Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022408.1 Corchorus olitorius cultivar O-4 contig22441, 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: 65543
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:1766 original size:333 final size:332
Alignment explanation
Indices: 1134--1984 Score: 1001
Period size: 333 Copynumber: 2.6 Consensus size: 332
1124 CCCGGCTCAG
* *
1134 TTTTG-CAAAATTTTAGTCGAAATCGTGTACTAACCATCATGGTTTTTGCCAAAAACGTATTTCG
1 TTTTGTCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTG-CAAAAACGCATTTCG
* * * * *
1198 GAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCTA-AAGATCCTTGAAATATCTATATCCATCT
65 GAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAGAA-CTCCTTGAAATATCCATATTCATCT
* ****
1262 ACCCAAATCCCAGCCAA-AGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTTTCGA
129 ACCCAAATCTCAG-CAACAACAAATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTTTCGA
* * *
1326 TTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAGGTTAAAAGCCAGTC
193 TTTAAATAGAAATTAATTAGGAAAAAAAATTGGAAAAATGATATTAAAAAGGTTAAAAGCCAGTC
* * * * *
1391 AATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGAACAAAAATAGAGG-AACATTT
258 AATCTTTTTTGCATTGAATTATAAATTTTTTATCAATATTTTGAACAAAAATAGAGGAAAAATGT
1455 TTCGGGTCAA
323 TTCGGGTCAA
* * *
1465 TTTTCTTCAAACTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGCATTT
1 TTTT-GTCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTT-GC-AAAAACGCATTT
** *
1530 CGGAGTTTCGACTCAGTTTTGCTTGATTTTTGGCGCCAGAACTCCTTGAAATATCCATATTCATT
63 CGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAGAACTCCTTGAAATATCCATATTCATC
* *
1595 TACCCAAATCTCAGCAACAACAAATTTAAGGAT-T-TCTTTTACTAGTATCTGAATCTAGTTTCG
128 TACCCAAATCTCAGCAACAACAAATTTAAGGATATGT-TTTTACGAGCATCTGAATCTAGTTTCG
* **
1658 ATTTAAATAGAAATTAATTAGGAAAAAAAATTGGAAAAATGATATTAAAAAGGTTAGAAGCCCTT
192 ATTTAAATAGAAATTAATTAGGAAAAAAAATTGGAAAAATGATATTAAAAAGGTTAAAAGCCAGT
* ** *
1723 CAATCTTTTTTGCATTGAATCT-TATATTTTTTATCAATATTTTGGCCAAAAATTGAGGAAAAAT
257 CAATCTTTTTTGCATTGAAT-TATAAATTTTTTATCAATATTTTGAACAAAAATAGAGGAAAAAT
1787 GTTTCGGGTCAA
321 GTTTCGGGTCAA
* * * * *
1799 TTTTGT-AAAATTTTAGTCGAAATCATG---T-ACCGTTACGGTTTTTAGCTAAAACTGCGTTTC
1 TTTTGTCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTT-GCAAAAAC-GCATTT-
* * * * * *
1859 CGG-GCCCCGGCTCAGTTTTGCATAATTTTTGACGTCATG-ACTCCTTGAAATATCCATATTCAT
63 CGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCA-GAACTCCTTGAAATATCCATATTCAT
* * *** * * * *
1922 CTACCCAAATATCAACAACAATGGATTTAAGGATATGATTTTATGAGCATCAGAATCTTGTTT
127 CTACCCAAATCTCAGCAACAACAAATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTTT
1985 TAGTCGAAAT
Statistics
Matches: 442, Mismatches: 64, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
327 5 0.01
328 98 0.22
329 26 0.06
331 4 0.01
332 19 0.04
333 178 0.40
334 110 0.25
335 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (332 bp):
TTTTGTCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGCAAAAACGCATTTCGG
AGCCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAGAACTCCTTGAAATATCCATATTCATCTAC
CCAAATCTCAGCAACAACAAATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTTTCGATTT
AAATAGAAATTAATTAGGAAAAAAAATTGGAAAAATGATATTAAAAAGGTTAAAAGCCAGTCAAT
CTTTTTTGCATTGAATTATAAATTTTTTATCAATATTTTGAACAAAAATAGAGGAAAAATGTTTC
GGGTCAA
Found at i:2382 original size:253 final size:254
Alignment explanation
Indices: 1799--2491 Score: 960
Period size: 253 Copynumber: 2.8 Consensus size: 254
1789 TTCGGGTCAA
* * * * * *
1799 TTTTGTAAAATTTTAGTCGAAATCATG---T-ACCGTTACGGTTTTTAGCTAAAACTGCGTTTCC
1 TTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAACCGCTTTTCC
* * *
1860 GGGCCCCGGCTCAGTTTTGCATAATTTTTGACG-TCATGACTCCTTGAAATATCCATATTCATCT
66 GAGCCCCGGCTCAGTTTTGCAT-ATTTTTGGCGCTCAAGACTCCTTGAAATATCCATATTCATCT
*
1924 ACCCAAATATCAACAACAATGGATTTAAGGATATGATTTTATGAGCATCAGAATCTTGTTTTAGT
130 ACCCAAATATCAACAACAATGGATTTAAGGATATGATTTTATGAGCATCAGAATCTTGTTTTAGC
* * *
1989 CGAAATTGTGTACGCATCACGGTTTTTGGCGAAAAACGTCATTTCGAGGCCCTGGCTCAG
