Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017575.1 Corchorus olitorius cultivar O-4 contig17608, 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: 51247
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:579 original size:319 final size:318
Alignment explanation
Indices: 1--1778 Score: 1541
Period size: 311 Copynumber: 5.6 Consensus size: 318
* * ** *
1 TTGGATTTTAAGGATTTGATTTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAAT
1 TTGGA-TTTAAGGATTTG-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT
* * * ** *
66 TCGGAAAAAATAA---AAAAAATGATATTAGAAGTGTGGAAAGCCCTTCAATTTTTTTGGCGCTG
64 TCGGAAAAAA-AATGGAAAAACT-TTATTAGAAGCGT-GAAA-AACTT-AATTTTTTTGGCGTTG
*
128 AATTATATATTTTTTATGAGTA-T-T---------TT-GGAAAAAATTTTCGGGTCAATTTTTAG
124 AATTATATATTTTTTATGAGTATTGTGGCAAAAAATTAGAAAAAAATTTTCGGGTCAA-TTTTAG
* * * * *
181 TCGAAATCGTGTACTAACCATCACAATTTTCCGCTAAAAATGCGTTTTGGGG-CCCTGGA-TCAG
188 CCGAAATCGTGTACTAACCATCACAGTTTTTCGCTAAAAACGCGTTTCGGGGTCCC--GACTCAG
* * * *
244 -TTAAGCAT-GATTTTTGGCAGAAACACTCCTTGAAATATCTATATTCATCTATCTGAATCTCAG
251 TTTTA-CATAG-TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAG
307 CCACA
314 CCACA
* * * * *
312 TTGGATTTAAGGATTTCTTTTTACGAGCATCCGAATCTTTTTTCTATTTAATTAAAAATAAATTC
1 TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
* * * * *
377 GGAAAAGAAATGGAAAAACTTTATTAGACGCGTGAAAAAC-TGATTTTTTTGGCGTTAAATTGTA
66 GGAAAAAAAATGGAAAAACTTTATTAGAAGCGTGAAAAACTTAATTTTTTTGGCGTTGAATTATA
* * *
441 TATTTATTATGAGTATTGTGGCAAAGAATTGAGATAAAAAATATTCGGGTCAATTTTAGCCGAAA
131 TATTTTTTATGAGTATTGTGGCAAAAAATT-AGA-AAAAAATTTTCGGGTCAATTTTAGCCGAAA
* ** * *
506 TCGTGTACTAACAATCACAGTTTTTAACTAAAAACGCATTTCGGGGTCTCGACTCAGTTTTACAT
194 TCGTGTACTAACCATCACAGTTTTTCGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTACAT
* * * *
571 AGTTTTTGGCAAAAAGACTCCTTGAAATATCTATAATCATCTAACCAAATCTCAGCCACA
259 AGTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCCACA
* * * *
631 TTGGATTTAAGAATTTGTTTTTACGAGCATCTCATTCTTGTTTCGATTTAATTAAAAATAAATTC
1 TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
* * * * *
696 GAAAAAAAAAAATGGAAAAACTTTTTTAGAACCATGAAAAATCTTTCATTTTTTTTGGCGTTGAA
66 G--GAAAAAAAATGGAAAAACTTTATTAGAAGCGTGAAAAA-C-TT-AATTTTTTTGGCGTTGAA
* * * *
761 TTATATATTTTTTATTAGTGTTGTGGCAAAAAATTTAG-AAAAAATGTTTCGGGTTAGTTTTTAG
126 TTATATATTTTTTATGAGTATTGTGGCAAAAAA-TTAGAAAAAAAT-TTTCGGGTCA-ATTTTAG
* * * * *
825 CCG--A--GTGTA-T----GTTAGAGCTTTTT-GCTAAAAACGCGTTTCGCGGTCCCGTCTCAGT
188 CCGAAATCGTGTACTAACCATCACAG-TTTTTCGCTAAAAACGCGTTTCGGGGTCCCGACTCAGT
* ** * **
880 TTTGCATTA-TTTTTGATAGAAATACTCCTTGAAATAAATATATTCATCTACCCGAATCTCAGCC
252 TTTACA-TAGTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCC
944 ACA
316 ACA
*
