Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000623.1 Kokia drynarioides strain JFW-HI SEQ_111578, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 113805
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:54 original size:2 final size:2
Alignment explanation
Indices: 47--71 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37 TTATTAACTA
47 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
72 AGAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3647 original size:20 final size:18
Alignment explanation
Indices: 3606--3662 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
3596 ACCTTTAATA
*
3606 TTAACTTAATTAATCACTT
1 TTAACTTAATTAAAC-CTT
3625 TTAATCTTAATTAAACCTAT
1 TTAA-CTTAATTAAACCT-T
3645 TTACACTTAATATAAACC
1 TTA-ACTTAAT-TAAACC
3663 ATACTAATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.18
20 20 0.61
21 7 0.21
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAACTTAATTAAACCTT
Found at i:7735 original size:3 final size:3
Alignment explanation
Indices: 7727--7752 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7717 ACTTTTTAAA
7727 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
7753 ATACAATAAC
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:9152 original size:25 final size:23
Alignment explanation
Indices: 9114--9159 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
9104 TGTTCATGCT
*
9114 TATAATATAATTTTTATAATTTG
1 TATAATATAATTTTTAAAATTTG
9137 TATATATATAATTTTTTAAAATT
1 TATA-ATATAA-TTTTTAAAATT
9160 GGATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 6 0.30
25 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATAATATAATTTTTAAAATTTG
Found at i:11395 original size:15 final size:16
Alignment explanation
Indices: 11374--11411 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
11364 AATCAAAGAA
11374 AAACAAAAATCAATTC
1 AAACAAAAATCAATTC
**
11390 -AACAAATTTCAATTC
1 AAACAAAAATCAATTC
11405 AAACAAA
1 AAACAAA
11412 GTTGCTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACAAAAATCAATTC
Found at i:14003 original size:15 final size:14
Alignment explanation
Indices: 13985--14025 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
13975 AACTTGACTA
13985 TTATTATTAATTATT
1 TTATT-TTAATTATT
*
14000 TTATTTTATTTTATT
1 TTATTTTA-ATTATT
14015 TTATTTTAATT
1 TTATTTTAATT
14026 TCTACTACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTTAATTATT
Found at i:14005 original size:5 final size:5
Alignment explanation
Indices: 13995--14022 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
13985 TTATTATTAA
13995 TTATT TTATT TTATT TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTA
14023 ATTTCTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:15027 original size:18 final size:18
Alignment explanation
Indices: 15004--15038 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14994 TTAAAAGTTT
* *
15004 TAAAAACTATTTAAAATA
1 TAAAAAATAATTAAAATA
15022 TAAAAAATAATTAAAAT
1 TAAAAAATAATTAAAAT
15039 TTCAATGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAAATAATTAAAATA
Found at i:15853 original size:29 final size:30
Alignment explanation
Indices: 15798--15876 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
15788 ATCTCAAAAT
*
15798 TATACATGAACTTTGATTTAATGTGCAATTA
1 TATACATGAACTTTAATTTAA-GTGCAATTA
*
15829 TATACATGAACTTTAATTTGA-TGCAATTA
1 TATACATGAACTTTAATTTAAGTGCAATTA
** *
15858 TGCACGTGAAACTTTAATT
1 TATACATG-AACTTTAATT
15877 GTGGGTCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.31
30 10 0.24
31 19 0.45
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAAGTGCAATTA
Found at i:19467 original size:2 final size:2
Alignment explanation
Indices: 19460--19484 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19450 TTGTCATTAG
19460 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
19485 TAAATTAAAG
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:30880 original size:17 final size:17
Alignment explanation
Indices: 30847--30880 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30837 GGTTGATATG
* *
30847 GAAAATGTTGTTGAAAT
1 GAAAATGTTATTAAAAT
30864 GAAAATGTTATTAAAAT
1 GAAAATGTTATTAAAAT
30881 AACGAGTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (17 bp):
GAAAATGTTATTAAAAT
Found at i:39151 original size:7 final size:7
Alignment explanation
Indices: 39139--39179 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
39129 AATGGAACCC
39139 AATTTTA
1 AATTTTA
39146 AATTTTA
1 AATTTTA
39153 AATTTTA
1 AATTTTA
*
39160 AATTATTT
1 AATT-TTA
*
39168 AAGTTTA
1 AATTTTA
39175 AATTT
1 AATTT
39180 ATTTTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 24 0.83
8 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:39167 original size:17 final size:18
Alignment explanation