195 CGAAATTGTGTACGCATCACGCTTTTTGGCGAAAAACGTCATTTCGAAGCCCCGGCTCAG
* * *
2049 TTTTGCAAAATGTTAGTCAAAATCGTGTACTAACCATCACGGTTTTT-GCCGAAAA-CG-TATTT
1 TTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAG-CTAAAACCGCT-TTT
* * ** ** * *
2111 CGGAGCCTCGATTCAGTTTTGTTTGACTTTTGGCGCTAAAGA-TCCTTGAAATATCCATATTCAT
64 CCGAGCCCCGGCTCAGTTTTGCAT-ATTTTTGGCGCTCAAGACTCCTTGAAATATCCATATTCAT
2175 CTACCCAAATATCAACAACAATGGATTTAAGGATATGATTTTATGAGCATCAGAATCTTGTTTTA
128 CTACCCAAATATCAACAACAATGGATTTAAGGATATGATTTTATGAGCATCAGAATCTTGTTTTA
2240 GCCGAAATTGTGTACGCATCACGCTTTTTGGCGAAAAACG-CATTTCGAAGCCCCGGCTCAG
193 GCCGAAATTGTGTACGCATCACGCTTTTTGGCGAAAAACGTCATTTCGAAGCCCCGGCTCAG
2301 TTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAACCGCTTTTCC
1 TTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAACCGCTTTTCC
* *
2366 GAGCCCCGGCTCAGTTTTCCATAGTTTTTGGCGC-CAAGACTCCTTCAAATATCCCA-ATTCATC
66 GAGCCCCGGCTCAGTTTTGCATA-TTTTTGGCGCTCAAGACTCCTTGAAATAT-CCATATTCATC
* * * * * *
2429 TACCCAAATCTCATCAACAATGGATTTAAGTATATGTTTTTACGAGCATCGGAATCTTGTTTT
129 TACCCAAATATCAACAACAATGGATTTAAGGATATGATTTTATGAGCATCAGAATCTTGTTTT
2492 GATTAAATGA
Statistics
Matches: 386, Mismatches: 44, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
250 23 0.06
252 74 0.19
253 263 0.68
254 26 0.07
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (254 bp):
TTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAACCGCTTTTCC
GAGCCCCGGCTCAGTTTTGCATATTTTTGGCGCTCAAGACTCCTTGAAATATCCATATTCATCTA
CCCAAATATCAACAACAATGGATTTAAGGATATGATTTTATGAGCATCAGAATCTTGTTTTAGCC
GAAATTGTGTACGCATCACGCTTTTTGGCGAAAAACGTCATTTCGAAGCCCCGGCTCAG
Found at i:3069 original size:331 final size:329
Alignment explanation
Indices: 2297--3467 Score: 1387
Period size: 333 Copynumber: 3.5 Consensus size: 329
2287 AAGCCCCGGC
* * *
2297 TCAGTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAACCGCTT
1 TCAGTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAAACGCAT
* * * *
2362 TTCCGAGCCCCGGCTCAGTTTTCCAT-AGTTTTTGGCGCCAAGACTCCTTCAAATATCCCA-ATT
66 TTCGGAGCCCCGACTCAGTTTTGCATGA-TTTTTGGCGCCAAGACTCCTTGAAATAT-CCATATT
* * * * *
2425 CATCTACCCAAATCTCATCAACAATGGATTTAAGTATATGTTTTTACGAGCATCGGAATCTTGTT
129 CATCTACCCAAATCCCACCAACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTT
* * * * * *
2490 TTGA-TTAAATGAAAAATTAATTAGG-AAAA-ACTTGGAAAAATGATATTAG-AAGCGTTAGAAT
194 TCGATTTAAAT-AGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAG-GTTAAAAG
* * * *
2551 CCCTTCAATCTTTTTTTTTGCGTTAAATTATATAAATTTTATAAGTATTTTGGCCAAAAATTGAG
257 CCATTCAA----TTTTTTTGCGTTGAA-T-CATAAATTTTATAAGTATTTTGGACAAAAATTGAG
*
2616 GTAAAAATTTT-GGG
316 G-AAAACTTTTCGGG
* * * * * **
2630 TCAATTTTGCAAAATTTTGGTCGAAATCGTGTATTAACCATCATGGTTTTTACCGAAAAACTTAT
1 TCAGTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAAACGCAT
* * * *
2695 TTCGGAGCCACGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGA-TCCTTGAAATATCTATATTC
66 TTCGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCGCC-AAGACTCCTTGAAATATCCATATTC
* *
2759 ATCTACCCAAATCCCAGCCAA-AGTGGATTTAAGGATATGTTTTTATGAGCATCTGAATCTAGTT
130 ATCTACCCAAATCCCA-CCAACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTT
*
2823 TCGATTTAAATAGGAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAGGTTAAAAGCC
194 TCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAGGTTAAAAGCC
* * * *
2888 ATTCAATTTTTTTGCATTGAATCATAAATTTTATCAGTGTTTTGGACAAAAATAGAGGAAAACTT
259 ATTCAATTTTTTTGCGTTGAATCATAAATTTTATAAGTATTTTGGACAAAAATTGAGGAAAACTT
2953 TTCGGG
324 TTCGGG
* * * * * *
2959 TCAGTTTTCTTCAAACTTTTAGCCGAAATCGTATACTAATCATCACGGTTTTTGGCGAAAAACGC
1 TCAG-TTT-TGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAAACGC
* * * *
3024 ATTTCGGAGTCTCGACTCAGTTTTGCTTGATTTTTGGCGCCAAAGA-TCCTTGAAATATCTATAT
64 ATTTCGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCGCC-AAGACTCCTTGAAATATCCATAT
* * *
3088 TAATCTACCCAAATCCCAGCCAA-AGTGGATTTAAAGATATGTTTTTACGAGCATCT-AGATCTA
128 TCATCTACCCAAATCCCA-CCAACAATGGATTTAAGGATATGTTTTTACGAGCATCTGA-ATCTA
*
3151 GTTTCGATTTAAATAGAAATTAAATAGGAAAAATAATTGGAAAAATGATTTTAGAAAGGTTAAAA