947 TTGAATTTAAGGATTTG---TT--GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
1 TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
*
1007 GGAAAAAAAATGGAAAAACTTTATTAGAAGCGT-AAAACCCTTCAATTTTTTT-GCGTTGAATTA
66 GGAAAAAAAATGGAAAAACTTTATTAGAAGCGTGAAAA-ACTT-AATTTTTTTGGCGTTGAATTA
* * **
1070 TATATTTGTTATGAGTATTGTGGCAAAAAATTTAGAAAAAAATTTTCGGGTCAGTTTATAGCAAA
129 TATATTTTTTATGAGTATTGTGGCAAAAAA-TTAGAAAAAAATTTTCGGGTCAATTT-TAGC-CG
* **** * * ** * *
1135 AAAT--TATA-TATTTGTTATGAGCATTTCGCTAAAAACGCGTTTTGGGGTCCCGGCTCAGTTTT
191 AAATCGTGTACTAACCATCA-CAGTTTTTCGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTT
* * * * * * ** ** *
1197 CCAT-GATTTTTTGCAGGAAGACTCGTTGGAATATCTATATTCATTTACATGAATCTCTTCTACA
255 ACATAG-TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCCACA
* * * *
1261 CTGGATTTAAGAATTTGTTTTTAGGAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
1 TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
* ** * * * *
1326 GG-AAAAGAATACAAAAA-TGATATTAGAATCGTGAAAAAACCCTTAATTTTTTTTGGCATTCAA
66 GGAAAAAAAATGGAAAAACT-TTATTAGAAGCGTG-AAAAA--CTTAA-TTTTTTTGGCGTTGAA
* * * * *
1389 TTATAT-TATTCTCATGATTATTTTGGC--------A-AAAAAAA--TTCGGGTCAGTTTATAGC
126 TTATATAT-TTTTTATGAGTATTGTGGCAAAAAATTAGAAAAAAATTTTCGGGTCAATTT-TAGC
* * *
1442 CAAAATCGTGTACTAACCATCACAGTTTTTCGATAAAAACGCGTTTCGGGGCCCCGACTCAGTTT
189 CGAAATCGTGTACTAACCATCACAGTTTTTCGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTT
** * * * * *
1507 TGTATAATTTTCGGAAGAAGGACTCCTTGAAATATCTACATTCATCTACCCGAATCTCAGCCACA
254 TACATAGTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCCACA
* * * *
1572 TTGGATTTAAGGACTTGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATTTGAAATAAATTC
1 TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
** * * * *
1637 GG-AAAAAAATGGAAAAACGATATTAGAAACTTGAAAAACACTTCAACTTTTTTGGCGCTGAATT
66 GGAAAAAAAATGGAAAAACTTTATTAGAAGCGTG-AAAA-ACTT-AATTTTTTTGGCGTTGAATT
* * *
1701 ATATATTTTTTATGAGTATTTTGGCAAAAAAAATTTG-AAAAAATTTTCGGGTCAATTTTTAGTC
128 ATATATTTTTTATGAGTATTGTGGC--AAAAAATTAGAAAAAAATTTTCGGGTCAA-TTTTAGCC
1765 GAAATCGTGTACTA
190 GAAATCGTGTACTA
1779 GTTTCCTCCC
Statistics
Matches: 1190, Mismatches: 195, Indels: 153
0.77 0.13 0.10
Matches are distributed among these distances:
305 3 0.00
306 89 0.07
307 20 0.02
308 9 0.01
309 88 0.07
310 76 0.06
311 227 0.19
312 12 0.01
313 11 0.01
314 94 0.08
316 100 0.08
317 12 0.01
318 25 0.02
319 210 0.18
320 36 0.03
321 48 0.04
322 54 0.05
323 11 0.01
324 9 0.01
325 54 0.05
326 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (318 bp):
TTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC
GGAAAAAAAATGGAAAAACTTTATTAGAAGCGTGAAAAACTTAATTTTTTTGGCGTTGAATTATA
TATTTTTTATGAGTATTGTGGCAAAAAATTAGAAAAAAATTTTCGGGTCAATTTTAGCCGAAATC
