Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016369.1 Corchorus olitorius cultivar O-4 contig16402, 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: 12504
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2208 original size:658 final size:651
Alignment explanation
Indices: 4--3049 Score: 3428
Period size: 658 Copynumber: 4.7 Consensus size: 651
1 ATT
* * *
4 TAAGGATTTATTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAATCAGAAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
* ** **
69 ATGGAAAAACGTTATTAGAAGCGTGAAAAGCCCAACAATCTTTTTGGAATTGAATTATATATTTT
66 ATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA-TTT
* * * * *
134 TTTCTTAGTATTATGGCAAAAAATTGACAAAAAAACCTTTCGGGTCAGTTTTTAGCCGAAATCGT
130 TTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAA-TTTTCGGGTCAGTTTTTAGCCGAAATCGT
* ** *
199 CTACTAATGATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGCTCCGACTCAGTTTTGCATGAT
194 GTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTC-GGGCCCCGACTCAGTTTTGCAT-AT
* * **
264 TTTTGGCAGAAAGA-TACCTTGAAATATGTATTTTCATCTAATGAAATCTCAGCCGA-ATTGGAT
257 TTTTGGCAGAAAGACT-CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC-ACATTGGAT
* * * *
327 TTATGAATTTGTGTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA
320 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GAAAA
** * * * * *
392 AAAGAAAGAAAAACGATATTTGAAGCGTGAAAAGCCCGTC-AATCTTTTTGGCGTTTG-ATTTTA
384 AAA-ATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTTGGCG-TTGAATTATA
* * * ** *
455 TATTTTTTATGAGTATTATGGCAAAAAATTGACAAAAAAATTTTCGGGTCA-----G----TTTT
447 TATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAAATTTTCAAGTCATTTTTGCAAAATTT
* * * * ** * *
511 TAGCCGAAATCGTGTACTAACAATCATGGTTTTGGGCTAAAAACGCGTTTTGGGACCCCGACTTA
511 TAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGAACCCCGACTCA
* * * *
576 GTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATGTATATTCATCTAATCAAATCTCAG
576 ATTTTGCATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAG
*
640 CCGA-ATTGGATT
640 CC-ACATTGGATA
*
652 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAAAT-AGAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT-AAATTCAGAAAA
* * *
716 AATGGAAAAACGATATTAGAAGCATGAAAAGCCCGACAATCTTTTTGGCATTGAATTATATATTT
65 AATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTT
* * * **
781 TTTCTGAGTATTATGGCAAAAAATTAACAAAAAACCTTTCGGGTCAGTTTTTA-CCGAAATCGTG
130 TTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTG
845 TACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGTCCCCGACTCA-----G-----TT
195 TACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGG-CCCCGACTCAGTTTTGCATATTT
* *
900 TT-GCAGATAGACT-CTATG-AACATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
259 TTGGCAGAAAGACTCCT-TGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
* * *
962 AGGATTTGTTTTTACGAGGATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCG-GAAAAAA
323 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAA
* * * *
1026 TGGTAAAACGATATTAGAAGCGTGAAAAACCTTTCCAA-TTTTTTGGTGTTGAATTATATATTTT
388 TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTTGGCGTTGAATTATATATTTT
***
1090 TT-T-AGTATTGTGGCAAAAAATTGAGGAAATGCTTTTCAAGTCAGTTTTTGCAAAA-TTTAGCC
453 TTCTGAGTATTGTGGCAAAAAATTGA-GAAAAAATTTTCAAGTCA-TTTTTGCAAAATTTTAGCC
* * **
