Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016261.1 Corchorus olitorius cultivar O-4 contig16294, 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: 34339
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:402 original size:36 final size:36
Alignment explanation
Indices: 330--405 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
320 TGAGAAGAGG
* ** *
330 CCAAGTACATAATTAAGTTGGCTTAATTCTATTGGC
1 CCAAATACATAATTAAGTTGGCCCAATTCTACTGGC
366 CCAAATACATAATTAAGTTGGCCCAACTT-TACTGGC
1 CCAAATACATAATTAAGTTGGCCCAA-TTCTACTGGC
402 CCAA
1 CCAA
406 TACTACCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (36 bp):
CCAAATACATAATTAAGTTGGCCCAATTCTACTGGC
Found at i:593 original size:13 final size:13
Alignment explanation
Indices: 530--715 Score: 92
Period size: 13 Copynumber: 14.8 Consensus size: 13
520 GTGAAACAAG
*
530 TCTTCATCAAAAT
1 TCTTCATCAAAGT
*
543 TATTCATCAAAGT
1 TCTTCATCAAAGT
* *
556 TCTTTAAC-AAG-
1 TCTTCATCAAAGT
*
567 TCTCCA-CGAAAGT
1 TCTTCATC-AAAGT
*
580 TATTCATCAAAGT
1 TCTTCATCAAAGT
*
593 TCTTCAAC-AAG-
1 TCTTCATCAAAGT
* *
604 TCTCCACCAAAGT
1 TCTTCATCAAAGT
*
617 TATTCATCAAAGT
1 TCTTCATCAAAGT
*
630 TCTTCAAC-AAG-
1 TCTTCATCAAAGT
641 TCTTCATC-AAGT
1 TCTTCATCAAAGT
* *
653 TGTTCTTCAACAAG-
1 TCTTCATC-A-AAGT
667 TCTTCATC-AAGT
1 TCTTCATCAAAGT
* *
679 TGTTCTTCAACAAGT
1 TCTTCATC-A-AAGT
694 T-TTCACTC--AGT
1 TCTTCA-TCAAAGT
705 TCTTCATCAAA
1 TCTTCATCAAA
716 TTTTCCACCA
Statistics
Matches: 129, Mismatches: 26, Indels: 36
0.68 0.14 0.19
Matches are distributed among these distances:
10 1 0.01
11 29 0.22
12 31 0.24
13 48 0.37
14 10 0.08
15 10 0.08
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (13 bp):
TCTTCATCAAAGT
Found at i:661 original size:15 final size:15
Alignment explanation
Indices: 641--694 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
631 CTTCAACAAG
*
641 TCTTCATCAAGTTGT
1 TCTTCAACAAGTTGT
656 TCTTCAACAA---G-
1 TCTTCAACAAGTTGT
*
667 TCTTCATCAAGTTGT
1 TCTTCAACAAGTTGT
682 TCTTCAACAAGTT
1 TCTTCAACAAGTT
695 TTCACTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.28
12 1 0.03
14 1 0.03
15 21 0.66
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (15 bp):
TCTTCAACAAGTTGT
Found at i:672 original size:37 final size:37
Alignment explanation
Indices: 524--643 Score: 195
Period size: 37 Copynumber: 3.2 Consensus size: 37
514 CCAAGAGTGA
* * * *
524 AACAAGTCTTCATCAAAATTATTCATCAAAGTTCTTT
1 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
*
561 AACAAGTCTCCACGAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
598 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
635 AACAAGTCT
1 AACAAGTCT
644 TCATCAAGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 77 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (37 bp):
AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
Found at i:710 original size:23 final size:24
Alignment explanation
Indices: 619--710 Score: 107
Period size: 26 Copynumber: 3.7 Consensus size: 24
609 ACCAAAGTTA
*
619 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAATGTTCTTCAACAAGTC
643 TTCATCAAGTTGTTCTTCAACAAGTC
1 TTCATCAA--TGTTCTTCAACAAGTC
*
669 TTCATCAAGTTGTTCTTCAACAAGTT
1 TTCATCAA--TGTTCTTCAACAAGTC
