Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019701.1 Corchorus olitorius cultivar O-4 contig19734, 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: 44880
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:605 original size:232 final size:231
Alignment explanation
Indices: 194--646 Score: 753
Period size: 232 Copynumber: 2.0 Consensus size: 231
184 CCGAAGGACT
* * * * *
194 CAATTCTTAGCTGAAATACTCATAGAGATATATATATTTCAACGCCAAAAATATTGAAGGTTTTT
1 CAATTCTTAGCTGAAATACTCAAAGAAATATATATAATTCAACACAAAAAATATTGAAGGTTTTT
* * * *
259 TTACGCTTCTAATATCATTTTTCTTACTTTTTCCGAATAAATTTCTAATTAAGTTGAAATAAGAT
66 TTACGCTTCTAATATCATTTTTCGTACTTTTTCCGAATAAATTTATAATTAAATTGAAACAAGAT
* *
324 ATAGATGCTCGTAAAAACAAATTCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGA
131 ATAGATACTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGA
*
389 CATTTGAAGGAGTCTCTACGCCGAAAGATATTTCCA
196 CATTTGAAGGAGTCTCGACGCCGAAAGATATTTCCA
*
425 CAATTTTTAGCTGAAATACTCAAAGAAATATATATAATTCAACACAAAAAAATATTGAAGGTTTT
1 CAATTCTTAGCTGAAATACTCAAAGAAATATATATAATTCAACAC-AAAAAATATTGAAGGTTTT
490 TTTACGCTTCTAATATCATTTTTCGTACTTTTTCCGAATAAATTTATAATTAAATTGAAACAAGA
65 TTTACGCTTCTAATATCATTTTTCGTACTTTTTCCGAATAAATTTATAATTAAATTGAAACAAGA
* *
555 TTTAGATACTCGTAAAAATAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAG
130 TATAGATACTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAG
*
620 ATATTTGAAGGAGTCTCGACGCCGAAA
195 ACATTTGAAGGAGTCTCGACGCCGAAA
647 ATCATGCAGA
Statistics
Matches: 205, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
231 40 0.20
232 165 0.80
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (231 bp):
CAATTCTTAGCTGAAATACTCAAAGAAATATATATAATTCAACACAAAAAATATTGAAGGTTTTT
TTACGCTTCTAATATCATTTTTCGTACTTTTTCCGAATAAATTTATAATTAAATTGAAACAAGAT
ATAGATACTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGA
CATTTGAAGGAGTCTCGACGCCGAAAGATATTTCCA
Found at i:1582 original size:334 final size:334
Alignment explanation
Indices: 409--1870 Score: 2124
Period size: 334 Copynumber: 4.4 Consensus size: 334
399 AGTCTCTACG
* * * *
409 CCGAAAGATATTTCCACAATTTTTAGCTGAAATACTCAAAGAAATATATATAATTCAACACAAAA
1 CCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATATATAATTCAACAC-CAA
* *
474 AAATATTGAAGGTTTTTTTACGCTTCTAATATCATTTTTCGTACTTTTTCCGAATAAATTTATAA
65 AAATATTGAAGGTTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTTCCGAATAAATTTCTAA
* *
539 TTAAATTGAAACAAGATTTAGATACTCGTAAAAATAAATCCTTAAATGCAATGTGGCTGAGATTT
130 TTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTT
604 GATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATGCAGAACTGAGTCGGGG
195 GATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATGCAGAACTGAGTCGGGG
669 CCCCGAAACGCGTTTTTAGCAAAAAAATCGTGATC-G-T-G-A-ACGATTTCGGCTAAAATTTTG
260 CCCCGAAACGCGTTTTTAGCAAAAAAATCGTGA-CGGTTAGTACACGATTTCGGCTAAAATTTTG
729 CAAAAATTGAC
324 CAAAAATTGAC
* *
