTCGATTTAAT-TAAAATAAATTCGGAATAAAATGGAAAAACGATATTAGAAGC
* * *** *
3498 GTGAAAAACCCTTCAATTTTTTTATTGTTGAATTATATATTTTTTCTGAGTATTTTCGG-AAAAA
128 ATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGT-GGCAAAAA
* * * * *
3562 ATTGTAGAAAATATTTTCGGCTTAGTTTTTGCAAAATTTTGCCTGAAATGGTATACTAACCATCA
192 ATT-AAGAAAATA-TTTCGGGTAAGTTTTT-----A----GCC-GAAATCGTGTACTAACCATCA
** * * * * * * *
3627 CGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAACTTTGCATGATTTTTGGCCAAAGAC
245 CGGGTTTTGGCTAAAAATGCTTTACGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGAAAGAC
3692 TCCTTGA
310 TCCTTGA
* * * *
3699 AATATCTG-TATTCATCGAACCAAATTTCAGCCATAGTGGATATACAAATTTGTTTTTACGAGCA
1 AATATC-GATATTCATC-TACCAAATCTCAGCCACAGTGGATATA-AGATTTGTTTTTACGAGCA
* * *
3763 TCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGGAAAAACGATATTGGAAGC
63 TCTGAATTTTGTTTCGATTTAATTAAAATAAATTCGGAATAAAATGGAAAAACGATATTAGAAGC
* ** * * * * * * *
3828 ATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATATTTTTTTTTAGTATTGTGGCGAAAAA
128 ATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
* * * *
3893 TTCAGAAGAAAATTTTTTGGGTAAGTTTTTAGCCGAAATCTTGTACTAACCATCA-TGGTTTTGG
193 TT---AAGAAAATATTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTT--
* * ** ** *
3957 GGCTAAAAACGCGTTACGG-GTAACCAACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTT-
253 GGCTAAAAATGCTTTACGGAG-CCCCGGCTCAATTTTGCATGATTTTTGGC-GAAAGACTCCTTG
4020 A
316 A
* * * * *
4021 CAATATCGATATTCATCTAACAGAATCTCAGCCACATTGGAAATAAGGTCTTGTTTTTACTAGCA
1 -AATATCGATATTCATCTACCA-AATCTCAGCCACAGTGGATATAAGAT-TTGTTTTTACGAGCA
* *
4086 TCTGAATTTTGTTTCGATTTAATTAAAAATAAAATT-GGAAAAAAAATGGAAAAATGATATTAGA
63 TCTGAATTTTGTTTCGATTTAATT-AAAAT-AAATTCGG-AATAAAATGGAAAAACGATATTAGA
* * *
4150 AGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTTGTGAGTATTGTGGCAA
125 AGCATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAA
* * * *
4215 AAAATTGAGGAAAAAATCTTCGGGTTAGTTTTTGCATAATTTTAGCTGAAATCGTGTACTAACCA
189 AAAATT-AAGAAAATAT-TTCGGG-TA-----AG--T--TTTTAGCCGAAATCGTGTACTAACCA
* * * *
4280 TCACGGTTTTTGGCT-AAAATCGCTTTCCGGAGCCCCGGCTCAATTTTGGATGATTTTTTGCGCA
242 TCACGGGTTTTGGCTAAAAAT-GCTTTACGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCG-A
* **
4344 AAGACACCTCAA
305 AAGACTCCTTGA
* * * * *
4356 AATATCTATATTCATCGAACCAAATTTCAGCCACAGTGGATATACAGATTTGCTTTTACGAGAAT
1 AATATCGATATTCATC-TACCAAATCTCAGCCACAGTGGATATA-AGATTTGTTTTTACGAGCAT
* *
4421 CTGAATTTTGTTTCGATTTAGTTAAAACT-AATTCGGAATAAAATGGAAAAACGATATGAGAAGC
64 CTGAATTTTGTTTCGATTTAATTAAAA-TAAATTCGGAATAAAATGGAAAAACGATATTAGAAGC
* ** * * *
4485 ATTAAAGGCCCGTCAATCTATTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTTGCAAAAAA
128 ATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
* * * *
4550 TTGAGGAAAAAATTTTCGTGTTAGTTTTT
193 TT-AAGAAAATA-TTTCGGGTAAGTTTTT
4579 GATAAATTTT
Statistics
Matches: 1254, Mismatches: 211, Indels: 144
0.78 0.13 0.09
Matches are distributed among these distances:
320 4 0.00
321 30 0.02
322 104 0.08
323 273 0.22
324 35 0.03
325 65 0.05
326 28 0.02
327 1 0.00
328 4 0.00
329 76 0.06
330 258 0.21
331 109 0.09
332 103 0.08
333 12 0.01
334 112 0.09
335 35 0.03
336 5 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (316 bp):
AATATCGATATTCATCTACCAAATCTCAGCCACAGTGGATATAAGATTTGTTTTTACGAGCATCT