695 TTCACTC-A-GTTCTTCA
1 TTCA-TCAATGTTCTTCA
711 TCAAATTTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
23 8 0.13
24 8 0.13
26 45 0.71
27 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (24 bp):
TTCATCAATGTTCTTCAACAAGTC
Found at i:714 original size:26 final size:26
Alignment explanation
Indices: 628--698 Score: 133
Period size: 26 Copynumber: 2.7 Consensus size: 26
618 ATTCATCAAA
628 GTTCTTCAACAAGTCTTCATCAAGTT
1 GTTCTTCAACAAGTCTTCATCAAGTT
654 GTTCTTCAACAAGTCTTCATCAAGTT
1 GTTCTTCAACAAGTCTTCATCAAGTT
*
680 GTTCTTCAACAAGTTTTCA
1 GTTCTTCAACAAGTCTTCA
699 CTCAGTTCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (26 bp):
GTTCTTCAACAAGTCTTCATCAAGTT
Found at i:2858 original size:318 final size:313
Alignment explanation
Indices: 2504--3135 Score: 749
Period size: 318 Copynumber: 2.0 Consensus size: 313
2494 AGATCCTCGT
* * *
2504 AAAAACAAATCCTTATATCCAATGTGGTTGAGATTTGGTTCCATGAATGA-AGATATTTCAAGGA
1 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATG-ATGATAGATATTTCAAGGA
* * * * * *
2568 GTCTTTGCACCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAAAC
65 GTCTTTACACCAAAAACCATGCAAAACTGAGCCGAGACCCCGGAACGCG-TTTTAGCCAAAAAAC
* * *
2633 TATGATGGTTAGTACACGATATT-GGCTAAAATTTTGAAAAAACTGACCCGAAATTTTTTTTTCT
129 CATGATGG-CA--A-ACGAT-TTCGGCTAAAATTTTGAAAAAACTGACCCGAAA--TATTTTTC-
* * * *
2697 TC-AATTCTCTGCCATAA-TACTCAGAAAAAATATATAATTCAACGCC-AAAAAGTTGAAGGATT
186 TCAAATT-TCAGCCACAATTA-TCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGACT
* * * * *
2759 TTTCACGCTTCT-ATATTGTTTTTCC-A-TTTTTTTTCCGAATTTAATTTCTTATTAAATCGAAA
249 TCTCACGCATCTAATATCGTTTTTCCTACTTTTTTTTCC-AAATTAATTTCTAATTAAATCGAAA
2821 C
313 C
* * *
2822 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGATTATAGGTATTTCAAGGAG
1 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGATGATAGATATTTCAAGGAG
** * * * * *
2887 TCTTTATGCCAGAAACCATGCAAAACTGCGTCGAGACCCCTGAACGCGTTTTAGCCAAAAAACCG
66 TCTTTACACCAAAAACCATGCAAAACTGAGCCGAGACCCCGGAACGCGTTTTAGCCAAAAAACCA
* * * * *
2952 TGATGGCAAACGATTTCGGCTGAAGTTTTGCAAAAATTGACCCGAGATATTTTTCTCAAATTTCA
131 TGATGGCAAACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGAAATATTTTTCTCAAATTTCA
* *
3017 GCCACAATTATCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCTTCTCACGCATCT
196 GCCACAATTATCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGACTTCTCACGCATCT
3082 AATATCGTTTTTCCTACTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAAC
261 AATATCGTTTTTCCTACTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAAC
3135 A
1 A
3136 TGATTCAAAT
Statistics
Matches: 268, Mismatches: 38, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
310 35 0.13
311 36 0.13
312 14 0.05
313 56 0.21
314 11 0.04
316 1 0.00
317 24 0.09
318 91 0.34
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (313 bp):
AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGATGATAGATATTTCAAGGAG
TCTTTACACCAAAAACCATGCAAAACTGAGCCGAGACCCCGGAACGCGTTTTAGCCAAAAAACCA
TGATGGCAAACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGAAATATTTTTCTCAAATTTCA
GCCACAATTATCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGACTTCTCACGCATCT
AATATCGTTTTTCCTACTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAAC
