Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018170.1 Corchorus olitorius cultivar O-4 contig18203, 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: 9499
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Found at i:1334 original size:337 final size:336
Alignment explanation
Indices: 293--3729 Score: 4022
Period size: 336 Copynumber: 10.3 Consensus size: 336
283 TCCCTAATAT
* *
293 TGATGCTCGTAAAA-CAAATCCTTAAATCCAATTTGGCTGAGATTTGCTTAGATGAATGTAGATA
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
* * *
357 TGTCAAGGAGTCTCGGGGCAAAAAATCATTAAAAACTGAGCTGGGGCCCCAGAACGCGTTTTTAG
66 TGTCAAGGAGTCTCGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
* *
422 CCAAAAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAATTGACCCGAAAG
131 CCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
*
487 TTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGTTTGA
196 TTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGA
* *
552 A-GGGTTTTCACGCTTCTAATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGATTAAATCG
261 AGGGGTTTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAATTAAATCG
616 AAACATGATTC
326 AAACATGATTC
*
627 TGATGCCCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * *
692 TGTCAAGGAGTCTCGGGGCCAAAAATCATTGAAAACTGAGCCGGGGCGCCAAAACGCGTTTTTAG
66 TGTCAAGGAGTCTCGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
757 CCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
131 CCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
*
822 TTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATAGATAATTCAACGCCAAAAAGATTGA
196 TTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGA
* *
887 A-GGGTTTCTCACGCTTCTAATATCGATTTTCCTATATCTTTCCGAATTAATTTCTGATTAAATC
261 AGGGGTTT-TCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAATTAAATC
951 GAAACATGATTC
325 GAAACATGATTC
* * *
963 TGATGGC-CGTAAAATCAAATCCTTAAACCCAATTTGGATGTGATTTGGTTAGATGAATATAGAT
1 TGAT-GCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGAT
*
1027 ATGTCAAGGAGTCTCGAGGCCAAAAATCATTAAAAACTGAGTCGGGGCCCCAGAACGCGTTTTTA
65 ATGTCAAGGAGTCTCGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTA
* *
1092 GCCAAAAAAAACCGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGCTAAAATTGACCCGAAA
130 GCCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
*
1157 GTTTTTTTCCATAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATT
195 G-TTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATT
* * *
1222 GAAGGGGTTTTCACGTTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTTTAATTTAAT
259 GAAGGGGTTTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAATTAAAT
1287 CGAAACATGATTC
324 CGAAACATGATTC
* * *
1300 TGATGTTCGTGAAATCAAATCCTTTAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * **
1365 TGTCAAGGAGTCTATG-GGCCGAAAATCATTGAAAACTGAGCCGATGCCCCAGAACGCGTTTTTA
66 TGTCAAGGAGTCT-CGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTA
* *
1429 GCCAAAAAATAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTGGCAAAAATTGACCCGAA
130 GCCAAAAAA-AACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAA
* * *
1494 ACTTTTATCCACAATCTTTGGCCAAAACACTTATAGAATATAGATAATTCAACGCCAAAAAGATT
