Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019401.1 Corchorus olitorius cultivar O-4 contig19434, 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: 52424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7819 original size:2 final size:2
Alignment explanation
Indices: 7812--7838 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7802 CTCGATACAA
7812 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
7839 GACACACACA
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:7845 original size:2 final size:2
Alignment explanation
Indices: 7840--7866 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7830 ATATATATAG
7840 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
7867 TACATAATAT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12490 original size:36 final size:36
Alignment explanation
Indices: 12443--12545 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
12433 TAAGCGCTTT
* *
12443 GATTTGTTACTTCCACTGAATCAACAAAACCCATTA
1 GATTTGTTACTTCCACTGAATGATCAAAACCCATTA
* *
12479 GATTTGTTACTTCGACT-AGATGTTCAAAACCCATTA
1 GATTTGTTACTTCCACTGA-ATGATCAAAACCCATTA
* * *
12515 GATTGGTTAGTTCCATTGAATGATCAAAACC
1 GATTTGTTACTTCCACTGAATGATCAAAACC
12546 TATATTATCT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 1 0.02
36 54 0.96
37 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (36 bp):
GATTTGTTACTTCCACTGAATGATCAAAACCCATTA
Found at i:13815 original size:23 final size:23
Alignment explanation
Indices: 13785--13831 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
13775 CCTAATTAAA
13785 TCTACCTCAAGTTTAGCCCCTAG
1 TCTACCTCAAGTTTAGCCCCTAG
13808 TCTACCTCAAGTTTAGCCCCTAG
1 TCTACCTCAAGTTTAGCCCCTAG
13831 T
1 T
13832 TATAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (23 bp):
TCTACCTCAAGTTTAGCCCCTAG
Found at i:18388 original size:23 final size:23
Alignment explanation
Indices: 18362--18408 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
18352 TTACTACTTT
*
18362 TATTATCAAACCAATTATATGTA
1 TATTATCAAACCAATTATAAGTA
18385 TATTATCAAACCAATTATAAGTA
1 TATTATCAAACCAATTATAAGTA
18408 T
1 T
18409 CAAGAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (23 bp):
TATTATCAAACCAATTATAAGTA
Found at i:20678 original size:332 final size:326
Alignment explanation
Indices: 19428--21371 Score: 1853
Period size: 330 Copynumber: 5.9 Consensus size: 326
19418 CCAAAAAAAT
* * *
19428 TTAATTTTTAATTAAATTGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
1 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGT
* * ** *
19493 GGCTGATAAATGGTTAGATGAATATAGATATTTCAAGGAGTTTTC-GCACAAAAAAATCATGCAA
65 GACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG-TCTCGGCAC-AAAAAATCATGCAA
* * * **
19557 AACTAAGCC-GGCTCCGGGAACGCGTTTTTAGCCGAAAACCGTGAT--GTAACACGATTTCGGCT
128 AACTAAGCCGGGGTCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGAGT-ACACGATTTCGGCT
* * * * *
19619 AAATTTTTGCAAAAATTGACCCGAAAGATTTTCCCTCAATTTCTAGCGAAAATACTCATAAAA-A
192 AAAATTTTGCAAAAATT-ACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATA
* * * ** * *
19683 TATATAATTCAACACCAAAAAAATTGAAAGCCTTTTTCACGCTTCCAATATCGTTTTTTCAATTT
256 TATATAATTCAACACCAAAAAGATTGAAGGAC-TTTTCACGCTTTTAATATCG--TTTTCCATAT
*
19748 TATTTCTAAA
318 T-TTTCTGAA
* * * *
19758 TTAATTTCTGATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTAAAT--ACG-G
