Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014915.1 Corchorus olitorius cultivar O-4 contig14948, 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: 40640
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:654 original size:335 final size:336
Alignment explanation
Indices: 1--787 Score: 1285
Period size: 335 Copynumber: 2.3 Consensus size: 336
* *
1 GTTACTACACGATTTCCGGTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTT
1 GTTAGTACACGATTTCCGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTT
* *
66 TTCAGAATACTCAGAAAAAATATGTAATTCAAAGCCATAAAAATTAATGGGTTATTCACGCTTCT
66 GTCAGAATACTCAGAAAAAATATGTAATTCAAAGCCATAAAAATTAAAGGGTTATTCACGCTTCT
131 CTTATCGTTTTTCCGTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCGAGACAAAATTCAGA
131 CTTATCGTTTTTCCGTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCGAGACAAAATTCAGA
196 TGCTCGTAAAAAAAATCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCA
196 TGCTCGTAAAAAAAATCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCA
* * * *
261 AGGAGACTTTATGCCAAAAATCAAGCAAAACTGAGTCGGGGCCTCGAAATGCGTTTTTAGCC-TA
261 AGGAGACTTTATGCCAAAAATCAAGCAAAACTGAGTCGCGGCCTCGAAACGAGTTTTTAGCCAAA
*
325 AAACCGTGATG
326 AAACCGTCATG
** * *
336 GTTAGTACATTATTTCCGCTAAACTTTTGCAAAAAATTACCCGAAAATTTTTTCCTCAATTTTTT
1 GTTAGTACACGATTTCCGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTT
*
401 GTCAGAATACTCATAAAAAATATGTAATTCAAAGCCATAAAAATTAAAGGGTTATTCACGCTTCT
66 GTCAGAATACTCAGAAAAAATATGTAATTCAAAGCCATAAAAATTAAAGGGTTATTCACGCTTCT
*
466 CTTATCGTTTTTCCG-TTTTTTCCCGAATTTATTTCTAATTATTTAAATCGAGACAAAATTCAGA
131 CTTATCGTTTTTCCGTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCGAGACAAAATTCAGA
530 TGCTCGTAAAAAAAATCCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTC
196 TGCTCGTAAAAAAAAT-CTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTC
* *
595 AAGGAGACTTTATGCCAAAAATCATGCAAAATTGAG-C-CGGCACTCCGAAACGAGTTTTTAGCC
260 AAGGAGACTTTATGCCAAAAATCAAGCAAAACTGAGTCGCGGC-CT-CGAAACGAGTTTTTAGCC
658 AAAAAACCGTCATG
323 AAAAAACCGTCATG
* ** *
672 GTTATTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCCGAAAAGTTTTTCCTCAATTTTTT
1 GTTAGTACACGATTTCCGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTT
* * * * *
737 GCCAGAATAGTCAGAAATAATATGTAATTCAAAGCCAAAAAAATTGAAGGG
66 GTCAGAATACTCAGAAAAAATATGTAATTCAAAGCCATAAAAATTAAAGGG
788 CTTTTGCAAA
Statistics
Matches: 417, Mismatches: 31, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
333 3 0.01
334 67 0.16
335 234 0.56
336 113 0.27
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (336 bp):
GTTAGTACACGATTTCCGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCTCAATTTTTT
GTCAGAATACTCAGAAAAAATATGTAATTCAAAGCCATAAAAATTAAAGGGTTATTCACGCTTCT
CTTATCGTTTTTCCGTTTTTTTCCCGAATTTATTTCTAATTAATTAAATCGAGACAAAATTCAGA
TGCTCGTAAAAAAAATCTTAAATCCATTGTGGCTTAGATTTGGTTAATTGAATATAGATATTTCA
AGGAGACTTTATGCCAAAAATCAAGCAAAACTGAGTCGCGGCCTCGAAACGAGTTTTTAGCCAAA
AAACCGTCATG
Found at i:894 original size:26 final size:27
