Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1195
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: 269935
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:183151 original size:21 final size:20
Alignment explanation
Indices: 183105--183152 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
183095 GTATCAATAT
* *
183105 AATATATCGATACTTTGAAT
1 AATATATCGATACTTTCAAG
*
183125 AATATATCGATACATTTCTAG
1 AATATATCGATAC-TTTCAAG
183146 AATATAT
1 AATATAT
183153 TAATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (20 bp):
AATATATCGATACTTTCAAG
Found at i:184115 original size:147 final size:146
Alignment explanation
Indices: 183835--184126 Score: 408
Period size: 147 Copynumber: 2.0 Consensus size: 146
183825 CATGCTATAC
* * * * *
183835 ATTTTTAATTTAGTATTTTTCTTTGAATTAAATTGAAAATATTTTTAAAAATATTAAATTAATAT
1 ATTTTTAAGTTAATATTTTTCGTTGAATTAAATGGAAAATATTTTGAAAAATATTAAATTAATAT
*** * * * *
183900 ATTTACCTTTTATTTTTTCAAAAATAATGTTTCTAATGAATATTTATATTTAGATTATTTTTGAG
66 ATTTACCTCCAATTTTCTCAAAAATAATGTTTCAAATGAATATTTATATGTAGAATATTTTTGAG
183965 ACAAGTTTAAATGATA
131 ACAAGTTTAAATGATA
183981 ATTTTTAAAGTTAATATTTTTCGTTGAATTAAATGGAAAATATTTTGAAAAATATTAAATTAAT-
1 ATTTTT-AAGTTAATATTTTTCGTTGAATTAAATGGAAAATATTTTGAAAAATATTAAATTAATA
*
184045 TTTCTTACCTCCAATTTTCTCAAAAATAAT-TATTCAAATGAATATTTATATGTAGAATATTTTT
65 TAT-TTACCTCCAATTTTCTCAAAAATAATGT-TTCAAATGAATATTTATATGTAGAATATTTTT
* *
184109 TAGACAAGTTTAAGTGAT
128 GAGACAAGTTTAAATGAT
184127 TTTCAAGTAA
Statistics
Matches: 128, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
146 9 0.07
147 119 0.93
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (146 bp):
ATTTTTAAGTTAATATTTTTCGTTGAATTAAATGGAAAATATTTTGAAAAATATTAAATTAATAT
ATTTACCTCCAATTTTCTCAAAAATAATGTTTCAAATGAATATTTATATGTAGAATATTTTTGAG
ACAAGTTTAAATGATA
Found at i:184311 original size:20 final size:20
Alignment explanation
Indices: 184258--184341 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
184248 ATTTATTGAT
*
184258 AAAATGTATTGATACATATC
1 AAAATGTATAGATACATATC
**
184278 -ATTTGTATCA-ATACATATC
1 AAAATGTAT-AGATACATATC
184297 AAAATGTATAGATACA-ATAC
1 AAAATGTATAGATACATAT-C
* * * *
184317 ACAATGTATTGATGCATCTC
1 AAAATGTATAGATACATATC
184337 AAAAT
1 AAAAT
184342 ATATCAATAC
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
19 18 0.37
20 30 0.61
21 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAATGTATAGATACATATC
Found at i:188784 original size:19 final size:19
Alignment explanation
Indices: 188756--188792 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
188746 GCATTTGGAA
*
188756 ATTTGGATTTAAAAAATAG
1 ATTTGAATTTAAAAAATAG
188775 ATTTGAATTTAAAAAATA
1 ATTTGAATTTAAAAAATA
188793 ATGTAAATTG
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:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATTTGAATTTAAAAAATAG
Found at i:188801 original size:18 final size:19
Alignment explanation
Indices: 188762--188801 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
188752 GGAAATTTGG
* *
188762 ATTTAAAAAATAGATTTGA
1 ATTTAAAAAATAGATGTAA
188781 ATTTAAAAAATA-ATGTAA
1 ATTTAAAAAATAGATGTAA
188799 ATT
1 ATT
188802 GTGTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (19 bp):
ATTTAAAAAATAGATGTAA
Found at i:191724 original size:15 final size:16
Alignment explanation
Indices: 191680--191734 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
191670 AGTTACTCTA
* *
191680 AACATAAGTTGTTTTG
1 AACACAAGTTGTTATG