1 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAATGTG
* * * * * *
19820 -CTGAGATTTGGTTACATGAATAAAGTTATATTTTAAGGAATCTTGGCGCAAAAAATCATGCAAA
66 ACTGAGATTTGGTTAGATGAATATAG--ATATTTCAAGGAGTCTCGGCACAAAAAATCATGCAAA
** *
19884 ACTGGGCAGGGG-CTCCGAAACGCGTTTTTAGCAAAAAAAAAAAACCGTGATG-GTACACGATTT
129 ACTAAGCCGGGGTC-CCGAAACGCGTTTTTAGC------AAAAAACCGTGATGAGTACACGATTT
* * * * *
19947 CGGCTAAAGTTTTACAAAAATTGACCCGAAATATTTTT-CTCATTTTTTAGCCTACAATACAT-A
187 CGGCTAAAATTTTGCAAAAATT-ACCCGAAAAATTTTTCCTCAATTTTTAG-CTAAAATAC-TCA
* * * * * *
20010 TAAAAAATATATAATTCAACACCAAAAACATTGAAAGACTTCTCACGCTTCTAATATTGTTTTTC
249 TAAAATATATATAATTCAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCG-TTTTC
* *
20075 C-TATTTTTTTCAAA
313 CATATTTTTCT-GAA
* * ** * * *
20089 TTAATTTATAATCAAATTAAGAACATGATTCAAATGCTCATAAAAACAAATCCTTAAATCCAATG
1 TTAATTTCTAATTAAATCGA-AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATG
* * * * * *
20154 TGACTAAGATTAGGTTAGATGACTATAGATATTTCAAGGAGTTTTGCCACAAAAAATCATGCAAA
64 TGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATGCAAA
* * ** * ** *
20219 ACTTACCCGGGACCCCGGATTGCGTTTTTAGCAAAAAAACTGTGATG-GTACACGATTTCGGCTA
129 ACTAAGCCGGGGTCCCGAAACGCGTTTTTAGC-AAAAAACCGTGATGAGTACACGATTTCGGCTA
* * * * * *
20283 AAATTTTGCAAAAATAGACCTGAAATATTTTTCCTCAATTTTTAGCCACAATACTCGTAAAATAT
193 AAATTTTGCAAAAAT-TACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATAT
* *
20348 ATATAATTCAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTCCATATTTTT
257 ATATAATTCAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTCCATATTTTT
20413 CTGAA
322 CTGAA
* **
20418 TTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCAATAAATTCAAATG
1 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA-TC-AATG
* * * * * * *
20483 TGACTGAGATTTGATTAGTTGAGTATAGTTATTTCAAGGAGTATCGGCACCAAAAATCATGGAAA
64 TGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATGCAAA
* * * *
20548 ACTAAGCCGGGGTCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTCCAGC
129 ACTAAGCCGGGGTCCCGAAACGCGTTTTTAGCAAAAAACCGTGAT-G--AGTACACGATTTCGGC
* *
20613 TAAAATTTTGTAGAAAATTACCTGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAT
191 TAAAATTTTGCA-AAAATTACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAT
* * * * ** *
20678 ATATATAATTTAACGCCAAAAATATTGCAGGACTTTTCATACTTTTAATATCGTTTTTCATA-TT
255 ATATATAATTCAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTCCATATTT
*
20742 TTCAGAA
320 TTCTGAA
* ** * *
20749 TTAATTTCTAAACTAAATCGTTACAAGATTTAGATGCTCGTATAAACAAATCCTTAAATGCAATG
1 TTAATTTCT-AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATG
* * * *
20814 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAA
64 TGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATGCAAA
* * * *
20879 ACTGAA-CCGGAGCCCCAAAACGCGTTTTTAGCAAAAAACCGTGATGGAGTATACGATTTCGGCT
129 ACT-AAGCCGGGGTCCCGAAACGCGTTTTTAGCAAAAAACCGTGAT-GAGTACACGATTTCGGCT
* *
20943 AAAATTTTGCAAAAAAATTACCCGAAAAATATTTT-CTCAATTTTTGGCTAAAATACTCATGAAA
192 AAAATTTTGC--AAAAATTACCCGAAAAAT-TTTTCCTCAATTTTTAGCTAAAATACTCATAAAA
* * * *
21007 TATATATAATTTAACACCAAAAAGGTTGAAGGA-TTTTCGA-GCTTTTCATATCGTTTTTCATAT
254 TATATATAATTCAACACCAAAAAGATTGAAGGACTTTTC-ACGCTTTTAATATCGTTTTCCATA-
21070 TTTTTCTGAA
317 TTTTTCTGAA
* * * * * **