Indices: 39147--39221 Score: 79
Period size: 17 Copynumber: 4.4 Consensus size: 18
39137 CCAATTTTAA
*
39147 ATTTTAAATTTTAAA-TT
1 ATTTTAAAGTTTAAATTT
39164 A-TTT-AAGTTTAAATTT
1 ATTTTAAAGTTTAAATTT
* *
39180 ATTTTAAA-TTAAAACTT
1 ATTTTAAAGTTTAAATTT
*
39197 ATTTT-GAGTTTAAATTT
1 ATTTTAAAGTTTAAATTT
39214 ATTTTAAA
1 ATTTTAAA
39222 TTAAAACTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
15 8 0.17
16 7 0.15
17 28 0.61
18 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (18 bp):
ATTTTAAAGTTTAAATTT
Found at i:39181 original size:16 final size:17
Alignment explanation
Indices: 39156--39220 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
39146 AATTTTAAAT
39156 TTTAAA-TTA-TTTAAG
1 TTTAAATTTATTTTAAG
*
39171 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAG
* * *
39188 TTAAAACTTATTTTGAG
1 TTTAAATTTATTTTAAG
39205 TTTAAATTTATTTTAA
1 TTTAAATTTATTTTAA
39221 ATTAAAACTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 6 0.15
16 3 0.08
17 31 0.77
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:39212 original size:34 final size:33
Alignment explanation
Indices: 39147--39231 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 33
39137 CCAATTTTAA
*
39147 ATTTTAAATTTTAAA-TTATTTAAGTTTAAATTT
1 ATTTTAAA-TTAAAACTTATTTAAGTTTAAATTT
*
39180 ATTTTAAATTAAAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTAAAACTTA-TTTAAGTTTAAATTT
39214 ATTTTAAATTAAAACTTA
1 ATTTTAAATTAAAACTTA
39232 AATTTAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
32 5 0.10
33 11 0.23
34 32 0.67
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (33 bp):
ATTTTAAATTAAAACTTATTTAAGTTTAAATTT
Found at i:41123 original size:29 final size:29
Alignment explanation
Indices: 41101--41157 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
41091 TTTTGCCCCA
41101 AAACATCCAAAAATCACATTTTTACCCTC
1 AAACATCCAAAAATCACATTTTTACCCTC
* *
41130 AAACTTCTAAAAATCACATTTTTACCCT
1 AAACATCCAAAAATCACATTTTTACCCT
41158 GAATTTCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (29 bp):
AAACATCCAAAAATCACATTTTTACCCTC
Found at i:41171 original size:28 final size:29
Alignment explanation
Indices: 40981--41199 Score: 114
Period size: 30 Copynumber: 7.4 Consensus size: 29
40971 GAAGGTCTCT
* *
40981 AAACTGTCCAAAAATCA-TTTTTTGACTCTC
1 AAACT-TCCAAAAATCACATTTTT-ACCCTC
* *
41011 AAACATTTCC-AAAATTACATTTTAACCC-C
1 AAAC--TTCCAAAAATCACATTTTTACCCTC
*
41040 TAAACTTTTCC-AAAATCACATTTTGACCCTC
1 -AAAC--TTCCAAAAATCACATTTTTACCCTC
** * * *
41071 AAGTTTCTAAAAAAAT-ACAATTTTGCCC-C
1 AAACTTC--CAAAAATCACATTTTTACCCTC
*
41100 AAAACATCCAAAAATCACATTTTTACCCTC
1 -AAACTTCCAAAAATCACATTTTTACCCTC
*
41130 AAACTTCTAAAAATCACATTTTTACCCT-
1 AAACTTCCAAAAATCACATTTTTACCCTC
* * * *
41158 GAATTTCCCAAAATGC-CA-TTTTACCCCTA
1 AAACTTCCAAAAAT-CACATTTTTA-CCCTC
41187 AAACTTTCCAAAA
1 AAAC-TTCCAAAA
41200 TTGCATTTTA
Statistics
Matches: 146, Mismatches: 28, Indels: 30
0.72 0.14 0.15
Matches are distributed among these distances:
27 5 0.03
28 25 0.17
29 41 0.28
30 61 0.42
31 13 0.09
32 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATCACATTTTTACCCTC
Found at i:41674 original size:97 final size:97
Alignment explanation
Indices: 41491--41778 Score: 470
Period size: 97 Copynumber: 3.0 Consensus size: 97
41481 AAAATGTTTA
* * *
41491 AAATCGAGGCAATATTCCTTTATTTCGAGTTTTGAAAATTTGTGCCTTAA-TTACTAGGCGCGAT
1 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
41555 TTTTCTTCAAACTAGGATAATCGAATACCCTT
66 TTTTCTTCAAACTAGGATAATCGAATACCCTT
* * *
41587 AAATCAAGGTAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
1 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
41652 TTTTCTTCAAACTAGGATAATCGAATACCCTT
66 TTTTCTTCAAACTAGGATAATCGAATACCCTT
* * * *
41684 AAATCGAGACAATATTCCTTTATCTCGGGTCTTGAAAATTTGTGTCTTAACTTACTAGGCATGAT
1 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
*
41749 TTTTCTTCAAACCAGGATAATCGAATACCC
66 TTTTCTTCAAACTAGGATAATCGAATACCC
41779 GTTTTCAAGG
Statistics
Matches: 177, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
96 46 0.26
97 131 0.74
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
TTTTCTTCAAACTAGGATAATCGAATACCCTT
Found at i:51437 original size:39 final size:39
Alignment explanation
Indices: 51398--51518 Score: 113
Period size: 39 Copynumber: 3.1 Consensus size: 39
51388 AGCTTGGGGT
* *
51398 AGATCATCATCAGCCAATCTCTTACCTCGAGCCTAGGGT
1 AGATCATCATCAGTCAATCTCTTACCTCGAGCCTAGGGC
* * * * *
51437 AGAT--TGCAGCAATTCGATCTTTTACCTCGAG-CTTGGAGC
1 AGATCAT-CATC-AGTCAATCTCTTACCTCGAGCCTAGG-GC
* *
51476 AGATCACCATCAGTCAATCTCTTACCTCGAGCCTGGGGC
1 AGATCATCATCAGTCAATCTCTTACCTCGAGCCTAGGGC
51515 AGAT
1 AGAT
51519 TGCAGCCATT
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
37 1 0.02
38 7 0.11
39 48 0.76
40 7 0.11
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
