Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold594
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: 328579
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:305614 original size:34 final size:35
Alignment explanation
Indices: 305576--305642 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
305566 CCTTACAACA
305576 CTATC-TTTC-AAGGATAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGATAAGATAG-AACCTCTCTCT
*
305610 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGATAAGATAGAACCTCTC
305643 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGATAAGATAGAACCTCTCTCT
Found at i:306164 original size:45 final size:46
Alignment explanation
Indices: 306082--306170 Score: 119
Period size: 45 Copynumber: 1.9 Consensus size: 46
306072 AGGCTTTGAT
* *
306082 TGAATAGTGATGAACAGTGATTTTTAACGATACATGAATAGTGATACG
1 TGAACAGTGATGAACAGTGA-TTGTAACGATACATGAA-AGTGATACG
*
306130 TGAACAGTG-TGAACAGTGA-TGTATCGATACATGAAAGTGAT
1 TGAACAGTGATGAACAGTGATTGTAACGATACATGAAAGTGAT
306171 GTATCGATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 6 0.16
45 14 0.37
47 10 0.26
48 8 0.21
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
TGAACAGTGATGAACAGTGATTGTAACGATACATGAAAGTGATACG
Found at i:306193 original size:22 final size:22
Alignment explanation
Indices: 306139--306193 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
306129 GTGAACAGTG
306139 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
306161 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
306182 TGAACAGTGATG
1 TGAACAGTGATG
306194 AATAGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:306200 original size:10 final size:10
Alignment explanation
Indices: 306181--306211 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
306171 GTATCGATAC
306181 ATGAACAGTG
1 ATGAACAGTG
*
306191 ATGAATAGTG
1 ATGAACAGTG
306201 ATGAACAGTG
1 ATGAACAGTG
306211 A
1 A
306212 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:306258 original size:18 final size:18
Alignment explanation
Indices: 306235--306270 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
306225 CTACTTCCAA
*
306235 TGTATCGATACATATTTG
1 TGTATCGATACAAATTTG
306253 TGTATCGATACAAATTTG
1 TGTATCGATACAAATTTG
306271 GCTACTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (18 bp):
TGTATCGATACAAATTTG
Found at i:306319 original size:53 final size:53
Alignment explanation
Indices: 306235--306370 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
306225 CTACTTCCAA
306235 TGTATCGATACATATT-TGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
306287 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCTATGTCC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
306340 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATA-TTGTGTGTATCGATAC
306371 TATCAATTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
52 16 0.20
53 48 0.60
54 16 0.20
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:306405 original size:20 final size:19
Alignment explanation
Indices: 306358--306410 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
306348 TACATATTTG
306358 TGTGTATCGATACTATC-AA
1 TGTGTATCGATACT-TCAAA
*
306377 T-TTTATCGATACATTCAAA
1 TGTGTATCGATAC-TTCAAA
306396 TGTGTATCGATACTT
1 TGTGTATCGATACTT
306411 TCAGGGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 12 0.41
19 7 0.24
20 10 0.34
