Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 100 of 106
Found at i:38166416 original size:21 final size:21
Alignment explanation
Indices: 38166390--38166431 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
38166380 GAGAGATGAA
38166390 AGACTAATCTAAACACCATGG
1 AGACTAATCTAAACACCATGG
38166411 AGACTAATCTAAACACCATGG
1 AGACTAATCTAAACACCATGG
38166432 TGTTTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (21 bp):
AGACTAATCTAAACACCATGG
Found at i:38168157 original size:3 final size:3
Alignment explanation
Indices: 38168149--38168174 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38168139 TGAGAAAATA
38168149 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
38168175 AGCAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38180264 original size:6 final size:6
Alignment explanation
Indices: 38180246--38180278 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
38180236 TTTTAGCAAA
*
38180246 TATATG TACATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TAT
38180279 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:38191427 original size:14 final size:14
Alignment explanation
Indices: 38191407--38191440 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
38191397 TACACAATTT
38191407 ATAATTATAAT-TA
1 ATAATTATAATGTA
38191420 ACTAATTATAATGTA
1 A-TAATTATAATGTA
38191435 ATAATT
1 ATAATT
38191441 GTAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 15 0.79
15 3 0.16
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (14 bp):
ATAATTATAATGTA
Found at i:38194978 original size:4 final size:4
Alignment explanation
Indices: 38194969--38195022 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
38194959 TGGTAATTTA
* * * * *
38194969 ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATGT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
38195017 GTAT AT
1 ATAT AT
38195023 GTGTATGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:38195023 original size:6 final size:6
Alignment explanation
Indices: 38194972--38195039 Score: 64
Period size: 6 Copynumber: 10.7 Consensus size: 6
38194962 TAATTTAATA
* * *
38194972 TATATA TATATA TATATA TATATG TATGTATG TATGTATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TA--TATG TA--TATG TATATG TATATG
*
38195024 TGTATG TATATG TATA
1 TATATG TATATG TATA
38195040 GGTTTTTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
6 43 0.75
8 14 0.25
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:38195027 original size:18 final size:18
Alignment explanation
Indices: 38194976--38195039 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
38194966 TTAATATATA
* * *
38194976 TATATATATATATATATA
1 TATATGTATATATGTATG
* *
38194994 TGTATGTATGTATGTATG
1 TATATGTATATATGTATG
*
38195012 TATATGTATATGTGTATG
1 TATATGTATATATGTATG
38195030 TATATGTATA
1 TATATGTATA
38195040 GGTTTTTTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (18 bp):
TATATGTATATATGTATG
Found at i:38195031 original size:4 final size:4
Alignment explanation
Indices: 38194992--38195032 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
38194982 TATATATATA
* *
38194992 TATG TATG TATG TATG TATG TA-- TATG TATA TGTG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
38195033 ATGTATAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
4 29 0.94
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:38206579 original size:15 final size:16
Alignment explanation
Indices: 38206561--38206596 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
38206551 GCCACCGCTT
*
38206561 CCTCCTCCT-CCGCCG
1 CCTCCTCCTCCCACCG
38206576 CCTCCTCCTCCCACCG
1 CCTCCTCCTCCCACCG
38206592 CCTCC
1 CCTCC
38206597 CCTGTCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.03, C:0.69, G:0.08, T:0.19
Consensus pattern (16 bp):
CCTCCTCCTCCCACCG
Found at i:38218418 original size:35 final size:35
Alignment explanation
Indices: 38218372--38218445 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
38218362 GCTCTCGAAA
38218372 CAAACACCAAACAAAATCAAACAACCTCCACAACC
1 CAAACACCAAACAAAATCAAACAACCTCCACAACC
* * * *
38218407 CAAACACCAAACGAAATCAAATATCGTCCACAACC
1 CAAACACCAAACAAAATCAAACAACCTCCACAACC
38218442 CAAA
1 CAAA
38218446 TGGGCAGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.53, C:0.36, G:0.03, T:0.08
Consensus pattern (35 bp):
CAAACACCAAACAAAATCAAACAACCTCCACAACC
Found at i:38219223 original size:30 final size:28
Alignment explanation
Indices: 38219182--38219246 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
38219172 TGTCAATCAT
* *
38219182 AAAATTAAAAATTTATTTGATATAAAATA
1 AAAATTAAAAATTTAATT-AAATAAAATA
*
38219211 AAAATATAAAAATTTAATTAAATATAATA
1 AAAAT-TAAAAATTTAATTAAATAAAATA
38219240 AAAATTA
1 AAAATTA
38219247 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 18 0.56
30 12 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAATTAAAAATTTAATTAAATAAAATA
Found at i:38219254 original size:21 final size:21
Alignment explanation
Indices: 38219209--38219254 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
38219199 TGATATAAAA
38219209 TAAAA-ATATAAAAATTTAAT
1 TAAAATATATAAAAATTTAAT
*
38219229 T-AAATATAATAAAAA-TTATT
1 TAAAATAT-ATAAAAATTTAAT
38219249 TAAAAT
1 TAAAAT
38219255 TTTTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 8 0.36
21 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAATATATAAAAATTTAAT
Found at i:38219254 original size:31 final size:28
Alignment explanation
Indices: 38219182--38219264 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
38219172 TGTCAATCAT
* *
38219182 AAAAT-TAAAAATTTATTTGATATAAAATA
1 AAAATATAAAAATTTA-TT-AAATATAATA
38219211 AAAATATAAAAATTTAATTAAATATAATA
1 AAAATATAAAAATTT-ATTAAATATAATA
*
38219240 AAAATTATTTAAAATTT-TTAAATAT
1 AAAA-TA-TAAAAATTTATTAAATAT
38219265 TTTAAAAACT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 25 0.53
30 13 0.28
31 9 0.19
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
AAAATATAAAAATTTATTAAATATAATA
Found at i:38219286 original size:21 final size:19
Alignment explanation
Indices: 38219250--38219299 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
38219240 AAAATTATTT
*
38219250 AAAATTTTTAAATATTTTA
1 AAAATTTTTAAATATTATA
*
38219269 AAAACTTTTTCAAGTATTATA
1 AAAA-TTTTT-AAATATTATA
38219290 AAAATATTTT
1 AAAAT-TTTT
38219300 TGATAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 6 0.23
21 16 0.62
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (19 bp):
AAAATTTTTAAATATTATA
Found at i:38234229 original size:2 final size:2
Alignment explanation
Indices: 38234222--38234330 Score: 113
Period size: 2 Copynumber: 57.0 Consensus size: 2
38234212 TGGATAAGAT
*
38234222 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G A- AG -G GG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
38234260 AA AA AG -G AG AG AA AA AG -G AG AG GG AG AG NAG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG
38234301 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38234331 GAGGGGGGGG
Statistics
Matches: 94, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
1 6 0.06
2 86 0.91
3 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38239670 original size:14 final size:14
Alignment explanation
Indices: 38239651--38239677 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38239641 TCTGGTGATA
38239651 GGAAGAATCACCAG
1 GGAAGAATCACCAG
38239665 GGAAGAATCACCA
1 GGAAGAATCACCA
38239678 CTCTAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.26, T:0.07
Consensus pattern (14 bp):
GGAAGAATCACCAG
Found at i:38245950 original size:2 final size:2
Alignment explanation
Indices: 38245945--38245969 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38245935 GGAGCGTGTG
