Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2485
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: 359192
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 4 of 4
Found at i:321980 original size:2 final size:2
Alignment explanation
Indices: 321975--322000 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
321965 CAAAAAAAAA
321975 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
322001 GCATGCGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322343 original size:27 final size:27
Alignment explanation
Indices: 322313--322369 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
322303 ACTCCTAATA
322313 TATATGAATAATTAAATTTA-ATATTTT
1 TATATGAAT-ATTAAATTTATATATTTT
** *
322340 TATATTTATATTATATTTATATATTTT
1 TATATGAATATTAAATTTATATATTTT
322367 TAT
1 TAT
322370 TATCATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TATATGAATATTAAATTTATATATTTT
Found at i:322355 original size:11 final size:11
Alignment explanation
Indices: 322339--322383 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
322329 TTTAATATTT
322339 TTATATTTATA
1 TTATATTTATA
322350 TTATATTTATA
1 TTATATTTATA
322361 -TAT-TTT-TA
1 TTATATTTATA
322369 TTATCATATTATA
1 TTAT-AT-TTATA
322382 TT
1 TT
322384 TAAGGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.07
9 6 0.21
10 3 0.10
11 12 0.41
12 2 0.07
13 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTTATA
Found at i:322355 original size:19 final size:19
Alignment explanation
Indices: 322333--322385 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
322323 ATTAAATTTA
322333 ATATTTTTATATTTATATT
1 ATATTTTTATATTTATATT
* *
322352 ATATTTATATATTTTTATT
1 ATATTTTTATATTTATATT
*
322371 ATCA-TATTATATTTA
1 AT-ATTTTTATATTTA
322386 AGGTATTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATTTTTATATTTATATT
Found at i:322377 original size:27 final size:26
Alignment explanation
Indices: 322323--322386 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
322313 TATATGAATA
* *
322323 ATTAAATTTAATATTTTTATATTTAT
1 ATTATATTTAATATTTTTATATTCAT
322349 ATTATATTTATATATTTTTAT-TATCAT
1 ATTATATTTA-ATATTTTTATAT-TCAT
322376 ATTATATTTAA
1 ATTATATTTAA
322387 GGTATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTATATTTAATATTTTTATATTCAT
Found at i:322397 original size:27 final size:25
Alignment explanation
Indices: 322323--322401 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 25
322313 TATATGAATA
* *
322323 ATTAAATTTAATATTTTTATATTTAT
1 ATTATATTT-ATATATTTATATTTAT
*
322349 ATTATATTTATATATTTTTATTATCAT
1 ATTATATTTATATATTTATATT-T-AT
322376 ATTATATTTA-AGGTA-TTATATTTAT
1 ATTATATTTATA--TATTTATATTTAT
322401 A
1 A
322402 ATTTTTGACA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
25 14 0.31
26 11 0.24
27 18 0.40
28 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTATATTTATATATTTATATTTAT
Found at i:322733 original size:21 final size:21
Alignment explanation
Indices: 322709--322748 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
322699 ATTTTTATTT
322709 TATTAAATAATAATCTTTACA
1 TATTAAATAATAATCTTTACA
* * *
322730 TATTCAATTATAATTTTTA
1 TATTAAATAATAATCTTTA
322749 TATGTAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTAAATAATAATCTTTACA
Found at i:324452 original size:6 final size:6
Alignment explanation
Indices: 324444--324473 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
324434 TTAATTTTTT
*
324444 ATTTAT ATTTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
324474 TATGATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:327405 original size:21 final size:22
Alignment explanation
Indices: 327381--327421 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
327371 ATTTCATCAT
327381 ATTTTA-CAAATTAAA-CAATGC
1 ATTTTATCAAA-TAAAGCAATGC
327402 ATTTTATCAAATAAAGCAAT
1 ATTTTATCAAATAAAGCAAT
327422 AACCAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (22 bp):
ATTTTATCAAATAAAGCAATGC
