Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016331.1 Corchorus olitorius cultivar O-4 contig16364, 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: 72263
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:938 original size:320 final size:320
Alignment explanation
Indices: 61--1286 Score: 1182
Period size: 331 Copynumber: 3.8 Consensus size: 320
51 ACCTGAAAAG
* * * * ** *
61 TTTTTCATGAATTTTTTGCCACAATACACAG-AAAAATATATAATTCAACTCCTGAAAAATTGAC
1 TTTTTC-TCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAAC-GCAAAAAAATTGAA
* * *
125 GGGCTTTT-CAC-ACTTCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAACTAAATCG
64 GGGCTTTTGCACGA-TTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCAAACTAAATCG
* * * * *
188 AAACAAGATTCGGATGCTAATAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGAT
128 AAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
* * * *
253 GAATATAGATATTCCAAGGAGTCTTTGCGCCAAAAATCT-TGCAAAATTGAGTCGGGGCTCCGGA
193 GAATATAGATATTTCGAGGACTCTTTGCGCCAAAAAT-TATGCAAAATTGAGTCGGGGCTCCGAA
* *
317 ACGCGTTTTTAGCCAAAAATCGTGTTGGTTAGTACACGATTTC-AGCTAAAATTTTAG-AAAAAT
257 ACGCGTTTTTAGCCAAAAATC----------GT-CACGA-TTCGA-TTAAAATTTT-GCAAAAAC
* *
380 TGACCCAAAAATT
308 TGACCCGAAATTT
* *
393 GTTTTCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAATGC-AAAAAA-TGAAGG
1 TTTTTCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCAAAAAAATTGAAGG
* * * * * *
456 GTTTTTTCACGCTTATAATATCATTTTTCTATTTTATTTCCGAATTAATTTCTAACTAAATCGAA
66 GCTTTTGCACGATTCTAATATCATTTTTCCATTTT-TTTCCGAATTAATTTCAAACTAAATCGAA
* * * * * *
521 ACAAGATTCAGATGCTCGTAAAAATAAATCC-TAATAACCAATGTGGTTGAGATTTGGTTCGATA
130 ACAAGATTCAGATGCTCATAAAAACAAATCCTTAA-ATCCAATGTGGCTGAGATTTGGTTAGATG
* *
585 AATATAGATATTTCGAGGACTCTTTGCGCCAAAAATTATGCAAAATTGCGTCGAGGCTCCGAAAC
194 AATATAGATATTTCGAGGACTCTTTGCGCCAAAAATTATGCAAAATTGAGTCGGGGCTCCGAAAC
* * * *
650 GCTTTTTTAGCCAGAAATCG-CACGATTCGATTGAAATTTTGCAAAAACTGGCCCGAAATTT
259 GCGTTTTTAGCCAAAAATCGTCACGATTCGATTAAAATTTTGCAAAAACTGACCCGAAATTT
*
711 TTTTTCTCAATTCTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCAAAAAAATTTGAAG
1 TTTTTCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCAAAAAAA-TTGAAG
* * ** *
776 GG-TTTTGCACGAATCTAAAATTGTTTTTCCATTTTATTTTCCGAATTTATTTCAAACTAAATCG
65 GGCTTTTGCACGATTCTAATATCATTTTTCCA-TTT-TTTTCCGAATTAATTTCAAACTAAATCG
* *
840 AAACAAGATTCAGATGCTCGTAAAAA-AAAACCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
128 AAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
*
904 GAATATAGATATTTCGAGGACTCTTT-CTGCCAAAAATCATGCAAAATTGAGAT-GGGGC-CCGA
193 GAATATAGATATTTCGAGGACTCTTTGC-GCCAAAAATTATGCAAAATTGAG-TCGGGGCTCCGA
* * * * * * * * *
966 AACACGTTTTTAGCCCAAAAACCGTGATGGTT--AGTACACGATTTCGGCTAAAAACTTACCCG-
256 AACGCGTTTTTAG-CCAAAAATCGTCACGATTCGATTA-A-AATTT-TGC-AAAAACTGACCCGA
1028 AATTT
316 AATTT
* * * * *
1033 TTCTTTTTCAAAATTTTTTGCAACAATACTCAGAAAAAATATATAATTAAACGCCAAAAAGATTG