AGATCATCATCAGTCAATCTCTTACCTCGAGCCTAGGGC
Found at i:51503 original size:78 final size:79
Alignment explanation
Indices: 51374--51632 Score: 337
Period size: 78 Copynumber: 3.3 Consensus size: 79
51364 GCAACAAGTT
* * * *
51374 GATCTTTTACC-CTGAGCTTGGGGTAGATCATCATCAGCCAATCTCTTACCTCGAGCCTAGGGTA
1 GATCTTTTACCTCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTGGGGTA
*
51438 GATTGCAGCAATTC
66 GATTGCAGCCATTC
* * *
51452 GATCTTTTACCTC-GAGCTTGGAGCAGATCACCATCAGTCAATCTCTTACCTCGAGCCTGGGGCA
1 GATCTTTTACCTCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTGGGGTA
*
51516 GATTGCAGCCATTA
66 GATTGCAGCCATTC
* * * * *
51530 GATCTTTTA-ATCAGAGCTTGGGGCAGATCACCATCAACCGATCTCTTACCCCGAGCTTGGGGTA
1 GATCTTTTACCTCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTGGGGTA
*
51594 GATTGTAGCCATTC
66 GATTGCAGCCATTC
* *
51608 GATCTTTTACC-CCGAACTTGGGGCA
1 GATCTTTTACCTCAGAGCTTGGGGCA
51633 AATTACAACC
Statistics
Matches: 157, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
77 2 0.01
78 154 0.98
79 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (79 bp):
GATCTTTTACCTCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTGGGGTA
GATTGCAGCCATTC
Found at i:51611 original size:39 final size:38
Alignment explanation
Indices: 51414--51827 Score: 250
Period size: 39 Copynumber: 10.6 Consensus size: 38
51404 TCATCAGCCA
* * * * *
51414 ATCTCTTACCTCGAGCCTAGGGTAGATTGCAGCAATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATT-CAGCCATTCG
* * * *
51453 ATCTTTTACCTCGAGCTTGGAGCAGA-TCA-CCATCAGTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTCAGCCAT---TCG
* * *
51492 ATCTCTTACCTCGAGCCTGGGGCAGATTGCAGCCATTAG
1 ATCTCTTACCCCGAGCTTGGGGCAGATT-CAGCCATTCG
* ** * *
51531 ATCTTTTAATCAGAGCTTGGGGCAGA-TCA-CCATCAACCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTCAGCCAT---TCG
* *
51570 ATCTCTTACCCCGAGCTTGGGGTAGATTGTAGCCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATT-CAGCCATTCG
* * * * * *
51609 ATCTTTTACCCCGAACTTGGGGCAAATTACAACCGTTTG
1 ATCTCTTACCCCGAGCTTGGGGCAGATT-CAGCCATTCG
* * * *
51648 ATCTCTTATCTCGAGCCTGGGGCAGATT-A-CCATGAGTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTCAGCCAT---TCG
* * *
51687 ATCTCTTACCCCGAGCCTAGGGCAGATTACAGCTATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATT-CAGCCATTCG
* *
51726 ATCTCTTACCCCGAGCTTGGGGCA-AATCA-CCATCAATCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTCAGCCAT---TCG
* * *
51765 ATCTCTTACCCCAAGCTTGGGGCAGATCGCAGTCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGAT-TCAGCCATTCG
* **
51804 ATCTTTTACCCTAAGCTTGGGGCA
1 ATCTCTTACCCCGAGCTTGGGGCA
51828 AATCACTATC
Statistics
Matches: 289, Mismatches: 62, Indels: 48
0.72 0.16 0.12
Matches are distributed among these distances:
36 13 0.04
37 7 0.02
38 4 0.01
39 242 0.84
40 3 0.01
41 6 0.02
42 14 0.05
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTCAGCCATTCG
Found at i:51651 original size:78 final size:78
Alignment explanation
Indices: 51374--51813 Score: 318
Period size: 78 Copynumber: 5.6 Consensus size: 78
51364 GCAACAAGTT
* * * ** * * *
51374 GATCTTTTACCCTGAGCTTGGGGTAGATCATC-ATCAGCCAATCTCTTACCTCGAGCCTAGGGTA
1 GATCTTTTACCCCGAGCTTGGGGCAGATCA-CAACCATTCGATCTCTTACCTCGAGCCTGGGGCA
*
51438 GATTGCAGCAATTC
65 GATTGCAGCCATTC
* * * * * *
51452 GATCTTTTACCTCGAGCTTGGAGCAGATCACCATCAGTCAATCTCTTACCTCGAGCCTGGGGCAG
1 GATCTTTTACCCCGAGCTTGGGGCAGATCACAACCATTCGATCTCTTACCTCGAGCCTGGGGCAG
*
51517 ATTGCAGCCATTA
66 ATTGCAGCCATTC
** * * * ** * * *
51530 GATCTTTTAATCAGAGCTTGGGGCAGATCACCATCAACCGATCTCTTACCCCGAGCTTGGGGTAG
1 GATCTTTTACCCCGAGCTTGGGGCAGATCACAACCATTCGATCTCTTACCTCGAGCCTGGGGCAG
*
51595 ATTGTAGCCATTC
66 ATTGCAGCCATTC
* * * * * *
51608 GATCTTTTACCCCGAACTTGGGGCAAATTACAACCGTTTGATCTCTTATCTCGAGCCTGGGGCAG
1 GATCTTTTACCCCGAGCTTGGGGCAGATCACAACCATTCGATCTCTTACCTCGAGCCTGGGGCAG
51673 ATT--A-CCATGAGTC
66 ATTGCAGCCAT---TC
* * * * * * * * *
51686 AATCTCTTACCCCGAGCCTAGGGCAGATTACAGCTATTCGATCTCTTACCCCGAGCTTGGGGCA-
1 GATCTTTTACCCCGAGCTTGGGGCAGATCACAACCATTCGATCTCTTACCTCGAGCCTGGGGCAG
*
51750 AAT-CA-CCATCAATC
66 ATTGCAGCCAT---TC
* * * * ** *
51764 AATCTCTTACCCCAAGCTTGGGGCAGATCGCAGTCATTCGATCTTTTACC
1 GATCTTTTACCCCGAGCTTGGGGCAGATCACAACCATTCGATCTCTTACC
51814 CTAAGCTTGG
Statistics
Matches: 295, Mismatches: 62, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
75 4 0.01
76 1 0.00
77 3 0.01
78 287 0.97
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (78 bp):
GATCTTTTACCCCGAGCTTGGGGCAGATCACAACCATTCGATCTCTTACCTCGAGCCTGGGGCAG
ATTGCAGCCATTC
Found at i:51661 original size:156 final size:156
Alignment explanation
Indices: 51387--51675 Score: 391
Period size: 156 Copynumber: 1.9 Consensus size: 156
51377 CTTTTACCCT
* * * *
51387 GAGCTTGGGGTAGATCATCATCAGCCAATCTCTTACCTCGAGCCTAGGGTAGATTGCAGCAATTC
