Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017838.1 Corchorus olitorius cultivar O-4 contig17871, 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: 29362
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:16547 original size:29 final size:28
Alignment explanation
Indices: 16505--16559 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
16495 ATGGGGAAGC
16505 ATATTCAAGTGATAATGAAATATATATTT
1 ATATTCAAGTGATAAT-AAATATATATTT
* *
16534 ATATTGAAGTGATAATAATTATATAT
1 ATATTCAAGTGATAATAAATATATAT
16560 ATGATGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATTCAAGTGATAATAAATATATATTT
Found at i:20625 original size:15 final size:16
Alignment explanation
Indices: 20600--20629 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20590 AATAATTATT
20600 TTTAGATTATAATATA
1 TTTAGATTATAATATA
20616 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
20630 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:21700 original size:333 final size:329
Alignment explanation
Indices: 21010--24748 Score: 2607
Period size: 333 Copynumber: 11.3 Consensus size: 329
21000 AATCTTGGCA
* * * * * *
21010 ACATTGGGTTTAAGAATTTCTTTTCACGAGCTTTTGAATCTTGTTTCAATTTAATTAGAAATT-A
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * ** * *
21074 TTGTAGAAAAAATAAGAAATACGATATTA-AAAGCGTAAAAAATCCTCCACTCTTTTTGGCGTTG
66 TT-TAGAAAAAATAGGAAAAACGATATTAGAAA-CGTGAAAAGCCCTCCAATCTTTTTGGTGTTG
** * *
21138 AATTATATAT-TTTTATGAGTATTTTAACCAAAAATTGAGGAGAA-ATATTTCGTGTCAATTTTT
129 AATTATATATATTTTATGAGTATTTTAGGCAAAAATTAAGGA-AATATATTTCGGGTCAATTTTT
* * * * * * **
21201 ACAAAATTTTAGTCGAAATCATGCACTAACAAACCATCAGGGGTTTTGGCTAAAAACGCGTTCCG
193 GCAAAATTTTAGCCGAAATCGTG---T-A-ATACCATCACGGTTTTTGGCTAAAAACGCGTTTGG
* * * * * * * * *
21266 AGACTCGGCTCAATTTTGCATGATTTTTGGCTCCGAGACTACTTGAAATATCTATATTCATTTGA
253 GGCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT-A
21331 TCAAATCTCAGCC
317 TCAAATCTCAGCC
* *
21344 AAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
21409 TTTGGAAAAAATAGGAAAAACGATATTAGAAATGTCAAAAGCCCTCCAATCTTCTTGGTGTTGAA
66 TTTAGAAAAAATAGGAAAAACGATATTAGAAACGTGAAAAGCCCTCCAATCTTTTTGGTGTTGAA
* * * * * * * *
21474 TTATATTTCTTTTATGAGTATTTTAGTCAAAAATTAAAGAAATATCTTCCGGGTCGATTTTTTAC
131 TTATATATATTTTATGAGTATTTTAGGCAAAAATTAAGGAAATATATTTCGGGTC-AATTTTTGC
* *
21539 AAAATTTTA-CCTGAAATCGTGTAATAGCCATCACAGTTTTTGGCTAAAAAAGCGCTTTGGGGCC
195 AAAATTTTAGCC-GAAATCGTGTAATA-CCATCACGGTTTTTGGCTAAAAACGCG-TTTGGGGCC
** * ** * *
21603 CCGAATCAGTTTTGCATGATTTTTGGCCCCAAGACTCCTTGAGGTATCGATATTAATCTGATCAA
257 CCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT-ATCAA
21668 ATCTCAGCC
321 ATCTCAGCC
* * *