740 CCGAAAGATATTTCCTCAATTTTTAGATGAAATACTCATAGAGATATATATAATTCAACGCCAAA
1 CCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATATATAATTCAACACCAAA
* ** * * *
805 AATATTGAAGGGTTTTTTACGCTTCTAATATTGTTTTACCTACTTTTTCCGAATTAATTTCAAAT
66 AATATTGAAGGTTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTTCCGAATAAATTTCTAAT
*
870 TAAATTGATACAAGATTTAGATGCTCGTAAAAA-AATATCCTTAAATGCAATGTGGCTGAGATTT
131 TAAATTGAAACAAGATTTAGATGCTCGTAAAAACAA-ATCCTTAAATGCAATGTGGCTGAGATTT
*
934 GATTAGATGAATATAGATATTTGAAGGAGTCTTGACGCCGAAAATCATGCAGAACTGAGTCGGGG
195 GATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATGCAGAACTGAGTCGGGG
* *
999 CCCCGAAACGCGTTTTTAGC-AAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTCTGC
260 CCCCGAAACGCGTTTTTAGCAAAAAAATCGTGACGGTTAGTACACGATTTCGGCTAAAATTTTGC
* *
1063 AAAAAATGAT
325 AAAAATTGAC
* * *
1073 CCGAAAAATTTTTCCTCAATTTTT-GCCT-AATATACTCGT-GTA-ATATATATAATTTC-ACAC
1 CCGAAAGATATTTCCTCAATTTTTAG-CTGAA-ATACTCATAG-AGATATATATAA-TTCAACAC
* ** * * * * * *
1133 C-AAAATGATTGGAGGACTTTTCACACTTTTCATATCATTTTTCATTAATTTTTCCGAATAAATT
62 CAAAAAT-ATTGAAGGTTTTTTTACGCTTCTAATATCATTTTTC-CTACTTTTTCCGAATAAATT
* * * * * * *
1197 TCTAATTAAATCGAAACAACATTCAGATGCTCGTAAAAACAAATACTTAAATGAAATTTGACTGA
125 TCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGA
* *
1262 GATTTGACTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATGCAGAACTGTGT
190 GATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATGCAGAACTGAGT
* *
1327 CGGGGCCCCGAAACGCGTTTTTAGCAAAGAAATCGTGACGGTTAGTACACGATTTAGGCTAAAAT
255 CGGGGCCCCGAAACGCGTTTTTAGCAAAAAAATCGTGACGGTTAGTACACGATTTCGGCTAAAAT
* *
1392 TTAGCAAAATTTGAC
320 TTTGCAAAAATTGAC
* *
1407 CCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATATATATTTCAACGCCAAA
1 CCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATATATAATTCAACACCAAA
*
1472 AATATTGAAGGTTTTTTTACGCTTCAAATATCATTTTTCCTACTTTTTCCGAATAAATTTCTAAT
66 AATATTGAAGGTTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTTCCGAATAAATTTCTAAT
* * *
1537 TAAGTTGAAATAAGATATAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTG
131 TAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTG
* *
1602 ATTAGATGAATATAGATATTTGAAGGAGTCTCAACGCCGAAAATCATGCAAAACTGAGTCGGGGC
196 ATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATGCAGAACTGAGTCGGGGC
* * *
1667 CCCGAAACGCGTTTTTAGCAAAAAAAAATCGTGATGGTTAGTATACGATTTCGCCT-AAATTTTG
261 CCCGAAACGCGTTTTTAGC--AAAAAAATCGTGACGGTTAGTACACGATTTCGGCTAAAATTTTG
1731 CAAAAATTGAC
324 CAAAAATTGAC
* * *
1742 CCAAAAGGTATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATATCTAATTCTAACACCAA
1 CCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATATATAATTC-AACACCAA
* * * * *
1807 AAATATTGAAAGTTTTTTTACTCTTCTAATATTATTTTTTCTACTTTTTCCGATTAAATTTCTA
65 AAATATTGAAGGTTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTTCCGAATAAATTTCTA
1871 CTCCATCCGT
Statistics
Matches: 1002, Mismatches: 106, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