38245945 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
38245970 TTATCAAATT
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:38251218 original size:2 final size:2
Alignment explanation
Indices: 38251211--38251238 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38251201 GGAATCAAAT
38251211 TA 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
38251239 ACAGATATAA
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):
TA
Found at i:38251900 original size:15 final size:15
Alignment explanation
Indices: 38251888--38251928 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
38251878 GTATTGTTAT
38251888 AAATGTAATTGTTGA
1 AAATGTAATTGTTGA
*
38251903 GAATGTAATTGTTGA
1 AAATGTAATTGTTGA
*
38251918 AAATGTGATTG
1 AAATGTAATTG
38251929 GTAATAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (15 bp):
AAATGTAATTGTTGA
Found at i:38253064 original size:18 final size:19
Alignment explanation
Indices: 38253029--38253064 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38253019 TAGTGAGTTA
38253029 TTTTAATTTTATGTTATTC
1 TTTTAATTTTATGTTATTC
*
38253048 TTTTTATTTTA-GTTATT
1 TTTTAATTTTATGTTATT
38253065 ATTTATTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (19 bp):
TTTTAATTTTATGTTATTC
Found at i:38253070 original size:25 final size:26
Alignment explanation
Indices: 38253026--38253080 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
38253016 TTTTAGTGAG
38253026 TTATTTTAATTTTATGTTATT-CTTT
1 TTATTTTAATTTTATGTTATTGCTTT
* *
38253051 TTATTTTAGTTATTAT-TTATTGGTTT
1 TTATTTTAATT-TTATGTTATTGCTTT
38253077 TTAT
1 TTAT
38253081 ATTTTTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (26 bp):
TTATTTTAATTTTATGTTATTGCTTT
Found at i:38255038 original size:21 final size:21
Alignment explanation
Indices: 38255014--38255053 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
38255004 ATTTTAAACA
38255014 ATTAAAATAATAA-ATAATAAC
1 ATTAAAA-AATAACATAATAAC
38255035 ATTAAAAAATAACATAATA
1 ATTAAAAAATAACATAATA
38255054 TTTTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTAAAAAATAACATAATAAC
Found at i:38255543 original size:25 final size:25
Alignment explanation
Indices: 38255507--38255572 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
38255497 GCGGACAATA
**
38255507 AGAAGAAAGAGAAGAAGGCAAGGTG
1 AGAAGAAAGAGAAGAAGGCAAGAAG
* *
38255532 AGAAGAAGGAGAAAAAGGCAAGAAG
1 AGAAGAAAGAGAAGAAGGCAAGAAG
38255557 -GAAGAAAGAGAAGAAG
1 AGAAGAAAGAGAAGAAG
38255573 ACGCAAAGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 14 0.40
25 21 0.60
ACGTcount: A:0.58, C:0.03, G:0.38, T:0.02
Consensus pattern (25 bp):
AGAAGAAAGAGAAGAAGGCAAGAAG
Found at i:38265767 original size:2 final size:2
Alignment explanation
Indices: 38265760--38265805 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
38265750 CGCCCCATCC
*
38265760 CT CT CT CT CT CT CT CT CT CT -T NT C- CT C- CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
38265799 CT CT CT C
1 CT CT CT C
38265806 CTTTTCTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:38267008 original size:3 final size:3
Alignment explanation
Indices: 38267002--38267026 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38266992 TGTGGTGGTT
38267002 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
38267027 AACCATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38267477 original size:14 final size:14
Alignment explanation
Indices: 38267458--38267496 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
38267448 ATTAATTGAA
* *
38267458 TAATTATATATATT
1 TAATTATATAAAAT
38267472 TAATTATATAAAAT
1 TAATTATATAAAAT
*
38267486 TAATAATATAA
1 TAATTATATAA
38267497 TTACCAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATTATATAAAAT
Found at i:38280015 original size:2 final size:2
Alignment explanation
Indices: 38280008--38280071 Score: 91
Period size: 2 Copynumber: 34.0 Consensus size: 2
38279998 AGTTCCTCAA
38280008 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
38280047 AT -T AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38280072 TATCATTTCT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 4 0.07
2 52 0.93
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:38280038 original size:23 final size:23
Alignment explanation
Indices: 38280008--38280071 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
38279998 AGTTCCTCAA
38280008 ATATATATATATATATATAATAT
1 ATATATATATATATATATAATAT
*
38280031 ATATATATAT-TATTATATTATAT
1 ATATATATATATA-TATATAATAT
*
38280054 ATATATATATATGTATAT
1 ATATATATATATATATAT
38280072 TATCATTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.05
23 34 0.92
24 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATATATATATATATATAATAT
Found at i:38280072 original size:23 final size:22
Alignment explanation
Indices: 38280008--38280074 Score: 102
Period size: 21 Copynumber: 3.1 Consensus size: 22
38279998 AGTTCCTCAA
*
38280008 ATATATATATATATA-TATAAT
1 ATATATATATATATATTATATT
38280029 ATATATATATAT-TATTATATT
1 ATATATATATATATATTATATT
38280050 ATATATATATATATATGTATATT
1 ATATATATATATATAT-TATATT
38280073 AT
1 AT
38280075 CATTTCTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 2 0.05
21 29 0.69
22 3 0.07
23 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
ATATATATATATATATTATATT
Found at i:38282586 original size:51 final size:51
Alignment explanation
Indices: 38282529--38282652 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 51
38282519 TTTTTTCAAA
** * * *
38282529 AAGAAAAGCTTTTAAGTATTTTGAGCATTTTAGAGTGACTTTTGATACACG
1 AAGAAAAATTTTTGAGTATTTTGAACATTTTAAAGTGACTTTTGATACACG
* * * * * *
38282580 AAGAAAATTTTTTGAGCATTTTGAATATTTTAAAGTGATTTTTGATATATG
1 AAGAAAAATTTTTGAGTATTTTGAACATTTTAAAGTGACTTTTGATACACG
38282631 AAGAAAAATTTTTGAGTATTTT
1 AAGAAAAATTTTTGAGTATTTT
38282653 TCGTTACGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (51 bp):
AAGAAAAATTTTTGAGTATTTTGAACATTTTAAAGTGACTTTTGATACACG
Found at i:38282920 original size:22 final size:22
Alignment explanation
Indices: 38282769--38282922 Score: 85
Period size: 22 Copynumber: 7.0 Consensus size: 22
38282759 TGCGTAATCG
* *
38282769 GTTTTTGAGTATTATGTGATTA
1 GTTTTTAAGTATTACGTGATTA
* * * *
38282791 GTTTTTAAGTAATAAGTTACTA
1 GTTTTTAAGTATTACGTGATTA
* * * *
38282813 ATTTTTAGGTATTGCGTTATTA
1 GTTTTTAAGTATTACGTGATTA
* * * * *
38282835 ATTTTTAATTATTGCGTGACTG
1 GTTTTTAAGTATTACGTGATTA
** *
38282857 GTTGAT-AGATATTACGTGATTG
1 GTTTTTAAG-TATTACGTGATTA
** *
38282879 GTTAGTAATGCATTACGTGATTA
1 GTTTTTAA-GTATTACGTGATTA
*
38282902 GTTTTTAAGTATTATGTGATT
1 GTTTTTAAGTATTACGTGATT
38282923 TAAGTATTGT
Statistics
Matches: 99, Mismatches: 30, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
21 1 0.01
22 79 0.80
23 18 0.18
24 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.49
Consensus pattern (22 bp):
GTTTTTAAGTATTACGTGATTA
Found at i:38283062 original size:22 final size:22
Alignment explanation
Indices: 38283037--38283089 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
38283027 TTGTAGTATC
* *
38283037 TAAAAATTAGTGACATAATGTT
1 TAAAAATTAGTAACATAATATT
* *
38283059 TAAAAATCAGTAATATAATATT
1 TAAAAATTAGTAACATAATATT
*
38283081 TAATAATTA
1 TAAAAATTA
38283090 ATTGATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (22 bp):
TAAAAATTAGTAACATAATATT
Found at i:38288971 original size:34 final size:35
Alignment explanation
Indices: 38288902--38288975 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
38288892 AAATTCAAAT
* * *
38288902 TTAAATAATAAAAAATAAATATCTCAAATATCAAC
1 TTAAATAATAAAAAACAAATATCTCAAACAACAAC
*
38288937 TTAAATAATTAAAAACAAATAT-TCAAACAACAAC
1 TTAAATAATAAAAAACAAATATCTCAAACAACAAC
38288971 TTAAA
1 TTAAA
38288976 CATTACAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 15 0.43
35 20 0.57