GTGTACTAACCATCACAGTTTTTCGCTAAAAACGCGTTTCGGGGTCCCGACTCAGTTTTACATAG
TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCCACA
Found at i:1220 original size:630 final size:620
Alignment explanation
Indices: 2--1759 Score: 1560
Period size: 630 Copynumber: 2.8 Consensus size: 620
1 T
* * * * *** *
2 TGGATTTTAAGGATTTGATTTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTAATT
1 TGGA-TTTAAGAATTTG-TTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAAAAATAAATT
*** * * ** *
67 CGGAAAAAATAA-A-AAAAATGATATTAGAAGTGTG-GAAAGCCCTTCAA-TTTTTTTGGCGCTG
64 C-GAAAAAA-AATACAAAAATGATATTAGAACCATGAAAAAACCCTT-AATTTTTTTTGGCATTC
* * * ** * * *
128 AATTATA-TATTTTTTATGAGTATTTTGG-AAAAAATTTTCGGGTCAATTTTTAGTCGAAATCGT
126 AATTATATTA-TTCTCATGATTATTTTGGCAAAAAAAATTCGGGTCAGTTTATAG-CCAAA-CGT
* * * * * * * ** *
191 GTACTAACCATCACAATTTTCCGCTAAAAATGCGTTTTGGGGCCCTGGA-TCAGTTAAGCATGAT
188 GTACT-A--ATCACAGTTTTTCGATAAAAACGCGTTTCGCGGCCC-CGACTCAGTTTTGCATAAT
* * *
255 TTTTGGCAGAAACACTCCTTGAAATATCTATATTCATCTATCTGAATCTCAGCCACATTGGATTT
249 TTTT-GAAGAAACACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCCACATTGGATTT
* * * * *
320 AAGGATTTCTTTTTACGAGCATCCGAATCTTTTTTCTATTTAATTAAAAATAAATTCGGAAAAGA
313 AAGGA-TTCTTTTTA-GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA
* * * *
385 AATGGAAAAACTTTATTAGACGCGTGAAAA-AC-T-GATTTTTTTGGCGTTAAATTGTATATTTA
376 AATGGAAAAACTTTATTAGAAGCGT-AAAACACTTCAATTTTTTT-GCGTTGAATTATATATTTA
* * * ** *
447 TTATGAGTATTGTGGCAAAGAATTGAGATAAAAAATATTCGGGTCAATTTTAGCCGAAATCGTGT
439 TTATGAGTATTGTGGCAAAAAATTTAGA-AAAAAATTTTCGGGTCAATTTTAGCAAAAATC-TAT
** *
512 ACTAACAATCACAGTTTTTAACTAAAAACGCATTTCGGGGTCTCGACTCAGTTTTACATAGTTTT
502 ACTAACAATCACAGCATTTAACTAAAAACGCATTTCGGGGTCCCGACTCAGTTTTACATAGTTTT
*
577 TGGCAAAAAGACTCCTTGAAATATCTATAATCATCTAACCA-AATCTCAGCCACAT
567 TGGCAAAAAGACTCCTTGAAATATCTATAATCAT-TAA-CAGAATCTCAGCCACAC
*
632 TGGATTTAAGAATTTGTTTTTACGAGCATCTCATTCTTGTTTCGATTTAATTAAAAATAAATTCG
1 TGGATTTAAGAATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAAAAATAAATTCG
** * * * * * * *
697 AAAAAAAAAAATGGAAAAACT-TTTTTAGAACCATG-AAAAATCTTTCATTTTTTTTGGCGTTGA
66 ---AAAAAAAATACAAAAA-TGATATTAGAACCATGAAAAAACCCTTAATTTTTTTTGGCATTCA
* * * *
760 ATTATA-TATT-T-TTTATTAGTGTTGTGGCAAAAAATTTAGAAAAAATGTTTCGGGTTAGTTTT
127 ATTATATTATTCTCATGATTA-T-TT-TGGC-----A---A-AAAAAA---TTCGGGTCAGTTTA
* * * * * * *
822 TAGCC-GA-GTGTA-T-GTTAGAGCTTTTT-GCTAAAAACGCGTTTCGCGGTCCCGTCTCAGTTT
177 TAGCCAAACGTGTACTAATCACAG-TTTTTCGATAAAAACGCGTTTCGCGGCCCCGACTCAGTTT
* * **
882 TGCATTATTTTTGATAGAAATACTCCTTGAAATAAATATATTCATCTACCCGAATCTCAGCCACA
241 TGCATAATTTTTGA-AGAAACACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCCACA
* *
