Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004939.1 Corchorus capsularis cultivar CVL-1 contig04957, 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: 15921
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:596 original size:33 final size:33
Alignment explanation
Indices: 549--613 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
539 CGGCGACTAG
549 CACAACAAACTTGGGAAATATCAAGGTTGAAAC
1 CACAACAAACTTGGGAAATATCAAGGTTGAAAC
* *
582 CACAACACAA-TTGGGAGATATCGAGGTTGAAA
1 CACAACA-AACTTGGGAAATATCAAGGTTGAAA
614 GTCGACAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (33 bp):
CACAACAAACTTGGGAAATATCAAGGTTGAAAC
Found at i:2215 original size:62 final size:63
Alignment explanation
Indices: 2067--2230 Score: 260
Period size: 67 Copynumber: 2.6 Consensus size: 63
2057 CAAGATCTGC
2067 TTCAAGGGTCAAATGACTTGATCTTGAACTTGATGATAATTTGAGAGTTTGATTTGATTTGATTT
1 TTCAAGGGTCAAATGACTTGATCTTGAACTTGATGATAATTTGAGA---T-ATTTGATTTGATTT
2132 GA
62 GA
2134 TTCAAGGGTCAAATGACTTGATCTTGAACTTGATGATAATTTGAGA-ATTTGATTTGATTTGA
1 TTCAAGGGTCAAATGACTTGATCTTGAACTTGATGATAATTTGAGATATTTGATTTGATTTGA
* *
2196 TTCAAGGTTCAGATGACTTGATCTTGAA-TTGATGA
1 TTCAAGGGTCAAATGACTTGATCTTGAACTTGATGA
2231 GGAAGTTTAA
Statistics
Matches: 95, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
61 7 0.07
62 42 0.44
67 46 0.48
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (63 bp):
TTCAAGGGTCAAATGACTTGATCTTGAACTTGATGATAATTTGAGATATTTGATTTGATTTGA
Found at i:2509 original size:26 final size:26
Alignment explanation
Indices: 2456--2510 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2446 TGGATCTTCT
**
2456 TTCAATAATTCCCCAATAACTGGGTC
1 TTCAATAATTCCCCAATAACTGAATC
* * *
2482 TTCAGTAATTCTCCAATAATTGAATC
1 TTCAATAATTCCCCAATAACTGAATC
2508 TTC
1 TTC
2511 CTTGAAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (26 bp):
TTCAATAATTCCCCAATAACTGAATC
Found at i:4275 original size:336 final size:331
Alignment explanation
Indices: 3766--6009 Score: 1223
Period size: 336 Copynumber: 6.7 Consensus size: 331
3756 TTCTAGTGAA
* * * *
3766 AATACTCAT-AAAAA-CTATAATTCAACACCAAAAAAATTGAAAGCCTTATTCACGCTTCTAATA
1 AATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAAGACTT-TCCACACTTCTAATA
* * * * * * * **
3829 TCATTTTTCCGATCTTATTTCCAAATTAATTTTTGATTAAATCA-AAACAAGATTTAAAAACTCG
65 TCGTTTTTCCTAT-TTTTTTCCAAATTAATCTCTAATTAAAT-AGAAACAAGATTCAAATGCTCG
* * *
3893 TAAAAACAAATCCTTAAATACAATGTGGGCGAGATTCGGTTAGATGAATATAGATATATTTCTAA
128 TAAAAACAAATCCTTAAATACAATGTGGCCGAGATTTGATTAGATGAATATAG--ATATTTC-AA
* * *
3958 GGAGTCTTGGTGCCAAAAATCATGTAAAAATGAACCAAGACCCCGGAACGCGTTTTTAGCCCATA
190 GGAGT-TTGGTGCCAAAAATCATGCAAAACTGAACCAAGGCCCCGGAACGCGTTTTTAGCCCA-A
*
4023 AAAAAACCATGATGGTATACAATTTCGGCTAAAATTTTGCAAAAAATTACTCGAAATATTTTTAT
