Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 34 of 82
Found at i:12393417 original size:4 final size:4
Alignment explanation
Indices: 12393410--12393458 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
12393400 TAAGTTCTTT
* * * * *
12393410 TATA TATA TATA TATA TATA CATA TATA TGTA TATG TATT TATA GATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
12393458 T
1 T
12393459 GTAGTTTATT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:12393421 original size:6 final size:6
Alignment explanation
Indices: 12393410--12393458 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
12393400 TAAGTTCTTT
* * * * *
12393410 TATATA TATATA TATATA TACATA TATATG TATATG TATTTA TAGATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
12393458 T
1 T
12393459 GTAGTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:12393425 original size:10 final size:10
Alignment explanation
Indices: 12393410--12393458 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
12393400 TAAGTTCTTT
12393410 TATATATATA
1 TATATATATA
12393420 TATATATATA
1 TATATATATA
* *
12393430 CATATATATG
1 TATATATATA
* *
12393440 TATATGTATT
1 TATATATATA
*
12393450 TATAGATAT
1 TATATATAT
12393459 GTAGTTTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (10 bp):
TATATATATA
Found at i:12393640 original size:161 final size:160
Alignment explanation
Indices: 12393331--12393640 Score: 450
Period size: 161 Copynumber: 1.9 Consensus size: 160
12393321 AATCTGTGAT
*
12393331 TGTTTGATTGCATTCTATTCCTCTGGATATCCCCTTGAAAAGGCTGAAGCATATGCTGTTTTAAG
1 TGTTTGATTGCATTCTATTCCTCTGGATATCCCCTTGAAAAGGCTGAAGCATATGCTGCTTTAAG
* * * *
12393396 GAAGTAAGTTCTTTTATATATATATATATATATACATATATATGTATATGTATTTATAGATATGT
66 GAAGTAAGTTCTTTTATATATACATACATACATACATATATA-GTATATGTATTTATAGATATGC
*
12393461 AGTTTATTCTTATGCATGTAATCTATGTGCA
130 AGTGTATTCTTATGCATGTAATCTATGTGCA
12393492 TGTTT-ATTGCATTCTATTCCTCTGGATATCCCCTTTGAAAAGGCTGAAGCATATGCTGCTTTAA
1 TGTTTGATTGCATTCTATTCCTCTGGATATCCCC-TTGAAAAGGCTGAAGCATATGCTGCTTTAA
*
12393556 GGAAGTAAGTTCTTTTATATTCATACATACATACATACATATATA-TA-ATGTAGTTTATTTG-T
65 GGAAGTAAGTTCTTTTATA-T-ATACATACATACATACATATATAGTATATGTA-TTTA-TAGAT
*
12393618 ATGCA-TGTATTCTATGTGCATGT
126 ATGCAGTGTATTCT-TATGCATGT
12393641 TTAAAATAAG
Statistics
Matches: 135, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
160 40 0.30
161 72 0.53
162 3 0.02
163 20 0.15
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (160 bp):
TGTTTGATTGCATTCTATTCCTCTGGATATCCCCTTGAAAAGGCTGAAGCATATGCTGCTTTAAG
GAAGTAAGTTCTTTTATATATACATACATACATACATATATAGTATATGTATTTATAGATATGCA
GTGTATTCTTATGCATGTAATCTATGTGCA
Found at i:12393730 original size:119 final size:119
Alignment explanation
Indices: 12393594--12394437 Score: 526
Period size: 119 Copynumber: 6.9 Consensus size: 119
12393584 ACATACATAC
*
12393594 ATATATATA-ATGTAGTTTATTTGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCAAT
1 ATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCAAT
* *
12393658 ATCTTTGCAAATTGCAGGAAA-ATTGCCTAATATTAGA-TCGAAATAAGTTCTTAT
66 ATCTTTGCAAATTGCAGGAAATATTACCTAATATTAGATTCGAAATAAGTT-GT-T
* *
12393712 ATATATATATATGTAGTTTATTCGTATGCCTGTATTCAATGTGCATGTTTAAAATAAGAATCAAT
1 ATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCAAT
* * * *
12393777 ATCTTTGCAAATTGCAGGAAATTTTACCTAATTTTAGATTGGAAGTAAGTTGTT
66 ATCTTTGCAAATTGCAGGAAATATTACCTAATATTAGATTCGAAATAAGTTGTT
* ** ****
12393831 -T-TATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCGTGTTTATTGCATTCTATTCC
1 ATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTA----A-AATAAGAA
* * ** * * ** * * *
12393894 TCTGGATATCCCCTTG-AAAAGGC-TGAAGCATA-T-GCTGCT-TTA-A--GGAAGTAAGTTCTT
61 TC--AATAT--CTTTGCAAATTGCAGGAA--ATATTACCTAATATTAGATTCGAAATAAG-T-TG
12393951 TT
118 TT
* ** * * * ** * * * *
12393953 ATATTCATACATACATACATACATATAT-ATATATATGTAGTTTTTTCGTATGCATGTATTCTAT
1 ATA-T-ATATATATGTA-GT--TTAT-TCGTATGCATGTA-TTCTAT-G--TGCATGT-TT-AAA
* * ** * **** * * *
12394017 GTGCATGTTTAAAATAAGAAT-CAATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGA-T
54 AT--AAGAAT-CAATATCTTTGCAA-A---TTGC--A--G--GAAATATTACCTAATATTAGATT
*
12394080 CGAAATAAGTTCTTAT
106 CGAAATAAGTT-GT-T
*
12394096 ATATATATATATGTAGTTTTTTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCAAT
1 ATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCAAT
* *
12394161 ATCTTTGCAAATTGCAGGAAA-ATTGCCTAATATTAGA-TCGAAATAAGTTCTTAT
66 ATCTTTGCAAATTGCAGGAAATATTACCTAATATTAGATTCGAAATAAGTT-GT-T
* *
12394215 ATATATATATATGTAGTTTATTCGTATGCCTGTATTCAATGTGCATGTTTAAAATAAGAATCAAT
1 ATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCAAT
* * * *
12394280 ATCTTTGCAAATTGCAGGAAATTTTACCTAATTTTAGATTGGAAGTAAGTTGTT
66 ATCTTTGCAAATTGCAGGAAATATTACCTAATATTAGATTCGAAATAAGTTGTT
* * **
12394334 -T-TATATATATGTAGTTTATTCGTATGCCTGTATTCTATGTGAATGTCCAAAATAAGAATCAAT
1 ATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCAAT
*
12394397 ATCTTTTCAAATTGCAGGAAA-ATTTACCTAAT-TATAGATTC
66 ATCTTTGCAAATTGCAGGAAATA-TTACCTAATAT-TAGATTC
12394438 TTAAATGATT
Statistics
Matches: 569, Mismatches: 99, Indels: 117
0.72 0.13 0.15
Matches are distributed among these distances:
116 1 0.00
117 138 0.24
118 11 0.02
119 191 0.34
120 40 0.07
121 22 0.04
122 9 0.02
123 4 0.01
124 11 0.02
125 7 0.01
126 18 0.03
127 1 0.00
129 20 0.04
130 14 0.02
131 5 0.01
132 5 0.01
133 10 0.02
134 9 0.02
136 1 0.00
137 5 0.01
138 12 0.02
139 1 0.00
140 6 0.01
141 12 0.02
142 5 0.01
143 11 0.02
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (119 bp):
ATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCAAT
ATCTTTGCAAATTGCAGGAAATATTACCTAATATTAGATTCGAAATAAGTTGTT
Found at i:12394162 original size:384 final size:382
Alignment explanation
Indices: 12393445--12394265 Score: 1407
Period size: 384 Copynumber: 2.1 Consensus size: 382
12393435 ATATGTATAT
* * *
12393445 GTATTTATAGATATGTAGTTTATTCTTATGCATGTAATCTATGTGCATGTTTATTGCATTCTATT
1 GTATTTATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTATTGCATTCTATT
12393510 CCTCTGGATATCCCCTTTGAAAAGGCTGAAGCATATGCTGCTTTAAGGAAGTAAGTTCTTTTATA
66 CCTCTGGATATCCCCTTTGAAAAGGCTGAAGCATATGCTGCTTTAAGGAAGTAAGTTCTTTTATA
12393575 TTCATACATACATACATACATATATATAATGTAGTTTATTTGTATGCATGTATTCTATGTGCATG
131 TTCATACATACATACATACATATATATAATGTAGTTTATTTGTATGCATGTATTCTATGTGCATG
12393640 TTTAAAATAAGAATCAATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAG
196 TTTAAAATAAGAATCAATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAG
*
12393705 TTCTTATATATATATATATGTAGTTTATTCGTATGCCTGTATTCAATGTGCATGTTTAAAATAAG
261 TTCTTATATATATATATATGTAGTTTATTCGTATGCATGTATTCAATGTGCATGTTTAAAATAAG
* * * *
12393770 AATCAATATCTTTGCAAATTGCAGGAAATTTTACCTAATTTTAGATTGGAAGTAAGTT-
326 AATCAATATCTTTGCAAATTGCAGGAAA-ATTACCTAATATTAGA-TCGAAATAAGTTC
*
12393828 GT-TTTATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCGTGTTTATTGCATTCTATT
1 GTATTTATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTATTGCATTCTATT
12393892 CCTCTGGATATCCCC-TTGAAAAGGCTGAAGCATATGCTGCTTTAAGGAAGTAAGTTCTTTTATA
66 CCTCTGGATATCCCCTTTGAAAAGGCTGAAGCATATGCTGCTTTAAGGAAGTAAGTTCTTTTATA