194 AGTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATT
* *
1559 GAA-GGGTCTTTCACGTTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTGATTAAA
259 GAAGGGGT-TTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAATTAAA
* *
1623 TCGAAACTTGATTT
323 TCGAAACATGATTC
*
1637 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAAATGAATATAGATA
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * * *
1702 TGTAAAGGAATCTCGGGGCAAAAAATCATTAAAAACTGAGCCGGGG-CCCAAAACGCGTTTTTAG
66 TGTCAAGGAGTCTCGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
* ** * *
1766 ACAAAAAAAAACTATGATGG---GTACACGATTTCGGCCAAAATTTTGCAAAAATTGGCCCGAAA
131 -CCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA
* * *
1828 GTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATATTTCAACTCCAAAAAGTTTG
195 GTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTG
** * * * * *
1893 AAGGATTTTTCACGTTTCTAATATCGATTTTCCTATATTTTTCTGAATTAATTTCTGATTTAATC
260 AAGGGGTTTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAATTAAATC
*
1958 GAAACGTGATTC
325 GAAACATGATTC
* *
1970 TGATGCCCGTAAAATCAAATCATTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * *
2035 TGACAAGGAGTCTCGGGGCCAAAAATCATTAAAAACTGAGCCGGGGCCACAAAACGCGTTTTTAG
66 TGTCAAGGAGTCTCGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
2100 CCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
131 CCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
* * *
2165 TTTTTTCCACAATCTTTGGCCAAAACAATTACAAAATATATATAATTCAACGCCAAAAAGATTGA
196 TTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGA
* * *
2230 AGGGGTTTTCACGTTTCTAATATCCATTTTCCTATATGTTTCCGAATTAATTT-TAATTTAATCG
261 AGGGGTTTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAATTAAATCG
2294 AAACATGATTC
326 AAACATGATTC
* * * *
2305 TGATGTTCGTAAAATCAAATCATTAAATCCAATTGTGGATGTGATTTGGTTAGATGAATATAGAT
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAATT-TGGCTGAGATTTGGTTAGATGAATATAGAT
* * * ** * * * *
2370 ATTTCAAGGAGTCTTTG-CGCCAAAAATCATGCAAAATTGAGTCGGGGCACCGGAACGCGTTTTT
65 ATGTCAAGGAGTC-TCGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCG-TTTT
* * * * * *
2434 TTGTC---AAAAA---T--TCG-T-G-ACACGATTTTGGCTAAAATTTTACAAAAACTGACCCGA
128 TAGCCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA
* * * * * * * * * * **
2488 TAAG-GTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATTTAATTCATTGCCAGAAAA-
193 -AAGTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCA-AAAAG
** * * * *
2551 ATTGAAGGATTTTTTCACGCTTCTAATATCG-TTTTTCTATTATTTTTTTTCGAATTAAATTCTA
256 ATTGAAGG-GGTTTTCACGCTTCTAATATCGATTTTCCTA-TA--TGTTTCCGAATTAATTTCTA
** *
2615 ATTAAATCGAAACAAAATTAA
317 ATTAAATCGAAACATGATT-C
* * * ** *
2636 T-ATGCTTGTAAAAACAATTAATTAAATCC-ATTGTGGATGAGATTTGGTTAGATGAATATAGAT
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAATT-TGGCTGAGATTTGGTTAGATGAATATAGAT
* * * * *** ** * **
2699 ATTTCAAGGAGTTTTTG-CGCCAAAAATCAGGCAAATTTGAGTCGGGGCTTC-GAAACGCGTTTT
65 ATGTCAAGGAG-TCTCGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAG-AACGCG----
* * *
2762 TTTTTTGTC--AAAAATCC-TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
124 TTTTTAGCCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC
* * * *
2824 CCGAAAGTTTTTTCCACATTCTTTGGCCAAAACACTTATAGAAAAGA-ATAATTCTACGCCAAAA
189 CCGAAAGTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAA
* * * *
2888 AAATTGAAGGGTTTTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTTTGAT
254 AGATTGAAGGGGTTTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAAT
2953 TAAATCGAAACATGATTC
319 TAAATCGAAACATGATTC
* * * * *
2971 TGATGCCCGTAAAATCAAATCCTTAAATCCGATTTGTCTGAGATATGGTTAGATGAATGTAGATA
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * *
3036 TTTCAAGGAGTC-CCAGGGCCAAAAATCATTACAAATTGAGCCGGGGCCCCAGAACGCGTTTTTA
66 TGTCAAGGAGTCTCGA-GGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTA
* * * *
3100 GCCAAAAAAAAACTGTGATGGTTAGTACACGATTTTGGCTAAAATTTTACAAAAACAT-ACCCGA
130 GCC-AAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA-TTGACCCGA
*** * * * * * * *
3164 AAAAATTTTACTCAATCTCCTT--CCACAATACTCATCAAAAT-TATA-AATATTAACGCCAAAA
193 AAGTTTTTTCCACAATCT--TTGGCCAAAACACTTAT-AGAATATATATAAT-TCAACGCCAAAA
* * * * **
3225 AGATTGAA-GGATTTTCACGCTTCTAATATCG-TTTTTCT-TATTTTTCCGAAATAAAATCTAAT
254 AGATTGAAGGGGTTTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAAT
* *
3287 TAAATCGAAATC-GGTTTTC
319 TAAATCGAAA-CATG-ATTC
* * * * * *
3306 TGATACTCGTAAAAACAAATTCTTAGAT-CAATGTT-GTTGAGATTTGGTCAGATGAATATAGAT
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAAT-TTGGCTGAGATTTGGTTAGATGAATATAGAT
* * ** * * * * * * *
3369 ATTTAAATAAGTCTTGACGCCAAAAATCGTGT-GAAACTAAGTCGGGGCCCCGGAACGCGTTTTT
65 ATGTCAAGGAGTCTCGAGGCCAAAAATCAT-TAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTT
* * * * * *
3433 AACC---AAAAACTGTGATGGTTAGTACACAATTTCAGC-AAAA-TTTCCAAAAAAAAAATGACC
129 AGCCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC----AAAAATTGACC
* * ** * * * *
3493 TG-AATTTATTTTCCTTAATTTTTGGCCAAAATACTCATA-AAAATATATAATTCAACGCCAAAA
190 CGAAAGTT-TTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAA
* * * *
3556 AGGTTGAAGGGATTTTCATGCTTCTAATATC-ATTTTTCT-TAAT-TTTCCGAATTAATTTCTAA
254 AGATTGAAGGGGTTTTCACGCTTCTAATATCGATTTTCCTAT-ATGTTTCCGAATTAATTTCTAA
* * * * *
3618 ATAAATTGATACCCT-TTTC
318 TTAAATCGA-AACATGATTC
* * * * *
3637 TGATGCTCGTAAAAACAAATCCTTAAATTCAATGTT-GCTAAGATTTGGTCATATGAATATAGAT
1 TGATGCTCGTAAAATCAAATCCTTAAATCCAAT-TTGGCTGAGATTTGGTTAGATGAATATAGAT
* * * *
3701 ATTTCAACGAGTCTTGACGCCAAAAATCA
65 ATGTCAAGGAGTCTCGAGGCCAAAAATCA
3730 GGAAAATTTG
Statistics
Matches: 2713, Mismatches: 311, Indels: 160
0.85 0.10 0.05
Matches are distributed among these distances:
326 91 0.03
327 28 0.01
328 6 0.00
329 103 0.04
330 75 0.03
331 58 0.02
332 161 0.06
333 292 0.11
334 143 0.05
335 339 0.12
336 715 0.26
337 520 0.19
338 89 0.03
339 29 0.01
340 64 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (336 bp):
TGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATA
TGTCAAGGAGTCTCGAGGCCAAAAATCATTAAAAACTGAGCCGGGGCCCCAGAACGCGTTTTTAG
CCAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG
TTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATATAATTCAACGCCAAAAAGATTGA
AGGGGTTTTCACGCTTCTAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTAATTAAATCG
AAACATGATTC
Found at i:4358 original size:328 final size:328