947 TTGAATTTAAGGA-T-TTGTT-GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG
305 TTGGATTTAAGGATTCTTTTTAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG
*
1009 AAAAAAAATGGAAAAACTTTATTAGAAGCGTAAAACCCTTCAATTTTTTTGCGTTGAATTATATA
370 AAAAAAAATGGAAAAACTTTATTAGAAGCGTAAAACACTTCAATTTTTTTGCGTTGAATTATATA
* *
1074 TTTGTTATGAGTATTGTGGCAAAAAATTTAGAAAAAAATTTTCGGGTCAGTTTATAGCAAAAAAT
435 TTTATTATGAGTATTGTGGCAAAAAATTTAGAAAAAAATTTTCGGGTCAATTT-TAGC-AAAAAT
**** * * ** * * * *
1139 -TATA-TATTTGTTATGAGCATTTCGCTAAAAACGCGTTTTGGGGTCCCGGCTCAGTTTTCCAT-
498 CTATACTAACAATCA-CAGCATTTAACTAAAAACGCATTTCGGGGTCCCGACTCAGTTTTACATA
* ** * * * * ** *
1201 GATTTTTTGCAGGAAGACTCGTTGGAATATCTATATTCATTTACATGAATCTCTTCTACAC
562 G-TTTTTGGCAAAAAGACTCCTTGAAATATCTATAATCATTAACA-GAATCTCAGCCACAC
* * * *
1262 TGGATTTAAGAATTTGTTTTTAGGAGCTTCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCG
1 TGGATTTAAGAATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAAAAATAAATTCG
* * * *
1327 GAAAAGAATACAAAAATGATATTAGAATCGTGAAAAAACCCTTAATTTTTTTTGGCATTCAATTA
66 AAAAAAAATACAAAAATGATATTAGAACCATGAAAAAACCCTTAATTTTTTTTGGCATTCAATTA
1392 TATTATTCTCATGATTATTTTGGCAAAAAAAATTCGGGTCAGTTTATAGCCAAAATCGTGTACTA
131 TATTATTCTCATGATTATTTTGGCAAAAAAAATTCGGGTCAGTTTATAGCC-AAA-CGTGTACT-
* * *
1457 ACCATCACAGTTTTTCGATAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGTATAATTTTCGGA
193 A--ATCACAGTTTTTCGATAAAAACGCGTTTCGCGGCCCCGACTCAGTTTTGCATAATTTT-TGA
** *
1522 AGAAGGACTCCTTGAAATATCTACATTCATCTACCCGAATCTCAGCCACATTGGATTTAAGGACT
255 AGAAACACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCCACATTGGATTTAAGGA-T
* * * *
1587 TGTTTTTACGAACATCTAAATCTTGTTTCGATTTAATTTGAAATAAATTCGG-AAAAAAATGGAA
319 TCTTTTTA-GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAA
** * * * * *
1651 AAACGATATTAGAAACTTGAAAAACACTTCAACTTTTTTGGCGCTGAATTATATATTTTTTATGA
383 AAACTTTATTAGAAGC--GTAAAACACTTCAA-TTTTTTTGCGTTGAATTATATATTTATTATGA
*
1716 GTATTTTGGCAAAAAAAATTT-G-AAAAAATTTTCGGGTCAATTTT
445 GTATTGTGGC--AAAAAATTTAGAAAAAAATTTTCGGGTCAATTTT
1760 TAGTCGAAAT
Statistics
Matches: 918, Mismatches: 149, Indels: 121
0.77 0.13 0.10
Matches are distributed among these distances:
616 17 0.02
618 1 0.00
619 6 0.01
620 6 0.01
621 1 0.00
623 1 0.00
624 5 0.01
625 100 0.11
626 3 0.00
627 24 0.03
628 83 0.09
629 57 0.06
630 288 0.31
631 110 0.12
632 75 0.08
633 2 0.00
634 11 0.01
635 95 0.10
636 4 0.00
637 1 0.00
639 1 0.00
640 6 0.01
641 4 0.00
642 1 0.00
643 1 0.00
644 15 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (620 bp):
TGGATTTAAGAATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAAAAATAAATTCG
AAAAAAAATACAAAAATGATATTAGAACCATGAAAAAACCCTTAATTTTTTTTGGCATTCAATTA
TATTATTCTCATGATTATTTTGGCAAAAAAAATTCGGGTCAGTTTATAGCCAAACGTGTACTAAT