12393956 TTCATACATACATACATACATATATATATATATGTAGTTT-TTTCGTATGCATGTATTCTATGTG
131 TTCATACATACATACATAC--ATATATATA-ATGTAGTTTATTT-GTATGCATGTATTCTATGTG
12394020 CATGTTTAAAATAAGAATCAATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAA
192 CATGTTTAAAATAAGAATCAATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAA
* *
12394085 TAAGTTCTTATATATATATATATGTAGTTTTTTCGTATGCATGTATTCTATGTGCATGTTTAAAA
257 TAAGTTCTTATATATATATATATGTAGTTTATTCGTATGCATGTATTCAATGTGCATGTTTAAAA
*
12394150 TAAGAATCAATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAGTTC
322 TAAGAATCAATATCTTTGCAAATTGCAGGAAAATTACCTAATATTAGATCGAAATAAGTTC
* * *
12394211 TTATATATATATATATGTAGTTTATTCGTATGCCTGTATTCAATGTGCATGTTTA
1 GTAT-T-TATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTA
12394266 AAATAAGAAT
Statistics
Matches: 414, Mismatches: 16, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
381 68 0.16
382 83 0.20
383 28 0.07
384 189 0.46
385 1 0.00
386 45 0.11
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (382 bp):
GTATTTATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTATTGCATTCTATT
CCTCTGGATATCCCCTTTGAAAAGGCTGAAGCATATGCTGCTTTAAGGAAGTAAGTTCTTTTATA
TTCATACATACATACATACATATATATAATGTAGTTTATTTGTATGCATGTATTCTATGTGCATG
TTTAAAATAAGAATCAATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAG
TTCTTATATATATATATATGTAGTTTATTCGTATGCATGTATTCAATGTGCATGTTTAAAATAAG
AATCAATATCTTTGCAAATTGCAGGAAAATTACCTAATATTAGATCGAAATAAGTTC
Found at i:12394216 original size:117 final size:119
Alignment explanation
Indices: 12393975--12394420 Score: 711
Period size: 119 Copynumber: 3.8 Consensus size: 119
12393965 ACATACATAC
*
12393975 ATATATATATATATGTAGTTTTTTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCA
1 ATATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCA
12394040 ATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAGTTCTT
66 ATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAGTTCTT
*
12394094 ATATATATATATATGTAGTTTTTTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCA
1 ATATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCA
12394159 ATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAGTTCTT
66 ATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAGTTCTT
* *
12394213 ATATATATATATATGTAGTTTATTCGTATGCCTGTATTCAATGTGCATGTTTAAAATAAGAATCA
1 ATATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCA
* * * * * *
12394278 ATATCTTTGCAAATTGCAGGAAATTTTACCTAATTTTAGATTGGAAGTAAGTT-GT
66 ATATCTTTGCAAATTGCAGGAAA-ATTGCCTAATATTAGA-TCGAAATAAGTTCTT
* * **
12394333 -T-T-TATATATATGTAGTTTATTCGTATGCCTGTATTCTATGTGAATGTCCAAAATAAGAATCA
1 ATATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCA
*
12394395 ATATCTTTTCAAATTGCAGGAAAATT
66 ATATCTTTGCAAATTGCAGGAAAATT
12394421 TACCTAATTA
Statistics
Matches: 310, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
116 2 0.01
117 78 0.25
118 1 0.00
119 205 0.66
120 14 0.05
121 10 0.03
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.41
Consensus pattern (119 bp):
ATATATATATATATGTAGTTTATTCGTATGCATGTATTCTATGTGCATGTTTAAAATAAGAATCA
ATATCTTTGCAAATTGCAGGAAAATTGCCTAATATTAGATCGAAATAAGTTCTT
Found at i:12401075 original size:2 final size:2
Alignment explanation
Indices: 12401068--12401258 Score: 168
Period size: 2 Copynumber: 94.5 Consensus size: 2
12401058 GTCATTTCTT
* * * * * *
12401068 TA TA TA TA TA CA TA TA TA TGA -A TA TG TA TA CA TA TA CA TG TT
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
12401110 TA TA TA TA CA TA TA CA TA TG TG TA TA TA TA CA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
12401152 TG TA TA TA TA CA CA TA CA TA TG TC TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
12401194 TA TA TA TA TA TA TA TA TA GTA GTN TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA TA TA TA TA TA TA TA
*
12401238 TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
12401259 GTGTGTGTGT
Statistics
Matches: 152, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
1 1 0.01
2 146 0.96
3 5 0.03
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:12408851 original size:18 final size:17
Alignment explanation
Indices: 12408811--12408858 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
12408801 AAAGATTACC
*
12408811 ATAAAACAAATACAAAAA
1 ATAAAA-AAATAAAAAAA
*
12408829 GTAAAAAAATAAAATAAA
1 ATAAAAAAATAAAA-AAA
*
12408847 ATAAAAACATAA
1 ATAAAAAAATAA
12408859 TTAATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (17 bp):
ATAAAAAAATAAAAAAA
Found at i:12414095 original size:19 final size:19
Alignment explanation
Indices: 12414071--12414112 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12414061 CTTCTTCTCC
*
12414071 TTCATGCTCTCACGCCATT
1 TTCATGCTCCCACGCCATT
* *
12414090 TTCATGCTCCCATGCTATT
1 TTCATGCTCCCACGCCATT
12414109 TTCA
1 TTCA
12414113 CCTTTCCACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.33, G:0.10, T:0.40
Consensus pattern (19 bp):
TTCATGCTCCCACGCCATT
Found at i:12423820 original size:61 final size:61
Alignment explanation
Indices: 12423754--12423870 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
12423744 TACCTTCTCA
* * * *
12423754 AATGTATAGATAGAAATGT-AACAGAATGCTTATTGCTTCAAAAGTATCGATACATTTCTTG
1 AATGTATAGATA-AAATGTCAACAAAATGCTTATTACCTCAAAAATATCGATACATTTCTTG
* * * *
12423815 AATGTATCGATACATTTTCAACAAAATGCTTATTACCTCAAAAATATCGATACATT
1 AATGTATAGATAAAATGTCAACAAAATGCTTATTACCTCAAAAATATCGATACATT
12423871 AGCAAATGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 3 0.06
61 44 0.94
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (61 bp):
AATGTATAGATAAAATGTCAACAAAATGCTTATTACCTCAAAAATATCGATACATTTCTTG
Found at i:12428697 original size:26 final size:26
Alignment explanation
Indices: 12428668--12428728 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
12428658 ACCATATACC
* *
12428668 CATCATCATCATGCACACCATCCCAT
1 CATCATCATCATACAAACCATCCCAT
12428694 CATCATCATCATACAAACCATCCCAT
1 CATCATCATCATACAAACCATCCCAT
12428720 CATCATCAT
1 CATCATCAT
12428729 TCCCAGCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.39, G:0.02, T:0.25
Consensus pattern (26 bp):
CATCATCATCATACAAACCATCCCAT
Found at i:12436965 original size:3 final size:3
Alignment explanation
Indices: 12436951--12436981 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
12436941 CCATCTTGAT
*
12436951 TTC TTC TAC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
12436982 CATTGAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:12453718 original size:32 final size:32
Alignment explanation
Indices: 12453677--12453740 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
12453667 AGACATATAC
12453677 AAATCATTCAAGTACCATAGCAGCACATTAAA
1 AAATCATTCAAGTACCATAGCAGCACATTAAA
*
12453709 AAATCATTCAAGTACCATGGCAGCACATTAAA
1 AAATCATTCAAGTACCATAGCAGCACATTAAA
12453741 CAATGTGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.22
Consensus pattern (32 bp):
AAATCATTCAAGTACCATAGCAGCACATTAAA
Found at i:12456252 original size:35 final size:35
Alignment explanation
Indices: 12456197--12456302 Score: 144
Period size: 35 Copynumber: 3.0 Consensus size: 35
12456187 AAGGGAAATG