*
191696 AACACAATTTGTTATG
1 AACACAAGTTGTTATG
191712 AACA-AAGTTGTTATAG
1 AACACAAGTTGTTAT-G
191728 AAC-CAAG
1 AACACAAG
191735 GTTTTCGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 9 0.27
16 24 0.73
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (16 bp):
AACACAAGTTGTTATG
Found at i:193865 original size:23 final size:25
Alignment explanation
Indices: 193834--193884 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
193824 GTTAGATAAG
*
193834 AAAGAAAGAAAATG-AAAAAGAA-A
1 AAAGAAAGAAAAAGAAAAAAGAAGA
*
193857 AAAGGAAGAAAAAGAAAAAAGAAGA
1 AAAGAAAGAAAAAGAAAAAAGAAGA
193882 AAA
1 AAA
193885 AAAACATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.50
24 8 0.33
25 4 0.17
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (25 bp):
AAAGAAAGAAAAAGAAAAAAGAAGA
Found at i:193869 original size:17 final size:16
Alignment explanation
Indices: 193834--193885 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
193824 GTTAGATAAG
*
193834 AAAGAAAGAAA-ATGAA
1 AAAGAAA-AAAGAAGAA
193850 AAAGAAAAAAGGAAGAA
1 AAAGAAAAAA-GAAGAA
193867 AAAGAAAAAAGAAGAA
1 AAAGAAAAAAGAAGAA
193883 AAA
1 AAA
193886 AAACATATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 3 0.09
16 16 0.48
17 14 0.42
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAAGAAGAA
Found at i:193886 original size:17 final size:17
Alignment explanation
Indices: 193847--193885 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
193837 GAAAGAAAAT
193847 GAAAAAGAAAAAAGGAA
1 GAAAAAGAAAAAAGGAA
193864 GAAAAAGAAAAAA-GAA
1 GAAAAAGAAAAAAGGAA
193880 GAAAAA
1 GAAAAA
193886 AAACATATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAAAAAGGAA
Found at i:194254 original size:2 final size:2
Alignment explanation
Indices: 194247--194271 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
194237 TTGTTTTATC
194247 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 T
194272 TTTGAAAATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:195565 original size:97 final size:96
Alignment explanation
Indices: 195445--195678 Score: 360
Period size: 97 Copynumber: 2.4 Consensus size: 96
195435 GGGGATAGTC
* *
195445 CAACCCTATTCTTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTAT
1 CAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTAT
195510 TCTCACTTAAATTGTCATCATCGGGGACACTT
66 TCTCACTTAAATTGTCATCATCGGGGACAC-T
* * ** *
195542 CAACCCCATTCCTCCAAGGGGATACTCCAACCTCGCTTTTAAATGCATCAAAGTTTAAATTTTAT
1 CAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTAT
*
195607 TCTCACTTAAATTGTCATCATCGGGGACTCT
66 TCTCACTTAAATTGTCATCATCGGGGACACT
* *
195638 CCACCCTCATTCCTCCGAGGGGATACTCCAACCCCGTTTTT
1 CAACCC-CATTCCTCCGAGGGGATACTCCAACCCCGCTTTT
195679 CAATAAAAAT
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
96 6 0.05
97 118 0.95
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (96 bp):
CAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTAT
TCTCACTTAAATTGTCATCATCGGGGACACT
Found at i:198819 original size:24 final size:25
Alignment explanation
Indices: 198773--198819 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
198763 TAAATTTAAC
198773 ATAATTTAAATTTTAAAAAAATTAT
1 ATAATTTAAATTTTAAAAAAATTAT
*
198798 ATAATTTAAA-TTTAAAATAATT
1 ATAATTTAAATTTTAAAAAAATT
198820 TAATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAATTTAAATTTTAAAAAAATTAT
Found at i:198886 original size:23 final size:24
Alignment explanation
Indices: 198860--198904 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