Alignment explanation
Indices: 858--909 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
848 TTTTGCAAAA
858 TTTGGCCG-AAATCGTGAACATCAATG
1 TTTGGCCGAAAATCGTGAACATCAATG
*
884 TTTGGCCGAAAATCGTGTACATCAAT
1 TTTGGCCGAAAATCGTGAACATCAAT
910 TTTTCGGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (27 bp):
TTTGGCCGAAAATCGTGAACATCAATG
Found at i:1580 original size:26 final size:26
Alignment explanation
Indices: 1551--1601 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1541 TTTGCAAAAT
*
1551 TTTGGCCGAAATCGTGTGCATCAATG
1 TTTGGCCGAAATCGTGTACATCAATG
*
1577 TTTGGCTGAAATCGTGTACATCAAT
1 TTTGGCCGAAATCGTGTACATCAAT
1602 TTTTCGGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (26 bp):
TTTGGCCGAAATCGTGTACATCAATG
Found at i:2567 original size:325 final size:325
Alignment explanation
Indices: 1941--2692 Score: 1040
Period size: 325 Copynumber: 2.3 Consensus size: 325
1931 AAACCATCAC
* * *
1941 AGTTTTGCATGATTTTCGGCAGCAAGACTCCTTAAAATATCTATTTTCATCTAACCAAATATCAG
1 AGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATCTAACCAAATATCAG
** * ** * * *
2006 ATACAATGGATTTAAGGATAAGGTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATT
66 CCACAATGGATTTAAGAATAATTTTTTAAGAGCATCTAAATTATGTTTCGATATAATTAGAAATT
* *
2071 AATTCGAAAAAATAGGAAAAATTATATTAGAAGCATGAAAAGCCCTTAAATTTTATTGGCGTTGA
131 AATTC--------AGGAAAAATGATATTAGAAGCATGAAAACCCCTTAAATTTTATTGGCGTTGA
* * * * *
2136 GTTACATATTTTGTATGAGTATTGTGGCCAAAAATTGAGGTAAAATTTTTCGGTATAGTTTTTGC
188 GTTAAATATTTTGTATGAGTATTGTGGCCAAAAATTGAGGAAAAAATTTTCGGCACAGTTTTTGC
* *
2201 AAAATTTTGGCAGAAATCGTATACTAAACATCACTGTTTTTTTGCTAAAAATGCGCGTTCTGGGG
253 AAAATTTTGGCAGAAATCGTATACTAAACATCACAG-TTTTTTGCTAAAAAAGCGCGTTCTGGGG
* **
2266 CCTCGTCTT
317 CCCCAACTT
* * *
2275 AGTTTTGCATGATTTTTGGAAGCAAGACTCCTTAAAATATTTATATTCATCTATCCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATCTAACCAAATATCAG
2340 CCACAATGGATTTAAGAATAATTTTTTAAGAGCATCTAAATTATGTTTCGATATAATTAGAAATT
66 CCACAATGGATTTAAGAATAATTTTTTAAGAGCATCTAAATTATGTTTCGATATAATTAGAAATT
* *
2405 TATTC-GGAAAAATGATATTAGAAGCCTGAAAACCCCTTAAATTTTATTGGCGTTGAGTTAAATA
131 AATTCAGGAAAAATGATATTAGAAGCATGAAAACCCCTTAAATTTTATTGGCGTTGAGTTAAATA
*
2469 TATTT-TATGAGTATTGTGGCCAGAAATTGAGGAAAAAATTTTCGGCACAGTTTTTGCAAAATTT
196 T-TTTGTATGAGTATTGTGGCCAAAAATTGAGGAAAAAATTTTCGGCACAGTTTTTGCAAAATTT
* * * * * *
2533 TGGCCGAAGTCGTGTACTAACCATCACAGTTTTTTGTTAAAAAAGCGTGTTCTGGGGCCCCAACT
260 TGGCAGAAATCGTATACTAAACATCACAGTTTTTTGCTAAAAAAGCGCGTTCTGGGGCCCCAACT
2598 T
325 T
* * * * *
2599 TGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAGTATTCATATTCTTCTAACCAAATTTCAG
1 AGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATCTAACCAAATATCAG
2664 CCACAATGGATTTAAGAATAATTTTTTAA
66 CCACAATGGATTTAAGAATAATTTTTTAA
2693 AATATTTATA
Statistics
Matches: 375, Mismatches: 42, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
324 118 0.31
325 134 0.36
326 3 0.01
334 120 0.32
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (325 bp):