1152 GAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGTGTTCCGGAGTCCCGACTCAATTTT
516 GAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGAACCCCGACTCAATTTT
* ** * *
1217 GCATGAATTTTGGCGCAAAGACTCCTTGAGTTATCTATATTCATCGAACCAAATCTCAGCTACAC
581 GCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAT
**
1282 CAGATA
646 TGGATA
* *
1288 TAAGGATTTGTTTTTACGAGCATCT-AAT-TTAGTTTCGATTTAATTAGAAATTAATTCGGAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTT-GTTTCGATTTAATTAGAAATAAATTC---AGA
* *
1351 AAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGATTTATATA
62 AAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA
* * *
1416 -TTTTTCTAAGTATTGCGGCAAAAAATTCAGAAAAAAATATTCGGGTCAGTTTTTAGCCGAAATC
127 TTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATC
* * * * * *
1480 GTGTACTAA-CACCACGGTTTTTGGGCTATAAACGCGTTTCAAGGCCCTGGCTCAGTTTTGCAAG
192 GTGTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTC-GGGCCCCGACTCAGTTTTGC-AT
**
1544 ATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTATGCAAATCTCAGCCACATTGGAT
255 ATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAT
* * * * *
1609 TTAAGAATTTGTTTTTACAAGCATATGAATCTTGTTTCTATTTAAATAGAAATAAATTCGAAAAA
320 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAA
* * * *
1674 AAATGGAAAAACAATATTAGATGCGTTAAAAACCCTTCAAATTTTTTTTTTTGCGTTGAATTATA
385 AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAA---TTTTTTTGGCGTTGAATTATA
* * * * ***
1739 TACTTTTTCTAAGTATTGTGGCAAAGAATTGAGGAAAAATTTTGGGGTCATTTTTTGCAAAATTT
447 TATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTTCAAGTCA-TTTTTGCAAAATTT
* * * *
1804 TAGCCGAAATCATGTACTAACCATCACAATATTTTTGCTAAAAATGCGTTCCGGAACCCCGACTC
511 TAGCCGAAATCGTGTACTAACCATCACGAT-TTTTGGCTAAAAACGCGTTCCGGAACCCCGACTC
* * * *
1869 AATTTTACATGATTTTTGGCGCAAAGACTCCTTGAAATATTTATTTTAATCGAACCAAATCTCAG
575 AATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAG
1934 CCACATTGGATA
640 CCACATTGGATA
* * *
1946 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAATTTAATTCAGAATAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
* * ** * * *
2011 ATTGAAAACCGATATTAGAAATGTGACAACCCCGTCAATCTTTTTGGCGTTGAGTTATATATTTT
66 ATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTT
* *
2076 TTCTGAGTATTGTGGCGAAAAATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCCAAAAATCGTG
131 TTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCC-GAAATCGTG
* * * * *
2141 TA-TCAACGATCACGGTTTTTGGGTTAAAAACGCGTTCCAGGGCCTCGACTCAGTTTTGTATATT
195 TACT-AACCATCACGGTTTTTGGGCTAAAAACGCGTTTC-GGGCCCCGACTCAGTTTTGCATATT
* * * * * *
2205 TTTGGCAAAAAGGCTCCTTAAAATATCTATATTCATGTAACCAAATCT-ATGCTACATTGGATTA
258 TTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA-GCCACATTGGATTT
* * *
2269 AAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCTATTTAATTAGGAATAAATTCTGGAAAAA
322 AAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC--G-AAAA
* * *
2334 AAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTTTAGTTGCATTGAGTT
384 AAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA--ATTTTTTT-G--GCGTTGAATT
* *
2399 ATATATTTTTTTCTGAGTATTGTGGCAAAGAATTGAGAAAAAAATTTTCAAGTCAACTTATT-CA
444 ATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAATTTTCAAGTC-A-TTTTTGCA
* * * ** *
2463 AAATTTTAGCCGAAATCGTG---T-ACCATCACGGTTTTTGGCTAAAAACGTGTTTCTTAGCCCC
