Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold364
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: 2089110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:115431 original size:26 final size:27
Alignment explanation
Indices: 115388--115439 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
115378 TTTTTATATT
*
115388 TATGAATAAATATGAAATTT-TTTTAA
1 TATGAATAAATATAAAATTTATTTTAA
115414 TATGAATAAA-ATAAAAATTTATTTTA
1 TATGAATAAATAT-AAAATTTATTTTA
115440 TCATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 16 0.70
27 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (27 bp):
TATGAATAAATATAAAATTTATTTTAA
Found at i:117371 original size:6 final size:6
Alignment explanation
Indices: 117360--117425 Score: 87
Period size: 6 Copynumber: 11.0 Consensus size: 6
117350 TTGTTATGCA
* *
117360 ATTGCC ATTGCC ATTGCC ATTGCC ATTGCC ATTGCC ACTGCC ACTGCC
1 ATTGCC ATTGCC ATTGCC ATTGCC ATTGCC ATTGCC ATTGCC ATTGCC
* * *
117408 ACTGCC ACTGCC ACTGCC
1 ATTGCC ATTGCC ATTGCC
117426 CACGCCTACT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.17, C:0.41, G:0.17, T:0.26
Consensus pattern (6 bp):
ATTGCC
Found at i:122426 original size:7 final size:7
Alignment explanation
Indices: 122414--122453 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
122404 TATATGTATA
122414 TGCACAT
1 TGCACAT
122421 TGCACAT
1 TGCACAT
122428 TGCACAT
1 TGCACAT
122435 TGCACAT
1 TGCACAT
*
122442 TGCACAA
1 TGCACAT
122449 TGCAC
1 TGCAC
122454 TACGTGTGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (7 bp):
TGCACAT
Found at i:125403 original size:2 final size:2
Alignment explanation
Indices: 125396--125429 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
125386 AGCAGCTGGT
125396 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
125430 GTACTTAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:125807 original size:18 final size:17
Alignment explanation
Indices: 125784--125823 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
125774 GCATTTGTTG
125784 AAAAAAACGTAATAAAAT
1 AAAAAAACGTAA-AAAAT
**
125802 AAAAAAATTTAAAAAAT
1 AAAAAAACGTAAAAAAT
125819 AAAAA
1 AAAAA
125824 CACATAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAAAAACGTAAAAAAT
Found at i:129572 original size:2 final size:2
Alignment explanation
Indices: 129565--129596 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
129555 CTTCTTTTTA
129565 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
129597 GAGATCAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130205 original size:2 final size:2
Alignment explanation
Indices: 130193--130224 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
130183 CATGATAACA
130193 AT AT A- 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 A
130225 AAGTTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:130927 original size:13 final size:14
Alignment explanation
Indices: 130909--130942 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
130899 AATTTTAATT
130909 TTATTAAA-TTATA
1 TTATTAAATTTATA
*
130922 TTATTAAATTTTTA
1 TTATTAAATTTATA
130936 TTATTAA
1 TTATTAA
130943 TAAATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTATA
Found at i:130947 original size:30 final size:29
Alignment explanation
Indices: 130888--130962 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
130878 TAATTTTTAT
* *
130888 TTAAGTTATAAAATTTTAATTTTATTAAA
1 TTAAGTTATTAAATTTTAATTTTAATAAA
*
130917 TTATA-TTATTAAATTTTTATTATTAATAAA
1 TTA-AGTTATTAAATTTTAATT-TTAATAAA
130947 TTAAGTTATTTAAATT
1 TTAAGTTA-TTAAATT
130963 AATTTCGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 18 0.46
30 14 0.36
31 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
TTAAGTTATTAAATTTTAATTTTAATAAA
Found at i:131790 original size:86 final size:86
Alignment explanation
Indices: 131645--132063 Score: 374
Period size: 86 Copynumber: 5.0 Consensus size: 86
131635 CTGAATTTAT
131645 AGCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGT
1 AGCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGT
*
131710 GGCCACAACCAATGCCGGCTA
66 GGCCACAACCAATGCCAGCTA
131731 AGCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGT
1 AGCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGT
131796 GGCCACAACCAATGCCAGCT-
66 GGCCACAACCAATGCCAGCTA
* * * * ** * * * * *
131816 A--TTT-CCT--TGTATTGTGATAGTGCAGCTACAATGTCTAA-AGCA--T-ATAGTGACATATA
1 AGCTTTAGCTGCTGCA--GGGA-AG-GAAGC-GGAATGGCTAAGA-AATTTGTTATTG-GATATA
* * * * * * ** *
131872 CA---ATGG--AAAATCTA-GACATATT
59 GAGTTGTGGCCACAACCAATGCCAGCTA
* * * * *
131894 AGCATTAGACATGAT-TA---TATGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTT
1 AGCTTTAG-C-TGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTT
*
131955 GTGACCACAACCAATGCCAGCTA
64 GTGGCCACAACCAATGCCAGCTA
131978 AGCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGT
1 AGCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGT
132043 GGCCACAACCAATGCCAGCTA
66 GGCCACAACCAATGCCAGCTA
132064 TTTCCTTGTA
Statistics
Matches: 256, Mismatches: 48, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
76 9 0.04
77 9 0.04
78 14 0.05
79 4 0.02
80 8 0.03
81 2 0.01
82 13 0.05
83 20 0.08
84 18 0.07
85 11 0.04
86 148 0.58
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (86 bp):
AGCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGT
GGCCACAACCAATGCCAGCTA
Found at i:132103 original size:247 final size:247
Alignment explanation
Indices: 131667--132160 Score: 970
Period size: 247 Copynumber: 2.0 Consensus size: 247
131657 TGCAGGGAAG
* *
131667 GAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTGGCCACAACCAATGCCGGCTAA
1 GAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTGACCACAACCAATGCCAGCTAA
131732 GCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTG
66 GCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTG
131797 GCCACAACCAATGCCAGCTATTTCCTTGTATTGTGATAGTGCAGCTACAATGTCTAAAGCATATA
131 GCCACAACCAATGCCAGCTATTTCCTTGTATTGTGATAGTGCAGCTACAATGTCTAAAGCATATA
131862 GTGACATATACAATGGAAAATCTAGACATATTAGCATTAGACATGATTATAT
196 GTGACATATACAATGGAAAATCTAGACATATTAGCATTAGACATGATTATAT
131914 GAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTGACCACAACCAATGCCAGCTAA
1 GAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTGACCACAACCAATGCCAGCTAA
131979 GCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTG
66 GCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTG
132044 GCCACAACCAATGCCAGCTATTTCCTTGTATTGTGATAGTGCAGCTACAATGTCTAAAGCATATA
131 GCCACAACCAATGCCAGCTATTTCCTTGTATTGTGATAGTGCAGCTACAATGTCTAAAGCATATA
132109 GTGACATATACAATGGAAAATCTAGACATATTAGCATTAGACATGATTATAT
196 GTGACATATACAATGGAAAATCTAGACATATTAGCATTAGACATGATTATAT
132161 TAGAGAATTA
Statistics
Matches: 245, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
247 245 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (247 bp):
GAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTGACCACAACCAATGCCAGCTAA
GCTTTAGCTGCTGCAGGGAAGGAAGCGGAATGGCTAAGAAATTTGTTATTGGATATAGAGTTGTG
GCCACAACCAATGCCAGCTATTTCCTTGTATTGTGATAGTGCAGCTACAATGTCTAAAGCATATA
GTGACATATACAATGGAAAATCTAGACATATTAGCATTAGACATGATTATAT
Found at i:133066 original size:8 final size:8
Alignment explanation
Indices: 133053--133081 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
133043 AAATCAAAGA
133053 TGGGCACT
1 TGGGCACT
133061 TGGGCACT
1 TGGGCACT
133069 TGGGCACT
1 TGGGCACT
133077 TGGGC
1 TGGGC
133082 TTAAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.24, G:0.41, T:0.24
Consensus pattern (8 bp):
TGGGCACT
Found at i:133120 original size:18 final size:18
Alignment explanation
Indices: 133097--133131 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
133087 TTAAAGATGC
*
133097 AATTATATTTTTTATTTT
1 AATTATATTATTTATTTT
133115 AATTATATTATTTATTT
1 AATTATATTATTTATTT
133132 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:133144 original size:18 final size:21
Alignment explanation
Indices: 133100--133146 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