Found at i:327589 original size:20 final size:20
Alignment explanation
Indices: 327518--327589 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
327508 TGATTTTTAA
327518 AAATTTAAATTAATT-TTATTT
1 AAATTTAAA-T-ATTATTATTT
327539 -AATTT-AA-ATTATTATTT
1 AAATTTAAATATTATTATTT
**
327556 AATAATAAAAATATTATTATTT
1 -A-AATTTAAATATTATTATTT
327578 AAATTTAAATAT
1 AAATTTAAATAT
327590 AAAAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
16 3 0.07
17 6 0.15
19 2 0.05
20 17 0.41
21 3 0.07
22 10 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTTAAATATTATTATTT
Found at i:327604 original size:20 final size:20
Alignment explanation
Indices: 327581--327626 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
327571 ATTATTTAAA
*
327581 TTTAAATATA-AAAATAATAT
1 TTTAAATA-ACAAAATAAAAT
327601 TTT-AATAACAAAATAAAAT
1 TTTAAATAACAAAATAAAAT
327620 TTTAAAT
1 TTTAAAT
327627 TAATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTAAATAACAAAATAAAAT
Found at i:328407 original size:41 final size:41
Alignment explanation
Indices: 328330--328407 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
328320 TTTTTTTGCA
* * *
328330 TAAATCTATTTTTAGACATAATATTTTATTCAAACCTTGAT
1 TAAATCTATTATTAGACATAATAATTTATTAAAACCTTGAT
*
328371 TAAATCTATTATTAG-TATAATAATTTATTAACAACCT
1 TAAATCTATTATTAGACATAATAATTTATTAA-AACCT
328408 AAAAATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 13 0.41
41 19 0.59
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.45
Consensus pattern (41 bp):
TAAATCTATTATTAGACATAATAATTTATTAAAACCTTGAT
Found at i:329060 original size:2 final size:2
Alignment explanation
Indices: 329048--329081 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
329038 CTATGTAATG
*
329048 TA TA TA CA 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
329082 CAACTACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:329741 original size:137 final size:140
Alignment explanation
Indices: 329566--329822 Score: 344
Period size: 137 Copynumber: 1.9 Consensus size: 140
329556 CAAAACTTTG
* * *
329566 AGGTTAAAAATGTAAATATTTTTAATTTTTAGATCATTTAGGGGTTGTTTTGGTTTATAGAAGCA
1 AGGTTAAAAATGTAAATATTTTTAATTTTAAGACCATTTAGGGGTTGTTTTGGTTCATAGAAGCA
* *
329631 TTTAT-AGGCACTATTTCATAA-TTTTTTT-AATTTTTTCAAACTCATTTAAGGGTGTTTAGGTT
66 CTTATAAAG-ACTATTTCATAATTTTTTTTCAATTTTTTCAAACTCATTTAAGGGTGTTTAGGTT
329693 AAAACCTATGA
130 AAAACCTATGA
* * * *
329704 AGGTT-AAAATGTAATTTTTTTTAATTCTTAAG-CCATTTAGGGGTTGTTTTGGTTCATGGTAGC
1 AGGTTAAAAATGTAAATATTTTTAATT-TTAAGACCATTTAGGGGTTGTTTTGGTTCATAGAAGC
* * * *
329767 ACTTATAAAGATTATTTTATAATTTTTTTTCAATTTTTTTAAACTCATTTAGGGGT
65 ACTTATAAAGACTATTTCATAATTTTTTTTCAATTTTTTCAAACTCATTTAAGGGT
329823 ATTCTTAACT
Statistics
Matches: 102, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
137 61 0.60
138 18 0.18
139 23 0.23
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.47
Consensus pattern (140 bp):
AGGTTAAAAATGTAAATATTTTTAATTTTAAGACCATTTAGGGGTTGTTTTGGTTCATAGAAGCA
CTTATAAAGACTATTTCATAATTTTTTTTCAATTTTTTCAAACTCATTTAAGGGTGTTTAGGTTA
AAACCTATGA
Found at i:330753 original size:21 final size:20
Alignment explanation
Indices: 330723--330767 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
330713 CTACAATTTA
*
330723 TATCGGTACAAACAGTAAATG
1 TATCGATACAAA-AGTAAATG
* *
330744 TATCGATACATAAGTGAATG
1 TATCGATACAAAAGTAAATG
330764 TATC
1 TATC
330768 ATTACATGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
TATCGATACAAAAGTAAATG
Found at i:333408 original size:79 final size:78
Alignment explanation
Indices: 333304--333566 Score: 225
Period size: 79 Copynumber: 3.3 Consensus size: 78
333294 TCCAATGCTG
* *
333304 TTATTTTTGAGAAG-ATGCTCTAACCCTGTTTTTATTTTCAAAATATTAAATTTTTCA-TAGCGA
1 TTATTTTTGA-AAGAATACTCCAACCCTGTTTTTATTTTCAAAATATTAAATTTTTCACTAG-GA
*
333367 GGATAC-TCTAACTCC-A
64 -AATACTTC-AAC-CCTA
** *
333383 TTATTTTTGAAAGAATACTCCAACCCCATTTTTA-TTTCTAAAATATTAAATTTTTCATCTTGGA