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (35 bp):
TTAAATAATAAAAAACAAATATCTCAAACAACAAC
Found at i:38300401 original size:6 final size:6
Alignment explanation
Indices: 38300390--38300414 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38300380 CTTCGTCTCT
38300390 CAAACC CAAACC CAAACC CAAACC C
1 CAAACC CAAACC CAAACC CAAACC C
38300415 CGCCGACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACC
Found at i:38303608 original size:27 final size:27
Alignment explanation
Indices: 38303570--38303628 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
38303560 TATAAACTAA
38303570 TGGCAAGTCTGATATCTACCACAGATC
1 TGGCAAGTCTGATATCTACCACAGATC
38303597 TGGCAAGTCTGATATCTACCACAGATC
1 TGGCAAGTCTGATATCTACCACAGATC
38303624 TGGCA
1 TGGCA
38303629 TTTTGGCGAG
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:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (27 bp):
TGGCAAGTCTGATATCTACCACAGATC
Found at i:38311094 original size:20 final size:19
Alignment explanation
Indices: 38311071--38311110 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38311061 AAATTATTTT
38311071 ATTTAAAATAAAATATAAAA
1 ATTTAAAAT-AAATATAAAA
**
38311091 ATTTAATGTAAATATAAAA
1 ATTTAAAATAAATATAAAA
38311110 A
1 A
38311111 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
ATTTAAAATAAATATAAAA
Found at i:38311120 original size:8 final size:9
Alignment explanation
Indices: 38311104--38311135 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
38311094 TAATGTAAAT
38311104 ATAAAAAAA
1 ATAAAAAAA
38311113 ATAAAAAAA
1 ATAAAAAAA
38311122 ATAAAAAAA
1 ATAAAAAAA
38311131 ATAAA
1 ATAAA
38311136 TTTTTTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:38311474 original size:67 final size:69
Alignment explanation
Indices: 38311303--38311489 Score: 227
Period size: 69 Copynumber: 2.7 Consensus size: 69
38311293 AAACTAAAAA
** * * ** *
38311303 CTCTTCTCGAAATTTCAAATTTTAATCAATTGAATATCTTATTTTGAGTATTAAAATTAGAATTT
1 CTCTTCTAAAAATTTAAAATTTTAAACGTTTGAATATCTTATTTCGAGTATTAAAATTAGAATTT
38311368 ATAT
66 ATAT
* *
38311372 CTCTTCTCAAAATTTAAAATTTTAAATGTTTGAATATCTTATTTCGAGTATTAAAATTTA-AA-T
1 CTCTTCTAAAAATTTAAAATTTTAAACGTTTGAATATCTTATTTCGAGTATTAAAA-TTAGAATT
*
38311435 T-TCT
65 TATAT
* * *
38311439 CTCTTTTAAAAATTTAAAATTTTAAACGTTTGAATATTTTACTTCGAGTAT
1 CTCTTCTAAAAATTTAAAATTTTAAACGTTTGAATATCTTATTTCGAGTAT
38311490 CTTATTCGAT
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
67 48 0.46
68 2 0.02
69 51 0.49
70 3 0.03
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (69 bp):
CTCTTCTAAAAATTTAAAATTTTAAACGTTTGAATATCTTATTTCGAGTATTAAAATTAGAATTT
ATAT
Found at i:38321186 original size:17 final size:17
Alignment explanation
Indices: 38321140--38321186 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
38321130 GACATTTTCA
38321140 TTATTTATCTT-TTATTT
1 TTATTTAT-TTATTATTT
* *
38321157 TTATTCATATATTATTT
1 TTATTTATTTATTATTT
38321174 TTATTTATTTATT
1 TTATTTATTTATT
38321187 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTATTTATTATTT
Found at i:38322419 original size:3 final size:3
Alignment explanation
Indices: 38322411--38322436 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38322401 CTCAATGCTT
38322411 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
38322437 TTTTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:38322914 original size:20 final size:22
Alignment explanation
Indices: 38322876--38322923 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
38322866 TAGATTAACC
38322876 AATTATTTGATTAAAAAAATT-
1 AATTATTTGATTAAAAAAATTA
* *
38322897 AATTATTT-TTTAATAAAATTA
1 AATTATTTGATTAAAAAAATTA
38322918 AATTAT
1 AATTAT
38322924 GACATAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTATTTGATTAAAAAAATTA
Found at i:38323903 original size:25 final size:26
Alignment explanation
Indices: 38323873--38323930 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
38323863 TTAATAATTA
*
38323873 ATTTAAAAT-AAAAATATAAAAAAGT
1 ATTTAAAATAAAAAATATAAAAAAAT
**
38323898 ATTTAATTTAAAAAATATAAAAAAAT
1 ATTTAAAATAAAAAATATAAAAAAAT
38323924 ATTTAAA
1 ATTTAAA
38323931 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
ATTTAAAATAAAAAATATAAAAAAAT
Found at i:38323918 original size:26 final size:27
Alignment explanation
Indices: 38323882--38323935 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
38323872 AATTTAAAAT
*
38323882 AAAAATATAAAAAAGTATTT-AATTTA
1 AAAAATATAAAAAAATATTTAAATTTA
38323908 AAAAATATAAAAAAATATTTAAATTTA
1 AAAAATATAAAAAAATATTTAAATTTA
38323935 A
1 A
38323936 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAAATATAAAAAAATATTTAAATTTA
Found at i:38329522 original size:29 final size:30
Alignment explanation
Indices: 38329490--38329567 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
38329480 GCTCTTAAAT
*
38329490 TATTTAAATAAGTTTTTA-ATTTT-TTATTA
1 TATTTAAATAAATTTTTATATTTTATT-TTA
*
38329519 TATTTAATTAAATTTTTATATTTTATTTTA
1 TATTTAAATAAATTTTTATATTTTATTTTA
* *
38329549 -AATTAAATAAATATTTATA
1 TATTTAAATAAATTTTTATA
38329568 ATTAATAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.76
30 8 0.19
31 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
TATTTAAATAAATTTTTATATTTTATTTTA
Found at i:38329552 original size:25 final size:22
Alignment explanation
Indices: 38329507--38329556 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 22
38329497 ATAAGTTTTT
38329507 AATTTTTTATTATATTTAATTA
1 AATTTTTTATTATATTTAATTA
*
38329529 AATTTTTATATTTTATTTTAAATTA
1 AATTTTT-TATTATA-TTT-AATTA
38329554 AAT
1 AAT
38329557 AAATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 3 0.12
25 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTTTTTATTATATTTAATTA
Found at i:38329591 original size:14 final size:15
Alignment explanation
Indices: 38329566--38329594 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38329556 TAAATATTTA
38329566 TAATTAATAATTAAT
1 TAATTAATAATTAAT
38329581 TAATT-ATAATTAAT
1 TAATTAATAATTAAT
38329595 AAAAATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTAATAATTAAT
Found at i:38329892 original size:31 final size:31
Alignment explanation
Indices: 38329833--38329892 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
38329823 TCATAAAGGC
*
38329833 TTATTTGACTCAAAATAAATAGTAAAAGAAT
1 TTATTTGACTCAAAATAAATAATAAAAGAAT
*
38329864 TTATTTGATTCAAAATAAA-AATATAAAGA
1 TTATTTGACTCAAAATAAATAATA-AAAGA
38329893 TTTGATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.33
Consensus pattern (31 bp):
TTATTTGACTCAAAATAAATAATAAAAGAAT
Found at i:38335529 original size:2 final size:2
Alignment explanation
Indices: 38335524--38335592 Score: 111
Period size: 2 Copynumber: 34.0 Consensus size: 2
38335514 AGAAGAAAAG
* *
38335524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC ACN AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
38335567 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
38335593 TAACCAGCTT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
2 62 0.98
3 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:38338358 original size:25 final size:25
Alignment explanation
Indices: 38338312--38338360 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
38338302 AAACTGAAAA
38338312 TATCAATATATTAATAATATACATG
1 TATCAATATATTAATAATATACATG
*
38338337 TATCAATATCATTGATAA-ATACAT
1 TATCAATAT-ATTAATAATATACAT
38338361 TGAGATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (25 bp):
TATCAATATATTAATAATATACATG
Found at i:38358583 original size:2 final size:2
Alignment explanation
Indices: 38358578--38358607 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38358568 TTAATAGATG
38358578 AT 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 AT