12456197 AGCTTTTT-ATGGGATCAAGTGAAATCC-TCACAAT
1 AGCTTTTTCATGGGATCAAGTGAAA-CCTTCACAAT
* *
12456231 AGCTTTTTCATGGGATTAAGTGAAACCTTTACAAT
1 AGCTTTTTCATGGGATCAAGTGAAACCTTCACAAT
*
12456266 AACTTTTTCATGGGATCAAGTGAAACCCTTCAACAAT
1 AGCTTTTTCATGGGATCAAGTGAAA-CCTTC-ACAAT
12456303 GGTTTTTAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
34 10 0.16
35 44 0.70
36 4 0.06
37 5 0.08
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (35 bp):
AGCTTTTTCATGGGATCAAGTGAAACCTTCACAAT
Found at i:12457933 original size:25 final size:25
Alignment explanation
Indices: 12457899--12457951 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
12457889 GCTTGCACAA
12457899 ATACCTAACTTAATTAGTTCACTAT
1 ATACCTAACTTAATTAGTTCACTAT
12457924 ATACCTAACTTAATTAGTTCACTAT
1 ATACCTAACTTAATTAGTTCACTAT
12457949 ATA
1 ATA
12457952 TCTATAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.40
Consensus pattern (25 bp):
ATACCTAACTTAATTAGTTCACTAT
Found at i:12463179 original size:20 final size:22
Alignment explanation
Indices: 12463154--12463227 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 22
12463144 GACGAAATGA
12463154 ATCGATACAT-TT-TGTG-ATGT
1 ATCGATACATGTTCT-TGCATGT
12463174 ATCGATACATGTTCTTGCATGT
1 ATCGATACATGTTCTTGCATGT
* * * *
12463196 ATAGATACATATGCAT--ATGT
1 ATCGATACATGTTCTTGCATGT
12463216 ATCGATACATGT
1 ATCGATACATGT
12463228 AATACAAGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 24 0.53
21 4 0.09
22 17 0.38
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (22 bp):
ATCGATACATGTTCTTGCATGT
Found at i:12474209 original size:37 final size:37
Alignment explanation
Indices: 12474159--12474314 Score: 208
Period size: 37 Copynumber: 4.2 Consensus size: 37
12474149 AATGCAATAT
12474159 CATCATCATGTGTGCACTCCCTACTCGCACACT-TCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTCT-AA
* * * *
12474196 CATCATAATGTGTGCACTCCTTACTTGCACACTCTAT
1 CATCATCATGTGTGCACTCCCTACTCGCACACTCTAA
* * *
12474233 CATCATCATGGGTACACTCCCTACTCGCACACTCTAT
1 CATCATCATGTGTGCACTCCCTACTCGCACACTCTAA
*
12474270 CATCATCATGTGTGCACTCCCTACTAGCACACT-TCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTCT-AA
12474307 CATCATCA
1 CATCATCA
12474315 CACAACATTA
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
36 1 0.01
37 102 0.98
38 1 0.01
ACGTcount: A:0.26, C:0.35, G:0.10, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTCTAA
Found at i:12475182 original size:13 final size:13
Alignment explanation
Indices: 12475164--12475188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12475154 GTTCTTATTA
12475164 AAACCCCACATGT
1 AAACCCCACATGT
12475177 AAACCCCACATG
1 AAACCCCACATG
12475189 AGTAAATCAC
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:0.40, C:0.40, G:0.08, T:0.12
Consensus pattern (13 bp):
AAACCCCACATGT
Found at i:12487191 original size:28 final size:29
Alignment explanation
Indices: 12487150--12487214 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
12487140 GTCTATGGGC
*
12487150 AATTTTTCAATTTT-TTGGGCAAAAATGT
1 AATTTTTCAATTTTATGGGGCAAAAATGT
* *
12487178 AATTTTTCACTTTTACTGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-TGGGGCAAAAATGT
*
12487208 AAATTTT
1 AATTTTT
12487215 AAAAATTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 13 0.42
30 18 0.58
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (29 bp):
AATTTTTCAATTTTATGGGGCAAAAATGT
Found at i:12491139 original size:76 final size:73
Alignment explanation
Indices: 12491032--12491175 Score: 202
Period size: 76 Copynumber: 1.9 Consensus size: 73
12491022 TTTTGTTTTG
*
12491032 TCATTTTTAAATTTTATTTTTTAATTCAAAAA-TAAAAA-TTTAAGTAAAAGTAATTTTTTATCT
1 TCATTTTTAAATTTTATTTCTTAATTCAAAAATTAAAAATTTTAAGTAAAA-TAA-TTTTTATCT
12491095 TCTATCTCTT
64 TCTATCTCTT
* *
12491105 TCATTTTTCAAAATTTATATTTCTTAATTTAAAAATTAAAAATTTTAAGTAAAATCATTTTTATC
1 TCATTTTT--AAATTT-TATTTCTTAATTCAAAAATTAAAAATTTTAAGTAAAATAATTTTTATC
12491170 TTCTAT
63 TTCTAT
12491176 TTTTTCTTCT
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
73 8 0.13
75 6 0.10
76 30 0.48
77 8 0.13
78 11 0.17
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.51
Consensus pattern (73 bp):
TCATTTTTAAATTTTATTTCTTAATTCAAAAATTAAAAATTTTAAGTAAAATAATTTTTATCTTC
TATCTCTT
Found at i:12498895 original size:23 final size:24
Alignment explanation
Indices: 12498869--12498915 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12498859 TTAAAATGAG
*
12498869 TCTTATT-ACATCAAAAGCCATTT
1 TCTTATTGACATCAAAAGCAATTT
* *
12498892 TCTTGTTGACATGAAAAGCAATTT
1 TCTTATTGACATCAAAAGCAATTT
12498916 GGGAGCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (24 bp):
TCTTATTGACATCAAAAGCAATTT
Found at i:12502456 original size:42 final size:42
Alignment explanation
Indices: 12502391--12502471 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
12502381 GTTGATTTGA
12502391 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
12502433 ACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
12502472 TTGCCTCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
Found at i:12502742 original size:26 final size:26
Alignment explanation
Indices: 12502706--12502767 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
12502696 TTGCATATGA
12502706 GATGATGATGATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
12502732 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
12502758 GTTGATGATG
1 GATGATGATG
12502768 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.40, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:12508195 original size:42 final size:42
Alignment explanation
Indices: 12508136--12508254 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
12508126 ATATGCAACA
* *
12508136 GCTTATGCGCACTCCCACTTGCACATAGCCGGGTCAGCAATG
1 GCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAATG
* *
12508178 GCTTATGTGCACTCCCACTCACACATAGTCGGGTCAGCAATG
1 GCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAATG
* *
12508220 GCTTATGTGCACTCCTACTCGCACATAGCCAGGTC
1 GCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
12508255 CACATCAACA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.24
Consensus pattern (42 bp):
GCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAATG
Found at i:12511420 original size:26 final size:26
Alignment explanation
Indices: 12511398--12511475 Score: 122
Period size: 27 Copynumber: 3.0 Consensus size: 26
12511388 TCTCTTTATA
12511398 ATTGGGCCATGCCCATTTTCTTTCTT
1 ATTGGGCCATGCCCATTTTCTTTCTT
*
12511424 ATTGGGCCATACCCATTTTTCTTTCTT
1 ATTGGGCCATGCCCA-TTTTCTTTCTT
*
12511451 ATTGGGTCATGCCCATTTT-TTTCTT
1 ATTGGGCCATGCCCATTTTCTTTCTT
12511476 TCTTGTTACT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
25 6 0.12
26 18 0.38
27 24 0.50
ACGTcount: A:0.13, C:0.24, G:0.14, T:0.49
Consensus pattern (26 bp):
ATTGGGCCATGCCCATTTTCTTTCTT
Found at i:12515533 original size:40 final size:40
Alignment explanation
Indices: 12515478--12515565 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
12515468 TAACTAAATA
12515478 AAACGACACTCAAGCTTAGTGTATCATTAGCTGGAGTATG
1 AAACGACACTCAAGCTTAGTGTATCATTAGCTGGAGTATG
12515518 AAACGACACTCAAGCTTAGTGTATCATTAGCTGGAGTATG