191 GTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAGGTTAAAA
*
3216 GCCATTCAATCTTTTTTGCGTTGAATCATAAATTTTTTATGAGTATTTTGGACAAAAATTGAGGA
256 GCCATTCAAT-TTTTTTGCGTTGAATCATAAA--TTTTATAAGTATTTTGGACAAAAATTGAGGA
3281 AAACTGTTTCGGG
318 AAACT-TTTCGGG
* * * * * * **
3294 TCAGTTTTGCAAAGTTTTAGTCGAAATTGTGTACTAACCATTACGATTTTTAGCTAAAACCGTGT
1 TCAGTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAAACGCAT
* * * * *
3359 TTCCGG-GCCCCGGCTCATTTTTGCATAATTTTTGACGCCATGACTCCTTGAAATATCCATATTC
66 TT-CGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTC
** * *
3423 ATCTACCCAAATATCAACAACAATGGATTTAAGGATATGATTTTA
130 ATCTACCCAAATCCCACCAACAATGGATTTAAGGATATGTTTTTA
3468 TGAGTATCAT
Statistics
Matches: 724, Mismatches: 95, Indels: 38
0.84 0.11 0.04
Matches are distributed among these distances:
328 8 0.01
329 37 0.05
330 5 0.01
331 249 0.34
332 28 0.04
333 295 0.41
334 57 0.08
335 42 0.06
336 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (329 bp):
TCAGTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCGAAAAACGCAT
TTCGGAGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTCA
TCTACCCAAATCCCACCAACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTTTC
GATTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAGGTTAAAAGCCAT
TCAATTTTTTTGCGTTGAATCATAAATTTTATAAGTATTTTGGACAAAAATTGAGGAAAACTTTT
CGGG
Found at i:5329 original size:334 final size:332
Alignment explanation
Indices: 3547--6150 Score: 3091
Period size: 335 Copynumber: 7.8 Consensus size: 332
3537 AAGCCCCTGC
* *
3547 TCAG-TTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTT-GCCAAAATAC-T
1 TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAA-ACGC
* * *
3609 TATTTCGGAGCCACGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGA-TCCTTGAAATATCTATA
65 T-TTTCGGAGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCC-AAGACTCCTTGAAATATCCATA
* * * * * *
3673 TTCATCTACCCATATCACAGCCAA-AGTGAATTTAAGGATATGTTTTTACGAGCATCTGAATCTA
128 TTCATCTACCCAAATCTCAG-CAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTT
* *
3737 GTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAG-GTTAAA
192 GTTTCGATTTAATTAGAAATTAATTAGG-AAAA-AATTGGAAAAATGATATTAG-AAGCGTTAAA
* * * * * * *
3801 ACCCATTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGGGAATTTTGGACAAAAATAGAGG
254 AGCCATTCAATCTATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGG
3866 AAAAA-TTTTCGGG
319 AAAAATTTTTCGGG
* * * * *
3879 TCATTTTTTTTTCAAAATTTTAGCCGAAATCGTCTACTAACCATCACGATTTTTGGCGAAAAACG
1 TCA--GTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACG
* ** * **
3944 CATTTCGGAATCTCGACTCAGAGTTGCTTGATTTTTGGCGCCATA-ACTCCTTGAAATATCCATA
64 CTTTTCGGAGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCCA-AGACTCCTTGAAATATCCATA
* * *
4008 TTCATCAACCCAAATCTCAACAACAATGGATTTAAGGATATTTTTTTACGAGCA-CTAGAATCTT
128 TTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATC-AGAATCTT
* *
4072 GTTTCGATTTAATTAGAAATTAATTAGGAAAAAATTTGCAAAAAATGATATTAGAAACGTTAAAA
192 GTTTCGATTTAATTAGAAATTAATTAGGAAAAAA-TTG-GAAAAATGATATTAGAAGCGTTAAAA
* * * * **
4137 GCCATTCAATCTATTTTGTGTTGAATTATATA-TTTTTATGAGTATCTTAGCCCAAAATTGAGTT
255 GCCATTCAATCTATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGA
*
4201 AAAATTTTTCGGA
320 AAAATTTTTCGGG
* * * *
4214 TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTAC---CCATCACAGTTTTTAGCTAAAACCGCT
1 TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGCT
* * * * * * * *
4276 TTTCTGAGCCCCGGCTAAGTTTTACATAATTTTTGGCGCCAGGACTCCTTCAAATATCCCA-ATT
66 TTTCGGAGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGAAATAT-CCATATT
*
4340 CATCTACCCAAATCTCAGCAACAATGGATTTAAGTATATGTTTTTACGAGCATCAGAATCTTGTT
130 CATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTT
* * ** *
4405 TCGATTTAATCAAAAATTAATTAGGAAAAACCTGGAAAAATGATATTAGAAGCGTTAGAAGCCAT
195 TCGATTTAATTAGAAATTAATTAGGAAAAAATTGGAAAAATGATATTAGAAGCGTTAAAAGCCAT
* * * * *
4470 TCAATAATTCT-TTTTGCGTTGAAATATATAATTTTTATGAGTATTTTGACCAAAAATAGTGGAA
260 TC---AA-TCTATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAA
* *
4534 AAATTGTTCGGA
321 AAATTTTTCGGG
* *