GAATTTTGTTTCGATTTAATTAAAATAAATTCGGAATAAAATGGAAAAACGATATTAGAAGCATG
AAAAACCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTA
AGAAAATATTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAA
ATGCTTTACGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGAAAGACTCCTTGA
Found at i:4019 original size:653 final size:654
Alignment explanation
Indices: 1100--4578 Score: 4670
Period size: 653 Copynumber: 5.3 Consensus size: 654
1090 TAAATATAAT
* * * * *
1100 GATTTGATTTTACGGGCATCTTAATTTTGTTTCCATTTAGTTATAATTAATTCGGAATAAAAT-G
1 GATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
* * * * * *
1164 AAAAACGATATTAGAAGCATGAAAAGCCCGTCAATCTCTTTGGCGTTGAATTATATATCTTTTCT
66 AAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATATTTTTTCT
* * * * *
1229 GA-TGGTTATGGCAAAAAATTCAGACGAAAATATTTCGGGTAAGTTTTTAGCCGAAATCATGTAC
131 GAGT-ATTGTGGCAAAAAATTCAGAAGAAAATTTTTCGGGTAAGTTTTTAGCCGAAATCTTGTAC
* * * * * * *
1293 TAACCATCACGGTTTTTGGGCCAAAAATGCGTTACGGGGACCCGACTAAGTTATGCATGATTTCT
195 TAACCATCACGGTTTTGGGGCTAAAAACGCGTTACGGGTAACCGACTCAGTTTTGCATGATTTCT
* * * **
1358 GGCAAAAAAACTCCTTGA-AATATCGATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAG
260 GGCAGAAAGACTCCTT-ATAATATCGATATTCATCTAACCAAATCTCAGCCACATTGGAAATAAG
* * ** *
1422 AAT-TTGTTTTTACTAGCATCTGAATCTTGTTTCGAATTAATTTGAAAT-AAATTCGAAAAAAAT
324 -GTCTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAATT-GGAAAAAAT
*
1485 GGAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTAGTGTTGAATTATATATTTTT
387 GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTTTTTAGTGTTGAATTATATATTTTT
*
1550 TTCTGAGTATTGTGGCAAAAAATTGTAGAAAATATTTTCGGCTTAGTTTTTGCAAAATTTTGGCC
451 TTCTGAGTATTGTGG-AAAAAATTGTAGAAAATATTTTCGGCTTAGTTTTTGCAAAATTTTAGCC
* *
1615 GAAATGGTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGAGTTAATTTT
515 GAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAATTTT
* * *
1680 GCATGATTTTTGGCACAAAAACTCCTTGAAATATCTGTATTCATCGAACCAAATTTCAACCATAG
580 GCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTGTATTCATCGAACCAAATTTCAGCCATAG
1745 TGGATATACA
645 TGGATATACA
*
1755 GATTTG--TTTACGAGCATTTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
1 GATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
* * *
1818 AAAAACGATATTAGAAGCATTAAAGGCTCGTGAATCTATTTGGCATTCAATTATATATTTTTTTT
66 AAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATA-TTTTTTC
* ** * *
1883 TTAGTATTGTGGTGAAAAATTCAGAAGAAAATTTTCCGTGTAAGTTTTTAGCCGAAATCTTGTAC
130 TGAGTATTGTGGCAAAAAATTCAGAAGAAAATTTTTCGGGTAAGTTTTTAGCCGAAATCTTGTAC
* *
1948 TAACCATCACGGTTTTGGGGCTAAAAACGCGTTACGGATAACCAACTCAGTTTTGCATGATTTCT
195 TAACCATCACGGTTTTGGGGCTAAAAACGCGTTACGGGTAACCGACTCAGTTTTGCATGATTTCT
* *
2013 GGCAGAAAGACTCCTTATAATATCGATATTAATCTAACCGAATCTCAGCCACATTGGAAATAAGG
260 GGCAGAAAGACTCCTTATAATATCGATATTCATCTAACCAAATCTCAGCCACATTGGAAATAAGG
*
2078 TCTTGTTTTTACTAGCATCTGAATCTTGTTTTGATTTAATTAAAAATAAAATTGGAAAAAAAATC
325 TCTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAATTGG--AAAAAAT-
* * *
2143 TGAAAAACGATATTAGAAGCGAGAAAAACCCTTTAATTTTTTTAGTGTTGAATTATATA-TTTTT
387 GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTAGTGTTGAATTATATATTTTTT
* * * * *
2207 TCTGATTATTATGACAAAAAATTGTAGAAAATATTTTCGGCTTAGTTTTTTGTAAAATTTTGGCC
452 TCTGAGTATTGTG-GAAAAAATTGTAGAAAATATTTTCGGCTTAG-TTTTTGCAAAATTTTAGCC