329 15 0.01
330 204 0.20
331 62 0.06
332 45 0.04
333 220 0.22
334 242 0.24
335 114 0.11
336 100 0.10
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (334 bp):
CCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATATATAATTCAACACCAAA
AATATTGAAGGTTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTTCCGAATAAATTTCTAAT
TAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTG
ATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATGCAGAACTGAGTCGGGGC
CCCGAAACGCGTTTTTAGCAAAAAAATCGTGACGGTTAGTACACGATTTCGGCTAAAATTTTGCA
AAAATTGAC
Found at i:6882 original size:51 final size:51
Alignment explanation
Indices: 6805--6902 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
6795 ATGTCATGTC
6805 TTACGTAAGTATTTAACAAATCCCTTGTTAAAACTAAGACAACAAAATTAA
1 TTACGTAAGTATTTAACAAATCCCTTGTTAAAACTAAGACAACAAAATTAA
* *
6856 TTACGTAAGTATTTAACATATTCCTTGTTAAAACTAAGACAACAAAA
1 TTACGTAAGTATTTAACAAATCCCTTGTTAAAACTAAGACAACAAAA
6903 CAAAATTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (51 bp):
TTACGTAAGTATTTAACAAATCCCTTGTTAAAACTAAGACAACAAAATTAA
Found at i:16612 original size:16 final size:16
Alignment explanation
Indices: 16591--16625 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
16581 ATGGTCAAAC
16591 TCTTTCTTACTACAAT
1 TCTTTCTTACTACAAT
16607 TCTTTCTTACTACAAT
1 TCTTTCTTACTACAAT
16623 TCT
1 TCT
16626 AAATCAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (16 bp):
TCTTTCTTACTACAAT
Found at i:20621 original size:328 final size:328
Alignment explanation
Indices: 19997--22889 Score: 2503
Period size: 330 Copynumber: 8.7 Consensus size: 328
19987 GGGAGGGAGT
* * * * ** * * *
19997 AATT-ATTCGGAAAAGTAGGAAAAACGATATTAGAAGCGTAAAAACCCCTTCAATATTTTTTGCG
1 AATTAATTCAGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCG
* * ** *
20061 TTAAATTATAT-T-TTATTATGAGTATTTTAGCCAAAAATTGAGGAATTATCTTTCCGGTCAATT
66 TTGAATTATATATATT-TTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATT
* * * * *
20124 CTTGCAAAATTTTAACCGAAATCGTGTAATAATCATCACGGTCTTTGGCTAAAAACGCGTTCCAG
130 TTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTT-C-G
* * * * *
20189 GGTCCCGAGTCAGTTTTGCATGATTTTTGGCGCTAAGACTACTTGAGATATCCATATTCATCTAA
193 GGACCCGACTCAGTTTTGCATGATTTTTGGCGC-AAGACTCCTTGAAATATCTATATTCATCTAA
* * **
20254 TCAAATATCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTATATTT
257 TCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
*
20319 AATTAAA
322 AATTAGA
* * * * * * *
20326 AATTAATTCAGAAAAATATGAAAAACGTTATGAAAAGCGTGAAAAATTCTCCAATCTTTTTGTCA
1 AATTAATTCAGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCG
* * * * * * *
20391 TTAAATTATCTATATTTCATGAGTATTTTAGCCAAAAATTAAGGAAAAAT-TTTCTGGTGC-TTT
66 TTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGT-CAATT
20454 TTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACTGGTTTTT-GCTAAAAACGCGTCTCG
130 TTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCAC-GGTTTTTGGCTAAAAACGCGT-TCG