1 TTATTTTTGAAAGAATACTCCAACCCTGTTTTTATTTTC-AAAATATTAAATTTTTCA-CTAGGA
333447 AATACTTCAACCCTA
64 AATACTTCAACCCTA
* * * **
333462 TTATTTTTG-AAGAGATACTTCAACACTGTTTTTATTTCCAAAATA-TCGATTTTTCACTATCGG
1 TTATTTTTGAAAGA-ATACTCCAACCCTGTTTTTATTTTCAAAATATTAAATTTTTCACTA--GG
* *
333525 AGATACTCCAACCCTA
63 AAATACTTCAACCCTA
* * * * *
333541 TCACTTCTGAAGGAAAACTCCAACCC
1 TTATTTTTGAAAGAATACTCCAACCC
333567 CATTTATCGA
Statistics
Matches: 150, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
77 2 0.01
78 22 0.15
79 114 0.76
80 10 0.07
81 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (78 bp):
TTATTTTTGAAAGAATACTCCAACCCTGTTTTTATTTTCAAAATATTAAATTTTTCACTAGGAAA
TACTTCAACCCTA
Found at i:333740 original size:23 final size:22
Alignment explanation
Indices: 333709--333757 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
333699 CGTCCCTCAT
**
333709 TTTTATATATTTTTGTGCGTTTA
1 TTTTATATAAATTTGTGCG-TTA
* *
333732 TTTTGTATAAATTTGTTCGTTA
1 TTTTATATAAATTTGTGCGTTA
333754 TTTT
1 TTTT
333758 CTTTTTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.18, C:0.04, G:0.12, T:0.65
Consensus pattern (22 bp):
TTTTATATAAATTTGTGCGTTA
Found at i:338399 original size:2 final size:2
Alignment explanation
Indices: 338392--338416 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
338382 GATAATAAAC
338392 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 A
338417 AAAGAGAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:338988 original size:6 final size:6
Alignment explanation
Indices: 338971--339001 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
338961 TAATTATATA
338971 ATTTAT -TTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
339002 ATATTGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:338988 original size:18 final size:18
Alignment explanation
Indices: 338958--339025 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
338948 TTTTACTTAT
338958 TTTTA-ATTATATAATTTA
1 TTTTATATTATAT-ATTTA
338976 TTTTATATT-TATATTTA
1 TTTTATATTATATATTTA
338993 TATTTATA-TATAT-TGTGTA
1 T-TTTATATTATATAT-T-TA
*
339012 ATTTATATTATATA
1 TTTTATATTATATA
339026 AAGAATATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
17 8 0.19
18 24 0.57
19 10 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTATATTATATATTTA
Found at i:339067 original size:24 final size:22
Alignment explanation
Indices: 339032--339094 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
339022 TATAAAGAAT
339032 ATATATAATATTTTAAATATTAAA
1 ATATATAATA-TTTAAAT-TTAAA
* *
339056 ATATATATTATTTATATTTAAA
1 ATATATAATATTTAAATTTAAA
* *
339078 ATTTATAA-AATTAAATT
1 ATATATAATATTTAAATT
339095 GTTAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.21
22 11 0.33
23 6 0.18
24 9 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATAATATTTAAATTTAAA
Found at i:339076 original size:22 final size:24
Alignment explanation
Indices: 339032--339085 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
339022 TATAAAGAAT
339032 ATATATAATATTTTAAATATTAAA
1 ATATATAATATTTTAAATATTAAA
* *
339056 ATATATATTA-TTTATAT-TTAAA
1 ATATATAATATTTTAAATATTAAA
*
339078 ATTTATAA
1 ATATATAA
339086 AATTAAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 11 0.42
23 6 0.23
24 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATATAATATTTTAAATATTAAA
Found at i:339114 original size:15 final size:16
Alignment explanation
Indices: 339096--339134 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
339086 AATTAAATTG
* *
339096 TTAAAAATTA-ATCTT
1 TTAAAAAATATATATT
339111 TTAAAAAATATATATT
1 TTAAAAAATATATATT
339127 TTAAAAAA
1 TTAAAAAA
339135 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATATATATT
Found at i:339193 original size:35 final size:33
Alignment explanation
Indices: 339147--339239 Score: 104
Period size: 35 Copynumber: 2.8 Consensus size: 33
339137 TAAAAAATAT
*
339147 AATATAAATATATTTAAATAAATTATTTATTTATA
1 AATATAAATATATTTAAATAAATT-TATATTT-TA