1 TT-TTTCTC--AATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACG-CAAAAAAATTG
* * * *
1098 ACGGGC-TTTGCACGCTTCTAATATCATTTTTCCATTTTTTT-CGAATTAA-TTAATAATTAAAG
62 AAGGGCTTTTGCACGATTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCA-AACTAAA-
* * * *
1160 TCGAAACAAGATTCAGATGCTCATAAAAACAAATCTTTAAATCGAATGTGGTTTG-GATTTGGCT
125 TCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGG-CTGAGATTTGGTT
* * * * * * * * * * * * *
1224 CGAAGATTATAGATATTCCAATGAGTCTTTACGTCAAAAATCATGTAAAACTGAGACGGGGCT
189 AGATGAATATAGATATTTCGAGGACTCTTTGCGCCAAAAATTATGCAAAATTGAGTCGGGGCT
1287 AAAAACTGAC
Statistics
Matches: 756, Mismatches: 104, Indels: 75
0.81 0.11 0.08
Matches are distributed among these distances:
317 1 0.00
318 74 0.10
319 30 0.04
320 110 0.15
321 77 0.10
322 23 0.03
323 48 0.06
324 77 0.10
325 71 0.09
326 7 0.01
329 10 0.01
330 31 0.04
331 175 0.23
332 22 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (320 bp):
TTTTTCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCAAAAAAATTGAAGG
GCTTTTGCACGATTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCAAACTAAATCGAAA
CAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAA
TATAGATATTTCGAGGACTCTTTGCGCCAAAAATTATGCAAAATTGAGTCGGGGCTCCGAAACGC
GTTTTTAGCCAAAAATCGTCACGATTCGATTAAAATTTTGCAAAAACTGACCCGAAATTT
Found at i:1522 original size:260 final size:264
Alignment explanation
Indices: 1044--1535 Score: 588
Period size: 260 Copynumber: 1.9 Consensus size: 264
1034 TCTTTTTCAA
* * * * *
1044 AATTTTTTGCAACAATACTCAGAAAAAATATATAATTAAACGCCAAAAAGATTGACGGGCTTTGC
1 AATTTTTTGCAACAATACTCAAAAAAAATATATAATTAAACACCAAAAAGATTCAAGAGCTTTGC
** *
1109 ACGCTTCTAATATCATTTTTCCATTTTTTTCGAATTAATTAATAATTAAAGTCGAAACAAGATTC
66 ACGCTTCTAATATCATTTTTCCA-TAATTT--AATT-ATT-ATAATTAAAGTCAAAACAAGATTC
** * * * *
1174 AGATGCTCATAAAAACAAATCTTTAAATCGAATGTGGTTTGGATTTGGCTCGAAGATTATAGATA
126 AGATGCTCATAAAAACAAATCCCTAAATCCAATGTGGTCTGGATTTGGCTAGAAGAATATAGATA
* * *
1239 TTCCAATGAGTCTTTACGTCAAAAATCATGTAAAACTGAGACGGGGCTAAAAACTGACACGAAAG
191 TT-CAAGGAATCTTTACGTCAAAAATCACGTAAAACTGAGACGGGGCTAAAAACTGACACGAAAG
1304 ATTTTTACTC
255 ATTTTTACTC
* * * *
1314 AATTTTTTGCCACAATACT-AAAAAAAATATATAATTCAACACCAAAAAGATTCAAGAGTTTTTC
1 AATTTTTTGCAACAATACTCAAAAAAAATATATAATTAAACACCAAAAAGATTCAAGAGCTTTGC
* *
1378 ACTCTTCTAATATCATTTTTTCC-TAATTT-ATT-TT-TAATTAAA-TCAAAACAAGATTTAGAT
66 ACGCTTCTAATATCA-TTTTTCCATAATTTAATTATTATAATTAAAGTCAAAACAAGATTCAGAT
* * *
1438 GCTCGTAAAAACAAATCCCTAAATCCAATGT-GTCTGAGATTTGGTTAGATGAATATAGATATAT
130 GCTCATAAAAACAAATCCCTAAATCCAATGTGGTCTG-GATTTGGCTAGAAGAATATAGATAT-T
1502 -AAGGAAATCTTT-CTGTCAAAAATCACGTAAAACT
193 CAAGG-AATCTTTAC-GTCAAAAATCACGTAAAACT
1536 AAGTTGGGCC
Statistics
Matches: 191, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
259 8 0.04
260 89 0.47
261 9 0.05
263 2 0.01
265 3 0.02
268 4 0.02
269 51 0.27
270 25 0.13
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (264 bp):
AATTTTTTGCAACAATACTCAAAAAAAATATATAATTAAACACCAAAAAGATTCAAGAGCTTTGC