133090 AAGATGCAAT
133100 TATATTT-TTTATTTTAATTA
1 TATATTTATTTATTTTAATTA
133120 TATTATTTATTTA-TTT-ATTA
1 TA-TATTTATTTATTTTAATTA
133140 -ATATTTA
1 TATATTTA
133147 ATTCGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.24
19 1 0.04
20 6 0.24
21 8 0.32
22 4 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATATTTATTTATTTTAATTA
Found at i:133841 original size:22 final size:22
Alignment explanation
Indices: 133791--133854 Score: 87
Period size: 20 Copynumber: 3.0 Consensus size: 22
133781 TTAAATGTAG
*
133791 TAAAAATAATATATTAAAT--A
1 TAAAAATAATATTTTAAATAAA
*
133811 TTAAAATAATATTTTAAATAAA
1 TAAAAATAATATTTTAAATAAA
133833 TAAAAATAATATTTATAAATAA
1 TAAAAATAATATTT-TAAATAA
133855 CAATTAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 17 0.45
22 14 0.37
23 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAATAATATTTTAAATAAA
Found at i:140028 original size:20 final size:21
Alignment explanation
Indices: 140003--140058 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
139993 AAACCCAAAG
*
140003 TGTATCAATACAATGAA-TAA
1 TGTATCAATACAATGAAGCAA
* *
140023 TGTATCGATACAATTTAAGCAA
1 TGTATCAATACAA-TGAAGCAA
140045 TGTATCAATACAAT
1 TGTATCAATACAAT
140059 CTCTTGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 12 0.40
21 4 0.13
22 14 0.47
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (21 bp):
TGTATCAATACAATGAAGCAA
Found at i:140197 original size:21 final size:23
Alignment explanation
Indices: 140171--140217 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
140161 GTTGGGACCT
140171 TGTATCGATACATTCA-A-AAAA
1 TGTATCGATACATTCAGACAAAA
*
140192 TGTATCGATAGATTCAGACAAAA
1 TGTATCGATACATTCAGACAAAA
140215 TGT
1 TGT
140218 GACTTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.65
22 1 0.04
23 7 0.30
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (23 bp):
TGTATCGATACATTCAGACAAAA
Found at i:144460 original size:15 final size:15
Alignment explanation
Indices: 144436--144481 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
144426 AATATGAAAT
144436 TTGCTTTGTACACAA
1 TTGCTTTGTACACAA
*
144451 TTGTTTTGTACACAA
1 TTGCTTTGTACACAA
*
144466 TTGCTTTGTAAACAA
1 TTGCTTTGTACACAA
144481 T
1 T
144482 GTGATTTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (15 bp):
TTGCTTTGTACACAA
Found at i:146041 original size:2 final size:2
Alignment explanation
Indices: 146036--146074 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
146026 TGTGTGTGTG
146036 TA TA TA TA 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 TA TA TA TA T
146075 TAGTGTGAGG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:146840 original size:3 final size:3
Alignment explanation
Indices: 146832--146862 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
146822 GAATACCATT
146832 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
146863 GATGATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:146867 original size:3 final size:3
Alignment explanation
Indices: 146861--146888 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
146851 TATTATTATT
146861 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
146889 GAGCGGCAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:147753 original size:2 final size:2
Alignment explanation
Indices: 147746--147770 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
147736 GACCTATTTC
147746 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
147771 GATAGATAGA
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:147793 original size:5 final size:5
Alignment explanation
Indices: 147771--147807 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
147761 TATATATATA
*
147771 GATA- GATA- GATAG CATAG GATAG GATAG GATAG GATA
1 GATAG GATAG GATAG GATAG GATAG GATAG GATAG GATA
147808 ATATAGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.43, C:0.03, G:0.32, T:0.22
Consensus pattern (5 bp):
GATAG
Found at i:149116 original size:18 final size:18
Alignment explanation
Indices: 149091--149139 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
149081 ATTAAATAAT
149091 TATT-AAAAATTATATTA
1 TATTAAAAAATTATATTA
149108 TATTAAAAAATTAT-TTA
1 TATTAAAAAATTATATTA
*
149125 -ATTATTAAAATTATA
1 TATTA-AAAAATTATA
149140 AACCCTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.14
17 15 0.54
18 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAAAAATTATATTA
Found at i:149131 original size:29 final size:29
Alignment explanation
Indices: 149068--149122 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
149058 ATTTAAATTT
*
149068 AAAA-TATATTAATATTAAATAATTATTA
1 AAAATTATATTAATATTAAAAAATTATTA
149096 AAAATTATATT-ATATTAAAAAATTATT
1 AAAATTATATTAATATTAAAAAATTATT
149123 TAATTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATTATATTAATATTAAAAAATTATTA
Found at i:149201 original size:36 final size:36
Alignment explanation
Indices: 149159--149271 Score: 127
Period size: 36 Copynumber: 3.3 Consensus size: 36
149149 CCCAAAAACT
*
149159 TATAATTATAATTATATTAAATAATAAAATATAAAA
1 TATAATTATATTTATATTAAATAATAAAATATAAAA
*
149195 TATAATTATTTTTATATTAAATAAT---A-ATAAAA
1 TATAATTATATTTATATTAAATAATAAAATATAAAA
149227 -AT--TTATATTTATATTAAA-AATAAAATATTAAAA
1 TATAATTATATTTATATTAAATAATAAAATA-TAAAA
149260 T-TATATTATATT
1 TATA-ATTATATT
149272 AAAATAAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
28 3 0.05
29 15 0.23
31 3 0.05
32 7 0.11
33 7 0.11
36 30 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
TATAATTATATTTATATTAAATAATAAAATATAAAA
Found at i:149272 original size:16 final size:16
Alignment explanation
Indices: 149224--149276 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
149214 AATAATAATA
149224 AAAATTTATATTTATATT
1 AAAA-TTATA-TTATATT
**
149242 AAAA--ATAAAATATT
1 AAAATTATATTATATT
149256 AAAATTATATTATATT
1 AAAATTATATTATATT
149272 AAAAT
1 AAAAT
149277 AAATTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 9 0.31
15 3 0.10
16 13 0.45
18 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTATATTATATT
Found at i:149284 original size:29 final size:31
Alignment explanation
Indices: 149164--149287 Score: 103
Period size: 29 Copynumber: 3.9 Consensus size: 31
149154 AAACTTATAA
* * *
149164 TTATAATTATATTAAATAATAAAATATAAAATAT
1 TTATATTTATATT-AA-AATAAATTATTAAA-AT
* * *
149198 AATTATTTTTATATT-AAAT-AATAATAAAAAT
1 --TTATATTTATATTAAAATAAATTATTAAAAT
*
149229 TTATATTTATATTAAAAATAAAATATTAAAA-
1 TTATATTTATATT-AAAATAAATTATTAAAAT
149260 TTATA-TTATATTAAAATAAATTATTAAA
1 TTATATTTATATTAAAATAAATTATTAAA
149288 TTAAATAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
29 27 0.36
30 7 0.09
31 11 0.14
32 16 0.21
33 3 0.04
34 1 0.01
36 11 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATATTTATATTAAAATAAATTATTAAAAT
Found at i:149290 original size:18 final size:17
Alignment explanation
Indices: 149263--149296 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
149253 ATTAAAATTA
*
149263 TATTATATTAAAATAAAT
1 TATTAAATT-AAATAAAT
149281 TATTAAATTAAATAAA
1 TATTAAATTAAATAAA
149297 AAAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATTAAATTAAATAAAT
Found at i:149652 original size:2 final size:2
Alignment explanation
Indices: 149645--149676 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
149635 CTCTATTCTG
149645 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
149677 ATTTATCCTA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:152882 original size:30 final size:30
Alignment explanation
Indices: 152848--152929 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 30
152838 TTTTGAAAAT
*
152848 TTAAATT-TTATAATATTTTATTTTATTTAA
1 TTAAATTATTATAATA-ATTATTTTATTTAA
* *
152878 TTAAATTATTATTATAATTATTTTATTTTA
1 TTAAATTATTATAATAATTATTTTATTTAA
*
152908 TT---TTA-TAAAATAATTATTTTAT
1 TTAAATTATTATAATAATTATTTTAT
152930 AAAATAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 15 0.33
27 3 0.07
30 21 0.46
31 7 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTAAATTATTATAATAATTATTTTATTTAA
Found at i:152900 original size:35 final size:34