Found at i:3885 original size:328 final size:326
Alignment explanation
Indices: 1770--4204 Score: 1667
Period size: 329 Copynumber: 7.5 Consensus size: 326
1760 AATTCAACAC
* * *
1770 CTTTTCACG-TTTCTAATATCGGTTTTC-CA-TTTTTCCGAATTAATTTCTAATTAAATCGAAAC
1 CTTTTCACGCTTT-TAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAAC
* * * *
1832 AAGATTCAGATGCATGCTCGTAAAAACAAA-TCGTTAAATCAAATGTGGCTGGGATTTGGGTTCG
65 AAGATTC--A-G-ATGCTCGTAAAAACAAATTC-TTAAATCCAATGTGGCTGAGATTT-GATTAG
* * * * * * *
1896 ATGAATATTGATATTTCAAAGAGTCTTTACGCCAAAGATTATGCAAAACTGAGTAGGGGCCCC-A
124 ATGAATATAGATATTTCAAGGAGT-TTGATGCCAAAAATCATGCAAAACT-AGT-TGGGCCCCGA
* * *
1960 GAACCCGTTTTTAGCC-AAAAATCGTGATGAGTA-A-ACGATTTCGGCTAAAATTTTGCAAAAAT
186 -AACGCG-TTTTAGCCAAAAAACCGTGATG-GTATACACGATTTCAGCTAAAATTTTGCAAAAAT
** * ** * * * *
2022 TGA-CC-AAATTTTTTTTTCTCCAATTCTTT-GTTACAATACACAGAAAAAATATATGATTCAAC
248 TGACCCGAAA-AATTTTTCCT-CAATT-TTTAGCCAAAATACTCA-TAAAAATATATAATTCAAC
*
2084 GCCAAAAA-ATTTGAAGGA
309 TCCAAAAATA-TTGAAGGA
* ** * ** * * *
2102 TTTTTCACGAATCTAATATCAATTTTCATAATTTTTTTTCGAATTTATTTCTAATTAAATCAAAA
1 CTTTTCACGCTTTTAATATCGTTTTTCAT-ATTTTTTCT-GAATTAATTTCTAATTAAATCGAAA
*
2167 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATTGTGGCTGAGATTTTG-TTAGATG
64 CAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAA-TGTGGCTGAGA-TTTGATTAGATG
* ** * *** *
2230 AATATCGATATTTCAAGGA-TTCGTTCTGCCAAAAATTATGCAAAACTGAGCCAAGG-CTCGAAA
127 AATATAGATATTTCAAGGAGTT--TGATGCCAAAAATCATGCAAAACT-AG-TTGGGCCCCGAAA
* * * *
2293 TGCGTTTTTAGCC-AAAAACGGTGAT-G-AGTACACGATTTCGGC--------T--AAAAACTGA
188 CGCG-TTTTAGCCAAAAAACCGTGATGGTA-TACACGATTTCAGCTAAAATTTTGCAAAAATTGA
* * * * * * *
2345 CCCGAAAATTTTTTTTCTCAAATGTTTT-GCCACAATACTCAGAAAAAAAATATAATTTAACGCC
251 CCCGAAAA-ATTTTTCCTC-AAT-TTTTAGCCAAAATACTCA-TAAAAATATATAATTCAACTCC
* *
2409 AAAAAAATTGACGG-
312 AAAAATATTGAAGGA
* * * ** *
2423 GTTTTCACGATTCTAATATTTTTTTTC-TATTTTATTC-GTAATTAATTTTTAATTAAATCGAAA
1 CTTTTCACGCTTTTAATATCGTTTTTCATATTTT-TTCTG-AATTAATTTCTAATTAAATCGAAA
* * * * * **
2486 CAAGATTCAGATCCTCGTAAAAACAAATCCTTATATCCAATGTGGTTGAGATTTGGTTCCATGAA
64 CAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* ** * *
2551 TGA-AGATATTTCAAGGAGTCTT--TGCACCAAAAATCATGCAAAATTGAGCCGGGGCTCCGGAA
129 T-ATAGATATTTCAAGGAGT-TTGATG--CCAAAAATCATGCAAAACT-AG-TTGGGCCCCGAAA
** * * *
2613 CGCGTTTTTAGCCAAAAAACTATGATGGTTAGTACACGATATT-GGCTAAAATTTTGAAAAAACT
188 CGCG-TTTTAGCCAAAAAACCGTGATGG-TA-TACACGAT-TTCAGCTAAAATTTTGCAAAAATT
** * * * * *
2677 GACCCGAAATTTTTTTTTCTTCAATTCTCT-GCCATAATACTCAGAAAAAATATATAATTCAACG
249 GACCCGAAA--AATTTTTCCTCAATT-TTTAGCCAAAATACTCA-TAAAAATATATAATTCAACT
*
2741 CCAAAAA-GTTGAAGGA
310 CCAAAAATATTGAAGGA
* * * * * *
2757 TTTTTCACGCTTCT-ATATTGTTTTTCCATTTTTTTTCCGAATTTAATTTCTTATTAAAT-----
1 CTTTTCACGCTTTTAATATCGTTTTT-CATATTTTTTCTGAA-TTAATTTCTAATTAAATCGAAA
* * *
2816 C--GA---A-A----C--AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAT
64 CAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * * * * *
2869 TATAGGTATTTCAAGGAGTCTTTATGCCAGAAACCATGCAAAACTGCGTCGAGACCCCTG-AACG
129 TATAGATATTTCAAGGAGT-TTGATGCCAAAAATCATGCAAAACT-AGTTG-GGCCCC-GAAACG
* * * *
2933 CGTTTTAGCCAAAAAACCGTGATGGCA-A-ACGATTTCGGCTGAAGTTTTGCAAAAATTGACCCG