21080 TTAATTTCTAATTGAATCGAAACAAAATTTAGATACTCGTAAAAACAAATCCATAAATGCAATAC
1 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGT
* * * * * * *
21145 GATTGAGATTTGATTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAA
65 GACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATGCAAAA
* *** * * * * *
21210 CTGA-CACGGGGCTTTGGGACAC-CTTTTTTTTGCCAAAAACCGTGATGTATTTTACACGATTTC
130 CTAAGC-CGGGG--TCCCGAAACGC-GTTTTTAGCAAAAAACCGTGATG-A--GTACACGATTTC
* * * * * * *
21273 AGCTAACATTTTGCAAAAAATGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAA
188 GGCTAAAATTTTGC-AAAAATTACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAA
* * * *
21338 AAAATATATAATTCAACGCCATAAATATTGAAGG
252 AATATATATAATTCAACACCAAAAAGATTGAAGG
21372 CTTGTCTTTG
Statistics
Matches: 1353, Mismatches: 210, Indels: 99
0.81 0.13 0.06
Matches are distributed among these distances:
325 20 0.01
326 24 0.02
327 34 0.03
328 44 0.03
329 160 0.12
330 366 0.27
331 174 0.13
332 238 0.18
333 159 0.12
334 56 0.04
335 56 0.04
336 2 0.00
337 20 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (326 bp):
TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAATGTG
ACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCACAAAAAATCATGCAAAAC
TAAGCCGGGGTCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGAGTACACGATTTCGGCTAAAA
TTTTGCAAAAATTACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATAT
AATTCAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTCCATATTTTTCTGA
A
Found at i:20736 original size:662 final size:652
Alignment explanation
Indices: 19451--21369 Score: 2057
Period size: 662 Copynumber: 2.9 Consensus size: 652
19441 AAATTGAAAT
*
19451 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-GATAAATGGTTAGATGAA
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAGAT-TA-GGTTAGATGAA
* *
19515 TATAGATATTTCAAGGAGTTTT-CGCACAAAAAAATCATGCAAAACTAAGCCGG-CTCCGGGAAC
64 TATAGATATTTCAAGGAGTTTTGC-CAC-AAAAAATCATGCAAAACTAAACCGGAC-CCCGGAAC
** * *
19578 GCGTTTTTAGCCGAAAACCGTGAT-GTAACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCG
126 GCGTTTTTAGCAAAAAACCGTGATGGT-ACACGATTTCGGCTAAAATTTTGCAAAAATAGACCCG
* * * * *
19642 AAAGATTTTCCCTCAATTTCTAGCGAAAATACTCATAAAA-ATATATAATTCAACACCAAAAAAA
190 AAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACACCAAAAAGA
* * ** * * * *
19706 TTGAAAGCCTTTTTCACGCTTCCAATATCGTTTTTTCAATTTTATTTCTAAATTAATTTCTGATT
255 TTGAAGGAC-TTTTCACGCTTTTAATATCG--TTTTCCATATT-TTTCTGAATTAATTTCTAATT
* * * *
19771 AAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTAAA-T--ACGG-CTGAGATTTGGT
316 AAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCATAAATTCAATGGACTGAGATTTGAT
* * * * * * *
19832 TACATGAATAAAGTTATATTTTAAGGAATCTTGGCGCAAAAAATCATGCAAAACTGGGCAGGGG-
381 TAGATGAATATAG-T-TATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGT
* * *
19896 CTCCGAAACGCGTTTTTAGCAAAAAAAAAAAACCGTGATG--GTACACGATTTCGGCTAAAGTTT
444 C-CCGAAACGCGTTTTTAGC------CAAAAACCGTGATGTTGTACACGATTTCAGCTAAAATTT
* * * * *
19959 TACAAAAATTGACCCGAAATATTTTT-CTCATTTTTTAGCCTACAATACAT-ATAAAAAATATAT
502 TGCAAAAATT-ACCTGAAAAATTTTTCCTCAATTTTTAG-CTAAAATAC-TCATAAAAAATATAT
* * * * *
20022 AATTCAACACCAAAAACATTGAAAGACTTCTCACGCTTCTAATATTGTTTTTCCTATTTTTTTCA
564 AATTCAACGCCAAAAATATTGAAAGACTTCTCACACTTCTAATATCGTTTTT-C-A-TATTTTCA
*
20087 -AATTAATTTATAATC-AAATTAAG-AAC