1 GAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATTGCAGCAATTC
* * * *
51452 GATCTTTTACCTCGAGCTTGGAGCAGATCACCATCAGTCAATCTCTTACCTCGAGCCTGGGGCAG
66 GATCTTTTACCCCGAACTTGGAGCAAATCACCAACAGTCAATCTCTTACCTCGAGCCTGGGGCAG
51517 ATTGCAGCCATTAGATCTTTTAATCA
131 ATTGCAGCCATTAGATCTTTTAATCA
* * * * *
51543 GAGCTTGGGGCAGATCACCATCAACCGATCTCTTACCCCGAGCTTGGGGTAGATTGTAGCCATTC
1 GAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATTGCAGCAATTC
* * * ** *
51608 GATCTTTTACCCCGAACTTGGGGCAAATTA-CAACCGTTTGATCTCTTATCTCGAGCCTGGGGCA
66 GATCTTTTACCCCGAACTTGGAGCAAATCACCAACAG-TCAATCTCTTACCTCGAGCCTGGGGCA
51672 GATT
130 GATT
51676 ACCATGAGTC
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
155 4 0.04
156 109 0.96
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (156 bp):
GAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGTAGATTGCAGCAATTC
GATCTTTTACCCCGAACTTGGAGCAAATCACCAACAGTCAATCTCTTACCTCGAGCCTGGGGCAG
ATTGCAGCCATTAGATCTTTTAATCA
Found at i:51710 original size:156 final size:154
Alignment explanation
Indices: 51374--51747 Score: 385
Period size: 156 Copynumber: 2.4 Consensus size: 154
51364 GCAACAAGTT
* * * * * * *
51374 GATCTTTTACCCTGAGCTTGGGGTAGATCATCATCAGCCAATCTCTTACCTCGAGCCTAGGGTAG
1 GATCTTTTACCCAGAGCTTGGGGCAGATCA-CATCAACCGATCTCTTACCCCGAGCTTGGGGTAG
* * * *
51439 ATTGCAGCAATTCGATCTTTTACCTCGAGCTTGGAGCAGATCACCATCAGTCAATCTCTTACCTC
65 ATTGCAGCAATTCGATCTTTTACCCCGAACTTGGAGCAAATCACCAACAGTCAATCTCTTACCTC
*
51504 GAGCCTGGGGCAGATTGCAGCCATTA
130 GAGCCTGGGGCAGATT-CAGCCATGA
**
51530 GATCTTTTAATCAGAGCTTGGGGCAGATCACCATCAACCGATCTCTTACCCCGAGCTTGGGGTAG
1 GATCTTTTACCCAGAGCTTGGGGCAGATCA-CATCAACCGATCTCTTACCCCGAGCTTGGGGTAG
* * * * * ** *
51595 ATTGTAGCCATTCGATCTTTTACCCCGAACTTGGGGCAAATTA-CAACCGTTTGATCTCTTATCT
65 ATTGCAGCAATTCGATCTTTTACCCCGAACTTGGAGCAAATCACCAACAG-TCAATCTCTTACCT
51659 CGAGCCTGGGGCAGATT-A-CCATGA
129 CGAGCCTGGGGCAGATTCAGCCATGA
* * * * * * **
51683 GTCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCTATTCGATCTCTTACCCCGAGCTTGGGG
1 G---ATCTTTTACCCAGAGCTTGGGGCAGATCACATC-AACCGATCTCTTACCCCGAGCTTGGGG
51748 CAAATCACCA
Statistics
Matches: 180, Mismatches: 33, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
153 6 0.03
154 1 0.01
155 7 0.04
156 166 0.92
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (154 bp):
GATCTTTTACCCAGAGCTTGGGGCAGATCACATCAACCGATCTCTTACCCCGAGCTTGGGGTAGA
TTGCAGCAATTCGATCTTTTACCCCGAACTTGGAGCAAATCACCAACAGTCAATCTCTTACCTCG
AGCCTGGGGCAGATTCAGCCATGA
Found at i:51769 original size:117 final size:117
Alignment explanation
Indices: 51543--51792 Score: 284
Period size: 117 Copynumber: 2.1 Consensus size: 117
51533 CTTTTAATCA
* * * * **
51543 GAGCTTGGGGCAGATCACCATCAACCGATCTCTTACCCCGAGCTTGGGGTAGATTGTAGCCATTC
1 GAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATTC
* * ** ** * *
51608 GATCTTTTACCCCGAACTTGGGGCAAATTACAACCGTTTGATCTCTTATCTC
66 GATCTCTTACCCCGAACTTGGGGCAAATCACAACCAATCAATCTCTTACCCC
* * * ** *
51660 GAGCCTGGGGCAGATTACCATGAGTCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCTATTC
1 GAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATTC
* * *
51725 GATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAATCAATCTCTTACCCC
66 GATCTCTTACCCCGAACTTGGGGCAAATCACAACCAATCAATCTCTTACCCC
*
51777 AAGCTTGGGGCAGATC
1 GAGCTTGGGGCAGATC
51793 GCAGTCATTC
Statistics
Matches: 107, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
117 107 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (117 bp):
GAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCCATTC
GATCTCTTACCCCGAACTTGGGGCAAATCACAACCAATCAATCTCTTACCCC
Found at i:51814 original size:78 final size:77
Alignment explanation
Indices: 51647--51932 Score: 270
Period size: 78 Copynumber: 3.7 Consensus size: 77
51637 ACAACCGTTT
* * * * * * * *
51647 GATCTCTTATCTCGAGCCTGGGGCAGATTACCATGAGTCAATCTCTTACCCCGAGCCTAGGGCAG
1 GATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAATCAATCTCTTACCCCGAGCCTGGGGCAG
*
51712 ATTACAGCTATTC
66 ATTGCAGC-ATTC
* *
51725 GATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAATCAATCTCTTACCCCAAGCTTGGGGCAG
1 GATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAATCAATCTCTTACCCCGAGCCTGGGGCAG
*
51790 ATCGCAGTCATTC
66 ATTGCAG-CATTC
* ** * * * * * * *
51803 GATCTTTTACCCTAAGCTTGGGGCAAATCACTATCAGTAAATCTCTTACCTCGATCCTGAGACAG
1 GATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAATCAATCTCTTACCCCGAGCCTGGGGCAG
* * *
51868 ATTGCAACCGTTT
66 ATTGC-AGCATTC
* * * *
51881 GATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAACCAATCTC--ACCCCGA
1 GATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAATCAATCTCTTACCCCGA
51933 TCATGGGGTA
Statistics
Matches: 167, Mismatches: 39, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
76 6 0.04