1 AAACGACACTCAAGCTTAGTGTATCATTAGCTGGAGTATG
12515558 AAACGACA
1 AAACGACA
12515566 TCATACTGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (40 bp):
AAACGACACTCAAGCTTAGTGTATCATTAGCTGGAGTATG
Found at i:12537738 original size:22 final size:20
Alignment explanation
Indices: 12537710--12537753 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
12537700 GTTTTTGGCT
12537710 AAGCTTGGTAAAAGCCATTGTA
1 AAGCTTGGTAAAAG-C-TTGTA
*
12537732 AAGCTTGGTGAAAGCTTGTA
1 AAGCTTGGTAAAAGCTTGTA
12537752 AA
1 AA
12537754 TTTCACCGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 1 0.05
22 13 0.62
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
AAGCTTGGTAAAAGCTTGTA
Found at i:12540490 original size:38 final size:38
Alignment explanation
Indices: 12540386--12540504 Score: 159
Period size: 38 Copynumber: 3.1 Consensus size: 38
12540376 CACACTTAGC
* *
12540386 TCATGTGCATCCCCCCACATCGTGCACATAGCTAGAGTCA
1 TCATGTGCATCCCCCCACATCGTGCACA-AGCAATA-TCA
12540426 TCATGTGCAT-CCCCCACATCGTGCACAAGCAATATCA
1 TCATGTGCATCCCCCCACATCGTGCACAAGCAATATCA
* * * *
12540463 TCGTGTGCGTCCCCCCACATCGGGCACAAGTAATATCA
1 TCATGTGCATCCCCCCACATCGTGCACAAGCAATATCA
12540501 TCAT
1 TCAT
12540505 CCACACTCCC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
37 11 0.15
38 33 0.46
39 17 0.24
40 10 0.14
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (38 bp):
TCATGTGCATCCCCCCACATCGTGCACAAGCAATATCA
Found at i:12542885 original size:31 final size:31
Alignment explanation
Indices: 12542793--12542885 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
12542783 AAAATTTGTT
* * *
12542793 GTAAAATGA-GGTAACATGCAATGCATATAAT
1 GTAAAAT-ATGGTAACACGCCATGCATATAAC
*
12542824 GTAAAATGTGGTAACACGCCATGCATATAAC
1 GTAAAATATGGTAACACGCCATGCATATAAC
12542855 GTAAAATATGGTAACACGCCATGCATATAAC
1 GTAAAATATGGTAACACGCCATGCATATAAC
12542886 CAATGTCGTG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (31 bp):
GTAAAATATGGTAACACGCCATGCATATAAC
Found at i:12548595 original size:36 final size:36
Alignment explanation
Indices: 12548543--12548643 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 36
12548533 ATTACAAAGT
* * *
12548543 GTGTGGTATGATGCCCCACATTTAGCCCTTG-ATCAC
1 GTGTGGTATGAAGCCCCACATCTAGCCCTAGTAT-AC
* * *
12548579 GTGTGGTATGAAGCCCCACATCTAGCTCAAGTATTC
1 GTGTGGTATGAAGCCCCACATCTAGCCCTAGTATAC
12548615 GTGTGGTAT-AACGCCCCACATCTAGCCCT
1 GTGTGGTATGAA-GCCCCACATCTAGCCCT
12548644 CTTACAGGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 2 0.04
36 51 0.93
37 2 0.04
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (36 bp):
GTGTGGTATGAAGCCCCACATCTAGCCCTAGTATAC
Found at i:12548655 original size:36 final size:34
Alignment explanation
Indices: 12548543--12548659 Score: 99
Period size: 36 Copynumber: 3.3 Consensus size: 34
12548533 ATTACAAAGT
* * *
12548543 GTGTGGTATGATGCCCCACATTTAGCCCTTGATCAC
1 GTGTGGTAT-AAGCCCCACATCTAGCCCTTTA-CAC
*** **
12548579 GTGTGGTATGAAGCCCCACATCTAGCTCAAGTATTC
1 GTGTGGTAT-AAGCCCCACATCTAGC-CCTTTACAC
*
12548615 GTGTGGTATAACGCCCCACATCTAGCCCTCTTACAG
1 GTGTGGTATAA-GCCCCACATCTAGCCCT-TTACAC
12548651 GTGTGGTAT
1 GTGTGGTAT
12548660 TGATATCTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
35 3 0.05
36 59 0.92
37 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.29
Consensus pattern (34 bp):
GTGTGGTATAAGCCCCACATCTAGCCCTTTACAC
Found at i:12549788 original size:39 final size:38
Alignment explanation
Indices: 12549713--12549799 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 38
12549703 AAAGTAAAGG
* *
12549713 GGTTGTGCTTTAACCTTAAAAAGGTAGAGACTTTGTGAAA
1 GGTTGTGCTTTAACCTTAAAAAGGCAGAGACGTTGTG--A
* **
12549753 GGTTGTGCTTTAACCTT-GAAAGGCATTGACGTTGTGA
1 GGTTGTGCTTTAACCTTAAAAAGGCAGAGACGTTGTGA
12549790 GGTTGTGCTT
1 GGTTGTGCTT
12549800 GCTCCTCTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 11 0.26
39 14 0.33
40 17 0.40
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.36
Consensus pattern (38 bp):
GGTTGTGCTTTAACCTTAAAAAGGCAGAGACGTTGTGA
Found at i:12549832 original size:40 final size:40
Alignment explanation
Indices: 12549779--12549900 Score: 156
Period size: 40 Copynumber: 3.0 Consensus size: 40
12549769 TGAAAGGCAT
*
12549779 TGACGTTGTGAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
1 TGACGTTGAGAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
* * * * *
12549819 TGATGTTGAGAGGTTGTGCTTGCTCTTTTTCAAAAGGCAG
1 TGACGTTGAGAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
* *
12549859 TGACATT-ATGAGGTTGTGCTTGCTCCTCTCGAAAAGGTAG
1 TGACGTTGA-GAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
12549899 TG
1 TG
12549901 CTTGTGAAAG
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 67 0.99
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (40 bp):
TGACGTTGAGAGGTTGTGCTTGCTCCTCTTGAAAAGGTAG
Found at i:12557726 original size:35 final size:35
Alignment explanation
Indices: 12557680--12557784 Score: 133
Period size: 35 Copynumber: 3.0 Consensus size: 35
12557670 ACTTAGCCAA
*
12557680 TGTGCACTCCCTACAT-GCACAAGGCAATATCATCG
1 TGTGCACTCCCTAC-TCGCACAAGGCAACATCATCG
***
12557715 TGTGCACTCCCTACTCGCACACTTCAACATCATCG
1 TGTGCACTCCCTACTCGCACAAGGCAACATCATCG
*
12557750 TGTGCACTCCCTACTCGCACACA-TCAACATCATCG
1 TGTGCACTCCCTACTCGCACA-AGGCAACATCATCG
12557785 ACCACACTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
34 1 0.02
35 62 0.98
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (35 bp):
TGTGCACTCCCTACTCGCACAAGGCAACATCATCG
Found at i:12560021 original size:21 final size:20
Alignment explanation
Indices: 12559972--12560021 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
12559962 AGAACAACGC
*
12559972 CATCATTCAAAATCAAGTAG
1 CATCATTCAAAATCAAGCAG
*
12559992 CTATCATTCAAAGTCAAGCAG
1 C-ATCATTCAAAATCAAGCAG
12560013 CATCGATTC
1 CATC-ATTC
12560022 GAGATCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (20 bp):
CATCATTCAAAATCAAGCAG
Found at i:12578252 original size:19 final size:20
Alignment explanation
Indices: 12578210--12578253 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12578200 AAAACACGAT
*
12578210 TTTTCCTTTGAATTTTCTAG
1 TTTTCCTTTGAATTTTCTAC
**
12578230 TTTTCCTTTGGTTTTTCT-C
1 TTTTCCTTTGAATTTTCTAC
12578249 TTTTC
1 TTTTC
12578254 TTCCTTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.07, C:0.18, G:0.09, T:0.66
Consensus pattern (20 bp):
TTTTCCTTTGAATTTTCTAC
Found at i:12590900 original size:19 final size:19
Alignment explanation
Indices: 12590876--12590937 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
12590866 AAAGCAATAC
*
12590876 TCATTCATTCGTCTCATCA
1 TCATTCATTCGTATCATCA
12590895 TCATTCATTC--ATCATTCA
1 TCATTCATTCGTATCA-TCA
* *
12590913 TCATTCATTTGTTTCATCA
1 TCATTCATTCGTATCATCA
12590932 TCATTC
1 TCATTC
12590938 TTTCATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 19 0.51
20 3 0.08
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.47
Consensus pattern (19 bp):
TCATTCATTCGTATCATCA
Found at i:12590928 original size:23 final size:23
Alignment explanation
Indices: 12590902--12590945 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12590892 TCATCATTCA