Alignment explanation
Indices: 152851--152954 Score: 111
Period size: 35 Copynumber: 2.9 Consensus size: 34
152841 TGAAAATTTA
*
152851 AATT-TTATAATATTTTATTTTATTTAATTAAAT
1 AATTATTATAATATTTTATTTTATTTAATAAAAT
* *
152884 TATTATTATAATTATTTTATTTTATTTTATAAAAT
1 AATTATTATAA-TATTTTATTTTATTTAATAAAAT
* *
152919 AATTATTTTATAAAATAATTATTTTATTTTAATAAA
1 AATTA--TTATAATAT-TTTATTTTA-TTTAATAAA
152955 TTAAATGAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
33 3 0.05
34 6 0.10
35 25 0.43
36 2 0.03
37 14 0.24
38 8 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
AATTATTATAATATTTTATTTTATTTAATAAAAT
Found at i:152924 original size:16 final size:16
Alignment explanation
Indices: 152905--152945 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
152895 TTATTTTATT
152905 TTATTTTATAAAATAA
1 TTATTTTATAAAATAA
152921 TTATTTTATAAAATAA
1 TTATTTTATAAAATAA
152937 TTATTTTAT
1 TTATTTTAT
152946 TTTAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTTTATAAAATAA
Found at i:152945 original size:21 final size:20
Alignment explanation
Indices: 152900--152954 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 20
152890 TATAATTATT
152900 TTATTTTATTTTATAAAATA
1 TTATTTTATTTTATAAAATA
152920 --A--TTATTTTATAAAATAA
1 TTATTTTATTTTATAAAAT-A
152937 TTATTTTATTTTAATAAA
1 TTATTTTATTTT-ATAAA
152955 TTAAATGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
16 14 0.48
17 1 0.03
18 1 0.03
19 1 0.03
21 7 0.24
22 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTTTATTTTATAAAATA
Found at i:152955 original size:21 final size:20
Alignment explanation
Indices: 152857--152955 Score: 68
Period size: 21 Copynumber: 5.1 Consensus size: 20
152847 TTTAAATTTT
152857 ATAA-TATTTTATTTTAT--
1 ATAATTATTTTATTTTATAA
* **
152874 TTAATTAAATTATTATTATAA
1 ATAATTATTTTATT-TTATAA
* *
152895 TTATTTTATTTTATTTTATAAA
1 ATA-ATTATTTTATTTTAT-AA
152917 ATAATTATTTTA---TA-AA
1 ATAATTATTTTATTTTATAA
152933 ATAATTATTTTATTTTAATAA
1 ATAATTATTTTATTTT-ATAA
152954 AT
1 AT
152956 TAAATGAGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
16 14 0.22
17 3 0.05
18 9 0.14
19 5 0.08
20 1 0.02
21 19 0.30
22 12 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATAATTATTTTATTTTATAA
Found at i:154735 original size:2 final size:2
Alignment explanation
Indices: 154728--154762 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
154718 CACATAAAAG
*
154728 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
154763 GAGTCAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:156692 original size:10 final size:9
Alignment explanation
Indices: 156668--156696 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
156658 TTTTATATAT
156668 AATTTTTTC
1 AATTTTTTC
156677 AATTTTTTC
1 AATTTTTTC
156686 AATTTTTTC
1 AATTTTTTC
156695 AA
1 AA
156697 CTTTAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (9 bp):
AATTTTTTC
Found at i:159223 original size:16 final size:17
Alignment explanation
Indices: 159181--159223 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
159171 TTTGATATTT
*
159181 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
*
159198 ATAAAA-TTATGATT-A
1 ATAAAATTTATAATTAA
159213 ATAAAATTTAT
1 ATAAAATTTAT
159224 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:159776 original size:10 final size:10
Alignment explanation
Indices: 159740--159776 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
159730 ATGCATAAAA
159740 TTTTTTTCTT
1 TTTTTTTCTT
*
159750 TTTCTTTCTT
1 TTTTTTTCTT
159760 TTCTTTTTCTT
1 TT-TTTTTCTT
159771 TTTTTT
1 TTTTTT
159777 ATCAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:159776 original size:15 final size:15
Alignment explanation
Indices: 159740--159776 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
159730 ATGCATAAAA
159740 TTTTTTTCTTTTTCT
1 TTTTTTTCTTTTTCT
*
159755 TTCTTTTCTTTTTCT
1 TTTTTTTCTTTTTCT
159770 TTTTTTT
1 TTTTTTT
159777 ATCAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTCTTTTTCT
Found at i:159944 original size:10 final size:9
Alignment explanation
Indices: 159912--159951 Score: 57
Period size: 8 Copynumber: 4.6 Consensus size: 9
159902 AAATAATTAA
159912 TAATATTTT
1 TAATATTTT
159921 TAAT-TTTT
1 TAATATTTT
159929 T-ATATTTT
1 TAATATTTT
159937 TAATTATTTT
1 TAA-TATTTT
159947 TAATA
1 TAATA
159952 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 2 0.07
8 10 0.36
9 7 0.25
10 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TAATATTTT
Found at i:160437 original size:155 final size:155
Alignment explanation
Indices: 160257--160728 Score: 822
Period size: 153 Copynumber: 3.0 Consensus size: 155
160247 ATAAATTTAT
* * * *
160257 AATATTTTAAACCATAAAAAATAACATAAATATAAATATAAACACATTAACTGTTCCTTTTATTT
1 AATACTTTAAACTATAAAAAATAACACAAATAAAAATATAAACACATTAACTGTTCCTTTTATTT
160322 CTCTTTCTCATTTTCTTTCTTCTCTTTTTTCTTTTTTTTCTTTTCTTCTCTCTCCCATGAAAAAT
66 CTCTTTCTCATTTTCTTTCTTCTCTTTTTTCTTTTTTTTCTTTTCTTCTCTCTCCCATGAAAAAT
160387 ATATCTAAATATATGAATATATCTA
131 ATATCTAAATATATGAATATATCTA
*
160412 AATACTTTAAATTATAAAAAATAACACAAATAAAAATATAAACACATTAACTGTTCCTTTTATTT
1 AATACTTTAAACTATAAAAAATAACACAAATAAAAATATAAACACATTAACTGTTCCTTTTATTT
160477 CTCTTTCTCATTTTCTTTCTTCTCTTTTTTC--TTTTTTCTTTTCTTCTCTCTCCCATGAAAAAT
66 CTCTTTCTCATTTTCTTTCTTCTCTTTTTTCTTTTTTTTCTTTTCTTCTCTCTCCCATGAAAAAT
160540 ATATCTAAATATATGAATATATCTA
131 ATATCTAAATATATGAATATATCTA
*
160565 AATACTTTAAACTATAAAAAATAACACAAATACAAATATAAACACATTAACTGTTCCTTTTATTT
1 AATACTTTAAACTATAAAAAATAACACAAATAAAAATATAAACACATTAACTGTTCCTTTTATTT
*
160630 CTCTTTCTTATTTTCTTTCTTCTCTTTTTTCTTTTTTTTTCTTTTCATCTTTCTCTCTCCCATGA
66 CTCTTTCTCATTTTCTTTCTTCTCTTTTTTC-TTTTTTTTC-TTT--TC-TTCTCTCTCCCATGA
160695 AAAATATATCTAAATATATGAATATATCTA
126 AAAATATATCTAAATATATGAATATATCTA
160725 AATA
1 AATA
160729 TATATAAATT
Statistics
Matches: 302, Mismatches: 8, Indels: 9
0.95 0.03 0.03
Matches are distributed among these distances:
153 150 0.50
155 91 0.30
156 7 0.02
157 3 0.01
159 2 0.01
160 49 0.16
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (155 bp):
AATACTTTAAACTATAAAAAATAACACAAATAAAAATATAAACACATTAACTGTTCCTTTTATTT
CTCTTTCTCATTTTCTTTCTTCTCTTTTTTCTTTTTTTTCTTTTCTTCTCTCTCCCATGAAAAAT
ATATCTAAATATATGAATATATCTA
Found at i:160444 original size:16 final size:18
Alignment explanation
Indices: 160425--160457 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
160415 ACTTTAAATT
160425 ATAAAAA-AT-AACACAA
1 ATAAAAATATAAACACAA
160441 ATAAAAATATAAACACA
1 ATAAAAATATAAACACA
160458 TTAACTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (18 bp):
ATAAAAATATAAACACAA
Found at i:160659 original size:16 final size:16
Alignment explanation
Indices: 160631--160663 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
160621 CTTTTATTTC
160631 TCTTTCTTATTTTCTT
1 TCTTTCTTATTTTCTT
160647 TCTTCTCTT-TTTTCTT
1 TCTT-TCTTATTTTCTT
160663 T
1 T
160664 TTTTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TCTTTCTTATTTTCTT
Found at i:160664 original size:21 final size:19
Alignment explanation
Indices: 160622--160675 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 19
160612 TAACTGTTCC
*
160622 TTTTATTTCTCTTTCTTAT
1 TTTTTTTTCTCTTTCTTAT
* *
160641 TTTCTTTCTTCTCTTTTTTCT
1 TTT-TTT-TTCTCTTTCTTAT
160662 TTTTTTTTCT-TTTC
1 TTTTTTTTCTCTTTC
160676 ATCTTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 3 0.10
19 7 0.24
20 5 0.17
21 14 0.48
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTTTCTCTTTCTTAT
Found at i:160682 original size:22 final size:23
Alignment explanation
Indices: 160627--160683 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
160617 GTTCCTTTTA
160627 TTTCTCTTTCTTATTTTCTTTCT
1 TTTCTCTTTCTTATTTTCTTTCT
* *
160650 TCTCTTTTTTCTT-TTTT-TTTCT
1 TTTC-TCTTTCTTATTTTCTTTCT
160672 TTTCATCTTTCT
1 TTTC-TCTTTCT
160684 CTCTCCCATG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 14 0.50
23 7 0.25
24 7 0.25
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTCTCTTTCTTATTTTCTTTCT
Found at i:160711 original size:10 final size:10
Alignment explanation