21677 ACATTGAATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTGTCGATTTAATTAGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * * * * ** *
21742 CTCAG-AAAAATATGAATAACGATATTAAGAGA-GTGAAAGGTCCTCTGATCTTTTTGGTGTTAA
66 TTTAGAAAAAATAGGAAAAACGATATT-AGAAACGTGAAAAGCCCTCCAATCTTTTTGGTGTTGA
* ** * * * * *
21805 ATTATATATATATTTTATGAGTATATTATCCAAAAATTGAGGAAAAAAATTTTGGGTCATTTTTT
130 A-T-TATATATATTTTATGAGTATTTTAGGCAAAAATTAAGGAAATATATTTCGGGTCA---ATT
* * * * *
21870 TTTGCGAAATTGTAGCCAAAATCGTG---TACCATCACGGTTTTTGGCT-GAAACGCGTTTCAGG
190 TTTGCAAAATTTTAGCCGAAATCGTGTAATACCATCACGGTTTTTGGCTAAAAACGCGTTT-GGG
*** * * * * *
21931 GCCCCAACTCAGTTTTGCATGATTTTTAGCGCCGACAATCCTTGAAATATCTATATTCATGTAAT
254 GCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT-AT
* * *
21996 AAAATATTAGCC
318 CAAATCTCAGCC
* ** *
22008 ACATTGCATTTAA-AGA-TT-TTTTTACGATAATCTGAATCTTGTTTCGATTTAATTAAAAATTA
1 ACATTGGATTTAAGA-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * *
22070 A-TT-CAAAAAATATGAAAAGCGATATTA-AAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTG
65 ATTTAGAAAAAATAGGAAAAACGATATTAGAAA-CGTGAAAAGCCCTCCAATCTTTTTGGTGTTG
* * * * * ** *
22132 AATTATATATTTTTTTTATGATTATTAT-GGCTAAAAATTGAGGAAAAACCTTTCGGGTAAATTT
129 AATTATATA--TATTTTATGAGTATTTTAGGC-AAAAATTAAGGAAATATATTTCGGGTCAATTT
* * ** * * *
22196 TTGCAAAATTTTAGCCAAAATCGTTTAATAATTTATCACGGTTTTCGACTAAAAACGTGTTTCGG
191 TTGCAAAATTTTAGCCGAAATCGTGTAAT-A-CCATCACGGTTTTTGGCTAAAAACGCGTTT-GG
* * * * * * * * *
22261 GG-CTCAGATCAATTTTGAATGATTTTTGGTGTCGAGACTCATTGAAATATCTATATTCATC---
253 GGCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAT
*
22322 C-AA-C-CAAACC
318 CAAATCTC-AGCC
* * *
22332 -CA---G-----A-CA-TTGTTTTTACAAGCATCTGAATCATT-TTTCGTTTTAATTAGAAATTA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATTTAATTAGAAATTA
* * * ** * * *
22385 ATTCGGAAAAAAAAAGAAGGAAAAACGATATTAGAAGTGTGAAAAGCCCTTCAATCTATTTGGCG
65 ATT---TAGAAAAAA-TAGGAAAAACGATATTAGAAACGTGAAAAGCCCTCCAATCTTTTTGGTG
* * * *
22450 TTGAATTATATAT-TTTTATGATTATTGTT--GCTAAAA-TGAGGAAAAATTATATATTTTGGGT
126 TTGAATTATATATATTTTATGAGTATT-TTAGGCAAAAATTAAGG---AA--ATATATTTCGGGT
* * * ***** *
22511 -AATTTTTTGCAAAATATTAG-CGAAATCGTGTAACATCACTTTTTTTTTTTGGCTAAAAATGCG
185 CAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAATACCA-TCACGGTTTTTGGCTAAAAACGCG
* * * * * *
22574 TTCTGGGGCCCCGAGTCAGTTTTACATGATTTTTGGCACCAAGATTCCTTGAAATATCAATGTTC
248 TT-TGGGGCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTC
* *
22639 ATATACTCAAATCTCAGTC
312 ATCTA-TCAAATCTCAGCC
* * * * * *
22658 ACAATGGATTTAAGGA-TT-TTTTTATGAGCATTTAAATCTTGTTTCGATTTAATAAGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * ** * * * * * *
22721 -TTCGAAAAAAGTAGGAAAAAACAATATTAGAAGTGTAAAAAACACTTCAATATTTTTGGGGTTG