Alignment explanation
Indices: 3755--4659 Score: 952
Period size: 328 Copynumber: 2.7 Consensus size: 328
3745 GGAGCCCGGA
* * * * * * *
3755 ACACGATTTCGGCTAAAATTTTGCAAATACTGAC-CCGAATAA-TTTATCC-TCATTTTCTTGCC
1 ACACGATTTCGACTAAAATTTTTCAAAAACTAACACC-AAAAACTTT-TCCTTC-TTTT-TGGCT
* * * * * * * *
3817 ACAATACT-TTAATAAAATATATAATTCAACACAAAAAAGATTGAAGGGTTTTTCAAGCTTCTAA
62 ACAATACTAGTAA-AAAATATATAATTCAACGCTAAAAA-ATTGAAGGGCTTTGCACGCTACAAA
* * * * * * ** *
3881 TATTGTTTTCCTCTTTTTTTTCCGAATTAATTTTTAATTAAATCAAAACCTGTTTTCGGTTCTCA
125 TATCG-TTTACAC-TTGTTTTCCGAATTAATTTGTAAATAAATCAAAACCTGTTTTCAATTCTCG
* * * *
3946 T-AAAAAAATCCATAAATCCAATGTTGTTGAGATTTGATCAAATGAATATATATATTTCAGTGAG
188 TAAAAAAAATCCTTAAATCCAATGTTGTTGAGATTTGGTTAAATGAATATATATATTTCAGCGAG
*
4010 TCTTGGCGCCAAAAATCATGCAAAACTAAG-CTGGGG-CCTCGGAACGCGTTATTAGCCAAAAAT
253 TCTTGGCGCCAAAAATCATGCAAAACTAAGAC-GGGGTCC-CAGAACGCGTTATTAGCCAAAAAT
* * *
4073 CATGATGGTTAGT
316 CATAATGGCTACT
* * *
4086 ACACGATTTCGACTAAAATCTTTT-AAAATCTGAC-CCAAAAACTTTTCCTT-TTTTTGGTTACA
1 ACACGATTTCGACTAAAAT-TTTTCAAAAACTAACACCAAAAACTTTTCCTTCTTTTTGGCTACA
* * * * *
4148 ATACTGGT-AAAAGTATATAATTTAATGCTGAGAAAATTGAAGGGCTTTGCACGCTAACAAATAT
65 ATACTAGTAAAAAATATATAATTCAACGCT-AAAAAATTGAAGGGCTTTGCACGCT-ACAAATAT
** * *
4212 CGTTTACACTTGTTTTCCGAATTAATTTGTAAATATGTCGAAATCTGTTTTCAATTCTCGTAAAA
128 CGTTTACACTTGTTTTCCGAATTAATTTGTAAATAAATCAAAACCTGTTTTCAATTCTCGTAAAA
* *
4277 ACAAATCCTTAAATCCAATGTTGTTGTGATTTGGTTAAATGAATATAGATATTTCAGCGAGTCTT
193 A-AAATCCTTAAATCCAATGTTGTTGAGATTTGGTTAAATGAATATATATATTTCAGCGAGTCTT
** * * *
4342 GGCGCCAAGGATCATGCAAAACTGAGACGGGGTCCCAGAACGCGTTATTAGTCAAAAATCGTAAT
257 GGCGCCAAAAATCATGCAAAACTAAGACGGGGTCCCAGAACGCGTTATTAGCCAAAAATCATAAT
4407 GGCTACT
322 GGCTACT
* * * * *
4414 ACACGATTTCGGCTAATATTTTTCAAAAACTAACACGAAAAATTTTTCCTTCTTTTTTGCTACAA
1 ACACGATTTCGACTAAAATTTTTCAAAAACTAACACCAAAAACTTTTCCTTCTTTTTGGCTACAA
* * *
4479 TACTAGTAAAAAAATATATAATTCAACGCTAAAAAATTGAAGGGTTTTGCACGCTTCTAATATCG
66 TACTAGT-AAAAAATATATAATTCAACGCTAAAAAATTGAAGGGCTTTGCACGCTACAAATATCG
* * * * * *
4544 TTTACCCTTTTTTTCCGAATTAATTTGTAAATAAATCAAAACCGGTTATGAATGCTCGTAAAAAT
130 TTTACACTTGTTTTCCGAATTAATTTGTAAATAAATCAAAACCTGTTTTCAATTCTCGTAAAAA-
* * *
4609 AAATCCTTAAATCCAACGTTATGGAGATTTGGTAATAAAT-AATATATATAT
194 AAATCCTTAAATCCAATGTTGTTGAGATTTGGT--TAAATGAATATATATAT
4660 ATATATATAT
Statistics
Matches: 477, Mismatches: 80, Indels: 34
0.81 0.14 0.06
Matches are distributed among these distances:
326 42 0.09
327 45 0.09
328 162 0.34
329 22 0.05
330 115 0.24
331 65 0.14
332 26 0.05
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (328 bp):
ACACGATTTCGACTAAAATTTTTCAAAAACTAACACCAAAAACTTTTCCTTCTTTTTGGCTACAA
TACTAGTAAAAAATATATAATTCAACGCTAAAAAATTGAAGGGCTTTGCACGCTACAAATATCGT
TTACACTTGTTTTCCGAATTAATTTGTAAATAAATCAAAACCTGTTTTCAATTCTCGTAAAAAAA
ATCCTTAAATCCAATGTTGTTGAGATTTGGTTAAATGAATATATATATTTCAGCGAGTCTTGGCG
CCAAAAATCATGCAAAACTAAGACGGGGTCCCAGAACGCGTTATTAGCCAAAAATCATAATGGCT
ACT
Found at i:4657 original size:2 final size:2
Alignment explanation
Indices: 4650--4683 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4640 GTAATAAATA
4650 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