12590902 TTCATCATTCA-TCATTCATTTGT
1 TTCATCA-TCATTCATTCATTTGT
*
12590925 TTCATCATCATTCTTTCATTT
1 TTCATCATCATTCATTCATTT
12590946 TTTTACCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55
Consensus pattern (23 bp):
TTCATCATCATTCATTCATTTGT
Found at i:12600274 original size:20 final size:20
Alignment explanation
Indices: 12600237--12600274 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12600227 TTTTTATTAT
*
12600237 TTTCTTACCTTTCTTTCTCG
1 TTTCTTACCTCTCTTTCTCG
12600257 TTTCTT-CCTCTCTCTTCT
1 TTTCTTACCTCTCT-TTCT
12600275 ACTCGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTCTTACCTCTCTTTCTCG
Found at i:12602636 original size:2 final size:2
Alignment explanation
Indices: 12602624--12602659 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12602614 ACCATATACC
*
12602624 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12602660 CAATCATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12610323 original size:14 final size:14
Alignment explanation
Indices: 12610304--12610330 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12610294 TTTTCTTTCA
12610304 TTTTCTTTTCCTTG
1 TTTTCTTTTCCTTG
12610318 TTTTCTTTTCCTT
1 TTTTCTTTTCCTT
12610331 TCCTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTCCTTG
Found at i:12610340 original size:19 final size:20
Alignment explanation
Indices: 12610294--12610340 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
12610284 GAAAAATCAA
*
12610294 TTTTCTTTCATTTTCTTTTCC
1 TTTT-TTTCATTTTCCTTTCC
*
12610315 TTGTTTTC-TTTTCCTTTCC
1 TTTTTTTCATTTTCCTTTCC
12610334 TTTTTTT
1 TTTTTTT
12610341 TCTTACATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 4 0.17
21 3 0.13
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTTTCATTTTCCTTTCC
Found at i:12611138 original size:30 final size:31
Alignment explanation
Indices: 12611104--12611166 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
12611094 CACGTGACGG
*
12611104 TGCCGGTGGTG-TATGGTGTGGGAGTGCACA
1 TGCCGGTGATGATATGGTGTGGGAGTGCACA
* *
12611134 TGCCGGTGATGATGTGGTGTGGGAGTGTACA
1 TGCCGGTGATGATATGGTGTGGGAGTGCACA
12611165 TG
1 TG
12611167 ATATTTGCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.14, C:0.11, G:0.46, T:0.29
Consensus pattern (31 bp):
TGCCGGTGATGATATGGTGTGGGAGTGCACA
Found at i:12615595 original size:4 final size:4
Alignment explanation
Indices: 12615581--12615655 Score: 68
Period size: 4 Copynumber: 18.8 Consensus size: 4
12615571 CAAACCGTGC
*
12615581 CTTT CCTTT CTTT CTCT C-TT -TTT CTTT CTTT CTTT CTTT CTTTT CTTTT
1 CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT C-TTT
*
12615630 CCTTT C-TT CTTT -ATT CTTT CTTT CTT
1 -CTTT CTTT CTTT CTTT CTTT CTTT CTT
12615656 CCCCTTCCTC
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
3 8 0.13
4 36 0.60
5 15 0.25
6 1 0.02
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:12615612 original size:22 final size:21
Alignment explanation
Indices: 12615581--12615655 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 21
12615571 CAAACCGTGC
12615581 CTTTCCTTTCTTTCTCTCTTTTT
1 CTTT-CTTTCTTTCT-TCTTTTT
12615604 CTTTCTTTCTTTCTT-TCTTTT
1 CTTTCTTTCTTTCTTCT-TTTT
*
12615625 C-TT-TTCCTTTCTTCTTTATT
1 CTTTCTTTCTTTCTTCTTT-TT
12615645 CTTTCTTTCTT
1 CTTTCTTTCTT
12615656 CCCCTTCCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
19 11 0.24
20 7 0.16
21 8 0.18
22 15 0.33
23 4 0.09
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (21 bp):
CTTTCTTTCTTTCTTCTTTTT
Found at i:12615655 original size:18 final size:17
Alignment explanation
Indices: 12615586--12615656 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 17
12615576 CGTGCCTTTC
12615586 CTTTCTTTCTCTCTTTTT
1 CTTTCTTTCT-TCTTTTT
12615604 CTTTCTTTCTTTCTTTCTTTT
1 CTTTCTTTC-TTC--T-TTTT
12615625 CTTTTCCTTTCTTCTTTATT
1 C-TTT-CTTTCTTCTTT-TT
12615645 CTTTCTTTCTTC
1 CTTTCTTTCTTC
12615657 CCCTTCCTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
18 19 0.41
19 6 0.13
20 5 0.11
21 5 0.11
22 6 0.13
23 5 0.11
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (17 bp):
CTTTCTTTCTTCTTTTT
Found at i:12620858 original size:23 final size:19
Alignment explanation
Indices: 12620807--12620853 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
12620797 AAAGCATTAC
12620807 TCATTCATTTGTCTCATCA
1 TCATTCATTTGTCTCATCA
*
12620826 TCATTCATTTGTTTCATCA
1 TCATTCATTTGTCTCATCA
12620845 TCATTCATT
1 TCATTCATT
12620854 CATTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.51
Consensus pattern (19 bp):
TCATTCATTTGTCTCATCA
Found at i:12626541 original size:22 final size:20
Alignment explanation
Indices: 12626515--12626557 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
12626505 TACATACCCA
12626515 TCATCATCATC-TCACCAGC
1 TCATCATCATCATCACCAGC
12626534 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
12626554 TCAT
1 TCAT
12626558 GCGCACTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.28, C:0.40, G:0.05, T:0.28
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:12626604 original size:43 final size:43
Alignment explanation
Indices: 12626556--12626708 Score: 211
Period size: 43 Copynumber: 3.6 Consensus size: 43
12626546 TCACCAGCTC
**
12626556 ATGCGCACTCCCTACTCGCACAT-GGCTGGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAATC-GGGTCATCACCGGGTT
* *
12626599 ATGCGCACTCCTTACTCGCACATAATCGGGTCATCATCGGGTT
1 ATGCGCACTCCCTACTCGCACATAATCGGGTCATCACCGGGTT
*
12626642 ATGCGCACTCCCTACTCGCACATAATCGGGTCATC-CTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAATCGGGTCATCAC-CGGGTT
* *
12626685 ATGTGCACTCCCTATTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
12626709 GCAGAGTCAA
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
43 98 0.99
44 1 0.01
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.26
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAATCGGGTCATCACCGGGTT
Found at i:12628975 original size:40 final size:40
Alignment explanation
Indices: 12628931--12629081 Score: 162
Period size: 40 Copynumber: 3.8 Consensus size: 40
12628921 TTAAACCCTA
* * * *
12628931 AAAAAGTAGTGACATTGTGACGTTGTGCTTGCTTTTATTG
1 AAAAAGCAATGACATTGTGAAGTTGTGCTTGCTTTTCTTG
** **
12628971 AAAAAGCAATGATTTTGTGAAGTTGTGCTTGCTGGTCTT-
1 AAAAAGCAATGACATTGTGAAGTTGTGCTTGCTTTTCTTG
* * *
12629010 AAAAAGACAGTGACGTTGTGAGGTTGTGCTT-CTTTCTCTTG
1 AAAAAG-CAATGACATTGTGAAGTTGTGCTTGCTTT-TCTTG
*
12629051 AAAAGGCAATGACATTGTGAAGTTGTGCTTG
1 AAAAAGCAATGACATTGTGAAGTTGTGCTTG
12629082 TGCAAGTTTG
Statistics
Matches: 89, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 8 0.09
40 76 0.85
41 5 0.06
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (40 bp):
AAAAAGCAATGACATTGTGAAGTTGTGCTTGCTTTTCTTG
Found at i:12629711 original size:42 final size:42
Alignment explanation
Indices: 12629663--12629754 Score: 100
Period size: 45 Copynumber: 2.1 Consensus size: 42
12629653 AAATATATTC
12629663 TTTATTAAATGT-A-AATAATACTAAATAATATTCTTTATTAA-A
1 TTTATTAAAT-TAATAATAATACTAAATAATATTC-TTA-TAATA
* *
12629705 TTTATTATATTCAAATAATAATATTAAATAATATTCTTATAATA
1 TTTATTAAATT--AATAATAATACTAAATAATATTCTTATAATA
12629749 TTTATT
1 TTTATT