* * *
2272 GAAATCGTGTATTAACCATCACGATATTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAACTTT
515 GAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAATTTT
*
2337 GCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTGTATTCATCGAACCAAATTTCAACCATAG
580 GCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTGTATTCATCGAACCAAATTTCAGCCATAG
*
2402 TGGATTTACA
645 TGGATATACA
* * *
2412 GATTTGTTTTTACAAGCATCCGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
1 GATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
* * *
2477 AAAAACGATATTAGAAGCATTAAAGGCTCGTGAATCTATTTGGCATTCAATTATATATTTTTACT
66 AAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATATTTTTTCT
* *
2542 GAGTATTGTGGCGAAAAATTCAGAAGAAAA-TTTTCAGGGTAAGTTTTTAGCCGAAATCTTGTAG
131 GAGTATTGTGGCAAAAAATTCAGAAGAAAATTTTTC-GGGTAAGTTTTTAGCCGAAATCTTGTAC
* *
2606 TAACCATCACGGTTTTGGGGCTAAAATCGCGTTACGGGTAACCGACTCATCTTCTTGCTATCTCG
195 TAACCATCACGGTTTTGGGGCTAAAAACGCGTTACGGGTAACCGACTCA-GTT-TTGC-A--T-G
** *
2671 AAAGTTAACACTCCGCTCTCTACCGAGGGTCCCCAAGACACCTTATAATATCGATATTCATCTAA
254 --A-TT-----T---CTGGC-A--GA--------AAGACTCCTTATAATATCGATATTCATCTAA
*
2736 CCGAATCTCAGCCACATTGG-AATAAGGTCTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTT
297 CCAAATCTCAGCCACATTGGAAATAAGGTCTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTT
2800 AATTAAAAATAAAATTGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTT
362 AATTAAAAATAAAATTGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTT
* * * * *
2865 TTTGGCGTTGAATCATATATTTTTTTCTGAGTATTGTGGAAAAAATTG-AGGAAAAAATCTTCGG
427 TTTAGTGTTGAATTATATATTTTTTTCTGAGTATTGTGGAAAAAATTGTA-GAAAATATTTTCGG
* * * * *
2929 GTTAG-TTTTGCAGAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGTCTAAAATCGC
491 CTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGC
* * * * * * * *
2993 TTTTCGGATCCCCGGCTCAATTTTGCATGATTTTTTGCGCAAAGACTCCTCGAAATATCTATATT
556 TTTCCAGAGCCCCGGGTTAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTGTATT
* * *
3058 CATCGTACCAAATTTCAGCCACAGTGGATATATA
621 CATCGAACCAAATTTCAGCCATAGTGGATATACA
*
3092 TATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
1 GATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
* * * * * * * *
3157 AAAAACGATTTTAGAAGCATGAAAAGCTCGTCAATATCTTTGGCGTTGAATTATATATTTTTTCT
66 AAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATATTTTTTCT
* * *
3222 GAGTATTGTGGCAAAAAATTCA-AACGAAAATATTTCGGGTAAGTTTTTAGCCGAAATCATGTAA
131 GAGTATTGTGGCAAAAAATTCAGAA-GAAAATTTTTCGGGTAAGTTTTTAGCCGAAATCTTGTAC
* * ***
3286 TAACCATCACGGGTTTT-GGTCTAAAAATGCGTTACGGGGCCCCGACT-ACGTTTTGCATGATTT
195 TAACCATCAC-GGTTTTGGGGCTAAAAACGCGTTACGGGTAACCGACTCA-GTTTTGCATGATTT
* **
3349 CTGGCAGAAAAACTCCTTGA-AATATCGATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
258 CTGGCAGAAAGACTCCTT-ATAATATCGATATTCATCTAACCAAATCTCAGCCACATTGGAAATA
** * * * *
3413 A-GAATTGTTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATGT-GAAAT-AAATTCGGATAA
322 AGGTCTTG-TTTTTACTAGCATCTGAATCTTGTTTCGATTTAAT-TAAAAATAAAATT-GGAAAA
* * *
3475 CATGGACAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTATTGTTGAATTATATA-TT
384 AATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTAGTGTTGAATTATATATTT
*
3539 TTTTCTGAGTATTTTCGGAAAAAATTGTAGAAAATATTTTCGGCTTAGTTTTTGCAAAATTTT-G