78 159 0.95
79 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (77 bp):
GATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAATCAATCTCTTACCCCGAGCCTGGGGCAG
ATTGCAGCATTC
Found at i:51852 original size:39 final size:38
Alignment explanation
Indices: 51684--51852 Score: 149
Period size: 39 Copynumber: 4.3 Consensus size: 38
51674 TTACCATGAG
* * * * * * *
51684 TCAATCTCTTACCCCGAGCCTAGGGCAGATTACAGCTAT
1 TCAATCTCTTACCCCAAGCTTGGGGCAAATCACATC-AA
* *
51723 TCGATCTCTTACCCCGAGCTTGGGGCAAATCACCATCAA
1 TCAATCTCTTACCCCAAGCTTGGGGCAAATCA-CATCAA
* * *
51762 TCAATCTCTTACCCCAAGCTTGGGGCAGATCGCAGTCAT
1 TCAATCTCTTACCCCAAGCTTGGGGCAAATCACA-TCAA
* * * *
51801 TCGATCTTTTACCCTAAGCTTGGGGCAAATCACTATCAG
1 TCAATCTCTTACCCCAAGCTTGGGGCAAATCAC-ATCAA
*
51840 TAAATCTCTTACC
1 TCAATCTCTTACC
51853 TCGATCCTGA
Statistics
Matches: 106, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
38 2 0.02
39 100 0.94
40 4 0.04
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (38 bp):
TCAATCTCTTACCCCAAGCTTGGGGCAAATCACATCAA
Found at i:52460 original size:6 final size:6
Alignment explanation
Indices: 52422--52501 Score: 60
Period size: 6 Copynumber: 13.8 Consensus size: 6
52412 GGAACCTAAT
* * * *
52422 TTTAAA TTTTAAA TTTATA TTT--A TGTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
52468 TTTAAA TTT-AT TTTAAA TTAAAA CTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
52502 TTAAAAATGT
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
4 3 0.05
5 8 0.14
6 39 0.70
7 6 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:52473 original size:17 final size:17
Alignment explanation
Indices: 52427--52486 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
52417 CTAATTTTAA
*
52427 ATTTTAAATTTATATTT
1 ATTTTAAATTTAAATTT
* *
52444 A-TGTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
52460 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
52477 ATTTTAAATT
1 ATTTTAAATT
52487 AAAACTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 13 0.35
17 24 0.65
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:54300 original size:29 final size:30
Alignment explanation
Indices: 54256--54727 Score: 311
Period size: 30 Copynumber: 15.7 Consensus size: 30
54246 CTGAATTGTC
* *
54256 CAAAAATCATATTTTTACCCTTAAACTTTT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* * *
54286 CTAAAATTACATTTTAACACC-TAGACTTTT
1 CAAAAATTACATTTTTAC-CCTTAAACTTTT
* * * **
54316 CCAAAATCACATTTTAACCCTCGAA--TTT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* * *
54344 CTAGAAAATTATA-TTTTACCCCTAAACTTCT
1 C-A-AAAATTACATTTTTACCCTTAAACTTTT
* ***
54375 CAAAAATTACATTTTTGCCCACGAAC-TTT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
** *
54404 CAAAAATTACATTTTTACCCTCGAAC-TTC
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* ** *
54433 CAATAATTACA-TTTTACCCTCGAATTTCCTGAACAT
1 CAAAAATTACATTTTTACCCTTAAACTT--T-----T
* *
54469 CCAAAAATTATATTTTTGCCCTTAAACTTTT
1 -CAAAAATTACATTTTTACCCTTAAACTTTT
* *
54500 CAAAAATTACATTTTTTGCCCATAAACTTTT
1 CAAAAATTACA-TTTTTACCCTTAAACTTTT
** *
54531 CAAAAATTACATTTTTACCCTCGAACTTCT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* *
54561 -AAAAATTACATTTTTACCCTCAAACTTCT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
** *
54590 CAAAAATTACATTTTTTGCCTCAAAACTTTT
1 CAAAAATTACATTTTTACCCT-TAAACTTTT
* *
54621 -AAAAATTATATTTTTACCCTTAAAC-TTC
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* * **
54649 CAAAAATCACATTTTTATCC-TAAGTTTTT
1 CAAAAATTACATTTTTACCCTTAAACTTTT
* * *
54678 CCAAAATGACATTTTTACCCCTAAAAC-TTT
1 CAAAAATTACATTTTTA-CCCTTAAACTTTT
* *
54708 CCAAAATTACATTTTAACCC
1 CAAAAATTACATTTTTACCC
54728 CGAACTCTCC
Statistics
Matches: 351, Mismatches: 67, Indels: 49
0.75 0.14 0.10
Matches are distributed among these distances:
28 22 0.06
29 126 0.36
30 136 0.39
31 45 0.13
36 1 0.00
37 9 0.03
38 12 0.03
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
CAAAAATTACATTTTTACCCTTAAACTTTT
Found at i:54420 original size:59 final size:59
Alignment explanation
Indices: 54256--54728 Score: 273
Period size: 59 Copynumber: 7.8 Consensus size: 59
54246 CTGAATTGTC
* * ** * * * * *
54256 CAAAAATCATATTTTTACCCTTAAACTTTTCTAAAATTACATTTTAACACCTAGACTTTT
1 CAAAAATTACATTTTTACCCACAAAC-TTTCAAAAATTACATTTTTACCCCTAAACTTCT
* * * * * *
54316 CCAAAATCACATTTTAACCCTCGAA-TTTCTAGAAAATTATA-TTTTACCCCTAAACTTCT
1 CAAAAATTACATTTTTACCCACAAACTTTC-A-AAAATTACATTTTTACCCCTAAACTTCT
* * *
54375 CAAAAATTACATTTTTGCCCACGAACTTTCAAAAATTACATTTTTA-CCCTCGAACTTC-
1 CAAAAATTACATTTTTACCCACAAACTTTCAAAAATTACATTTTTACCCCT-AAACTTCT
* * * * * * *
54433 CAATAATTACA-TTTTACCCTCGAATTTCCTGAACATCCAAAAATTATATTTTTGCCCTTAAACT
1 CAAAAATTACATTTTTA-CC-C--A----C-AAACTTTCAAAAATTACATTTTTACCCCTAAACT
*
54497 TTT
57 TCT
* * *