190 CGTTTTAGCCAAAAAACCGTGATGGTATACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCG
* * * * * * *
2996 AGATATTTTT-CTCAAATTTCAGCCACAATTA-TCATAAAAAATATATAATTCAACGCCAAAAAA
255 AAAAATTTTTCCTCAATTTTTAGCCA-AAATACTCAT-AAAAATATATAATTCAACTCCAAAAAT
*
3059 ATTGAAGGG
318 ATTGAAGGA
* * * * **
3068 CTTCTCACGCATCTAATATCGTTTTTCCTACTTTTTTTTCCAAATTAATTTCTAATTAAATCGAA
1 CTTTTCACGCTTTTAATATCGTTTTT-C-A-TATTTTTTCTGAATTAATTTCTAATTAAATCGAA
* * * * *
3133 ACATGATTCAAATGCTCGTAAAAA-AAATTCTTAAATCCAATGTGGCTAAGATTTGGTTAAATGA
63 ACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
* * * *
3197 ATATAAATATTTTAAGGAGTTT--TGCCACAAAAAATCATGCAAAAC----T--GACCCGGAACG
128 ATATAGATATTTCAAGGAGTTTGATG-C-C-AAAAATCATGCAAAACTAGTTGGGCCCCGAAACG
* *
3254 CGTTTTTAGCCAAAAAATCGTGATGGT-T-CACAATTTCAGCTAAAATTTTGCAAAAATTGACCC
190 CG-TTTTAGCCAAAAAACCGTGATGGTATACACGATTTCAGCTAAAATTTTGCAAAAATTGACCC
* * * * *
3317 GAAATATTTTTCCTAAATTTTTAGCCACAATACTCATAATATATATATATATATATATAATTCAA
254 GAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAA-A-A-ATATATA-AT-T-CAACTC--
* *
3382 CATGAAAAAGATTGGAGGA
311 C---AAAAATATTGAAGGA
* *
3401 TTTTTCACGCTTTTAATATCGTTTTTCGTA-TTTTTCTGAATTAATTTCTAATTAAA-CGAAACA
1 CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
* ** *
3464 AGATTTAGATGCTCGTAAAAACAAA-TCATTAAATTTAATGTGGCTGAGATTTGATTAGATAAAT
66 AGATTCAGATGCTCGTAAAAACAAATTC-TTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* *
3528 ATAGATATATCAAGGAGTTTCAGTGCCAAAAATCATGCAAAACTAAGTTGGGCCCCGAAACGCGT
130 ATAGATATTTCAAGGAGTTTGA-TGCCAAAAATCATGCAAAACT-AGTTGGGCCCCGAAACGCGT
*
3593 TGTTAGTC-AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAA-TGACCCG
193 T-TTAGCCAAAAAACCGTGATGG-TA-TACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCG
* * * * *
3656 AAAAATTTTTCCTCAATTTTTGGCTAAAATACTCAT-AATATGTATAATTTAACTCCAAAAATAT
255 AAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCAACTCCAAAAATAT
*
3720 TGGAGGA
320 TGAAGGA
* * * * *
3727 CTTTTCACGCTTTTAATTTTGTTTTTCATATTTTTTCTGAATTAATTTCTGATTGAATTGAAACA
1 CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
* * * *
3792 AGATTCAGATGCTCGTAAAAATAAATTCTTAAATCCAATATAGCTGAGATTTGATAAGATGAATA
66 AGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * * * * * * * *
3857 TGGATATCTCAAAGATTCTTGATGCCAAAAATCATTCAAAACTTAGTCGGGGCCTC-AGAATGCA
131 TAGATATTTCAAGGAGT-TTGATGCCAAAAATCATGCAAAAC-TAGT-TGGGCCCCGA-AACGCG
* * * * * *
3921 TTTTAACC-AAAAATCGTGACGATTATTACACGATTTCAGTTAAAATTTTGTAAAAATTGACCCG
192 TTTTAGCCAAAAAACCGTGATG-GTA-TACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCG
* * * * *
3985 -AAAGTTATTTCCTCAATTTTTAGTCACAATACTTATAAAAATTATATAATTCAA-TGACAAAAA
255 AAAAATT-TTTCCTCAATTTTTAGCCAAAATACTCATAAAAA-TATATAATTCAACT-CCAAAAA
*
4048 TATTGAAGGG
317 TATTGAAGGA
* * * * *
4058 TTTTTCATGCTTTTATTATCGTTTTTCCTATTATTTTCCT-AATTAATTTCTAATTAAATTGAAA
1 CTTTTCACGCTTTTAATATCGTTTTTCATATT-TTTT-CTGAATTAATTTCTAATTAAATCGAAA
* * *** *
4122 CATGATTCAGATGTTCGT-TTTACAAA-TCATTAAATCCAATGTGGCTGAGATTTGGTTAGATGA
64 CAAGATTCAGATGCTCGTAAAAACAAATTC-TTAAATCCAATGTGGCTGAGATTTGATTAGATGA
4185 ATATAGATATTTCAAGGAGT
128 ATATAGATATTTCAAGGAGT
4205 CTCGGCGCCT
Statistics
Matches: 1721, Mismatches: 245, Indels: 275