AGTTTTGCATGATTTTTGGCAGCAAGACTCCTTAAAATATTTATATTCATCTAACCAAATATCAG
CCACAATGGATTTAAGAATAATTTTTTAAGAGCATCTAAATTATGTTTCGATATAATTAGAAATT
AATTCAGGAAAAATGATATTAGAAGCATGAAAACCCCTTAAATTTTATTGGCGTTGAGTTAAATA
TTTTGTATGAGTATTGTGGCCAAAAATTGAGGAAAAAATTTTCGGCACAGTTTTTGCAAAATTTT
GGCAGAAATCGTATACTAAACATCACAGTTTTTTGCTAAAAAAGCGCGTTCTGGGGCCCCAACTT
Found at i:3078 original size:58 final size:58
Alignment explanation
Indices: 3004--3123 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
2994 GCACTACTCC
*
3004 TTAAAGTATTTATATTCATCTAACCAAAT-TCCAGCCACAATGGATTTAAA-ATAATTTT
1 TTAAAATATTTATATTCATCTAACCAAATCT-CAGCCACAATGGA-TTAAAGATAATTTT
3062 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAATTTT
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAA-GATAATTTT
3121 TTA
1 TTA
3124 CGAGCATCTA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
57 5 0.09
58 41 0.71
59 12 0.21
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (58 bp):
TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGATAATTTT
Found at i:3189 original size:384 final size:386
Alignment explanation
Indices: 2306--3454 Score: 1632
Period size: 384 Copynumber: 3.0 Consensus size: 386
2296 GCAAGACTCC
* * *
2306 TTAAAATATTTATATTCATCTATCCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTAAGA
1 TTAAAATATTTATATTCATCTA-CCAAATCTCAGCCACAATGGATTAAAGGATAATTTTTTACGA
* * *
2371 GCATCTAAATTATGTTTCGATATAATTAGAAATTTATTC-G-------GAAAAATGATATTAGAA
65 GCATCTAAATTATGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGAAAAATTATATTAGAA
* * * *
2428 GCCTGAAAACCCCTTAAATTTTATTGGCGTTGAGTTAAATATATTTTATGAGTATTGTGGCCAGA
130 TCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTAAATATTTTTTATGAGTATTGTGGCCAAA
* *
2493 AATTGAGGAAAAAATTTTCGGCACAGTTTTTGCAAAATTTTGGCCGAAGTCGTGTACTAACCATC
195 AATTGAGGAAAAATTTTTCGGCACAGTTTTTGCAAAATTTTGGCCGAAATCG-GTACT-A--ATC
* * * * * *
2558 ACAGTTTTTTGTTAAAAAAGCGTGTTCTGGGGCCCCAACTTTGTTTTGCATGATTTTTGGCAGCA
256 ATAGTTTTTTGCTAAAAACGCGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCA
* * *
2623 AGACTCCTTAAAGTATTCATATTCTTCTAACCAAATTTCAGCCACAATGGATTTAAGAATAATTT
321 AGACTCCTTAAAGTATTTATATTCATCTAACCAAATTCCAGCCACAATGGATTTAAGAATAATTT
2688 T
386 T
*
2689 TTAAAATA-TT-TA-T-AT-T--C--ATCT-AGCCACAATGGATTAAAGGATAAGTTTTTACGAG
1 TTAAAATATTTATATTCATCTACCAAATCTCAGCCACAATGGATTAAAGGATAATTTTTTACGAG
2744 CATCTAAATTATGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAAAAATTATATTAGAA
66 CATCTAAATTATGTTTCGATTTAATTAGAAATTAATTCAGAAAAATA-GAAAAATTATATTAGAA
*
2809 TCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAAA
130 TCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTAAATATTTTTTATGAGTATTGTGGCCAAA
* *
2874 AAGTGA-GAAACAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATC-GTA-T-ATCATA
195 AATTGAGGAAA-AATTTTTCGGCACAGTTTTTGCAAAATTTTGGCCGAAATCGGTACTAATCATA
* * **
2935 GCTTTTTGCTAAAAACGTGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCACTA
259 GTTTTTTGCTAAAAACGCGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGA
3000 CTCCTTAAAGTATTTATATTCATCTAACCAAATTCCAGCCACAATGGATTTAA-AATAATTTT
324 CTCCTTAAAGTATTTATATTCATCTAACCAAATTCCAGCCACAATGGATTTAAGAATAATTTT
3062 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAATTTTTTACGA
1 TTAAAATATTTATATTCATCT-ACCAAATCTCAGCCACAATGGATTAAAGGATAATTTTTTACGA
* *
3127 GCATCTAAATTATGTTTCAATTTAATTAGAAATTCATTCAGAAAAATATGAAAAATTATATTAGA
65 GCATCTAAATTATGTTTCGATTTAATTAGAAATTAATTCAGAAAAATA-GAAAAATTATATTAGA
*
3192 ATCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATA-TTTTTATGAGTATTGTGAG-CA
129 ATCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTAAATATTTTTTATGAGTATTGTG-GCCA
* * *
3255 AAAATTGAGGAAAAATTTTTCGGTATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCA
193 AAAATTGAGGAAAAATTTTTCGGCACAGTTTTTGCAAAATTTTGGCCGAAATCG-GTACTAATCA
*
3320 TCACTGTTTTTTGCT-AAAACGCGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGAAG
257 T-A--GTTTTTTGCTAAAAACGCGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAG
* *
3384 CAAGACTCCTTAAAATATTTATATTCATCTAACCAAA-TCTCAGCCACAAAGGATTTAAGAATAA
319 CAAGACTCCTTAAAGTATTTATATTCATCTAACCAAATTC-CAGCCACAATGGATTTAAGAATAA
3448 TTTT
383 TTTT
3452 TTA
1 TTA
3455 CGAGCATCTG
Statistics
Matches: 689, Mismatches: 45, Indels: 57
0.87 0.06 0.07
Matches are distributed among these distances:
372 66 0.10
373 22 0.03
374 113 0.16
375 3 0.00
376 1 0.00
377 2 0.00
378 3 0.00
379 5 0.01
380 5 0.01
381 121 0.18
382 2 0.00
383 76 0.11
384 140 0.20
385 3 0.00
386 1 0.00
387 4 0.01
388 3 0.00
389 98 0.14
390 21 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (386 bp):
TTAAAATATTTATATTCATCTACCAAATCTCAGCCACAATGGATTAAAGGATAATTTTTTACGAG
CATCTAAATTATGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGAAAAATTATATTAGAAT
CCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTAAATATTTTTTATGAGTATTGTGGCCAAAA
ATTGAGGAAAAATTTTTCGGCACAGTTTTTGCAAAATTTTGGCCGAAATCGGTACTAATCATAGT
TTTTTGCTAAAAACGCGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGCAAGACT
CCTTAAAGTATTTATATTCATCTAACCAAATTCCAGCCACAATGGATTTAAGAATAATTTT
Found at i:4414 original size:651 final size:655
Alignment explanation
Indices: 3062--4976 Score: 2510
Period size: 651 Copynumber: 2.9 Consensus size: 655
3052 AAATAATTTT
*
3062 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAATTTTTTACGA
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
* * * * * *
3127 GCATCTAAATTATGTTTCAATTTAATTAGAAATTCATTCAGAAAAATATGAAAAATTATATTAGA
66 GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
* *
3192 ATCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTATGAGTATTGTGAG-CAA
131 ATCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTTGAGTATTGTG-GCCAA
* *
3256 AAATTGAGGAAAAATTTTTCGGTATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCAT
195 AAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCAT
* * *
3321 CACTGTTTTTTGCTAAAACGCGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGAAGCA
260 CACAGTTTTTTGCTAAAA-ACGCGTTCTTGGGCCCCGAC-TAGTTTTGCATGATTTTT-G-AGC-
* *