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (19 bp):
TGTGTATCGATACTTCAAA
Found at i:306413 original size:20 final size:20
Alignment explanation
Indices: 306358--306413 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
306348 TACATATTTG
*
306358 TGTGTATCGATACTATC-AA
1 TGTGTATCGATACTTTCAAA
* *
306377 T-TTTATCGATACATTCAAA
1 TGTGTATCGATACTTTCAAA
306396 TGTGTATCGATACTTTCA
1 TGTGTATCGATACTTTCA
306414 GGGTTTTGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 12 0.40
19 4 0.13
20 14 0.47
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (20 bp):
TGTGTATCGATACTTTCAAA
Found at i:306478 original size:21 final size:21
Alignment explanation
Indices: 306448--306487 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
306438 TCAACCTGTG
306448 GTATTAATACCAATA-GTATAT
1 GTATTAATA-CAATACGTATAT
*
306469 GTATTGATACAATACGTAT
1 GTATTAATACAATACGTAT
306488 TTGGACTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
GTATTAATACAATACGTATAT
Found at i:306855 original size:31 final size:31
Alignment explanation
Indices: 306815--306883 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
306805 TTATCCACAC
*
306815 TCATTAAAAATTGGTACCATTCATTAAACTT
1 TCATCAAAAATTGGTACCATTCATTAAACTT
306846 TCATCAAAAATTGGTACCATTCATTAAACTT
1 TCATCAAAAATTGGTACCATTCATTAAACTT
306877 TCATCAA
1 TCATCAA
306884 TTGGTATCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (31 bp):
TCATCAAAAATTGGTACCATTCATTAAACTT
Found at i:307639 original size:87 final size:87
Alignment explanation
Indices: 307493--307672 Score: 299
Period size: 87 Copynumber: 2.1 Consensus size: 87
307483 ATTCGGTTTA
*
307493 AATTTGGTTTTATCAACTTAGCTTATAACACAAAGGGGGAGAAATTATTGTTTATTGGTTTAAGG
1 AATTTGGTTTTATCAACTTAGCTTATAACACAAAGGGGGAGAAATTATTATTTATTGGTTTAAGG
307558 GTGAGAACATATT-AAGGGGGAG
66 GTGAGAACATATTGAA-GGGGAG
* *
307580 AATTTGGTTTTATCAACTTAGTTTATAACACAAAGGGGGAGAGATTATTATTTATTGGTTTAAGG
1 AATTTGGTTTTATCAACTTAGCTTATAACACAAAGGGGGAGAAATTATTATTTATTGGTTTAAGG
*
307645 GTGAGAACGTATTGAAGGGGAG
66 GTGAGAACATATTGAAGGGGAG
*
307667 AGTTTG
1 AATTTG
307673 CATAAAATTC
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 85 0.98
88 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.34
Consensus pattern (87 bp):
AATTTGGTTTTATCAACTTAGCTTATAACACAAAGGGGGAGAAATTATTATTTATTGGTTTAAGG
GTGAGAACATATTGAAGGGGAG
Found at i:308429 original size:21 final size:21
Alignment explanation
Indices: 308386--308429 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
308376 GTTAAGTATA
*
308386 AATGTTTTTCAAGCATAAGAAT
1 AATGTTTTTCAAG-ATAAAAAT
308408 AATGTTTTTCAA-AGTAAAAAT
1 AATGTTTTTCAAGA-TAAAAAT
308429 A
1 A
308430 TTTCAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 7 0.35
22 12 0.60
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (21 bp):
AATGTTTTTCAAGATAAAAAT
Found at i:308566 original size:13 final size:13
Alignment explanation
Indices: 308548--308572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
308538 ATATTGCTTA
308548 GTATCGATACATT
1 GTATCGATACATT
308561 GTATCGATACAT
1 GTATCGATACAT
308573 GTTCTTGGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:308589 original size:32 final size:33
Alignment explanation
Indices: 308527--308591 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
308517 CACACCTAGA
308527 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
* *