626 GAATTAATTTATAAACTAAA-T-AGTAAC
* * * * *
20113 ATGATTCAAATGCTCATAAAAACAAATCCTTAAATCCAATGTGACTAAGATTAGGTTAGATGACT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-AGATTAGGTTAGATGAAT
* * **
20178 ATAGATATTTCAAGGAGTTTTGCCACAAAAAATCATGCAAAACTTACCCGGGACCCCGGATTGCG
65 ATAGATATTTCAAGGAGTTTTGCCACAAAAAATCATGCAAAACTAAACC-GGACCCCGGAACGCG
* *
20243 TTTTTAGCAAAAAAACTGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATAGACCTGAAA
129 TTTTTAGC-AAAAAACCGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATAGACCCGAAA
* * * *
20308 TATTTTTCCTCAATTTTTAGCCACAATACTCGTAAAATATATATAATTCAACTCCAAAAAGATTG
193 AATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACACCAAAAAGATTG
* *
20373 GAGGACTTTTCACGCTTTTAATATCGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCAA
258 AAGGACTTTTCACGCTTTTAATATCGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCGA
* * *
20438 AACAAGATTCAGATGCTCGTAAAAACAAATCAATAAATTCAAATGTGACTGAGATTTGATTAGTT
323 AACAAGATTTAGATGCTCGTAAAAACAAATCCATAAATTC-AATG-GACTGAGATTTGATTAGAT
* * * * * *
20503 GAGTATAGTTATTTCAAGGAGTATCGGCACCAAAAATCATGGAAAACTAAGCCGGGGTCCCGAAA
386 GAATATAGTTATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGTCCCGAAA
* * *
20568 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTCCAGCTAAAATTTTGTAGAAAATTA
451 CGCGTTTTTAGCCAAAAACCGTGAT-GTT-GTACACGATTTCAGCTAAAATTTTGCA-AAAATTA
* *
20633 CCTGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAAA
513 CCTGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAA
* * * * * *
20698 AATATTGCAGGACTTTTCATACTTTTAATATCGTTTTTCATATTTTCAGAATTAATTTCTAAACT
578 AATATTGAAAGACTTCTCACACTTCTAATATCGTTTTTCATATTTTCAGAATTAATTTATAAACT
* *
20763 AAATCGTTAC
643 AAATAGTAAC
* * * *
20773 AAGATTTAGATGCTCGTATAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAAT
1 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-AGATTAGGTTAGATGAAT
* * * * * * **
20838 ATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAACCGGAGCCCCAAAACGCG
65 ATAGATATTTCAAGGAGTTTTGCCACAAAAAATCATGCAAAACTAAACCGGA-CCCCGGAACGCG
* * *
20903 TTTTTAGCAAAAAACCGTGATGGAGTATACGATTTCGGCTAAAATTTTGCAAAAAAATTACCCGA
129 TTTTTAGCAAAAAACCGTGAT-G-GTACACGATTTCGGCTAAAATTTTGCAAAAATA-GACCCGA
* * * * *
20968 AAAATATTTT-CTCAATTTTTGGCTAAAATACTCATGAAATATATATAATTTAACACCAAAAAGG
191 AAAAT-TTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACACCAAAAAGA
* * *
21032 TTGAAGGA-TTTTCGA-GCTTTTCATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTGA
255 TTGAAGGACTTTTC-ACGCTTTTAATATCGTTTTCCATA-TTTTTCTGAATTAATTTCTAATTAA
* * * * *
21095 ATCGAAACAAAATTTAGATACTCGTAAAAACAAATCCATAAATGCAATACGATTGAGATTTGATT
318 ATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCATAAATTCAAT-GGACTGAGATTTGATT
* * *
21160 AGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA-CACGGGGCTT
382 AGATGAATATAGTTATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGC-CGGGG--T
*** * * * * *
21224 TGGGACAC-CTTTTTTTTGCCAAAAACCGTGATGTATTTTACACGATTTCAGCTAACATTTTGCA
444 CCCGAAACGC-GTTTTTAGCCAAAAACCGTGATG--TTGTACACGATTTCAGCTAAAATTTTGC-
* * * *
21288 AAAAATGA-CTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
505 AAAAATTACCT-GAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTC
*
21352 AACGCCATAAATATTGAA
569 AACGCCAAAAATATTGAA
21370 GGCTTGTCTT
Statistics
