Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014823.1 Corchorus olitorius cultivar O-4 contig14856, 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: 138161
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1766 original size:25 final size:25
Alignment explanation
Indices: 1732--1779 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1722 GTATTCAACG
*
1732 CATGCAAGTTTATGAAATTTGAACT
1 CATGCAAGTTTATGAAACTTGAACT
1757 CATGCAAGTTTATGAAACTTGAA
1 CATGCAAGTTTATGAAACTTGAA
1780 TATTATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (25 bp):
CATGCAAGTTTATGAAACTTGAACT
Found at i:2623 original size:3 final size:3
Alignment explanation
Indices: 2615--2675 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
2605 ATATCTACTA
2615 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2663 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
2676 TATGATTTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3914 original size:21 final size:21
Alignment explanation
Indices: 3888--3995 Score: 67
Period size: 22 Copynumber: 5.0 Consensus size: 21
3878 TCTTAGACAG
*
3888 AGGTTATCAAAAATCATAGGA
1 AGGTTATCAAAATTCATAGGA
* *
3909 AGGTTA-CAAATTTTAATAGGA
1 AGGTTATCAAA-ATTCATAGGA
* **
3930 AGGTTTATTAAAACTTCATAGTT
1 AGG-TTATCAAAA-TTCATAGGA
*
3953 AGGTTATCAAAGTTTCATATGG-
1 AGGTTATCAAA-ATTCATA-GGA
* *
3975 AGTTTATCACAATTTCATAGG
1 AGGTTATCA-AAATTCATAGG
3996 TAAATCATCA
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
20 4 0.06
21 18 0.26
22 31 0.46
23 15 0.22
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTCATAGGA
Found at i:3969 original size:22 final size:22
Alignment explanation
Indices: 3934--4059 Score: 96
Period size: 22 Copynumber: 5.7 Consensus size: 22
3924 ATAGGAAGGT
* * *
3934 TTATTAAAACTTCATAGTTAGG
1 TTATCAAAATTTCATAGTTAGA
* * *
3956 TTATCAAAGTTTCATA-TGGAGT
1 TTATCAAAATTTCATAGT-TAGA
* * *
3978 TTATCACAATTTCATAGGTAAA
1 TTATCAAAATTTCATAGTTAGA
*
4000 TCATCAAAATTTCATAGTGT-GA
1 TTATCAAAATTTCATAGT-TAGA
* *
4022 TTATCAAAATTTAATAGGGTAG-
1 TTATCAAAATTTCATA-GTTAGA
4044 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
4060 AAAATATTCA
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
21 1 0.01
22 76 0.95
23 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTTAGA
Found at i:3992 original size:44 final size:43
Alignment explanation
Indices: 3934--4059 Score: 121
Period size: 44 Copynumber: 2.9 Consensus size: 43
3924 ATAGGAAGGT
* * * *
3934 TTATTAAAACTTCATAGTTAGGTTATCAAAGTTTCATA-TG-GA
1 TTATCAAAATTTCATAGGTA-GTTATCAAAATTTCATAGTGTGA
* * *
3976 GTTTATCACAATTTCATAGGTAAATCATCAAAATTTCATAGTGTGA
1 --TTATCAAAATTTCATAGGT-AGTTATCAAAATTTCATAGTGTGA
*
4022 TTATCAAAATTTAATAGGGTAGTTATCAAAATTTCATA
1 TTATCAAAATTTCATA-GGTAGTTATCAAAATTTCATA
4060 AAAATATTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
44 59 0.88
45 6 0.09
46 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGTAGTTATCAAAATTTCATAGTGTGA
Found at i:5398 original size:34 final size:31
Alignment explanation
Indices: 5301--5508 Score: 207
Period size: 34 Copynumber: 6.6 Consensus size: 31
5291 TTAAATTTAA
* **
5301 TTGACACTAGAAGTTGTCATATTAAATTATC
1 TTGACACCAGAAGTTGTCATACAAAATTATC
* *
5332 TTGACACCAAAAGTTGTCAT-GAAAATTA--
1 TTGACACCAGAAGTTGTCATACAAAATTATC
5360 TTGACACCAGAAGTTGTCATACCAAATTATTATC
1 TTGACACCAGAAGTTGTCATA-CAAA--ATTATC
*
5394 TTGACACCAGAAGTTGTCAT-GAAAATTA--
1 TTGACACCAGAAGTTGTCATACAAAATTATC
5422 TTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATA-CAAA--ATTATC
*
5456 TTGACACCAGAAGTTGTCATGCTGAGGAAATTA--
1 TTGACACCAGAAGTTGTCATAC--A--AAATTATC
5489 TTGACACCAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCAT
5509 CCCAAGATTG
Statistics
Matches: 152, Mismatches: 9, Indels: 30
0.80 0.05 0.16
Matches are distributed among these distances:
28 39 0.26
30 16 0.11
31 18 0.12
32 11 0.07
33 21 0.14
34 40 0.26
35 5 0.03
37 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (31 bp):
TTGACACCAGAAGTTGTCATACAAAATTATC
Found at i:5416 original size:62 final size:62
Alignment explanation
Indices: 5300--5513 Score: 308
Period size: 62 Copynumber: 3.4 Consensus size: 62
5290 TTTAAATTTA
* ** *
5300 ATTGACACTAGAAGTTGTCATA-TTAA--ATTATCTTGACACCAAAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
5359 ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
*
5421 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCA---TGA--AAA
5486 TT
61 TT
*
5488 ATTGACACCAGAAGTTGTCATCCCAA
1 ATTGACACCAGAAGTTGTCATACCAA
5514 GATTGGAATT
Statistics
Matches: 140, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
59 21 0.15
60 2 0.01
62 85 0.61
65 3 0.02
67 29 0.21
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (62 bp):
ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
Found at i:23260 original size:45 final size:42
Alignment explanation
Indices: 23209--23302 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
23199 GCAACAATTA
* *
23209 AATATTAGTTTTATTTTGATAAATTATCTAGAGATTGAGGAGTAG
1 AATATTAGCTTTATTTTGATAAATTACCTAGAGA-T--GGAGTAG
*
23254 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATAAATTACCTAGAGATGGAGTAG
23296 AAT-TTAG
1 AATATTAG
23303 ATAATGCACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.22
44 1 0.02
45 31 0.67
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.40
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATAAATTACCTAGAGATGGAGTAG
Found at i:27856 original size:23 final size:24
Alignment explanation
Indices: 27802--27857 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