66 TTTAGAAAAAA-TAGG-AAAAACGATATTAGAAACGTGAAAAGCCCTCCAATCTTTTTGGTGTTG
** * * * *
22785 AATTATATATATTTTATGAGTATTTTAATCCAAAATTGAGGAAATATCTTTCCGGTCAATTTTTG
129 AATTATATATATTTTATGAGTATTTTAGGCAAAAATTAAGGAAATATATTTCGGGTCAATTTTTG
* * * * *** *
22850 CAAAATTTTAGCCGAAATCGTGTTATAATCATCACGGTTTTTTGCTAAAAATGCGTTCCACGGCT
194 CAAAATTTTAGCCGAAATCGTGTAAT-ACCATCACGGTTTTTGGCTAAAAACGCGTT-TGGGGCC
* * * * * * *
22915 CCGGGTCAATTTTGCATGATTTTTGGCGCTAAAACTCCTTGAGATATCCATATTCATCTAGTTAT
257 CCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTA-TCAA
*
22980 ATATCAGCC
321 ATCTCAGCC
* * *
22989 ACATTGCATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATAAGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * *
23054 TTCAGAAAAATATA-AAAAAACGATATTA-AAAGCGTGAAAAGTCCTCCAATCTTTTTGGGGTTG
66 TTTAGAAAAA-ATAGGAAAAACGATATTAGAAA-CGTGAAAAGCCCTCCAATCTTTTT--GG-TG
* * * *
23117 AATATATATATATATATATATATATATATTATGAGTATTTTAGACAAAAATTGAGGAAAAATATT
126 ------T-T-GA-AT-TATATATAT-T-TTATGAGTATTTTAGGCAAAAATTAAGGAAATATATT
* * * * *
23182 TCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTATATATTAGTCGAGATCACAGTTTTTGGC
179 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-A-TA--C--CATCACGGTTTTTGGC
* * * *
23247 TAAAAACGCGTTCCGGGG-CCCGGTTCAGTGTTGCATTGCATGATTTTTGGCGTCGAGACTCCTT
238 TAAAAACGCGTT-TGGGGCCCCGGGTCA--GTT---TTGCATGATTTTTGGCGCCAAGACTCCTT
* *
23311 GAAATATCTATATTCATTTAACTAAATCTCAGCC
297 GAAATATCTATATTCATCTATC-AAATCTCAGCC
* ** * * * **
23345 ACATTGGATTTTAGAATTTG--TAAAAGAAGCATCCGAATCATGTTTTAATTTAATTAGAAATTA
1 ACATTGGATTTAAGAATTTGTTTTTACG-AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * * *
23408 ATTCAGAAAATAATAGGAAAAACGATAGTAGAAGCAT-AAAAGCCCTTCAACCTTTTTGTTGTTG
65 ATTTAGAAAA-AATAGGAAAAACGATATTAGAAACGTGAAAAGCCCTCCAATCTTTTTGGTGTTG
* * **
23472 AATTATATA-ATTTTTATGAGTATTGT-GGCTAAAAATTGAGGAAATA-ACTTTCAAGTCAATTT
129 AATTATATATA-TTTTATGAGTATTTTAGGC-AAAAATTAAGGAAATATA-TTTCGGGTCAATTT
* * * * * * * **
23534 TTACAAAATTCTAGCCGAAGTCGTGTAATAATCATCACAGTATTTGGCT-AAAACGCATTCCGGG
191 TTGCAAAATTTTAGCCGAAATCGTGTAAT-ACCATCACGGTTTTTGGCTAAAAACGCGTTTGGGG
** * * * * * *
23598 -CCCGCCTAAGTTTTGCATGATTTTTGGTGTCAAGACTCTTTGAGATATCCATATTCATCTAATC
255 CCCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT-ATC
* * *
23662 AAACCTTAGCT
319 AAATCTCAGCC
* * * * * *
23673 ATATTGGATTT-A-AATTTATTTTTACAAGCATCTGAATCTTTTTTCGATTAAATTATAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* ** * *
23736 TTCAG-AAAAATTTGAAAAACGATATTA-AAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTAA
66 TTTAGAAAAAATAGGAAAAACGATATTAGAAA-CGTGAAAAGCCCTCCAATCTTTTTGGTGTTGA
* * * * * *
23799 ATTATATATATTTTATGAGTATCTTAGCCAAAAAATTGACGGAAAAATTTTTTGGGT-AATTTTT
