Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013259.1 Corchorus capsularis cultivar CVL-1 contig13280, 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: 81054
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:11382 original size:50 final size:49
Alignment explanation
Indices: 11305--11402 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 49
11295 AAGATTAAAT
* * * *
11305 TTTATTGAAATGGTGTTTATGTCTGTAGATTGTGTTTCCTGTCTTTGAA
1 TTTATTGAAATGGTGTCTATATCTGTAGACTGTGTTTCCTGTCCTTGAA
* *
11354 TTTATTGAAATGTTGTCTATTATCTGTAGGCTGTGTTTCCTGTCCTTGA
1 TTTATTGAAATGGTGTCTA-TATCTGTAGACTGTGTTTCCTGTCCTTGA
11403 GAACCTACAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 17 0.40
50 25 0.60
ACGTcount: A:0.17, C:0.11, G:0.21, T:0.50
Consensus pattern (49 bp):
TTTATTGAAATGGTGTCTATATCTGTAGACTGTGTTTCCTGTCCTTGAA
Found at i:19704 original size:19 final size:19
Alignment explanation
Indices: 19680--19716 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19670 GTAGAGTACC
19680 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
19699 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
19717 TGTTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:35518 original size:13 final size:13
Alignment explanation
Indices: 35500--35524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35490 TCTAATATCC
35500 TTTTTTCAAATTT
1 TTTTTTCAAATTT
35513 TTTTTTCAAATT
1 TTTTTTCAAATT
35525 AATTTCTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTCAAATTT
Found at i:36198 original size:332 final size:329
Alignment explanation
Indices: 35261--37432 Score: 1567
Period size: 332 Copynumber: 6.4 Consensus size: 329
35251 TTACATGTGA
* * * ** *
35261 CTGAGGTTTGATTAGATGAATATTGATATATTTTAAGGAGTCTTGACGGTAAAAATCATGAAAAA
1 CTGAGATTTGATTAGATGAATA-T-AGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAA
* * ** * *
35326 CTGA-CACAGGG-CCTTAGAACGTGTTTTTAGCCAAAAAAACC--GA---TACACA--ATTTCGG
64 CTAAGC-CGGGGCCCCGA-AACGCGTTTTTAGCC-AAAAAACCGTGATGGTACACACGATTTCGA
* * ** * *
35382 CTAAAATTTAGCAAAAATTGAGCCGAAATAA--TTTT-CTCAATTTTTAACCACAATACTCATAA
126 CTAAAATTTTGCAAAAAATGA-CC-AAA-AATTTTTTCCTCAATTTTTGGCTAAAATACTCATAA
* * * * * * * *
35444 AAAATATATAATTCAACGGCAAAAAGATTGAAAAGA-TTCTCACACTTCTAATATCCTTTTTTCA
188 AATATATATAATTTAACGCCAAAAAGATTG-AAGGACTTTTCACGCTTTTAATAT-CGTTTTTC-
* * * * * * *
35508 AATTTTTTTTTCAAATTAATTTCTTATTAAATCGAAACATGATTCAAATGCTCGTAAAAACAAAT
250 -ATATTTTTCT-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAAT
*
35573 CCTTAAA-TCTAATGTGG
313 CCTTAAATTC-AATGTAG
* * * * *
35590 C-GAAGATTTGATTATATGAATATAGATATTTCAAGGAGTTTTGCCACCAAAAATCATCCAAAAC
1 CTG-AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAAC
* * * * * * *
35654 TGATCCGGAGCCCGGAAACGTGTTTTTAGCCAAAAAAACCGTGATGGTACTCA--ATTTCGGCTA
65 TAAGCCGGGGCCCCGAAACGCGTTTTTAGCC-AAAAAACCGTGATGGTACACACGATTTCGACTA
* * ** * * * * * *
35717 AAATTTTACAAAAATTGACCTGAAATATTTGTCTTCAATTTTTAGCCACAATACCCATAAAATAT
129 AAATTTTGCAAAAAATGACCAAAAAT-TTTTTCCTCAATTTTTGGCTAAAATACTCATAAAATAT
* * * *
35782 ATATAATTCAACGCCAAAAAGATTGTAGGACTTTTCACGGTTTTAATATCATTTTTCATATTTTT
193 ATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTT
* *