12629755 TTAGTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
41 1 0.02
42 9 0.21
43 3 0.07
44 11 0.26
45 19 0.44
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (42 bp):
TTTATTAAATTAATAATAATACTAAATAATATTCTTATAATA
Found at i:12629767 original size:44 final size:45
Alignment explanation
Indices: 12629676--12629768 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
12629666 ATTAAATGTA
12629676 AATAATACTAAATAATATTCTTTATTAAATTTATTATATTCAAAT
1 AATAATACTAAATAATATTCTTTATTAAATTTATTATATTCAAAT
* *
12629721 AATAATATTAAATAATATTC-TTA-TAATATTTATTTTAGTT-AAAT
1 AATAATACTAAATAATATTCTTTATTAA-ATTTATTATA-TTCAAAT
12629765 AATA
1 AATA
12629769 TTAACATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 3 0.07
44 20 0.45
45 21 0.48
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (45 bp):
AATAATACTAAATAATATTCTTTATTAAATTTATTATATTCAAAT
Found at i:12629782 original size:18 final size:18
Alignment explanation
Indices: 12629759--12629796 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
12629749 TTTATTTTAG
12629759 TTAAATAAT-ATTAACATA
1 TTAAATAATAATTAA-ATA
12629777 TTAAATAATAATTAAATA
1 TTAAATAATAATTAAATA
12629795 TT
1 TT
12629797 TTTGTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATAATAATTAAATA
Found at i:12639668 original size:34 final size:34
Alignment explanation
Indices: 12639584--12639730 Score: 147
Period size: 34 Copynumber: 4.3 Consensus size: 34
12639574 AAAGGAATGA
*
12639584 GCTTTTT-ATGAGATCAAGTGAAACCCTCACAAT
1 GCTTTTTCATGAGATCAAGCGAAACCCTCACAAT
* *
12639617 AGATTTTT-ACGAGATCAAGCGAAACCCTCACAAT
1 -GCTTTTTCATGAGATCAAGCGAAACCCTCACAAT
*** *
12639651 GCTTTTTCATG-GTATCAAGCGAAATGTTTACAAT
1 GCTTTTTCATGAG-ATCAAGCGAAACCCTCACAAT
* *
12639685 GCTTTTTCATGGGATCAAGTGAAACCCTTCAACAAT
1 GCTTTTTCATGAGATCAAGCGAAACCC-TC-ACAAT
*
12639721 GGTTTTTCAT
1 GCTTTTTCAT
12639731 AAGCTCAACC
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
33 7 0.08
34 70 0.75
35 2 0.02
36 14 0.15
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (34 bp):
GCTTTTTCATGAGATCAAGCGAAACCCTCACAAT
Found at i:12641752 original size:63 final size:63
Alignment explanation
Indices: 12641650--12641773 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 63
12641640 GAGAAATGGT
* * *
12641650 TAAGTATTTATAAAAGAAAACCAACCCAAAAAGCTTTCAAAATTGGATTCTACACCAAAAGGC
1 TAAGTATTTATAAAAGAAAACCAACACAAAAAGCCTTCAAAATTAGATTCTACACCAAAAGGC
* * * *
12641713 TAAGTATTTATAAAAGATAACCAGCACAACAAGCCTTCAAAATTAGATTCTACACTAAAAG
1 TAAGTATTTATAAAAGAAAACCAACACAAAAAGCCTTCAAAATTAGATTCTACACCAAAAG
12641774 TATAGAAACT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (63 bp):
TAAGTATTTATAAAAGAAAACCAACACAAAAAGCCTTCAAAATTAGATTCTACACCAAAAGGC
Found at i:12644494 original size:22 final size:21
Alignment explanation
Indices: 12644437--12644495 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
12644427 TTAGGTATAT
12644437 ATTTTATAAGTTTATATAAATA
1 ATTTTATAAG-TTATATAAATA
***
12644459 AAGATATATA-TTATACTAAATA
1 ATTTTATA-AGTTATA-TAAATA
12644481 ATTTTATAAGTTATA
1 ATTTTATAAGTTATA
12644496 ACTTTTGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
21 6 0.21
22 21 0.75
23 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTTTATAAGTTATATAAATA
Found at i:12664064 original size:17 final size:17
Alignment explanation
Indices: 12664026--12664071 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
12664016 TGCATTCAGG
*
12664026 TATTATTTTTTTTCTTTA
1 TATT-TTTTTTTTATTTA
12664044 TATTTTGTTTTTTATTT-
1 TATTTT-TTTTTTATTTA
12664061 TATTTTTTTTT
1 TATTTTTTTTT
12664072 GTACTTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 13 0.50
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (17 bp):
TATTTTTTTTTTATTTA
Found at i:12665501 original size:18 final size:18
Alignment explanation
Indices: 12665459--12665501 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12665449 TCTCTCTAAA
* *
12665459 TTCACTATCTAATTCTTT
1 TTCACTTTCTAATTCTCT
*
12665477 TTTACTTTCTAATTCTCT
1 TTCACTTTCTAATTCTCT
12665495 TTCACTT
1 TTCACTT
12665502 ACCACGACAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (18 bp):
TTCACTTTCTAATTCTCT
Found at i:12669658 original size:2 final size:2
Alignment explanation
Indices: 12669651--12669680 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12669641 TATGAATAAA
12669651 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
12669681 TCTCTCTTGC
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:12671335 original size:16 final size:17
Alignment explanation
Indices: 12671293--12671336 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
12671283 CGGTCAAAAA
* *
12671293 TATTATTTAATCGAGAT
1 TATTATTTTATCGAGAG
*
12671310 TATTAATTTATCG-GAG
1 TATTATTTTATCGAGAG
12671326 TATTATTTTAT
1 TATTATTTTAT
12671337 AGAGGTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (17 bp):
TATTATTTTATCGAGAG
Found at i:12679431 original size:4 final size:4
Alignment explanation
Indices: 12679422--12679446 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12679412 AATCATTTTG
12679422 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
12679447 ATTGTTTACC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:12685716 original size:74 final size:74
Alignment explanation
Indices: 12685590--12685742 Score: 270
Period size: 74 Copynumber: 2.1 Consensus size: 74
12685580 CTAGATTAAG
* *
12685590 TTAAGCAATTTTCATATTTGTGGATTGTCATATTTCTATTAGGTCTATATGGGTTATCACTATAA
1 TTAAGCAATTTTCATATATGTGGATTGTCATATTTCTATTAGGTCTAGATGGGTTATCACTATAA
*
12685655 ATAATTCCT
66 ATAACTCCT
*
12685664 TTAAGCAATTTTCATATATGTGGATTGTCGTATTTCTATTAGGTCTAGATGGGTTATCACTATAA
1 TTAAGCAATTTTCATATATGTGGATTGTCATATTTCTATTAGGTCTAGATGGGTTATCACTATAA
12685729 ATAACTCCT
66 ATAACTCCT
12685738 TTAAG
1 TTAAG
12685743 TTTCATTATA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (74 bp):
TTAAGCAATTTTCATATATGTGGATTGTCATATTTCTATTAGGTCTAGATGGGTTATCACTATAA
ATAACTCCT
Found at i:12687340 original size:29 final size:29
Alignment explanation
Indices: 12687289--12687351 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
12687279 ATGTTGAAAA
** * *
12687289 AAAAAATACTTTTGTTATTCGTCATGTTG
1 AAAAAATACTTTTGTTACACGTCATATTC
12687318 AAAAAATA-TTATTGTTACACGTCATATTC
1 AAAAAATACTT-TTGTTACACGTCATATTC
12687347 AAAAA
1 AAAAA
12687352 CATTTTGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (29 bp):
AAAAAATACTTTTGTTACACGTCATATTC
Found at i:12688776 original size:25 final size:26
Alignment explanation
Indices: 12688723--12688779 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
12688713 CGCTATATAT
*
12688723 AAAAATATATTACACGTTATGGTTAA
1 AAAAATATATTACACGTCATGGTTAA
*
12688749 AAAAATTTATTACACGTCAT-GTTGAA
1 AAAAATATATTACACGTCATGGTT-AA
12688775 AAAAA
1 AAAAA
12688780 AAATATCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (26 bp):
AAAAATATATTACACGTCATGGTTAA
Found at i:12688810 original size:30 final size:31
Alignment explanation
Indices: 12688758--12688898 Score: 114
Period size: 30 Copynumber: 4.7 Consensus size: 31
12688748 AAAAAATTTA
* * **
12688758 TTACACGTCATGTTGAAAAAAAAAATATCGTTG
1 TTACACGCCATGTT--ACAAAAAAATATTATTG
* *