308560 TGTATCGATACATGTT-CTTGGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
308592 ATGGAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTAGTATCGATACAT
Found at i:308657 original size:13 final size:13
Alignment explanation
Indices: 308639--308663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
308629 AAACTCACTT
308639 TGTATCGATACAA
1 TGTATCGATACAA
308652 TGTATCGATACA
1 TGTATCGATACA
308664 TGGTGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:308677 original size:20 final size:20
Alignment explanation
Indices: 308652--308704 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
308642 ATCGATACAA
308652 TGTATCGATACATGGTGAAT
1 TGTATCGATACATGGTGAAT
308672 TGTATCGATACATGGTGAAT
1 TGTATCGATACATGGTGAAT
308692 TGTATCGATACAT
1 TGTATCGATACAT
308705 TGAGCCCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGGTGAAT
Found at i:309204 original size:33 final size:31
Alignment explanation
Indices: 309167--309250 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 31
309157 AAGATAGTAT
309167 AGAGGTTCTATCTTAGCCTGC-AAAAGATAGGG
1 AGAGGTTCTATCTTAGCCTGCGAAAAGATA--G
* *
309199 AAGAGGTTCTACCTTAGCCCGCGAAAAGATAG
1 -AGAGGTTCTATCTTAGCCTGCGAAAAGATAG
309231 AGAGGTTTCTATCTTAGCCT
1 AGAGG-TTCTATCTTAGCCT
309251 TGAAAGATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
31 5 0.11
32 13 0.29
33 19 0.42
34 8 0.18
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (31 bp):
AGAGGTTCTATCTTAGCCTGCGAAAAGATAG
Found at i:310340 original size:20 final size:20
Alignment explanation
Indices: 310315--310369 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
310305 TTTTCACAAT
310315 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
** *
310335 TTGTATCGATACCCTGTTCA
1 TTGTATCGATACATTATTCA
310355 TTGTATCGATACATT
1 TTGTATCGATACATT
310370 GTATCGATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:310371 original size:13 final size:13
Alignment explanation
Indices: 310353--310382 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
310343 ATACCCTGTT
310353 CATTGTATCGATA
1 CATTGTATCGATA
310366 CATTGTATCGATA
1 CATTGTATCGATA
310379 CATT
1 CATT
310383 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:310425 original size:20 final size:20
Alignment explanation
Indices: 310400--310450 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
310390 TACCCAGATG
*
310400 ATCGATACATT-TTGCATTGT
1 ATCGATACATTGCT-CATTGT
310420 ATCGATACATTGCTCATTGT
1 ATCGATACATTGCTCATTGT
310440 ATCGATACATT
1 ATCGATACATT
310451 ATATTGATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (20 bp):
ATCGATACATTGCTCATTGT
Found at i:310460 original size:81 final size:81
Alignment explanation
Indices: 310316--310512 Score: 288
Period size: 81 Copynumber: 2.4 Consensus size: 81
310306 TTTCACAATT
** * *
310316 TGTATCGATACATTATTCATTGTATCGATACCCTGTTCATTGTATCGATACATTGTATCGATACA
1 TGTATCGATACATT-TTCATTGTATCGATACATTGCTCATTGTATCGATACATTATATCGATACA
*
310381 TTCTGGGTTTACCCAGA
65 TTCTGGATTTACCCAGA
*
310398 TG-ATCGATACATTTTGCATTGTATCGATACATTGCTCATTGTATCGATACATTATATTGATACA
1 TGTATCGATACATTTT-CATTGTATCGATACATTGCTCATTGTATCGATACATTATATCGATACA
*
310462 TTTTGGATTTACCCAGA
65 TTCTGGATTTACCCAGA
*
310479 TGTATCGATACATTTTACAATGTATCGATACATT
1 TGTATCGATACATTTT-CATTGTATCGATACATT
310513 CAGGCATTTT
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
80 2 0.02
81 71 0.68
82 31 0.30