198850 TTAAAAATTT
* *
198860 AAATTTTTTTTAAAAT-AAAATAA
1 AAATTTTATTAAAAATCAAAATAA
198883 AAATTTTATTAAAAATCAAAAT
1 AAATTTTATTAAAAATCAAAAT
198905 CAAGGGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATTTTATTAAAAATCAAAATAA
Found at i:199432 original size:2 final size:2
Alignment explanation
Indices: 199425--199452 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
199415 TATTAATAGC
199425 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
199453 GGTTACTTAA
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
Found at i:201106 original size:14 final size:14
Alignment explanation
Indices: 201087--201117 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
201077 CATGTTTAGA
201087 AGGATTTTCAGAAG
1 AGGATTTTCAGAAG
201101 AGGATTTTCAGAAG
1 AGGATTTTCAGAAG
201115 AGG
1 AGG
201118 CTTCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (14 bp):
AGGATTTTCAGAAG
Found at i:212745 original size:95 final size:95
Alignment explanation
Indices: 212544--212736 Score: 368
Period size: 95 Copynumber: 2.0 Consensus size: 95
212534 TAATATCTAG
*
212544 GTTTTGGTATTTTTTCTATCACTGATATTGGCCTTGACATTATCTTCAATAAGGCCTTATCTTCA
1 GTTTTGGTATTTTTTCTATCACTGATATAGGCCTTGACATTATCTTCAATAAGGCCTTATCTTCA
212609 TTCTAGTTAGGCAAACAGGATATTTCCAAA
66 TTCTAGTTAGGCAAACAGGATATTTCCAAA
*
212639 GTTTTGGTATTTTTTCTATCACTGATATAGGCCTTGACATTATCTTCGATAAGGCCTTATCTTCA
1 GTTTTGGTATTTTTTCTATCACTGATATAGGCCTTGACATTATCTTCAATAAGGCCTTATCTTCA
212704 TTCTAGTTAGGCAAACAGGATATTTCCAAA
66 TTCTAGTTAGGCAAACAGGATATTTCCAAA
212734 GTT
1 GTT
212737 CTTTTATTTA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (95 bp):
GTTTTGGTATTTTTTCTATCACTGATATAGGCCTTGACATTATCTTCAATAAGGCCTTATCTTCA
TTCTAGTTAGGCAAACAGGATATTTCCAAA
Found at i:215346 original size:2 final size:2
Alignment explanation
Indices: 215339--215377 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
215329 TAATCATCCA
215339 TC TC TC 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 TC TC TC T
215378 GCTATTTGCT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:215638 original size:22 final size:23
Alignment explanation
Indices: 215603--215645 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
215593 TAAAATTTTT
215603 TAAATTTTATTATTTTATTTAAA
1 TAAATTTTATTATTTTATTTAAA
*
215626 TAAATTTTA-TATTTTTTTTA
1 TAAATTTTATTATTTTATTTA
215646 CATTCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TAAATTTTATTATTTTATTTAAA
Found at i:215685 original size:30 final size:30
Alignment explanation
Indices: 215651--215713 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
215641 TTTTACATTC
* *
215651 AAATAAATTTTTAATATTT-AATTAATA-TCT
1 AAATAAA-TCTTAACATTTAAATT-ATACTCT
215681 AAATAAATCTTAACATTTAAATTATACTCT
1 AAATAAATCTTAACATTTAAATTATACTCT
215711 AAA
1 AAA
215714 AGTCATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATAAATCTTAACATTTAAATTATACTCT
Found at i:215892 original size:22 final size:22
Alignment explanation
Indices: 215867--215908 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
215857 ATAAAAATTT
215867 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
215889 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
215909 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:219117 original size:38 final size:39
Alignment explanation
Indices: 219044--219122 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
219034 ATATTTCATG
*