4684 TTCAATGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5534 original size:33 final size:33
Alignment explanation
Indices: 5492--5556 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
5482 GACGGGTCCC
*
5492 AATACACGTTATTAGCCGAAAATCGTGATAATT
1 AATACACGTTATTAGCCAAAAATCGTGATAATT
5525 AATACACGTTATTAGCCAAAAATCGTGATAAT
1 AATACACGTTATTAGCCAAAAATCGTGATAAT
5557 CGTGAAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (33 bp):
AATACACGTTATTAGCCAAAAATCGTGATAATT
Found at i:7784 original size:20 final size:19
Alignment explanation
Indices: 7757--8075 Score: 129
Period size: 20 Copynumber: 15.7 Consensus size: 19
7747 CGCGGCATAT
7757 TCACATTGAACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* *
7776 TCAACATTGAACTTGCCTTAA
1 TC-ACATTGAACTTTCC-CAA
*
7797 TTCACATTCAACTTTCCCAA
1 -TCACATTGAACTTTCCCAA
* * *
7817 TCGACATTGAACTTGCCTTGAT
1 TC-ACATTGAACTTTCC--CAA
***
7839 TCACATCCCACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* * *
7858 TTCACATTGAACTTGCCTTGAT
1 -TCACATTGAACTTTCC--CAA
* * *
7880 TCACATTCAAATTTCCTAA
1 TCACATTGAACTTTCCCAA
* *
7899 TTCACATTGAACTTGCCTTAA
1 -TCACATTGAACTTTCC-CAA
* * *
7920 TTCTACATTCAAATTTCCTAA
1 -TC-ACATTGAACTTTCCCAA
* *
7941 TTCACATTGAACTTGCCTTAA
1 -TCACATTGAACTTTCC-CAA
*
7962 TTCACATTCAACTTTCCCAA
1 -TCACATTGAACTTTCCCAA
* * *
7982 TTCACATTGAACTTGCCTTGAT
1 -TCACATTGAACTTTCC--CAA
*
8004 TCACA--CAACTTTCCCAA
1 TCACATTGAACTTTCCCAA
* *
8021 TTCACATTGAACTTGCCTTCAT
1 -TCACATTGAACTTTCC--CAA
* *
8043 TCACATTCAACTTTTCCAA
1 TCACATTGAACTTTCCCAA
*
8062 TTGACATTGAACTT
1 -TCACATTGAACTT
8076 GCCTTGATTC
Statistics
Matches: 224, Mismatches: 55, Indels: 41
0.70 0.17 0.13
Matches are distributed among these distances:
17 1 0.00
18 5 0.02
19 15 0.07
20 98 0.44
21 85 0.38
22 20 0.09
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (19 bp):
TCACATTGAACTTTCCCAA
Found at i:7812 original size:41 final size:41
Alignment explanation
Indices: 7755--8131 Score: 537
Period size: 41 Copynumber: 9.2 Consensus size: 41
7745 TACGCGGCAT
* *
7755 ATTCACATTGAACTTTCCCAA-TCAACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTC-ACATTGAACTTGCCTTG
7796 ATTCACATTCAACTTTCCCAA-TCGACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTC-ACATTGAACTTGCCTTG
* *
7837 ATTCACATCCCACTTTCCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
* * *
7878 ATTCACATTCAAATTTCCTAATTCACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
* * *
7919 ATTCTACATTCAAATTTCCTAATTCACATTGAACTTGCCTTA
1 ATTC-ACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
7961 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
*
8002 ATTCACA--CAACTTTCCCAATTCACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
* *
8041 ATTCACATTCAACTTTTCCAATTGACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
** * * *
8082 ATTCTTATTCAACTTTCCAAATTGACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
8123 ATTCACATT
1 ATTCACATT
8132 AGCCCTTAAT
Statistics
Matches: 308, Mismatches: 24, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
39 38 0.12
41 227 0.74
42 43 0.14
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (41 bp):
ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
Done.