449 TTTTCTGAGTATTGT-GGAAAAAATTGTAGAAAATATTTTCGGCTTAGTTTTTGCAAAATTTTAG
* * *
3603 CCTGAAATGGTATACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAAC
513 CC-GAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAAT
3668 TTTGCATGATTTTTGGC-CAAAGACTCCTTGAAATATCTGTATTCATCGAACCAAATTTCAGCCA
577 TTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTGTATTCATCGAACCAAATTTCAGCCA
3732 TAGTGGATATACA
642 TAGTGGATATACA
* *
3745 AATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
1 GATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
* *
3810 AAAAACGATATTGGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATATTTTTTTT
66 AAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATATTTTTTCT
* * *
3875 TAGTATTGTGGCGAAAAATTCAGAAGAAAATTTTTTGGGTAAGTTTTTAGCCGAAATCTTGTACT
131 GAGTATTGTGGCAAAAAATTCAGAAGAAAATTTTTCGGGTAAGTTTTTAGCCGAAATCTTGTACT
* * *
3940 AACCATCATGGTTTTGGGGCTAAAAACGCGTTACGGGTAACCAACTCAGTTTTGCATGATTTTTG
196 AACCATCACGGTTTTGGGGCTAAAAACGCGTTACGGGTAACCGACTCAGTTTTGCATGATTTCTG
*
4005 GCAGAAAGACTCCTTACAATATCGATATTCATCTAA-CAGAATCTCAGCCACATTGGAAATAAGG
261 GCAGAAAGACTCCTTATAATATCGATATTCATCTAACCA-AATCTCAGCCACATTGGAAATAAGG
*
4069 TCTTGTTTTTACTAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAAATTGGAAAAAAAATG
325 TCTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAATTGG--AAAAAATG
* * *
4134 GAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTT
388 GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTAGTGTTGAATTATATATTTTTTT
* * * * * *
4199 GTGAGTATTGTGGCAAAAAATTG-AGGAAAAAATCTTCGGGTTAGTTTTTGCATAATTTTAGCTG
453 CTGAGTATTGTGG-AAAAAATTGTA-GAAAATATTTTCGGCTTAGTTTTTGCAAAATTTTAGCCG
* * * * *
4263 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAATCGCTTTCCGGAGCCCCGGCTCAATTTTG
516 AAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAATTTTG
* * * ** * *
4328 GATGATTTTTTGCGCAAAGACACCTCAAAATATCTATATTCATCGAACCAAATTTCAGCCACAGT
581 CATGATTTTTGGCGCAAAGACTCCTTGAAATATCTGTATTCATCGAACCAAATTTCAGCCATAGT
4393 GGATATACA
646 GGATATACA
* *
4402 GATTTGCTTTTACGAGAATCTGAATTTTGTTTCGATTTAGTTAAAACTAATTCGGAATAAAATGG
1 GATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
* * *
4467 AAAAACGATATGAGAAGCATTAAAGGCCCGTCAATCTATTTGGCGTTGAATTATATATTTTTTCT
66 AAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATATTTTTTCT
* * * *
4532 GAGTATTGTTGCAAAAAATTGAGGAA-AAAA-TTTTCGTGTTAGTTTTT
131 GAGTATTGTGGCAAAAAATTCA-GAAGAAAATTTTTCGGGTAAGTTTTT
4579 GATAAATTTT
Statistics
Matches: 2491, Mismatches: 261, Indels: 143
0.86 0.09 0.05
Matches are distributed among these distances:
652 81 0.03
653 551 0.22
654 147 0.06
655 279 0.11
656 189 0.08
657 390 0.16
658 141 0.06
659 113 0.05
660 6 0.00
661 1 0.00
662 1 0.00
663 4 0.00
664 1 0.00
666 2 0.00
667 2 0.00
671 2 0.00
672 2 0.00
674 1 0.00
675 4 0.00
676 1 0.00
677 1 0.00
678 6 0.00
679 5 0.00
680 339 0.14
681 11 0.00
682 78 0.03
683 23 0.01
685 61 0.02
686 49 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (654 bp):
GATTTGCTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAATTAATTCGGAATAAAATGG
AAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATATTTTTTCT
GAGTATTGTGGCAAAAAATTCAGAAGAAAATTTTTCGGGTAAGTTTTTAGCCGAAATCTTGTACT
AACCATCACGGTTTTGGGGCTAAAAACGCGTTACGGGTAACCGACTCAGTTTTGCATGATTTCTG