0.77 0.11 0.12
Matches are distributed among these distances:
309 1 0.00
310 38 0.02
311 27 0.02
312 14 0.01
313 47 0.03
314 13 0.01
316 1 0.00
317 25 0.01
318 95 0.06
319 117 0.07
320 38 0.02
321 45 0.03
322 128 0.07
323 20 0.01
324 16 0.01
325 10 0.01
326 44 0.03
327 27 0.02
328 183 0.11
329 209 0.12
330 52 0.03
331 158 0.09
332 101 0.06
333 61 0.04
334 86 0.05
335 49 0.03
336 49 0.03
337 1 0.00
338 39 0.02
339 27 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (326 bp):
CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
AGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
TAGATATTTCAAGGAGTTTGATGCCAAAAATCATGCAAAACTAGTTGGGCCCCGAAACGCGTTTT
AGCCAAAAAACCGTGATGGTATACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAAT
TTTTCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCAACTCCAAAAATATTGAAGG
A
Found at i:4080 original size:657 final size:658
Alignment explanation
Indices: 2094--4206 Score: 1516
Period size: 657 Copynumber: 3.2 Consensus size: 658
2084 GCCAAAAAAT
** * ** * * * * *
2094 TTGAAGGATTTTTCACGAATCTAATATCAATTTTCATAATTTTTTTTCGAATTTATTTCTAATTA
1 TTGAAGGATTTTTCACGCTTTTAATATCGTTTTTCCT-ATTATTTTCCTAATTAATTTCTAATTA
* * *
2159 AATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATTGTGGCTGAGATTTTG
65 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAA-TGTGGCTGAGATTTGG
* * ** * * * *
2223 TTAGATGAATATCGATATTTCAAGGATTCGTTC-TGCCAAAAATTATGCAAAACTGAGCCAAG-G
129 TTAGATGAATATAGATATTTCAAGGAGTC-TTCATGCCAAAAACCATGCAAAACTAAGTCGAGAC
* * * * * *
2286 CTC-GAAATGCGTTTTTAGCC-AAAAACGGTGATGAGTACACGATTTCGGC--------T--AAA
193 CCCTG-AACGCG-TTTTAGCCAAAAAACCGTGATG-GCAAACGATTTCAGCTAAAATTTTGCAAA
* * ** * * *
2339 AACTGACCCGAAAATTTTTTTTCTCAAATGTTTTGCCAC-AATACTCAGAAAAAAAATATAATTT
255 AATTGACCCGAAAA--ATTTTTCTCAAAT-TTCAGCCACAAATA-TCA-TAAAAATATATAATTC
* * * * **
2403 AACGCCAAAAAAATTGACGG-GTTTTCACG-ATTCTAATAT--TTTTT--TTCTATTTTATTCGT
315 AACGCCAAAAAAATTGAAGGACTTCTCACGCA-TCTAATATCGTTTTTCCTACTATTTT-TTCCA
* * * * *
2462 AATTAATTTTTAATTAAATCGAAACAAGATTCAGATCCTCGTAAAAACAAATCCTTATATCCAAT
378 AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAA-AAATTCTTAAATCCAAT
* * * * * ** * * * *
2527 GTGGTTGAGATTTGGTTCCATGAATGA-AGATATTTCAAGGAGTCTTTG-CACCAAAAATCATGC
442 ATAGCTAAGATTTGGATAAATGAAT-ATAAATATCTCAAAGAGT-TTTGACACAAAAAATCATGC
* * * * * * *
2590 AAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAAA-CTATGATGGTTAGTACACGATA
505 AAAACTGA-------C-CCAGAACGCGATTTTAACCAAAAAATC-GTGAT-G--A-TTCACAAT-
* * * * * * * * *
2654 TT-GGCTAAAATTTTGAAAAAACTGACCCGAAATTTTTTTTTCTTCAATTCTCT-GCCATAATA-
556 TTCAGCTAAAATTTTGCAAAAATTGACCCGAAA--TATATTTCCTAAATT-TTTAGCCACAATAC
* * ***
2716 C-T-CAGA-A-A-A-A-ATATATAATTCAACGCCAAAAAG-
618 CATATATATATATATATATATATAATTCAACATGAAAAAGA
* * * * *
2749 TTGAAGGATTTTTCACGCTTCT-ATATTGTTTTTCC-ATTTTTTTTCCGAATTTAATTTCTTATT
1 TTGAAGGATTTTTCACGCTTTTAATATCGTTTTTCCTA-TTATTTTCCTAA-TTAATTTCTAATT
*
2812 AAAT-----C--GA---A-A----C--AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG
64 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGATTTGG
* * * * **
2860 TTAGATGATTATAGGTATTTCAAGGAGTCTTTATGCCAGAAACCATGCAAAACTGCGTCGAGACC
129 TTAGATGAATATAGATATTTCAAGGAGTCTTCATGCCAAAAACCATGCAAAACTAAGTCGAGACC