3386 AGACTCCTTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAAAGGATTTAAGAATAATTT
320 AGACTCCTT--AATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTT
*
3451 TTTACGAGCATCTGAATTATGTTTTGATTTAATTAGAAATTAATTCGGAAAAAT-------TATA
383 TTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAATATA
*
3509 TTAGAA--GTCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTTATGAGTATTT
448 TTAGAAGCGTCTGAAAAGCCCTTAAATTTT-TTGGCGTTGAGTTACATAATTTTTATGAGT-TTT
3572 -TGGGCAAAAATTGAGGAAAAATTTTTCGGGATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTA
511 GTGGGCAAAAATTGAGGAAAAATTTTTCGGGATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTA
* * **
3636 CGTT--ATCACTGTTTTTTGCTTAAAATGCGCGTTCTAGGGCCCCGACTTAGTTTTGCATGATTT
576 CGTTACATCACTGTTTTTTGCTAAAAAT-CACGTTCTAGGGCCCCGACACAGTTTTGCATGATTT
* *
3699 TTGGCAGCAAGACTTC
640 TTGACAGCAAGACTCC
*
3715 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACGA
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
* * *
3780 GCATCTGAATTATATTTTGATTTAATTAGAGATTAATTCGGAAAAATAGGAAAAATGATATTAGA
66 GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
*
3845 ATCCTGAAAAGCCCTTAAATTTTATTGGCATTGAGTTATATTATTTTTTTGAGTATTGTGGCCAA
131 ATCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATA-TATTTTTTTGAGTATTGTGGCCAA
* *
3910 AAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAGAATTTTGGCCGAAATCGTGTACTAACGAT
195 AAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCAT
* * * * *
3975 CACAGTTTTTGGCTAAAAACTCATTCTTGGGCCCGGCAC-AGTTTTGCATGATCTTTG-GC-G-C
260 CACAGTTTTTTGCTAAAAACGCGTTCTTGGGCCCCG-ACTAGTTTTGCATGATTTTTGAGCAGAC
* * * * * * *
4036 -CATGT-GTCATTGA-AAT-ATCTAACCAATTCTCAGCCACATTGGATTTAAGGAT-TTGTTTTT
324 TCCT-TAAT-ATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAT-TTTTT
* *
4096 ATGAGCATCTGAATTATGTTTCGATTTAATTAGAAAGTAATTCGGAAAAAATAGGAAAAATGATA
386 ACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAATAGG-AAAAT-AT-
* * ** * *
4161 ATT-GAAGCGTCT-AAAA-CCCTTCAGTCTTTTTGGATTTGAATTATATAATTTTTATGA-TTTT
447 ATTAGAAGCGTCTGAAAAGCCCTTAAAT-TTTTTGGCGTTGAGTTACATAATTTTTATGAGTTTT
* * * * *
4222 GTGGCCAAAAATTGAGGAAAAGTTTTTCGGGACAATTTTTGCAAAATTTTGGCCGAAATTGTGTA
511 GTGGGCAAAAATTGAGGAAAAATTTTTCGGGATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTA
* * *
4287 CGTTACATCACAGTTTTTGGCTAAAAAT-ACGTTC-ATGGGCCCCGACACAGTTTTGGATGATTT
576 CGTTACATCACTGTTTTTTGCTAAAAATCACGTTCTA-GGGCCCCGACACAGTTTTGCATGATTT
4350 TTGACAGCAAGACTCC
640 TTGACAGCAAGACTCC
* * * * **
4366 TTAAAATATCTATATTTATCTAACCAAATCTCAGCCATAATAGATTTAAGGATAAGGTTTTACGA
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
*
4431 GCATCTGAATTATGTTTCGATTTAGTTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
66 GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
*
4496 AGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAA
131 ATCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTT-TGAGTATTGTGGCCAA
* * * *
4561 AAATTGAGGAAAAATTTTTCGTGACAGTTTTTCCAAAATTTAT-GTCGAAATCATGTACTAACCA