130 ATTATATATATTTTATGAGTATTTTAGGC-AAAAATT-AAGGAAATATATTTCGGGTCAA-TTTT
* ** * * *
23863 TGTAAAATTTTAGTTGAAAT--TG------CGT-A--ATTTTT-GCTAAAAACGCGTTTCGGAGC
192 TGCAAAATTTTAGCCGAAATCGTGTAATACCATCACGGTTTTTGGCTAAAAACGCGTTT-GGGGC
* * * * * *
23916 CCCGGCTTAGTTTTGCATGATTTTTAGCGCCGAGACCCCTTGAAAAATCTATATTCATCTAATTA
256 CCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATC----TA
23981 TCAAATCTCAGCC
317 TCAAATCTCAGCC
* * * * * *
23994 ACATTGAATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGCTTCAATTTAATTTGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * *
24059 TTCA-AAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTCGA
66 TTTAGAAAAAATAGGAAAAACGATATTAGAAA-CGTGAAAAGCCCTCCAATCTTTTTGGTGTTGA
* * * * * * **
24122 ATTATATATATATTATGAGTATTGT-GGCTAAAAATTCAGGAAAAATATTTTGGATTGATTTTTG
130 ATTATATATATTTTATGAGTATTTTAGGC-AAAAATTAAGGAAATATATTTCGGGTCAATTTTTG
* * *
24186 -AAAATTTTAGCCAAAATCGTG---TACAATCACGGTTTTTTCGCTAAAAACGCGTTTCGGGG-C
194 CAAAATTTTAGCCGAAATCGTGTAATACCATCACGG-TTTTTGGCTAAAAACGCGTTT-GGGGCC
* ** * * *
24246 CCTGGTCAGTTTTGCATGATTTTTTGTAG-CAAAACTCCTTGAAATATCTATATTCATATAACTA
257 CCGGGTCAGTTTTGCATGA-TTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTATC-A
24310 AATCAT-AGCC
320 AATC-TCAGCC
* * * * *
24320 ACATTGGATTTAAGGATTTGTTATTACGAGCATTTGAATCATGTTTTGATTTAATTAGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * *
24385 TTTGAAAAAAGAAATAGGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTT
66 TTT--AGAAA-AAATAGGAAAAACGATATTAGAAACGTGAAAAGCCCTCCAATCTTTTTGGTGTT
* * * * ** *
24450 GAATTATATATTTTTTATGAGTATTGT-GGCTAAAAATTGA-GAAAAATATTTCAAGTTAATTTT
128 GAATTATATATATTTTATGAGTATTTTAGGC-AAAAATTAAGGAAATATATTTCGGGTCAATTTT
* * * * **
24513 TGAAAAATTTTAGCCGAAATCGT-T-TTACCATCATGGTTTTTTTTGGCTAAAATCGCGTTCCGG
192 TGCAAAATTTTAGCCGAAATCGTGTAATACCATCACGG---TTTTTGGCTAAAAACGCGTTTGGG
* * * * * * * * *
24576 GCCCTGTGTTAGTTTTGCATGAGTTTTGGCGTCAAGACTCATTAAAATATATTTATATTCATGTA
254 GCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GAA-ATATCTATATTCATCT-
*
24641 ACCAAATCTCA-CAC
316 ATCAAATCTCAGC-C
* * ** * * * *
24655 ACATTGTATTTAAGGATTTGTTTTTACGAGTTTTTAAATCATGTTTCGATTTAATCAGAAATTAA
1 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
*
24720 TTTGGAAATAAATAGGAAAAACGATATTA
66 TTTAGAAA-AAATAGGAAAAACGATATTA
24749 TAAGCTTTAA
Statistics
Matches: 2717, Mismatches: 522, Indels: 333
0.76 0.15 0.09
Matches are distributed among these distances:
314 3 0.00
315 41 0.02
316 21 0.01
317 6 0.00
318 66 0.02
319 28 0.01
320 77 0.03
321 117 0.04
322 16 0.01
323 123 0.05
324 6 0.00
325 51 0.02
326 134 0.05
327 55 0.02
328 176 0.06
329 112 0.04
330 220 0.08
331 232 0.09
332 184 0.07
333 269 0.10
334 187 0.07