505 AAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGAACCCC
* * * *
2524 -AGCTCAATTTTGTATGATTTTT-ACGCAAAGACTCCTTCAAATATCTATATGCATCGAACCAAA
570 GA-CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAA
2587 TCTCAGCCACATTGGATA
634 TCTCAGCCACATTGGATA
* * * *
2605 TAA-GATTTTTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAACTAAATTCGGGAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-AGAAAA
** * * *
2669 AATGGAAAAACGATATTAGAAGCGTGAAGAA-CCTTTCAATTTTTTTTGAGTTGAATTATATA-T
65 AATGGAAAAACGATATTAGAAGCGTGAA-AAGCCCGTCAATCTTTTTGGCGTTGAATTATATATT
* * * *
2732 TTTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAG
129 TTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAATTTTCGGGTCAG----T------TTTTAG
* * * * *
2797 CCGAAATCGTGTACTAACCATCACAGTATTTT-GGCTAAAAACTCGTTTCGAAGCCCCGACTTAA
184 CCGAAATCGTGTACTAACCATCACGGT-TTTTGGGCTAAAAACGCGTTTCG-GGCCCCGACTCAG
* * *
2861 TTTTGCATGATTTTTGAC-GCAAAGACTCCTTGAAATATCTAGATTCATCGAACCAAATCTCAGC
247 TTTTGCAT-ATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
* * * *
2925 CACATTGGATATAAGGATTTGTTTTTAGGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTA
310 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
* * * * *
2990 ATTTGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAATCCTTC-AATCTTTTTGGC
375 ATTCGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTTGGC
3050 AATAAATTGA
Statistics
Matches: 2046, Mismatches: 266, Indels: 161
0.83 0.11 0.07
Matches are distributed among these distances:
627 32 0.02
628 4 0.00
629 50 0.02
630 7 0.00
631 2 0.00
632 89 0.04
633 11 0.01
634 10 0.00
635 25 0.01
636 140 0.07
637 84 0.04
638 81 0.04
640 1 0.00
642 1 0.00
644 3 0.00
645 55 0.03
646 18 0.01
647 35 0.02
648 118 0.06
649 17 0.01
650 93 0.05
651 38 0.02
655 25 0.01
656 81 0.04
657 106 0.05
658 336 0.16
659 181 0.09
660 52 0.03
661 52 0.03
662 8 0.00
663 13 0.01
664 30 0.01
665 73 0.04
666 7 0.00
667 50 0.02
668 117 0.06
669 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (651 bp):
TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
ATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTT
TTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGT
ACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGCCCCGACTCAGTTTTGCATATTTTT
GGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGG
ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGG
AAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTTGGCGTTGAATTATATATTTTTTC
TGAGTATTGTGGCAAAAAATTGAGAAAAAATTTTCAAGTCATTTTTGCAAAATTTTAGCCGAAAT
CGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGAACCCCGACTCAATTTTGCATG
ATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGAT
A
Found at i:2857 original size:990 final size:965
Alignment explanation
Indices: 4--3048 Score: 3402
Period size: 990 Copynumber: 3.1 Consensus size: 965
1 ATT
* * *
4 TAAGGATTTATTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAATCAGAAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
* * * *
69 ATGGAAAAACGTTATTAGAAGCGTGAAAAGCCCAACAATCTTTTTGGAATTGAATTATATATTTT
66 ATGG-AAAACGATATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGAGTTGAATTATATA-TTT
* * *
134 TTTCTTAGTATTATGGCAAAAAATTGACAAAAAAACCTTTCGGGTCAGTTTTTAGCCGAAATCGT
129 TTTC-TAGTATTGTGGCAAAAAATTGAGAAAAAAA-TTTTCGGGTCAGTTTTTAGCCGAAATCGT