GCAGAAAGACTCCTTATAATATCGATATTCATCTAACCAAATCTCAGCCACATTGGAAATAAGGT
CTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAATTGGAAAAAATGGAA
AAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTAGTGTTGAATTATATATTTTTTTCTG
AGTATTGTGGAAAAAATTGTAGAAAATATTTTCGGCTTAGTTTTTGCAAAATTTTAGCCGAAATC
GTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAATTTTGCATGA
TTTTTGGCGCAAAGACTCCTTGAAATATCTGTATTCATCGAACCAAATTTCAGCCATAGTGGATA
TACA
Found at i:5326 original size:332 final size:322
Alignment explanation
Indices: 4644--5996 Score: 1251
Period size: 332 Copynumber: 4.2 Consensus size: 322
4634 ACCACAGTAA
* * * *
4644 ATATAAGGATTTGATTTTAC-AGGCATCTTAATTTTGTTTCCATTT-AGTTAAAATTAATTCGGA
1 ATATAA-GATTTGTTTTTACGA-GCATCTGAATTTTGTTTCGATTTAAGTTAAAATAAATTCGGA
* * *
4707 ATAAAATGGAAAAACGATATTAAAAGCATGAAAAGCCCGTCAATCTCTTTT-GCGTTGAATTATA
64 ATAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCGTCAAT-TTTTTTGGCGTTGAATTATA
* *
4771 TATTTTTTCTGAGTATTGTGGCAAAAAATTCAGATGAAAATATTTCGGGTAAGTTTTT-A---GC
128 TATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA--AAAAT-TTTC-GGTTAGTTTTTAATTTGC
* * * *
4832 CGAAATCATGTACTAACCATCACGATTTTTGGGCTAAAAATGCGTTACGGGGTCCCGAC-TAAGT
189 CGAAATCATGTACTAACCATCACGATTTTTGGGCTAAAAACGCGTTAC-GAGCCCCGGCTTAA-T
* * *
4896 TTTGCATGATTTCTGGCAGAAAAACTCCTTGAAATATCGATATTCATCTAAACAAATCTCAGCCA
252 TTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCGATATTCATCGAAACAAATCTCAGCCA
4961 CATTGG
317 CATTGG
* * * *
4967 ATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGGAA
1 ATATAAG-ATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAGTTAAAATAAATTCGGAA
* * * * *
5032 -AAAATGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATTTTTTTAGTGTTGAATTAT-TA
65 TAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATATA
* *
5095 TTTTTTTCTGAGTATTGTGGCAAAAAAATTGTAGATTATATTTTCGGCTTAGTTTTTGCAAAATT
130 -TTTTTTCTGAGTATTGTGGC-AAAAAATTG-AGA-AAAATTTTCGG-TTAGTTTTT----AA-T
* * * *
5160 TTGGCCGAAATCGTGTACTAACCATCACGATTTTT-GGCTAAAAACGCTTTCCAGAGCCCCGGGT
185 TT-GCCGAAATCATGTACTAACCATCACGATTTTTGGGCTAAAAACGCGTTAC-GAGCCCCGGCT
* * * *
5224 TAACTTTGCATAATTTTTGGC-GCAAAGACTTCTTGAAATATCTG-TATTCATCGAAACAAATTT
248 TAATTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATC-GATATTCATCGAAACAAATCT
* *
5287 CAGCCATAGTGG
311 CAGCCACATTGG
*
5299 ATATACAGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTT-AGTTAAAACT-AATTCGAA
1 ATATA-AGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAGTTAAAA-TAAATTCGGA
* ** * * * *
5362 ATAAAATGGAAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATAT
64 ATAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATAT
* * * *
5427 ATTTTTT-TGAGTATTGTGGCGAAATATTCAGAAGAAAATTTTCCGG---G----TAAGTT-CCG
129 ATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-A-AAAATTTT-CGGTTAGTTTTTAATTTGCCG
* * ** * *
5483 AAATCTTGTACTAACCATCAC-AGTTTTTGGGCTAAAAACGCGTTACGGGTAACCGACTTAGTTT
191 AAATCATGTACTAACCATCACGA-TTTTTGGGCTAAAAACGCGTTACGAG-CCCCGGCTTAATTT
* * *
5547 TGCATGATTTTTGGCAGAAAGACTCCTT-ATAATATCGATATTCAT-GTAACCGAGTCTCAGCCA
254 TGCATGATTTTTGGCAGAAAGACTCCTTGA-AATATCGATATTCATCG-AAACAAATCTCAGCCA
*
5610 CATTAG
317 CATTGG
* * *
5616 ATATAAGGACTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAA-TTAAAAATAAA-T----
1 ATATAA-GATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAGTT-AAAATAAATTCGGA