27792 TTTCATGTTC
*
27802 CAATAT-AGAAATCTTGATAACCA
1 CAATATGAAAAATCTTGATAACCA
* * *
27825 CATTGTGAAAAAT-TTGATAACCT
1 CAATATGAAAAATCTTGATAACCA
27848 CAATATGAAA
1 CAATATGAAA
27858 TTTCGATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (24 bp):
CAATATGAAAAATCTTGATAACCA
Found at i:27924 original size:22 final size:22
Alignment explanation
Indices: 27805--28044 Score: 94
Period size: 22 Copynumber: 10.9 Consensus size: 22
27795 CATGTTCCAA
* * *
27805 TATAGAAATCTTGATAACCACAT
1 TATA-AAATTTTGATAACCTCAG
* * *
27828 TGTGAAAAATTTGATAACCTCAA
1 TAT-AAAATTTTGATAACCTCAG
* * * **
27851 TATGAAATTTCGATAATCTCCC
1 TATAAAATTTTGATAACCTCAG
* * * *
27873 TATGAAAA-TTTGTTAATCACAT
1 TAT-AAAATTTTGATAACCTCAG
* * *
27895 TGTGAAATTTTGATAACCTGAG
1 TATAAAATTTTGATAACCTCAG
* * **
27917 TGTAAAATTTTGATAATCTCCT
1 TATAAAATTTTGATAACCTCAG
* *
27939 TATAAAATTTTGATAACCACAC
1 TATAAAATTTTGATAACCTCAG
* *
27961 TATAAAA--TTGGTAACCGC-G
1 TATAAAATTTTGATAACCTCAG
* *
27980 CTATGAAAATTTTGATGACCTC-C
1 -TAT-AAAATTTTGATAACCTCAG
* *
28003 TCATAAAATTTTGATAACCACAC
1 T-ATAAAATTTTGATAACCTCAG
* **
28026 TATGAAATTTCAATAACCT
1 TATAAAATTTTGATAACCT
28045 TCTTATGAGA
Statistics
Matches: 160, Mismatches: 48, Indels: 19
0.70 0.21 0.08
Matches are distributed among these distances:
20 12 0.08
21 7 0.04
22 107 0.67
23 33 0.21
24 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCAG
Found at i:27932 original size:66 final size:66
Alignment explanation
Indices: 27805--27948 Score: 173
Period size: 66 Copynumber: 2.2 Consensus size: 66
27795 CATGTTCCAA
* * *
27805 TATAGAAATCTTGATAACCACATTGTGAAAAATTTGATAACCTCAATATGAAATTTCGATAATCT
1 TATA-AAAT-TTGTTAATCACATTGTGAAAAATTTGATAACCTCAATATAAAATTTCGATAATCT
27870 CCC
64 CCC
* * * * *
27873 TATGAAAATTTGTTAATCACATTGTG-AAATTTTGATAACCTGAGTGTAAAATTTTGATAATCTC
1 TAT-AAAATTTGTTAATCACATTGTGAAAAATTTGATAACCTCAATATAAAATTTCGATAATCTC
*
27937 CT
65 CC
27939 TATAAAATTT
1 TATAAAATTT
27949 TGATAACCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
65 7 0.11
66 36 0.55
67 15 0.23
68 7 0.11
69 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (66 bp):
TATAAAATTTGTTAATCACATTGTGAAAAATTTGATAACCTCAATATAAAATTTCGATAATCTCC
C
Found at i:27967 original size:44 final size:43
Alignment explanation
Indices: 27833--28044 Score: 131
Period size: 44 Copynumber: 4.9 Consensus size: 43
27823 CACATTGTGA
* * * * *
27833 AAAATTTGATAACCTCAATATGAAATTTCGATAATCTCCCTAT
1 AAAATTTGATAACCTCATTATAAAATTTTGATAACCTCACTAT
* * * * * * * *
27876 GAAAATTTGTTAATCACATTGTGAAATTTTGATAACCTGAGTGT
1 -AAAATTTGATAACCTCATTATAAAATTTTGATAACCTCACTAT
* * *
27920 AAAATTTTGATAATCTCCTTATAAAATTTTGATAACCACACTAT
1 AAAA-TTTGATAACCTCATTATAAAATTTTGATAACCTCACTAT
* * ** *
27964 AAAA-TTGGTAACCGCGCTATGAAAATTTTGATGACCTC-CTCAT
1 AAAATTTGATAACCTCATTAT-AAAATTTTGATAACCTCACT-AT
* * * **
28007 AAAATTTTGATAACCACACTATGAAATTTCAATAACCT
1 AAAA-TTTGATAACCTCATTATAAAATTTTGATAACCT
28045 TCTTATGAGA
Statistics
Matches: 129, Mismatches: 34, Indels: 10
0.75 0.20 0.06
Matches are distributed among these distances:
42 13 0.10
43 25 0.19
44 78 0.60
45 13 0.10
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (43 bp):
AAAATTTGATAACCTCATTATAAAATTTTGATAACCTCACTAT
Found at i:28093 original size:20 final size:20
Alignment explanation
Indices: 28064--28128 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 20
28054 AATGAAACTG
*
28064 TGATATCCTCT-ATATAATTT
1 TGATAACCTCTCATA-AATTT
28084 TGATAACCTCTCCATAAATTT
1 TGATAACCTCT-CATAAATTT
*
28105 TCCATAACCTCTCTATGAAATTT
1 T-GATAACCTCTC-AT-AAATTT
28128 T
1 T
28129 TTTAACCTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 10 0.26
21 7 0.18
22 14 0.37
23 7 0.18
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.43
Consensus pattern (20 bp):
TGATAACCTCTCATAAATTT
Found at i:28114 original size:22 final size:23
Alignment explanation
Indices: 28086--28128 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
28076 TATAATTTTG
28086 ATAACCTCTCCAT-AAATTTTCC
1 ATAACCTCTCCATGAAATTTTCC
*
28108 ATAACCTCTCTATGAAATTTT
1 ATAACCTCTCCATGAAATTTT
28129 TTTAACCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.40
Consensus pattern (23 bp):
ATAACCTCTCCATGAAATTTTCC
Found at i:28149 original size:22 final size:22
Alignment explanation
Indices: 28109--28150 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28099 AAATTTTCCA
* *
28109 TAACCTCTCTATGAAATTTTTT
1 TAACCTCCCTAGGAAATTTTTT
*
28131 TAACCTCCCTAGGATATTTT
1 TAACCTCCCTAGGAAATTTT
28151 GATAGGCACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (22 bp):
TAACCTCCCTAGGAAATTTTTT
Found at i:28188 original size:25 final size:23
Alignment explanation
Indices: 28160--28285 Score: 75
Period size: 22 Copynumber: 5.6 Consensus size: 23
28150 TGATAGGCAC
28160 AAATTTTGATAACCCCCTCCCTATG
1 AAATTTTGATAA--CCCTCCCTATG
* * *
28185 AAATTTTGTTAA-CCTTCTTATG
1 AAATTTTGATAACCCTCCCTATG
* *
28207 AAATTTTGATAA--CTACACTATA
1 AAATTTTGATAACCCT-CCCTATG
* ***
28229 AAATTTCGATAA-CCTTTGTATG
1 AAATTTTGATAACCCTCCCTATG
* *
28251 AAATTTT-ATTAA-CCTCGCTAAG
1 AAATTTTGA-TAACCCTCCCTATG
28273 AAATTTTGATAAC
1 AAATTTTGATAAC
28286 TTTTTTATGA
Statistics
Matches: 78, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
21 3 0.04
22 61 0.78
23 3 0.04
25 11 0.14
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAACCCTCCCTATG
Found at i:28209 original size:22 final size:22
Alignment explanation
Indices: 28181--28372 Score: 101
Period size: 22 Copynumber: 8.7 Consensus size: 22
28171 ACCCCCTCCC
*
28181 TATGAAATTTTGTTAACCTTCT
1 TATGAAATTTTGATAACCTTCT