54500 CAAAAATTACATTTTTTGCCCATAAACTTTTCAAAAATTACATTTTTA-CCCTCGAACTTCT
1 CAAAAATTACA-TTTTTACCCACAAAC-TTTCAAAAATTACATTTTTACCCCT-AAACTTCT
* * * *
54561 -AAAAATTACATTTTTACCCTCAAACTTCTCAAAAATTACATTTTTTGCCTCAAAACTT-T
1 CAAAAATTACATTTTTACCCACAAACTT-TCAAAAATTACA-TTTTTACCCCTAAACTTCT
* * ** * * * ** *
54620 TAAAAATTATATTTTTACCCTTAAACTTCCAAAAATCACATTTTTA-TCCTAAGTTTTT
1 CAAAAATTACATTTTTACCCACAAACTTTCAAAAATTACATTTTTACCCCTAAACTTCT
* * * *
54678 CCAAAATGACATTTTTACCC-CTAAAACTTTCCAAAATTACATTTTAACCCC
1 CAAAAATTACATTTTTACCCAC--AAACTTTCAAAAATTACATTTTTACCCC
54729 GAACTCTCCA
Statistics
Matches: 320, Mismatches: 65, Indels: 56
0.73 0.15 0.13
Matches are distributed among these distances:
57 9 0.03
58 52 0.16
59 102 0.32
60 85 0.27
61 25 0.08
65 2 0.01
66 25 0.08
67 14 0.04
68 2 0.01
69 4 0.01
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCACAAACTTTCAAAAATTACATTTTTACCCCTAAACTTCT
Found at i:55179 original size:97 final size:96
Alignment explanation
Indices: 55008--55297 Score: 427
Period size: 97 Copynumber: 3.0 Consensus size: 96
54998 AAAATATTTA
* * * *
55008 AAATTGAGGCAATATTCATTTATTTCGGGTTTTTAAAATTTGTGCCTTAATTTACTAGGCACGAT
1 AAATCGAGGCAATATTCATTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA-
55073 TTTTCTTCAAATCGGGATAATCGAATACCCTT
65 TTTTCTTCAAATCGGGATAATCGAATACCCTT
* * *
55105 AAATCGAGGCAATATTCTTTTATCTCGGGTTTTGAAAATTTGTGTCTTAACTTACTAGGCACAAC
1 AAATCGAGGCAATATTCATTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA-
*
55170 TTTTCTTCAAATCGGGATAATCAAATACCCTT
65 TTTTCTTCAAATCGGGATAATCGAATACCCTT
* * * * * *
55202 AAATCAAGGCAGTATTCCTTTATCTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAAGCGCGAT
1 AAATCGAGGCAATATTCATTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
*
55267 TTTTTTCAAATCGGGATAATCGAATACCCTT
66 TTTCTTCAAATCGGGATAATCGAATACCCTT
55298 TTTCAAGGTT
Statistics
Matches: 174, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
96 30 0.17
97 144 0.83
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (96 bp):
AAATCGAGGCAATATTCATTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
TTTCTTCAAATCGGGATAATCGAATACCCTT
Found at i:61840 original size:17 final size:17
Alignment explanation
Indices: 61818--61863 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
61808 TTAAATGTGT
*
61818 AATTATCATT-TTTATTA
1 AATTATAATTATTT-TTA
61835 AATTATAATTATTTTTA
1 AATTATAATTATTTTTA
61852 AATGTATAATTA
1 AAT-TATAATTA
61864 CTACCATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTATAATTATTTTTA
Found at i:62890 original size:5 final size:5
Alignment explanation
Indices: 62880--62904 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62870 TCAAAGACTT
62880 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
62905 TAAAACAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:64000 original size:2 final size:2
Alignment explanation
Indices: 63995--64033 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
63985 ATATAAGAGA
63995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64034 GAAATGTGAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65330 original size:19 final size:20
Alignment explanation
Indices: 65308--65348 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
65298 ATATTTTTTA
65308 ATATTTACA-TTTATA-TAAT
1 ATATTTA-ATTTTATATTAAT
65327 ATATTTAATTTTATATTAAT
1 ATATTTAATTTTATATTAAT
65347 AT
1 AT
65349 TTAAAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.05
19 13 0.65
20 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTAATTTTATATTAAT
Found at i:69878 original size:28 final size:28
Alignment explanation
Indices: 69824--69878 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
69814 TTCATTATAT
* *
69824 ATATATTTATTTTAATTATTTCTACTTC
1 ATATATTTATTTAAATTATTTCAACTTC
*
69852 ATAT-TTTATTTAAATTTATTTGAACTT
1 ATATATTTATTTAAA-TTATTTCAACTT
69879 ATAATTGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (28 bp):
ATATATTTATTTAAATTATTTCAACTTC
Found at i:71243 original size:40 final size:40
Alignment explanation
Indices: 71198--71282 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 40
71188 GGCTGAAGCT
*
71198 ATTTTGACTT-GTTTGAAAAATATTTTGA-A-GTGTTAAAATG
1 ATTTTGACTTAG-TT-AAAAATATTTTGACATGT-TTAAAATC
*
71238 ATTTTGACTTAGTTAAAATTATTTTGACATGTTTAAAATC
1 ATTTTGACTTAGTTAAAAATATTTTGACATGTTTAAAATC
71278 ATTTT
1 ATTTT
71283 AATTTGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
39 12 0.30
40 25 0.62
41 3 0.08
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (40 bp):
ATTTTGACTTAGTTAAAAATATTTTGACATGTTTAAAATC
Found at i:71273 original size:20 final size:20
Alignment explanation
Indices: 71197--71282 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
71187 GGGCTGAAGC
* *
71197 TATTTTGACTTGTTTGAAAAA
1 TATTTTGACATGTTT-AAAAT
71218 TATTTTGA-A-GTGTTAAAAT