* * * *
199 CTACTAATGATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGCTCCGACTCAGTTTTGCATGAT
192 GTACTAACGATCACGGTTTTTGGGCTAAAAACGCGTTCCGGGCCT-CGACTCAGTTTTGCATGAT
* * * * * ** *
264 TTTTGGCAGAAA-GATACCTTGAAATATGTATTTTCATCTAATGAAATCTCAGCCGA-ATTGGAT
256 TTTTGGCAAAAAGGCT-CCTTGAAATATCTATATTCATGTAACCAAATCTCAG-CTACATTGGAT
* * * *
327 TTATGAATTTGTGTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA
319 TAAAGGATTTGTTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA
* * *
392 AAAGAA-AGAAAAACGATATTTGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTTGATTT-TA
383 AAA-AATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGC-ATTGATTTATA
* * *
455 TATTTTTTATGAGTATTATGGCAAAAAATTGACAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAA
446 T-TTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAA
* * ** *
520 TCGTGTACTAACAATCATGGTTTTGGGCTAAAAACGCGTTT-TGGGACCCCGACTTAGTTTTGCA
510 TCGTGTAC--AC-ATCACGGTTTTTGGCTAAAAACGCGTTTCTAAG-CCCCG-CTCAGTTTTGCA
* *
584 TGATTTTTGGCAGAAAGACTCCTTGAAATATGTATATTCATCTAATCAAATCTCAGCCGA-ATTG
570 TGATTTTTGGCA-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC-ACATTG
* *
648 GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAAAT--A
633 GATTTAA-GATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAAT-AAATTCGA
* ** * *
711 GAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGCCCGACAATCTTTTTGGCA-TTGAATTAT
696 GAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTTTG-AGTTGAATTAT
* * * * ** *
775 ATATTTTTTCTGAGTATTATGGCAAAAAATTAACAAAAAACCTTTCGGGTCAG----T------T
759 ATACTTTTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAA-TTTTCGGGTCAGTTTTTGCAAAAT
* * *
830 TTTA-CCGAAATCGTGTACTAACCATCACGGT-TTTTGGGCTAAAAACGCGTTTCG-GGTCCCCG
823 TTTAGCCGAAATCGTGTACTAACCATCACAGTATTTT-GGCTAAAAACTCGTTTCGAAG-CCCCG
* * *
892 ACTCAGTTTTGCA-GA----T------AGACT-CTATG-AACATCTATATTCATCTAACCAAATC
886 ACTCAATTTTGCATGATTTTTGCGCAAAGACTCCT-TGAAATATCTATATTCATCGAACCAAATC
*
944 TCAGCCACATTGGATT
950 TCAGCCACATTGGATA
* * *
960 TAAGGATTTGTTTTTACGAGGATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
** *
1025 ATGGTAAAACGATATTAGAAGCGTGAAAAACCTTTCCAAT-TTTTTGGTGTTGAATTATATATTT
66 ATGG-AAAACGATATTAGAAGCGTGAAAAACCCAT-CAATCTTTTTGGAGTTGAATTATATATTT
* *** **
1089 TTT-TAGTATTGTGGCAAAAAATTGAGGAAATGCTTTTCAAGTCAGTTTTTGCAAAATTTAGCCG
129 TTTCTAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAG---TT------TTTAGCCG
* * * * *
1153 AAATCGTGTACTAACCATCACGATTTTT-GGCTAAAAATGTGTTCCGGAGTCC-CGACTCAATTT
185 AAATCGTGTACTAACGATCACGGTTTTTGGGCTAAAAACGCGTTCCGG-G-CCTCGACTCAGTTT
* ** * **
1216 TGCATGAATTTTGGCGCAAAGACTCCTTGAGTTATCTATATTCATCG-AACCAAATCTCAGCTAC
248 TGCATGATTTTTGGCAAAAAGGCTCCTTGAAATATCTATATTCAT-GTAACCAAATCTCAGCTAC
*** *
1280 ACCAGA-TATAAGGATTTGTTTTTACGAGCATCTAAT-TTAGTTTCGATTTAATTAGAAATTAAT
312 ATTGGATTA-AAGGATTTGTTTTTACGAGCATCTAATCTT-GTTTCGATTTAATTAGAAATAAAT
* *
1343 TCGGAAAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
375 TCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGA
* * * * *
1408 TTTATATATTTTTCTAAGTATTGCGGCAAAAAATTCAGAAAAAAATATTCGGGTCAGTTTTTAGC
440 TTTATATTTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGC
* * *
1473 CGAAATCGTGTACTAACACCACGGTTTTTGGGCTATAAACGCGTTTC-AAGGCCCTGGCTCAGTT
505 CGAAATCGTGTAC--ACATCACGGTTTTT-GGCTAAAAACGCGTTTCTAA-GCCC-CGCTCAGTT