195 AAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTT-TGGCCGAAATCGTGTACTAACCA
* *
4625 TCATAGTTTTTTGCTAAAAACGCGCGTTCTTTGGCCCCGACTTAGTTTTGCATGATTTTTGACAG
259 TCACAGTTTTTTGCTAAAAA--CGCGTTCTTGGGCCCCGAC-TAGTTTTGCATGATTTTTG--AG
*
4690 CAAGACTCCTTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAAT
319 C-AGACTCCTT--AATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAT
* * *
4755 TTTTTACGAGCATCTAAATTATGTTTCGATTTAATTAAAAATTAATTCAGAAAAATAGGAATAAT
381 TTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAA-AA-
*
4820 TATATTAGAAGC--CTGAAAAGCCCTTAAATATTATTGGCGTTGAGTTACAT-ATTTTTATGAGT
444 TATATTAGAAGCGTCTGAAAAGCCCTTAAAT-TTTTTGGCGTTGAGTTACATAATTTTTATGAGT
* ** * *
4882 ATTGTGGGCAAAAATTGAGGAAAAATTTTTCGATATAGTTTTTGCAAAATTTTGGTCAAAATCGT
508 TTTGTGGGCAAAAATTGAGGAAAAATTTTTCGGGATAGTTTTTGCAAAATTTTGGCCGAAATCGT
* *
4947 GTAC-TAACCATCATTGTTTTTTGCTAAAAA
573 GTACGTTA-CATCACTGTTTTTTGCTAAAAA
4977 CAGTGATGGT
Statistics
Matches: 1092, Mismatches: 120, Indels: 90
0.84 0.09 0.07
Matches are distributed among these distances:
641 1 0.00
642 79 0.07
643 9 0.01
644 4 0.00
645 2 0.00
646 2 0.00
647 1 0.00
649 2 0.00
650 12 0.01
651 356 0.33
652 54 0.05
653 213 0.20
654 121 0.11
657 2 0.00
659 1 0.00
660 2 0.00
661 4 0.00
662 25 0.02
663 122 0.11
664 79 0.07
665 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (655 bp):
TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
ATCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTTGAGTATTGTGGCCAAA
AATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCATC
ACAGTTTTTTGCTAAAAACGCGTTCTTGGGCCCCGACTAGTTTTGCATGATTTTTGAGCAGACTC
CTTAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGAG
CATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAATATATTAGAAGC
GTCTGAAAAGCCCTTAAATTTTTTGGCGTTGAGTTACATAATTTTTATGAGTTTTGTGGGCAAAA
ATTGAGGAAAAATTTTTCGGGATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACGTTACATCA
CTGTTTTTTGCTAAAAATCACGTTCTAGGGCCCCGACACAGTTTTGCATGATTTTTGACAGCAAG
ACTCC
Found at i:4559 original size:331 final size:330
Alignment explanation
Indices: 3062--4976 Score: 2470
Period size: 331 Copynumber: 5.8 Consensus size: 330
3052 AAATAATTTT
*
3062 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAATTTTTTACGA
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
* * * * * *
3127 GCATCTAAATTATGTTTCAATTTAATTAGAAATTCATTCAGAAAAATATGAAAAATTATATTAGA
66 GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
*
3192 ATCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATA-TTTTTATGAGTATTGTGAG-CA
131 AGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTTATGAGTATTGTG-GCCA
* *
3255 AAAATTGAGGAAAAATTTTTCGGTATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCA
195 AAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCA
* **
3320 TCACTGTTTTTTGCTAAAACGCGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGA-AG
260 TCACAGTTTTTTGCTAAAA-ATGCGTTCT-GGGCCCCGACTTAGTTTTGCATGATTTTT-GACAG
3384 CAAGACTCC
322 CAAGACTCC
* *