35847 CTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATACTTGTAAAAACAAATTCC-TAAATT
258 CTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAA-TCCTTAAATT
*
35911 CAATGTGG
322 CAATGTAG
* * * *
35919 CTGAGATTTGAATAGCTGATTATAGATATTTCAAGGAGTCTTGATGCCAAAAATCATGCAAAACT
1 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACT
* * * *
35984 AAGACGAGGCCCCGAAACGCATTTTTAGCCAAAAAACCGTGATGGTTAGCACACGATTTCAACT-
66 AAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGG-TA-CACACGATTTCGACTA
*
36048 AAATTTTGCAAAAAATGACCAAAAAATTTTTTCCGTCAATTTTTGGCTAAAATACTCGTAAAATA
129 AAATTTTGCAAAAAATGACC-AAAAATTTTTTCC-TCAATTTTTGGCTAAAATACTCATAAAATA
* * * *
36113 TATATAGTTTAACGCCAAAAAGATTGGAGGACTTTTCATGCTTTTAATATTGTTTTTCATATTTT
192 TATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* * *
36178 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTCATAAAAACAAATTCTTAAATT
257 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATT
36243 CAAT-TAG
322 CAATGTAG
* * * *
36250 CTGAGATTTGATTAGATGAATATTGATATCTCAAAGAGTCTTGCCGCCAAAAATCATGCAAAACT
1 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACT
* * * * * *
36315 TAGCTGGGGCCCCGTAACGCGTTTTTAACCAAAAAAACCGTGATGATATTACACGATTTCGGA-T
66 AAGCCGGGGCCCCGAAACGCGTTTTTAGCC-AAAAAACCGTGATGGTA-CACACGATTTC-GACT
* * * * * * *
36379 AGAATTTTGC-AAAAATGACTCGAAAGTTATTTGCC-CAATTTGTAGCCT-TAATACTCATAAAA
128 AAAATTTTGCAAAAAATGAC-CAAAAATT-TTTTCCTCAATTT-TTGGCTAAAATACTCATAAAA
* * * * * *
36441 -ATTATATAATTCAACGCAAAAAAGATTCAAGGGCTTTTCATGCTTCTAATATCGTTTTTTC-TA
190 TA-TATATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCG-TTTTTCATA
* * * * *
36504 TTATTTTCCGAATTAATTTCTAATTAAATAGAAATATGATTCAGATGCTTGTTTTCGGATGCTTG
253 -T-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATAC------TC----G--T-
**** * *
36569 TTTTACAAATCCTTGAATCCAATGT-G
303 AAAAACAAATCCTTAAATTCAATGTAG
* ** * * * ** *
36595 ACTGAGAATTGGCTAGATGGATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCATCAT
1 -CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAAC
* * ** *
36660 TGAA-CCGGTGCCTC-AGAACATGTTTTTAGCC-AAAAACCGTGATTTCGACTAACATACACGAT
65 T-AAGCCGGGGCCCCGA-AACGCGTTTTTAGCCAAAAAACCGTGA--T-G-GT-AC--ACACGAT
* * * * * * *
36722 TTCGACTAATATTTTGCAAAAATTGATCTAGAAATATTTTCC-CTATTTTTTGTCTAAAATACTC
121 TTCGACTAAAATTTTGCAAAAAATGA-CCAAAAATTTTTTCCTC-AATTTTTGGCTAAAATACTC
**** * *
36786 ATAAAATATATATAATTCTTTTTTTTTAAAATAAAAATATATATAATTCAACTCCAAGAATATTG
184 ATAAAATATATATAA---------TTT--AACGCCAA-A-A-A-GA-T----T----G-A-AG--
* * * *
36851 GAGGACTTTTCACGATTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTTTAATTAAATAGA
221 ---GACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGA
* * * *
36916 AACAAGATTCAAATTCTCGTAAAAACAAATCCTTAAATGCAATGTAT
283 AACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATTCAATGTAG
* * ** * *
36963 CTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGCCTCCAAGCCAAAAATCATGCAAAATT
1 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACT
* * *
37028 AAGTCGGGGCACCGAAACGCGTTTTTAG-CAAAAAACCGTGAT-GT--ACACGATTTCGGCTAAA
66 AAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTACACACGATTTCGACTAAA
* ** * * * *
37089 ATTTTGCAAAAAATTACCAGAAAAAATTTTCCTCAATTTTTGGTTAAAATATTCATGAATTATAT