* **
1537 TTGCAAGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTATGCAAATCTCAGCCAC
565 TTGCATGATTTTTGGCA-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
* * *
1602 ATTGGATTTAAGAATTTGTTTTTACAAGCATATGAATCTTGTTTCTATTTAAATAGAAATAAATT
629 ATTGGATTTAAG-ATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATAAATT
* * * * *
1667 CGAAAAAAAATGGAAAAACAATATTAGATGCGTTAAAAACCCTTCAAATTTTTTTTTTTGCGTTG
693 CGAGAAAAAATGGAAAAACGATATTAGAAGCG-TGAAAACCCTTC-AA---TTTTTTTTGAGTTG
* * *
1732 AATTATATACTTTTTCTAAGTATTGTGGCAAAGAATTGAGGAAAAATTTTGGGGTCATTTTTTGC
753 AATTATATACTTTTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAATTTTCGGGTCAGTTTTTGC
* * * *
1797 AAAATTTTAGCCGAAATCATGTACTAACCATCACAATATTTTTGCTAAAAA-TGCGTTCCGGAA-
818 AAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTATTTTGGCTAAAAACT-CGTTTC-GAAG
* * * *
1860 CCCCGACTCAATTTTACATGATTTTTGGCGCAAAGACTCCTTGAAATATTTATTTTAATCGAACC
881 CCCCGACTCAATTTTGCATGATTTTT-GCGCAAAGACTCCTTGAAATATCTATATTCATCGAACC
1925 AAATCTCAGCCACATTGGATA
945 AAATCTCAGCCACATTGGATA
* * *
1946 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAATTTAATTCAGAATAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
* ** * * * * *
2011 ATTGAAAACCGATATTAGAAATGTGACAACCCCGTCAATCTTTTTGGCGTTGAGTTATATATTTT
66 ATGGAAAA-CGATATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGAGTTGAATTATATATTTT
* * *
2076 TTCTGAGTATTGTGGCGAAAAATTCAGAAAAAAATTTTCGGGTCAGTTTTTAGCCAAAAATCGTG
130 TTCT-AGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCC-GAAATCGTG
* *
2141 TA-TCAACGATCACGGTTTTTGGGTTAAAAACGCGTTCCAGGGCCTCGACTCAGTTTTGTAT-AT
193 TACT-AACGATCACGGTTTTTGGGCTAAAAACGCGTTCC-GGGCCTCGACTCAGTTTTGCATGAT
*
2204 TTTTGGCAAAAAGGCTCCTTAAAATATCTATATTCATGTAACCAAATCT-ATGCTACATTGGATT
256 TTTTGGCAAAAAGGCTCCTTGAAATATCTATATTCATGTAACCAAATCTCA-GCTACATTGGATT
* *
2268 AAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCTATTTAATTAGGAATAAATTCTGGAAAA
320 AAAGGATTTGTTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAA
* * *
2333 AAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTTTAGTTGCATTGAGT
383 AAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAA---TCTTTTT-G--GCATTGA-T
* ** *
2398 TATATATTTTTTTCTGAGTATTGTGGCAAAGAATTGAGAAAAAAATTTTCAAGTCAACTTATTCA
441 T-TATATTTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGT---C--AGT--
* *
2463 AAATTTTAGCCGAAATCGTGTAC-CATCACGGTTTTTGGCTAAAAACGTGTTTCTTAGCCCCAGC
498 ---TTTTAGCCGAAATCGTGTACACATCACGGTTTTTGGCTAAAAACGCGTTTCTAAGCCCC-GC
* * * * * *
2527 TCAATTTTGTATGATTTTTACGC-AAAGACTCCTTCAAATATCTATATGCATCGAACCAAATCTC
559 TCAGTTTTGCATGATTTTT-GGCAAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTC
* * * *
2591 AGCCACATTGGATATAAGATTTTTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAACT
623 AGCCACATTGGATTTAAGATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAAT
* *
2656 AAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAGAACCTTTCAATTTTTTTTGAGTT
688 AAATTCGAGAAAAAATGGAAAAACGATATTAGAAGCGTGAA-AACCCTTCAATTTTTTTTGAGTT
2721 GAATTATATA-TTTTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAATTTTTCGGGTCAGTTTTT
752 GAATTATATACTTTTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAA-TTTTCGGGTCAGTTTTT
2785 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTATTTTGGCTAAAAACTCGTTTCGAAG