* * *
2925 CCTGAACGCGTTTTAGCCAAAAAACCGTGATGGCAAACGATTTCGGCTGAAGTTTTGCAAAAATT
194 CCTGAACGCGTTTTAGCCAAAAAACCGTGATGGCAAACGATTTCAGCTAAAATTTTGCAAAAATT
* * *
2990 GACCCGAGATATTTTTCTCAAATTTCAGCCACAATTATCATAAAAAATATATAATTCAACGCCAA
259 GACCCGAAAAATTTTTCTCAAATTTCAGCCACAAATATCAT-AAAAATATATAATTCAACGCCAA
* *
3055 AAAAATTGAAGGGCTTCTCACGCATCTAATATCGTTTTTCCTACTTTTTTTTCCAAATTAATTTC
323 AAAAATTGAAGGACTTCTCACGCATCTAATATCGTTTTTCCTACTATTTTTTCCAAATTAATTTC
* * *
3120 TAATTAAATCGAAACATGATTCAAATGCTCGTAAAAAAAATTCTTAAATCCAATGTGGCTAAGAT
388 TAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAAAAATTCTTAAATCCAATATAGCTAAGAT
* * * * * *
3185 TTGGTTAAATGAATATAAATATTTTAAGGAGTTTTGCCACAAAAAATCATGCAAAACTGACCCGG
453 TTGGATAAATGAATATAAATATCTCAAAGAGTTTTGACACAAAAAATCATGCAAAACTGACCCAG
* * *
3250 AACGCGTTTTTAGCCAAAAAATCGTGATGGTTCACAATTTCAGCTAAAATTTTGCAAAAATTGAC
518 AACGCGATTTTAACCAAAAAATCGTGATGATTCACAATTTCAGCTAAAATTTTGCAAAAATTGAC
*
3315 CCGAAATATTTTTCCTAAATTTTTAGCCACAATACTCATAATATATATATATATATATATAATTC
583 CCGAAATATATTTCCTAAATTTTTAGCCACAATAC-CAT-ATATATATATATATATATATAATTC
3380 AACATGAAAAAGA
646 AACATGAAAAAGA
* *
3393 TTGGAGGATTTTTCACGCTTTTAATATCGTTTTTCGTA-T-TTTT-CTGAATTAATTTCTAATTA
1 TTGAAGGATTTTTCACGCTTTTAATATCGTTTTTCCTATTATTTTCCT-AATTAATTTCTAATTA
* ** *
3455 AA-CGAAACAAGATTTAGATGCTCGTAAAAACAAATCATTAAATTTAATGTGGCTGAGATTTGAT
65 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGATTTGGT
* * * * *
3519 TAGATAAATATAGATATATCAAGGAGT-TTCAGTGCCAAAAATCATGCAAAACTAAGTTG-GGCC
130 TAGATGAATATAGATATTTCAAGGAGTCTTCA-TGCCAAAAACCATGCAAAACTAAGTCGAGACC
* *
3582 CC-GAAACGCGTTGTTAGTC-AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCA
194 CCTG-AACGCGTT-TTAGCCAAAAAACCGTGATGG-CA--A-ACGATTTCAGCTAAAATTTTGCA
* ** * * * *
3645 AAAA-TGACCCGAAAAATTTTTCCTCAATTTTTGGCTA-AAATACTCAT-AATATGTATAATTTA
253 AAAATTGACCCGAAAAATTTTT-CTCAAATTTCAGCCACAAATA-TCATAAAAATATATAATTCA
* * * * * * * * **
3707 ACTCCAAAAATATTGGAGGACTTTTCACGCTTTTAATTTTGTTTTT-C-A-TATTTTTTCTGAAT
316 ACGCCAAAAAAATTGAAGGACTTCTCACGCATCTAATATCGTTTTTCCTACTATTTTTTCCAAAT
* * * *
3769 TAATTTCTGATTGAATTGAAACAAGATTCAGATGCTCGTAAAAATAAATTCTTAAATCCAATATA
381 TAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAA-AAATTCTTAAATCCAATATA
* ** ** * *
3834 GCTGAGATTT-GATAAGATGAATATGGATATCTCAAAGA-TTCTTGATGCCAAAAATCATTCAAA
445 GCTAAGATTTGGATAA-ATGAATATAAATATCTCAAAGAGTT-TTGACACAAAAAATCATGCAAA
* * * *
3897 ACTTAGTCGGGGCCTCAGAATGC-ATTTTAACC-AAAAATCGTGACGATTATTACACGATTTCAG
508 AC----T---GACC-CAGAACGCGATTTTAACCAAAAAATCGT---GATGATT-CACAATTTCAG
* * * *
3960 TTAAAATTTTGTAAAAATTGACCCGAAAGT-TATTTCCTCAATTTTTAGTCACAATA-C-T-TAT
561 CTAAAATTTTGCAAAAATTGACCCGAAA-TATATTTCCTAAATTTTTAGCCACAATACCATATAT
*
4021 A-A-A-A-AT-TATATAATTC-A-ATGACAAAAATA
625 ATATATATATATATATAATTCAACATG--AAAAAGA
* * *
4050 TTGAAGGGTTTTTCATGCTTTTATTATCGTTTTTCCTATTATTTTCCTAATTAATTTCTAATTAA
1 TTGAAGGATTTTTCACGCTTTTAATATCGTTTTTCCTATTATTTTCCTAATTAATTTCTAATTAA
* * * ***
4115 ATTGAAACATGATTCAGATGTTCGT-TTTACAAATCATTAAATCCAATGTGGCTGAGATTTGGTT
66 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGATTTGGTT
4179 AGATGAATATAGATATTTCAAGGAGTCT
131 AGATGAATATAGATATTTCAAGGAGTCT
4207 CGGCGCCTTA