253 AAAAAACTATGATGGTATACAATTTCGGCTAAAATTTTGCAAAAAATTACTCGAAATATTTTTAT
4088 CAATTTTTAGCCAC
318 CAATTTTTAGCCAC
* * * *
4102 AATACTCATAAAAAATATATAATTCAACACCAAAAATATTGAAATACTTCCCACACTACTAATAT
1 AATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAAGACTTTCCACACTTCTAATAT
* * *
4167 CGTTTTTCCTATTTTTTTCCAAATTAATCTCTAATTAAATTGAAACATGATTCAAATGCTCATAA
66 CGTTTTTCCTATTTTTTTCCAAATTAATCTCTAATTAAATAGAAACAAGATTCAAATGCTCGTAA
* * * * *
4232 AAACAAATACTTAAATCCAGTGTGGCCAAGATTTGTTTAGATGAATATAGATATTTCAAGGAGTT
131 AAACAAATCCTTAAATACAATGTGGCCGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTT
* * * * * ** *
4297 T-TTCCACAAAAAATAATGCAATACTG-ACCTGAGGTTCCGGAACGCGTTTTTAG-CC--AAAAG
196 TGGTGC-C-AAAAATCATGCAAAACTGAACC-AAGGCCCCGGAACGCGTTTTTAGCCCAAAAAAA
* *** * * **
4357 ACTGTGATGGTACGTAATTTCGGCTAAAATTTTGC-AAAAATTGACCCAAAATATTTTCCCTCAA
258 ACTATGATGGTATACAATTTCGGCTAAAATTTTGCAAAAAATT-ACTCGAAATATTTT-TATCAA
4421 TTTTTAGCCAC
321 TTTTTAGCCAC
* ** * * * *
4432 AATACTCATAAAATATATATAATTCAAC-GTAAAAAGATTGGAGGACTTTCCACGA-TTTTAATA
1 AATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAAGACTTTCCAC-ACTTCTAATA
* * *
4495 TCGTTTTTCATA-TTTTTT--AGAATTAA-CTTCTAGTTAAATAGAAACAAGATTCAGATGCTCG
65 TCGTTTTTCCTATTTTTTTCCA-AATTAATC-TCTAATTAAATAGAAACAAGATTCAAATGCTCG
* * * * *
4556 TAAAAATAAATCCTTAAATTCAATTTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGA
128 TAAAAACAAATCCTTAAATACAATGTGGCCGAGATTTGATTAGATGAATATAGATATTTCAAGGA
* * * * *** *
4621 GTTTAGGCGCCAAAAATCAAGCAAAACT-AAACAGGGGCCCTAAAACGCGTTTTTAGCCAAAAAA
193 GTTT-GGTGCCAAAAATCATGCAAAACTGAACCA-AGGCCCCGGAACGCGTTTTTAGCC-CAAAA
* *
4685 AAAACTATGATGGTTAATACAAGATTTCGGCTAAAATTTTGCAAAAAATGACTCGAAAAATTTTT
255 AAAACTATGATGG-T-ATAC-A-ATTTCGGCTAAAATTTTGCAAAAAATTACTCGAAATATTTTT
* * ** *
4750 CCGTCAATTTTTGGTTAA
316 --ATCAATTTTTAGCCAC
* * * * * * *
4768 AATAATCATAATATATATATATATATATAATTTAACGCC-AAAAGATTGGAGGAGTATT-CACAC
1 AAT-A-C-TCATA-A-A-A-A-ATATATAATTCAACACCAAAAAAATTGAAAGACT-TTCCACAC
* * * * * * *
4831 TTTTAATATCGTTTTT-C-ATATTTTTCTAAATTTATTTCT-A--AAATTGAATCAAGATTCAGA
57 TTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATCTCTAATTAAATAGAAACAAGATTCA-A
* * * * * * * * *
4891 A-ACTCGTAAAAACAAATTCTTAGATTCAATATATATAGCTGAGTTTTGATTAGATGAATATGGA
121 ATGCTCGTAAAAACAAATCCTTA-AAT--ACA-ATGTGGCCGAGATTTGATTAGATGAATATAGA
* * * * * * ** *
4955 TATCTGAAAGAGTGTTGGCGCCAAAAATCATGCAAAACTTAGCCGGGGCCTCGGAACGCGTTTTT
182 TATTTCAAGGAGT-TTGGTGCCAAAAATCATGCAAAACTGAACCAAGGCCCCGGAACGCGTTTTT
* * * * *
5020 AG-CC---AAAAACTGTGATGATTATTACACGATTTTTCGGGTAGAATTTTG-TAAAAATTGACT
246 AGCCCAAAAAAAACTATGATG-GTA-TACA--A--TTTCGGCTAAAATTTTGCAAAAAATT-ACT
* *
5080 CGAAAT-TTATTTCCTCAATTTTTAGACAC
304 CGAAATATT-TTT-ATCAATTTTTAGCCAC
* * * **