3393 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAAAGGATTTAAGAATAATTTTTTACGA
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
*
3458 GCATCTGAATTATGTTTTGATTTAATTAGAAATTAATTCGGAAAAAT--------T-ATATTAGA
66 GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
* * *
3514 AGTCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTTATGAGTATTTTGGGCAA
131 AGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAA
* *
3579 AAATTGAGGAAAAATTTTTCGGGATAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACGT---TA
196 AAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTAC-TAACCA
* * *
3641 TCACTGTTTTTTGCTTAAAATGCGCGTTCTAGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAG
260 TCACAGTTTTTTGCTAAAAAT--GCGTTCT-GGGCCCCGACTTAGTTTTGCATGATTTTTGACAG
*
3706 CAAGACTTC
322 CAAGACTCC
*
3715 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGAATAATTTTTTACGA
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
* * *
3780 GCATCTGAATTATATTTTGATTTAATTAGAGATTAATTCGGAAAAATAGGAAAAATGATATTAGA
66 GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
* * *
3845 ATCCTGAAAAGCCCTTAAATTTTATTGGCATTGAGTTATATTATTTTTT-TGAGTATTGTGGCCA
131 AGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACA-TATTTTTTATGAGTATTGTGGCCA
* *
3909 AAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAGAATTTTGGCCGAAATCGTGTACTAACGA
195 AAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCA
* * * *
3974 TCACAGTTTTTGGCTAAAAACT-CATTCTTGGGCCCGGCAC--AGTTTTGCATGATCTTTG---G
260 TCACAGTTTTTTGCTAAAAA-TGCGTTC-TGGGCCCCG-ACTTAGTTTTGCATGATTTTTGACAG
*
4033 C--G-C-CA
322 CAAGACTCC
* * * * * *
4038 TGT---GTCATTGA-AAT-ATCTAACCAATTCTCAGCCACATTGGATTTAAGGAT-TTGTTTTTA
1 T-TAAAAT-ATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAAT-TTTTTA
* *
4097 TGAGCATCTGAATTATGTTTCGATTTAATTAGAAAGTAATTCGGAAAAAATAGGAAAAATGATAA
63 CGAGCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAATAGGAAAAATGAT-A
* * ** * * * *
4162 TT-GAAGCGTCT-AAAA-CCCTTCAGTCTTT-TTGGATTTGAATTATATAATTTTTATGA-TTTT
126 TTAGAAGC--CTGAAAAGCCCTTAAAT-TTTATTGGCGTTGAGTTACATATTTTTTATGAGTATT
* * *
4222 GTGGCCAAAAATTGAGGAAAAGTTTTTCGGGACAATTTTTGCAAAATTTTGGCCGAAATTGTGTA
188 GTGGCCAAAAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTA
* * * ** *
4287 CGTTA-CATCACAGTTTTTGGCTAAAAATACGTTCATGGGCCCCGACACAGTTTTGGATGATTTT
253 C-TAACCATCACAGTTTTTTGCTAAAAATGCGTTC-TGGGCCCCGACTTAGTTTTGCATGATTTT
4351 TGACAGCAAGACTCC
316 TGACAGCAAGACTCC
* * * * **
4366 TTAAAATATCTATATTTATCTAACCAAATCTCAGCCATAATAGATTTAAGGATAAGGTTTTACGA
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
*
4431 GCATCTGAATTATGTTTCGATTTAGTTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
66 GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
*
4496 AGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTATATATTTTTTATGAGTATTGTGGCCAA
131 AGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAA
* * * *
4561 AAATTGAGGAAAAATTTTTCGTGACAGTTTTTCCAAAATTTAT-GTCGAAATCATGTACTAACCA