12688791 TTACACGCCAT-TTACAAAAAAA-A--AATA
1 TTACACGCCATGTTACAAAAAAATATTATTG
* *
12688818 TTACACGTCATGTTA-AAAAAAATATTGTTG
1 TTACACGCCATGTTACAAAAAAATATTATTG
* * *
12688848 TTACGCGCCATGTTAAAAAAAAATGTTATTG
1 TTACACGCCATGTTACAAAAAAATATTATTG
*
12688879 TTACACGTCATG-TACAAAAA
1 TTACACGCCATGTTACAAAAA
12688899 CATGTTACAT
Statistics
Matches: 87, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
27 18 0.21
28 4 0.05
29 1 0.01
30 29 0.33
31 23 0.26
32 2 0.02
33 10 0.11
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (31 bp):
TTACACGCCATGTTACAAAAAAATATTATTG
Found at i:12688810 original size:31 final size:31
Alignment explanation
Indices: 12688758--12688891 Score: 118
Period size: 31 Copynumber: 4.4 Consensus size: 31
12688748 AAAAAATTTA
* *
12688758 TTACACGTCATGTTGAAAAAAAAAATATCGTTG
1 TTACACGCCATGTT--AAAAAAAAATATTGTTG
* *
12688791 TTACACGCCAT-TTACAAAAAAAA-A---ATA
1 TTACACGCCATGTTA-AAAAAAAATATTGTTG
*
12688818 TTACACGTCATGTT-AAAAAAAATATTGTTG
1 TTACACGCCATGTTAAAAAAAAATATTGTTG
* * *
12688848 TTACGCGCCATGTTAAAAAAAAATGTTATTG
1 TTACACGCCATGTTAAAAAAAAATATTGTTG
*
12688879 TTACACGTCATGT
1 TTACACGCCATGT
12688892 ACAAAAACAT
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
26 8 0.10
27 12 0.15
28 2 0.02
30 15 0.18
31 33 0.40
32 2 0.02
33 10 0.12
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (31 bp):
TTACACGCCATGTTAAAAAAAAATATTGTTG
Found at i:12688848 original size:57 final size:58
Alignment explanation
Indices: 12688747--12688870 Score: 171
Period size: 57 Copynumber: 2.1 Consensus size: 58
12688737 CGTTATGGTT
**
12688747 AAAAAAATTTATTACACGTCATGTTGAAAAAAAAAATATCGTTGTTACACGCCAT-TTACA
1 AAAAAAAAATATTACACGTCATGTT--AAAAAAAAATATCGTTGTTACACGCCATGTTA-A
* *
12688807 AAAAAAAAATATTACACGTCATGTT-AAAAAAAATATTGTTGTTACGCGCCATGTTAA
1 AAAAAAAAATATTACACGTCATGTTAAAAAAAAATATCGTTGTTACACGCCATGTTAA
12688864 AAAAAAA
1 AAAAAAA
12688871 TGTTATTGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
57 33 0.56
58 3 0.05
60 23 0.39
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.28
Consensus pattern (58 bp):
AAAAAAAAATATTACACGTCATGTTAAAAAAAAATATCGTTGTTACACGCCATGTTAA
Found at i:12688961 original size:29 final size:31
Alignment explanation
Indices: 12688919--12688977 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
12688909 GCTATGACTC
12688919 AAAATGATTGTTACACGCCATGT-TAAAAAA
1 AAAATGATTGTTACACGCCATGTATAAAAAA
* *
12688949 AAAAT-ATTTTTACACGCTATGTATAAAAA
1 AAAATGATTGTTACACGCCATGTATAAAAA
12688978 CATGCTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (31 bp):
AAAATGATTGTTACACGCCATGTATAAAAAA
Found at i:12689121 original size:29 final size:29
Alignment explanation
Indices: 12689060--12689141 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
12689050 TACAAAAATA
* * *
12689060 TGTTACACGTCATGTTGAAAAAAATGTTGT
1 TGTTACACGCCATATTG-AAAAAATGTTAT
12689090 TGTTACACGCCATATTGAAAAAATGTTAT
1 TGTTACACGCCATATTGAAAAAATGTTAT
* *
12689119 TGTTACATGCCATATTTAAAAAA
1 TGTTACACGCCATATTGAAAAAA
12689142 AAATTGTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 32 0.68
30 15 0.32
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (29 bp):
TGTTACACGCCATATTGAAAAAATGTTAT
Found at i:12689147 original size:27 final size:28
Alignment explanation
Indices: 12689089--12689150 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
12689079 AAAAATGTTG
**
12689089 TTGTTACACGCCATATTGAAAAAATGTTA
1 TTGTTACACGCCATATTGAAAAAA-GAAA
* *
12689118 TTGTTACATGCCATATTTAAAAAA-AAA
1 TTGTTACACGCCATATTGAAAAAAGAAA
12689145 TTGTTA
1 TTGTTA
12689151 TATTTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.24
29 22 0.76
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (28 bp):
TTGTTACACGCCATATTGAAAAAAGAAA
Found at i:12690846 original size:41 final size:41
Alignment explanation
Indices: 12690797--12691107 Score: 158
Period size: 41 Copynumber: 7.6 Consensus size: 41
12690787 ATATTTAAAT
12690797 TAAATAAAATATTAATATTTTAAATATTAATGATTAAATTA
1 TAAATAAAATATTAATATTTTAAATATTAATGATTAAATTA
* * *
12690838 TAAATAAAATATCAATA-TTTAAATTATCAATTATTAATATTTA
1 TAAATAAAATATTAATATTTTAAA-TATTAATGATTAA-A-TTA
* * *** *
12690881 AAAATAAAATA-AAATAAAAATAAATTGATCATAATAATACTTAAA-T-
1 TAAATAAAATATTAAT-ATTTTAAA-T-AT--TAAT--GA-TTAAATTA
*
12690927 TAAATAAAATATTAATATTTTAAATATTGATGATTAAATT-
1 TAAATAAAATATTAATATTTTAAATATTAATGATTAAATTA
* *
12690967 TAATATTTAAATTATCAAT-TTTT-AATATTTAA--ATATAAA--A
1 TAA-A--TAAAATATTAATATTTTAAATA-TTAATGAT-TAAATTA
* *
12691007 TGAAATAAAAAATTAATCA---T-AATAAT-AT--TTAAA-T-
1 T-AAATAAAATATTAAT-ATTTTAAATATTAATGATTAAATTA
* * *
12691041 TAAATGAAATGTTAATATTTTAAAATATTAAAGATTAAATTA
1 TAAATAAAATATTAATATTTT-AAATATTAATGATTAAATTA
12691083 TAAATAAAATATTAATATTTTAAAT
1 TAAATAAAATATTAATATTTTAAAT
12691108 TATCAATTAT
Statistics
Matches: 207, Mismatches: 29, Indels: 68
0.68 0.10 0.22
Matches are distributed among these distances:
32 1 0.00
33 12 0.06
34 5 0.02
35 3 0.01
36 1 0.00
37 10 0.05
38 10 0.05
39 5 0.02
40 20 0.10
41 43 0.21
42 33 0.16
43 24 0.12
44 8 0.04
45 3 0.01
46 15 0.07
47 7 0.03
49 3 0.01
50 4 0.02
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (41 bp):
TAAATAAAATATTAATATTTTAAATATTAATGATTAAATTA
Found at i:12690882 original size:48 final size:44
Alignment explanation
Indices: 12690820--12690951 Score: 112
Period size: 48 Copynumber: 2.9 Consensus size: 44
12690810 AATATTTTAA
12690820 ATATTAATGATTAAATTATAAATAAAATATCAATATTTAAATT-ATC
1 ATATTAAT-ATTAAA-TATAAATAAAATAT-AATATTTAAATTGATC
* *
12690866 AATTATTAATATTTAAAAATAAAATAAAATA-AA-A-ATAAATTGATC
1 -A-TATTAATA-TTAAATAT-AAATAAAATATAATATTTAAATTGATC
*
12690911 ATAATAATACTTAAAT-TAAATAAAATATTAATATTTTAAAT
1 ATATTAATA-TTAAATATAAATAAAATA-TAATA-TTTAAAT
12690952 ATTGATGATT
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
41 10 0.14
42 1 0.01
43 14 0.20
44 8 0.11
45 4 0.06
46 7 0.10
47 4 0.06
48 22 0.31
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.39
Consensus pattern (44 bp):
ATATTAATATTAAATATAAATAAAATATAATATTTAAATTGATC
Found at i:12690953 original size:15 final size:14
Alignment explanation
Indices: 12690933--12690978 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
12690923 AAATTAAATA
12690933 AAATATTAATATTTT
1 AAATATTAATA-TTT
*
12690948 AAATATTGATGA-TT
1 AAATATTAAT-ATTT
12690962 AAAT-TTAATATTT
1 AAATATTAATATTT
12690975 AAAT
1 AAAT
12690979 TATCAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 1 0.04
13 10 0.37
14 6 0.22
15 9 0.33
16 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (14 bp):
AAATATTAATATTT
Found at i:12690997 original size:117 final size:115
Alignment explanation
Indices: 12690851--12691081 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 115
12690841 ATAAAATATC
*
12690851 AATATTTAAATTATCAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAATTGATCATAAT
1 AATATTTAAATTATCAATTATTAATATTTAAAAATAAAATAAAAT--AAA-AAATTAATCATAAT
* *
12690916 AATACTTAAATTAAATAAAATATTAATATTTT-AAATATTGATGATTAAATTT
63 AATACTTAAATTAAATAAAATATTAATATTTTAAAATATTAAAGATTAAATTT
* * *
12690968 AATATTTAAATTATCAATTTTTAATATTTAAATATAAAATGAAATAAAAAATTAATCATAATAAT