* *
28203 TATGAAATTTTGATAA-CTACAC
1 TATGAAATTTTGATAACCTTC-T
* *
28225 TATAAAATTTCGATAACCTT-T
1 TATGAAATTTTGATAACCTTCT
*
28246 GTATGAAATTTT-ATTAACC-TCGC
1 -TATGAAATTTTGA-TAACCTTC-T
* * *
28269 TAAGAAATTTTGATAACTTTTT
1 TATGAAATTTTGATAACCTTCT
* * **
28291 TATGAAATTTTG-TTAGCGACT
1 TATGAAATTTTGATAACCTTCT
* * *
28312 GTATGGAATTTTGATAA-CTACAC
1 -TATGAAATTTTGATAACCTTC-T
* * *
28335 TAT-AAAGTTTTGATAATCTCCA
1 TATGAAA-TTTTGATAACCTTCT
28357 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
28373 TCACAAAGAA
Statistics
Matches: 128, Mismatches: 28, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
21 10 0.08
22 106 0.83
23 12 0.09
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCT
Found at i:28244 original size:44 final size:44
Alignment explanation
Indices: 28175--28302 Score: 129
Period size: 44 Copynumber: 2.9 Consensus size: 44
28165 TTGATAACCC
* * *
28175 CCTCCCTATGAAATTTTGTTAACCTTCTTATGAAATTTTGA-TAA
1 CCTCACTATAAAATTTTGATAACCTT-TTATGAAATTTTGATTAA
*
28219 -CTACACTATAAAATTTCGATAACCTTTGTATGAAATTTT-ATTAA
1 CCT-CACTATAAAATTTTGATAACCTTT-TATGAAATTTTGATTAA
* *
28263 CCTCGCTA-AGAAATTTTGATAACTTTTTTATGAAATTTTG
1 CCTCACTATA-AAATTTTGATAAC-CTTTTATGAAATTTTG
28303 TTAGCGACTG
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
43 5 0.07
44 60 0.86
45 5 0.07
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (44 bp):
CCTCACTATAAAATTTTGATAACCTTTTATGAAATTTTGATTAA
Found at i:29881 original size:13 final size:13
Alignment explanation
Indices: 29863--29890 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29853 TATATAGTAG
29863 TAAGATAGTAAGA
1 TAAGATAGTAAGA
29876 TAAGATAGTAAGA
1 TAAGATAGTAAGA
29889 TA
1 TA
29891 GTCTATACTG
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:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (13 bp):
TAAGATAGTAAGA
Found at i:30104 original size:213 final size:213
Alignment explanation
Indices: 29829--30249 Score: 824
Period size: 213 Copynumber: 2.0 Consensus size: 213
29819 AATTTCCCAA
*
29829 TTAAAATTTTTGAGTTCGTGATTTTATATAGTAGTAAGATAGTAAGATAAGATAGTAAGATAGTC
1 TTAAAATTTTTGAGTTCGTGATTTTATATAGTAGTAAGATAATAAGATAAGATAGTAAGATAGTC
*
29894 TATACTGCATTTGGTGATATCATTAAGAACATATATTAAATGACTATGTTTACAAAATTAATTAG
66 TATACTGCATTTGCTGATATCATTAAGAACATATATTAAATGACTATGTTTACAAAATTAATTAG
29959 ATTTCTTTAGGTGATACTTGACAATTTTTGCTGCAATATCAAACTCAATCCTGATTGAAGGGATT
131 ATTTCTTTAGGTGATACTTGACAATTTTTGCTGCAATATCAAACTCAATCCTGATTGAAGGGATT
30024 GTGCTGCAAAACCTAATT
196 GTGCTGCAAAACCTAATT
30042 TTAAAATTTTTGAGTTCGTGATTTTATATAGTAGTAAGATAATAAGATAAGATAGTAAGATAGTC
1 TTAAAATTTTTGAGTTCGTGATTTTATATAGTAGTAAGATAATAAGATAAGATAGTAAGATAGTC
30107 TATACTGCATTTGCTGATATCATTAAGAACATATATTAAATGACTATGTTTACAAAATTAATTAG
66 TATACTGCATTTGCTGATATCATTAAGAACATATATTAAATGACTATGTTTACAAAATTAATTAG
30172 ATTTCTTTAGGTGATACTTGACAATTTTTGCTGCAATATCAAACTCAATCCTGATTGAAGGGATT
131 ATTTCTTTAGGTGATACTTGACAATTTTTGCTGCAATATCAAACTCAATCCTGATTGAAGGGATT
30237 GTGCTGCAAAACC
196 GTGCTGCAAAACC
30250 AGGCTCCATT
Statistics
Matches: 206, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 206 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (213 bp):
TTAAAATTTTTGAGTTCGTGATTTTATATAGTAGTAAGATAATAAGATAAGATAGTAAGATAGTC
TATACTGCATTTGCTGATATCATTAAGAACATATATTAAATGACTATGTTTACAAAATTAATTAG
ATTTCTTTAGGTGATACTTGACAATTTTTGCTGCAATATCAAACTCAATCCTGATTGAAGGGATT
GTGCTGCAAAACCTAATT
Found at i:31266 original size:12 final size:12
Alignment explanation
Indices: 31249--31285 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
31239 GTCAATGGAC
31249 TCTTTGAATCCA
1 TCTTTGAATCCA
31261 TCTTTGAATCCA
1 TCTTTGAATCCA
31273 TCTTTGAATCCA
1 TCTTTGAATCCA
31285 T
1 T
31286 TAATAAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.43
Consensus pattern (12 bp):
TCTTTGAATCCA
Found at i:32233 original size:6 final size:6
Alignment explanation
Indices: 32222--32248 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
32212 GTAGGAGCTC
32222 TGGGAT TGGGAT TGGGAT TGGGAT TGG
1 TGGGAT TGGGAT TGGGAT TGGGAT TGG
32249 ATCAGGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
TGGGAT
Found at i:39978 original size:32 final size:32
Alignment explanation
Indices: 39936--40017 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
39926 TCCAGTGATA
*
39936 TGTGCATCTCCCGCACACCTTAACAATACT-TG
1 TGTGCATCTCCCGCACACCATAACAATA-TATG
* * *
39968 TGTGCTTCTCCCGCACATCATAATAATATATG
1 TGTGCATCTCCCGCACACCATAACAATATATG
*
40000 TGTGCACCTCCCGCACAC
1 TGTGCATCTCCCGCACAC
40018 TATACATGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 1 0.02
32 41 0.98
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.28
Consensus pattern (32 bp):
TGTGCATCTCCCGCACACCATAACAATATATG
Found at i:40070 original size:29 final size:29
Alignment explanation
Indices: 39935--40161 Score: 155
Period size: 29 Copynumber: 7.7 Consensus size: 29
39925 TTCCAGTGAT
*
39935 ATGTGCATCTCCCGCACACCTTAACAATACTT-
1 ATGTGCATCTCCCGCACA-C-T-ATAATA-TTC
* *
39967 GTGTGCTTCTCCCGCACATCATAATAATATAT-
1 ATGTGCATCTCCCGCACA-C-T-ATAATAT-TC
* *
39999 GTGTGCACCTCCCGCACAC--T-ATA--C
1 ATGTGCATCTCCCGCACACTATAATATTC
* * *
40023 ATGTACATCTTCCGTACACTATAATATTC
1 ATGTGCATCTCCCGCACACTATAATATTC
40052 ATGTGCATCTCCCGCACACT-TGAATATTC
1 ATGTGCATCTCCCGCACACTAT-AATATTC
* **
40081 ATGTGCATCTGCTACACACTATATTAATATTC
1 ATGTGCATCTCCCGCACAC--TA-TAATATTC
* * * *
40113 GTGTACATCTCCCGTACACTATAATATTG
1 ATGTGCATCTCCCGCACACTATAATATTC
40142 ATGTGCATCTCCCGCACACT
1 ATGTGCATCTCCCGCACACT
40162 TTATTTATCA
Statistics
Matches: 155, Mismatches: 28, Indels: 27