339182 AATATAAATATATTT--A-AAATTTATATTTTA
1 AATATAAATATATTTAAATAAATTTATATTTTA
* *
339212 AAT-TAAATTAAATTTAAATAAATATATA
1 AATATAAA-TATATTTAAATAAATTTATA
339240 ATATTAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
29 4 0.08
30 11 0.22
31 6 0.12
32 6 0.12
33 9 0.18
35 15 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AATATAAATATATTTAAATAAATTTATATTTTA
Found at i:339203 original size:29 final size:30
Alignment explanation
Indices: 339171--339229 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
339161 TAAATAAATT
*
339171 ATTTAT-TTATAAATATAAA-TATATTTAAA
1 ATTTATATTATAAAT-TAAATTAAATTTAAA
*
339200 ATTTATATTTTAAATTAAATTAAATTTAAA
1 ATTTATATTATAAATTAAATTAAATTTAAA
339230 TAAATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTATATTATAAATTAAATTAAATTTAAA
Found at i:340458 original size:27 final size:27
Alignment explanation
Indices: 340395--340465 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
340385 ATAATTAATT
*
340395 TAAAATAAATATAAATTACATTTATTA
1 TAAAATAAATATAAATTACATATATTA
340422 TAATAA-AAATATAAAATGTA-ATATATTA
1 TAA-AATAAATAT-AAAT-TACATATATTA
340450 -AAAATAAATA-AAATTA
1 TAAAATAAATATAAATTA
340466 TACATACAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
24 2 0.05
25 4 0.10
26 2 0.05
27 16 0.41
28 13 0.33
29 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (27 bp):
TAAAATAAATATAAATTACATATATTA
Found at i:342760 original size:22 final size:21
Alignment explanation
Indices: 342707--342760 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
342697 TTAACATTAT
*
342707 TTTTAAATAATTTATAAAAAAA
1 TTTTAAA-AATTCATAAAAAAA
* *
342729 TCTTATAAATTCATAAAAACAA
1 TTTTAAAAATTCATAAAAA-AA
342751 TTTTAAAAAT
1 TTTTAAAAAT
342761 AATATCTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTTAAAAATTCATAAAAAAA
Found at i:343487 original size:20 final size:21
Alignment explanation
Indices: 343446--343491 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
343436 TTTTACTAAA
343446 AATTTTATTGAAAAAAAGTTT
1 AATTTTATTGAAAAAAAGTTT
* *
343467 AATTTTGTTGAAAATAA-TTT
1 AATTTTATTGAAAAAAAGTTT
343487 AATTT
1 AATTT
343492 CTCTTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
AATTTTATTGAAAAAAAGTTT
Found at i:344066 original size:15 final size:16
Alignment explanation
Indices: 344046--344078 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
344036 TCTAATTTGC
344046 AAGTTG-GAAATAAGA
1 AAGTTGAGAAATAAGA
*
344061 AAGTTGAGATATAAGA
1 AAGTTGAGAAATAAGA
344077 AA
1 AA
344079 TGGCAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (16 bp):
AAGTTGAGAAATAAGA
Found at i:344307 original size:23 final size:21
Alignment explanation
Indices: 344262--344307 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
344252 TTTTTTTACA
* *
344262 ATTATTTTTTATATTTAATAT
1 ATTATTTTTTAAATTTAAAAT
344283 ATTATTTTTATTAAATTTAAAAT
1 ATTA-TTTT-TTAAATTTAAAAT
344306 AT
1 AT
344308 ATAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 4 0.19
23 13 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTATTTTTTAAATTTAAAAT
Found at i:347122 original size:30 final size:29
Alignment explanation
Indices: 347076--347132 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
347066 TTTACTTGAT
*
347076 AAATTTTTTTATTATTAAAAAATATTTAA
1 AAATTTTTTTAATATTAAAAAATATTTAA
*
347105 AAATTTATTTTAATATTAAAATATATTT
1 AAATTT-TTTTAATATTAAAAAATATTT
347133 TATAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
AAATTTTTTTAATATTAAAAAATATTTAA
Found at i:347147 original size:30 final size:30
Alignment explanation
Indices: 347083--347170 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
347073 GATAAATTTT
* * * * * *
347083 TTTATTATTAAAAAATATTTAAAAATTTAT
1 TTTAATATTAAAATATATTTTATAATTAAA
347113 TTTAATATTAAAATATATTTTATAATTAAA
1 TTTAATATTAAAATATATTTTATAATTAAA
347143 TTTAA-A-T-AAATA-ATTTTATAATTTAAA
1 TTTAATATTAAAATATATTTTATAA-TTAAA
347170 T
1 T