5109 AATACTCATTAAAATTATATAATTCAACACCAAAAAAGATTGAAAGACTTTTCATGCTTCTAATA
1 AATACTCATAAAAAATATATAATTCAACACCAAAAAA-ATTGAAAGACTTTCCACACTTCTAATA
* * * *
5174 TCGTTTTTCCTACTATTTTTT--GAATTAAAT-TCTAATTAAATCGAAACAAGATTCAGATGCTT
65 TCGTTTTTCCTA-T-TTTTTTCCAAATT-AATCTCTAATTAAATAGAAACAAGATTCAAATGCTC
*** * * * *
5236 GT-TTTACAAATCCTTAATTCCAATGTGGCTGAGATTTTG-TTACATGAATATAGATATCTT-AA
127 GTAAAAACAAATCCTTAAATACAATGTGGCCGAGA-TTTGATTAGATGAATATAGATAT-TTCAA
* ** * * * * ** *
5298 AGAGTCTTGACG-CAAAAATTCATGCAACACTGAACCGAGGCCCTGGTACGTATTTTTAG-TCAA
190 GGAGT-TTGGTGCCAAAAA-TCATGCAAAACTGAACCAAGGCCCCGGAACGCGTTTTTAGCCCAA
* * * * * * * **
5361 AAACCGTGATTTCAACTA--A-CGTACACGATTTCGGCTAATATTTTGCAACAACTGAGC-AAAA
253 AAA-----A----AACTATGATGGTATACAATTTCGGCTAAAATTTTGCAAAAAATTA-CTCGAA
* *
5422 ATATTTTTCCTCAATTTTT-GTCTAC
308 ATATTTTT-ATCAATTTTTAG-CCAC
* * * * * * * * * *
5447 -ATACTCATAACATATATATATTTCAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATAT
1 AATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAAGACTTTCCACACTTCTAATAT
* * * *
5511 CGTTTTGTGC-A--TTTTTCTAAATTAATTTCTAATTAAATCG-AACAAGATTCAAATGCTCGTA
66 CGTTTT-TCCTATTTTTTTCCAAATTAATCTCTAATTAAATAGAAACAAGATTCAAATGCTCGTA
** * **
5572 AAAACAAATCCTTAAATGA-AATGTGGTTGAGATTTGATTAGATGATTATAGATACATCAAGGAG
130 AAAACAAATCCTTAAAT-ACAATGTGGCCGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* * * * * * * *
5636 TCTTGATGTCAAAAATCATGCAAATCTGAGCC-AGTGCCCCGAAATGTGTTTTTTTGCGAAAAAA
194 T-TTGGTGCCAAAAATCATGCAAAACTGAACCAAG-GCCCCGGAACGCG-TTTTTAGC-------
** * * *
5700 AAAAAAAAAAAAAACTGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC-CA
249 ----CCAAAAAAAACTATGATGG-TA-TACA--ATTTCGGCTAAAATTTTGCAAAAAATTACTC-
* * * * * ** *
5764 GAAAAAAATCTTCTCAATTTTTGGTTAA
305 G-AAATATTTTTATCAATTTTTAGCCAC
* * * * * ** * * ** * *
5792 AATACTCATAATATATATATAGTTTAACGCCAAAACGATT-AGAGGACCTTATACACTTTTCATA
1 AATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGA-AAGACTTTCCACACTTCTAATA
* * * * * * *
5856 TTGTTTTTCATATTTTTTT--GAATTAATTTCTAATTAAATCGAAACAAGATTCAGACGCTCGTA
65 TCGTTTTTCCTATTTTTTTCCAAATTAATCTCTAATTAAATAGAAACAAGATTCAAATGCTCGTA
* * *** ** * *
5919 AAAATATCATTAATAAATGA-AATGTGGTTGAGATTTGATTAGATGAATATGGATATCTCAAGGA
130 AAAACA-AATCCTTAAAT-ACAATGTGGCCGAGATTTGATTAGATGAATATAGATATTTCAAGGA
* *
5983 ATCTTAGTGCCAAAAATCATGCAAAAC
193 GT-TTGGTGCCAAAAATCATGCAAAAC
6010 AGGCCTAGGG
Statistics
Matches: 1489, Mismatches: 293, Indels: 240
0.74 0.14 0.12
Matches are distributed among these distances:
326 2 0.00
327 126 0.08
328 15 0.01
329 82 0.06
330 43 0.03
331 15 0.01
332 14 0.01
333 83 0.06
334 112 0.08
335 138 0.09
336 153 0.10
337 69 0.05
338 81 0.05
339 30 0.02
340 42 0.03
341 59 0.04
342 36 0.02
343 11 0.01
344 58 0.04
345 120 0.08
346 91 0.06
347 33 0.02
348 76 0.05