38358608 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38358651 original size:2 final size:2
Alignment explanation
Indices: 38358644--38358688 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
38358634 TAATAGATGG
38358644 TA TA TA TA TA TA TA TA 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 TA TA TA TA
38358686 TA T
1 TA T
38358689 TAGTAAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38359185 original size:20 final size:21
Alignment explanation
Indices: 38359145--38359185 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38359135 TTATAATTAA
* *
38359145 ATATTTTTTTATTTAATATGT
1 ATATTTTTTGAATTAATATGT
38359166 ATATTTTTTGAATTAA-ATGT
1 ATATTTTTTGAATTAATATGT
38359186 GCAAATGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
ATATTTTTTGAATTAATATGT
Found at i:38360710 original size:13 final size:13
Alignment explanation
Indices: 38360692--38360719 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38360682 GGAAAACCAC
38360692 ATAATATATATGT
1 ATAATATATATGT
38360705 ATAATATATATGT
1 ATAATATATATGT
38360718 AT
1 AT
38360720 TGCAGTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
ATAATATATATGT
Found at i:38363133 original size:10 final size:10
Alignment explanation
Indices: 38363110--38363173 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
38363100 AATTAAAAAT
38363110 AAATAT-ATAA
1 AAATATAAT-A
* *
38363120 AAATTTAATT
1 AAATATAATA
38363130 AAATATAATA
1 AAATATAATA
*
38363140 AAAAAT-A-A
1 AAATATAATA
38363148 AAATATAATA
1 AAATATAATA
* *
38363158 AAATTTAATT
1 AAATATAATA
38363168 AAATAT
1 AAATAT
38363174 TTTTAAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
8 6 0.14
9 2 0.05
10 32 0.76
11 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATATAATA
Found at i:38363137 original size:18 final size:18
Alignment explanation
Indices: 38363114--38363173 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
38363104 AAAAATAAAT
38363114 ATATAAAAATTTAATTAA
1 ATATAAAAATTTAATTAA
* *
38363132 ATATAATAAA--AAATAAAA
1 ATATAA-AAATTTAAT-TAA
38363150 ATATAATAAAATTTAATTAA
1 ATAT-A-AAAATTTAATTAA
38363170 ATAT
1 ATAT
38363174 TTTTAAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
17 3 0.09
18 12 0.38
19 7 0.22
20 7 0.22
21 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATATAAAAATTTAATTAA
Found at i:38363154 original size:36 final size:38
Alignment explanation
Indices: 38363099--38363173 Score: 118
Period size: 36 Copynumber: 2.0 Consensus size: 38
38363089 ACAATTTATT
* *
38363099 TAATTAAAAATAAATATAT-A-AAAATTTAATTAAATA
1 TAATAAAAAATAAAAATATAATAAAATTTAATTAAATA
38363135 TAATAAAAAATAAAAATATAATAAAATTTAATTAAATA
1 TAATAAAAAATAAAAATATAATAAAATTTAATTAAATA
38363173 T
1 T
38363174 TTTTAAGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 17 0.49
37 1 0.03
38 17 0.49
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (38 bp):
TAATAAAAAATAAAAATATAATAAAATTTAATTAAATA
Found at i:38365410 original size:23 final size:23
Alignment explanation
Indices: 38365384--38365428 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
38365374 GGAAGTAAGT
38365384 ACAAATGCTAAATGGGATATAAA
1 ACAAATGCTAAATGGGATATAAA
38365407 ACAAATGCTAAATGGGATATAA
1 ACAAATGCTAAATGGGATATAA
38365429 TCTAATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (23 bp):
ACAAATGCTAAATGGGATATAAA
Found at i:38365617 original size:16 final size:16
Alignment explanation
Indices: 38365598--38365649 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
38365588 TTTATACTTC
38365598 AAAT-TTTATACTTTAA
1 AAATATTTATA-TTTAA
*
38365614 AAATATTTATATTTAC
1 AAATATTTATATTTAA
* *
38365630 ATATAATTATCATTTAA
1 AAATATTTAT-ATTTAA
38365647 AAA
1 AAA
38365650 ATAAATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATTTATATTTAA
Found at i:38366158 original size:16 final size:16
Alignment explanation
Indices: 38366137--38366167 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
38366127 TTCAAATTGC
38366137 ATTAAAATATAAAAAT
1 ATTAAAATATAAAAAT
38366153 ATTAAAATATAAAAA
1 ATTAAAATATAAAAA
38366168 ATCATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTAAAATATAAAAAT
Found at i:38369575 original size:30 final size:30
Alignment explanation
Indices: 38369541--38369665 Score: 130
Period size: 30 Copynumber: 4.2 Consensus size: 30
38369531 AACTATTAGT
* *
38369541 TATAAAGACATATTTAACTTAAAATAAAAA
1 TATAAAGACTTATTTAATTTAAAATAAAAA
* **
38369571 TATAAAAACTTATTTGTTTTAAAATAAAAA
1 TATAAAGACTTATTTAATTTAAAATAAAAA
* *
38369601 TATAAAAACTTATTT-ATTTCAAAATAAAAG
1 TATAAAGACTTATTTAATTT-AAAATAAAAA
* * *
38369631 TACAAAGACTTAATTAA--TACAATAAAAA
1 TATAAAGACTTATTTAATTTAAAATAAAAA
38369659 TATAAAG
1 TATAAAG
38369666 GTTTACTAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
28 14 0.17
29 4 0.05
30 61 0.76
31 1 0.01
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (30 bp):
TATAAAGACTTATTTAATTTAAAATAAAAA
Found at i:38375092 original size:2 final size:2
Alignment explanation
Indices: 38375085--38375111 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38375075 TGGAAGAGGA
38375085 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
38375112 TTAATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38381254 original size:2 final size:2
Alignment explanation
Indices: 38381247--38381282 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
38381237 GTTAACACTT
38381247 TA TA TA TA TA 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 TA
38381283 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38381287 original size:2 final size:2
Alignment explanation
Indices: 38381282--38381313 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38381272 ATATATATAT
38381282 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38381314 TCAAACTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38383864 original size:35 final size:34
Alignment explanation
Indices: 38383823--38383896 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
38383813 AAATTTAAAT
* *
38383823 TTAAATAA-TAAAAAACAAACATCTCAAATATCAAC
1 TTAAATAACT-AAAAACAAACATCT-AAACAACAAC
* *
38383858 TTAAATAACTACAAACAAATATCTAAACAACAAC
1 TTAAATAACTAAAAACAAACATCTAAACAACAAC
38383892 TTAAA
1 TTAAA
38383897 CAACATTGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 13 0.38
35 20 0.59
36 1 0.03
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.23
Consensus pattern (34 bp):
TTAAATAACTAAAAACAAACATCTAAACAACAAC
Found at i:38385584 original size:17 final size:17
Alignment explanation
Indices: 38385562--38385602 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
38385552 TCCTTTCCCT
38385562 TATATAAAAAAAATATA
1 TATATAAAAAAAATATA
** *
38385579 TATATACTAAAAGTATA
1 TATATAAAAAAAATATA
38385596 TATATAA
1 TATATAA
38385603 CAGTAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
TATATAAAAAAAATATA
Found at i:38387154 original size:42 final size:42
Alignment explanation
Indices: 38387072--38387155 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
38387062 TATTGTGTAA
* **
38387072 TGATATTGACTCGACAATATGAGAGTGGGAGTGCGTATAAGC
1 TGATATTGACTCGACAATATGAGAGTGGGAGTCCACATAAGC
* * *
38387114 TGATATTGACTCGACTATGTGCGAGTGGGAGTCCACATAAGC
1 TGATATTGACTCGACAATATGAGAGTGGGAGTCCACATAAGC
38387156 CAATGCTAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (42 bp):
TGATATTGACTCGACAATATGAGAGTGGGAGTCCACATAAGC
Found at i:38390358 original size:19 final size:19
Alignment explanation
Indices: 38390334--38390371 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
38390324 CTGTCAAACC
*
38390334 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
38390353 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
38390372 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:38391943 original size:17 final size:16
Alignment explanation