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (81 bp):
TGTATCGATACATTTTCATTGTATCGATACATTGCTCATTGTATCGATACATTATATCGATACAT
TCTGGATTTACCCAGA
Found at i:312191 original size:51 final size:50
Alignment explanation
Indices: 312081--312350 Score: 158
Period size: 51 Copynumber: 5.3 Consensus size: 50
312071 TTTCATCTCG
* * ** * * * ** *
312081 GGGATACTCCAATCCCGGTTCCATTTCCAAAACATCAATTTTTCTTAATC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAAGC
*
312131 GAGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAAGC
1 G-GGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAAGC
* *** ** *
312182 GGGAGTACTCCAATCCC-A--TTATTTCATCGGGGATACTCCAATCTCGTTATTTCTGAG-
1 GGGA-TACTCCAACCCCGATTTTATTTC-T--AAAATA--CCAAT-T--TT-TCAC-AAGC
*
312239 GGGATACTCCAACCTCGATTTTATTTCTAAAATACCAATTTTTCACAAGC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAAGC
* * * *
312289 AGGGATACTCCAACTCCGATTTTATTTC-CAAA-A-CAATTTCTCACAATC
1 -GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAAGC
312337 GGGGATACTCCAAC
1 -GGGATACTCCAAC
312351 TCCGTTATTT
Statistics
Matches: 170, Mismatches: 33, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
48 33 0.19
49 4 0.02
50 10 0.06
51 80 0.47
53 6 0.04
54 6 0.04
56 15 0.09
57 6 0.04
58 3 0.02
59 7 0.04
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAAGC
Found at i:312218 original size:28 final size:28
Alignment explanation
Indices: 312182--312250 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
312172 TTCCACAAGC
*
312182 GGGAGTACTCCAATCCCATTATTTCAT-CG
1 GGGA-TACTCCAATCCCATTATTTC-TGAG
* *
312211 GGGATACTCCAATCTCGTTATTTCTGAG
1 GGGATACTCCAATCCCATTATTTCTGAG
312239 GGGATACTCCAA
1 GGGATACTCCAA
312251 CCTCGATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.03
28 31 0.86
29 4 0.11
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (28 bp):
GGGATACTCCAATCCCATTATTTCTGAG
Found at i:312345 original size:48 final size:51
Alignment explanation
Indices: 312238--312354 Score: 161
Period size: 48 Copynumber: 2.4 Consensus size: 51
312228 TTATTTCTGA
*
312238 GGGGATACTCCAAC-CTCGATTTTATTTCTAAAATACCAATTTTTCACAAGC
1 GGGGATACTCCAACTC-CGATTTTATTTCTAAAATACCAATTTCTCACAAGC
* * *
312289 AGGGATACTCCAACTCCGATTTTATTTC-CAAA-A-CAATTTCTCACAATC
1 GGGGATACTCCAACTCCGATTTTATTTCTAAAATACCAATTTCTCACAAGC
312337 GGGGATACTCCAACTCCG
1 GGGGATACTCCAACTCCG
312355 TTATTTTTGC
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
48 30 0.50
49 1 0.02
50 3 0.05
51 25 0.42
52 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGATTTTATTTCTAAAATACCAATTTCTCACAAGC
Found at i:312438 original size:79 final size:78
Alignment explanation
Indices: 312290--312591 Score: 333
Period size: 79 Copynumber: 3.8 Consensus size: 78
312280 TTCACAAGCA
* * *
312290 GGGATACTCCAACTCCGATTTTATTTCCAAAACA---ATTTCTC-ACAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTATTT-TAAAACACTGATTT-TCAACAATCAGGGATACTCCAAC
* * *
312351 TCCGTTATTTTTGCG
64 CCCATTATTTTTGAG
*** * *
312366 GGGATACTCCAACCCCGGCCTTATTTCTAAAGCATTGATTTTCAACAATCAGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTT-TAAAACACTGATTTTCAACAATCAGGGATACTCCAACC
*
312431 CCATTATTTTCGAG
65 CCATTATTTTTGAG
** * *
312445 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTT-AAAACACTGATTTTCAACAATCAGGGATACTCCAACC
*
312510 CTATTATTTTTGAG
65 CCATTATTTTTGAG
* * * *