4546 TCAGTTTTGTGCAAAATTTTAGCCGAAATCGTGTACT-ACCATCACGGTTTTTGGCGAAAACCG-
1 TCAGTTTT-TGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGC
* * * * *
4609 TATTTCGGAGCCACGACTTAGTTTTGCTTGACTTTTGGCGCGAAAGA-TCCTTGAAATATCTATA
65 T-TTTCGGAGCCCCGACTCAGTTTTGCTTGATTTTTGGCGC-CAAGACTCCTTGAAATATCCATA
*
4673 TTCATCTACCCAAATC-CTAGC--CAATGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATC
128 TTCATCTACCCAAATCTC-AGCAACAA--TGGATTTAAGGATATGTTTTTACGAGCATCAGAATC
* * *
4735 TAGTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAG-GTTA
190 TTGTTTCGATTTAATTAGAAATTAATTAGG-AAAA-AATTGGAAAAATGATATTAG-AAGCGTTA
* * * *
4799 AAAGCCATTCAATCTTTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGACAAAAATAG
252 AAAGCCATTCAATC-TATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTG
4864 AGGAAAAA-TTTTCGGG
316 AGGAAAAATTTTTCGGG
* * *
4880 TCAATTTTCTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGC
1 TCAGTTTT-TGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGC
* * * *
4945 ATTTCGGAGTCTCGGCTCAGTTTTGCTTGATTTTTGGCGCC-AGAACTCCTTGAAATATCCATAT
65 TTTTCGGAGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAG-ACTCCTTGAAATATCCATAT
* *
5009 TCATTTACCCAAATCTCAGCAACAATGGATTTAAGGATATTTTTTTACGAGCATCAGAATCTTGT
129 TCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGT
* *
5074 TCCGATTTAATTAGAAATTAATTAGGAAAAAATTTGCAAAAAATGATATTAGAAGCGTTAAAAGC
194 TTCGATTTAATTAGAAATTAATTAGGAAAAAA-TTG-GAAAAATGATATTAGAAGCGTTAAAAGC
* *
5139 CATTCAATCTATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGTAAA
257 CATTCAATCTATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAA
*
5204 AATTTTTCGGA
322 AATTTTTCGGG
* * *
5215 TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTAGCTAAAACCGCT
1 TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGCT
* * * * *
5280 TTTCCGAGCCCCGGCTCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTCAAATATCCCA-ATT
66 TTTCGGAGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGAAATAT-CCATATT
*
5344 CATCTACCCAAATCTCAGCAACAATGGATTTAAGTATATGTTTTTACGAGCATCAGAATCTTGTT
130 CATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTT
* * * * *
5409 TCGATTTAATCAAAAATTAATTAGGAAAAACTTGGAAAAATGATATTAGAAGCGTTAGAAGCCCT
195 TCGATTTAATTAGAAATTAATTAGGAAAAAATTGGAAAAATGATATTAGAAGCGTTAAAAGCCAT
* ** * * **
5474 TCAATCTTTTTTTTATGCTAAATTATATAAATTTTATGAGTATTTTGGCCAAAAATTGAGGAAAA
260 TCAATC--TATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAA
5539 ATTTTTCGGG
323 ATTTTTCGGG
* * *
5549 TCAATTTTTGCAAAATTTTAGTCGAAATCGTGTAC-AACGATCACGG-TTTTGGCGAAAAACGCA
1 TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGCT
* * *
5612 TTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGA-TCCTTGAAATATCTATATT
66 TTTCGGAGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCC-AAGACTCCTTGAAATATCCATATT
* * * * *
5676 AATCTACCCAAATCCCAGCCAA-AGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGT
130 CATCTACCCAAATCTCAG-CAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGT
* * *
5740 TTCGATTTAAATAGAAATTAATTAGGAAAAAATTGGAAAAATAATATTAGAAAG-GTTAGAAGCC
194 TTCGATTTAATTAGAAATTAATTAGGAAAAAATTGGAAAAATGATATTAG-AAGCGTTAAAAGCC
* * * *
5804 CTTCAATCTATTTTGCATTGAATCATATATTTTTTATCAGTATTTTGGCCAAAAATTGAGGAAAA
258 ATTCAATCTATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAA
*
5869 TTTTTTCGGG
323 ATTTTTCGGG
** * * *
5879 TCAG-TTTTGCAAAATATTT-GTCGAAATCGTGTACTAACCATTGCGGTTTTTAGCTAAAACCGC
1 TCAGTTTTTGCAAAAT-TTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGC
* * ** * **
5942 GTTTCCGACTTTCCGG-GCCCCCG-CTCAGTTTTGCATAATTTTTGTTGCCATGACTATTTGAAA
65 ---T-----TTT-CGGAG-CCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGAAA
* * *
6005 TATCC-TATTCATCTACCCAAATTTCAGCAACAATGGAATTAAGGATATGTTTTTACGAGCATCT
120 TATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCA
* * * *
6069 GAATCTCGTTTCGATTTAATCAAAAATTAATTAGGAAAAAATTGGAAAAATAATATTAGAAGCGT
185 GAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAATTGGAAAAATGATATTAGAAGCGT
* * *
6134 TAGAAGCCCTTCTATCT
250 TAAAAGCCATTCAATCT
6151 TTCCGGAGCC
Statistics