219044 TTTAGATATGGCAAATGATTCTTTTAACTTTATTTTTCA
1 TTTAGATATGACAAATGATTCTTTTAACTTTATTTTTCA
219083 TTTAGATATGACAAATGATTC-TTTAACTTTATTTTTCA
1 TTTAGATATGACAAATGATTCTTTTAACTTTATTTTTCA
219121 TT
1 TT
219123 GTTATCTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 19 0.49
39 20 0.51
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (39 bp):
TTTAGATATGACAAATGATTCTTTTAACTTTATTTTTCA
Found at i:221649 original size:15 final size:17
Alignment explanation
Indices: 221631--221668 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
221621 TTACGTTTTG
*
221631 TTTAATTAAGTCA-A-A
1 TTTAATTAAATCACATA
221646 TTTAATTAAATCACATA
1 TTTAATTAAATCACATA
221663 TTTAAT
1 TTTAAT
221669 CCAACAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 1 0.05
17 7 0.35
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAATTAAATCACATA
Found at i:225619 original size:18 final size:18
Alignment explanation
Indices: 225592--225629 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
225582 AAAATAAAAT
225592 AATTGATAA-TTAGTTGAA
1 AATTGATAATTTA-TTGAA
*
225610 AATTGGTAATTTATTGAA
1 AATTGATAATTTATTGAA
225628 AA
1 AA
225630 AAGGAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (18 bp):
AATTGATAATTTATTGAA
Found at i:228667 original size:20 final size:20
Alignment explanation
Indices: 228642--228696 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
228632 ATTGGGCTCA
* *
228642 ATGTATCGATACATTTTACC
1 ATGTATCGATACAATTCACC
*
228662 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
*
228682 ATGTGTCGATACAAT
1 ATGTATCGATACAAT
228697 GTATCGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:228799 original size:20 final size:19
Alignment explanation
Indices: 228756--228805 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
228746 CTTTTCAAGG
* *
228756 TGTATCGATACTATGGACA
1 TGTATCGATACTAAGAACA
*
228775 TGTATCGATACTAAGCAATA
1 TGTATCGATACTAAG-AACA
*
228795 TGTATCAATAC
1 TGTATCGATAC
228806 ATCTGGGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
TGTATCGATACTAAGAACA
Found at i:231515 original size:13 final size:13
Alignment explanation
Indices: 231494--231581 Score: 96
Period size: 13 Copynumber: 7.1 Consensus size: 13
231484 TAGTATCCAT
231494 GTATCGATACTAA
1 GTATCGATACTAA
*
231507 GTCTCGATA-TAA
1 GTATCGATACTAA
231519 TGTATCGATACTAA
1 -GTATCGATACTAA
* *
231533 GTCTCGATA--AT
1 GTATCGATACTAA
231544 GTATCGATACTAA
1 GTATCGATACTAA
*
231557 GTATCGATA--AT
1 GTATCGATACTAA
231568 GTATCGATACTAA
1 GTATCGATACTAA
231581 G
1 G
231582 AACACAGTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
11 19 0.31
12 3 0.05
13 36 0.59
14 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (13 bp):
GTATCGATACTAA
Found at i:231547 original size:24 final size:24
Alignment explanation
Indices: 231492--231581 Score: 153
Period size: 24 Copynumber: 3.7 Consensus size: 24
231482 AATAGTATCC
231492 ATGTATCGATACTAAGTCTCGATATA
1 ATGTATCGATACTAAGTCTCG--ATA
231518 ATGTATCGATACTAAGTCTCGATA
1 ATGTATCGATACTAAGTCTCGATA
*
231542 ATGTATCGATACTAAGTATCGATA
1 ATGTATCGATACTAAGTCTCGATA
231566 ATGTATCGATACTAAG
1 ATGTATCGATACTAAG
231582 AACACAGTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
24 42 0.67
26 21 0.33
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (24 bp):
ATGTATCGATACTAAGTCTCGATA
Found at i:231552 original size:11 final size:11
Alignment explanation
Indices: 231515--231576 Score: 61
Period size: 11 Copynumber: 5.3 Consensus size: 11
231505 AAGTCTCGAT