ACGCTTCTAATATCATTTTTCCATAATTTAATTATTATAATTAAAGTCAAAACAAGATTCAGATG
CTCATAAAAACAAATCCCTAAATCCAATGTGGTCTGGATTTGGCTAGAAGAATATAGATATTCAA
GGAATCTTTACGTCAAAAATCACGTAAAACTGAGACGGGGCTAAAAACTGACACGAAAGATTTTT
ACTC
Found at i:2088 original size:589 final size:576
Alignment explanation
Indices: 687--2453 Score: 1866
Period size: 589 Copynumber: 3.0 Consensus size: 576
677 CGATTGAAAT
* *
687 TTTGCAAAAACTGGCCCGAAATT-TTTTTTCTCAATTCTTTGCCACAATACTTAG--AAAAAATA
1 TTTGCAAAAACTGACCCG-AATTATTTTTACTCAATTCTTTGCCACAATAC-TAGAAAAAAAATA
* * *
749 TATAATTCAACG-CAAAAAAATTTGAAGGGTTTTGCACGAATCTAAAATT-GTTTTTCCATTTTA
64 TATAATTCAACGCCAAAAAAAATTGAA-GGTTTTTCA-G-CTCT---ATTCGTTTTTCCA-TTT-
* * * * * *
812 TTTTCCGAATTTATTTCAAACTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAACCTTAAA
121 TTTTCCAAATTTATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAACAAATCCTTAAA
* *
877 TCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCGAGGACTCTTTCTGCCAAAAATC
186 TCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTGCCAAAAATC
* * *
942 ATGCAAAATTGAGATGGGGCCCGAAACACGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGA
251 ATGCAAAATTGAG-TCGGGCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGA
* *** ** *
1007 TTTCGGCTAAAAACTTACCCGAATTTTTCTTTTTCAAAATTTTTTGCAACAATACTCAGAAAAAA
315 TTTCGGCTAAAAACTGACCC-AA-AAAT-TTTTTCTGAATTTTTTGCCACAATACTCA-AAAAAA
* * * *
1072 TATATAATTAAACGCCAAAAAGATTGACGGGCTTTGCACGCTTCTAATATCATTTTTCCATTTTT
376 TATATAATTCAACGCCAAGAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCC------
** * *
1137 TTCGAATTAATTAATAATTAAAGTCGAAACAAGATTCAGATGCTCATAAAAACAAATCTTTAAAT
435 -TCGAATTAATTTCTAATTAAA-TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
** * *
1202 CGAATGTGGTTTG-GATTTGGCTCGAAGATTATAGATATTCCAATGAGTCTTTACGTCAAAAATC
498 C-AATGT-GAATGAGATTTGGTTCGAAGATTATAGATATTCCAATGAGTCTTTACGCCAAAAATC
* *
1266 ATGTAAAACTGAGACG
561 ATGCAAAACTGAGTCG
** * ** *
1282 -GGGCTAAAAACTGACACGAAAGATTTTTACTCAATTTTTTGCCACAATACT--AAAAAAAATAT
1 TTTGC-AAAAACTGACCCGAATTATTTTTACTCAATTCTTTGCCACAATACTAGAAAAAAAATAT
* * * * * *
1344 ATAATTCAACACC-AAAAAGATTCAAGAGTTTTTCA-CTC--TTC-TAATAT-CA-TTTTTTCCT
65 ATAATTCAACGCCAAAAAAAATTGAAG-GTTTTTCAGCTCTATTCGT-TTTTCCATTTTTTTCCA
* * * *
1402 AATTTATTTTTAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAATCCCTAAATCCAAT
128 AATTTATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGT-AAAACAAATCCTTAAATCCAAT
* * * * *
1467 GTGTCTGAGATTTGGTTAGATGAATATAGATATAT-AAGGAAATCTTTCTGTCAAAAATCACGTA
192 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG-AATCTTTCTGCCAAAAATCATGCA
* * * * * ** *
1531 AAACTAAGTTGGGCCGTCGAAACGCGTTTTTAGCCAAAAAAAATCATGATAATTAGTACAAGATT
256 AAATTGAGTCGGGCC--CGAAACGCGTTTTTAGCC--AAAAAACCGTGATGGTTAGTACACGATT
*** * *
1596 T-TAATCAAAAACCGACCCAAAAATTTTTTCTGAATTTTTTGCCATAATACTCAAAAAAATATAT
317 TCGGCT-AAAAACTGACCCAAAAATTTTTTCTGAATTTTTTGCCACAATACTCAAAAAAATATAT
*
1660 AATTCAACGCCAAGAAGATTGACGGGCTTTTCACGCATCTAATATCGTTTTT-C-CGAATTAATT
381 AATTCAACGCCAAGAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCTCGAATTAATT
* * *
1723 TCTGATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAACGTGAATGA
446 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGAATGA
* * * *
1788 GATTTGGTTCGAAAAATATAGATATTTCAAGGAGTCTTTACGCCGAAAAATCATGCAAAACTGAG
510 GATTTGGTTCGAAGATTATAGATATTCCAATGAGTCTTTACGCC-AAAAATCATGCAAAACTGAG
1853 TCG
574 TCG
* * *
1856 TTTGCAAAAACTAACCCGAATTATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAAAAAAT
1 TTTGCAAAAACTGACCCGAATTATTTTTACTCAATTCTTTGCCACAATACT-AGAAAAAAAATAT
1921 ATAATTCAACGCCAAAAAAAAATTGAAGGCTTTTTCATGCTTCTAGTTTCGTTTTTCCATTTTTT
65 ATAATTCAACGCC-AAAAAAAATTGAAGG-TTTTTCA-GC-TCTA--TTCGTTTTTCCATTTTTT
* *
1986 TCCAAATTTAATTTCTAATTAAATCGAAATAAGATTAAGATACTCGTGAAAACAAATCCTTAAAT
124 TCCAAATTT-ATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGT-AAAACAAATCCTTAAAT
* * *
2051 CCAACGTGGCTGAGATTTGGTTAAATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCA
187 CCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTGCCAAAAATCA
* * * *
2116 TACAAAATTGAGTCGGAACCCCGAAAGGCGTTTTTAGCCCGAAAAACCGTGATGGTTAGTACACG
252 TGCAAAATTGAGTCGG--GCCCGAAACGCGTTTTTAG-CCAAAAAACCGTGATGGTTAGTACACG
** * * *
2181 ATTTCGGCTAAAAACTGACCTGAAAAGTTTTTCATGAATTTTTTGCCACAATACTCAGAATAATA
314 ATTTCGGCTAAAAACTGACCCAAAAATTTTTTC-TGAATTTTTTGCCACAATACTCAAAAAAATA
* *
2246 TATAATTCAACGCC-TGAAAGATTGACGGGCTTTTCACACTTCTAATATCGTTTTTCCTTTTTTT
378 TATAATTCAACGCCAAG-AAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCC-------
* * *
2310 TCGAATAAATTTCTAATTAAAGCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCC
435 TCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-C
** * * ** *
2375 AATGTGGCTGAGATTTGGTTTGATGATTATAGATATTCCAATGAGTCTTTGTGCCAAAAATTATG
499 AATGTGAATGAGATTTGGTTCGAAGATTATAGATATTCCAATGAGTCTTTACGCCAAAAATCATG
* *
2440 CCAAATTGAGTCG
564 CAAAACTGAGTCG
2453 T
1 T
2454 GGCTCCGGAA
Statistics
Matches: 969, Mismatches: 151, Indels: 102
0.79 0.12 0.08
Matches are distributed among these distances:
572 3 0.00
573 81 0.08
574 79 0.08
575 2 0.00
577 22 0.02
578 1 0.00
579 18 0.02
581 1 0.00
582 3 0.00
583 110 0.11
584 105 0.11
585 18 0.02
586 13 0.01
587 38 0.04
588 57 0.06
589 206 0.21
590 7 0.01
591 4 0.00
593 1 0.00
594 40 0.04
595 37 0.04
597 21 0.02
598 102 0.11
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (576 bp):
TTTGCAAAAACTGACCCGAATTATTTTTACTCAATTCTTTGCCACAATACTAGAAAAAAAATATA
TAATTCAACGCCAAAAAAAATTGAAGGTTTTTCAGCTCTATTCGTTTTTCCATTTTTTTCCAAAT
TTATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAACAAATCCTTAAATCCAATGTGG
CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTGCCAAAAATCATGCAAAATT
GAGTCGGGCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
AACTGACCCAAAAATTTTTTCTGAATTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGC
CAAGAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCTCGAATTAATTTCTAATTAAA
TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAATGTGAATGAGATTTGGTTCG
AAGATTATAGATATTCCAATGAGTCTTTACGCCAAAAATCATGCAAAACTGAGTCG
Found at i:15112 original size:2 final size:2
Alignment explanation
Indices: 15105--15137 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15095 TTCCCATACA
15105 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
15138 TTAATGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16619 original size:6 final size:6
Alignment explanation
Indices: 16608--16646 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
16598 GTGATGATGG
*
16608 ATGAAC ATGAAC ATGAAC ATGAAC ATGAAT ATTGAAC AT
1 ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC A-TGAAC AT
16647 AACCCATGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (6 bp):
ATGAAC
Found at i:19155 original size:21 final size:22
Alignment explanation
Indices: 19112--19156 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
19102 ATTTACAGAA
* *
19112 GAAGGGTCAAATTAGATAGATT
1 GAAGGGTAAAATTAGAGAGATT
19134 GAAGGGTAAAATT-GAGAGATT
1 GAAGGGTAAAATTAGAGAGATT
19155 GA
1 GA
19157 CGGATTAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (22 bp):
GAAGGGTAAAATTAGAGAGATT
Found at i:19589 original size:14 final size:15
Alignment explanation
Indices: 19563--19592 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19553 AACTTTCGGC
19563 AAAGCAAACGCTGCA
1 AAAGCAAACGCTGCA
19578 AAAGCAAA-GCTGCA
1 AAAGCAAACGCTGCA
19592 A
1 A
19593 GTGAAGGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.50, C:0.23, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAGCAAACGCTGCA
Found at i:25321 original size:26 final size:30
Alignment explanation
Indices: 25289--25354 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
25279 TTTATTAGGT
25289 TGGTAGTTTTT-TCTT-T-G-AAAAGTTAG
1 TGGTAGTTTTTCTCTTATGGCAAAAGTTAG
*
25315 TGGTAGTTTTTCTTTTATGGCCAAAAGTTAG
1 TGGTAGTTTTTCTCTTATGG-CAAAAGTTAG
25346 TGGTAGTTT
1 TGGTAGTTT
25355 AGATTTAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.32
27 3 0.09
28 1 0.03
29 1 0.03
31 18 0.53
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.48
Consensus pattern (30 bp):
TGGTAGTTTTTCTCTTATGGCAAAAGTTAG
Found at i:32551 original size:33 final size:33
Alignment explanation
Indices: 32485--32551 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
32475 CCTTGCAGCT
* *
32485 TCGAGTTTCTCAGTCAGGTCCTTTTTCTGTTGC
1 TCGAGTTCCTCAGTCAGGTCCTTTTCCTGTTGC
32518 TCGAGTTCCTCAGTCAGGTCCTTTCTCCT-TTGC
1 TCGAGTTCCTCAGTCAGGTCCTTT-TCCTGTTGC
32551 T
1 T
32552 ACTATGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.09, C:0.28, G:0.19, T:0.43
Consensus pattern (33 bp):
TCGAGTTCCTCAGTCAGGTCCTTTTCCTGTTGC
Found at i:36126 original size:2 final size:2
Alignment explanation
Indices: 36119--36157 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
36109 ATCTATCATT
36119 TA TA TA TA TA TA TA TA TA TA 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