Indices: 160696--160737 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
160686 CTCCCATGAA
160696 AAATATATCT
1 AAATATATCT
160706 AAATATA--T
1 AAATATATCT
*
160714 GAATATATCT
1 AAATATATCT
*
160724 AAATATATAT
1 AAATATATCT
160734 AAAT
1 AAAT
160738 TAATAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.26
10 20 0.74
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (10 bp):
AAATATATCT
Found at i:160720 original size:18 final size:18
Alignment explanation
Indices: 160697--160731 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
160687 TCCCATGAAA
160697 AATATATCTAAATATATG
1 AATATATCTAAATATATG
160715 AATATATCTAAATATAT
1 AATATATCTAAATATAT
160732 ATAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (18 bp):
AATATATCTAAATATATG
Found at i:161162 original size:21 final size:22
Alignment explanation
Indices: 161123--161164 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
161113 TATAGATAGA
161123 TAAATATATAGATATAAAAAAT
1 TAAATATATAGATATAAAAAAT
161145 TAAA-ATATA-ATATAAAAAAT
1 TAAATATATAGATATAAAAAAT
161165 AATATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAATATATAGATATAAAAAAT
Found at i:161170 original size:17 final size:17
Alignment explanation
Indices: 161124--161171 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 17
161114 ATAGATAGAT
161124 AAAT-ATATAGATATAAA
1 AAATAATATA-ATATAAA
161141 AAATTAAAATATAATATAAA
1 AAA-T--AATATAATATAAA
161161 AAATAATATAA
1 AAATAATATAA
161172 ATATTGTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 10 0.37
18 1 0.04
19 1 0.04
20 10 0.37
21 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AAATAATATAATATAAA
Found at i:161344 original size:38 final size:36
Alignment explanation
Indices: 161297--161371 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 36
161287 TGATATGTAC
*
161297 ATAATATAAATATACGT-ATATATAAAAATATAAATAAA
1 ATAAAATAAAT-TA-GTAATATATAAAAA-ATAAATAAA
* *
161335 ATAAAATAAATTATTAATATATAAAAAATATATAAA
1 ATAAAATAAATTAGTAATATATAAAAAATAAATAAA
161371 A
1 A
161372 ATATCATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 10 0.30
37 13 0.39
38 10 0.30
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (36 bp):
ATAAAATAAATTAGTAATATATAAAAAATAAATAAA
Found at i:161373 original size:37 final size:34
Alignment explanation
Indices: 161313--161404 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 34
161303 TAAATATACG
*
161313 TATATATAAAAATATAAATAAAATAAAATAAATTATTAA
1 TATATA-AAAAATATATA-AAAATAAAAT--ATT-TTAA
**
161352 TATATAAAAAATATATAAAAATATCATATTTTAA
1 TATATAAAAAATATATAAAAATAAAATATTTTAA
161386 -ATATAAAAAATAATATAAA
1 TATATAAAAAAT-ATATAAA
161405 TACCAACATA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
33 11 0.22
34 11 0.22
35 3 0.06
37 8 0.16
38 10 0.20
39 6 0.12
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (34 bp):
TATATAAAAAATATATAAAAATAAAATATTTTAA
Found at i:161448 original size:20 final size:20
Alignment explanation
Indices: 161423--161468 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
161413 TATAATTTTT
161423 TTTCTTTTTTTTCTCCTTTC
1 TTTCTTTTTTTTCTCCTTTC
* *
161443 TTTCTTTTTTTTTTTCTTTC
1 TTTCTTTTTTTTCTCCTTTC
161463 TTTCTT
1 TTTCTT
161469 GCCTTCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTTTCTCCTTTC
Found at i:163667 original size:2 final size:2
Alignment explanation
Indices: 163658--163690 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
163648 AGTTTTTTAG
163658 TA TA -A 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
163691 AAGAAAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:164119 original size:6 final size:6
Alignment explanation
Indices: 164109--164152 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
164099 CCATGGGATT
* * * *
164109 GATGAT GATGAA GATGAA GATGAA GAAGAA GACGAA GAAGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GA
164153 AGGATTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.52, C:0.02, G:0.34, T:0.11
Consensus pattern (6 bp):
GATGAA
Found at i:164130 original size:12 final size:12
Alignment explanation
Indices: 164115--164152 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
164105 GATTGATGAT
*
164115 GATGAAGATGAA
1 GATGAAGAAGAA
164127 GATGAAGAAGAA
1 GATGAAGAAGAA
*
164139 GACGAAGAAGAA
1 GATGAAGAAGAA
164151 GA
1 GA
164153 AGGATTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.55, C:0.03, G:0.34, T:0.08
Consensus pattern (12 bp):
GATGAAGAAGAA
Found at i:164848 original size:2 final size:2
Alignment explanation
Indices: 164841--164888 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
164831 GTAGGGAGGG
164841 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
164883 GA GA GA
1 GA GA GA
164889 ACAAAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:165630 original size:4 final size:4
Alignment explanation
Indices: 165621--165645 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
165611 GGCTGCGGCT
165621 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
165646 CGAAGGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:169883 original size:2 final size:2
Alignment explanation
Indices: 169876--169916 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
169866 TGATCGTGAA
*
169876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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 AT A
169917 ATCTCCACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:172121 original size:2 final size:2
Alignment explanation
Indices: 172114--172158 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
172104 CATTCGAACA
172114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
172155 AT AT
1 AT AT
172159 GCGCATGCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:173299 original size:2 final size:2
Alignment explanation
Indices: 173292--173332 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
173282 TAAAAGTTTA
173292 AG AG 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 AG AG A
173333 ATAAACATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:179328 original size:12 final size:12
Alignment explanation
Indices: 179313--179348 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
179303 ATAATATAAG
*
179313 ATATATATATAT
1 ATATATGTATAT
179325 ATATATGTATAT
1 ATATATGTATAT
*
179337 ATGTATGTATAT
1 ATATATGTATAT
179349 TGGAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:179457 original size:3 final size:3
Alignment explanation
Indices: 179449--179514 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
179439 TCTTCCTAAA
*
179449 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
179497 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
179515 GGCTTTCATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:179906 original size:2 final size:2
Alignment explanation
Indices: 179899--179937 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
179889 TAACCCATTT
179899 TA TA TA TA 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 TA TA TA TA T
179938 TGCGTTTGCC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:180084 original size:2 final size:2
Alignment explanation
Indices: 180079--180109 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
180069 CATATATGAC
180079 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 A
180110 CATACATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:180751 original size:2 final size:2
Alignment explanation
Indices: 180744--180773 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
180734 CTTGTTGGCA
180744 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
180774 GTGTGTGTGT
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:197573 original size:3 final size:3
Alignment explanation
Indices: 197565--197593 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
197555 AAAGAAGCAA
197565 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
197594 ATAGACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:201312 original size:82 final size:82
Alignment explanation
Indices: 201175--201340 Score: 287