816 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTATTTTGGCTAAAAACTCGTTTCGAAG
* *
2850 CCCCGACTTAATTTTGCATGATTTTTGACGCAAAGACTCCTTGAAATATCTAGATTCATCGAACC
881 CCCCGACTCAATTTTGCATGATTTTTG-CGCAAAGACTCCTTGAAATATCTATATTCATCGAACC
2915 AAATCTCAGCCACATTGGATA
945 AAATCTCAGCCACATTGGATA
* * * **
2936 TAAGGATTTGTTTTTAGGAGAATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAA
1 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAA
* * *
3001 AATGGAAAAATGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTGG
65 AATGG-AAAACGATATTAGAAGCGTGAAAAACCCATCAATCTTTTTGG
3049 CAATAAATTG
Statistics
Matches: 1754, Mismatches: 230, Indels: 175
0.81 0.11 0.08
Matches are distributed among these distances:
952 9 0.01
953 24 0.01
955 8 0.00
956 107 0.06
957 19 0.01
958 215 0.12
959 118 0.07
960 102 0.06
961 34 0.02
962 10 0.01
963 49 0.03
966 1 0.00
972 5 0.00
973 53 0.03
974 7 0.00
978 1 0.00
979 10 0.01
980 100 0.06
981 57 0.03
982 49 0.03
985 23 0.01
986 146 0.08
987 1 0.00
988 39 0.02
989 41 0.02
990 269 0.15
991 39 0.02
992 4 0.00
993 6 0.00
994 81 0.05
995 55 0.03
996 37 0.02
997 15 0.01
1000 20 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (965 bp):
TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
ATGGAAAACGATATTAGAAGCGTGAAAAACCCATCAATCTTTTTGGAGTTGAATTATATATTTTT
TCTAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTAC
TAACGATCACGGTTTTTGGGCTAAAAACGCGTTCCGGGCCTCGACTCAGTTTTGCATGATTTTTG
GCAAAAAGGCTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGCTACATTGGATTAAAGGA
TTTGTTTTTACGAGCATCTAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAATGG
AAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCATTGATTTATATTTTTTTCTG
AGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACACA
TCACGGTTTTTGGCTAAAAACGCGTTTCTAAGCCCCGCTCAGTTTTGCATGATTTTTGGCAAAAG
ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGATTTGTTTTT
ACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATAAATTCGAGAAAAAATGGAAAAACGATA
TTAGAAGCGTGAAAACCCTTCAATTTTTTTTGAGTTGAATTATATACTTTTTCTGAGTATTGTGG
CAAAGAATTGAGGAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
CATCACAGTATTTTGGCTAAAAACTCGTTTCGAAGCCCCGACTCAATTTTGCATGATTTTTGCGC
AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATA
Found at i:5495 original size:27 final size:27
Alignment explanation
Indices: 5432--5500 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 27
5422 GTTAATATGT
* *
5432 TGTTGCAATTTTTCTTCCTGGTTGGCGC
1 TGTT-CAATTTTTCTTCTTGGTTGGAGC
*
5460 TG--CAA-TTTTCTTCTTGGTTGGATC
1 TGTTCAATTTTTCTTCTTGGTTGGAGC
5484 TGTTCAATTTTTCTTCT
1 TGTTCAATTTTTCTTCT
5501 AAAAACCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 18 0.51
25 3 0.09
26 3 0.09
27 9 0.26
28 2 0.06
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (27 bp):
TGTTCAATTTTTCTTCTTGGTTGGAGC
Found at i:6868 original size:2 final size:2
Alignment explanation
Indices: 6861--6899 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
6851 CGTGGCAAAT
*
6861 TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6900 CTTCATAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11104 original size:219 final size:220
Alignment explanation
Indices: 10708--11128 Score: 551
Period size: 219 Copynumber: 1.9 Consensus size: 220
10698 TAGTTCAATG
* * *
10708 CCAAAAGGACTGGAGAACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTT
1 CCAAAAAGACTGGAGAACTTTTCACACTTTTAATATCGATTTTCATATTTTTTCTGAATTAATTT
* * * *
10773 CTAATTAAATCGAAACAAGATTCAGATGCGCATAAAAACAAATCCTTAAATTCAATGTACCTGAG
66 CAAACTAAATCGAAACAAGATTCAGATGCGCATAAAAAAAAATCCTTAAATCCAATGTACCTGAG
* *
10838 ATTTGATTAGATGAATAAAGATATTTAAAGGAGTCCCAGTGCCAAAAATCATACAAAACAGAGTC
131 ATTTGATTAGATGAATAAAGATATCTAAAGGAGTCCCAGCGCCAAAAATCATACAAAACAGAGTC
10903 GTGGCCCTGAAACGTGTTTTTAATA
196 GTGGCCCTGAAACGTGTTTTTAATA
* *
10928 CCAAAAAGATTGGAGGACTTTTCACACTTTTAATAT-GAATTTTCATA-TTTTTCTGAATTAATT
1 CCAAAAAGACTGGAGAACTTTTCACACTTTTAATATCG-ATTTTCATATTTTTTCTGAATTAATT
* *** ** **
10991 TCAAACTAAATCGACACAAGATTCAGATGCTTGTAAAAAAAAATTTTTAAATCCAATGTGGCTGA
65 TCAAACTAAATCGAAACAAGATTCAGATGCGCATAAAAAAAAATCCTTAAATCCAATGTACCTGA
** * * ** ** *
11056 GATTTGATTAGATGAATATGGGTATCTCAAGGAG-CCTTGACGCCAAAAATCATGTAAAACTGAG
130 GATTTGATTAGATGAATAAAGATATCTAAAGGAGTCCCAG-CGCCAAAAATCATACAAAACAGAG
11120 TCGTGGCCC
194 TCGTGGCCC
11129 CAGAACGCTT
Statistics
Matches: 171, Mismatches: 28, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
218 3 0.02
219 128 0.75
220 40 0.23
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (220 bp):
CCAAAAAGACTGGAGAACTTTTCACACTTTTAATATCGATTTTCATATTTTTTCTGAATTAATTT
CAAACTAAATCGAAACAAGATTCAGATGCGCATAAAAAAAAATCCTTAAATCCAATGTACCTGAG
ATTTGATTAGATGAATAAAGATATCTAAAGGAGTCCCAGCGCCAAAAATCATACAAAACAGAGTC
GTGGCCCTGAAACGTGTTTTTAATA
Found at i:12265 original size:655 final size:634
Alignment explanation
Indices: 10944--12500 Score: 1707
Period size: 655 Copynumber: 2.4 Consensus size: 634
10934 AGATTGGAGG
* * * *
10944 ACTTTTCACACTTTTAATAT-GAATTTTCATATTTTTCTGAATTAATTTCAAACTAAATCGACAC
1 ACTTTTCACAC-TTTAATATAG-TTTTTCATA---TT-TGAATTAATTTCTAATTAAATCGAAAC
* * * *
11008 AAGATTCAGATGCTTGTAAAAAAAAATTTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
60 AAGATTCAGATACTCGTAAAAAAAAATTTTTAAATCTAATGTGGCTAAGATTTGATTAGATGAAT
* * * * * * * * * *
11073 ATGGGTATCTCAAGGAGCCTTGACGCCAAAAATCATGTAAAACTGAGTCGTGGCCCCAGAACGCT
125 ATAGATATTTTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGTGG-CCCGGAACGCG
* * * *
11138 TTTTTATCCAAAAACTATGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTGG
189 TTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CG
*
11203 AAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATTTTATAATTCGACATAAAAAAGA
253 AAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATTATATAATTCGACATAAAAAAGA
* * *
11268 TTGAAGGGCTTTTAACACTTCTATTATTGTTTTTCCTAATTTTTTCAAATTAATTTCAAATTAAA
318 TTGAAGGGCTTTTAACACTTCCAATATTATTTTTCCTAATTTTTTCAAATTAATTTCAAATTAAA
* *
11333 TCAAAACAAGATTCATATAAAAAACAAATCCTTAAATTTAATGTTGCTGAGATATTGTTAGATGA
383 TCAAAACAAGATTCATATAAAAAACAAATCCTTAAATCTAATGTGGCTGAGATATTGTTAGATGA
11398 ATATAGATATTTCAAGAAGTCTTGGCACCAAAAATCATGCAAAACTGGGCTGGGCCCCGGAACGC
448 ATATAGATATTTCAAGAAGTCTTGGCACCAAAAATCATGCAAAACTGGGCTGGGCCCCGGAACGC
** *
11463 GGTTTTAGTTGAAAACTGTGATAGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAAATTTATC
513 GGTTTTAGCCGAAAACCGTGATAG-T-GT--ATG---TCA-C-AAAA-TTTG-----AA--TATC
**
11528 CAAAAGATTTTTCCTCGATTTCTAGCGAAAATACTCATAAAAAATATATAATTCAACGTTGAAAG
561 CAAAAGATTTTTCCTCGATTTCTAGCGAAAATACTCATAAAAAATATATAATTCAAAATTGAAAG
* * **
11593 GATTTGAGG
626 CATTTAAAA
11602 ACTTTTCACACATTTAATATAGTTTTTCATATATTGAATTAATTTCTAATTAAATCGAAACAAGA