Matches: 1058, Mismatches: 158, Indels: 81
0.82 0.12 0.06
Matches are distributed among these distances:
658 12 0.01
659 24 0.02
660 190 0.18
661 158 0.15
662 321 0.30
663 236 0.22
664 94 0.09
665 3 0.00
666 20 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (652 bp):
AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAGATTAGGTTAGATGAATA
TAGATATTTCAAGGAGTTTTGCCACAAAAAATCATGCAAAACTAAACCGGACCCCGGAACGCGTT
TTTAGCAAAAAACCGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATAGACCCGAAAAAT
TTTTCCTCAATTTTTAGCCAAAATACTCATAAAATATATATAATTCAACACCAAAAAGATTGAAG
GACTTTTCACGCTTTTAATATCGTTTTCCATATTTTTCTGAATTAATTTCTAATTAAATCGAAAC
AAGATTTAGATGCTCGTAAAAACAAATCCATAAATTCAATGGACTGAGATTTGATTAGATGAATA
TAGTTATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGTCCCGAAACGCGT
TTTTAGCCAAAAACCGTGATGTTGTACACGATTTCAGCTAAAATTTTGCAAAAATTACCTGAAAA
ATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAATATTGA
AAGACTTCTCACACTTCTAATATCGTTTTTCATATTTTCAGAATTAATTTATAAACTAAATAGTA
AC
Found at i:27368 original size:15 final size:16
Alignment explanation
Indices: 27342--27372 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
27332 TCTTTTTTTC
27342 AACAATTCCCATCTTG
1 AACAATTCCCATCTTG
27358 AACAA-TCCCATCTTG
1 AACAATTCCCATCTTG
27373 TTGCTGGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.29
Consensus pattern (16 bp):
AACAATTCCCATCTTG
Found at i:27979 original size:3 final size:3
Alignment explanation
Indices: 27938--27963 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27928 ATCTCCCCTT
27938 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
27964 GTTTCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:32932 original size:19 final size:19
Alignment explanation
Indices: 32904--32940 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
32894 CTGTTTAGCA
32904 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
32923 ACTGTGCAGATTAGATTA
1 ACTGTACAGATGAGATTA
32941 GGTATTGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:34444 original size:30 final size:29
Alignment explanation
Indices: 34371--34446 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
34361 ACTTGTAGTG
* *
34371 TTTGGACGTTTTGCCCTATGAACTTCAAT
1 TTTGGACGTTTTGCCCCATAAACTTCAAT
**
34400 TTTGGATATTTTGCCCCATAAACTTCAAT
1 TTTGGACGTTTTGCCCCATAAACTTCAAT
34429 TTTGGGACGTTTTGCCCC
1 TTT-GGACGTTTTGCCCC
34447 CTCAAACTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 28 0.70
30 12 0.30
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCATAAACTTCAAT
Found at i:34589 original size:32 final size:30
Alignment explanation
Indices: 34533--34610 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 30
34523 CGTTAGTCTG
*
34533 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAATTC
34563 AGGGGGCAAAATCATGT-CCAAAATTGAAATTC
1 AGGGGGCAAAA-C--GTCCCAAAATTGAAATTC
* *
34595 AGTGGGTAAAACGTCC
1 AGGGGGCAAAACGTCC
34611 AAACGCTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 2 0.05
30 12 0.29
31 2 0.05
32 23 0.56
33 2 0.05
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAATTC
Found at i:35640 original size:14 final size:13
Alignment explanation
Indices: 35615--35645 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
35605 TATTATTCTC
35615 ATAATAATAATTA
1 ATAATAATAATTA
35628 ATAATAGATAATTA
1 ATAATA-ATAATTA
35642 ATAA