0.74 0.13 0.13
Matches are distributed among these distances:
24 14 0.09
26 4 0.03
27 4 0.03
28 1 0.01
29 65 0.42
30 2 0.01
31 3 0.02
32 61 0.39
33 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.32
Consensus pattern (29 bp):
ATGTGCATCTCCCGCACACTATAATATTC
Found at i:40160 original size:61 final size:61
Alignment explanation
Indices: 40044--40166 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 61
40034 CCGTACACTA
* * *
40044 TAATATTCATGTGCATCTCCCGCACACTTGAATATTCATGTGCATCTGCTACACACTATAT
1 TAATATTCATGTACATCTCCCGCACACTTGAATATTCATGTGCATCTCCCACACACTATAT
* * * * *
40105 TAATATTCGTGTACATCTCCCGTACACTAT-AATATTGATGTGCATCTCCCGCACACTTTAT
1 TAATATTCATGTACATCTCCCGCACACT-TGAATATTCATGTGCATCTCCCACACACTATAT
40166 T
1 T
40167 TATCACATTC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 52 0.98
62 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (61 bp):
TAATATTCATGTACATCTCCCGCACACTTGAATATTCATGTGCATCTCCCACACACTATAT
Found at i:46964 original size:22 final size:22
Alignment explanation
Indices: 46939--47007 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
46929 TGAAATTTCA
*
46939 ATAATCACCCTATTAAATTTTG
1 ATAATCACCCTATAAAATTTTG
* ** *
46961 ATAACCACAATATGAAATTTTG
1 ATAATCACCCTATAAAATTTTG
* *
46983 ATAATTA-CCTATAAAATTGTG
1 ATAATCACCCTATAAAATTTTG
47004 ATAA
1 ATAA
47008 ACTCCATAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (22 bp):
ATAATCACCCTATAAAATTTTG
Found at i:47026 original size:43 final size:43
Alignment explanation
Indices: 46947--47029 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
46937 CAATAATCAC
* * * * *
46947 CCTATTAAATTTTGATAACCACAATATGAAATTTTGATAATTA
1 CCTATAAAATTGTGATAAACACAATAAGAAACTTTGATAATTA
* *
46990 CCTATAAAATTGTGATAAACTCCATAAGAAACTTTGATAA
1 CCTATAAAATTGTGATAAACACAATAAGAAACTTTGATAA
47030 CCTAACTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (43 bp):
CCTATAAAATTGTGATAAACACAATAAGAAACTTTGATAATTA
Found at i:48642 original size:20 final size:22
Alignment explanation
Indices: 48600--48644 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
48590 AAGCATGAAA
48600 AGAACTAATCAATACCATACCT
1 AGAACTAATCAATACCATACCT
*
48622 AGAACTAATC-AT-CCATTCCT
1 AGAACTAATCAATACCATACCT
48642 AGA
1 AGA
48645 CGATAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (22 bp):
AGAACTAATCAATACCATACCT
Found at i:58047 original size:25 final size:25
Alignment explanation
Indices: 58019--58107 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 25
58009 CAACGAGGTT
58019 CAGCGAGCTTCAACGAGCTTCCCAG
1 CAGCGAGCTTCAACGAGCTTCCCAG
**
58044 CAGCGAGCTTCAACGAGCTTCCTGG
1 CAGCGAGCTTCAACGAGCTTCCCAG
* * * *
58069 CAGCGAGTTTCAGCGAACTT-CCTG
1 CAGCGAGCTTCAACGAGCTTCCCAG
58093 ACAGCGAGCTTCAAC
1 -CAGCGAGCTTCAAC
58108 AAATATTTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 2 0.04
25 52 0.96
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.19
Consensus pattern (25 bp):
CAGCGAGCTTCAACGAGCTTCCCAG
Found at i:64995 original size:19 final size:19
Alignment explanation
Indices: 64971--65019 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
64961 AAAACCGTTA
*
64971 CGTAACAGCCGTTACGTCG
1 CGTAACGGCCGTTACGTCG
64990 CGTAACGGCCGTTACGTCG
1 CGTAACGGCCGTTACGTCG
65009 CGTAACGGCCG
1 CGTAACGGCCG
65020 ATATTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.18, C:0.33, G:0.31, T:0.18
Consensus pattern (19 bp):
CGTAACGGCCGTTACGTCG
Found at i:70722 original size:21 final size:21
Alignment explanation
Indices: 70670--70723 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
70660 AAAAAAGTGT
* *
70670 TAAAAAT-TTTATAAGATTAT
1 TAAAAATGCTTATAAGATTAC
* *
70690 TAAAAAAAGCTTATAAGGTTAC
1 T-AAAAATGCTTATAAGATTAC
70712 TAAAAATGCTTA
1 TAAAAATGCTTA
70724 AAAACTTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.04
21 15 0.56
22 11 0.41
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (21 bp):
TAAAAATGCTTATAAGATTAC
Found at i:77000 original size:25 final size:25
Alignment explanation
Indices: 76959--77008 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
76949 ACTACTATAT
*
76959 AAAATCACAAATTATAAATATCGCA
1 AAAATCACAAATCATAAATATCGCA
*
76984 AAAATCACGAATCATAAATATCGCA
1 AAAATCACAAATCATAAATATCGCA
77009 GGGATACGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.18, G:0.06, T:0.22
Consensus pattern (25 bp):
AAAATCACAAATCATAAATATCGCA
Found at i:85772 original size:13 final size:13
Alignment explanation
Indices: 85754--85778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85744 GATACAAAGA
85754 GACAAAGGAATAT
1 GACAAAGGAATAT
85767 GACAAAGGAATA
1 GACAAAGGAATA
85779 CGCAAGCACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GACAAAGGAATAT
Found at i:90469 original size:12 final size:12
Alignment explanation
Indices: 90454--90478 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90444 TCTTCTTCTT
90454 GATCTTTGTAAA
1 GATCTTTGTAAA
90466 GATCTTTGTAAA
1 GATCTTTGTAAA
90478 G
1 G
90479 TTTAGTAGCC
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:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (12 bp):
GATCTTTGTAAA
Found at i:91310 original size:38 final size:39
Alignment explanation
Indices: 91254--91329 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 39
91244 ATCTTCTTCA
*
91254 CCATTTTTAACCATCATACCTTCTTAT-AATGATAAACT
1 CCATCTTTAACCATCATACCTTCTTATAAATGATAAACT
91292 CCATCTTTAACCATCATACCTTCTTATAAATGATAAAC
1 CCATCTTTAACCATCATACCTTCTTATAAATGATAAAC
91330 CCCGTAAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 26 0.72
39 10 0.28
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (39 bp):