131 ATTTTGCAAAAAATGACCA-AAAATTTTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATAT
*
37154 ATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTCATATCGTTTTTCATATTATTTC
195 ATAATTTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT-TTTC
* * * * * * *
37219 TGAATTAACTTCTTATTAAATTGAAATAAGATTCAGATACTCATAAAAGCAAATCCTTAAATGCA
259 TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATTCA
37284 ATGTAG
324 ATGTAG
* * * *
37290 CTGAGATTTGAGTT-GATAAATATGGATATCTCAAGGAGGCTT-AGCGCCAAAAATCATGCAAAA
1 CTGAGATTTGA-TTAGATGAATATAGATATTTCAAGGAGTCTTGA-CGCCAAAAATCATGCAAAA
* * * * * ** * *
37353 CTGATCCGGGGCACTGGAACGCGTTTTTAGCC-AAAAACCGTGATAATTATAACACGATTTCGGC
64 CTAAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGAT-GGTA-CACACGATTTCGAC
37417 TAAAATTTTGCAAAAA
127 TAAAATTTTGCAAAAA
37433 TTGAGGGTCA
Statistics
Matches: 1473, Mismatches: 260, Indels: 217
0.76 0.13 0.11
Matches are distributed among these distances:
326 33 0.02
327 213 0.14
328 24 0.02
329 158 0.11
330 82 0.06
331 148 0.10
332 298 0.20
333 67 0.05
337 1 0.00
338 2 0.00
341 1 0.00
342 1 0.00
343 1 0.00
344 13 0.01
345 18 0.01
346 78 0.05
347 2 0.00
348 4 0.00
349 3 0.00
350 29 0.02
351 34 0.02
352 2 0.00
356 2 0.00
357 68 0.05
358 1 0.00
360 2 0.00
362 6 0.00
363 1 0.00
364 1 0.00
365 2 0.00
366 4 0.00
367 100 0.07
368 2 0.00
370 1 0.00
371 1 0.00
374 2 0.00
376 1 0.00
377 1 0.00
380 38 0.03
381 7 0.00
382 21 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (329 bp):
CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACT
AAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTACACACGATTTCGACTAAA
ATTTTGCAAAAAATGACCAAAAATTTTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATA
TAATTTAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTG
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATTCAAT
GTAG
Found at i:38562 original size:2 final size:2
Alignment explanation
Indices: 38555--38579 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38545 CAAGCTTTCC
38555 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
38580 ATGAAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:41767 original size:15 final size:16
Alignment explanation
Indices: 41747--41776 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41737 ATGAATAATA
41747 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
41762 ATATTATAATCTAAA
1 ATATTATAATCTAAA
41777 AATAAATATT
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:50063 original size:27 final size:27
Alignment explanation
Indices: 50033--50091 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
50023 TTGTTTAAAT
50033 ATTCATTATATATATTTCTTTTGAAGA
1 ATTCATTATATATATTTCTTTTGAAGA
50060 ATTCATTATATATATTTCTTTTGAAGA
1 ATTCATTATATATATTTCTTTTGAAGA
50087 ATTCA
1 ATTCA
50092 CCTCTGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (27 bp):
ATTCATTATATATATTTCTTTTGAAGA
Found at i:53702 original size:157 final size:155
Alignment explanation
Indices: 53368--53731 Score: 393
Period size: 157 Copynumber: 2.3 Consensus size: 155
53358 GAGCTTCTCA
*
53368 CCTCAAACTGTCCTTAAATGAAAAACTAGCAT-AGTTTTTCATTCTAAGTCTGAATGAGACGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATGAGACG-AA
* * *
53432 TTTTGCCAAGGATCTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCTAGCTC
65 TTTTGCCAAGGATCTTAGAATATCCACATAAAACTATGGAAAAAATTCTAAGTAAAACCGAACTC
* * * * *
53497 TCCTCGATGGTGAACTAGGTTTCTCT
130 TCCTAGATAGAGAACTAGGTTACACT
* ** *
53523 CCCCAAGTTGTCCTTAAATGAAAAACCAGCATAAGTTTTTCATTCTAAGTC-CAATGA-AGCTG-
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATGAGA-C-GA
* * *
53585 ATTTT-CCACCAGTAGA-CTTAGATTAT-CACCATAAAAGCTATGGGAAAATTTCTAAGTAAAAC
64 ATTTTGCCA--AG--GATCTTAGAATATCCA-CATAAAA-CTATGGAAAAAATTCTAAGTAAAAC
* * *
53647 CGAACTCT-CTAGCATAGAGAAGTTGGTTAGACT
123 CGAACTCTCCTAG-ATAGAGAACTAGGTTACACT
* *
53680 CCTCAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATGCTAAGTCT
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
53732 GTTTGAGATG
Statistics
Matches: 173, Mismatches: 25, Indels: 19
0.80 0.12 0.09
Matches are distributed among these distances:
153 3 0.02
154 6 0.03
155 38 0.22
156 37 0.21
157 89 0.51
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (155 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATGAGACGAAT
TTTGCCAAGGATCTTAGAATATCCACATAAAACTATGGAAAAAATTCTAAGTAAAACCGAACTCT
CCTAGATAGAGAACTAGGTTACACT
Found at i:59095 original size:14 final size:14
Alignment explanation
Indices: 59076--59116 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
59066 AATAGTAACA
59076 ATATATTACTATAT
1 ATATATTACTATAT
*
59090 ATATATTACAATAT
1 ATATATTACTATAT
*
59104 ATATATTATTATA
1 ATATATTACTATA
59117 ATTATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTACTATAT
Found at i:59130 original size:17 final size:17
Alignment explanation
Indices: 59085--59132 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
59075 AATATATTAC
*
59085 TATATAT-ATATTACAA
1 TATATATAATATTATAA
*
59101 TATATATATTATTATAA
1 TATATATAATATTATAA
59118 T-TATAATAATATTAT
1 TATAT-ATAATATTAT
59133 TATAATAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATATAATATTATAA
Found at i:59913 original size:99 final size:99
Alignment explanation
Indices: 59797--59997 Score: 393
Period size: 99 Copynumber: 2.0 Consensus size: 99
59787 CTAGTACTTA
59797 CTCCAAATTAACAGGAAAAAATAAAAAATAAAATAAAGTAATGCAAATTGTAATATGAAATTCAC
1 CTCCAAATTAACAGGAAAAAATAAAAAATAAAATAAAGTAATGCAAATTGTAATATGAAATTCAC
59862 AATTATGCGCATTCTAATAAGTGACATCGATATC
66 AATTATGCGCATTCTAATAAGTGACATCGATATC
59896 CTCCAAATTAACAGGAAAAAATAAAAAATAAAATAAAGTAATGCAAATTGTAATATGAAATTCAC
1 CTCCAAATTAACAGGAAAAAATAAAAAATAAAATAAAGTAATGCAAATTGTAATATGAAATTCAC
*
59961 AATTATGCGCATTCTGATAAGTGACATCGATATC
66 AATTATGCGCATTCTAATAAGTGACATCGATATC
59995 CTC
1 CTC
59998 GTATCAATCG
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.26
Consensus pattern (99 bp):
CTCCAAATTAACAGGAAAAAATAAAAAATAAAATAAAGTAATGCAAATTGTAATATGAAATTCAC
AATTATGCGCATTCTAATAAGTGACATCGATATC
Found at i:64360 original size:20 final size:20
Alignment explanation
Indices: 64335--64374 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
64325 TAACTCCAAT
64335 TTCTTTTCTTTTCTTGGTAC
1 TTCTTTTCTTTTCTTGGTAC
64355 TTCTTTTCTTTTCTTGGTAC
1 TTCTTTTCTTTTCTTGGTAC
64375 GTTGAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.20, G:0.10, T:0.65
Consensus pattern (20 bp):
TTCTTTTCTTTTCTTGGTAC
Found at i:65588 original size:13 final size:13