*** * * * *
20518 GGATTTGACTCAGTTTTGCAT-ATTTTTGGAGTCGAGACTCCTTGAAATATATATATTCATCTGA
193 GGACCCGACTCAGTTTTGCATGATTTTTGGCG-CAAGACTCCTTGAAATATCTATATTCATCTAA
* * * *
20582 TCAAATTTCAGCCACATTGCATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTCCGATTT
257 TCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
20647 AATTAGA
322 AATTAGA
* * * *
20654 AATTAATTCAGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGAG
1 AATTAATTCAGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCG
* * * * * *
20719 TTGAATTATATATATTTTATGAGTATTTTAGATAAAAATCGAGGAAAACTATTTCTGGTCAGTTT
66 TTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATTT
** * * * * ** * *
20784 TTTAAAAATATTAGCCGAAATCGTGTACGTTAGTCGAACTCACAGTTTTTGGCTAAATTCACATT
131 TTGCAAAATTTTAGCCGAAATCGTGTA--TTA-AC-CA-TCACGGTTTTTGGCTAAAAACGCGTT
** * * ** * * *
20849 CCGGGGACCCGGTTTCAGTGTTCCATGATTTTTTTCGCCGAGATTCCTTGAAATATCTATATTAA
191 -C-GGGACCC-GACTCAGTTTTGCATGATTTTTGGCG-CAAGACTCCTTGAAATATCTATATTCA
* * * *** *
20914 TCTAACCAAATCTCATCCACATTGAATTTAAGAATTTGTAAAATA--AGCATCTGAATCATGTTT
252 TCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGT-TTTTACGAGCATCTGAATCTTGTTT
*
20977 CGATTTAAGTAGA
316 CGATTTAATTAGA
* ** * * *
20990 AATTAGTTCAGAAAATAATAGGAAAAACGATATTCGAAGCATGAAAAGCCCTTCAATCTTTTTGG
1 AATTAATTCAG-AAA-AATAGGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGG
* * * * * * *
21055 CGTTGAATTAT-T-TTTTTTATGATTATTGTGGCTAAAAATTGAGGACATAA-CATTCGAGTCAA
64 CGTTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGA-AAAATCTTTCGGGTCAA
* * * * * * *
21117 ATTTTACAAAATTCTAGCCAAAATCGTGTAATAATCATCACGGTTTTTGGCT-AAAACGCATTCC
128 TTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTT-C
* * * * * *
21181 GGGGCCCCAGCTAAGTTTTGCATGATTTTTGGCGTCAAGACTCTTTGAGATATCCATATTCATCT
192 GGGACCCGA-CTCAGTTTTGCATGATTTTTGGCG-CAAGACTCCTTGAAATATCTATATTCATCT
* * ** ** * * *
21246 AATCAAATTTCAGCTACATTGGTTTTAAAAATTTGTTTTTATGAGCATCTGAACCTTGTTTTGAT
255 AATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
21311 TTAATTAGA
320 TTAATTAGA
* * * *
21320 AATTAATTC-TAAAAATATGAAAAATGATATTAAAATCGTGAAAAGTCCTCCAATCTTTTTGGCG
1 AATTAATTCAGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCG
* * * * *
21384 TTAAATTATATATA--TTATGAGTA-TTTATGCCAAAAATTGACGAAAAAATTTTTCGGGTCATT
66 TTGAATTATATATATTTTATGAGTATTTTA-GCTAAAAATTGA-GGAAAAATCTTTCGGGTCAAT
* * * *
21446 TTTTGCAAACTTTTAGCTGAAATCGTGTATTAACCATCACGATTTTTTTGCTAAAAACGCGTTTC
129 TTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACG-GTTTTTGGCTAAAAACGCG-TTC
* * * * *
21511 GGGACCCCGACTTAGTTTTGCATGATTTTTAGCACCGAGACTCCTTGAAACATCTATATTCATCT
192 GGGA-CCCGACTCAGTTTTGCATGATTTTTGGC-GCAAGACTCCTTGAAATATCTATATTCATCT
* ** *
21576 AATCAAATATCAATCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGAT
255 AATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
21641 TTAATTAGA
320 TTAATTAGA
* * * * *