CACAGTTTTTCGATAAAAACGCGTTTCGCGGCCCCGACTCAGTTTTGCATAATTTTTGAAGAAAC
ACTCCTTGAAATATCTATATTCATCTACCCGAATCTCAGCCACATTGGATTTAAGGATTCTTTTT
AGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAAAACTTTA
TTAGAAGCGTAAAACACTTCAATTTTTTTGCGTTGAATTATATATTTATTATGAGTATTGTGGCA
AAAAATTTAGAAAAAAATTTTCGGGTCAATTTTAGCAAAAATCTATACTAACAATCACAGCATTT
AACTAAAAACGCATTTCGGGGTCCCGACTCAGTTTTACATAGTTTTTGGCAAAAAGACTCCTTGA
AATATCTATAATCATTAACAGAATCTCAGCCACAC
Found at i:2878 original size:320 final size:321
Alignment explanation
Indices: 2298--3779 Score: 1437
Period size: 320 Copynumber: 4.7 Consensus size: 321
2288 TTTGGTTCTC
* * * *
2298 GACTCAGTTTTGCATG-GTTTTTGACAAAAAGACTCCTTGAAATATCTATAATCATCTAACCAAA
1 GACTCAGTTTTGCATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
* *
2362 TCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTG-ATTTGTGTTTCGATTTAATT
66 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TGTTTCGATTTAATT
* * * * *
2426 AGAAATAAATTCGAAAAAAAATGGAAAAAATTTATTAGAAGCATGAAAAATCCTTCAATTTTTTG
130 AGAAATAAATTCGAAAAAAAATGGAAAAACTATATTAGAAGCGTAAAAAATACTTCAATTTTTT-
* * * *
2491 GGCGTTGAATTATATATTTTTTATTAGTGTTGT-GGCAAAAATTTAGACAAAAAATTTCGGATCA
194 GGCGTTGAATTATATATTTTTTATTAGTATTGTGGGAAAAAATGTAGA-AAAAATTTTCGGATCA
* *
2555 GTTTTTAGCCGAAATCGTGTACTAACCATCAGAGATTTTT-GCTAAAACCGCGTTTCGGGGTCCT
258 GTTTTTAGCCGAAATCGTGTACTAACCATCAGAG-TTTTTCGCTAAAAACGCGTTTCGGGGACCT
* * * ** *
2619 GTCTCAGTTTT-CATTA-TTTTTGGCAGAAATACTCCTTGAAATAAATATATTCATCTACCCAAA
1 GACTCAGTTTTGCATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
2682 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
66 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* * * * * *
2747 GAATTAAATTCGGAAAAAATTGGAAAAACGATATTAGAATCGTAAAAAATACTTCAATTTTTTTG
131 GAAATAAATTCGAAAAAAAATGGAAAAACTATATTAGAAGCGTAAAAAATACTTCAATTTTTTGG
*
2812 CGTTGAATTATATATTTTTTATTAGTATTGTGGGAAAAAATGTAGAAACAAATTTTCGGGTCAGT
196 CGTTGAATTATATATTTTTTATTAGTATTGTGGGAAAAAATGTAGAAA-AAATTTTCGGATCAGT
* * * **
2877 TTTTAGTCGAAATCATTTACTAACCATCAGAGTTTTTCGCTAAAAACGCAATTCGGGGACCT
260 TTTTAGCCGAAATCGTGTACTAACCATCAGAGTTTTTCGCTAAAAACGCGTTTCGGGGACCT
* * * * * * * * *
2939 GGCTCAGTTTCGCATTATTTTTTGGTAGAAAGACTGCTTGGAATATCTACATTCATCTACCCGAA
1 GACTCAGTTTTGCATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
* * *
3004 TCGCAGCCACATTGGATTTAAGGATTTTTTTTTACGAGCATCTGAATCTTGCTTCGATTTAATTA
66 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* * * *
3069 GAAATATATTCGAAAAAAAATGGAAAAACTATATTTGAAGCGT-GAAAACACTTCAATTTTTTTG
131 GAAATAAATTCGAAAAAAAATGGAAAAACTATATTAGAAGCGTAAAAAATACTTCAA-TTTTTTG
* * * ** * *
3133 GAGTTGAATTATATATTTTTTCTAAGTATTGTGGCCAAAAAT-TGAGGAAAAACTTTTCGAATCA
195 GCGTTGAATTATATATTTTTTATTAGTATTGTGGGAAAAAATGT-A-GAAAAAATTTTCGGATC-