Statistics
Matches: 1192, Mismatches: 173, Indels: 181
0.77 0.11 0.12
Matches are distributed among these distances:
632 2 0.00
633 20 0.02
634 2 0.00
635 34 0.03
636 3 0.00
637 102 0.09
638 25 0.02
639 32 0.03
640 3 0.00
641 1 0.00
642 17 0.01
643 27 0.02
644 64 0.05
645 42 0.04
646 8 0.01
647 92 0.08
648 48 0.04
649 8 0.01
651 1 0.00
652 2 0.00
653 11 0.01
654 24 0.02
655 23 0.02
656 59 0.05
657 143 0.12
658 90 0.08
659 129 0.11
660 43 0.04
661 41 0.03
662 4 0.00
663 9 0.01
664 11 0.01
665 7 0.01
666 5 0.00
667 59 0.05
668 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (658 bp):
TTGAAGGATTTTTCACGCTTTTAATATCGTTTTTCCTATTATTTTCCTAATTAATTTCTAATTAA
ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTGAGATTTGGTT
AGATGAATATAGATATTTCAAGGAGTCTTCATGCCAAAAACCATGCAAAACTAAGTCGAGACCCC
TGAACGCGTTTTAGCCAAAAAACCGTGATGGCAAACGATTTCAGCTAAAATTTTGCAAAAATTGA
CCCGAAAAATTTTTCTCAAATTTCAGCCACAAATATCATAAAAATATATAATTCAACGCCAAAAA
AATTGAAGGACTTCTCACGCATCTAATATCGTTTTTCCTACTATTTTTTCCAAATTAATTTCTAA
TTAAATCGAAACAAGATTCAAATGCTCGTAAAAAAAATTCTTAAATCCAATATAGCTAAGATTTG
GATAAATGAATATAAATATCTCAAAGAGTTTTGACACAAAAAATCATGCAAAACTGACCCAGAAC
GCGATTTTAACCAAAAAATCGTGATGATTCACAATTTCAGCTAAAATTTTGCAAAAATTGACCCG
AAATATATTTCCTAAATTTTTAGCCACAATACCATATATATATATATATATATATAATTCAACAT
GAAAAAGA
Found at i:5035 original size:326 final size:328
Alignment explanation
Indices: 4557--5213 Score: 835
Period size: 326 Copynumber: 2.0 Consensus size: 328
4547 TTGGTTGGAG
* * * *
4557 GAATATAGATATTTCAAGGAGTCTTGGAGCAAAAAATCATGCAAAACTGAATCGGGCCTCGGAAC
1 GAATATAGATATTTCAAGGAGTCTCGGAGC-AAAAATCATACAAAAATGAATCGGGCCTCGAAAC
* * *
4622 GCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGAC
65 GCGTTTTTAGCCAAAAACCGTGATG---AGTACACGATTTCAGCTAAAATTTTGTAAAAAATGAC
* *
4687 CCGAAAGATTTTTCCTCAATTTTCAGCCACAATACGCATAAAAAATATATA-ATTCAACACCAAA
127 CCGAAAGATATTTCCTCAATTTTCAGCCAAAATACGCAT-AAAAATATA-ACATTCAACACCAAA
* **
4751 AATATTGAAGAG-CTTTCACACTTT-TAATATCGTTTGTCATA-TTTTTTTCTGAATTAATTTCT
190 AATATTGAAGAGACTTTCAC-CTTTCTAATATCATTTGTCATATTTTTTTTCCAAATTAATTTCT
** * *
4813 AATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAATGCAATGTGGCTAAGA
254 AATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCATT-AAATCCAATGTGGCTAAGA
*
4878 TTTTATTAGAT
318 TTTGATTAGAT
* * *
4889 GAATATAGATATTTCAAGGAGTCTCGGTGC-CAAA-CATACAAAAATGAGTCGAGGTCC-CGAAA
1 GAATATAGATATTTCAAGGAGTCTCGGAGCAAAAATCATACAAAAATGAATCG-GG-CCTCGAAA
4951 CGCGTTTTTAGCCAAAAACCGTGATG-GTACACGATTTCAGCTAAAATTTTGTAAAAAATGACCC
64 CGCGTTTTTAGCCAAAAACCGTGATGAGTACACGATTTCAGCTAAAATTTTGTAAAAAATGACCC
** * * * ** *
5015 GAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATAACTTTCAATGCTAAAAATA
129 GAAAGATATTTCCTCAATTTTCAGCCAAAATACGCATAAAAATATAACATTCAACACCAAAAATA
* * * * * * *
5080 TTGAAGGGATTTTGACGTTTCTAATATCATTTTTCCTATTTTTTTTCCAAATTAATTTCTTATTA
194 TTGAAGAGACTTTCACCTTTCTAATATCATTTGTCATATTTTTTTTCCAAATTAATTTCTAATTA
* *
5145 AATCAAAACAAGATTCAGATGCTTGTAAAAACAAATCATTAAATCCAATGTGGCTGAGATTTGAT
259 AATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTAAGATTTGAT
5210 TAGA
324 TAGA
5214 GAAGTTGAGA
Statistics
Matches: 282, Mismatches: 37, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
324 1 0.00