196 AAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTT-TGGCCGAAATCGTGTACTAACCA
* * *
4625 TCATAGTTTTTTGCTAAAAACGCGCGTTCTTTGGCCCCGACTTAGTTTTGCATGATTTTTGACAG
260 TCACAGTTTTTTGCTAAAAA--TGCGTTC-TGGGCCCCGACTTAGTTTTGCATGATTTTTGACAG
4690 CAAGACTCC
322 CAAGACTCC
*
4699 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATAATTTTTTACGA
1 TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
* * * * *
4764 GCATCTAAATTATGTTTCGATTTAATTAAAAATTAATTCAGAAAAATAGGAATAATTATATTAGA
66 GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
* *
4829 AGCCTGAAAAGCCCTTAAATATTATTGGCGTTGAGTTACATA-TTTTTATGAGTATTGTGGGCAA
131 AGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAA
** * * *
4893 AAATTGAGGAAAAATTTTTCGATATAGTTTTTGCAAAATTTTGGTCAAAATCGTGTACTAACCAT
196 AAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCAT
**
4958 CATTGTTTTTTGCTAAAAA
261 CACAGTTTTTTGCTAAAAA
4977 CAGTGATGGT
Statistics
Matches: 1394, Mismatches: 132, Indels: 115
0.85 0.08 0.07
Matches are distributed among these distances:
319 4 0.00
320 183 0.13
321 86 0.06
322 218 0.16
323 80 0.06
324 5 0.00
325 1 0.00
326 1 0.00
327 4 0.00
328 4 0.00
329 13 0.01
330 78 0.06
331 388 0.28
332 108 0.08
333 220 0.16
334 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (330 bp):
TTAAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATAATTTTTTACGA
GCATCTGAATTATGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAATGATATTAGA
AGCCTGAAAAGCCCTTAAATTTTATTGGCGTTGAGTTACATATTTTTTATGAGTATTGTGGCCAA
AAATTGAGGAAAAATTTTTCGGGACAGTTTTTGCAAAATTTTGGCCGAAATCGTGTACTAACCAT
CACAGTTTTTTGCTAAAAATGCGTTCTGGGCCCCGACTTAGTTTTGCATGATTTTTGACAGCAAG
ACTCC
Found at i:5571 original size:2 final size:2
Alignment explanation
Indices: 5564--5598 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5554 TAATCTAAAC
5564 AT AT AT AT 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 AT AT AT AT A
5599 ATGATAACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12192 original size:17 final size:16
Alignment explanation
Indices: 12152--12194 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
12142 CATATAATCT
*
12152 TTGATCACCGATGATC
1 TTGATCACTGATGATC
*
12168 TTGCATCACTGGTGATC
1 TTG-ATCACTGATGATC
12185 TTAGATCACT
1 TT-GATCACT
12195 AGTGGTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (16 bp):
TTGATCACTGATGATC
Found at i:18541 original size:19 final size:19
Alignment explanation
Indices: 18514--18554 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
18504 ATAATAATAA
*
18514 TAACGGTGTAAATTGAGGT
1 TAACAGTGTAAATTGAGGT
*
18533 TAACAGTGTGAATTGAGGT
1 TAACAGTGTAAATTGAGGT
18552 TAA
1 TAA
18555 TTGAGCTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (19 bp):
TAACAGTGTAAATTGAGGT
Found at i:30577 original size:2 final size:2
Alignment explanation
Indices: 30566--30600 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
30556 CATCAACTTT
30566 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30601 CTCTACAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.