36158 TCTGGTTCGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36816 original size:1 final size:1
Alignment explanation
Indices: 36810--36841 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
36800 ACCTTTTCGC
36810 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
36842 ATCGCTTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46400 original size:63 final size:63
Alignment explanation
Indices: 46276--46400 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
46266 ATAGTGGCAT
* * * * *
46276 CATCCAGCTTCGAATAGAGTTCTTCCCTTTCCTCATTCCAACTGTGACGCTTTTCTACGAATC
1 CATCCAGCTTCAAATAGAGATCTTCCCTTTCCTCATTCCAAATGAGACGCTCTTCTACGAATC
* *
46339 CATCCAGCTTCAAATAGAGATCTTGCCTTTCCTCATTCCAAATGCAG-CGCTCTTCTTCGAAT
1 CATCCAGCTTCAAATAGAGATCTTCCCTTTCCTCATTCCAAATG-AGACGCTCTTCTACGAAT
46401 TCTTTTTCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 53 0.98
64 1 0.02
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (63 bp):
CATCCAGCTTCAAATAGAGATCTTCCCTTTCCTCATTCCAAATGAGACGCTCTTCTACGAATC
Found at i:46647 original size:33 final size:33
Alignment explanation
Indices: 46585--46648 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
46575 GCAGCTTCAT
*
46585 GTTTCTCAGTCAGGTCCTTCCTCTGTTGCTCGA
1 GTTTCTCAGTCAGGTCCTTCCTCTCTTGCTCGA
**
46618 GTTTCTCAGTCAGGTCCTTTTTCTCTTGCTC
1 GTTTCTCAGTCAGGTCCTTCCTCTCTTGCTC
46649 CACCTTGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.08, C:0.30, G:0.19, T:0.44
Consensus pattern (33 bp):
GTTTCTCAGTCAGGTCCTTCCTCTCTTGCTCGA
Found at i:46716 original size:27 final size:27
Alignment explanation
Indices: 46678--46729 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
46668 TCATATCCAC
46678 GCAATCGCTCAGCCAGCTCCTCTTCAT
1 GCAATCGCTCAGCCAGCTCCTCTTCAT
* *
46705 GCAATCGCTCAGCCCGTTCCTCTTC
1 GCAATCGCTCAGCCAGCTCCTCTTC
46730 CCTTTGCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.42, G:0.15, T:0.27
Consensus pattern (27 bp):
GCAATCGCTCAGCCAGCTCCTCTTCAT
Found at i:47665 original size:54 final size:54
Alignment explanation
Indices: 47606--47717 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
47596 TCCCCTTCTC
*
47606 CCTTCTGCTTCAACTCAACTTTCTTTTCCAGCAATTCAACATCGGCATTCTCCT
1 CCTTCTGCTCCAACTCAACTTTCTTTTCCAGCAATTCAACATCGGCATTCTCCT
47660 CCTTCTGCTCCAACTCAACTTTCTTTTCCAGCAATTCAACATCGGCATTCTCCT
1 CCTTCTGCTCCAACTCAACTTTCTTTTCCAGCAATTCAACATCGGCATTCTCCT
47714 CCTT
1 CCTT
47718 TTTCTGATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.20, C:0.37, G:0.07, T:0.37
Consensus pattern (54 bp):
CCTTCTGCTCCAACTCAACTTTCTTTTCCAGCAATTCAACATCGGCATTCTCCT
Found at i:61430 original size:36 final size:36
Alignment explanation
Indices: 61383--61453 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
61373 TTTCTCGTCT
61383 AGCATGAACATGTCATGCTCTGCTTGAATTGTCTCA
1 AGCATGAACATGTCATGCTCTGCTTGAATTGTCTCA
61419 AGCATGAACATGTCATGCTCTGCTTGAATTGTCTC
1 AGCATGAACATGTCATGCTCTGCTTGAATTGTCTC
61454 CATTACTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (36 bp):