Indices: 38391921--38391953 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
38391911 TAAGATTAAG
38391921 AAGAAAAAAGATAAAAA
1 AAGAAAAAAGA-AAAAA
38391938 AAGAAAAAAGAAAAAA
1 AAGAAAAAAGAAAAAA
38391954 GAGGGTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:38396144 original size:2 final size:2
Alignment explanation
Indices: 38396132--38396170 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
38396122 AAACTTTATT
38396132 TA TA TA T- TA TA TA TA T- TA -A TA TA -A 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 TA TA TA TA
38396170 T
1 T
38396171 TAAGAAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38396153 original size:17 final size:16
Alignment explanation
Indices: 38396131--38396172 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
38396121 CAAACTTTAT
38396131 TTATATATTATATATA
1 TTATATATTATATATA
*
38396147 TTA-ATATAATATATA
1 TTATATATTATATATA
38396162 TATATATATTA
1 T-TATATATTA
38396173 AGAAGAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATATATTATATATA
Found at i:38397443 original size:2 final size:2
Alignment explanation
Indices: 38397436--38397478 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
38397426 TATTTATAAT
38397436 TA TA TA TA TA TA -A TA TA TA TA -A TA TA -A TA GTA 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
38397476 TA T
1 TA T
38397479 CATTTTACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.08
2 32 0.86
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38397453 original size:9 final size:9
Alignment explanation
Indices: 38397439--38397478 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
38397429 TTATAATTAT
38397439 ATATATATA
1 ATATATATA
38397448 ATATATATA
1 ATATATATA
38397457 ATATA-ATA
1 ATATATATA
*
38397465 GTATATAT-
1 ATATATATA
38397473 ATATAT
1 ATATAT
38397479 CATTTTACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 12 0.43
9 16 0.57
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (9 bp):
ATATATATA
Found at i:38417855 original size:16 final size:17
Alignment explanation
Indices: 38417825--38417857 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
38417815 TTTCTCCCTC
38417825 TTATCTTTAACCATTAA
1 TTATCTTTAACCATTAA
*
38417842 TTATC-TTAATCATTAA
1 TTATCTTTAACCATTAA
38417858 CCAACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATCTTTAACCATTAA
Found at i:38425325 original size:21 final size:21
Alignment explanation
Indices: 38425295--38425362 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
38425285 GGATATGTTC
38425295 ATGCAATTCATGACAAAGACTG
1 ATGC-ATTCATGACAAAGACTG
* *
38425317 ATGCATTCATAACAAAGACCG
1 ATGCATTCATGACAAAGACTG
* *
38425338 ATGCATTTATGACAAGGACTG
1 ATGCATTCATGACAAAGACTG
38425359 ATGC
1 ATGC
38425363 TTCCATTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 36 0.90
22 4 0.10
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTG
Found at i:38426516 original size:21 final size:21
Alignment explanation
Indices: 38426491--38426532 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
38426481 GAATTCTTAG
38426491 CTTTTGGTGAATAAGGTTTTT
1 CTTTTGGTGAATAAGGTTTTT
38426512 CTTTTGGTGAATAAGGTTTTT
1 CTTTTGGTGAATAAGGTTTTT
38426533 GTTTGGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.24, T:0.52
Consensus pattern (21 bp):
CTTTTGGTGAATAAGGTTTTT
Found at i:38426537 original size:20 final size:21
Alignment explanation
Indices: 38426493--38426538 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
38426483 ATTCTTAGCT
*
38426493 TTTGGTGAATAAGGTTTTTCT
1 TTTGGTGAATAAGGTTTTTCG
38426514 TTTGGTGAATAAGGTTTTT-G
1 TTTGGTGAATAAGGTTTTTCG
38426534 TTTGG
1 TTTGG
38426539 ATTCATGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.52
Consensus pattern (21 bp):
TTTGGTGAATAAGGTTTTTCG
Found at i:38427559 original size:3 final size:3
Alignment explanation
Indices: 38427551--38427576 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38427541 ACTTTATCTC
38427551 TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TA
38427577 ACTATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:38429733 original size:21 final size:20
Alignment explanation
Indices: 38429709--38429756 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
38429699 CTTAATATCT
*
38429709 TTTTGAAATATTTTAAAAAA
1 TTTTGAAATATATTAAAAAA
38429729 CTTTTG-AAT-TATTAAAAAA
1 -TTTTGAAATATATTAAAAAA
38429748 TTTT-AAATA
1 TTTTGAAATA
38429757 AATTTTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 7 0.29
19 9 0.38
20 3 0.12
21 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (20 bp):
TTTTGAAATATATTAAAAAA
Found at i:38429788 original size:26 final size:26
Alignment explanation
Indices: 38429747--38429809 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
38429737 TTATTAAAAA
38429747 ATTTTAAAT-AAA-TTTT-TACTTTTT
1 ATTTTAAATCAAACTTTTATA-TTTTT
38429771 ATATTT-AATCAAACTTTTATATTTTT
1 AT-TTTAAATCAAACTTTTATATTTTT
38429797 ATTTTAAATCAAA
1 ATTTTAAATCAAA
38429810 TAAATATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
24 5 0.15
25 9 0.26
26 18 0.53
27 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTTAAATCAAACTTTTATATTTTT
Found at i:38429955 original size:20 final size:19
Alignment explanation
Indices: 38429912--38429949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
38429902 TATTATATTA
38429912 TATTAATATATCACATCAC
1 TATTAATATATCACATCAC
*
38429931 TATTAATCATATCATATCA
1 TATTAAT-ATATCACATCA
38429950 ACATTATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAATATATCACATCAC
Found at i:38430800 original size:86 final size:86
Alignment explanation
Indices: 38430615--38431036 Score: 577
Period size: 86 Copynumber: 5.0 Consensus size: 86
38430605 TTATATTACT
* * * * *
38430615 TATAAAATTTTAATATTAGTTAAATTTGTAAATTAAAAAATATAAAATTAATTTATATTAC-T--
1 TATAAAATTTTTATATTAGTTAAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
*
38430677 --TATGATGTAAACTTAAATA
66 ACTATGATGCAAACTTAAATA
* *
38430696 TATAAAATTTTTACATTAGTTAAACTTGTAAGCTAACAAATGTAAAATTAAATTT-TATTACTTG
1 TATAAAATTTTTATATTAGTTAAACTTGTAAACTAACAAATGTAAAATT-AATTTATATTACTTG
* *
38430760 AACTATTATGCAAACTTAAGTA
65 AACTATGATGCAAACTTAAATA
* * *
38430782 TATAAAATTTTTGTATTAGTTGAACTTGTAAACTAACAAATTTAAAATTAATTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTAAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
*
38430847 ATTATGATGCAAACTTAAATA
66 ACTATGATGCAAACTTAAATA
* * *
38430868 TATAAAATTTTTATATTAGTTAATCTTGTAAACTAACAAATGTGAAATTGATTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTAAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
* * *
38430933 ACTATCATACAAATTTAAATA
66 ACTATGATGCAAACTTAAATA
* * * *
38430954 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAATGTAAAATTAATTTATATTATTTAA
1 TATAAAATTTTTATATTAGTTAAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
38431019 ACTATGATGCAAACTTAA
66 ACTATGATGCAAACTTAA
38431037 TAACAATTAT
Statistics
Matches: 296, Mismatches: 38, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
81 48 0.16
82 6 0.02
85 5 0.02
86 237 0.80
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (86 bp):
TATAAAATTTTTATATTAGTTAAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
ACTATGATGCAAACTTAAATA
Found at i:38430805 original size:44 final size:44
Alignment explanation
Indices: 38430685--38430979 Score: 172
Period size: 42 Copynumber: 6.8 Consensus size: 44
38430675 CTTATGATGT
* * * *
38430685 AAACTTAAATATATAAAATTTTTACATTAGTTAAACT-TGTAAGC
1 AAACTTAAATATATAAAATTTTTATATTACTTGAACTAT-TATGC
* *
38430729 TAAC---AA-ATGTAAAATTAAATTT-TATTACTTGAACTATTATGC
1 AAACTTAAATATATAAAATT---TTTATATTACTTGAACTATTATGC
* * * *
38430771 AAACTTAAGTATATAAAATTTTTGTATTAGTTGAAC---T-TGT
1 AAACTTAAATATATAAAATTTTTATATTACTTGAACTATTATGC