231515 ATAATGTATCG
1 ATAATGTATCG
* *
231526 ATACTAAGTCTCG
1 ATA--ATGTATCG
231539 ATAATGTATCG
1 ATAATGTATCG
*
231550 ATACTAAGTATCG
1 ATA--ATGTATCG
231563 ATAATGTATCG
1 ATAATGTATCG
231574 ATA
1 ATA
231577 CTAAGAACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
11 22 0.54
13 19 0.46
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (11 bp):
ATAATGTATCG
Found at i:237240 original size:22 final size:23
Alignment explanation
Indices: 237206--237248 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
237196 TCTCTCAATC
237206 TCTTCAAGAATTATA-CCCAAAT
1 TCTTCAAGAATTATATCCCAAAT
237228 TCTT-AAGAGATTATATCCCAA
1 TCTTCAAGA-ATTATATCCCAA
237249 GGTAGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (23 bp):
TCTTCAAGAATTATATCCCAAAT
Found at i:237668 original size:20 final size:20
Alignment explanation
Indices: 237643--237697 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
237633 ATTGGGCTCA
*
237643 ATGTATCGATACATTTTACC
1 ATGTATCGATACATTTCACC
* *
237663 ATGTATCGATACAATTCATC
1 ATGTATCGATACATTTCACC
237683 ATGTATCGATACATT
1 ATGTATCGATACATT
237698 GTATCGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTCACC
Found at i:237781 original size:19 final size:18
Alignment explanation
Indices: 237757--237818 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
237747 CTTTTTAAGG
237757 TGTATCGATACTATGAATA
1 TGTATCGATACTATG-ATA
237776 TGTATCG-T--TAT-A-A
1 TGTATCGATACTATGATA
*
237789 TGTATCGATACTAAGCATA
1 TGTATCGATACTATG-ATA
237808 TGTATCGATAC
1 TGTATCGATAC
237819 ATCTGGGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
13 8 0.22
14 2 0.06
16 5 0.14
18 2 0.06
19 19 0.53
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACTATGATA
Found at i:245148 original size:36 final size:35
Alignment explanation
Indices: 245069--245156 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 35
245059 AAAATTAATA
*
245069 TTATTATTCAAAATAATATTAAAAATAAAAATATT
1 TTATTATTTAAAATAATATTAAAAATAAAAATATT
*
245104 TT-TATATTTATAATTAAT-TTAAAAATAAAAAATATT
1 TTAT-TATTTA-AAATAATATTAAAAAT-AAAAATATT
245140 TTATTATTT-AAATAATA
1 TTATTATTTAAAATAATA
245157 ATTTGAGCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
34 7 0.16
35 15 0.33
36 22 0.49
37 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (35 bp):
TTATTATTTAAAATAATATTAAAAATAAAAATATT
Found at i:245694 original size:27 final size:29
Alignment explanation
Indices: 245663--245738 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 29
245653 AGTTATTCAA
245663 TAAAAAATTAATTATT-TAAAATAA-AAT
1 TAAAAAATTAATTATTATAAAATAATAAT
*
245690 T--AAAATTAATTATATTATAAAATAATATT
1 TAAAAAATTAA-T-TATTATAAAATAATAAT
*
245719 TAACAAATTAAATTATTATA
1 TAAAAAATT-AATTATTATA
245739 TTAGTATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
25 8 0.20
26 1 0.03
27 5 0.12
28 8 0.20
29 3 0.08
30 7 0.17
31 6 0.15
32 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAAAAATTAATTATTATAAAATAATAAT
Found at i:250475 original size:43 final size:43
Alignment explanation
Indices: 250427--250516 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
250417 ATTTTATCTT
*
250427 TTAAAGATTATGAAACTTTTGAACACGAATTTCAAAGTTTACA
1 TTAAAGATTATGAAACTTTTGAACACGAATCTCAAAGTTTACA
250470 TTAAAGATTATGAAACTTTTGAACACGAATCTCAAAGTTTACA
1 TTAAAGATTATGAAACTTTTGAACACGAATCTCAAAGTTTACA
250513 TTAA
1 TTAA
250517 TTAAAGATTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (43 bp):
TTAAAGATTATGAAACTTTTGAACACGAATCTCAAAGTTTACA