CCATCTTTAACCATCATACCTTCTTATAAATGATAAACT
Found at i:94726 original size:32 final size:30
Alignment explanation
Indices: 94639--94738 Score: 125
Period size: 28 Copynumber: 3.4 Consensus size: 30
94629 CCCATTGCTG
*
94639 AACTATGA-TTATTATTTGTGCAAAAAAAA
1 AACTAGGATTTATTATTTGTGCAAAAAAAA
* *
94668 AACTAGGATTTATTA-TGGTGC-CAAAAAA
1 AACTAGGATTTATTATTTGTGCAAAAAAAA
94696 AACTAGGATTTATTAGTCTTGTGCAAAAAAAA
1 AACTAGGATTTATTA-T-TTGTGCAAAAAAAA
*
94728 AGCTAGGATTT
1 AACTAGGATTT
94739 CTTAGTTATC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
28 21 0.35
29 12 0.20
30 6 0.10
31 5 0.08
32 16 0.27
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (30 bp):
AACTAGGATTTATTATTTGTGCAAAAAAAA
Found at i:96163 original size:22 final size:22
Alignment explanation
Indices: 96138--96260 Score: 92
Period size: 22 Copynumber: 5.6 Consensus size: 22
96128 ATCCAATGTA
* *
96138 GAAATATTGATAACCACATTTT
1 GAAATATTGATAACCACAGTGT
* * *
96160 GAAA-ATTTGATAACCTCATTTT
1 GAAATA-TTGATAACCACAGTGT
*
96182 GAAAT-TTCGATAACCACACTGT
1 GAAATATT-GATAACCACAGTGT
* *
96204 GAAA-ATTTGGTAACCACAGTAT
1 GAAATA-TTGATAACCACAGTGT
*
96226 GAAAT-TTCGATAACCTCAGTGT
1 GAAATATT-GATAACCACAGTGT
*
96248 GAAATTTTGATAA
1 GAAATATTGATAA
96261 TCTGTCTATA
Statistics
Matches: 83, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
21 5 0.06
22 74 0.89
23 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (22 bp):
GAAATATTGATAACCACAGTGT
Found at i:96194 original size:44 final size:44
Alignment explanation
Indices: 96138--96260 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 44
96128 ATCCAATGTA
* * * * *
96138 GAAATATT-GATAACCACATTTTGAAAATTTGATAACCTCATTTT
1 GAAAT-TTCGATAACCACACTGTGAAAATTTGATAACCACAGTAT
*
96182 GAAATTTCGATAACCACACTGTGAAAATTTGGTAACCACAGTAT
1 GAAATTTCGATAACCACACTGTGAAAATTTGATAACCACAGTAT
* * *
96226 GAAATTTCGATAACCTCAGTGTGAAATTTTGATAA
1 GAAATTTCGATAACCACACTGTGAAAATTTGATAA
96261 TCTGTCTATA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.03
44 66 0.97
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (44 bp):
GAAATTTCGATAACCACACTGTGAAAATTTGATAACCACAGTAT
Found at i:96441 original size:22 final size:23
Alignment explanation
Indices: 96415--96484 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 23
96405 TATATTTTCG
96415 ATAACCTCTCC-ATAAAATTTT-T
1 ATAACCTC-CCTATAAAATTTTGT
96437 ATAACCTCCCTATAAAATTTTGT
1 ATAACCTCCCTATAAAATTTTGT
**
96460 -TAACCTCCCTAGGAAATTTTG-
1 ATAACCTCCCTATAAAATTTTGT
96481 ATAA
1 ATAA
96485 GCACAAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.05
22 40 0.93
23 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (23 bp):
ATAACCTCCCTATAAAATTTTGT
Found at i:96561 original size:22 final size:22
Alignment explanation
Indices: 96507--96565 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
96497 GTAACCTCCC
* *
96507 TCCCTATGAAATTTTGTTAACT
1 TCCCTATGAAATTTTATTAACA
* *
96529 TTCATATGAAATTTTATTAACA
1 TCCCTATGAAATTTTATTAACA
*
96551 TCCCTAAGAAATTTT
1 TCCCTATGAAATTTT
96566 GATAATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (22 bp):
TCCCTATGAAATTTTATTAACA
Found at i:96586 original size:44 final size:45
Alignment explanation
Indices: 96507--96632 Score: 132
Period size: 44 Copynumber: 2.8 Consensus size: 45
96497 GTAACCTCCC
* * *
96507 TCCCTATGAAATTTTGTTAA-CTTTCATATGAAATTTT-ATTAACA
1 TCCCTATGAAATTTTGATAATCTTTC-TATGTAATTTTGATGAACA
* * * **
96551 TCCCTAAGAAATTTTGATAATTTTTCTATGTAATTTTGGTGGCCA
1 TCCCTATGAAATTTTGATAATCTTTCTATGTAATTTTGATGAACA
* *
96596 -CACTATGAAAGTTTGATAATCTTTCTATGTAATTTTG
1 TCCCTATGAAATTTTGATAATCTTTCTATGTAATTTTG
96633 GTTTGATTGT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 61 0.90
45 7 0.10
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (45 bp):
TCCCTATGAAATTTTGATAATCTTTCTATGTAATTTTGATGAACA
Found at i:96632 original size:22 final size:22
Alignment explanation
Indices: 96560--96632 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
96550 ATCCCTAAGA
*
96560 AATTTTGATAATTTTTCTATGT
1 AATTTTGATAATCTTTCTATGT
* *** *** *
96582 AATTTTGGTGGCCACACTATGA
1 AATTTTGATAATCTTTCTATGT
*
96604 AAGTTTGATAATCTTTCTATGT
1 AATTTTGATAATCTTTCTATGT
96626 AATTTTG
1 AATTTTG
96633 GTTTGATTGT
Statistics
Matches: 32, Mismatches: 19, Indels: 0
0.63 0.37 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (22 bp):
AATTTTGATAATCTTTCTATGT
Found at i:97925 original size:63 final size:67
Alignment explanation
Indices: 97805--97938 Score: 204
Period size: 63 Copynumber: 2.0 Consensus size: 67
97795 ATTATTGATA
97805 AGTCACTCAATTAGAATTTCTTACACTTTCTTTCCCCTGCCCTATTTTGGTAATAAATAGTGTCA
1 AGTCACTCAATTAG-ATTTCTTACACTTTC-TT-CCCTGCCCTATTTTGGTAATAAATAGTGTCA
97870 TTAAT
63 TTAAT
*
97875 AGTCCCTCAATTAG-TTTCTTACACTTTC-T-CC-GCCCTATTTTGGTAATAAATAGTGTCATTA
1 AGTCACTCAATTAGATTTCTTACACTTTCTTCCCTGCCCTATTTTGGTAATAAATAGTGTCATTA
97936 AT
66 AT
97938 A
1 A
97939 TTCATTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
63 33 0.52
64 2 0.03
66 1 0.02
68 14 0.22
70 13 0.21
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (67 bp):
AGTCACTCAATTAGATTTCTTACACTTTCTTCCCTGCCCTATTTTGGTAATAAATAGTGTCATTA
AT
Found at i:98482 original size:52 final size:52
Alignment explanation
Indices: 98415--98520 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
98405 TAGCTAGGTC
*
98415 TGCAAAATATGACAAATTCTTCATAATTCCTGGTTCAGCAACTGCAACTGGG
1 TGCAAAATATGACAAATTCTTCATAATTACTGGTTCAGCAACTGCAACTGGG
98467 TGCAAAATATGACAAATTCTTCATAATTACTGGTTCAGCAACTGCAACTGGG
1 TGCAAAATATGACAAATTCTTCATAATTACTGGTTCAGCAACTGCAACTGGG