AGCATGAACATGTCATGCTCTGCTTGAATTGTCTCA
Found at i:62841 original size:69 final size:69
Alignment explanation
Indices: 62730--62867 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
62720 CAGGTAAAGA
62730 ACTCCAAATCAGCAAATAAACAATTCTAAAATTCAAACAAGGACATGCTTCAAGAAAGATGGGAA
1 ACTCCAAATCAGCAAATAAACAATTCTAAAATTCAAACAAGGACATGCTTCAAGAAAGATGGGAA
62795 TGTG
66 TGTG
62799 ACTCCAAATCAGCAAATAAACAATTCTAAAATTCAAACAAGGACATGCTTCAAGAAAGATGGGAA
1 ACTCCAAATCAGCAAATAAACAATTCTAAAATTCAAACAAGGACATGCTTCAAGAAAGATGGGAA
62864 TGTG
66 TGTG
62868 TCTGGTATGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.20
Consensus pattern (69 bp):
ACTCCAAATCAGCAAATAAACAATTCTAAAATTCAAACAAGGACATGCTTCAAGAAAGATGGGAA
TGTG
Found at i:64040 original size:25 final size:26
Alignment explanation
Indices: 64005--64054 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
63995 ACACTTAACT
*
64005 TAAAATCCTAATTCTAATAGGAAAAG
1 TAAAATCCTAATCCTAATAGGAAAAG
*
64031 TAAAA-CCTAATCCTACTAGGAAAA
1 TAAAATCCTAATCCTAATAGGAAAA
64055 ACCATAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (26 bp):
TAAAATCCTAATCCTAATAGGAAAAG
Found at i:65477 original size:20 final size:22
Alignment explanation
Indices: 65452--65501 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
65442 TCTATGAATT
65452 TTATTTTGATAATTTA-AAA-A
1 TTATTTTGATAATTTATAAAGA
*
65472 TTATTTTAATAATTTATAAAGA
1 TTATTTTGATAATTTATAAAGA
65494 -TATTTTGA
1 TTATTTTGA
65502 GAAATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 15 0.58
21 10 0.38
22 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (22 bp):
TTATTTTGATAATTTATAAAGA
Found at i:66173 original size:80 final size:80
Alignment explanation
Indices: 66059--66218 Score: 257
Period size: 80 Copynumber: 2.0 Consensus size: 80
66049 GCATTCGTTA
* *
66059 TGCAACTCCCCCTCGTTTTCATTTCTCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTGAAAA
1 TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
66124 GTCGTCTAAGATCCG
66 GTCGTCTAAGATCCG
* * * **
66139 TGCAACTCCCCCTCGTTTTTATTTCCCTTCCCAAAATAGGTTTTTCAGCCGACTTATCTTCAAAA
1 TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
66204 GTCGTCTAAGATCCG
66 GTCGTCTAAGATCCG
66219 AAACCACTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.33
Consensus pattern (80 bp):
TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
GTCGTCTAAGATCCG
Found at i:69121 original size:50 final size:51
Alignment explanation
Indices: 69067--69166 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 51
69057 AGGAAGAGAG
69067 TTGTTTTGAGCAACTTAATAAATGAGTAACAGC-TTAGCAAAA-AAGAGGAA
1 TTGTTTTGAGCAACTTAATAAATGAGTAACAGCATTAG-AAAATAAGAGGAA
*
69117 TTGTTTTGAGCAACTTAATAAATGAGTTACAGCATTTAGAAAATAAGAGG
1 TTGTTTTGAGCAACTTAATAAATGAGTAACAGCA-TTAGAAAATAAGAGG
69167 GGGCAAAAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
50 32 0.70
51 4 0.09
52 10 0.22
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (51 bp):
TTGTTTTGAGCAACTTAATAAATGAGTAACAGCATTAGAAAATAAGAGGAA
Done.