Alignment explanation
Indices: 65567--65603 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
65557 GATAATTCTT
65567 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
65580 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
65593 TTTGACTCTCC
1 TTTGACCCTCC
65604 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.38, G:0.08, T:0.38
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:65646 original size:40 final size:38
Alignment explanation
Indices: 65602--65685 Score: 123
Period size: 40 Copynumber: 2.2 Consensus size: 38
65592 ATTTGACTCT
*
65602 CCTAATAATTAAGGAAATAAATTAAATCCAAGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCC-AGTTTAG-CC
* *
65642 CCTAATAATTAAGGTAAGAAATTAAATCCGGTTTAGCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGTTTAGCC
65680 CCTAAT
1 CCTAAT
65686 TATAAATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 8 0.20
39 6 0.15
40 27 0.66
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.29
Consensus pattern (38 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGTTTAGCC
Found at i:68328 original size:45 final size:45
Alignment explanation
Indices: 68214--68331 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 45
68204 TTGCCTGGAC
* *
68214 GACTGCATTGAGCCAACTACAAACTACTCCTACCTCGACAGACCT
1 GACTGCATTGAGCCAATTACAAACTATTCCTACCTCGACAGACCT
*
68259 GACTGCATTGAGCCAATTACAAACTATTCCCT-CCTGGACAGACCT
1 GACTGCATTGAGCCAATTACAAACTATT-CCTACCTCGACAGACCT
* **
68304 GACTGCATTAAGCCAATTTGAAACTATT
1 GACTGCATTGAGCCAATTACAAACTATT
68332 GCATTAAGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 63 0.95
46 3 0.05
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (45 bp):
GACTGCATTGAGCCAATTACAAACTATTCCTACCTCGACAGACCT
Found at i:68339 original size:24 final size:24
Alignment explanation
Indices: 68307--68353 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
68297 CAGACCTGAC
68307 TGCATTAAGCCAATTTGAAACTAT
1 TGCATTAAGCCAATTTGAAACTAT
68331 TGCATTAAGCCAATTTGAAACTA
1 TGCATTAAGCCAATTTGAAACTA
68354 CTCCTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (24 bp):
TGCATTAAGCCAATTTGAAACTAT
Found at i:69790 original size:2 final size:2
Alignment explanation
Indices: 69773--69814 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
69763 TCCTATTCAT
*
69773 TA TA CA TA TA -A TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69813 TA
1 TA
69815 ACCATTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:69797 original size:21 final size:21
Alignment explanation
Indices: 69773--69814 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
69763 TCCTATTCAT
69773 TATACATATAATATATATATA
1 TATACATATAATATATATATA
*
69794 TATATATATAATATATATATA
1 TATACATATAATATATATATA
69815 ACCATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATACATATAATATATATATA
Found at i:70458 original size:30 final size:29
Alignment explanation
Indices: 70403--70459 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
70393 TGGAATTAGT
*
70403 GACAGAAATACTCATAAATAATTTTTTGC
1 GACACAAATACTCATAAATAATTTTTTGC
*
70432 GACACAAATACTCACT-AATAAATTTTTG
1 GACACAAATACTCA-TAAATAATTTTTTG
70460 GGTGAGGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (29 bp):
GACACAAATACTCATAAATAATTTTTTGC
Done.