Found at i:252003 original size:28 final size:27
Alignment explanation
Indices: 251972--252035 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
251962 ACAAGTGGGC
*
251972 AATTAAAATTTTATATATGATAAAA-TTT
1 AATTAAAATTTAAT-TATG-TAAAATTTT
252000 AATTAAGAATTTAATTATGTAAAATTTT
1 AATTAA-AATTTAATTATGTAAAATTTT
252028 AATTAAAA
1 AATTAAAA
252036 AATCATAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 7 0.21
28 19 0.58
29 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
AATTAAAATTTAATTATGTAAAATTTT
Found at i:253085 original size:17 final size:15
Alignment explanation
Indices: 253057--253102 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
253047 CTTTTACAAC
*
253057 AATAATTTAAAATATA
1 AATAATTAAAAAT-TA
253073 AACTAATTAAAAATTA
1 AA-TAATTAAAAATTA
253089 AA-AATTAAAAATTA
1 AATAATTAAAAATTA
253103 TTATAATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 12 0.43
16 6 0.21
17 10 0.36
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATTAAAAATTA
Found at i:253098 original size:6 final size:7
Alignment explanation
Indices: 253077--253102 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
253067 AATATAAACT
253077 AATTAAA
1 AATTAAA
253084 AATTAAA
1 AATTAAA
253091 AATTAAA
1 AATTAAA
253098 AATTA
1 AATTA
253103 TTATAATAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATTAAA
Found at i:253477 original size:19 final size:18
Alignment explanation
Indices: 253453--253566 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
253443 TTTTAACGAT
253453 TTGTATCGATACAAAAATG
1 TTGTATCGATACAAAAA-G
253472 TTGTATCGATAC----A-
1 TTGTATCGATACAAAAAG
253485 TTGTATCGATACAAAAATG
1 TTGTATCGATACAAAAA-G
253504 TTGTATCGATAC----A-
1 TTGTATCGATACAAAAAG
* *
253517 TTGTATCGATAC-AACAC
1 TTGTATCGATACAAAAAG
**
253534 TTGTATCGATACATAAGTG
1 TTGTATCGATACA-AAAAG
253553 TTGTATCGATACAA
1 TTGTATCGATACAA
253567 TGTATCGCTA
Statistics
Matches: 80, Mismatches: 3, Indels: 25
0.74 0.03 0.23
Matches are distributed among these distances:
13 24 0.30
15 2 0.03
16 1 0.01
17 13 0.16
18 1 0.01
19 39 0.49
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACAAAAAG
Found at i:253490 original size:13 final size:13
Alignment explanation
Indices: 253472--253529 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
253462 TACAAAAATG
253472 TTGTATCGATACA
1 TTGTATCGATACA
253485 TTGTATCGATACAAAAA
1 TTGTATCGATAC----A
253502 TGTTGTATCGATACA
1 --TTGTATCGATACA
253517 TTGTATCGATACA
1 TTGTATCGATACA
253530 ACACTTGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 25 0.64
15 1 0.03
17 1 0.03
19 12 0.31
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:253491 original size:32 final size:32
Alignment explanation
Indices: 253453--253547 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
253443 TTTTAACGAT
253453 TTGTATCGATACAAAAATGTTGTATCGATACA
1 TTGTATCGATACAAAAATGTTGTATCGATACA
253485 TTGTATCGATACAAAAATGTTGTATCGATACA
1 TTGTATCGATACAAAAATGTTGTATCGATACA
* *
253517 TTGTATCGATAC-AACA-CTTGTATCGATACA
1 TTGTATCGATACAAAAATGTTGTATCGATACA
253547 T
1 T
253548 AAGTGTTGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 14 0.23
31 3 0.05
32 44 0.72
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACAAAAATGTTGTATCGATACA
Found at i:253636 original size:13 final size:13
Alignment explanation
Indices: 253618--253642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253608 ATTACCCAAA
253618 TGTATCGATACAT
1 TGTATCGATACAT
253631 TGTATCGATACA