1 ACTTTTCACAC-TTTAATATAGTTTTTCATAT-TTGAATTAATTTCTAATTAAATCGAAACAAGA
* * * * * * *
11667 TTCAGATTCACATAAAAACAAATTTTTAAATCTAATGTGACTAAAATTTGATTAGATGAATAAAG
64 TTCAGATACTCGTAAAAAAAAATTTTTAAATCTAATGTGGCTAAGATTTGATTAGATGAATATAG
** ** **
11732 ATATTTTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAAAACCGTGGTCTTGGAACGCGTTTT
129 ATATTTTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGTGG-CCCGGAACGCGTTTT
*
11797 TAGCCAAAAACTGTGATGCTTAGTACACGATTTCGGCTAAAAATTTTGCAAAAATTGATCCGAAA
193 TAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCT-AAAATTTTGCAAAAATTGA-CCGAAA
* * *
11862 GATATTTCCTCAATTTTTGGCTAAAATCCTCATAACAAA-TATATAATTCGACGTCAAAAAGATT
256 GATATTTCCTCAATTTTTGGCTAAAATACTCATAA-AAATTATATAATTCGACATAAAAAAGATT
* *
11926 GAAGGG-TTTTAACGCTTCCAATATTATTTTTCCT-ATTTTTTCAAATTAATTTCTAATTAAATC
320 GAAGGGCTTTTAACACTTCCAATATTATTTTTCCTAATTTTTTCAAATTAATTTCAAATTAAATC
* * * * * *
11989 GAAATAAGATTCAGATGCTCACAAAAACAAATCTTTAAGTCTAATGTGGTTGAGAT-TTGATTAG
385 AAAACAAGATTC--AT-AT-A-AAAAACAAATCCTTAAATCTAATGTGGCTGAGATATTG-TTAG
* * * *
12053 ATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCGTGCAAAACTGAG-TCGGGCCCTGG
444 ATGAATATAGATATTTCAAGAAGTCTTGGCACCAAAAATCATGCAAAACTGGGCT-GGGCCCCGG
* *
12117 AACGCGGTTTTAGCCGAAAACCGTGAT-G-GT-TG-CA-AAAA-TTG-A-CT-CGAAAGATTTTT
508 AACGCGGTTTTAGCCGAAAACCGTGATAGTGTATGTCACAAAATTTGAATATCCAAAAGATTTTT
* * ** * *
12173 CCTCGATTTCTAGTGAAAATACTCATAAAAAATATATAATT--AAATTCCCAAAAAATTGAAAG
573 CCTCGATTTCTAGCGAAAATACTCATAAAAAATATATAATTCAAAATT--GAAAGCATTTAAAA
* * *
12235 CCTTTTTCACACATTTAATAAAGTTTTTCACATTTTTCTGAATTAATTTCTAATTAAATCGAAAC
1 AC-TTTTCACAC-TTTAATATAGTTTTT--CA-TATT-TGAATTAATTTCTAATTAAATCGAAAC
* * **
12300 AAGATTTAGATACTCGT-AAAAGAAATCCTTAAAT-TCAATGTGGCTAAGATTTGATTAGATGAA
60 AAGATTCAGATACTCGTAAAAAAAAATTTTTAAATCT-AATGTGGCTAAGATTTGATTAGATGAA
*
12363 TATAGATATTTCATTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACTGAGTCG-GGCCCGGAA
124 TATAGATA-TT--TT-AAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGTGGCCCGGAA
* * * * *
12427 TGCGTTTTTAAG-CGAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAGTTTTGCAAAAATTG
185 CGCGTTTTT-AGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
*
12491 ACCTAAAGAT
249 ACCGAAAGAT
12501 TTTT
Statistics
Matches: 775, Mismatches: 99, Indels: 72
0.82 0.10 0.08
Matches are distributed among these distances:
631 3 0.00
633 60 0.08
634 25 0.03
635 1 0.00
636 57 0.07
637 63 0.08
638 43 0.06
639 6 0.01
640 34 0.04
643 3 0.00
645 4 0.01
648 2 0.00
652 2 0.00
654 38 0.05
655 192 0.25
656 88 0.11
657 5 0.01
658 33 0.04
659 116 0.15
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (634 bp):
ACTTTTCACACTTTAATATAGTTTTTCATATTTGAATTAATTTCTAATTAAATCGAAACAAGATT
CAGATACTCGTAAAAAAAAATTTTTAAATCTAATGTGGCTAAGATTTGATTAGATGAATATAGAT
ATTTTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGTGGCCCGGAACGCGTTTTTAG
CCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCGAAAGATAT
TTCCTCAATTTTTGGCTAAAATACTCATAAAAATTATATAATTCGACATAAAAAAGATTGAAGGG
CTTTTAACACTTCCAATATTATTTTTCCTAATTTTTTCAAATTAATTTCAAATTAAATCAAAACA
AGATTCATATAAAAAACAAATCCTTAAATCTAATGTGGCTGAGATATTGTTAGATGAATATAGAT
ATTTCAAGAAGTCTTGGCACCAAAAATCATGCAAAACTGGGCTGGGCCCCGGAACGCGGTTTTAG
CCGAAAACCGTGATAGTGTATGTCACAAAATTTGAATATCCAAAAGATTTTTCCTCGATTTCTAG
CGAAAATACTCATAAAAAATATATAATTCAAAATTGAAAGCATTTAAAA
Done.