Period size: 82 Copynumber: 2.0 Consensus size: 82
201165 ATTGTGTGTA
*
201175 TTTTCTAGTAATATTCTAAGTCTAATCATTCCCTTTTCTGAAAGTTTATTATACTAGCCACTGCT
1 TTTTCTAGTAATATTCTAAGTCTAATCATTCCCTTTTCTGAAAATTTATTATACTAGCCACTGCT
201240 GCATTTATAATGCTATT
66 GCATTTATAATGCTATT
* *
201257 TTTTCTAGTAATATTCTAAGTCTAATCATTCCCTTTTTTGAAAATTTGTTATACTAGCCACTGCT
1 TTTTCTAGTAATATTCTAAGTCTAATCATTCCCTTTTCTGAAAATTTATTATACTAGCCACTGCT
* *
201322 GCTTTTATAATTCTATT
66 GCATTTATAATGCTATT
201339 TT
1 TT
201341 CCAATACGGG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (82 bp):
TTTTCTAGTAATATTCTAAGTCTAATCATTCCCTTTTCTGAAAATTTATTATACTAGCCACTGCT
GCATTTATAATGCTATT
Found at i:204796 original size:16 final size:16
Alignment explanation
Indices: 204777--204808 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
204767 AATATATATA
204777 TATGTATATGTGTGTG
1 TATGTATATGTGTGTG
*
204793 TATGTGTATGTGTGTG
1 TATGTATATGTGTGTG
204809 CATACTGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (16 bp):
TATGTATATGTGTGTG
Found at i:205185 original size:2 final size:2
Alignment explanation
Indices: 205178--205210 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
205168 ATTCATGGAT
*
205178 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
205211 TTTAATTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:213989 original size:13 final size:14
Alignment explanation
Indices: 213971--214009 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
213961 ATTAAAAAAC
*
213971 TTAATATTTTTAA-
1 TTAATATTTTAAAT
*
213984 TTAATATTATAAAT
1 TTAATATTTTAAAT
213998 TTAATATTTTAA
1 TTAATATTTTAA
214010 TAGATGATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATATTTTAAAT
Found at i:218600 original size:74 final size:74
Alignment explanation
Indices: 218479--218636 Score: 289
Period size: 74 Copynumber: 2.1 Consensus size: 74
218469 TTATTGTGAG
**
218479 TTAATTTCCAAAGTAGTGCAGAAACTTGTGCTTTCTAATGTGTATACATTATGATTGAAGGTGTC
1 TTAATTTTTAAAGTAGTGCAGAAACTTGTGCTTTCTAATGTGTATACATTATGATTGAAGGTGTC
218544 TGGAGTTCT
66 TGGAGTTCT
218553 TTAATTTTTAAAGTAGTGCAGAAACTTGTGCTTTCTAATGTGTATACATTATGATTGAAGGTGTC
1 TTAATTTTTAAAGTAGTGCAGAAACTTGTGCTTTCTAATGTGTATACATTATGATTGAAGGTGTC
*
218618 TGTAGTTCT
66 TGGAGTTCT
218627 TTAATTTTTA
1 TTAATTTTTA
218637 GTTGTCATGC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 81 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (74 bp):
TTAATTTTTAAAGTAGTGCAGAAACTTGTGCTTTCTAATGTGTATACATTATGATTGAAGGTGTC
TGGAGTTCT
Found at i:218757 original size:2 final size:2
Alignment explanation
Indices: 218750--218786 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
218740 CCAATGCCAC
218750 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
218787 GTAGTATAGA
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:219544 original size:2 final size:2
Alignment explanation
Indices: 219537--219564 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
219527 CAAAGGATAC
219537 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
219565 GGAGGCTGAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:220014 original size:2 final size:2
Alignment explanation
Indices: 220007--220037 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
219997 ACTACCTACC
220007 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
220038 GTTTTTGAAC
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:228923 original size:19 final size:19
Alignment explanation
Indices: 228899--228939 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
228889 AATTTGATTT
*
228899 CTTCCCATTATATTGTTGA
1 CTTCCCATTATACTGTTGA
*
228918 CTTCCCATTATGCTGTTGA
1 CTTCCCATTATACTGTTGA
228937 CTT
1 CTT
228940 GACTTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.24, G:0.12, T:0.46
Consensus pattern (19 bp):
CTTCCCATTATACTGTTGA
Found at i:231334 original size:30 final size:30
Alignment explanation
Indices: 231298--231410 Score: 79
Period size: 30 Copynumber: 3.6 Consensus size: 30
231288 TGTAGTGGTT
231298 ATATTTTATTATAATATAATAATATTTAAA
1 ATATTTTATTATAATATAATAATATTTAAA
* *
231328 ATATTTTA-TATTTATATAAATTAAAATATGTTAAT
1 ATATTTTATTA-TAATAT-AA-T--AATAT-TTAAA
* * *
231363 A-ATTTATATTATATTAT-ATTATATTTTAA
1 ATATTT-TATTATAATATAATAATATTTAAA
*
231392 ATATTTTATTTATATTATA
1 ATATTTTA-TTATAATATA
231411 TTTATATCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 21
0.70 0.08 0.23
Matches are distributed among these distances:
29 8 0.12
30 30 0.46
31 2 0.03
32 2 0.03
33 1 0.02
34 9 0.14
35 11 0.17
36 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
ATATTTTATTATAATATAATAATATTTAAA
Found at i:231376 original size:5 final size:5
Alignment explanation
Indices: 231366--231417 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
231356 TGTTAATAAT
* * *
231366 TTATA TTATA TTATA TTATA TTTTA -AATA TTTTA TTTATA TTATA TTTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA -TTATA
231417 T
1 T
231418 CAATGTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 2 0.05
5 27 0.71
6 9 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:231411 original size:30 final size:31
Alignment explanation
Indices: 231304--231417 Score: 99
Period size: 31 Copynumber: 3.6 Consensus size: 31
231294 GGTTATATTT
* * *
231304 TATTATAATATAATAATATTTAAAATATTTTA
1 TATTATATTAT-ATTATATTTTAAATATTTTA
* * *
231336 TATT-TATATAAATTAAAATATGTT-AATAATTTA
1 TATTATAT-TATATT---ATATTTTAAATATTTTA
231369 TATTATATTATATTATATTTTAAATATTTTA
1 TATTATATTATATTATATTTTAAATATTTTA
231400 T-TTATATTATATTTATAT
1 TATTATATTATA-TTATAT
231418 CAATGTAACT
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
30 16 0.24
31 19 0.29
32 6 0.09
33 17 0.26
34 8 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
TATTATATTATATTATATTTTAAATATTTTA
Found at i:232150 original size:22 final size:20
Alignment explanation
Indices: 232123--232163 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
232113 AAAATATTAA
232123 TTAATAAAATAATTTTTTAAAC
1 TTAAT-AAAT-ATTTTTTAAAC
*
232145 TTAATACATATTTTTTAAA
1 TTAATAAATATTTTTTAAA
232164 TATGTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATAAATATTTTTTAAAC
Found at i:232247 original size:16 final size:17
Alignment explanation
Indices: 232222--232266 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
232212 AATACATCAA
232222 TTAAAAAT-AAAATAAT
1 TTAAAAATAAAAATAAT
*
232238 TTAAATATAAAAATAAT
1 TTAAAAATAAAAATAAT
*
232255 TAATAAAATAAA
1 TTA-AAAATAAA
232267 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 7 0.29
17 10 0.42
18 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAAATAAAAATAAT
Found at i:232266 original size:24 final size:22
Alignment explanation
Indices: 232223--232267 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
232213 ATACATCAAT
**
232223 TAAAAATAAAATAATTTAAATA
1 TAAAAATAAAATAAAATAAATA
232245 TAAAAATAATTAATAAAATAAAT
1 TAAAAATAA--AATAAAATAAAT
232268 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
24 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAAATAAAATAAAATAAATA
Found at i:233459 original size:100 final size:100
Alignment explanation
Indices: 233352--233972 Score: 922
Period size: 100 Copynumber: 6.2 Consensus size: 100
233342 AAAGTTTTAG
* * * * *
233352 TATAAAATGATATTAATTTAAATGATATTAATGTTTACTAAATTTATAATATATAACATCATATT
1 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATATT
* *
233417 TATTTTTATCAAA-TTTTTGATATATAGAGTAGTAT
66 TATTTTTATCAAACTTTTAG-TATATAGAGTAGCAT
* * *
233452 TATAAAATGATATTAATTTAAGTAATATTAATTTTTACCAAACTTATAATATATAACGTCATATT
1 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATA-T
*
233517 TTATTTTTATCAAACTTTT-GATATATAAAGTAGCAT
65 TTATTTTTATCAAACTTTTAG-TATATAGAGTAGCAT
* *
233553 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTATCAAACTTATAGTATATAACATCATATT
1 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATATT
* *
233618 TATTTTTATCAAACTTTTAGCATATAGAGTAGTAT
66 TATTTTTATCAAACTTTTAGTATATAGAGTAGCAT
* * *
233653 TATAAAGTAATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAGTATATAATATCATATT
1 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATATT
* **
233718 TATTTTTGTCAAACTTTTAGTATATAGAAAAGCAT
66 TATTTTTATCAAACTTTTAGTATATAGAGTAGCAT
* *
233753 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAGTATATAACGTCATATT
1 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATATT
* * * *
233818 TAGTGTTGTCAAACTTTTAGTATATAGACTAGCAT
66 TATTTTTATCAAACTTTTAGTATATAGAGTAGCAT
* *
233853 TATAAAAGTGATATTAACTTAAGTGATATTAATTTTTATCAAACTTATAATATATAACATCATAT
1 TAT-AAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATAT
*
233918 TTATTTTTATCAAACTTTTAGTATATAAAGTAGCAT
65 TTATTTTTATCAAACTTTTAGTATATAGAGTAGCAT
233954 TATAAAGTGATATTAATTT
1 TATAAAGTGATATTAATTT
233973 TTACCAAATT
Statistics
Matches: 476, Mismatches: 41, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
100 292 0.61
101 180 0.38
102 4 0.01
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (100 bp):
TATAAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATATT
TATTTTTATCAAACTTTTAGTATATAGAGTAGCAT
Found at i:233568 original size:201 final size:200
Alignment explanation
Indices: 233352--234190 Score: 1111
Period size: 201 Copynumber: 4.3 Consensus size: 200
233342 AAAGTTTTAG
* * * * *
233352 TATAAAATGATATTAATTTAAATGATATTAATGTTTACTAAATTTATAATATATAACATCATATT
1 TATAAAGTGATATTAATTTAAATGATATTAATTTTTACCAAACTTATAGTATATAACATCATATT
* *
233417 TATTTTTATCAAA-TTTTTGATATATAGAGTAGTATTATAAAATGATATTAATTTAAGTAATATT
66 TATTTTTATCAAACTTTTAG-TATATAGAGTAGCATTATAAAATGATATTAATTTAAGTAATATT
*
233481 AATTTTTACCAAACTTATAATATATAACGTCATATTTTATTTTTATCAAACTTTT-GATATATAA
130 AATTTTTACCAAACTTATAATATATAACATCATA-TTTATTTTTATCAAACTTTTAG-TATATAA
233545 AGTAGCAT
193 AGTAGCAT
* *
233553 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTATCAAACTTATAGTATATAACATCATATT
1 TATAAAGTGATATTAATTTAAATGATATTAATTTTTACCAAACTTATAGTATATAACATCATATT
* * * * *
233618 TATTTTTATCAAACTTTTAGCATATAGAGTAGTATTATAAAGTAATATTAATTTAAGTGATATTA
66 TATTTTTATCAAACTTTTAGTATATAGAGTAGCATTATAAAATGATATTAATTTAAGTAATATTA
* * *
233683 ATTTTTACCAAACTTATAGTATATAATATCATATTTATTTTTGTCAAACTTTTAGTATATAGAA-
131 ATTTTTACCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTAGTATATA-AAG
*
233747 AAGCAT
195 TAGCAT
* *
233753 TATAAAGTGATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAGTATATAACGTCATATT
1 TATAAAGTGATATTAATTTAAATGATATTAATTTTTACCAAACTTATAGTATATAACATCATATT
* * * * * *
233818 TAGTGTTGTCAAACTTTTAGTATATAGACTAGCATTATAAAAGTGATATTAACTTAAGTGATATT
66 TATTTTTATCAAACTTTTAGTATATAGAGTAGCATTATAAAA-TGATATTAATTTAAGTAATATT
*
233883 AATTTTTATCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTAGTATATAAAG
130 AATTTTTACCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTAGTATATAAAG
233948 TAGCAT
195 TAGCAT
* *
233954 TATAAA--G-------------TGATATTAATTTTTACCAAATTTATAGTATATAACGTCATATT
1 TATAAAGTGATATTAATTTAAATGATATTAATTTTTACCAAACTTATAGTATATAACATCATATT
* * *
234004 TATTTTTGTCAAATTTTTAGTATATAGAGTAGCATTATAAAGTGATATTAATTTAAGTAATATTA
66 TATTTTTATCAAACTTTTAGTATATAGAGTAGCATTATAAAATGATATTAATTTAAGTAATATTA
** * * * *
234069 ATTTTTATTAAACTTATAGTATATAACGTCATATTTATTTTTGTCAAACTTTTAATATATAAAGT
131 ATTTTTACCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTAGTATATAAAGT
**
234134 AATAT
196 AGCAT
* * *
234139 TATAAAATGATATTAATTTAAATAATATTAATTTTTACCAAACTTCTAGTAT
1 TATAAAGTGATATTAATTTAAATGATATTAATTTTTACCAAACTTATAGTAT
234191 CCAATATAAA
Statistics
Matches: 567, Mismatches: 51, Indels: 41
0.86 0.08 0.06
Matches are distributed among these distances:
185 90 0.16
186 79 0.14
187 1 0.00
199 1 0.00
200 157 0.28
201 234 0.41
202 5 0.01
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (200 bp):
TATAAAGTGATATTAATTTAAATGATATTAATTTTTACCAAACTTATAGTATATAACATCATATT
TATTTTTATCAAACTTTTAGTATATAGAGTAGCATTATAAAATGATATTAATTTAAGTAATATTA
ATTTTTACCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTAGTATATAAAGT
AGCAT
Found at i:233575 original size:15 final size:15
Alignment explanation
Indices: 233557--233586 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
233547 TAGCATTATA
233557 AAGTGATATTAATTT
1 AAGTGATATTAATTT
233572 AAGTGATATTAATTT
1 AAGTGATATTAATTT
233587 TTATCAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
AAGTGATATTAATTT
Found at i:233624 original size:36 final size:35
Alignment explanation
Indices: 233577--233946 Score: 118
Period size: 36 Copynumber: 10.9 Consensus size: 35
233567 AATTTAAGTG
*
233577 ATATTAATTTTTATCAAACTTATAGTATATAACATC
1 ATATTTATTTTTATCAAACTTATAGTATATAA-ATC
* * *
233613 ATATTTATTTTTATCAAACTTTTAGCATATAGA--
1 ATATTTATTTTTATCAAACTTATAGTATATAAATC
* * * * * * * *
233646 GTA-GTA---TTAT-AAAGTAATATTAATTTAAGTG
1 ATATTTATTTTTATCAAACTTATAGT-ATATAAATC
* *
233677 ATATTAATTTTTACCAAACTTATAGTATATAATATC
1 ATATTTATTTTTATCAAACTTATAGTATATAA-ATC
* *
233713 ATATTTATTTTTGTCAAACTTTTAGTATATAGAA--
1 ATATTTATTTTTATCAAACTTATAGTATATA-AATC
** * * * * * *
233747 A-A-GCA---TTAT-AAAGTGATATTAATTTAAGTG
1 ATATTTATTTTTATCAAACTTATAGT-ATATAAATC
* * *
233777 ATATTAATTTTTACCAAACTTATAGTATATAACGTC
1 ATATTTATTTTTATCAAACTTATAGTATATAA-ATC
* * * * *
233813 ATATTTAGTGTTGTCAAACTTTTAGTATATAGA-C
1 ATATTTATTTTTATCAAACTTATAGTATATAAATC
** * * * * * *
233847 -TA-GCA---TTATAAAAGTGATATTA-ACTTAAGTG
1 ATATTTATTTTTATCAAACTTATAGTATA--TAAATC
* *
233878 ATATTAATTTTTATCAAACTTATAATATATAACATC
1 ATATTTATTTTTATCAAACTTATAGTATATAA-ATC
*
233914 ATATTTATTTTTATCAAACTTTTAGTATATAAA
1 ATATTTATTTTTATCAAACTTATAGTATATAAA
233947 GTAGCATTAT
Statistics
Matches: 229, Mismatches: 75, Indels: 61
0.63 0.21 0.17
Matches are distributed among these distances:
28 15 0.07
29 26 0.11
30 3 0.01
31 3 0.01
32 8 0.03
33 6 0.03
34 2 0.01
35 21 0.09
36 143 0.62
37 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (35 bp):
ATATTTATTTTTATCAAACTTATAGTATATAAATC
Found at i:233680 original size:15 final size:15
Alignment explanation
Indices: 233657--233686 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
233647 TAGTATTATA
233657 AAGTAATATTAATTT
1 AAGTAATATTAATTT
*
233672 AAGTGATATTAATTT
1 AAGTAATATTAATTT
233687 TTACCAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (15 bp):
AAGTAATATTAATTT
Found at i:233758 original size:301 final size:285
Alignment explanation
Indices: 233346--234190 Score: 1158
Period size: 301 Copynumber: 2.9 Consensus size: 285
233336 AAAAATAAAG
* * * * *
233346 TTTTAGTATA-AAA-TGATATTAATTTAAATGATATTAATGTTTACTAAATTTATAATATATAAC
1 TTTTAGTATATAAAGTAATATTAATTTAAGTGATATTAATTTTTACCAAATTTATAGTATATAAC
* * * *
233409 ATCATATTTATTTTTATCAAATTTTTGATATATAGAGTAGTATTATAAAATGATATTAATTTAAG
66 ATCATATTTATTTTTGTCAAATTTTAG-TATATAGAGTAGCATTATAAAGTGATATTAATTTAAG
* *
233474 TAATATTAATTTTTACCAAACTTATAATATATAACGTCATATTTTATTTTTATCAAACTTTTGAT
130 TAATATTAATTTTTACCAAACTTATAGTATATAACGTCATA-TTTATTTTTGTCAAACTTTT-AT
233539 ATATAAAGTAGCATTATAAAGTGATATTAATTTAAGTGATATTAATTTTTATCAAACTTATAGTA
193 ATATAAAGTAGCATTATAAAGTGATATTAATTTAAGTGATATTAATTTTTATCAAACTTATAGTA
233604 TATAACATCATATTTATTTTTATCAAAC
258 TATAACATCATATTTATTTTTATCAAAC
*
233632 TTTTAGCATATAGAGTAGTATTATAAAGTAATATTAATTTAAGTGATATTAATTTTTACCAAACT
1 ---T----T-T----TAGTA-TATAAAGTAATATTAATTTAAGTGATATTAATTTTTACCAAATT
* **
233697 TATAGTATATAATATCATATTTATTTTTGTCAAACTTTTAGTATATAGAAAAGCATTATAAAGTG
53 TATAGTATATAACATCATATTTATTTTTGTCAAA-TTTTAGTATATAGAGTAGCATTATAAAGTG
* * *
233762 ATATTAATTTAAGTGATATTAATTTTTACCAAACTTATAGTATATAACGTCATATTTAGTGTTGT
117 ATATTAATTTAAGTAATATTAATTTTTACCAAACTTATAGTATATAACGTCATATTTATTTTTGT
* * *
233827 CAAACTTTTAGTATATAGACTAGCATTATAAAAGTGATATTAACTTAAGTGATATTAATTTTTAT
182 CAAACTTTTA-TATATAAAGTAGCATTAT-AAAGTGATATTAATTTAAGTGATATTAATTTTTAT
*
233892 CAAACTTATAATATATAACATCATATTTATTTTTATCAAAC
245 CAAACTTATAGTATATAACATCATATTTATTTTTATCAAAC
** *
233933 TTTTAGTATATAAAGTAGCATT-A-TAAAGTGATATTAATTTTTACCAAATTTATAGTATATAAC
1 TTTTAGTATATAAAGTAATATTAATTTAAGTGATATTAATTTTTACCAAATTTATAGTATATAAC
*
233996 GTCATATTTATTTTTGTCAAATTTTTAGTATATAGAGTAGCATTATAAAGTGATATTAATTTAAG
66 ATCATATTTATTTTTGTCAAA-TTTTAGTATATAGAGTAGCATTATAAAGTGATATTAATTTAAG
**
234061 TAATATTAATTTTTATTAAACTTATAGTATATAACGTCATATTTATTTTTGTCAAACTTTTAATA