* * * *
38430811 AAAC-TAACAAATTTAAAATTAATTTATATTACTTGAATTATGATGC
1 AAACTTAA-ATATATAAAATT--TTTATATTACTTGAACTATTATGC
* * *
38430857 AAACTTAAATATATAAAATTTTTATATTAGTT-AA-T-CT-TGT
1 AAACTTAAATATATAAAATTTTTATATTACTTGAACTATTATGC
* * * * *
38430897 AAAC-TAACAAATGTGAAATTGATTTATATTACTTGAACTATCATAC
1 AAACTTAA-ATATATAAAATT--TTTATATTACTTGAACTATTATGC
* *
38430943 AAATTTAAATATATAAAATTTTTATATTAGTTGAACT
1 AAACTTAAATATATAAAATTTTTATATTACTTGAACT
38430980 TGTAAACTAA
Statistics
Matches: 188, Mismatches: 38, Indels: 50
0.68 0.14 0.18
Matches are distributed among these distances:
39 6 0.03
40 39 0.21
41 3 0.02
42 42 0.22
43 11 0.06
44 42 0.22
45 1 0.01
46 38 0.20
47 6 0.03
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.41
Consensus pattern (44 bp):
AAACTTAAATATATAAAATTTTTATATTACTTGAACTATTATGC
Found at i:38431010 original size:42 final size:40
Alignment explanation
Indices: 38430615--38431013 Score: 229
Period size: 40 Copynumber: 9.5 Consensus size: 40
38430605 TTATATTACT
* * * *
38430615 TATAAAATT-TTAATATTAGTTAAATTTGTAAATTAAAAAA
1 TATAAAATTATTTATATTAGTTGAACTTGTAAACT-AAAAA
* *** *
38430655 TATAAAATTAATTTATATTACTT-ATGATGTAAACTTAAATA
1 TATAAAATT-ATTTATATTAGTTGAACTTGTAAAC-TAAAAA
* * *
38430696 TATAAAATT-TTTACATTAGTTAAACTTGTAAGCTAACAAA
1 TATAAAATTATTTATATTAGTTGAACTTGTAAACTAA-AAA
* * * **
38430736 TGTAAAATTAAATTT-TATTACTTGAACTATTATGCAAACTTAAGTA
1 TATAAAATT--ATTTATATTAGTTGAAC---T-TGTAAAC-TAAAAA
*
38430782 TATAAAATT-TTTGTATTAGTTGAACTTGTAAACTAACAAA
1 TATAAAATTATTTATATTAGTTGAACTTGTAAACTAA-AAA
* * * *
38430822 TTTAAAATTAATTTATATTACTTGAATTATGATGCAAACTTAAATA
1 TATAAAATT-ATTTATATTAGTTGAACT-TG-T--AAAC-TAAAAA
38430868 TATAAAATT-TTTATATTAGTT-AATCTTGTAAACTAACAAA
1 TATAAAATTATTTATATTAGTTGAA-CTTGTAAACTAA-AAA
* * * * * *
38430908 TGTGAAATTGATTTATATTACTTGAACTATCATACAAATTTAAATA
1 TATAAAATT-ATTTATATTAGTTGAACT-T-GT--AAA-CTAAAAA
38430954 TATAAAATT-TTTATATTAGTTGAACTTGTAAACTAATAAA
1 TATAAAATTATTTATATTAGTTGAACTTGTAAACTAA-AAA
*
38430994 TGTAAAATTAATTTATATTA
1 TATAAAATT-ATTTATATTA
38431014 TTTAAACTAT
Statistics
Matches: 275, Mismatches: 49, Indels: 68
0.70 0.12 0.17
Matches are distributed among these distances:
39 22 0.08
40 67 0.24
41 21 0.08
42 58 0.21
43 16 0.06
44 41 0.15
45 1 0.00
46 40 0.15
47 9 0.03
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (40 bp):
TATAAAATTATTTATATTAGTTGAACTTGTAAACTAAAAA
Found at i:38432129 original size:30 final size:28
Alignment explanation
Indices: 38432056--38432130 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 28
38432046 TTAGAAAATT
38432056 TTAAATAAATTTTTAT-TTTTTATTAAA
1 TTAAATAAATTTTTATATTTTTATTAAA
* * *
38432083 TTTAATCATATCTTTATATTTTTATTTTAAA
1 TTAAAT-AAATTTTTATATTTTTA--TTAAA
38432114 TTAAATAAATTTTTATA
1 TTAAATAAATTTTTATA
38432131 ACTAATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.13
28 8 0.21
29 6 0.16
30 9 0.24
31 10 0.26
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
TTAAATAAATTTTTATATTTTTATTAAA
Found at i:38439156 original size:7 final size:7
Alignment explanation
Indices: 38439144--38439174 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
38439134 CTTGGATTTG
38439144 GGAAATT
1 GGAAATT
38439151 GGAAATT
1 GGAAATT
38439158 GGAAATT
1 GGAAATT
38439165 GGAAATT
1 GGAAATT
38439172 GGA
1 GGA
38439175 GTCCCCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (7 bp):
GGAAATT
Found at i:38440596 original size:2 final size:2
Alignment explanation
Indices: 38440589--38440619 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38440579 GTTATAAAAT
38440589 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38440620 GTATGTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38441372 original size:25 final size:25
Alignment explanation
Indices: 38441327--38441375 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38441317 TATCATTTTA
*
38441327 AATTAAATAACTTTTTATAATTAAT
1 AATTAAATAACTTATTATAATTAAT
*
38441352 AATTAATTAA-TTATTATTAATTAA
1 AATTAAATAACTTATTA-TAATTAA
38441376 AATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTAAATAACTTATTATAATTAAT
Found at i:38441545 original size:21 final size:21
Alignment explanation
Indices: 38441505--38441563 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
38441495 ATTGATAAAT
**
38441505 ATTATTAATAATAATTATTTA
1 ATTATTAATAATAAAAATTTA
*
38441526 ATTATTAATTATAAAAATTTA
1 ATTATTAATAATAAAAATTTA
*
38441547 TTTAATTTAA-AATAAAA
1 ATT-A-TTAATAATAAAA
38441564 TTATGAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 20 0.65
22 7 0.23
23 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATTAATAATAAAAATTTA
Found at i:38450047 original size:29 final size:28
Alignment explanation
Indices: 38450007--38450061 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
38449997 TTTGATTTAA
*
38450007 AATAAAATATAAAAATTTAATTAAATAT
1 AATAAAATATAAAAAATTAATTAAATAT
*
38450035 AATAAAATAATAAAAAATTATTTAAAT
1 AATAAAAT-ATAAAAAATTAATTAAAT
38450062 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
AATAAAATATAAAAAATTAATTAAATAT
Found at i:38450633 original size:18 final size:18
Alignment explanation
Indices: 38450593--38450653 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
38450583 TATAAAATTC
* **
38450593 TTTATTCAATAAATATATT
1 TTTATT-AAAAAATATAAA
38450612 TTTATTAAAAAATATAAA
1 TTTATTAAAAAATATAAA
*
38450630 TTTATAATAAATAATATTAAA
1 TTTAT--TAAAAAATA-TAAA
38450651 TTT
1 TTT
38450654 TATTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 14 0.40
19 6 0.17
20 8 0.23
21 7 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTATTAAAAAATATAAA
Found at i:38455722 original size:2 final size:2
Alignment explanation
Indices: 38455717--38455759 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
38455707 TATATACCTA
38455717 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
38455759 A
1 A
38455760 GGATACGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38456034 original size:2 final size:2
Alignment explanation
Indices: 38456027--38456069 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
38456017 TATCTATAGT
*
38456027 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA GA TA 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
38456068 TA
1 TA
38456070 AAATAATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38461262 original size:22 final size:22
Alignment explanation
Indices: 38461232--38461282 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
38461222 TTATTTTTTA
* *
38461232 TTATATTCAATCAAATATATTT
1 TTATATTCAATAAAATAAATTT
*
38461254 TTATTTTCAATAAAATAAATTT
1 TTATATTCAATAAAATAAATTT
38461276 TTATATT
1 TTATATT
38461283 TTTAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATATTCAATAAAATAAATTT
Found at i:38461283 original size:30 final size:30
Alignment explanation
Indices: 38461247--38461309 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
38461237 TTCAATCAAA
*
38461247 TATATTTTT-ATTTTCAATAAAATAAATTTT
1 TATATTTTTAATTTT-AACAAAATAAATTTT
*
38461277 TATATTTTTAATTTTTACAAAATAAATTTT
1 TATATTTTTAATTTTAACAAAATAAATTTT
38461307 TAT
1 TAT
38461310 GACTAATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TATATTTTTAATTTTAACAAAATAAATTTT
Found at i:38463444 original size:2 final size:2
Alignment explanation
Indices: 38463437--38463469 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38463427 TTGCCTTAGT
38463437 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38463470 TGCCTACCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38465610 original size:30 final size:28
Alignment explanation
Indices: 38465575--38465653 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 28
38465565 TCTGAAAATA
38465575 AAAATATAAAAATTTATTTAATTTAAGAT-AT
1 AAAATATAAAAATTTATTTAA---AA-ATAAT
*