347171 ATTTTTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
26 9 0.18
27 11 0.22
28 1 0.02
29 1 0.02
30 29 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTAATATTAAAATATATTTTATAATTAAA
Found at i:347733 original size:14 final size:15
Alignment explanation
Indices: 347708--347740 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
347698 ATTTTTTATC
347708 AATTATATTTAAAAT
1 AATTATATTTAAAAT
347723 AATTA-ATTTAAAAT
1 AATTATATTTAAAAT
347737 AATT
1 AATT
347741 TTTTAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATATTTAAAAT
Found at i:348261 original size:13 final size:13
Alignment explanation
Indices: 348226--348272 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
348216 AATTTTGATG
348226 ATTTTTAATT-TT
1 ATTTTTAATTATT
* *
348238 AATTGTAATTATT
1 ATTTTTAATTATT
*
348251 ATTTTTAATTATC
1 ATTTTTAATTATT
*
348264 ACTTTTAAT
1 ATTTTTAAT
348273 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 8 0.29
13 20 0.71
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (13 bp):
ATTTTTAATTATT
Found at i:348468 original size:3 final size:3
Alignment explanation
Indices: 348460--348490 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
348450 ATTAATTTAT
348460 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
348491 CTAGTTATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:348630 original size:27 final size:26
Alignment explanation
Indices: 348544--348632 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
348534 TTTTAATTAA
348544 ATAAAATTATAATTAAT-AAAATTTAT
1 ATAAAATT-TAATTAATAAAAATTTAT
* * * *
348570 TTAAAA-ATATTTAATAAATAAATTTAA
1 ATAAAATTTAATTAAT-AA-AAATTTAT
348597 AGTTAAAATTTAATTATATAAAAATTTAT
1 A--TAAAATTTAATTA-ATAAAAATTTAT
348626 ATAAAAT
1 ATAAAAT
348633 ATAAAATGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
24 7 0.15
26 6 0.12
27 13 0.27
29 13 0.27
30 7 0.15
31 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
ATAAAATTTAATTAATAAAAATTTAT
Found at i:348994 original size:22 final size:24
Alignment explanation
Indices: 348954--349000 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
348944 ACACGAAATG
348954 AATACAACATAGAAAATAAT-TAA
1 AATACAACATAGAAAATAATATAA
*
348977 AATACAGCATA-AAAATAATATAA
1 AATACAACATAGAAAATAATATAA
349000 A
1 A
349001 TATAATACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.66, C:0.09, G:0.04, T:0.21
Consensus pattern (24 bp):
AATACAACATAGAAAATAATATAA
Found at i:349625 original size:11 final size:9
Alignment explanation
Indices: 349602--349644 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
349592 AAATACATAA
349602 TTTTTTTCT
1 TTTTTTTCT
349611 TTTTTTTCT
1 TTTTTTTCT
*
349620 CCTTTTTTCTAT
1 --TTTTTT-TCT
349632 TTTTTTTCT
1 TTTTTTTCT
349641 TTTT
1 TTTT
349645 CTCTTGACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 15 0.52
10 6 0.21
11 6 0.21
12 2 0.07
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:349627 original size:19 final size:17
Alignment explanation
Indices: 349603--349649 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 17
349593 AATACATAAT
349603 TTTTTTCTTTTTTTTCTCC
1 TTTTTTCTTTTTTTT-T-C
349622 TTTTTTCTATTTTTTTTC
1 TTTTTTCT-TTTTTTTTC
349640 TTTTTCTCTT
1 TTTTT-TCTT
349650 GACAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.27
19 12 0.46
20 7 0.27
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTTC
Found at i:349634 original size:21 final size:20
Alignment explanation
Indices: 349602--349640 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
349592 AAATACATAA
*
349602 TTTTTTTCTTTTTTTTCTCC
1 TTTTTTTATTTTTTTTCTCC
349622 TTTTTTCTATTTTTTTTCT
1 TTTTTT-TATTTTTTTTCT
349641 TTTTCTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTATTTTTTTTCTCC
Found at i:349853 original size:58 final size:59
Alignment explanation
Indices: 349774--349886 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
349764 CAATTTTTTT
* * *
349774 AATTAAATCATTATAACAAATTATG-AAAAAATGTCACGAATTGAGATATGATACATTA