98519 TG
1 TG
98521 ATCTCAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (52 bp):
TGCAAAATATGACAAATTCTTCATAATTACTGGTTCAGCAACTGCAACTGGG
Found at i:99337 original size:27 final size:25
Alignment explanation
Indices: 99307--99359 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
99297 AATTGAATTG
99307 AAGAAAAAAAGAATTGAATTTTTTCTT
1 AAGAAAAAAAG-ATT-AATTTTTTCTT
* *
99334 AAGAAGACAAGATTAATTTTTTCTT
1 AAGAAAAAAAGATTAATTTTTTCTT
99359 A
1 A
99360 GTAAGAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
27 9 0.38
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (25 bp):
AAGAAAAAAAGATTAATTTTTTCTT
Found at i:106989 original size:2 final size:2
Alignment explanation
Indices: 106982--107018 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
106972 GAAGAACACA
106982 AG AG AG AG AG 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 AG AG AG AG AG A
107019 AAATTACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:121887 original size:29 final size:30
Alignment explanation
Indices: 121829--121889 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
121819 GTTTTAATTA
* *
121829 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
121859 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
121888 AT
1 AT
121890 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:122189 original size:12 final size:13
Alignment explanation
Indices: 122167--122192 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
122157 AAGATGTAGA
122167 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
122180 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
122193 CCTTAGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:123973 original size:35 final size:35
Alignment explanation
Indices: 123909--123983 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
123899 AGTTCGTTTA
* **
123909 TGTTCACGAACAAACTTGTTTATCATTCATTTAAG
1 TGTTCACGAACAAACTCGTTTATCATTCATAAAAG
* * **
123944 TGTTCACGAACAAGCTCGTTTGTTGTTCATAAAAG
1 TGTTCACGAACAAACTCGTTTATCATTCATAAAAG
123979 TGTTC
1 TGTTC
123984 GTTTATATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (35 bp):
TGTTCACGAACAAACTCGTTTATCATTCATAAAAG
Found at i:124043 original size:14 final size:14
Alignment explanation
Indices: 124013--124054 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
124003 GTTCGTTTAT
*
124013 TATA-TAATAATTTA
1 TATATTAATAA-TAA
124027 TATATTAATAATAA
1 TATATTAATAATAA
*
124041 TATATTATTAATAA
1 TATATTAATAATAA
124055 AAATCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATTAATAATAA
Found at i:124051 original size:17 final size:17
Alignment explanation
Indices: 124009--124054 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
123999 GAATGTTCGT
*
124009 TTATTATATAATAATTTA
1 TTATTA-ATAATAATATA
124027 TATATTAATAATAATATA
1 T-TATTAATAATAATATA
124045 TTATTAATAA
1 TTATTAATAA
124055 AAATCATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
19 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTAATAATAATATA
Found at i:124130 original size:15 final size:14
Alignment explanation
Indices: 124103--124144 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
124093 AATTAAAATT
124103 TAATTAT-TATATA
1 TAATTATATATATA
124116 TAATATATATATATA
1 TAAT-TATATATATA
124131 TAATTATATA-ATA
1 TAATTATATATATA
124144 T
1 T
124145 TCTGTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.30
14 9 0.33
15 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:124788 original size:2 final size:2
Alignment explanation
Indices: 124783--124895 Score: 59
Period size: 2 Copynumber: 61.0 Consensus size: 2
124773 TATATTTAAG
* *
124783 AT AT AT AT AT AT AT -T AT AT AT -T AGT A- AT CA- AT TT TT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT
* * * *
124822 AT AT AT AT AA AT AT AT AT -T TT AT -T AT AA AT AT -T AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
124861 AT TT A- AG AT AT AT AT AT AT -T AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124896 TAGTCATCAA
Statistics
Matches: 86, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
1 11 0.13
2 72 0.84
3 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:124842 original size:24 final size:24
Alignment explanation
Indices: 124772--124895 Score: 82
Period size: 24 Copynumber: 5.2 Consensus size: 24
124762 TAAATATTAA
* *
124772 ATATATTTAAGATATATATATATATT
1 ATATATATAA-ATATATAT-TTTATT
124798 ATATAT-TAGTAATCA-AT-TTTTATT
1 ATATATATA--AAT-ATATATTTTATT
124822 ATATATATAAATATATATTTTATT
1 ATATATATAAATATATATTTTATT
* * **
124846 ATAAATATTAA-ATATA-TTTAAG
1 ATATATATAAATATATATTTTATT
* *
124868 ATATATATATAT-TATA-TATATT
1 ATATATATAAATATATATTTTATT
124890 ATATAT
1 ATATAT
124896 TAGTCATCAA
Statistics
Matches: 80, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
22 26 0.32
23 10 0.12
24 27 0.34
25 5 0.06
26 10 0.12
27 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATATATAAATATATATTTTATT
Found at i:124861 original size:35 final size:35
Alignment explanation
Indices: 124822--124895 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
124812 AATTTTTATT
*
124822 ATATATATAA-ATATATATTTTATTATAAATATTAA
1 ATATATATAAGATATATA-TATATTATAAATATTAA
* * *
124857 ATATATTTAAGATATATATATATTATATATATTAT
1 ATATATATAAGATATATATATATTATAAATATTAA
124892 ATAT
1 ATAT
124896 TAGTCATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 27 0.79
36 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (35 bp):
ATATATATAAGATATATATATATTATAAATATTAA
Found at i:124924 original size:92 final size:85
Alignment explanation