312524 GGGATACTCCAACCCCGATTTTATTTTTAAAATACTGATTTTCCATAATCAGGGGATACTCCAGC
1 GGGATACTCCAACCCCGATTTTA-TTTTAAAACACTGATTTTCAACAATCA-GGGATACTCCAAC
312589 CCC
64 CCC
312592 GTTGTCATCT
Statistics
Matches: 191, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
76 28 0.15
78 3 0.02
79 142 0.74
80 18 0.09
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGATTTTATTTTAAAACACTGATTTTCAACAATCAGGGATACTCCAACCC
CATTATTTTTGAG
Found at i:312532 original size:158 final size:156
Alignment explanation
Indices: 312290--312591 Score: 394
Period size: 158 Copynumber: 1.9 Consensus size: 156
312280 TTCACAAGCA
* * * *
312290 GGGATACTCCAACTCCGATTTTATTTCCAAAACAATTTCTCACAATCGGGGATACTCCAACTCCG
1 GGGATACTCCAACCCCGATTTTATTTCAAAAACAATTTCTCACAATCAGGGATACTCCAACTCCA
* * * *
312355 TTATTTTTGCGGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATTGATTTTCAACAATCA-GG
66 TTATTTTTGAGGGGATACTCCAACCCCGACCTTATTTCTAAAACACTGATTTTCAACAATCAGGG
312419 GATACTCCAACCCCATTATTTTCGAG
131 GATACTCCAACCCCATTATTTTCGAG
*
312445 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTT-TCTATAATCAGGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTTA-TTTCAAAA-A-CAATTTCTC-ACAATCAGGGATACTCCAAC
** * * * *
312509 -CCTATTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTTTAAAATACTGATTTTCCATAAT
62 TCC-ATTATTTTTGAGGGGATACTCCAACCCCGACCTTATTTCTAAAACACTGATTTTCAACAAT
*
312573 CAGGGGATACTCCAGCCCC
126 CAGGGGATACTCCAACCCC
312592 GTTGTCATCT
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
155 22 0.18
156 7 0.06
157 5 0.04
158 76 0.61
159 15 0.12
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (156 bp):
GGGATACTCCAACCCCGATTTTATTTCAAAAACAATTTCTCACAATCAGGGATACTCCAACTCCA
TTATTTTTGAGGGGATACTCCAACCCCGACCTTATTTCTAAAACACTGATTTTCAACAATCAGGG
GATACTCCAACCCCATTATTTTCGAG
Found at i:324657 original size:20 final size:22
Alignment explanation
Indices: 324622--324662 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
324612 TGGACATGTT
324622 AAAATGCATGGAACAT-GGCTC
1 AAAATGCATGGAACATAGGCTC
324643 AAAATGCAT-GAACATAGGCT
1 AAAATGCATGGAACATAGGCT
324663 GTTTAGCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (22 bp):
AAAATGCATGGAACATAGGCTC
Found at i:325597 original size:52 final size:50
Alignment explanation
Indices: 325536--325700 Score: 195
Period size: 52 Copynumber: 3.2 Consensus size: 50
325526 TTAGCTAGAC
* *
325536 GTATCGATACATTGAAGAATGTATCGATACATTTGGTTCAAAAACCTAAAAT
1 GTATCGATACAATGAAGAATGTATCGATACATTTGG-ACAAAAACC-AAAAT
* * *
325588 GTATCGATACAATGAAGAATGTATCGATACATTCGGGCAAAAAACCGAGAAT
1 GTATCGATACAATGAAGAATGTATCGATACATTTGGAC-AAAAACC-AAAAT
* * * * * *
325640 GTGTCGATACAAAGAAAAATGTATCGATACATTTAGACTAAATCCAAAAT
1 GTATCGATACAATGAAGAATGTATCGATACATTTGGACAAAAACCAAAAT
325690 GTATCGATACA
1 GTATCGATACA
325701 TTTTTTCCAA
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
50 14 0.14
51 6 0.06
52 77 0.79
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (50 bp):
GTATCGATACAATGAAGAATGTATCGATACATTTGGACAAAAACCAAAAT
Found at i:325781 original size:20 final size:21
Alignment explanation
Indices: 325758--325811 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
325748 CATTTCAAAC
325758 ATGTATCGATACATTCACTT-
1 ATGTATCGATACATTCACTTG
325778 ATGTATCGATACATTCACTTG
1 ATGTATCGATACATTCACTTG
* *
325799 TTGTATCAATACA
1 ATGTATCGATACA
325812 AATTGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTCACTTG
Done.