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (331 bp):
AATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAAGACTTTCCACACTTCTAATAT
CGTTTTTCCTATTTTTTTCCAAATTAATCTCTAATTAAATAGAAACAAGATTCAAATGCTCGTAA
AAACAAATCCTTAAATACAATGTGGCCGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTT
TGGTGCCAAAAATCATGCAAAACTGAACCAAGGCCCCGGAACGCGTTTTTAGCCCAAAAAAAACT
ATGATGGTATACAATTTCGGCTAAAATTTTGCAAAAAATTACTCGAAATATTTTTATCAATTTTT
AGCCAC
Found at i:5323 original size:335 final size:331
Alignment explanation
Indices: 3637--6057 Score: 1585
Period size: 335 Copynumber: 7.2 Consensus size: 331
3627 AATATAGATA
* * * * *** **
3637 AAAAATCAAGCAAAACTGAGCCG-GGCCCCGGAACGCGTTTTCAGTTGAAAACCATGATGATTAG
1 AAAAATCATGCAAAACTGAACCGAGGCCCTGGAACGCGTTTTTAGCCAAAAACTGTGATGATTAG
* * * * ** * **
3701 TATACGATTTCGTCTAAAATTTTGCAAAACTTGAC-CTGAAAGATTTTTCCTTGATTTCTAGTGA
66 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACTC-GAAATATTTTTCCTCAATTTTTAGCCA
* * * * * * *
3765 AAATACTCA-TAAAA-A-CTATAATTCAACACCAAAAAAATTGAAAGCCTTATTCACGCTTCTAA
130 CAATACTCATTAAAATATATATAATTCAACACCAAAAAGATTGGAGGACTT-TTCACGCTTTTAA
* * * * * * * * * **
3827 TATCATTTTTCCGATCTTATTTCCAAATTAATTTTTGATTAAATCAAAACAAGATTTAAAAACTC
194 TATCGTTTTT-C-ATATT-TTT-TAAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * *
3892 GTAAAAACAAATCCTTAAATACAATGTGGGC-GAGATTCGGTTAGATGAATATAGATATATTTCT
255 GTAAAAACAAATCCTTAATTCCAATGT-GGCTGAGATTTGATTAGATGAATATAG--ATATCT-T
* **
3956 AAGGAGTCTTGGTGCC
316 AAAGAGTCTTGACGCC
* * * * * *****
3972 AAAAATCATGTAAAAATGAACCAAGACCCCGGAACGCGTTTTTAGCCCATAAAAAAACCATGA-T
1 AAAAATCATGCAAAACTGAACCGAGGCCCTGGAACGCGTTTTTAG-CCA-AAAACTGTGATGATT
* * * *
4036 GGTATACAATTTCGGCTAAAATTTTGCAAAAAATT-ACTCGAAATATTTTT-ATCAATTTTTAGC
64 AGTACACGATTTCGGCTAAAATTTTGC-AAAAATTGACTCGAAATATTTTTCCTCAATTTTTAGC
* * * ** ** * **
4099 CACAATACTCA-TAAAAAATATATAATTCAACACCAAAAATATTGAAATACTTCCCACACTACTA
128 CACAATACTCATTAAAATATATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTA
* * * *
4163 ATATCGTTTTTCCTATTTTTTTCCAAATT-AATCTCTAATTAAATTGAAACATGATTCAAATGCT
193 ATATCGTTTTTCATA-TTTTTT--AAATTAAAT-TCTAATTAAATCGAAACAAGATTCAGATGCT
* * * * ** *
4227 CATAAAAACAAATACTTAAATCCAGTGTGGCCAAGATTTGTTTAGATGAATATAGATAT-TTCAA
254 CGTAAAAACAAATCCTTAATTCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATCTT-AA
* * ** * *
4291 GGAGTTTTTCCACA
318 AGAGTCTTGACGCC
* * * *
4305 AAAAATAATGCAATACTG-ACCTGAGGTTCC-GGAACGCGTTTTTAGCCAAAAGACTGTGATG-G
1 AAAAATCATGCAAAACTGAACC-GAGG-CCCTGGAACGCGTTTTTAGCCAAAA-ACTGTGATGAT
* * *
4367 TACGT--A--ATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTCCCTCAATTTTTAG
63 TA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATTTTTCCTCAATTTTTAG
** * *
4428 CCACAATACTCA-TAAAATATATATAATTCAAC-GTAAAAAGATTGGAGGACTTTCCACGATTTT
127 CCACAATACTCATTAAAATATATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTT
* * *
4491 AATATCGTTTTTCATATTTTTTAGAATTAACTTCTAGTTAAATAGAAACAAGATTCAGATGCTCG
192 AATATCGTTTTTCATATTTTTTA-AATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* *
4556 TAAAAATAAATCCTTAAATT-CAATTTGGCTGAGATTTGATTAGATGAATATAGATAT-TTCAAA
256 TAAAAACAAATCCTT-AATTCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATCTT-AAA
*
4619 GAGT-TTAGGCGCC
319 GAGTCTT-GACGCC
* * * * ** *
4632 AAAAATCAAGCAAAACTAAACAGGGGCCCTAAAACGCGTTTTTAGCCAAAAAAAAAACTATGATG
1 AAAAATCATGCAAAACTGAACCGAGGCCCTGGAACGCGTTTTTAGCC-----AAAAACTGTGATG
* * * * *
4697 GTTAATACAAGATTTCGGCTAAAATTTTGCAAAAAATGACTCGAAAAATTTTTCCGTCAATTTTT
61 ATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATTTTTCC-TCAATTTTT
* ** * * * * * *
4762 GGTTAAAATAATCATAATATATATATATATATATAATTTAACGCC-AAAAGATTGGAGGAGTATT
125 AGCCACAAT-A-C-TCAT-TA-A-A-ATATATATAATTCAACACCAAAAAGATTGGAGGACTTTT
* * * * *
4826 CACACTTTTAATATCGTTTTTCATATTTTTCTAAATTTATTTCT-A--AAATTGAATCAAGATTC
183 CACGCTTTTAATATCGTTTTTCATATTTTT-TAAATTAAATTCTAATTAAATCGAAACAAGATTC
** * * * * * *
4888 AGAAACTCGTAAAAACAAATTCTTAGATTCAATATATATAGCTGAGTTTTGATTAGATGAATATG
247 AGATGCTCGTAAAAACAAATCCTTA-ATTC--CA-ATGTGGCTGAGATTTGATTAGATGAATATA
* * *
4953 GATATCTGAAAGAGTGTTGGCGCC
308 GATATCTTAAAGAGTCTTGACGCC
* * *
4977 AAAAATCATGCAAAACTTAGCCG-GGGCCTCGGAACGCGTTTTTAGCCAAAAACTGTGATGATTA
1 AAAAATCATGCAAAACTGAACCGAGGCCCT-GGAACGCGTTTTTAGCCAAAAACTGTGATGATTA
* * * *
5041 TTACACGATTTTTCGGGTAGAATTTTGTAAAAATTGACTCGAAAT-TTATTTCCTCAATTTTTAG
65 GTACACGA--TTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATT-TTTCCTCAATTTTTAG
* * * * *
5105 ACACAATACTCATTAAAAT-TATATAATTCAACACCAAAAAAGATTGAAAGACTTTTCATGCTTC
127 CCACAATACTCATTAAAATATATATAATTCAACACC-AAAAAGATTGGAGGACTTTTCACGCTTT
*
5169 TAATATCGTTTTTCCTACTATTTTTTGAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGC
191 TAATATCGTTTTT-C-A-TATTTTTTAAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGC
* *** *
5234 TTGT-TTTACAAATCCTTAATTCCAATGTGGCTGAGATTTTG-TTACATGAATATAGATATCTTA
253 TCGTAAAAACAAATCCTTAATTCCAATGTGGCTGAGA-TTTGATTAGATGAATATAGATATCTTA
5297 AAGAGTCTTGACG-C
317 AAGAGTCTTGACGCC
* * ** * * *
5311 AAAAATTCATGCAACACTGAACCGAGGCCCTGGTACGTATTTTTAGTCAAAAACCGTGATTTCAA
1 AAAAA-TCATGCAAAACTGAACCGAGGCCCTGGAACGCGTTTTTAGCCAAAAACTGTGA--T-GA
* * * * **
5376 CTAACGTACACGATTTCGGCTAATATTTTGCAACAACTGAGC-AAAAATATTTTTCCTCAATTTT
62 -TTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CTCGAAATATTTTTCCTCAATTTT
* * * *
5440 T-GTCTAC-ATACTCA-TAACATATATATATTTCAACTCCAAAAAGATTGGAGGACTTTTCACGC
124 TAG-CCACAATACTCATTAAAATATATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGC
* * *
5502 TTTTAATATCGTTTTGTGCAT-TTTTCTAAATTAATTTCTAATTAAATCG-AACAAGATTCAAAT