1 TGTATCGATACA
253643 CTGATCTTTG
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):
TGTATCGATACAT
Found at i:258488 original size:3 final size:3
Alignment explanation
Indices: 258480--258514 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
258470 ATAAATGCAA
258480 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
258515 AGTTTGAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:260853 original size:23 final size:23
Alignment explanation
Indices: 260822--260867 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
260812 ATACTTATTT
*
260822 ATTTGATATTTAAAAATTTAAAA
1 ATTTAATATTTAAAAATTTAAAA
* *
260845 ATTTAATATTTATAATTTTAAAA
1 ATTTAATATTTAAAAATTTAAAA
260868 TTTTTATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTAATATTTAAAAATTTAAAA
Found at i:263345 original size:15 final size:16
Alignment explanation
Indices: 263322--263352 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
263312 AGGAAATCTC
263322 ATTCTAACTCTATCAT
1 ATTCTAACTCTATCAT
263338 ATTC-AACTCTATCAT
1 ATTCTAACTCTATCAT
263353 TGATTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTCTAACTCTATCAT
Found at i:264428 original size:58 final size:58
Alignment explanation
Indices: 264229--264432 Score: 182
Period size: 58 Copynumber: 3.5 Consensus size: 58
264219 TAATTATCTC
* * * * * * * *
264229 TAAAATACATTAAATCGCATAAAAGTCTTCAGATCATAG-AAATGACCTAAATGATAT
1 TAAAATTCATAAAATTGCATAAAAGTCTTTAGACCATGGAAAATGATCTAAATGACAT
* * * * *
264286 TAACATTCATAAAATTGTATCAAAA-TCCTTAG-CTCATGAAAAATGATCTACATGACAT
1 TAAAATTCATAAAATTGCAT-AAAAGTCTTTAGAC-CATGGAAAATGATCTAAATGACAT
** * ***
264344 CGATATTCATAAAATTGCACCCAAGTCTTTAGACCATGGAAAATGATCTAAATGACAT
1 TAAAATTCATAAAATTGCATAAAAGTCTTTAGACCATGGAAAATGATCTAAATGACAT
264402 TAAAATTCATAAAA-TGACATAAAAGTCTTTA
1 TAAAATTCATAAAATTG-CATAAAAGTCTTTA
264433 AGTCATGAAA
Statistics
Matches: 112, Mismatches: 29, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
57 27 0.24
58 84 0.75
59 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (58 bp):
TAAAATTCATAAAATTGCATAAAAGTCTTTAGACCATGGAAAATGATCTAAATGACAT
Found at i:266642 original size:616 final size:615
Alignment explanation
Indices: 265736--266971 Score: 1827
Period size: 616 Copynumber: 2.0 Consensus size: 615
265726 TATGTTTTAA
* **
265736 TGTAAAAATGTTTGTTAAGGACCTCTTGTATGGTTATAAAGTAATCCAAGGTCATTAGGAAGGTG
1 TGTAAAAATGTTTGTTAAGGACCTCTTGTATGATTATAAAGTAATCCAAGGTCATTAAAAAGGTG
* * *
265801 AAATTGAGAAAACTTGGGTAAAAAGCTTAATTCTTGGTGAAAAATTCTATGTAGTATCAATATAT
66 AAATTGAGAAAACTTGGGTAAAAAGCTTAATTCATGGTGAAAAATTCTATGCAATATCAATATAT
* * * * * * * * *
265866 TGGTATTTGTGTCGATATAAGTTATTCCTAGAACCAAATAATCTAGAAATTTTGAATTTGCGAGT
131 TGGTATTTATGTCAATAGAAGTGATTCCTAGAACAAAAAAATATAGAAATTTTGAATTTACGACT
* *
265931 TTCGAGAATATCCCTATTCATAGGTTTGAGATCCATATCTATGAATTAAAAGGTCTGAATGATCA
196 TTCAAAAATATCCCTATTCATAGGTTTGAGATCCATATCTATGAATTAAAAGGTCTGAATGATCA
* * *
265996 ACTTTGTAATTAGTTGTTAGAATTAATAGGTTTTTAAATCATTCATTTGAAAAAATTCAAACCTT
261 ACTTTGCAATTAGTTGTTAAAATTAATAGGTCTTTAAATCATTCATTTGAAAAAATTCAAACCTT
* * **
266061 CTTACTATATTATCATAATACTTCTCAAAAATAAAAAATTTTGATCTATGGAGGAAGAATAACAT
326 CTTACTAGATTATCATAATACTT-TCAAAAAT-AAAAATTTTGATCAATAAAGGAAGAATAACAT
* * * *
266126 TATTTTTTTTCAATAAAATACCAAAGTGGATGATTAACTCATTCCAT-ACTAGAAATAATCATAG
389 TATTTTTGTTCAATAAAATACCAAAATGGATGATTAACTCATTCCATGA-TAG-AATAATCACAA
* * *
266190 GATATC-TTTGATAACACAGATCCCTGTTTCTCAATGATATCCCACGATTAAGACAATTGCCTGA