1 ATAA
35646 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
ATAATAATAATTA
Found at i:42383 original size:5 final size:5
Alignment explanation
Indices: 42373--42401 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
42363 TTTGGCTCCC
42373 TTATT TTATT TTATT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTAT
42402 CATTACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:43650 original size:24 final size:24
Alignment explanation
Indices: 43613--43664 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
43603 GCCAAGTGCA
43613 TTTATCTGGAAAAAAAGGTACAAT
1 TTTATCTGGAAAAAAAGGTACAAT
43637 TTTATACTGG-AAAAAAGGTACAAT
1 TTTAT-CTGGAAAAAAAGGTACAAT
43661 TTTA
1 TTTA
43665 AAGAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (24 bp):
TTTATCTGGAAAAAAAGGTACAAT
Found at i:43766 original size:134 final size:133
Alignment explanation
Indices: 43527--43787 Score: 486
Period size: 134 Copynumber: 2.0 Consensus size: 133
43517 ATTGATAATT
* *
43527 TTTTAAAGAAATATTCCAGAATTGTAATAATACAAATGGTGTGTCCTTCTAATTACAGAGAATCC
1 TTTTAAAGAAATATTACACAATTGTAATAATACAAATGGTGTGTCCTTCTAATTACAGAGAATCC
43592 AGTCTCTTGAAGCCAAGTGCATTTATCTGGAAAAAAAGGTACAATTTTATACTGGAAAAAAGGTA
66 AGTCTCTTGAAGCCAAGTGCATTTATCTGGAAAAAAAGGTACAATTTTATACTGGAAAAAAGGTA
43657 CAA
131 CAA
*
43660 TTTTAAAGAAATATTATACAATTTGTAATAATACAAATGGTGTGTCCTTCTAATTACAGAGAATC
1 TTTTAAAGAAATATTACACAA-TTGTAATAATACAAATGGTGTGTCCTTCTAATTACAGAGAATC
43725 CAGTCTCTTGAAGCCAAGTGCATTTATCTGGAAAAAAAGGTACAATTTTATACTGGAAAAAAG
65 CAGTCTCTTGAAGCCAAGTGCATTTATCTGGAAAAAAAGGTACAATTTTATACTGGAAAAAAG
43788 ATGAAAACGA
Statistics
Matches: 124, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
133 18 0.15
134 106 0.85
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (133 bp):
TTTTAAAGAAATATTACACAATTGTAATAATACAAATGGTGTGTCCTTCTAATTACAGAGAATCC
AGTCTCTTGAAGCCAAGTGCATTTATCTGGAAAAAAAGGTACAATTTTATACTGGAAAAAAGGTA
CAA
Found at i:43929 original size:21 final size:21
Alignment explanation
Indices: 43900--43957 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
43890 TGTTTTGAGT
43900 AAGGA-AGAAGCCAAATGG-A
1 AAGGAGAGAAGCCAAATGGAA
* *
43919 GAGAGAGAGAAGCCGAATGGAA
1 AAG-GAGAGAAGCCAAATGGAA
*
43941 AAGGAGAGAAGCTAAAT
1 AAGGAGAGAAGCCAAAT
43958 TACAACAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 24 0.77
22 3 0.10
ACGTcount: A:0.50, C:0.09, G:0.34, T:0.07
Consensus pattern (21 bp):
AAGGAGAGAAGCCAAATGGAA
Found at i:44559 original size:21 final size:21
Alignment explanation
Indices: 44510--44550 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44500 GATTCACACA
*
44510 GATCGAAACGGCCAGGAGGGT
1 GATCGAAACTGCCAGGAGGGT
44531 GATCGAAACTGCCAGGAGGG
1 GATCGAAACTGCCAGGAGGG
44551 ATCAGGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.41, T:0.10
Consensus pattern (21 bp):
GATCGAAACTGCCAGGAGGGT
Found at i:45841 original size:21 final size:21
Alignment explanation
Indices: 45815--45870 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
45805 AGGATCCGAA
*
45815 GAAGAAGAAGAGGAAGAAACC
1 GAAGAAGAAGAAGAAGAAACC
* **
45836 GAAGAAGACGAAGAAGATTCC
1 GAAGAAGAAGAAGAAGAAACC
*
45857 GAAGAAGAACAAGA
1 GAAGAAGAAGAAGA
45871 GCAAGAACAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.55, C:0.11, G:0.30, T:0.04
Consensus pattern (21 bp):
GAAGAAGAAGAAGAAGAAACC
Done.