Matches: 1957, Mismatches: 245, Indels: 134
0.84 0.10 0.06
Matches are distributed among these distances:
328 30 0.02
329 28 0.01
330 224 0.11
331 38 0.02
332 262 0.13
333 88 0.04
334 434 0.22
335 628 0.32
336 14 0.01
337 39 0.02
338 129 0.07
339 36 0.02
340 7 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (332 bp):
TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGCT
TTTCGGAGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGAAATATCCATATTC
ATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTT
CGATTTAATTAGAAATTAATTAGGAAAAAATTGGAAAAATGATATTAGAAGCGTTAAAAGCCATT
CAATCTATTTTGCGTTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATT
TTTCGGG
Found at i:6807 original size:14 final size:14
Alignment explanation
Indices: 6788--6815 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6778 AAATCGTGTA
6788 CTAACCATCACGGT
1 CTAACCATCACGGT
6802 CTAACCATCACGGT
1 CTAACCATCACGGT
6816 TTTTAGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (14 bp):
CTAACCATCACGGT
Found at i:7279 original size:336 final size:332
Alignment explanation
Indices: 6156--7631 Score: 1648
Period size: 334 Copynumber: 4.4 Consensus size: 332
6146 TATCTTTCCG
* * * * *
6156 GAGCCCTGGCTCAGTTTTGCTTTACTTTTGGCACCAAAGATACTTGAAATATCTATATTCATCTA
1 GAGCCCCGGCTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATCCATATTCATCTA
* * * *
6221 CCTAAATCTCAGCCAA-ATTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTTTCGAT
66 CCCAAATCTCAG-CAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGAT
*
6285 TTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAGAAAGGTTAAAAGCCCTTCA
130 TTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATATTAG-AAGGTTAAAAGCCCTTCA
* *
6350 ATATTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGCCAAAAATAGAGG-AAAAATTT
194 ATATTTTTTGCGTTGAATTATAAA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAATTT
* * * * * *
6414 TCGGGTCAGTTTTCTTCAAAATTTTAGCCGAAATCGTATACTAACCA-CTACGGTTTTTGGCAAA
258 TCTGGTCAGTTTT-TGCAAAATTTTAGTCGAAATCGTATACTAACCATC-ATGGTTTTTAGC-TA
*
6478 AAAACGCATTTCG
320 AAAACGCATTTCA
* * * * *
6491 GAGTCTCGGCTCAGTTTTGCTTGATTTTTGGCGCCCAAA-CTCCTTGAAATATCCATATTCATCA
1 GAGCCCCGGCTCAGTTTTGCTTGACTTTTGGCG-CCAAAGATCCTTGAAATATCCATATTCATCT
* *
6555 ACCCAAATCTCAGCAACAACGGATTTAAGGATA-GTTTTTTACGAGCATCAGAATCTTATTTCGA
65 ACCCAAATCTCAGCAACAATGGATTTAAGGATATG-TTTTTACGAGCATCAGAATCTTGTTTCGA
* * * *
6619 -TTAAATTAGAAATTTATTAGG-AAAA-AGTTGCAAAAAATGATATTAGAAGCGTTAAAAGCCAT
129 TTTAAA-TAGAAATTAATTAGGAAAAATAATTG-GAAAAATGATATTAGAAG-GTTAAAAGCCCT
* *
6681 TCAATATATTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTAGCCAAAAATT-AGGTAAAAA
191 TCAATATTTTTTGCGTTGAATTATAAA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAA
6745 TTTT-TCGGATCAGTTTTTGCAAAATATTT-GTCGAAATCGTGTACTAACCATCACGGTCTAACC
255 TTTTCT-GG-TCAGTTTTTGCAAAAT-TTTAGTCGAAATC--G---T----AT-A----CTAACC
* * * *
6808 ATCACGGTTTTTAGCTAAAACCGCGTTTCT
303 ATCATGGTTTTTAGCTAAAAACGCATTTCA
** * * *
6838 GAGCCCCGGCTCAGTTTTGAATAATTTTTGGCGCC-AAGACTCCTTCAAATATCCCA-ATTCATC
1 GAGCCCCGGCTCAGTTTTGCTTGACTTTTGGCGCCAAAGA-TCCTTGAAATAT-CCATATTCATC
* *
6901 TACCCAAATCTCAGCAACAATGGATTTAAGTATATGTTTTTACGAGCATCGGAATCTTGTTTCGA
64 TACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGA
* * * *
6966 TTT-AATCAAAAATTAATTAGG-AAAA-ACTTGGAAAAATGATATTAGAAGCGTTAGAATCCCTT
129 TTTAAAT-AGAAATTAATTAGGAAAAATAATTGGAAAAATGATATTAGAAG-GTTAAAAGCCCTT
* * * *
7028 CAATCTTTTTTTTTGCGTTAAATTATATTAA-TTTTATGAGTATTTTGGCCAAAATTTGAGGAAA
192 CAA---TATTTTTTGCGTTGAATTATA--AATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * * *
7092 AAATTTTCTGGTCAATTTTTGTAAAATTTTTGTCGAAAATCGTGTACTAACCATCATGGTTTTTG
252 AAATTTTCTGGTCAGTTTTTGCAAAATTTTAGTCG-AAATCGTATACTAACCATCATGGTTTTTA
*
7157 GCGAAAAACGCATTTCA
316 GCTAAAAACGCATTTCA
* * ** *
7174 GAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATTTATACTCATCTA
1 GAGCCCCGGCTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATCCATATTCATCTA
* * * *
7239 CCCAAATCCCAGCCAA-AATGGATTTAAGGATATATTTTTACGAGCATCTGAATCTAGTTTCGAT
66 CCCAAATCTCAG-CAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGAT
*
7303 TTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATATTAGAATGGTTAGAAGCCCTTCA
130 TTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATATTAGAA-GGTTAAAAGCCCTTCA
* * * *
7368 AT-CTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTAGCTAAAAATTGAGAAAAAAAATT
194 ATATTTTTTGCGTTGAATTATAAA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAATTT
* *
7432 TC-GCGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTATACTAACCATTATGGTTTTTAACTAAA
258 TCTG-GTCAGTTTTTGCAAAATTTTAGTCGAAATCGTATACTAACCATCATGGTTTTTAGCTAAA
* *
7496 ACCGCGTTTCCA
322 AACGCATTT-CA
* * *
7508 G-GCCCCGGCTCAGTTTTGCAT-AATGTTTGGCGCC-GAGACTCCTTGAAATATCCATATTCATC
1 GAGCCCCGGCTCAGTTTTGCTTGACT-TTTGGCGCCAAAGA-TCCTTGAAATATCCATATTCATC
* **
7570 TACCCAAATATCAGCAACAATGGATTTAAGGATATGTTTTTATTAGCATCAGAATCTTGTTT
64 TACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTT
7632 TAGCCGAAAT
Statistics
Matches: 971, Mismatches: 116, Indels: 110
0.81 0.10 0.09
Matches are distributed among these distances:
332 10 0.01
333 145 0.15
334 193 0.20
335 127 0.13
336 154 0.16
337 14 0.01
338 36 0.04
339 2 0.00
340 1 0.00
341 1 0.00
343 2 0.00
344 1 0.00
345 3 0.00
346 34 0.04
347 137 0.14
348 28 0.03
349 61 0.06
350 19 0.02
351 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (332 bp):
GAGCCCCGGCTCAGTTTTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATCCATATTCATCTA
CCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATT
TAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATATTAGAAGGTTAAAAGCCCTTCAAT
ATTTTTTGCGTTGAATTATAAATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAAATTTTCT
GGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTATACTAACCATCATGGTTTTTAGCTAAAAACG
CATTTCA
Found at i:7467 original size:683 final size:667
Alignment explanation
Indices: 6202--7631 Score: 1844
Period size: 683 Copynumber: 2.1 Consensus size: 667
6192 AAGATACTTG
* * *
6202 AAATATCTATATTCATCTACCTAAATCTCAGCCAA-ATTGGATTTAAGGATATGTTTTTACGAGC
1 AAATATCCATATTCATCTACCCAAATCTCAG-CAACAATGGATTTAAGGATATGTTTTTACGAGC
* * * *
6266 ATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATTGGAAAAATGATTTTAG
65 ATCAGAATCTTGTTTCGATTTAAATAAAAATTAATTAGGAAAAATAATTGGAAAAATGATATTAG
*
6331 AAAGGTTAAAAGCCCTTCAATATTTTTTGCGTTGAATTATAAATTTTTTATGAGTATTTTGGCCA
130 AAAGGTTAAAAGCCCTTCAATATTTTTTGCGTTAAATTATAAA-TTTTTATGAGTATTTTGGCCA
*
6396 AAAATAGAGGAAAAATTTTCGGGTCAGTTTTCTTCAAAATTTTAGCCGAAATCGTATACTAACCA
194 AAAATAGAGGAAAAATTTTCGGGTCAATTTTCTTCAAAATTTTAGCCGAAATCGTATACTAACCA
* * * *
6461 CTACGGTTTTTGGCAAAAAAACGCATTTCGGAGTCTCGGCTCAGTTTTGCTTGATTTTTGGCGCC
259 CTACGGTTTTTGGCAAAAAAACGCATTTCAGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCC
* * *
6526 CAAACTCCTTGAAATATCCATATTCATCAACCCAAATCTCAGCAACAACGGATTTAAGGATAGTT
324 CAAAATCCTTGAAATATCCATACTCATCAACCCAAATCCCAGCAACAACGGATTTAAGGATAGTT
* *
6591 TTTTACGAGCATCAGAATCTTATTTCGATTAAATTAGAAATTTATTAGGAAAAAGTTGCAAAAAA
389 TTTTACGAGCATCAGAATCTTATTTCGATTAAATTAGAAATTAATTAGGAAAAAATTGCAAAAAA
6656 TGATATTAGAAGCGTTAAAAGCCATTCAATATATTTTGCGTTGAATTATAAATTTTTTATGAGTA
454 TGATATTAGAAGCGTTAAAAGCCATTCAATATATTTTGCGTTGAATTATAAATTTTTTATGAGTA
* ** *
6721 TTTTAGCCAAAAATTAGGTAAAAATTTTTCGGATCAGTTTTTGCAAAATATTTGTCGAAATCGTG
519 TTTTAGCCAAAAATTAGGAAAAAAAATTTCGGATCAGTTTTTGCAAAATATTTGTCGAAATCGTA
* *
6786 TACTAACCATCACGGTCTAACCATCACGGTTTTTAGCTAAAACCGCGTTT-CTGAGCCCCGGCTC
584 TACTAA-C--CA---T-T----AT---GGTTTTTAACTAAAACCGCGTTTCCAG-GCCCCGGCTC
*
6850 AGTTTTGAATAATTTTTGGCGCCAAGACTCCTTC
634 AGTTTTGAATAATGTTTGGCGCCAAGACTCCTTC
*
6884 AAATATCCCA-ATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGTATATGTTTTTACGAGC
1 AAATAT-CCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGC
* *
6948 ATCGGAATCTTGTTTCGATTT-AATCAAAAATTAATTAGG-AAAA-ACTTGGAAAAATGATATTA
65 ATCAGAATCTTGTTTCGATTTAAAT-AAAAATTAATTAGGAAAAATAATTGGAAAAATGATATTA
* * *
7010 G-AAGCGTTAGAATCCCTTCAATCTTTTTTTTTGCGTTAAATTATATTAA-TTTTATGAGTATTT
129 GAAAG-GTTAAAAGCCCTTCAA---TATTTTTTGCGTTAAATTATA--AATTTTTATGAGTATTT
* * * * * *
7073 TGGCCAAAATTTGAGGAAAAAATTTTCTGGTCAATTTT-TGT-AAAATTTTTGTCGAAAATCGTG