188 TTTTAATATCGTTTT-T-CATATTTTTTAAATTAAATTCTAATTAAATCGAAACAAGATTCAGAT
* ** * *
5565 GCTCGTAAAAACAAATCCTTAAATGAAATGTGGTTGAGATTTGATTAGATGATTATAGATA-CAT
251 GCTCGTAAAAACAAATCCTTAATTCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATC-T
* * * *
5629 CAAGGAGTCTTGATGTC
315 TAAAGAGTCTTGACGCC
* * * * * * * *
5646 AAAAATCATGCAAATCTGAGCC-AGTGCCCCGAAATGTGTTTTTTTGCGAAAAAAAAAAAAAAAA
1 AAAAATCATGCAAAACTGAACCGAG-GCCCTGGAACGCG-TTTTTAGC---------------CA
* * * * * *
5710 AAAACTGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAAATGAC-CAGAAAAAAATC
49 AAAACTGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTC-G-AAATATTT
* ** * * * * * * *
5774 TT-CTCAATTTTTGGTTAAAATACTCA-TAATATATATATAGTTTAACGCCAAAACGATTAGAGG
112 TTCCTCAATTTTTAGCCACAATACTCATTAAAATATATATAATTCAACACCAAAAAGATTGGAGG
* * * * * *
5837 ACCTTAT-ACACTTTTCATATTGTTTTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAAC
177 A-CTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTAAATTAAATTCTAATTAAATCGAAAC
* * * ** *
5901 AAGATTCAGACGCTCGT-AAAA-ATATCATTAATAAATGAAATGTGGTTGAGATTTGATTAGATG
240 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAT---TCCAATGTGGCTGAGATTTGATTAGATG
* * * * *
5964 AATATGGATATCTCAAGGAATCTT-AGTGCC
302 AATATAGATATCTTAAAGAGTCTTGA-CGCC
* * * * * *
5994 AAAAATCATGCAAAACAG-GCCTAGGGCCATGGAACTCGTTTTTAGCCAAAAACCGTGATGATTA
1 AAAAATCATGCAAAACTGAACCGA-GGCCCTGGAACGCGTTTTTAGCCAAAAACTGTGATGATTA
6058 TTGAAGGGTT
Statistics
Matches: 1660, Mismatches: 311, Indels: 233
0.75 0.14 0.11
Matches are distributed among these distances:
326 5 0.00
327 120 0.07
328 20 0.01
329 66 0.04
330 42 0.03
331 13 0.01
332 33 0.02
333 84 0.05
334 114 0.07
335 190 0.11
336 184 0.11
337 95 0.06
338 103 0.06
339 18 0.01
340 52 0.03
341 56 0.03
342 36 0.02
343 1 0.00
344 78 0.05
345 132 0.08
346 98 0.06
347 33 0.02
348 75 0.05
349 2 0.00
350 10 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (331 bp):
AAAAATCATGCAAAACTGAACCGAGGCCCTGGAACGCGTTTTTAGCCAAAAACTGTGATGATTAG
TACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATTTTTCCTCAATTTTTAGCCAC
AATACTCATTAAAATATATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATA
TCGTTTTTCATATTTTTTAAATTAAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
ACAAATCCTTAATTCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATCTTAAAGAGTCTT
GACGCC
Found at i:7978 original size:225 final size:224
Alignment explanation
Indices: 7578--8016 Score: 594
Period size: 225 Copynumber: 2.0 Consensus size: 224
7568 GCTAAAATAA
* * * * * *
7578 TCATAAAATTATATAATTTAACACCAAAAAGGTTGAAAGGATTATGACATTTCTAGTATCTTTTT
1 TCATAAAAATATATAATTCAACACCAAAAAGATTGAAAGGATTATGACATTTCGAATATCGTTTT
* * *
7643 TCCTATTTTTTGAAAATAATTTCTAATTGAACCGAAACAAAATTCAAATACTCGTAAAAATCAAA