335 184 0.07
336 52 0.02
337 2 0.00
338 1 0.00
339 5 0.00
340 61 0.02
341 3 0.00
342 8 0.00
343 3 0.00
344 3 0.00
345 10 0.00
346 2 0.00
347 67 0.02
348 2 0.00
349 1 0.00
351 7 0.00
352 30 0.01
353 3 0.00
354 3 0.00
355 61 0.02
356 83 0.03
357 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (329 bp):
ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTTAGAAAAAATAGGAAAAACGATATTAGAAACGTGAAAAGCCCTCCAATCTTTTTGGTGTTGAA
TTATATATATTTTATGAGTATTTTAGGCAAAAATTAAGGAAATATATTTCGGGTCAATTTTTGCA
AAATTTTAGCCGAAATCGTGTAATACCATCACGGTTTTTGGCTAAAAACGCGTTTGGGGCCCCGG
GTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTATCAAATCTC
AGCC
Found at i:22994 original size:981 final size:980
Alignment explanation
Indices: 21361--24474 Score: 2334
Period size: 981 Copynumber: 3.1 Consensus size: 980
21351 ATTTAAGGAT
* * *
21361 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAA
1 TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAA
* *
21426 AAACGATATTAGAAATGTCAAAAGCCCTCCAATCTTCTTGGTGTTGAATTATATTTCTTTTATGA
66 AAACGATATTAGAAATGTCAAAAGCCCTCCAATCTTCTTGGCGTTGAATTATATATCTTTTATGA
* * * * *
21491 GTATTTTAGTCAAAAATTAAAGAAATATCTTCCGGGTCGATTTTTTACAAAATTTTACCTGAAAT
131 GTATTTTAGTCAAAAATGAAAAAAATATATTCCGGGTCAATTTTTTACAAAATATTACCTGAAAT
* *
21556 CGTGTAATAGCCATCACAGTTTTTGGCTAAAAAAGCGCTTTGGGGCCCCGAATCAGTTTTGCATG
196 CGTGTAACAGCCATCACAGTTTTTGGCTAAAAAAGCGCTTTGGGGCCCCGAATCAGTTTTACATG
* ** * * *
21621 ATTTTTGGCCCCAAGACTCCTTGAGGTATCGATATTAATCTGATCAAATCTCAGCCACATTGAAT
261 ATTTTTGGCACCAAGACTCCTTGAAATATCAATATTAATATGATCAAATCTCAGCCACAATGAAT
* *
21686 TTAAGAATTTGTTTTTACAAGCATCTGAATCTTGTGTCGATTTAATTAGAAATTAACTCAGAAAA
326 TTAAGAATTTGTTTTTACAAGCATCTAAATCTTGTGTCGATTTAATAAGAAATTAACTCAGAAAA
* * * *** * * *
21751 ATATGAATAACGATATTAAGAGAGTGAAAGGTCCTCTGATCTTTTTGGTGTTAAATTATATATAT
391 ATAGGAAAAACAATATTAAGAGAGTGAAAAAACCTCTAATATTTTTGGGGTTAAATTATATATAT
** * *
21816 ATTTTATGAGTATATTATCCAAAAATTGAGGAAAAAAATTTTGGGTCATTTTTTTTTGCGAAATT
456 ATTTTATGAGTATATTATCCAAAAATTGAGGAAAAAAATTTCCGGTCA--TATTTTTGCAAAATT
* * * *
21881 GTAGCCAAAATCGTGTACCATCACGGTTTTTGGCTGAAACGCGTTTCAGGGCCCCAACTCAGTTT
519 GTAGCCAAAATCGTGTACCATCACGGTTTTTGGCTAAAACGCGTTCCACGGCCCCAACTCAATTT
* * * *
21946 TGCATGATTTTTAGCGCCGACAATCCTTGAAATATCTATATTCATGTAATAAAATATTAGCCACA
584 TGCATGATTTTTAGCGCCGAAAATCCTTGAAATATCCATATTCATCTAATAAAATATCAGCCACA
*
22011 TTGCATTTAAAG-A-TT-TTTTTACGATAATCTGAATCTTGTTTCGATTTAATTAA-AAATTAAT
649 TTGCATTT-AAGTATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAA-TAAGAAATTAAT
* * * *
22072 TCA-AAAAATAT-GAAAAGCGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTGTTGAAT
712 TCAGAAAAATATAAAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGGGTTGAAT
22135 -TATATATTTTTTTTATGATTATTATGGCTAAAAATTGAGGAAAAACCTTTCGGGTAAATTTTTG
777 ATATATATTTTTTTTATGATTATTATGGCTAAAAATTGAGGAAAAACCTTTCGGGTAAATTTTTG
22199 CAAAATTTTAGCCAAAATCGTTTAATAATTTATCACGGTTTTCGACTAAAAACGTGTTTCGGGGC
842 CAAAATTTTAGCCAAAATCGTTTAATAATTTATCACGGTTTTCGACTAAAAACGTGTTTCGGGGC
22264 TCAGATCAATTTTGAATGATTTTTGGTGTCGAGACTCATTGAAATATCTATATTCATCCAACCAA
907 TCAGATCAATTTTGAATGATTTTTGGTGTCGAGACTCATTGAAATATCTATATTCATCCAACCAA
22329 ACCCAGACA
972 ACCCAGACA
*
22338 TTGTTTTTACAAGCATCTGAATCATT-TTTCGTTTTAATTAGAAATTAATTCGGAAAAAAAAAGA
1 TTGTTTTTACAAGCATCTGAATC-TTGTTTCGATTTAATTAGAAATTAATTCGG---AAAAAA-A
* * *
22402 AGGAAAAACGATATTAGAAGTGTGAAAAGCCCTTCAATCTAT-TTGGCGTTGAATTATATAT-TT
61 AGGAAAAACGATATTAGAAATGTCAAAAGCCCTCCAATCT-TCTTGGCGTTGAATTATATATCTT
* * ** *
22465 TTATGATTATTGTT-G-CTAAAATGAGGAAAAATTATATATTTTGGGT-AATTTTTTGCAAAATA
125 TTATGAGTATT-TTAGTCAAAAATGA--AAAAA--ATATATTCCGGGTCAATTTTTTACAAAATA
* * ***** * *
22527 TTAGC-GAAATCGTGTAACA-TCACTTTTTTTTTTTGGCTAAAAATGCG-TTCTGGGGCCCCGAG
185 TTACCTGAAATCGTGTAACAGCCA-TCACAGTTTTTGGCTAAAAAAGCGCTT-TGGGGCCCCGAA
* * *
22589 TCAGTTTTACATGATTTTTGGCACCAAGATTCCTTGAAATATCAATGTTCATAT-ACTCAAATCT
248 TCAGTTTTACATGATTTTTGGCACCAAGACTCCTTGAAATATCAATATTAATATGA-TCAAATCT
* * * ** * *
22653 CAGTCACAATGGATTTAAGGA-TT-TTTTTATGAGCATTTAAATCTTGTTTCGATTTAATAAGAA
312 CAGCCACAATGAATTTAAGAATTTGTTTTTACAAGCATCTAAATCTTGTGTCGATTTAATAAGAA
*
22716 ATTAATTC-GAAAAAAGTAGGAAAAAACAATATT-AGA-AGTGTAAAAAACACT-TCAATATTTT
377 ATTAACTCAG-AAAAA-TAGG-AAAAACAATATTAAGAGAGTG-AAAAAAC-CTCT-AATATTTT
* * * **
22777 TGGGGTTGAA-T-TATATATATTTTATGAGTATTTTAATCC-AAAATTGAGGAAATATCTTTCCG
436 TGGGGTTAAATTATATATATATTTTATGAGTATATT-ATCCAAAAATTGAGGAAAAAAATTTCCG
* * * * *
22839 GTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTTATAATCATCACGGTTTTTTGCTAAAAATG
500 GTCATATTTTTGCAAAATTGTAGCCAAAATCGTG---T-ACCATCACGGTTTTTGGCT-AAAACG
* *** * * *
22903 CGTTCCACGGCTCCGGGTCAATTTTGCATGATTTTTGGCG-CTAAAACTCCTTGAGATATCCATA
560 CGTTCCACGGCCCCAACTCAATTTTGCATGATTTTTAGCGCCGAAAA-TCCTTGAAATATCCATA
* * * *
22967 TTCATCTAGTTATATATCAGCCACATTGCATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTG
624 TTCATCTAATAAAATATCAGCCACATTGCATTTAAGTATTTGTTTTTACGAGAATCTGAATCTTG
*
23032 TTTCGATTTAATAAGAAATTAATTCAGAAAAATATAAAAAAACGATATTAAAAGCGTGAAAAGTC
689 TTTCGATTTAATAAGAAATTAATTCAGAAAAATATAAAAAAACGATATTAAAAGCGTGAAAAGCC
*
23097 CTCCAATCTTTTTGGGGTTGAATATATATATATATATATATATATAT-ATTATGAGTATTTTAGA
754 CTCCAATCTTTTTGGGGTTGAATATATATAT-T-T-T-T-T-T-TATGATTAT---TA---T-GG
** * * * * *
23161 C-AAAAATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTATATATT
805 CTAAAAATTGAGGAAAAACCTTTCGGGTAAATTTTTGCAAAATTTTAGCCAAAATCGT-T-TAAT
* ** * * * * * * * * * *