188 TGGCCAAAAATAGAGG-AAAAATTTTCGGGTCAATTTTCT-TCAAAATTTTAGCCG-AAATCGTA
* *
7136 TACTAACCA-TCATGGTTTTTGGC-GAAAAACGCATTTCAGAGCCTCGACTCAGTTTTGCTTGAC
250 TACTAACCACT-ACGGTTTTTGGCAAAAAAACGCATTTCAGAGCCTCGACTCAGTTTTGCTTGAC
** * *
7199 TTTTGGCG-CCAAAGATCCTTGAAATATTTATACTCATCTACCCAAATCCCAGCCAA-AATGGAT
314 TTTTGGCGCCCAAA-ATCCTTGAAATATCCATACTCATCAACCCAAATCCCAG-CAACAACGGAT
*
7262 TTAAGGATA-TATTTTTACGAGCATCTGAATC-TAGTTTCGATTTAAA-TAGAAATTAATTAGGA
377 TTAAGGATAGT-TTTTTACGAGCATCAGAATCTTA-TTTCGA-TTAAATTAGAAATTAATTAGG-
* * * *
7324 AAAATAATTG-GAAAAATGATATTAGAATG-GTTAGAAGCCCTTCAATCT-TTTTGCGTTGAATT
438 AAAA-AATTGCAAAAAATGATATTAGAA-GCGTTAAAAGCCATTCAATATATTTTGCGTTGAATT
*
7386 ATAAATTTTTTATGAGTATTTTAGCTAAAAATT-GAGAAAAAAAATTTCGCG-TCAGTTTTTGCA
501 ATAAATTTTTTATGAGTATTTTAGCCAAAAATTAG-GAAAAAAAATTTCG-GATCAGTTTTTGCA
7449 AAAT-TTTAGTCGAAATCGTATACTAACCATTATGGTTTTTAACTAAAACCGCGTTTCCAGGCCC
564 AAATATTT-GTCGAAATCGTATACTAACCATTATGGTTTTTAACTAAAACCGCGTTTCCAGGCCC
* * *
7513 CGGCTCAGTTTTGCATAATGTTTGGCGCCGAGACTCCTTG
628 CGGCTCAGTTTTGAATAATGTTTGGCGCCAAGACTCCTTC
* **
7553 AAATATCCATATTCATCTACCCAAATATCAGCAACAATGGATTTAAGGATATGTTTTTATTAGCA
1 AAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCA
7618 TCAGAATCTTGTTT
66 TCAGAATCTTGTTT
7632 TAGCCGAAAT
Statistics
Matches: 666, Mismatches: 56, Indels: 65
0.85 0.07 0.08
Matches are distributed among these distances:
668 3 0.00
669 132 0.20
670 2 0.00
672 2 0.00
676 1 0.00
677 1 0.00
679 3 0.00
680 34 0.05
681 10 0.02
682 98 0.15
683 281 0.42
684 92 0.14
685 7 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (667 bp):
AAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATGTTTTTACGAGCA
TCAGAATCTTGTTTCGATTTAAATAAAAATTAATTAGGAAAAATAATTGGAAAAATGATATTAGA
AAGGTTAAAAGCCCTTCAATATTTTTTGCGTTAAATTATAAATTTTTATGAGTATTTTGGCCAAA
AATAGAGGAAAAATTTTCGGGTCAATTTTCTTCAAAATTTTAGCCGAAATCGTATACTAACCACT
ACGGTTTTTGGCAAAAAAACGCATTTCAGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCCCA
AAATCCTTGAAATATCCATACTCATCAACCCAAATCCCAGCAACAACGGATTTAAGGATAGTTTT
TTACGAGCATCAGAATCTTATTTCGATTAAATTAGAAATTAATTAGGAAAAAATTGCAAAAAATG
ATATTAGAAGCGTTAAAAGCCATTCAATATATTTTGCGTTGAATTATAAATTTTTTATGAGTATT
TTAGCCAAAAATTAGGAAAAAAAATTTCGGATCAGTTTTTGCAAAATATTTGTCGAAATCGTATA
CTAACCATTATGGTTTTTAACTAAAACCGCGTTTCCAGGCCCCGGCTCAGTTTTGAATAATGTTT
GGCGCCAAGACTCCTTC
Found at i:7772 original size:176 final size:177
Alignment explanation
Indices: 7452--7801 Score: 458
Period size: 176 Copynumber: 2.0 Consensus size: 177
7442 TTTTGCAAAA
* * * * * *
7452 TTTTAGTCGAAATCGTATACTAACCATTATGGTTTTTAACTAAAACCGCGTTTCCAGGCCCCGGC
1 TTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTAACGAAAAACGCATTTCCAGGCCCCGGC
*
7517 TCAGTTTTGCATAATGTTTGGCGCCGAGACTCCTTGAAATATCCATATTCATCTACCCAAATATC
66 TCAGTTTTGCATAATGTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTACCCAAATATC
**
7582 AGCAACAATGGATTTAAGGATATGTTTTTATTAGCATCAGAATCTTG
131 AGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTG
* ** *
7629 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGCATTT-CGGAGCCCCGG
1 TTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTAACGAAAAACGCATTTCCAG-GCCCCGG
* * *
7693 CTCAG-TTTGCTTGACT-TTTGGCGCCAAAGA-TCCTTGAAATATCTATATTCATCTACCCAAAT
65 CTCAGTTTTGCAT-AATGTTTGGCGCC-AAGACTCCTTGAAATATCCATATTCATCTACCCAAAT
* * *
7755 CTCATGCAA-AGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATC
128 ATCA-GCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATC
7802 AAAGTTCGAT
Statistics
Matches: 150, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
176 85 0.57
177 65 0.43
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (177 bp):
TTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTAACGAAAAACGCATTTCCAGGCCCCGGC
TCAGTTTTGCATAATGTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTACCCAAATATC
AGCAACAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTG
Found at i:12681 original size:47 final size:47
Alignment explanation
Indices: 12612--12701 Score: 180
Period size: 47 Copynumber: 1.9 Consensus size: 47