38465606 -AAATATAAAAATTTAATTAAAAATAAT
1 AAAATATAAAAATTTATTTAAAAATAAT
*
38465633 AAAAAATAAAAATTTATTTAA
1 AAAATATAAAAATTTATTTAA
38465654 GTTTTTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.05
27 4 0.09
28 18 0.42
30 19 0.44
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (28 bp):
AAAATATAAAAATTTATTTAAAAATAAT
Found at i:38465653 original size:28 final size:30
Alignment explanation
Indices: 38465571--38465653 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 30
38465561 AGTGTCTGAA
38465571 AATAAAAATATAAAAATTTATTTAATTTAAGAT
1 AATAAAAA-ATAAAAATTTATTTAA--TAAGAT
* *
38465604 -AT-AAATATAAAAATTTAATTAA-AA-AT
1 AATAAAAAATAAAAATTTATTTAATAAGAT
38465630 AATAAAAAATAAAAATTTATTTAA
1 AATAAAAAATAAAAATTTATTTAA
38465654 GTTTTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
26 2 0.05
27 4 0.09
28 18 0.41
30 15 0.34
31 3 0.07
32 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (30 bp):
AATAAAAAATAAAAATTTATTTAATAAGAT
Found at i:38466991 original size:2 final size:2
Alignment explanation
Indices: 38466984--38467020 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
38466974 TTGTTCTTCA
38466984 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38467021 ATTAATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38466999 original size:11 final size:11
Alignment explanation
Indices: 38466983--38467029 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
38466973 TTTGTTCTTC
38466983 AATATATATAT
1 AATATATATAT
38466994 AATATATATAT
1 AATATATATAT
38467005 -ATATATATAT
1 AATATATATAT
*
38467015 TATATA-AT-T
1 AATATATATAT
38467024 AATATA
1 AATATA
38467030 AACATATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
9 6 0.18
10 12 0.35
11 16 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATATATATAT
Found at i:38467008 original size:19 final size:19
Alignment explanation
Indices: 38466984--38467020 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
38466974 TTGTTCTTCA
38466984 ATATATATATAATATATAT
1 ATATATATATAATATATAT
*
38467003 ATATATATATATTATATA
1 ATATATATATAATATATA
38467021 ATTAATATAA
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:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATATAATATATAT
Found at i:38470037 original size:33 final size:33
Alignment explanation
Indices: 38469999--38470164 Score: 111
Period size: 33 Copynumber: 4.8 Consensus size: 33
38469989 ATTATATTAG
* *
38469999 TATGTCATCTTATTATTAATTATTATTCGTGAA
1 TATGTCATGTCATTATTAATTATTATTCGTGAA
* * *
38470032 TATGTCATGTCATTATCAACTATTATT-GATAAA
1 TATGTCATGTCATTATTAATTATTATTCG-TGAA
* * *
38470065 CATGTCATGTCATCATAATAATGTTATTATATCAT-ATTA
1 TATGTCATGTCAT--TATTAA--TTATTAT-TCGTGA--A
* * * *
38470104 GTATGTCATCTTATTATTAATTATGATTAGTGAA
1 -TATGTCATGTCATTATTAATTATTATTCGTGAA
* *
38470138 TATGTAATGTCATTATCAATTATTATT
1 TATGTCATGTCATTATTAATTATTATT
38470165 GATCAACATA
Statistics
Matches: 100, Mismatches: 22, Indels: 22
0.69 0.15 0.15
Matches are distributed among these distances:
32 1 0.01
33 60 0.60
34 1 0.01
35 6 0.06
36 7 0.07
37 7 0.07
38 7 0.07
39 1 0.01
40 10 0.10
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (33 bp):
TATGTCATGTCATTATTAATTATTATTCGTGAA
Found at i:38470155 original size:106 final size:106
Alignment explanation
Indices: 38469970--38470182 Score: 336
Period size: 106 Copynumber: 2.0 Consensus size: 106
38469960 TAGCAATAGA
* * *
38469970 ATCATAATAATGTCATCATATTATATTAGTATGTCATCTTATTATTAATTATTATTCGTGAATAT
1 ATCATAATAATGTCATCATATCATATTAGTATGTCATCTTATTATTAATTATGATTAGTGAATAT
* * *
38470035 GTCATGTCATTATCAACTATTATTGATAAACATGTCATGTC
66 GTAATGTCATTATCAACTATTATTGATAAACATATCACGTC
* *
38470076 ATCATAATAATGTTATTATATCATATTAGTATGTCATCTTATTATTAATTATGATTAGTGAATAT
1 ATCATAATAATGTCATCATATCATATTAGTATGTCATCTTATTATTAATTATGATTAGTGAATAT
* *
38470141 GTAATGTCATTATCAATTATTATTGATCAACATATCACGTC
66 GTAATGTCATTATCAACTATTATTGATAAACATATCACGTC
38470182 A
1 A
38470183 ACATTATGTT
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 97 1.00
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (106 bp):
ATCATAATAATGTCATCATATCATATTAGTATGTCATCTTATTATTAATTATGATTAGTGAATAT
GTAATGTCATTATCAACTATTATTGATAAACATATCACGTC
Found at i:38471518 original size:15 final size:15
Alignment explanation
Indices: 38471498--38471545 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
38471488 TTTTTTAAAT
*
38471498 ATTAATAATTTTATA
1 ATTAATAATTTAATA
38471513 ATTAATTAAAATATTAATA
1 ATTAA-T--AAT-TTAATA
38471532 ATTAATAATTTAAT
1 ATTAATAATTTAAT
38471546 TTAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 10 0.36
16 4 0.14
18 4 0.14
19 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTAATAATTTAATA
Found at i:38471524 original size:27 final size:27
Alignment explanation
Indices: 38471494--38471643 Score: 95
Period size: 27 Copynumber: 5.7 Consensus size: 27
38471484 TTTATTTTTT
*
38471494 AAATATTAATAATTTTATAA-TTAATTA
1 AAATATTAATAA-TTAATAATTTAATTA
*
38471521 AAATATTAATAATTAATAATTTAATTT
1 AAATATTAATAATTAATAATTTAATTA
*
38471548 AAATATT-TTAA-T-ATAATTTAATTA
1 AAATATTAATAATTAATAATTTAATTA
* * * *
38471572 CTTATATTTTAATTAA-TAATATTTTATTTA
1 ---AAATATTAA-TAATTAATAATTTAATTA
* *
38471602 TAAT-TTAAT-ATT-AT--TTTGATTA
1 AAATATTAATAATTAATAATTTAATTA
38471624 AAATATTAATAATTTAATAA
1 AAATATTAATAA-TTAATAA
38471644 ATAAAACATT
Statistics
Matches: 95, Mismatches: 14, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
22 9 0.09
23 5 0.05
24 15 0.16
25 5 0.05
26 15 0.16
27 32 0.34
29 4 0.04
30 10 0.11
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
AAATATTAATAATTAATAATTTAATTA
Found at i:38471564 original size:19 final size:19
Alignment explanation
Indices: 38471537--38471613 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
38471527 TAATAATTAA
*
38471537 TAATTTAATTTAAATATTT
1 TAATATAATTTAAATATTT
* *
38471556 TAATATAATTTAATTACTTA
1 TAATATAATTTAAATA-TTT
* * *
38471576 TATTTTAATTAATAATATTT
1 TAATATAATTTA-AATATTT
*
38471596 TATTTATAATTT-AATATT
1 TA-ATATAATTTAAATATT
38471614 ATTTTGATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 20 0.44
20 15 0.33
21 10 0.22
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATATAATTTAAATATTT
Found at i:38471582 original size:15 final size:15
Alignment explanation
Indices: 38471555--38471597 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38471545 TTTAAATATT
*
38471555 TTAA-TATAATTTAA
1 TTAATTATATTTTAA
*
38471569 TTACTTATATTTTAA
1 TTAATTATATTTTAA
*
38471584 TTAATAATATTTTA
1 TTAATTATATTTTA
38471598 TTTATAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATTATATTTTAA
Found at i:38471598 original size:22 final size:22
Alignment explanation
Indices: 38471542--38471636 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
38471532 ATTAATAATT
*
38471542 TAATTT-A-AATATTTTA-ATA
1 TAATTTAATAATATTTTATTTA
*
38471561 TAATTTAAT--TACTTATATTT-
1 TAATTTAATAATA-TTTTATTTA
38471581 TAA-TTAATAATATTTTATTTA
1 TAATTTAATAATATTTTATTTA
*
38471602 TAATTTAATATTATTTTGA-TTA
1 TAATTTAATAATATTTT-ATTTA
*
38471624 AAATATTAATAAT
1 TAAT-TTAATAAT
38471637 TTAATAAATA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
19 13 0.22
20 15 0.25
21 6 0.10
22 18 0.30
23 8 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (22 bp):
TAATTTAATAATATTTTATTTA
Found at i:38471648 original size:23 final size:24
Alignment explanation
Indices: 38471622--38471738 Score: 80
Period size: 23 Copynumber: 4.8 Consensus size: 24
38471612 TTATTTTGAT
38471622 TAAAATATTAATAATTTAATA-AA
1 TAAAATATTAATAATTTAATATAA
* * *
38471645 TAAAACATTAATAGTTTAA-ATAT
1 TAAAATATTAATAATTTAATATAA
* * *
38471668 TAATATTTTAATATTTTAATCAT-A
1 TAAAATATTAATAATTTAAT-ATAA
*
38471692 T-TAATATTAATAATGTTTCAATTATATA
1 TAAAATATTAATAA--TTT-AA-TATA-A
*
38471720 TAAAATATTAATATTTTAA