Indices: 124748--124929 Score: 256
Period size: 92 Copynumber: 2.1 Consensus size: 85
124738 AGAACCCGAG
124748 TATATATTGTATTATAAATATTAAATATATTTAAGATATATATATATATTATATATTAGTAATCA
1 TATATATTGTATTATAAATATTAAATATATTTAAGATATATATATATATTATATATTAGTAATCA
* *
124813 ATTTTTATTATATATATAAA
66 ATTTTTATTATAAAAATAAA
*
124833 TATATATTTTATTATAAATATTAAATATATTTAAGATATATATATATTATATATATTATATATTA
1 TATATATTGTATTATAAATATTAAATATATTTAAG------ATATA-TATATATATTATATATTA
*
124898 GTCATCAATTTTTATTATAAAAATAAA
59 GTAATCAATTTTTATTATAAAAATAAA
*
124925 AATAT
1 TATAT
124930 TCCCTCGGTT
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
85 34 0.40
91 5 0.06
92 46 0.54
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.49
Consensus pattern (85 bp):
TATATATTGTATTATAAATATTAAATATATTTAAGATATATATATATATTATATATTAGTAATCA
ATTTTTATTATAAAAATAAA
Found at i:127705 original size:35 final size:36
Alignment explanation
Indices: 127638--127708 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
127628 CTAAGTCTTG
127638 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAA
1 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAA
*
127674 AAAATTCTTTGTAAATTAAG-AATACTCAACTCAAA
1 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAA
127709 TCTTGATCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 15 0.44
36 19 0.56
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (36 bp):
AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAA
Found at i:127879 original size:56 final size:57
Alignment explanation
Indices: 127777--127891 Score: 214
Period size: 56 Copynumber: 2.0 Consensus size: 57
127767 TTTATTCTGT
127777 AGAATAATTAAGTAGAGATAGGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
*
127834 AGAATAATTAAGTAGAGATA-GGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
127890 AG
1 AG
127892 GAAACGGATA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 37 0.65
57 20 0.35
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
Found at i:136221 original size:20 final size:20
Alignment explanation
Indices: 136184--136222 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
136174 TCCTATTATT
136184 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
136204 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
136223 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:136448 original size:22 final size:21
Alignment explanation
Indices: 136414--136623 Score: 123
Period size: 22 Copynumber: 9.5 Consensus size: 21
136404 ATAAGATATT
* *
136414 GGTTATTATAATTTCATGAGAA
1 GGTTATCAAAATTTCAT-AGAA
* **
136436 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-AA
* *
136458 GGTTACCAAAATTGCATATGAA
1 GGTTATCAAAATTTCATA-GAA
* *
136480 AGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCAT-AGAA
* **
136502 GGTTATCAAAATATCATAGTGT
1 GGTTATCAAAATTTCATAG-AA
*
136524 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATA-GA--A
* * *
136548 GGTTATTAGAATTTCTTAGGAA
1 GGTTATCAAAATTTCATA-GAA
** **
136570 GGTTATTGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-AA
* *
136592 GGTTATCACAATTTTATAGAGA
1 GGTTATCAAAATTTCATAGA-A
136614 GGTTATCAAA
1 GGTTATCAAA
136624 GAGATTATCA
Statistics
Matches: 141, Mismatches: 38, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
21 4 0.03
22 118 0.84
23 2 0.01
24 17 0.12
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGAA
Found at i:136497 original size:66 final size:66
Alignment explanation
Indices: 136423--136596 Score: 208
Period size: 66 Copynumber: 2.6 Consensus size: 66
136413 TGGTTATTAT
*
136423 AATTTCATGAGAAGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTGCATATGA-AAGTTATC
1 AATTTCATGAGAAGGTTATCAAAATT-CATAGTGTGGTTACCAAAATTGCATAGGACAAGTTATC
136487 AA
65 AA
* * *
136489 AATTTCATGGGAAGGTTATCAAAATATCATAGTGTGGTTACCAAAATTTCATAGGATCAGGTTAT
1 AATTTCATGAGAAGGTTATCAAAAT-TCATAGTGTGGTTACCAAAATTGCATAGGA-CAAGTTAT
* *
136554 TAG
64 CAA
* * *
136557 AATTTC-TTAGGAAGGTTATTGAAATTTCATAGTGTGGTTA
1 AATTTCATGA-GAAGGTTA-TCAAAATTCATAGTGTGGTTA
136597 TCACAATTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
66 51 0.55
67 2 0.02
68 35 0.38
69 5 0.05
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.35
Consensus pattern (66 bp):
AATTTCATGAGAAGGTTATCAAAATTCATAGTGTGGTTACCAAAATTGCATAGGACAAGTTATCA
A
Found at i:136682 original size:22 final size:22
Alignment explanation
Indices: 136628--137066 Score: 145
Period size: 22 Copynumber: 19.9 Consensus size: 22
136618 ATCAAAGAGA
* * * *
136628 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATAGTGTGG
136650 TTAT-AATAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGTGG
* * *
136672 TTAACAAAATTTCATAAG-GAGA
1 TTATCAAAATTTCAT-AGTGTGG
* * *
136694 TTA-CTAATATATCAT-GGGTAGG
1 TTATC-AAAATTTCATAGTGT-GG
136716 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
**
136738 --ATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
*
136758 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-TGG
* * *
136780 TTAT-AAAAGTCTCAATTTGATGAGG
1 TTATCAAAA-TTTC-A-TAG-TGTGG
* * **
136805 AGTA-CTAAAATTTGATAG-AAGG
1 -TTATC-AAAATTTCATAGTGTGG
* * *
136827 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGTGG
* *
136848 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTG-T-GG
* * *
136872 ATTATCGAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-TGG
*
136894 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGTGG
* * * *
136916 TTATCAAAGTTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGTGG
* * **
136938 TTATCAAAATTACATAATGTTA