* * * *
3197 ATTTTTGCAAAATTTTAGCCGAAATCTTGTACTAACCATCACG-GTTTTTGGCTAAAAATGCGTT
257 A-----G----TTTTTAGCCGAAATCGTGTACTAACCATCA-GAGTTTTTCGCTAAAAACGCGTT
* * * *
3261 CCGGAGCCCC
312 TCGGGGACCT
* * **
3271 GACTCAATTTTGCATGATTTTTTGTGC--AAAGACTCCTTGAAATATCTATGTTCATGGAACCAA
1 GACTCAGTTTTGCATGATTTTTTG-GCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAA
* * * *
3334 ATCTCAACCACATTGGATATAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTAAATT
65 ATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* ** * * * *
3399 AGAAATTAATTCG--GGAAAATGGAAAAACAATATTAAAAGCGTGAAAAGA-ACATCAATCTTTT
130 AGAAATAAATTCGAAAAAAAATGGAAAAACTATATTAGAAGCGT-AAAAAATACTTCAAT-TTTT
* * * * * *
3461 TGGCGTTTAATTATATA-TTTTCACTGAGTATTGTGGCAAAAAAACTG-AGAAAAACTTTTCGGG
193 TGGCGTTGAATTATATATTTTTTA-TTAGTATTGTGG-GAAAAAA-TGTAGAAAAAATTTTCGGA
*
3524 TCAGTTTTTAGCCGAAACCGTGTACATAA--AT-A-A---------T------GCGTTTCGGGG-
255 TCAGTTTTTAGCCGAAATCGTGTAC-TAACCATCAGAGTTTTTCGCTAAAAACGCGTTTCGGGGA
*
3569 CCAC
319 CC-T
* * * * * *
3573 GATTCTGTTTTGCATGA-TTTTTGACGCCG--AGACTCCTTGATATATCTTTATTCATCTAATCA
1 GACTCAGTTTTGCATGATTTTTTG--GCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCA
* * * *
3635 AATCTTAGCTACATTTGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAAT
64 AATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * * * * * *
3700 TAGAAATTAATTC--AAAAAAAT-AAAAAACGATATTAGAAGCGTGAAAAGTCCTCCAATCTTTT
129 TAGAAATAAATTCGAAAAAAAATGGAAAAACTATATTAGAAGCGTAAAAAATACTTCAAT-TTTT
*
3762 TGGTGTTGAATTATATAT
193 TGGCGTTGAATTATATAT
3780 ATATATATAT
Statistics
Matches: 971, Mismatches: 152, Indels: 95
0.80 0.12 0.08
Matches are distributed among these distances:
300 3 0.00
301 51 0.05
302 128 0.13
308 1 0.00
318 1 0.00
319 40 0.04
320 257 0.26
321 33 0.03
322 191 0.20
323 5 0.01
324 1 0.00
328 1 0.00
329 30 0.03
330 51 0.05
331 106 0.11
332 70 0.07
333 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (321 bp):
GACTCAGTTTTGCATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
GAAATAAATTCGAAAAAAAATGGAAAAACTATATTAGAAGCGTAAAAAATACTTCAATTTTTTGG
CGTTGAATTATATATTTTTTATTAGTATTGTGGGAAAAAATGTAGAAAAAATTTTCGGATCAGTT
TTTAGCCGAAATCGTGTACTAACCATCAGAGTTTTTCGCTAAAAACGCGTTTCGGGGACCT
Found at i:12672 original size:14 final size:14
Alignment explanation
Indices: 12653--12682 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12643 TTATTACTAA
12653 ATGGTGTATATGCT
1 ATGGTGTATATGCT
12667 ATGGTGTATATGCT
1 ATGGTGTATATGCT
12681 AT
1 AT
12683 AAATGATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (14 bp):
ATGGTGTATATGCT
Found at i:18256 original size:20 final size:20
Alignment explanation
Indices: 18231--18272 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