1 TAAAATATTAATAATTTAA
38471739 ATTTTACAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
22 1 0.01
23 41 0.59
24 1 0.01
25 5 0.07
26 6 0.09
27 4 0.06
28 2 0.03
29 10 0.14
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.46
Consensus pattern (24 bp):
TAAAATATTAATAATTTAATATAA
Found at i:38471740 original size:15 final size:15
Alignment explanation
Indices: 38471651--38471740 Score: 62
Period size: 15 Copynumber: 6.0 Consensus size: 15
38471641 TAAATAAAAC
*
38471651 ATTAATAGTTTAAAT
1 ATTAATATTTTAAAT
38471666 ATTAATATTTTAATAT
1 ATTAATATTTTAA-AT
* *
38471682 TTTAATCATATT-AAT
1 ATTAAT-ATTTTAAAT
*
38471697 ATTAATAATGTTT-CA-
1 ATTAAT-AT-TTTAAAT
* *
38471712 ATT-ATATATAAAAT
1 ATTAATATTTTAAAT
38471726 ATTAATATTTTAAAT
1 ATTAATATTTTAAAT
38471741 TTTACAAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 5 0.09
15 33 0.58
16 11 0.19
17 4 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTAATATTTTAAAT
Found at i:38471774 original size:11 final size:10
Alignment explanation
Indices: 38471752--38471794 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
38471742 TTACAAATAA
38471752 TTTATTCTTT
1 TTTATTCTTT
38471762 TTTATTCTATT
1 TTTATTCT-TT
**
38471773 TTTACCCTTT
1 TTTATTCTTT
*
38471783 TTTTTTCTTT
1 TTTATTCTTT
38471793 TT
1 TT
38471795 CATGGGCCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTCTTT
Found at i:38485405 original size:2 final size:2
Alignment explanation
Indices: 38485393--38485447 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
38485383 AAAGGGAAAC
* * *
38485393 AG AG GG AG AG AG AA AG AG AG AG TG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38485435 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
38485448 TTCCCCAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:38487199 original size:15 final size:15
Alignment explanation
Indices: 38487179--38487207 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38487169 GCCTTTTATC
38487179 AGGAAAAAAAAAAGA
1 AGGAAAAAAAAAAGA
38487194 AGGAAAAAAAAAAG
1 AGGAAAAAAAAAAG
38487208 GTAATTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGGAAAAAAAAAAGA
Found at i:38494205 original size:29 final size:30
Alignment explanation
Indices: 38494165--38494244 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 30
38494155 TATTTTTAAA
*
38494165 TTTTTATATAAATATAAAATAA-AATTTAT
1 TTTTTAAATAAATATAAAATAATAATTTAT
*
38494194 TTTTTAAATAAATA-ATAATAATAATTTAT
1 TTTTTAAATAAATATAAAATAATAATTTAT
38494223 TTAATTTAAAATAAAATATAAA
1 TT--TTT-AAAT-AAATATAAA
38494245 TATTTAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.14
29 22 0.52
31 3 0.07
32 4 0.10
33 5 0.12
34 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTTTAAATAAATATAAAATAATAATTTAT
Found at i:38496466 original size:16 final size:16
Alignment explanation
Indices: 38496445--38496478 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38496435 TCCTGGGGCG
38496445 CCTATTTTGGGGTGCA
1 CCTATTTTGGGGTGCA
38496461 CCTATTTTGGGGTGCA
1 CCTATTTTGGGGTGCA
38496477 CC
1 CC
38496479 AAGAGTGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.35
Consensus pattern (16 bp):
CCTATTTTGGGGTGCA
Found at i:38522557 original size:28 final size:27
Alignment explanation
Indices: 38522509--38522571 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
38522499 GTAAGAAAAT
*
38522509 TTAAA-TAAATTTTTATCTTTTATTATG
1 TTAAATTAAATTTTTATATTTT-TTATG
* *
38522536 TTAAATTAAGTTTTTATATTTTTTATT
1 TTAAATTAAATTTTTATATTTTTTATG
*
38522563 TTGAATTAA
1 TTAAATTAA
38522572 TAAAATCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (27 bp):
TTAAATTAAATTTTTATATTTTTTATG
Found at i:38526333 original size:34 final size:34
Alignment explanation
Indices: 38526292--38526358 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
38526282 CATCCCCGAC
*
38526292 TTTTTAAAATATTTGATTCAATAATAAATATATT
1 TTTTTAAAATATTTAATTCAATAATAAATATATT
* *
38526326 TTTTTAAAATATTTAATTTAGTAATAAATATAT
1 TTTTTAAAATATTTAATTCAATAATAAATATAT
38526359 GTATTTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (34 bp):
TTTTTAAAATATTTAATTCAATAATAAATATATT
Found at i:38536791 original size:116 final size:114
Alignment explanation
Indices: 38536586--38536809 Score: 279
Period size: 116 Copynumber: 1.9 Consensus size: 114
38536576 ATTTTGAGTT
* * * *
38536586 TTATTTTCTGGAGATGAGGATTTTGGAAGTGTGGGATTAGTGGAGTTGTCTTCTTAGGTGCTCAT
1 TTATTTACTGGAGATGAGAATTTTGGAAGTGTGGAATTAGTGGAATTGTCTTC-TAGGTGCTCAT
*
38536651 CTGTGCCTGTACATGATGCACTTGTTACCATATAGAGTGAGCAGTTTATC
65 CTGTGCATGTACATGATGCACTTGTTACCATATAGAGTGAGCAGTTTATC
* * *
38536701 TTATTTACTGGAGATGAGAATTTTGGGAAGTGTGGAATTAGTGTAATTGTCTGTGC-ATGTGCTT
1 TTATTTACTGGAGATGAGAATTTT-GGAAGTGTGGAATTAGTGGAATTGTCT-T-CTAGGTGCTC
* * * ***
38536765 ATTTGTGTATGTACATGATGCGCTTGTTATGGTATAGAGTGAGCA
63 ATCTGTGCATGTACATGATGCACTTGTTACCATATAGAGTGAGCA
38536810 TGGGAGTGGG
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
115 22 0.24
116 68 0.74
117 1 0.01
118 1 0.01
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (114 bp):
TTATTTACTGGAGATGAGAATTTTGGAAGTGTGGAATTAGTGGAATTGTCTTCTAGGTGCTCATC
TGTGCATGTACATGATGCACTTGTTACCATATAGAGTGAGCAGTTTATC
Found at i:38552821 original size:19 final size:18
Alignment explanation
Indices: 38552799--38552843 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
38552789 TCATAAAGAG
38552799 TATTTATTA-AATAATTTTT
1 TATTTATTACAAT--TTTTT
38552818 TATTTATTACGAATTTTTT
1 TATTTATTAC-AATTTTTT
38552837 TATTTAT
1 TATTTAT
38552844 AATAAAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 21 0.88
21 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTTATTACAATTTTTT
Found at i:38555375 original size:218 final size:216
Alignment explanation
Indices: 38555140--38555536 Score: 598
Period size: 218 Copynumber: 1.8 Consensus size: 216
38555130 TAATTGTATA
* * *
38555140 AATATATTTTATATACATATATTTAATTTATACATAAACATTATTATAATTTATAATAGACTTTA
1 AATATATTTTATATACATATATTTAATTTATACATAAACATTACTATAACTTATAATAAACTTTA
* *
38555205 TCTATATGATTACACTTAATAACTTTATTAGTTATCA-CGCTAGATTTTATAACATATTGTTTAT
66 TCTATATGATTACACTTAATAACTTTATTAGCTATCATC-CTAGATTTTATAACATATTATTTAT
* *
38555269 AATTAGTTATTATTTATACAAACTCTGATATAAAACATTTTAACATATAATTTGCATCAATAATT
130 AATTAATTATTATTTATACAAACTCTGATATAAAACATTATAACATATAATTTGCATCAATAATT
38555334 TTATATATATATATAATAAAAG
195 TTATATATATATATAATAAAAG
** *
38555356 AATATATTATATATATACATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAATTT
1 AATATATT-T-TATATACATATATTTAATTTATACATAAACATTACTATAACTTATAATAAACTT
* * * * *
38555421 TATTTATATGATTATACTTAATAAGTTTATTTGCTATCATCTTAGATTTTATAACATATTATTTA
64 TATCTATATGATTACACTTAATAACTTTATTAGCTATCATCCTAGATTTTATAACATATTATTTA
* * *
38555486 TAATTAATTATTATTTATATAAATTTTGATATAAAACATTATAACATATAA
129 TAATTAATTATTATTTATACAAACTCTGATATAAAACATTATAACATATAA
38555537 GTTATATAAT
Statistics
Matches: 160, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
216 8 0.05
217 1 0.01
218 150 0.94
219 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (216 bp):
AATATATTTTATATACATATATTTAATTTATACATAAACATTACTATAACTTATAATAAACTTTA
TCTATATGATTACACTTAATAACTTTATTAGCTATCATCCTAGATTTTATAACATATTATTTATA
ATTAATTATTATTTATACAAACTCTGATATAAAACATTATAACATATAATTTGCATCAATAATTT
TATATATATATATAATAAAAG
Found at i:38555717 original size:27 final size:26
Alignment explanation
Indices: 38555662--38555718 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
38555652 ACCAAATCAA
* **
38555662 TTTTATATTTGATCGGTTTGATTTTT
1 TTTTATATTTGATCAGTTTGATTGAT
*
38555688 TTTTATATTTGATCAATTTTGATTGAT
1 TTTTATATTTGATC-AGTTTGATTGAT
38555715 TTTT
1 TTTT
38555719 TCAAAAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.19, C:0.04, G:0.12, T:0.65
Consensus pattern (26 bp):
TTTTATATTTGATCAGTTTGATTGAT
Done.