66 TCCTATTTTTTCAAAATAATTTCTAATTAAACCGAAACAAAAATCAAATACTCGTAAAAATCAAA
* ***
7708 TCCTTAAAAACCAATGTGGCTGAGATTTAATTAGATGAATATAGATATCTCAAGGAGTCTTGGTG
131 ACCTTAAAAACCAATGTGGCTGAGATTTAATTAGATGAATATAGATATCTCAAGGAGTCTTGACA
*
7773 TTAAAAATCATGCAAAACTAAGCCGGTAC
196 CTAAAAATCATGCAAAACTAAGCCGGTAC
* * * * *
7802 TCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCGAATATCGTTT
1 TCAT-AAAAATATATAATTCAACACCAAAAAGATTGAAAGGATTATGACATTTCGAATATCGTTT
* * ** * *
7867 TTCCTCTTTTTTTCCAAATTAATTTCTAATTAAATTGAAACAAAAATCAAATGCTCGTTAAAA-C
65 TTCCT-ATTTTTT-CAAAATAATTTCTAATTAAACCGAAACAAAAATCAAATACTCGTAAAAATC
* *
7931 AAAACCTT-AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTG
128 AAAACCTTAAAAACCAATGTGGCTGAGATTTAATTAGATGAATATAGATATCTCAAGGAGTCTTG
7995 ACACTAAAAATCATGCAAAACT
193 ACACTAAAAATCATGCAAAACT
8017 GAGTGGGCCC
Statistics
Matches: 185, Mismatches: 27, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
224 4 0.02
225 126 0.68
226 14 0.08
227 41 0.22
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (224 bp):
TCATAAAAATATATAATTCAACACCAAAAAGATTGAAAGGATTATGACATTTCGAATATCGTTTT
TCCTATTTTTTCAAAATAATTTCTAATTAAACCGAAACAAAAATCAAATACTCGTAAAAATCAAA
ACCTTAAAAACCAATGTGGCTGAGATTTAATTAGATGAATATAGATATCTCAAGGAGTCTTGACA
CTAAAAATCATGCAAAACTAAGCCGGTAC
Found at i:9215 original size:20 final size:19
Alignment explanation
Indices: 9190--9229 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
9180 GCTCTGTTCA
* *
9190 TCTTTTTTTTTTTCTTTCTT
1 TCTTTTTCTTGTTC-TTCTT
9210 TCTTTTTCTTGTTCTTCTT
1 TCTTTTTCTTGTTCTTCTT
9229 T
1 T
9230 AAAGGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (19 bp):
TCTTTTTCTTGTTCTTCTT
Found at i:10703 original size:27 final size:25
Alignment explanation
Indices: 10656--10751 Score: 68
Period size: 27 Copynumber: 3.5 Consensus size: 25
10646 AACAATTAGC
*
10656 ACAGCAGCAATCCCAATTCCAAGCACA
1 ACAGCAGCAA--CAAATTCCAAGCACA
10683 ACAGCAGCAACAAATACTCCAA-CAACTA
1 ACAGCAGCAACAAAT--TCCAAGC-AC-A
* *
10711 GCACAGAAGCAATCCCAATTCCAAGCACA
1 --ACAGCAGCAA--CAAATTCCAAGCACA
10740 ACAGCAGCAACA
1 ACAGCAGCAACA
10752 GCAAGAGCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
25 5 0.09
26 1 0.02
27 26 0.47
28 1 0.02
29 1 0.02
30 16 0.29
31 1 0.02
32 4 0.07
ACGTcount: A:0.45, C:0.34, G:0.11, T:0.09
Consensus pattern (25 bp):
ACAGCAGCAACAAATTCCAAGCACA
Found at i:10715 original size:33 final size:31
Alignment explanation
Indices: 10677--10787 Score: 77
Period size: 33 Copynumber: 3.4 Consensus size: 31
10667 CCCAATTCCA
10677 AGCACAACAGCAGCAACAAATACTCCAACAACT
1 AGCACAACAGCAG-AACAAATA-TCCAACAACT
* *
10710 AGCACAGA-AGCA-ATCCCAAT-TCCAAGCACAAC-
1 AGCACA-ACAGCAGA-ACAAATATCC-A--ACAACT
*
10742 AGCAGCAACAGCAAGAGCAAATATTCCAACAACT
1 AGCA-CAACAGC-AGAACAAATA-TCCAACAACT
10776 AGCACAACAGCA