23225 AGTCGAGATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGTTCAGTGTTGCATTGCATGA
868 AAT--TTATCACGGTTTTCGACTAAAAACGTGTTTCGGGGCTCAGATCA--ATT---TTGAATGA
* * ** * *
23290 TTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATTTAACTAAATCTCAGCCACA
926 TTTTTGGTGTCGAGACTCATTGAAATATCTATATTCATCCAACCAAA-CCCAG--ACA
* * * ** *
23348 TTGGATTTTAGAATTTGTAAAAGAAGCATCCGAATCATGTTTTAATTTAATTAGAAATTAATTCA
1 TT-G----T----TTT-T---ACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG
* * *** * * * **
23413 GAAAATAATAGGAAAAACGATAGTAGAAGCAT-AAAAGCCCTTCAACCTTTTTGTTGTTGAATTA
53 GAAAA-AAAAGGAAAAACGATATTAGAAATGTCAAAAGCCCTCCAATCTTCTTGGCGTTGAATTA
* * ** * **
23477 TATAAT-TTTTATGAGTATTGT-GGCTAAAAATTG-AGGAAATA-ACTTTCAAGTCAA-TTTTTA
117 TAT-ATCTTTTATGAGTATTTTAGTC-AAAAA-TGAAAAAAATATA-TTCCGGGTCAATTTTTTA
* * ** * **
23537 CAAAAT-TCTAGCC-GAAGTCGTGTAATAATCATCACAGTATTTGGCT--AAAA-CGCATTCCGG
178 CAAAATAT-TA-CCTGAAATCGTGTAACAGCCATCACAGTTTTTGGCTAAAAAAGCGC-TTTGGG
** * * *** * * * * * *
23597 G-CCCGCCTAAGTTTTGCATGATTTTTGGTGTCAAGACTCTTTGAGATATCCATATTCATCTAAT
240 GCCCCGAATCAGTTTTACATGATTTTTGGCACCAAGACTCCTTGAAATATCAATATTAATATGAT
* * * * * * * * * * *
23661 CAAACCTTAGCTATATTGGATTT-A-AATTTATTTTTACAAGCATCTGAATCTTTTTTCGATTAA
305 CAAATCTCAGCCACAATGAATTTAAGAATTTGTTTTTACAAGCATCTAAATCTTGTGTCGATTTA
* * * ** * * * ** * *
23724 ATTATAAATTAATTCAGAAAAATTTGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTT
370 ATAAGAAATTAACTCAGAAAAATAGGAAAAACAATATTAAGAGAGTGAAAAAACCTCTAATATTT
* * * ** *
23789 TTGGTGTTAAA-T-TATATATATTTTATGAGTATCTTAGCCAAAAAATTGACGGAAAAATTTTTT
435 TTGGGGTTAAATTATATATATATTTTATGAGTATATTATCC-AAAAATTGA-GGAAAAAAATTTC
* * * * *** * *
23852 GGGTAAT-TTTTTGTAAAATTTTAGTTGAAAT--TG---CGT-A--ATTTTT-GCTAAAAACGCG
498 CGGTCATATTTTTGCAAAATTGTAGCCAAAATCGTGTACCATCACGGTTTTTGGCT-AAAACGCG
* * ** * * * ** * *
23907 TTTC-GGAGCCCCGGCTTAGTTTTGCATGATTTTTAGCGCCGAGACCCCTTGAAAAATCTATATT
562 TTCCACG-GCCCCAACTCAATTTTGCATGATTTTTAGCGCCGAAAATCCTTGAAATATCCATATT
* * * * *
23971 CATCTAATTATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATATGAATCTT
626 CATCTAA-TA--AAATATCAGCCACATTGCATTTAAGTATTTGTTTTTACGAGAATCTGAATCTT
* * ** * * *
24036 GCTTCAATTTAATTTGAAATTAATTCAAAAAAATAT-GAAAAACGATATTAAAAGCGTGAAAAGT
688 GTTTCGATTTAATAAGAAATTAATTCAGAAAAATATAAAAAAACGATATTAAAAGCGTGAAAAGC
* * * * * * *
24100 CCTCCAATCTTTTTGGCGTCGAAT-TATATA--TATATTATGAGTATTGTGGCTAAAAATTCAGG
753 CCTCCAATCTTTTTGGGGTTGAATATATATATTTTTTTTATGATTATTATGGCTAAAAATTGAGG
** * * ** * *
24162 AAAAATATTTTGGATTGATTTTTG-AAAATTTTAGCCAAAATCGTGT-A-CA---ATCACGGTTT
818 AAAAACCTTTCGGGTAAATTTTTGCAAAATTTTAGCCAAAATCGTTTAATAATTTATCACGG--T
* * * * * * * * * *
24221 TTTCG-CTAAAAACGCGTTTCGGGGCCCTGGTCAGTTTTGCATGATTTTTTGTAG-CAAAACTCC