130 TAATATTAATTTTTACCAAACTTATAGTATATAACGTCATATTTATTTTTGTCAAACTTTT-ATA
** * * * * *
234126 TATAAAGTAATATTATAAAATGATATTAATTTAAATAATATTAATTTTTACCAAACTTCTAGTAT
194 TATAAAGTAGCATTATAAAGTGATATTAATTTAAGTGATATTAATTTTTATCAAACTTATAGTAT
234191 CCAATATAAA
Statistics
Matches: 493, Mismatches: 47, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
285 42 0.09
286 168 0.34
287 2 0.00
288 12 0.02
289 6 0.01
293 2 0.00
294 2 0.00
298 6 0.01
299 3 0.01
300 36 0.07
301 209 0.42
302 5 0.01
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (285 bp):
TTTTAGTATATAAAGTAATATTAATTTAAGTGATATTAATTTTTACCAAATTTATAGTATATAAC
ATCATATTTATTTTTGTCAAATTTTAGTATATAGAGTAGCATTATAAAGTGATATTAATTTAAGT
AATATTAATTTTTACCAAACTTATAGTATATAACGTCATATTTATTTTTGTCAAACTTTTATATA
TAAAGTAGCATTATAAAGTGATATTAATTTAAGTGATATTAATTTTTATCAAACTTATAGTATAT
AACATCATATTTATTTTTATCAAAC
Found at i:233775 original size:15 final size:15
Alignment explanation
Indices: 233757--233786 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
233747 AAGCATTATA
233757 AAGTGATATTAATTT
1 AAGTGATATTAATTT
233772 AAGTGATATTAATTT
1 AAGTGATATTAATTT
233787 TTACCAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
AAGTGATATTAATTT
Found at i:233994 original size:36 final size:36
Alignment explanation
Indices: 233954--234029 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
233944 AAAGTAGCAT
*
233954 TATAAAGTGATATTAATTTTTACCAAATTTATAGTA
1 TATAAAGTCATATTAATTTTTACCAAATTTATAGTA
* * ** *
233990 TATAACGTCATATTTATTTTTGTCAAATTTTTAGTA
1 TATAAAGTCATATTAATTTTTACCAAATTTATAGTA
234026 TATA
1 TATA
234030 GAGTAGCATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.49
Consensus pattern (36 bp):
TATAAAGTCATATTAATTTTTACCAAATTTATAGTA
Found at i:234002 original size:85 final size:85
Alignment explanation
Indices: 233873--234057 Score: 307
Period size: 85 Copynumber: 2.2 Consensus size: 85
233863 ATATTAACTT
*
233873 AAGTGATATTAATTTTTATCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTA
1 AAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTA
233938 GTATATAAAGTAGCATTATA
66 GTATATAAAGTAGCATTATA
* * * * *
233958 AAGTGATATTAATTTTTACCAAATTTATAGTATATAACGTCATATTTATTTTTGTCAAATTTTTA
1 AAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTA
*
234023 GTATATAGAGTAGCATTATA
66 GTATATAAAGTAGCATTATA
234043 AAGTGATATTAATTT
1 AAGTGATATTAATTT
234058 AAGTAATATT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (85 bp):
AAGTGATATTAATTTTTACCAAACTTATAATATATAACATCATATTTATTTTTATCAAACTTTTA
GTATATAAAGTAGCATTATA
Found at i:234061 original size:15 final size:15
Alignment explanation
Indices: 234043--234072 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
234033 TAGCATTATA
*
234043 AAGTGATATTAATTT
1 AAGTAATATTAATTT
234058 AAGTAATATTAATTT
1 AAGTAATATTAATTT
234073 TTATTAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (15 bp):
AAGTAATATTAATTT
Found at i:234067 original size:100 final size:100
Alignment explanation
Indices: 233958--234190 Score: 358
Period size: 100 Copynumber: 2.3 Consensus size: 100
233948 TAGCATTATA
* * *
233958 AAGTGATATTAATTTTTACCAAATTTATAGTATATAACGTCATATTTATTTTTGTCAAATTTTTA
1 AAGTAATATTAATTTTTACCAAACTTATAGTATATAACGTCATATTTATTTTTGTCAAACTTTTA
* * * *
234023 GTATATAGAGTAGCATTATAAAGTGATATTAATTT
66 ATATATAAAGTAACATTATAAAATGATATTAATTT
**
234058 AAGTAATATTAATTTTTATTAAACTTATAGTATATAACGTCATATTTATTTTTGTCAAACTTTTA
1 AAGTAATATTAATTTTTACCAAACTTATAGTATATAACGTCATATTTATTTTTGTCAAACTTTTA
*
234123 ATATATAAAGTAATATTATAAAATGATATTAATTT
66 ATATATAAAGTAACATTATAAAATGATATTAATTT
* *
234158 AAATAATATTAATTTTTACCAAACTTCTAGTAT
1 AAGTAATATTAATTTTTACCAAACTTATAGTAT
234191 CCAATATAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 119 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (100 bp):
AAGTAATATTAATTTTTACCAAACTTATAGTATATAACGTCATATTTATTTTTGTCAAACTTTTA
ATATATAAAGTAACATTATAAAATGATATTAATTT
Found at i:234110 original size:36 final size:36
Alignment explanation
Indices: 234058--234140 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
234048 ATATTAATTT
* *
234058 AAGTAATATTAATTTTTATTAAACTTATAGTATATA
1 AAGTAATATTAATTTTTATCAAACTTATAATATATA
* * * * *
234094 ACGTCATATTTATTTTTGTCAAACTTTTAATATATA
1 AAGTAATATTAATTTTTATCAAACTTATAATATATA
234130 AAGTAATATTA
1 AAGTAATATTA
234141 TAAAATGATA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (36 bp):
AAGTAATATTAATTTTTATCAAACTTATAATATATA
Found at i:234161 original size:15 final size:15
Alignment explanation
Indices: 234143--234172 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
234133 TAATATTATA
*
234143 AAATGATATTAATTT
1 AAATAATATTAATTT
234158 AAATAATATTAATTT
1 AAATAATATTAATTT
234173 TTACCAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATAATATTAATTT
Found at i:236144 original size:29 final size:28
Alignment explanation
Indices: 236087--236145 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
236077 TTATATTTGA
* * *
236087 TAAAAAATATATTTATTCTCATCATATT
1 TAAAAAATATATTTATTATCATAAAATT
236115 TAAAAAATATTCATTT-TTATCATAAAATT
1 TAAAAAATA-T-ATTTATTATCATAAAATT
236144 TA
1 TA
236146 GTTAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.35
29 13 0.50
30 4 0.15
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAAAAATATATTTATTATCATAAAATT
Found at i:236435 original size:23 final size:25
Alignment explanation
Indices: 236409--236462 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
236399 AAATTTAAAA
*
236409 TAAATTTATTAA-AATATT-TCATT
1 TAAATTAATTAATAATATTATCATT
*
236432 TAAATTAATTAATTAATATTATTATT
1 TAAATTAATTAA-TAATATTATCATT
236458 TAAAT
1 TAAAT
236463 ATTTAGTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
25 6 0.23
26 9 0.35
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAATTAATTAATAATATTATCATT
Found at i:236436 original size:27 final size:26
Alignment explanation
Indices: 236401--236463 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
236391 TATCTATTAA
*
236401 ATTTAAAATAAATTTATTAAAATATT-TC
1 ATTT-AAATAAATTAATT--AATATTATC
* *
236429 ATTTAAATTAATTAATTAATATTATT
1 ATTTAAATAAATTAATTAATATTATC
236455 ATTTAAATA
1 ATTTAAATA
236464 TTTAGTGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 6 0.20
26 9 0.30
27 11 0.37
28 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAAATAAATTAATTAATATTATC
Found at i:236681 original size:22 final size:21
Alignment explanation
Indices: 236654--236705 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
236644 AATTTATTTT
236654 TAAATAAAAATATT-ATAATATA
1 TAAATAAAAA-ATTAAT-ATATA
*
236676 TTAATATAAAAATTAATATATA
1 TAAATA-AAAAATTAATATATA
236698 TAAATAAA
1 TAAATAAA
236706 TTAAACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.08
22 18 0.69
23 6 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATAAAAAATTAATATATA
Found at i:236698 original size:24 final size:23
Alignment explanation
Indices: 236634--236699 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
236624 TTTTTAAAAT
* * *
236634 AATAACAATTAATTTAT-TTTTA
1 AATAAAAATTAATATATATATTA
*
236656 AATAAAAA-TATTATAATATATTA
1 AATAAAAATTAATAT-ATATATTA
236679 ATATAAAAATTAATATATATA
1 A-ATAAAAATTAATATATATA
236700 AATAAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.11
22 9 0.26
23 5 0.14
24 12 0.34
25 5 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAAAATTAATATATATATTA
Found at i:236916 original size:17 final size:16
Alignment explanation
Indices: 236894--236935 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
236884 AATTTAATAA
236894 TAATTAAAAAATATTTT
1 TAATTAAAAAATA-TTT
236911 TAATT-AAAAATATTT
1 TAATTAAAAAATATTT
*
236926 TAAATAAAAA
1 TAATTAAAAA
236936 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
17 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTAAAAAATATTT
Found at i:236921 original size:16 final size:15
Alignment explanation
Indices: 236894--236937 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
236884 AATTTAATAA
236894 TAATTAAAAAATATTTT
1 TAATT-AAAAATA-TTT
236911 TAATTAAAAATATTT
1 TAATTAAAAATATTT
*
236926 TAAATAAAAATA