18221 CATACTTTAC
18231 CCTCTTCCATAATTCCAAAA
1 CCTCTTCCATAATTCCAAAA
18251 CCTCTTCCATAATTCCAAAA
1 CCTCTTCCATAATTCCAAAA
18271 CC
1 CC
18273 GTTTTGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.38, G:0.00, T:0.29
Consensus pattern (20 bp):
CCTCTTCCATAATTCCAAAA
Found at i:28888 original size:40 final size:40
Alignment explanation
Indices: 28833--28914 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
28823 AGTCTACCAA
*
28833 TATTAATCATTGAATATTTACATTTATTCCCTAAGAGGTT
1 TATTAATCATTGAATATTTACATTTATTCCCTAAGAGATT
28873 TATTAATCATTGAATATTTACATTTATTCCCTAAGAGATT
1 TATTAATCATTGAATATTTACATTTATTCCCTAAGAGATT
28913 TA
1 TA
28915 ACTACACACG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (40 bp):
TATTAATCATTGAATATTTACATTTATTCCCTAAGAGATT
Found at i:31490 original size:26 final size:26
Alignment explanation
Indices: 31453--31530 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 26
31443 AGATGATGAA
* *
31453 CGATGATCGGAAATCCCGAGTTGGAG
1 CGATGATCGGAAATACTGAGTTGGAG
*
31479 CGATGATTGGAAATACTGAGTTGGAG
1 CGATGATCGGAAATACTGAGTTGGAG
31505 CGATGATCGGAAATACTGAGTTGGAG
1 CGATGATCGGAAATACTGAGTTGGAG
31531 ATGAAATCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.29, C:0.13, G:0.35, T:0.23
Consensus pattern (26 bp):
CGATGATCGGAAATACTGAGTTGGAG
Found at i:36966 original size:23 final size:23
Alignment explanation
Indices: 36940--36987 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
36930 CTTTCATAAC
36940 TATTTTTTATTTATGCTTTACCA
1 TATTTTTTATTTATGCTTTACCA
36963 TATTTTTTATTTATGCTTTACCA
1 TATTTTTTATTTATGCTTTACCA
36986 TA
1 TA
36988 ACAACTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.04, T:0.60
Consensus pattern (23 bp):
TATTTTTTATTTATGCTTTACCA
Found at i:36996 original size:27 final size:26
Alignment explanation
Indices: 36934--36990 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 26
36924 AATTCCCTTT
36934 CATAACTATTTTTTATTTATGCTTTAC
1 CATAAC-ATTTTTTATTTATGCTTTAC
36961 CAT---ATTTTTTATTTATGCTTTAC
1 CATAACATTTTTTATTTATGCTTTAC
36984 CATAACA
1 CATAACA
36991 ACTTTTGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
23 23 0.85
26 1 0.04
27 3 0.11
ACGTcount: A:0.28, C:0.16, G:0.04, T:0.53
Consensus pattern (26 bp):
CATAACATTTTTTATTTATGCTTTAC
Found at i:40215 original size:40 final size:40
Alignment explanation
Indices: 40160--40236 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
40150 CCGTCTATTT
40160 TATGTTCAATTAACTGAATTTACGGCACTAAAATAACATA
1 TATGTTCAATTAACTGAATTTACGGCACTAAAATAACATA
40200 TATGTTCAATTAACTGAATTTACGGCACTAAAATAAC
1 TATGTTCAATTAACTGAATTTACGGCACTAAAATAAC
40237 GAGTTCTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (40 bp):
TATGTTCAATTAACTGAATTTACGGCACTAAAATAACATA
Done.