881 TTTCGACTAAAAACGTGTTTCGGGGCTCAGATCAATTTTGAATGATTTTTGGT-GTCGAGACTCA
* * * *
24284 TTGAAATATCTATATTCATATAACTAAATCATAGCCACATTGGATTTAAGGA
945 TTGAAATATCTATATTC--AT--C-CAACCA-AACC-CA---G-----A-CA
* * * * * * *
24336 TTTGTTATTACGAGCATTTGAATCATGTTTTGATTTAATTAGAAATTAATTTGAAAAAAGAAATA
1 -TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-GAAAA-AAA-A
** * * * * *
24401 GGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTT
62 GGAAAAACGATATTAGAAATGTCAAAAGCCCTCCAATCTTCTTGGCGTTGAATTATATATCTTTT
24466 ATGAGTATT
127 ATGAGTATT
24475 GTGGCTAAAA
Statistics
Matches: 1718, Mismatches: 292, Indels: 252
0.76 0.13 0.11
Matches are distributed among these distances:
975 38 0.02
976 63 0.04
977 55 0.03
978 29 0.02
979 153 0.09
980 97 0.06
981 286 0.17
982 23 0.01
983 53 0.03
984 10 0.01
985 47 0.03
986 8 0.00
987 2 0.00
988 23 0.01
989 33 0.02
990 1 0.00
991 1 0.00
992 7 0.00
993 3 0.00
994 3 0.00
995 7 0.00
997 1 0.00
998 51 0.03
999 4 0.00
1000 5 0.00
1001 1 0.00
1002 95 0.06
1003 15 0.01
1004 51 0.03
1005 80 0.05
1006 2 0.00
1007 49 0.03
1008 4 0.00
1010 5 0.00
1011 1 0.00
1012 3 0.00
1013 54 0.03
1014 20 0.01
1015 151 0.09
1016 10 0.01
1017 23 0.01
1018 25 0.01
1019 41 0.02
1020 40 0.02
1021 6 0.00
1022 3 0.00
1023 36 0.02
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (980 bp):
TTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAA
AAACGATATTAGAAATGTCAAAAGCCCTCCAATCTTCTTGGCGTTGAATTATATATCTTTTATGA
GTATTTTAGTCAAAAATGAAAAAAATATATTCCGGGTCAATTTTTTACAAAATATTACCTGAAAT
CGTGTAACAGCCATCACAGTTTTTGGCTAAAAAAGCGCTTTGGGGCCCCGAATCAGTTTTACATG
ATTTTTGGCACCAAGACTCCTTGAAATATCAATATTAATATGATCAAATCTCAGCCACAATGAAT
TTAAGAATTTGTTTTTACAAGCATCTAAATCTTGTGTCGATTTAATAAGAAATTAACTCAGAAAA
ATAGGAAAAACAATATTAAGAGAGTGAAAAAACCTCTAATATTTTTGGGGTTAAATTATATATAT
ATTTTATGAGTATATTATCCAAAAATTGAGGAAAAAAATTTCCGGTCATATTTTTGCAAAATTGT
AGCCAAAATCGTGTACCATCACGGTTTTTGGCTAAAACGCGTTCCACGGCCCCAACTCAATTTTG
CATGATTTTTAGCGCCGAAAATCCTTGAAATATCCATATTCATCTAATAAAATATCAGCCACATT
GCATTTAAGTATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATAAGAAATTAATTCAG
AAAAATATAAAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGGGTTGAATATAT
ATATTTTTTTTATGATTATTATGGCTAAAAATTGAGGAAAAACCTTTCGGGTAAATTTTTGCAAA
ATTTTAGCCAAAATCGTTTAATAATTTATCACGGTTTTCGACTAAAAACGTGTTTCGGGGCTCAG
ATCAATTTTGAATGATTTTTGGTGTCGAGACTCATTGAAATATCTATATTCATCCAACCAAACCC
AGACA
Found at i:23125 original size:2 final size:2
Alignment explanation
Indices: 23118--23145 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23108 TTGGGGTTGA
23118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23146 TATGAGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.