1 TATTTTGACATGT-TTAAAAT
* *
71237 GATTTTGACTTAG-TTAAAAT
1 TATTTTGACAT-GTTTAAAAT
71257 TATTTTGACATGTTTAAAAT
1 TATTTTGACATGTTTAAAAT
*
71277 CATTTT
1 TATTTT
71283 AATTTGATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
19 14 0.26
20 30 0.57
21 8 0.15
22 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.49
Consensus pattern (20 bp):
TATTTTGACATGTTTAAAAT
Found at i:71331 original size:12 final size:12
Alignment explanation
Indices: 71314--71338 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71304 CAAACTTTTC
71314 TAAGAGTTTAAA
1 TAAGAGTTTAAA
71326 TAAGAGTTTAAA
1 TAAGAGTTTAAA
71338 T
1 T
71339 TTTATCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TAAGAGTTTAAA
Found at i:76251 original size:37 final size:37
Alignment explanation
Indices: 76210--76287 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
76200 AACTCATAGT
76210 TCTAATGGGTCCAAAAAGGTCAATATGAATAAGTTGG
1 TCTAATGGGTCCAAAAAGGTCAATATGAATAAGTTGG
76247 TCTAATGGGTCCAAAAAGGTCAATATGAATAAGTTGG
1 TCTAATGGGTCCAAAAAGGTCAATATGAATAAGTTGG
76284 TCTA
1 TCTA
76288 CTCTGGATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (37 bp):
TCTAATGGGTCCAAAAAGGTCAATATGAATAAGTTGG
Found at i:80196 original size:21 final size:21
Alignment explanation
Indices: 80172--80213 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
80162 GCTTCATGCT
80172 GGTGTTTTCAAGCTTTGTGCC
1 GGTGTTTTCAAGCTTTGTGCC
*
80193 GGTGTTTTCAGGCTTTGTGCC
1 GGTGTTTTCAAGCTTTGTGCC
80214 TAGTAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.19, G:0.31, T:0.43
Consensus pattern (21 bp):
GGTGTTTTCAAGCTTTGTGCC
Found at i:80304 original size:37 final size:37
Alignment explanation
Indices: 80183--80307 Score: 171
Period size: 37 Copynumber: 3.4 Consensus size: 37
80173 GTGTTTTCAA
*
80183 GCTTTGTGCCGGTGTTTTCAGGCTTTGTGCCTAGTAG
1 GCTTTGTGCCAGTGTTTTCAGGCTTTGTGCCTAGTAG
* * *
80220 G-TTTCGTGCCGGTGTTTTTAGGCTTTGTGCCTGGTAG
1 GCTTT-GTGCCAGTGTTTTCAGGCTTTGTGCCTAGTAG
* * *
80257 GCTTCGTGCCAGTGTTTTCAGGCTATGTGCCTAGCAG
1 GCTTTGTGCCAGTGTTTTCAGGCTTTGTGCCTAGTAG
80294 GCTTTGTGCCAGTG
1 GCTTTGTGCCAGTG
80308 ATCCAAGAGC
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
36 3 0.04
37 72 0.94
38 2 0.03
ACGTcount: A:0.09, C:0.20, G:0.33, T:0.38
Consensus pattern (37 bp):
GCTTTGTGCCAGTGTTTTCAGGCTTTGTGCCTAGTAG
Found at i:82732 original size:27 final size:26
Alignment explanation
Indices: 82694--82793 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 26
82684 GAAGGAAAGA
82694 AATGGCGAACTCTTAAAGAGCATTATG
1 AATGGCGAACTC-TAAAGAGCATTATG
* *
82721 AATGGCGAACTCTAAAGGAACATATACG
1 AATGGCGAACTCTAAA-GAGCAT-TATG
* **
82749 AATGGTGAACTCTGAAAGAGTGTTATG
1 AATGGCGAACTCT-AAAGAGCATTATG
82776 AATGGCGAACTCTAAAGA
1 AATGGCGAACTCTAAAGA
82794 AACAAATAGG
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
26 9 0.15
27 32 0.52
28 18 0.29
29 3 0.05
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (26 bp):
AATGGCGAACTCTAAAGAGCATTATG
Found at i:82775 original size:55 final size:55
Alignment explanation
Indices: 82694--82797 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
82684 GAAGGAAAGA
* *
82694 AATGGCGAACTCTTAAAGAGCATTATGAATGGCGAACTCTAAAGGAACATATACG
1 AATGGCGAACTCTGAAAGAGCATTATGAATGGCGAACTCTAAAGAAACATATACG
* **
82749 AATGGTGAACTCTGAAAGAGTGTTATGAATGGCGAACTCTAAAGAAACA
1 AATGGCGAACTCTGAAAGAGCATTATGAATGGCGAACTCTAAAGAAACA
82798 AATAGGCGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.22
Consensus pattern (55 bp):
AATGGCGAACTCTGAAAGAGCATTATGAATGGCGAACTCTAAAGAAACATATACG
Found at i:82814 original size:55 final size:54
Alignment explanation
Indices: 82694--82820 Score: 155
Period size: 55 Copynumber: 2.3 Consensus size: 54
82684 GAAGGAAAGA
* * *
82694 AATGGCGAACTCTTAAAGAGCATTATGAATGGCGAACTCTAAAGGAACATATACG
1 AATGGGGAACTC-TAAAGAGCATTATGAATGGCGAACTCTAAAGAAACAAATACG
* ** *
82749 AATGGTGAACTCTGAAAGAGTGTTATGAATGGCGAACTCTAAAGAAACAAATAGG
1 AATGGGGAACTCT-AAAGAGCATTATGAATGGCGAACTCTAAAGAAACAAATACG
**
82804 CGTGGGGAACTCTAAAG
1 AATGGGGAACTCTAAAG
82821 GAAGAGCACT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
54 5 0.08
55 57 0.92
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (54 bp):
AATGGGGAACTCTAAAGAGCATTATGAATGGCGAACTCTAAAGAAACAAATACG
Found at i:84476 original size:21 final size:21
Alignment explanation
Indices: 84452--84491 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
84442 TCATAATCTA
84452 AAAAGTATATTAAAAATTAAT
1 AAAAGTATATTAAAAATTAAT
* *
84473 AAAAGTATTTTTAAAATTA
1 AAAAGTATATTAAAAATTA
84492 TTTCCATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAAGTATATTAAAAATTAAT
Found at i:85080 original size:264 final size:264
Alignment explanation
Indices: 84610--85139 Score: 1033
Period size: 264 Copynumber: 2.0 Consensus size: 264
84600 TTGGGATTCT