* * *
5675 -T----TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTGTAT
64 ATAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATAT
* * *
5735 TTTTTTTCTGAGTATTGTGGCAAGAAATTGAGGAAAAATCTTCGAGTTAGTTTTTGCAGAATTTT
129 ATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAATTTTCG-GTTAGTTTTT----AA-TTT
* * * * *
5800 AGCCGAAATTATGTACTAACCATCACGGTTTTT-GGCTAAAATCGC-TTTCTGAAGCCCCGGCTC
187 -GCCGAAATCATGTACTAACCATCACGATTTTTGGGCTAAAAACGCGTTAC-G-AGCCCCGGCTT
* * * * *
5863 AATTTTGCATGATTTTTTGC-GCAAAGACTCCTCGAAATATCTATATTCATCGAACCAAATTTCA
249 AATTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCGATATTCATCGAAACAAATCTCA
*
5927 GCCACAATGG
313 GCCACATTGG
* * *
5937 ATATACGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTT-AGTTAAAATTAATTC
1 ATATA-AGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAGTTAAAATAAATTC
5997 AGAAACGCAC
Statistics
Matches: 840, Mismatches: 125, Indels: 131
0.77 0.11 0.12
Matches are distributed among these distances:
307 2 0.00
308 63 0.08
309 20 0.02
310 1 0.00
311 1 0.00
312 1 0.00
315 2 0.00
316 34 0.04
317 119 0.14
318 10 0.01
319 4 0.00
320 14 0.02
321 118 0.14
322 40 0.05
323 117 0.14
324 28 0.03
325 3 0.00
327 1 0.00
328 1 0.00
329 2 0.00
330 13 0.02
331 31 0.04
332 176 0.21
333 39 0.05
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (322 bp):
ATATAAGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAGTTAAAATAAATTCGGAAT
AAAATGGAAAAACGATATTAGAAGCATGAAAAACCCGTCAATTTTTTTGGCGTTGAATTATATAT
TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAATTTTCGGTTAGTTTTTAATTTGCCGAAATC
ATGTACTAACCATCACGATTTTTGGGCTAAAAACGCGTTACGAGCCCCGGCTTAATTTTGCATGA
TTTTTGGCAGAAAGACTCCTTGAAATATCGATATTCATCGAAACAAATCTCAGCCACATTGG
Found at i:5981 original size:638 final size:648
Alignment explanation
Indices: 4644--6001 Score: 1881
Period size: 638 Copynumber: 2.1 Consensus size: 648
4634 ACCACAGTAA
* * * * *
4644 ATATAAGGATTTGATTTTAC-AGGCATCTTAATTTTGTTTCCATTTAGTTAAAATTAATTCGGAA
1 ATATACGGATTTGTTTTTACGA-GCATCTAAATTTTGTTTCGATTTAGTTAAAATTAATTCGAAA
* * * *
4708 TAAAATGGAAAAACGATATTAAAAGCATGAAAAGCCCGTCAATCTCTTTTGCGTTGAATTATATA
65 TAAAATGGAAAAACGATATTAAAAGCATGAAAAGCCCGTCAATCTATTTGGCATTCAATTATATA
*
4773 TTTTTTCTGAGTATTGTGGCAAAAAATTCAGATGAAAATATTTCGGGTAAGTTTTTAGCCGAAAT
130 TTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAGAAAATATTTCGGGTAAG--TTTA-CCGAAAT
* *
4838 CATGTACTAACCATCACGATTTTTGGGCTAAAAATGCGTTACGGGGTCCCGACTAAGTTTTGCAT
192 CATGTACTAACCATCACGATTTTTGGGCTAAAAACGCGTTACGGGGTACCGACTAAGTTTTGCAT
*
4903 GATTTCTGGCAGAAAAACTCCTTGAAATATCGATATTCATCTAAACAAATCTCAGCCACATTGGA
257 GATTTCTGGCAGAAAAACTCCTTGAAATATCGATATTCATCTAAACAAATCTCAGCCACATTAGA
* *
4968 TTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATAAATTCGGAAA
322 TATAAGAACTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTT-AAATAAATT--G-AA
*
5033 AAATGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATTTTTTTAGTGTTGAATTATTATTT
383 AAATGGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATTTTTTTAGCGTTGAATTATTATTT
* * * *
5098 TTTTCTGAGTATTGTGGCAAAAAAATTGTAGATTATATTTTCGGCTTAGTTTTTGCAAAATTTTG
448 TTTTCTGAGTATTGTGGCAAAAAAATTGTAGATAAAATCTTCGGCTTAGTTTTTGCAAAATTTTA
* * *
5163 GCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGGTTAAC
513 GCCGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGCTCAAC
* * *
5228 TTTGCATAATTTTTGGCGCAAAGACTTCTTGAAATATCTGTATTCATCGAAACAAATTTCAGCCA
578 TTTGCATAATTTTTGGCGCAAAGACTCCTCGAAATATCTATATTCATCGAAACAAATTTCAGCCA
* *
5293 TAGTGG
643 CAATGG
* * *
5299 ATATACAGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAAAACTAATTCGAAAT
1 ATATACGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAGTTAAAATTAATTCGAAAT
* * *
5364 AAAATGGAAAAACGATATTAGAAGCATTAAAGGCCCGTCAATCTATTTGGCATTCAATTATATAT
66 AAAATGGAAAAACGATATTAAAAGCATGAAAAGCCCGTCAATCTATTTGGCATTCAATTATATAT
* * *
5429 TTTTT-TGAGTATTGTGGCGAAATATTCAGAAGAAAAT-TTTCCGGGTAAG-TT-CCGAAATCTT
131 TTTTTCTGAGTATTGTGGCAAAAAATTCAGAAGAAAATATTT-CGGGTAAGTTTACCGAAATCAT
*
5490 GTACTAACCATCAC-AGTTTTTGGGCTAAAAACGCGTTAC-GGGTAACCGACTTAGTTTTGCATG
195 GTACTAACCATCACGA-TTTTTGGGCTAAAAACGCGTTACGGGGT-ACCGACTAAGTTTTGCATG
* * * * * *
5553 ATTTTTGGCAGAAAGACTCCTT-ATAATATCGATATTCATGTAACCGAGTCTCAGCCACATTAGA
258 ATTTCTGGCAGAAAAACTCCTTGA-AATATCGATATTCATCTAAACAAATCTCAGCCACATTAGA
* * **
5617 TATAAGGACTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAA-TT-AA-AAA-T-AAATTT
322 TATAAGAACTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAATAAATTGAAAAAT
* * *
5677 GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATT-GTATTTTTTT
387 GGAAAAACGATATTAGAAGCGTAAAAAACCCTTCAATTTTTTTAGCGTTGAATTATTA-TTTTTT
* *
5741 TCTGAGTATTGTGGC-AAGAAATTG-AGGA-AAAATCTTCGAG-TTAGTTTTTGCAGAATTTTAG
451 TCTGAGTATTGTGGCAAAAAAATTGTA-GATAAAATCTTCG-GCTTAGTTTTTGCAAAATTTTAG
* * * * *
5802 CCGAAATTATGTACTAACCATCACGGTTTTTGGCTAAAATCGCTTT-CTGAAGCCCCGGCTCAAT
514 CCGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAG-AGCCCCGGCTCAAC
* * *
5866 TTTGCATGATTTTTTGCGCAAAGACTCCTCGAAATATCTATATTCATCGAACCAAATTTCAGCCA
578 TTTGCATAATTTTTGGCGCAAAGACTCCTCGAAATATCTATATTCATCGAAACAAATTTCAGCCA
5931 CAATGG
643 CAATGG
5937 ATATACGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAGTTAAAATTAATTCAGAAA
1 ATATACGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAGTTAAAATTAATTC-GAAA
6002 CGCACGCGCT
Statistics
Matches: 630, Mismatches: 63, Indels: 36
0.86 0.09 0.05
Matches are distributed among these distances:
637 2 0.00
638 200 0.32
639 17 0.03
640 76 0.12
644 1 0.00
645 3 0.00
646 2 0.00
648 8 0.01
649 159 0.25
651 2 0.00
653 3 0.00
654 37 0.06
655 119 0.19
656 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (648 bp):
ATATACGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAGTTAAAATTAATTCGAAAT
AAAATGGAAAAACGATATTAAAAGCATGAAAAGCCCGTCAATCTATTTGGCATTCAATTATATAT
TTTTTCTGAGTATTGTGGCAAAAAATTCAGAAGAAAATATTTCGGGTAAGTTTACCGAAATCATG
TACTAACCATCACGATTTTTGGGCTAAAAACGCGTTACGGGGTACCGACTAAGTTTTGCATGATT
TCTGGCAGAAAAACTCCTTGAAATATCGATATTCATCTAAACAAATCTCAGCCACATTAGATATA
AGAACTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAAATAAATTGAAAAATGGAA
AAACGATATTAGAAGCGTAAAAAACCCTTCAATTTTTTTAGCGTTGAATTATTATTTTTTTCTGA
GTATTGTGGCAAAAAAATTGTAGATAAAATCTTCGGCTTAGTTTTTGCAAAATTTTAGCCGAAAT
CATGTACTAACCATCACGATTTTTGGCTAAAAACGCTTTCCAGAGCCCCGGCTCAACTTTGCATA
ATTTTTGGCGCAAAGACTCCTCGAAATATCTATATTCATCGAAACAAATTTCAGCCACAATGG
Found at i:7922 original size:26 final size:26
Alignment explanation
Indices: 7879--7928 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
7869 GGACATCTGG
7879 TATACTTGAAGTACTTTTACTTTTAA