1 AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
* * *
349832 AATTAAATTATTA-AGAAAAATTATGTAAAATATGTCATGAATGGAGATACGATAC
1 AATTAAATCATTATA-AAAAATTATGTAAAAAATGTCACGAATGGAGATACGATAC
349887 GAATATGACA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.02
58 21 0.45
59 25 0.53
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (59 bp):
AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
Found at i:350589 original size:34 final size:33
Alignment explanation
Indices: 350519--350612 Score: 84
Period size: 34 Copynumber: 2.8 Consensus size: 33
350509 ATACACGTAC
* *
350519 ATATAAAAAAATAT-GAAATAAAATGAATTATGCAT
1 ATATAAAAAAATATAAAAAT-AAAT--ATTATACAT
*
350554 ATATAAAAAAATATAAAAATATAATATTTTACAT
1 ATATAAAAAAATATAAAAATA-AATATTATACAT
* *
350588 ATA-AAAAATAACATAAATATAAATA
1 ATATAAAAA-AATATAAAAATAAATA
350613 CAAATATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
33 9 0.18
34 20 0.39
35 15 0.29
36 7 0.14
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (33 bp):
ATATAAAAAAATATAAAAATAAATATTATACAT
Found at i:350664 original size:15 final size:15
Alignment explanation
Indices: 350619--350666 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
350609 AATACAAATA
*
350619 TTTTTCTTTTTCCTCC
1 TTTTT-TTTTTCCTTC
350635 TTTCTTTTTTT--TTC
1 TTT-TTTTTTTCCTTC
350649 TTTTTTTTTTCCTTC
1 TTTTTTTTTTCCTTC
350664 TTT
1 TTT
350667 CTTTCTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 6 0.21
16 8 0.29
17 2 0.07
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTTCCTTC
Found at i:351009 original size:2 final size:2
Alignment explanation
Indices: 351002--351043 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
350992 CTTATTTGCC
*
351002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
351042 AT
1 AT
351044 TCAAGCTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:351100 original size:18 final size:18
Alignment explanation
Indices: 351077--351111 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
351067 AAGAAAGTAT
351077 AGTAAAAATTTGTTATAG
1 AGTAAAAATTTGTTATAG
351095 AGTAAAAATTTGTTATA
1 AGTAAAAATTTGTTATA
351112 AAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (18 bp):
AGTAAAAATTTGTTATAG
Found at i:352422 original size:20 final size:20
Alignment explanation
Indices: 352397--352440 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
352387 CTTTTATTTA
*
352397 TATCGATACATATA-AAAATG
1 TATCGACACA-ATACAAAATG
*
352417 TATCGACACAATACACAATG
1 TATCGACACAATACAAAATG
352437 TATC
1 TATC
352441 AATATATTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (20 bp):
TATCGACACAATACAAAATG
Found at i:354038 original size:18 final size:18
Alignment explanation
Indices: 354011--354054 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
354001 TGATAATAAT
*
354011 GATGACGAGGTTGAGAAA
1 GATGAAGAGGTTGAGAAA
*
354029 GATGAAGAGGTTGAGGAA
1 GATGAAGAGGTTGAGAAA
*
354047 GATAAAGA
1 GATGAAGA
354055 AATGGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.39, T:0.16
Consensus pattern (18 bp):
GATGAAGAGGTTGAGAAA
Found at i:356992 original size:24 final size:23
Alignment explanation
Indices: 356944--356994 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
356934 AAGCAAGCTC
*
356944 TTAAAGCTTTTTGTGAAAGACTT
1 TTAAAGCTTTTTGTGAAAAACTT
*
356967 TTAAA-CTTTTTGATTGAAAAAGTT
1 TTAAAGCTTTTTG--TGAAAAACTT
356991 TTAA
1 TTAA
356995 TAGAAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 5 0.21
24 12 0.50
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (23 bp):
TTAAAGCTTTTTGTGAAAAACTT
Found at i:359024 original size:16 final size:16
Alignment explanation
Indices: 359003--359033 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
358993 ATGGCCAATT
*
359003 GATGATTTTTGTGAAA
1 GATGATGTTTGTGAAA
359019 GATGATGTTTGTGAA
1 GATGATGTTTGTGAA
359034 TTGAGAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (16 bp):
GATGATGTTTGTGAAA
Done.