1 AGCACAACAGCA
10788 ACAACAATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 25
0.68 0.04 0.27
Matches are distributed among these distances:
30 3 0.05
31 2 0.03
32 10 0.16
33 32 0.52
34 10 0.16
35 2 0.03
36 3 0.05
ACGTcount: A:0.47, C:0.32, G:0.13, T:0.09
Consensus pattern (31 bp):
AGCACAACAGCAGAACAAATATCCAACAACT
Found at i:10734 original size:30 final size:30
Alignment explanation
Indices: 10645--10734 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
10635 ACTCCAACAA
*
10645 CAACAATTAGCACAGCAGCAATCCCAATTC
1 CAACAACTAGCACAGCAGCAATCCCAATTC
*
10675 CAAGC-AC-A--ACAGCAGCAA--CAAATACTC
1 CAA-CAACTAGCACAGCAGCAATCCCAAT--TC
*
10702 CAACAACTAGCACAGAAGCAATCCCAATTC
1 CAACAACTAGCACAGCAGCAATCCCAATTC
10732 CAA
1 CAA
10735 GCACAACAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
25 4 0.09
26 1 0.02
27 17 0.36
28 1 0.02
29 1 0.02
30 18 0.38
31 1 0.02
32 4 0.09
ACGTcount: A:0.44, C:0.33, G:0.10, T:0.12
Consensus pattern (30 bp):
CAACAACTAGCACAGCAGCAATCCCAATTC
Found at i:11309 original size:2 final size:2
Alignment explanation
Indices: 11302--11330 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11292 AATTAAAGGG
11302 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 T
11331 TCTTTACCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11798 original size:27 final size:27
Alignment explanation
Indices: 11763--11855 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
11753 GGTATAACTT
11763 AATTCGGTATTTGTATGTATATTGTGG
1 AATTCGGTATTTGTATGTATATTGTGG
* * * * * **
11790 AATTTGGTATTTGCATTTGTATTATTT
1 AATTCGGTATTTGTATGTATATTGTGG
*
11817 AATTCGGTATCTGTATGTATATTGTGG
1 AATTCGGTATTTGTATGTATATTGTGG
*
11844 AATTTGGTATTT
1 AATTCGGTATTT
11856 ACATTTGTAT
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.23, C:0.04, G:0.22, T:0.52
Consensus pattern (27 bp):
AATTCGGTATTTGTATGTATATTGTGG
Found at i:11843 original size:54 final size:54
Alignment explanation
Indices: 11761--11865 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
11751 AGGGTATAAC
* *
11761 TTAATTCGGTATTTGTATGTATATTGTGGAATTTGGTATTTGCATTTGTATTAT
1 TTAATTCGGTATCTGTATGTATATTGTGGAATTTGGTATTTACATTTGTATTAT
11815 TTAATTCGGTATCTGTATGTATATTGTGGAATTTGGTATTTACATTTGTAT
1 TTAATTCGGTATCTGTATGTATATTGTGGAATTTGGTATTTACATTTGTAT
11866 AATACGGGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (54 bp):
TTAATTCGGTATCTGTATGTATATTGTGGAATTTGGTATTTACATTTGTATTAT
Found at i:13654 original size:2 final size:2
Alignment explanation
Indices: 13647--13686 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
13637 CACGTACTTT
* *
13647 TA TA TA TA GTA TA GA TA TA GA 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 TA TA TA TA T
13687 TTTATCATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Done.