21650 AATTAATTCAGAAAAATATGAAAAATGATATTAAAAGCTTGAAGAGTCCTCAAATCTTTTTGGCG
1 AATTAATTCAGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCG
* * * *** * * *
21715 TTTAATCATATATATTCTATGAGTATTGCGGCTTAAAATTGAGGAAAAATATTTCGAGTCAATTT
66 TTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATTT
* * *
21780 TTACAAAATTTTAGCCGAAA-C-TGT-GT-ACCATCACGGTTTTTTTAGCTAAAAACGCGTTCTA
131 TTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGG--TTTTTGGCTAAAAACGCGTTC--
* * * *
21841 GGGTCCC-AGGTCAGTTTTGCATGATTTTTTGTG-GCAACACTCCTTGAAATATCTATATTCATT
192 GGGACCCGA-CTCAGTTTTGCATGA-TTTTTG-GCGCAAGACTCCTTGAAATATCTATATTCATC
* * * * * ** * * * **
21904 TAACCAAATTTTAGCCACATTGGATTGAAGGA-TT-TTTTTAATAGAATTTGAATCATGTTTTAA
254 TAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
21967 TTTAATTAGA
319 TTTAATTAGA
* * * * * *
21977 AATTAAATTGATAAAAGTAGGAAAAACGATATTAAAAGCGTGAGAAA-CCCTTCAATCCTTTTGG
1 AATT-AATTCAGAAAAATAGGAAAAACGATATTAAAAGCGTGA-AAAGTCCTCCAATCTTTTTGG
* * * * * * ** *
22041 TGTTGAATTATATATTTTTTATGAGTATTGTGGCTATAAATTTAGGAAAAAAAATTTGGGGTCAA
64 CGTTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGG-AAAAATCTTTCGGGTCAA
* * * *
22106 TTTTTGCAAAATTATAGTCGAAATCGTG---T-ACCATCATGGTTTTTTTTGGCTAAAAACGCAT
128 TTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGG---TTTTTGGCTAAAAACGC-G
* * * * * *
22167 TTTGGGGCCCTAGGTCAGTTTTGCATGATTTTTGGTGGCAAGACTCCTCAATATATATATATATA
189 TTCGGGACCCGA-CTCAGTTTTGCATGATTTTTGG-CGCAAGACT-C-C------T-T-GA-A-A
* * * ** *
22232 TATATATATTCATCTAATCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTATGAGTTTCC
240 TATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCT
* * *
22297 GAATCTTGTTTCGATTGAATCAAA
305 GAATCTTGTTTCGATTTAATTAGA
** * * * *
22321 AATTAATTTTGAATTAAAATAGGAAAAAACGATATTAGAAA-CGTGAAAAAGGCTTTTC-ATTTT
1 AATTAATTCAG-A--AAAATAGG-AAAAACGATATTA-AAAGCGTG-AAAAGTC-CTCCAATCTT
* * *
22384 TTTGGCGTTGAATTATAT-T-TTGTTATGAGTATTTTCGCTAGAAATCGAGGAAAAATCTTTCGG
59 TTTGGCGTTGAATTATATATATT-TTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGG
* * * *
22447 GTCAATTTTTGCAAAA-TTTAGCCGAAATCATGTACTAACCATCATGGTTTTCGGCTAAAAACGC
123 GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGC
* * *
22511 GTTCTGGGACCCGACTCTGTGTTTGCATGATTTTTGGTGCAAAAACTCCTTGAAATATCTATATT
188 GTTC-GGGACCCGACTCAGT-TTTGCATGATTTTTGGCGC-AAGACTCCTTGAAATATCTATATT
* * * * *
22576 TATCTAACCAAATCTCAGCTACATT-AGATTTAAGGATTTCTTTTTACGAGTATCTGAATCTTGT
250 CATCTAATCAAATCTCAGCCACATTGA-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
*
22640 TTCGATTTAAATAGA
314 TTCGATTTAATTAGA
* * * * * * **
22655 AATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATATTTTTTAA
1 AATTAATTCAG-AAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAAT-CTTTTTGG
* * * * *
22720 TGTCGAATTATATATGTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAAT
64 CGTTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAA-
* * *