1 TATACTTGAAGTACTTTTACTTTTAA
* *
7905 TATACTCTTAAGTA-TTTTTCTTTT
1 TATACT-TGAAGTACTTTTACTTTT
7929 TTGGCCAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (26 bp):
TATACTTGAAGTACTTTTACTTTTAA
Found at i:12091 original size:19 final size:19
Alignment explanation
Indices: 12051--12091 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12041 ATGCATATGA
*
12051 TCTAATGACGGAAATTAGT
1 TCTAATGACGGAAATTACT
12070 TCTAA-GACGGAAATCTACT
1 TCTAATGACGGAAAT-TACT
12089 TCT
1 TCT
12092 GCTCTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (19 bp):
TCTAATGACGGAAATTACT
Found at i:22658 original size:31 final size:31
Alignment explanation
Indices: 22615--22681 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
22605 GAGGGGAGCA
* **
22615 AGTCCCTGACAGTGTGAAATC-AGCTCAAATC
1 AGTCCCTAACAGTGCAAAATCGA-CTCAAATC
*
22646 AGTCCCTAACAGTGCAAAATCGACTCAATTC
1 AGTCCCTAACAGTGCAAAATCGACTCAAATC
22677 AGTCC
1 AGTCC
22682 TTAAAGTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (31 bp):
AGTCCCTAACAGTGCAAAATCGACTCAAATC
Found at i:33138 original size:15 final size:15
Alignment explanation
Indices: 33118--33146 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33108 TGGGCAGTTT
33118 CAGAATTTATTGAAC
1 CAGAATTTATTGAAC
33133 CAGAATTTATTGAA
1 CAGAATTTATTGAA
33147 TCTATCAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (15 bp):
CAGAATTTATTGAAC
Found at i:46663 original size:2 final size:2
Alignment explanation
Indices: 46656--46687 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
46646 TACATATACC
*
46656 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46688 TTTTGGCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:60684 original size:27 final size:27
Alignment explanation
Indices: 60649--60703 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
60639 TTTGCTCTTA
60649 ATTCAGAACTTATACTTACTTTACCTT
1 ATTCAGAACTTATACTTACTTTACCTT
60676 ATTCAGAACTTATACTTACTTTACCTT
1 ATTCAGAACTTATACTTACTTTACCTT
60703 A
1 A
60704 GACAAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.44
Consensus pattern (27 bp):
ATTCAGAACTTATACTTACTTTACCTT
Found at i:62336 original size:33 final size:33
Alignment explanation
Indices: 62294--62364 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
62284 CCATCCTAAT
62294 TTGATTTAACAATGTATTTCAATAATCAAAAAC
1 TTGATTTAACAATGTATTTCAATAATCAAAAAC
*
62327 TTGATTTAACAATGTATTTCAATCATCAAAAAC
1 TTGATTTAACAATGTATTTCAATAATCAAAAAC
62360 -TGATT
1 TTGATT
62365 GGCAATCTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 5 0.14
33 32 0.86
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (33 bp):
TTGATTTAACAATGTATTTCAATAATCAAAAAC
Found at i:82501 original size:16 final size:17
Alignment explanation
Indices: 82480--82511 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
82470 GATTCTTTAT
82480 TTTCTTT-TATTTTTTC
1 TTTCTTTATATTTTTTC
82496 TTTCTTTATATTTTTT
1 TTTCTTTATATTTTTT
82512 AGAACAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTCTTTATATTTTTTC
Found at i:87892 original size:2 final size:2
Alignment explanation
Indices: 87885--87925 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
87875 CCTCTAGAAC
87885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
87926 CAAAAATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.