84610 ATGAAATGAAATTTAAGAACATTTTTATTTTTTCTTATTTTATTCTTTTTCTAGGTATTCCTTTC
1 ATGAAATGAAATTTAAGAACATTTTTATTTTTTCTTATTTTATTCTTTTTCTAGGTATTCCTTTC
84675 TTCTTCTTTCATCCTCTCGTCATTTTACTTTTTTCTTTTTTTAATTCATTCAACATTTCCAAATT
66 TTCTTCTTTCATCCTCTCGTCATTTTACTTTTTTCTTTTTTTAATTCATTCAACATTTCCAAATT
*
84740 CATTCAACATTTCTAGGTTTCTTTGAAAAGAAATTTAAGAACATTTCTAAGCCGCGCAACTGTAA
131 CATTCAACATTTCTAGGTTTCTTTGAAAAGAAATTTAAGAACATTTCTAAGCCGCGCAACTATAA
*
84805 ATATGAAGCAAGTTAAATCTGATTAAATCATGCAAAAACAAACAAAACATTTATAATCAGAATAT
196 ATATGAAGCAAGTTAAATCTAATTAAATCATGCAAAAACAAACAAAACATTTATAATCAGAATAT
84870 CTCC
261 CTCC
84874 ATGAAATGAAATTTAAGAACATTTTTATTTTTTCTTATTTTATTCTTTTTCTAGGTATTCCTTTC
1 ATGAAATGAAATTTAAGAACATTTTTATTTTTTCTTATTTTATTCTTTTTCTAGGTATTCCTTTC
*
84939 TTCTTCTTTCTTCCTCTCGTCATTTTACTTTTTTCTTTTTTTAATTCATTCAACATTTCCAAATT
66 TTCTTCTTTCATCCTCTCGTCATTTTACTTTTTTCTTTTTTTAATTCATTCAACATTTCCAAATT
85004 CATTCAACATTTCTAGGTTTCTTTGAAAAGAAATTTAAGAACATTTCTAAGCCGCGCAACTATAA
131 CATTCAACATTTCTAGGTTTCTTTGAAAAGAAATTTAAGAACATTTCTAAGCCGCGCAACTATAA
85069 ATATGAAGCAAGTTAAATCTAATTAAATCATGCAAAAACAAACAAAACATTTATAATCAGAATAT
196 ATATGAAGCAAGTTAAATCTAATTAAATCATGCAAAAACAAACAAAACATTTATAATCAGAATAT
85134 CTCC
261 CTCC
85138 AT
1 AT
85140 TAATGATTAA
Statistics
Matches: 263, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
264 263 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.43
Consensus pattern (264 bp):
ATGAAATGAAATTTAAGAACATTTTTATTTTTTCTTATTTTATTCTTTTTCTAGGTATTCCTTTC
TTCTTCTTTCATCCTCTCGTCATTTTACTTTTTTCTTTTTTTAATTCATTCAACATTTCCAAATT
CATTCAACATTTCTAGGTTTCTTTGAAAAGAAATTTAAGAACATTTCTAAGCCGCGCAACTATAA
ATATGAAGCAAGTTAAATCTAATTAAATCATGCAAAAACAAACAAAACATTTATAATCAGAATAT
CTCC
Found at i:90037 original size:22 final size:22
Alignment explanation
Indices: 90012--90053 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
90002 AATGAAGAAT
90012 AAAACCTAAG-AAAACTAAAGAG
1 AAAA-CTAAGCAAAACTAAAGAG
*
90034 AAAACTAAGCTAAACTAAAG
1 AAAACTAAGCAAAACTAAAG
90054 CTAATGTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12
Consensus pattern (22 bp):
AAAACTAAGCAAAACTAAAGAG
Found at i:94458 original size:5 final size:5
Alignment explanation
Indices: 94448--94485 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
94438 ATGAACAATA
94448 ACCAC ACCAC ACCAC ACCAC ACCAC ACCAC ACCAC ACC
1 ACCAC ACCAC ACCAC ACCAC ACCAC ACCAC ACCAC ACC
94486 CATGGTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.61, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCAC
Found at i:105091 original size:29 final size:28
Alignment explanation
Indices: 104996--105091 Score: 95
Period size: 29 Copynumber: 3.4 Consensus size: 28
104986 AAGGAATATT
* * *
104996 TTATCG-TATTATTTAGCACTTCGGAGC
1 TTATCGTTATTATTTTGCACTTTGGTGC
* * * *
105023 TTATCGTTGTAAAATTTGCACTTTAGTGC
1 TTATCGTTAT-TATTTTGCACTTTGGTGC
*
105052 TTATCATTATTATTTTTGCACTTTGGTGC
1 TTATCGTTATTA-TTTTGCACTTTGGTGC
105081 TTATCGTTATT
1 TTATCGTTATT
105092 TGCACTTTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
27 6 0.11
28 3 0.06
29 44 0.83
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.49
Consensus pattern (28 bp):
TTATCGTTATTATTTTGCACTTTGGTGC
Found at i:105323 original size:5 final size:5
Alignment explanation
Indices: 105313--105337 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
105303 AATGAATATA
105313 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
105338 TATATAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:105903 original size:18 final size:18
Alignment explanation
Indices: 105869--105903 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105859 AGAGAGTAGT
*
105869 TTTGGTATCGATTTTGAC
1 TTTGGTATCGATATTGAC
*
105887 TTTGGTATTGATATTGA
1 TTTGGTATCGATATTGA
105904 AGGCCCGGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.51
Consensus pattern (18 bp):
TTTGGTATCGATATTGAC
Found at i:109448 original size:31 final size:30
Alignment explanation
Indices: 109412--109493 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
109402 GATTAAATCA
109412 AAATTAAAGCTTCA-AGTATACATTTGAACC
1 AAATTAAAGCTTCACAGTATACATTT-AACC
* *
109442 ACAATTAGAGCTTCACATGTATA-ATTTCACC
1 A-AATTAAAGCTTCACA-GTATACATTTAACC
*
109473 AAATTAAAG-TTCATA-TATACA
1 AAATTAAAGCTTCACAGTATACA
109494 ATTACACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
27 4 0.09
28 1 0.02
29 5 0.11
30 8 0.18
31 16 0.36
32 5 0.11
33 5 0.11
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (30 bp):
AAATTAAAGCTTCACAGTATACATTTAACC
Found at i:113775 original size:2 final size:2
Alignment explanation
Indices: 113768--113805 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
113758 TTTTAATTTC
113768 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
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.