1 TAATTAAAAATA
236938 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 14 0.54
16 7 0.27
17 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATTAAAAATATTT
Found at i:237002 original size:13 final size:15
Alignment explanation
Indices: 236984--237015 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
236974 TTTTAAATTA
236984 ATTTAT-AAATA-AT
1 ATTTATAAAATATAT
236997 ATTTATAAAATATAT
1 ATTTATAAAATATAT
237012 ATTT
1 ATTT
237016 TATATTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATAAAATATAT
Found at i:244937 original size:15 final size:15
Alignment explanation
Indices: 244917--244945 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
244907 AATACTACGT
244917 GATATAACTTTCTAC
1 GATATAACTTTCTAC
244932 GATATAACTTTCTA
1 GATATAACTTTCTA
244946 AATTTCTGTC
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:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
GATATAACTTTCTAC
Found at i:248097 original size:2 final size:2
Alignment explanation
Indices: 248090--248130 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
248080 TGCCTAATAA
* * *
248090 AT AT AT AT AT GT AT AT AC AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
248131 ACCTTTCGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:248274 original size:2 final size:2
Alignment explanation
Indices: 248267--248299 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
248257 AAATCCTAGC
248267 TA 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 TA T
248300 GCGTTCTATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:250256 original size:1 final size:1
Alignment explanation
Indices: 250252--250285 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
250242 GTTCTTCGTG
* *
250252 TTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
250286 AAAGAAGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:254060 original size:14 final size:14
Alignment explanation
Indices: 254041--254091 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
254031 ATTTTTAAGT
254041 ATATTATTAAAATA
1 ATATTATTAAAATA
254055 ATATTAATTTAAAATA
1 ATATT-A-TTAAAATA
*
254071 A-ATTATCAAAATA
1 ATATTATTAAAATA
*
254084 CTATTATT
1 ATATTATT
254092 TTAATTTACG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 7 0.23
14 11 0.35
15 4 0.13
16 9 0.29
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTATTAAAATA
Found at i:254401 original size:17 final size:16
Alignment explanation
Indices: 254380--254423 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
254370 GGATTAGTTA
254380 ATTATTATTATTATAAT
1 ATTATTATTATT-TAAT
*
254397 GTTATTATTTATTTAAT
1 ATTATTA-TTATTTAAT
*
254414 AATATTATTA
1 ATTATTATTA
254424 GAGTTGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 3 0.13
17 15 0.65
18 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTATTATTATTTAAT
Found at i:254405 original size:20 final size:20
Alignment explanation
Indices: 254380--254423 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
254370 GGATTAGTTA
254380 ATTATTA-TTA-TT-ATAAT
1 ATTATTATTTATTTAATAAT
*
254397 GTTATTATTTATTTAATAAT
1 ATTATTATTTATTTAATAAT
254417 ATTATTA
1 ATTATTA
254424 GAGTTGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 3 0.14
19 2 0.09
20 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTATTATTTATTTAATAAT
Found at i:254628 original size:13 final size:13
Alignment explanation
Indices: 254610--254653 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
254600 CGATTACAAC
254610 TTAAATTAAAATT
1 TTAAATTAAAATT
*
254623 TTAAATTTAAAA-A
1 TTAAA-TTAAAATT
254636 TTAAATTAAATATT
1 TTAAATTAAA-ATT
254650 TTAA
1 TTAA
254654 TAATTACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.19
13 11 0.42
14 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATTAAAATT
Found at i:254954 original size:29 final size:28
Alignment explanation
Indices: 254921--254983 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
254911 TTTTTGTGAG
254921 TTAAAATAATAGTATTTT-AGTAATTTGAT
1 TTAAAATAATAGTATTTTGA-TAATTT-AT
* *
254950 TTAAATTAATATTATTTTGATAATTTAT
1 TTAAAATAATAGTATTTTGATAATTTAT
254978 TTAAAA
1 TTAAAA
254984 AACAGCAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 22 0.73
30 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (28 bp):
TTAAAATAATAGTATTTTGATAATTTAT
Found at i:257840 original size:6 final size:6
Alignment explanation
Indices: 257823--257851 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
257813 CTGTGGATGG
257823 CTAATT -TAATT CTAATT CTAATT CTAATT
1 CTAATT CTAATT CTAATT CTAATT CTAATT
257852 AACGGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (6 bp):
CTAATT
Found at i:267388 original size:2 final size:2
Alignment explanation
Indices: 267383--267419 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
267373 AATCATGCTT
267383 TA TA TA 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 TA TA TA T
267420 GGAATTTAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:269562 original size:20 final size:21
Alignment explanation
Indices: 269531--269578 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
269521 ATAAAAATAC
269531 TTATAAATTAATAAATTAATT
1 TTATAAATTAATAAATTAATT
* **
269552 TTATAAA-TAATAATTTAAAA
1 TTATAAATTAATAAATTAATT
269572 TTATAAA
1 TTATAAA
269579 AAAACACCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTATAAATTAATAAATTAATT
Found at i:280293 original size:26 final size:28
Alignment explanation
Indices: 280237--280297 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 28
280227 TTTATTTTTA
280237 TAATAAATTAATTAAATTAATTAAATTT
1 TAATAAATTAATTAAATTAATTAAATTT
*
280265 TAATAAATT-TTTAAA-T-ATTAAAATTT
1 TAATAAATTAATTAAATTAATT-AAATTT
280291 TAATAAA
1 TAATAAA
280298 AAAATTTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 3 0.10
26 14 0.45
27 5 0.16
28 9 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATAAATTAATTAAATTAATTAAATTT
Found at i:282932 original size:27 final size:28
Alignment explanation
Indices: 282883--282954 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 28
282873 AACAAGTCAC
282883 CATTTTTTACAAA-A-AAAAGGAACCAT
1 CATTTTTTACAAACACAAAAGGAACCAT
*
282909 CATTTTTTACAAACACAAAA-GAACTAT
1 CATTTTTTACAAACACAAAAGGAACCAT
* *
282936 TATTTTTGACAAACACAAA
1 CATTTTTTACAAACACAAA
282955 GGGTGGCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.32
27 24 0.59
28 4 0.10
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.29
Consensus pattern (28 bp):
CATTTTTTACAAACACAAAAGGAACCAT
Found at i:285715 original size:13 final size:13
Alignment explanation
Indices: 285697--285721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
285687 ATACACAGTA
285697 TGTATCGATACAT
1 TGTATCGATACAT
285710 TGTATCGATACA
1 TGTATCGATACA
285722 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:288651 original size:27 final size:27
Alignment explanation
Indices: 288557--288652 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 27
288547 TAGCCATCAA
*
288557 TTTTGACAAACAACAA-G--CCACCAT
1 TTTTGACAAACAAAAAGGAACCACCAT
* * * *
288581 TTTTGACAAGCAAAAAAGAATCACCGT
1 TTTTGACAAACAAAAAGGAACCACCAT
* * *
288608 TTCTGACAAATACAAAGGAACCACCAT
1 TTTTGACAAACAAAAAGGAACCACCAT
*
288635 TTTTGACAAACATAAAGG
1 TTTTGACAAACAAAAAGG
288653 GTGGCTTTTG
Statistics
Matches: 55, Mismatches: 14, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
24 14 0.25
25 1 0.02
27 40 0.73
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (27 bp):
TTTTGACAAACAAAAAGGAACCACCAT
Found at i:289220 original size:37 final size:37
Alignment explanation
Indices: 289174--289249 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
289164 AAATCTGGAC
289174 AAGCCAATTTGGACTAACTTCG-TCATAATCAAATCGA
1 AAGCCAATTTGGACTAA-TTCGATCATAATCAAATCGA
*
289211 AAGCTAATTTGGACTAATTCGATCATAATCAAATCGA
1 AAGCCAATTTGGACTAATTCGATCATAATCAAATCGA
289248 AA
1 AA
289250 TAGTTGAAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 4 0.11
37 33 0.89
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (37 bp):
AAGCCAATTTGGACTAATTCGATCATAATCAAATCGA
Done.