325 32 0.11
326 111 0.39
327 59 0.21
329 14 0.05
330 35 0.12
331 2 0.01
332 28 0.10
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
GAATATAGATATTTCAAGGAGTCTCGGAGCAAAAATCATACAAAAATGAATCGGGCCTCGAAACG
CGTTTTTAGCCAAAAACCGTGATGAGTACACGATTTCAGCTAAAATTTTGTAAAAAATGACCCGA
AAGATATTTCCTCAATTTTCAGCCAAAATACGCATAAAAATATAACATTCAACACCAAAAATATT
GAAGAGACTTTCACCTTTCTAATATCATTTGTCATATTTTTTTTCCAAATTAATTTCTAATTAAA
TCAAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGGCTAAGATTTGATTA
GAT
Found at i:13700 original size:57 final size:57
Alignment explanation
Indices: 13612--13720 Score: 209
Period size: 57 Copynumber: 1.9 Consensus size: 57
13602 TTCCTTTCAT
13612 ACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTCCAC
1 ACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTCCAC
*
13669 ACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATTCT
1 ACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCT
13721 ACAAAATGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.38
Consensus pattern (57 bp):
ACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATTCTTCCAC
Found at i:14855 original size:42 final size:43
Alignment explanation
Indices: 14809--14896 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 43
14799 TGCATTACCT
* * *
14809 AAATTCTA-CTCCATCTTTAGGTAATTCATCAAAATAAAGCTA
1 AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
*
14851 AAATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAAAACTA
1 AAATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTA
14896 A
1 A
14897 TATTAATTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
42 8 0.21
45 31 0.79
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (43 bp):
AAATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTA
Found at i:16487 original size:32 final size:32
Alignment explanation
Indices: 16444--16536 Score: 161
Period size: 31 Copynumber: 2.9 Consensus size: 32
16434 CAATCATGTC
* *
16444 AGGGGGCAAATTGGCCTAAATTTCCAAATTTA
1 AGGGGGTAAATTGGCCTAAATTTCTAAATTTA
16476 AGGGGGTAAATTGGCCTAAATTTCTAAA-TTA
1 AGGGGGTAAATTGGCCTAAATTTCTAAATTTA
16507 AGGGGGTAAATTGGCCTAAATTTCTAAATT
1 AGGGGGTAAATTGGCCTAAATTTCTAAATT
16537 CAATAGGGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 31 0.53
32 27 0.47
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (32 bp):
AGGGGGTAAATTGGCCTAAATTTCTAAATTTA
Found at i:19588 original size:19 final size:19
Alignment explanation
Indices: 19566--19613 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
19556 GGGCTGAAAT
19566 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
19585 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
19604 TAATT-ATTAT
1 TAATTAATTAT
19614 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:21456 original size:51 final size:50
Alignment explanation
Indices: 21355--21460 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 50
21345 GTTCTTCATA
* **
21355 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
21405 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
21456 TTTTC
1 TTTTC
21461 ATTCAGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
50 7 0.15
51 40 0.83
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Done.