1 TTATCAAAATTTCATAGTGTGG
* * *
136960 TTATCAAAATTTCATCGAGGGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
136982 TCAAT-AAAATTTTATA--GAGA
1 T-TATCAAAATTTCATAGTGTGG
** *
137002 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
137024 TTATCAAATTTTCAAAATGTGAT
1 TTATCAAAATTTCATAGTGTG-G
*
137047 TTACCAAAATTTCATAGTGT
1 TTATCAAAATTTCATAGTGT
137067 TGTTTTTGGG
Statistics
Matches: 308, Mismatches: 77, Indels: 63
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.01
20 41 0.13
21 29 0.09
22 171 0.56
23 31 0.10
24 8 0.03
25 16 0.05
26 6 0.02
27 4 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:136743 original size:20 final size:21
Alignment explanation
Indices: 136717--136773 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
136707 ATGGGTAGGT
136717 TATCAAAATTTCATAGTGTGG
1 TATCAAAATTTCATAGTGTGG
**
136738 -ATCAAAATTTTTTAGTGTGG
1 TATCAAAATTTCATAGTGTGG
136758 TTATCAAAATTTCATA
1 -TATCAAAATTTCATA
136774 TGAAGGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 18 0.60
22 12 0.40
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (21 bp):
TATCAAAATTTCATAGTGTGG
Found at i:136895 original size:21 final size:24
Alignment explanation
Indices: 136846--136910 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
136836 CTCATAGAGT
*
136846 GATTATCGAAATTTCATAGAGATCG
1 GATTATCGAAATTTCATAGAGA-CA
136871 GATTATCGAAATTT-ATAG-GA-A
1 GATTATCGAAATTTCATAGAGACA
*
136892 GATTATCAAAATTTCATAG
1 GATTATCGAAATTTCATAG
136911 TGTTGTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.35
22 4 0.11
23 2 0.05
24 4 0.11
25 14 0.38
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (24 bp):
GATTATCGAAATTTCATAGAGACA
Found at i:137234 original size:22 final size:21
Alignment explanation
Indices: 137163--137455 Score: 93
Period size: 22 Copynumber: 13.5 Consensus size: 21
137153 TCAGGGAGAA
* *
137163 TATCAAAATTTTATATGAAGGT
1 TATCAAAATTTCATA-GAGGGT
* ***
137185 CATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAG-AGGGT
*
137207 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCAT-AGAGGGT
*
137229 TATCAAAATTTCATAGTA-TGT
1 TATCAAAATTTCATAG-AGGGT
* * *
137250 AGATTAAAAGTTCATAG-GGAGAT
1 -TATCAAAATTTCATAGAGG-G-T
*
137273 TAACAAAATTTCATA-ATGAGGT
1 TATCAAAATTTCATAGA-G-GGT
** *
137295 TATCAAAAAATCATAGAGAGAT
1 TATCAAAATTTCATAGAG-GGT
* *
137317 TATCAAAATTT-GT--A--GC
1 TATCAAAATTTCATAGAGGGT
* *
137333 TATCAAGATATCATA-AGGATGT
1 TATCAAAATTTCATAGAGG--GT
* *
137355 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATA--GAGGGT
* *
137378 TATCAAAATTTTATAGAAAGGTT
1 TATCAAAATTTCATAG--AGGGT
*
137401 TATCAAAATTTCAT-GACGAAGT
1 TATCAAAATTTCATAGA-G-GGT
* * * *
137423 TATTACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGAG-GGT
137445 TATCAAAATTT
1 TATCAAAATTT
137456 TAGAGTGTGA
Statistics
Matches: 198, Mismatches: 48, Indels: 50
0.67 0.16 0.17
Matches are distributed among these distances:
16 9 0.05
17 1 0.01
18 1 0.01
19 1 0.01
20 1 0.01
21 8 0.04
22 132 0.67
23 41 0.21
24 1 0.01
25 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (21 bp):
TATCAAAATTTCATAGAGGGT
Found at i:137264 original size:44 final size:44
Alignment explanation
Indices: 137186--137327 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 44
137176 TATGAAGGTC
* *
137186 ATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGG-G-TT
1 ATCAAAATTTCATAGTTTAGTATTCAAAAGTTCAT-AG-GGAGATT
137230 ATCAAAATTTCATAGTATGTAG-ATT-AAAAGTTCATAGGGAGATT
1 ATCAAAATTTCATAGT-T-TAGTATTCAAAAGTTCATAGGGAGATT
* * * ** *
137274 AACAAAATTTCATA-ATGAGGT-TATCAAAAAATCATAGAGAGATT
1 ATCAAAATTTCATAGTTTA-GTAT-TCAAAAGTTCATAGGGAGATT
137318 ATCAAAATTT
1 ATCAAAATTT
137328 GTAGCTATCA
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
41 1 0.01
42 5 0.06
43 4 0.05
44 65 0.80
45 3 0.04
46 3 0.04
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (44 bp):
ATCAAAATTTCATAGTTTAGTATTCAAAAGTTCATAGGGAGATT
Found at i:137384 original size:23 final size:23
Alignment explanation
Indices: 137354--137411 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
137344 CATAAGGATG
**
137354 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAAAGGT
137377 TTATCAAAATTTTATAGAAAGGT
1 TTATCAAAATTTTATAGAAAGGT
137400 TTATCAAAATTT
1 TTATCAAAATTT
137412 CATGACGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAAAGGT
Found at i:137599 original size:22 final size:22
Alignment explanation
Indices: 137558--137600 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
137548 TTGTTGGTTA
* *
137558 TTCAAAATTTCATAGTGAGGTC
1 TTCAAAATTCCATAGGGAGGTC
*
137580 TTCAAAATTCCTTAGGGAGGT
1 TTCAAAATTCCATAGGGAGGT
137601 TAACAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (22 bp):
TTCAAAATTCCATAGGGAGGTC
Found at i:137637 original size:21 final size:22
Alignment explanation
Indices: 137597--137644 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
137587 TTCCTTAGGG
* * *
137597 AGGTTAACAAAATTTTATAAGA
1 AGGTTAACAAAAATTAATAACA
137619 AGGTTAA-AAAAATTAATAACA
1 AGGTTAACAAAAATTAATAACA
137640 AGGTT
1 AGGTT
137645 CTCGAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (22 bp):
AGGTTAACAAAAATTAATAACA
Found at i:137717 original size:22 final size:22
Alignment explanation
Indices: 137670--137717 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
137660 TATCGTTTTT
* *
137670 AAAATTTCATAGGAAGATTATC
1 AAAATTTCATAGGAAGATCATA
*
137692 AAAATTTCATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAGATCATA
137714 AAAA
1 AAAA
137718 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAGATCATA
Done.