22785 TTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAACACGT
128 --TTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGG-TTTTTGGCTAAAAACGCG-
* * * *
22850 TATAGGG-CCACGGCTCTGTTTTGCATGATTTTTCGCGCAA
189 T-TCGGGACC-CGACTCAGTTTTGCATGATTTTTGGCGCAA
22890 ATCTCAGCCA
Statistics
Matches: 2075, Mismatches: 388, Indels: 195
0.78 0.15 0.07
Matches are distributed among these distances:
326 2 0.00
327 109 0.05
328 347 0.17
329 289 0.14
330 349 0.17
331 163 0.08
332 91 0.04
333 28 0.01
334 104 0.05
335 16 0.01
336 138 0.07
337 105 0.05
338 67 0.03
339 2 0.00
340 1 0.00
341 1 0.00
342 40 0.02
343 6 0.00
344 33 0.02
345 22 0.01
346 79 0.04
347 44 0.02
348 26 0.01
349 13 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (328 bp):
AATTAATTCAGAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCG
TTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATTT
TTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTTCGGGA
CCCGACTCAGTTTTGCATGATTTTTGGCGCAAGACTCCTTGAAATATCTATATTCATCTAATCAA
ATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
AGA
Found at i:23145 original size:19 final size:19
Alignment explanation
Indices: 23121--23158 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23111 TTTTTGGCTA
23121 ATATTATCTAATAAAATCT
1 ATATTATCTAATAAAATCT
23140 ATATTATCTAATAAAATCT
1 ATATTATCTAATAAAATCT
23159 CAGGCATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATTATCTAATAAAATCT
Found at i:27151 original size:12 final size:11
Alignment explanation
Indices: 27125--27150 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27115 ATTTTGTGAG
27125 TTTTGTTTTTT
1 TTTTGTTTTTT
27136 TTTTGTTTTTT
1 TTTTGTTTTTT
27147 TTTT
1 TTTT
27151 TTGGCCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:34235 original size:26 final size:26
Alignment explanation
Indices: 34199--34252 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
34189 GAAAGTCCAA
34199 TGGGTCCGTAAATCCCAAAAATGGGT
1 TGGGTCCGTAAATCCCAAAAATGGGT
34225 TGGGTCCGTAAATCCCAAAAATGGGT
1 TGGGTCCGTAAATCCCAAAAATGGGT
34251 TG
1 TG
34253 ACGGTTTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (26 bp):
TGGGTCCGTAAATCCCAAAAATGGGT
Found at i:44326 original size:20 final size:20
Alignment explanation
Indices: 44282--44333 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
44272 AAGTAAAATA
**
44282 ATTAGCCAAGATTAATTTAG
1 ATTAGCCAAGATTAATCCAG
*
44302 ATTAGCCAAGATTAATCCGG
1 ATTAGCCAAGATTAATCCAG
*
44322 CTTAGCCAAGAT
1 ATTAGCCAAGAT
44334 ATTAGCCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (20 bp):
ATTAGCCAAGATTAATCCAG
Found at i:44367 original size:17 final size:17
Alignment explanation
Indices: 44334--44367 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44324 TAGCCAAGAT
**
44334 ATTAGCCAAGATTAATA
1 ATTAGCCAAGACAAATA
44351 ATTAGCCAAGACAAATA
1 ATTAGCCAAGACAAATA
44368 TGACACTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (17 bp):
ATTAGCCAAGACAAATA
Done.