452 GATATCTTTTGATAACACAGATCCCTATTTATCAATGATATCCCACGATTAAGACAATTGCCTAA
266254 ATCCCGT-GAAACCA-TTCATAGAAGTTCATTGATAACTTCTTTTTATAAAGCAAATTGATTTTG
517 ATCCCGTGGAAACCATTTCATAGAAGTTCATTGATAACTTCTTTTTATAAAGCAAATTGATTTTG
*
266317 ATTCTTGAATAATCCATATCACTTCTACTTCTAT
582 ATTCTTGAATAATCCACATCACTTCTACTTCTAT
266351 TGTAAAAATGTTTGTTAAGGACCTCTTGTATGATTATAAAAGTAATCCAAGGTCATTAAAAAGGT
1 TGTAAAAATGTTTGTTAAGGACCTCTTGTATGATTAT-AAAGTAATCCAAGGTCATTAAAAAGGT
* * *
266416 GAAATGTGAGAAAATTTGGGTGAAAAAG-TTTATTCATGGTGAAAAATTCTATGCAATATCGATA
65 GAAAT-TGAGAAAACTTGGGT-AAAAAGCTTAATTCATGGTGAAAAATTCTATGCAATATCAATA
* * * *
266480 TATTGGTATTTATGTCAATAGCAGTGCTTCTTAGAACAAAAAAATATAGAAA-TTTGAATTTATG
128 TATTGGTATTTATGTCAATAGAAGTGATTCCTAGAACAAAAAAATATAGAAATTTTGAATTTACG
* * *
266544 ACTTTCAAAAATATCCTTATTCATATGTTTGAGATCCATATCTATGAATTGAAAGGTCTGAATGA
193 ACTTTCAAAAATATCCCTATTCATAGGTTTGAGATCCATATCTATGAATTAAAAGGTCTGAATGA
* *
266609 TCAACTTTGCAATTAGTTGTTAAAATTAATAGGTCTTTAAGTCATTCATTTGAAAAAATTGAAAC
258 TCAACTTTGCAATTAGTTGTTAAAATTAATAGGTCTTTAAATCATTCATTTGAAAAAATTCAAAC
* * * * *
266674 CTTCTTATTGGATTATCATATTACTTTTAAAAATAAAAATTTTGATCAATAAAGGAAGAATATCA
323 CTTCTTACTAGATTATCATAATACTTTCAAAAATAAAAATTTTGATCAATAAAGGAAGAATAACA
* * *
266739 TTATTTTTGTTCAATAAGATACCAAAATGGATGATTGACTTATTCCATGATAGAATAATCACAAG
388 TTATTTTTGTTCAATAAAATACCAAAATGGATGATTAACTCATTCCATGATAGAATAATCACAAG
* * * *
266804 ATATCTTTTGATAACACAGATTCCTATTTATTAATGATATCCCATGATTAAGACAATTGTCTAAA
453 ATATCTTTTGATAACACAGATCCCTATTTATCAATGATATCCCACGATTAAGACAATTGCCTAAA
* * *
266869 TCCTGTGGAAACCATTTCATAGAAGTTCATTGATAATTTTTTTTTATAAAGCAAATTGATTTTGA
518 TCCCGTGGAAACCATTTCATAGAAGTTCATTGATAACTTCTTTTTATAAAGCAAATTGATTTTGA
*
266934 TTCTTGAATAATCCACATCACTTCTATTTCTAT
583 TTCTTGAATAATCCACATCACTTCTACTTCTAT
266967 TGTAA
1 TGTAA
266972 CGAAAGATTC
Statistics
Matches: 554, Mismatches: 60, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
613 15 0.03
614 130 0.23
615 51 0.09
616 265 0.48
617 87 0.16
618 6 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (615 bp):
TGTAAAAATGTTTGTTAAGGACCTCTTGTATGATTATAAAGTAATCCAAGGTCATTAAAAAGGTG
AAATTGAGAAAACTTGGGTAAAAAGCTTAATTCATGGTGAAAAATTCTATGCAATATCAATATAT
TGGTATTTATGTCAATAGAAGTGATTCCTAGAACAAAAAAATATAGAAATTTTGAATTTACGACT
TTCAAAAATATCCCTATTCATAGGTTTGAGATCCATATCTATGAATTAAAAGGTCTGAATGATCA
ACTTTGCAATTAGTTGTTAAAATTAATAGGTCTTTAAATCATTCATTTGAAAAAATTCAAACCTT
CTTACTAGATTATCATAATACTTTCAAAAATAAAAATTTTGATCAATAAAGGAAGAATAACATTA
TTTTTGTTCAATAAAATACCAAAATGGATGATTAACTCATTCCATGATAGAATAATCACAAGATA
TCTTTTGATAACACAGATCCCTATTTATCAATGATATCCCACGATTAAGACAATTGCCTAAATCC
CGTGGAAACCATTTCATAGAAGTTCATTGATAACTTCTTTTTATAAAGCAAATTGATTTTGATTC
TTGAATAATCCACATCACTTCTACTTCTAT
Found at i:267553 original size:19 final size:20
Alignment explanation
Indices: 267529--267581 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
267519 TGCTTTGTAA
*
267529 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGCTCAAT
* *
267548 TGTATCGATGCATACTCAAT
1 TGTATCGATACATGCTCAAT
267568 TGTATCGATACATG
1 TGTATCGATACATG
267582 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:269261 original size:3 final size:3
Alignment explanation
Indices: 269240--269280 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
269230 AACCATCAAA
* * *
269240 GAT GAT GAA GAT GAA GAT GAT GAT GAT GAT GAT AAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
269281 AGTTGACTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (3 bp):
GAT
Done.