12602 TCAGTCCCCA
12612 AATGTCATAAACTAGACAGCCTCCTTCCCATAAAACCTGAGTACCCG
1 AATGTCATAAACTAGACAGCCTCCTTCCCATAAAACCTGAGTACCCG
12659 AATGTCATAAACTAGACAGCCTCCTTCCCATAAAACCTGAGTA
1 AATGTCATAAACTAGACAGCCTCCTTCCCATAAAACCTGAGTA
12702 GTACGTCTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (47 bp):
AATGTCATAAACTAGACAGCCTCCTTCCCATAAAACCTGAGTACCCG
Found at i:25648 original size:27 final size:27
Alignment explanation
Indices: 25615--25671 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
25605 ATAATAATGG
25615 TAAATGTACTGGCCAACAAAAATAAAT
1 TAAATGTACTGGCCAACAAAAATAAAT
*
25642 TAAATGTACTGGCCAACAGAAATAAAT
1 TAAATGTACTGGCCAACAAAAATAAAT
25669 TAA
1 TAA
25672 GAGTGGGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (27 bp):
TAAATGTACTGGCCAACAAAAATAAAT
Found at i:41693 original size:2 final size:2
Alignment explanation
Indices: 41686--41712 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41676 TATATCTAAA
41686 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 A
41713 AAGGCTAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44844 original size:10 final size:10
Alignment explanation
Indices: 44815--44844 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
44805 CATATACCAA
*
44815 ACCAAAATTA
1 ACCAAAATTT
44825 ACCAAAATTT
1 ACCAAAATTT
44835 ACCAAAATTT
1 ACCAAAATTT
44845 GGTTGATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (10 bp):
ACCAAAATTT
Found at i:48432 original size:36 final size:35
Alignment explanation
Indices: 48374--48460 Score: 144
Period size: 36 Copynumber: 2.5 Consensus size: 35
48364 GGTCAAAACT
48374 AAAATTCAACC---TTTTTTTTTTTTTTTTAGGAA
1 AAAATTCAACCTTGTTTTTTTTTTTTTTTTAGGAA
48406 AAAATTTCAACCTTGTTTTTTTTTTTTTTTTAGGAA
1 AAAA-TTCAACCTTGTTTTTTTTTTTTTTTTAGGAA
48442 AAAATTCAACCTTGTTTTT
1 AAAATTCAACCTTGTTTTT
48461 AAATTCTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
32 4 0.08
33 7 0.14
35 15 0.29
36 25 0.49
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (35 bp):
AAAATTCAACCTTGTTTTTTTTTTTTTTTTAGGAA
Found at i:48956 original size:2 final size:2
Alignment explanation
Indices: 48949--48979 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48939 CGCTATTCAC
48949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48980 GTGAGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51029 original size:16 final size:18
Alignment explanation
Indices: 51008--51044 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
50998 TTAAGAGGTT
*
51008 AAAA-ATACACCCGACAA
1 AAAATATACACCAGACAA
51025 AAAATATACACCAGACAA
1 AAAATATACACCAGACAA
51043 AA
1 AA
51045 GGATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.24, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAATATACACCAGACAA
Found at i:55489 original size:4 final size:4
Alignment explanation
Indices: 55480--55505 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
55470 AATACTCCAT
55480 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
55506 GTTATGCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:56590 original size:30 final size:30
Alignment explanation
Indices: 56556--56617 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
56546 CGACATGTTT
*
56556 TTCTTTAAAGTTAACTATATATTTTTAGGG
1 TTCTTTAAAATTAACTATATATTTTTAGGG
56586 TTCTTTAAAATTAACTATATATTTTTAGGG
1 TTCTTTAAAATTAACTATATATTTTTAGGG
56616 TT
1 TT
56618 TTTTTTTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (30 bp):
TTCTTTAAAATTAACTATATATTTTTAGGG
Found at i:57087 original size:16 final size:16
Alignment explanation
Indices: 57066--57099 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
57056 TCGATTATTC
57066 TCGCTCCTTGTATATA
1 TCGCTCCTTGTATATA
57082 TCGCTCCTTGTATATA
1 TCGCTCCTTGTATATA
57098 TC
1 TC
57100 TATATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.44
Consensus pattern (16 bp):
TCGCTCCTTGTATATA
Found at i:65509 original size:2 final size:2
Alignment explanation
Indices: 65502--65543 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
65492 TGGGATTGAG
65502 AT AT AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.