1 AATATTTAAATTATCAATTATTAATATTTAAAAATAAAATAAAATAAAAAATTAATCATAATAAT
* * *
12691033 ATTTAAATTAAATGAAATGTTAATATTTTAAAATATTAAAGATTAAATT
66 ACTTAAATTAAATAAAATATTAATATTTTAAAATATTAAAGATTAAATT
12691082 ATAAATAAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
114 42 0.40
115 20 0.19
117 42 0.40
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (115 bp):
AATATTTAAATTATCAATTATTAATATTTAAAAATAAAATAAAATAAAAAATTAATCATAATAAT
ACTTAAATTAAATAAAATATTAATATTTTAAAATATTAAAGATTAAATTT
Found at i:12691133 original size:27 final size:27
Alignment explanation
Indices: 12691103--12691178 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
12691093 ATTAATATTT
*
12691103 TAAATTATCAATTATTAATATTTTGAA-
1 TAAATTATCAATTATTAATATTAT-AAG
12691130 TAAA-TA-CTAATTATTAATATTATAAG
1 TAAATTATC-AATTATTAATATTATAAG
*
12691156 CAAATTATCAATTATTAATATTA
1 TAAATTATCAATTATTAATATTA
12691179 AAAAATAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 3 0.07
26 19 0.44
27 20 0.47
28 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (27 bp):
TAAATTATCAATTATTAATATTATAAG
Found at i:12691148 original size:26 final size:23
Alignment explanation
Indices: 12691052--12691177 Score: 73
Period size: 23 Copynumber: 5.3 Consensus size: 23
12691042 AAATGAAATG
* **
12691052 TTAATATTTTAAA-ATATTAAAGA
1 TTAATATTTTAAATA-ATCAATTA
*
12691075 TTAA-ATTATAAATAA--AA-TA
1 TTAATATTTTAAATAATCAATTA
*
12691094 TTAATATTTTAAATTATCAATTA
1 TTAATATTTTAAATAATCAATTA
*
12691117 TTAATATTTTGAATAAATACTAATTA
1 TTAATATTTTAAAT-AAT-C-AATTA
* *
12691143 TTAATATTATAAGCAAATTATCAATTA
1 TTAATATT-T---TAAATAATCAATTA
12691170 TTAATATT
1 TTAATATT
12691178 AAAAAATAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
19 5 0.06
20 11 0.13
22 10 0.12
23 20 0.24
24 2 0.02
25 1 0.01
26 13 0.16
27 14 0.17
28 1 0.01
29 2 0.02
30 3 0.04
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAATATTTTAAATAATCAATTA
Found at i:12691226 original size:26 final size:26
Alignment explanation
Indices: 12691168--12691242 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
12691158 AATTATCAAT
* * *
12691168 TATTAATATTAAAAAATAAAAATAAAA
1 TATTAATATT-TAAATTATAAATAAAA
*
12691195 TATTAATGA-TTAAATTATAAATAAGA
1 TATTAAT-ATTTAAATTATAAATAAAA
*
12691221 TGTTAATATTTAAATTATAAAT
1 TATTAATATTTAAATTATAAAT
12691243 TATTCATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 1 0.02
26 31 0.76
27 8 0.20
28 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
TATTAATATTTAAATTATAAATAAAA
Found at i:12691251 original size:22 final size:22
Alignment explanation
Indices: 12691226--12691283 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 22
12691216 TAAGATGTTA
12691226 ATATTTAAATTATAAATTATTC
1 ATATTTAAATTATAAATTATTC
12691248 ATATTTTAATTAAATTATAAATTATTC
1 ATA---T--TTAAATTATAAATTATTC
12691275 ATATTTAAA
1 ATATTTAAA
12691284 AAATCAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
22 8 0.26
24 1 0.03
25 1 0.03
27 21 0.68
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTTAAATTATAAATTATTC
Found at i:12699184 original size:39 final size:41
Alignment explanation
Indices: 12699130--12699212 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 41
12699120 GATGTCAAAA
12699130 GTACATAATGCTCCTC-T-GTATTCTATATAATTTTATCAG
1 GTACATAATGCTCCTCATGGTATTCTATATAATTTTATCAG
12699169 GTACATAATGCTCCTCTAATATGGTATTCTATATAATTTTATCA
1 GTACATAATGCTCCTC----ATGGTATTCTATATAATTTTATCA
12699213 AGCACATTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
39 16 0.42
44 1 0.03
45 21 0.55
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (41 bp):
GTACATAATGCTCCTCATGGTATTCTATATAATTTTATCAG
Found at i:12701894 original size:22 final size:21
Alignment explanation
Indices: 12701866--12701918 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12701856 TTTTGTTTAA
*
12701866 TTTTTTCTTTTTCTTTATTCTT
1 TTTTTTCTTTTT-TTTATCCTT
* *
12701888 TTTTTTCTTGTTTTTCTCCTT
1 TTTTTTCTTTTTTTTATCCTT
12701909 TTTTTTCTTT
1 TTTTTTCTTT
12701919 CTCTCTCCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTATCCTT
Found at i:12701925 original size:20 final size:21
Alignment explanation
Indices: 12701885--12701927 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12701875 TTTCTTTATT
* *
12701885 CTTTTTTTTCTTGTTTTTCTC
1 CTTTTTTTTCTTGTCTCTCTC
12701906 CTTTTTTTTCTT-TCTCTCTC
1 CTTTTTTTTCTTGTCTCTCTC
12701926 CT
1 CT
12701928 CTCACCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (21 bp):
CTTTTTTTTCTTGTCTCTCTC
Found at i:12702172 original size:12 final size:13
Alignment explanation
Indices: 12702138--12702184 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
12702128 GATGAGAGAG
12702138 AGAAAA-AAAAGA
1 AGAAAAGAAAAGA
12702150 A-AAAAGAAAA-A
1 AGAAAAGAAAAGA
*
12702161 GAGGAAAGAAAAGA
1 -AGAAAAGAAAAGA
12702175 AGAAAAGAAA
1 AGAAAAGAAA
12702185 CAAAAGCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 5 0.17
12 6 0.21
13 17 0.59
14 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAAGA
Found at i:12702172 original size:26 final size:26
Alignment explanation
Indices: 12702134--12702184 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12702124 GTGAGATGAG
12702134 AGAGAGAAAAAAAAGAA-AAAAGAAAA
1 AGAGAG-AAAAAAAGAAGAAAAGAAAA
12702160 AGAG-GAAAGAAAAGAAGAAAAGAAA
1 AGAGAGAAA-AAAAGAAGAAAAGAAA
12702185 CAAAAGCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.13
25 8 0.35
26 12 0.52
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (26 bp):
AGAGAGAAAAAAAGAAGAAAAGAAAA
Found at i:12705340 original size:5 final size:5
Alignment explanation
Indices: 12705320--12705372 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
12705310 ATTTAACTGA
* * *
12705320 AAAAG AAAAC ATAAAA AAAAA AAAAG AAAAG AAAAG AAAAG AAAAGG AAAAG
1 AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA-G AAAAG
12705372 A
1 A
12705373 CAGATGTACA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
5 34 0.79
6 9 0.21
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:12705359 original size:21 final size:21
Alignment explanation
Indices: 12705319--12705372 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
12705309 AATTTAACTG
*
12705319 AAAAAGAAAACATAAAAAAAA
1 AAAAAGAAAAGATAAAAAAAA
*
12705340 AAAAAGAAAAGA-AAAGAAAAG
1 AAAAAGAAAAGATAAA-AAAAA
*
12705361 AAAAGGAAAAGA
1 AAAAAGAAAAGA
12705373 CAGATGTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAAGAAAAGATAAAAAAAA
Found at i:12708015 original size:3 final size:3
Alignment explanation
Indices: 12708007--12708037 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
12707997 AAAGAATGTT
*
12708007 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12708038 ACAAACTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12709095 original size:90 final size:90
Alignment explanation
Indices: 12708986--12709160 Score: 223
Period size: 90 Copynumber: 1.9 Consensus size: 90
12708976 AAGTTTTGGA
* *
12708986 ATTATTTTGTTTCATCATCTTC-AAGCT-TCAAAAGGATTTCAATGATTCGG-TTTTGATTTATA
1 ATTACTTTGTTTCATCATC-TCAAAGCTCT-AAAAGGATTTCAATGATT-GGTTTTTAATTTATA
* *
12709048 GTTTTAGC-AAATCAGGTAAGTGTTGCT
63 GTTGTAACAAAATCAGGTAAGTGTTGCT
* * *
12709075 ATTACTTTGTTTTCATCATCTCAAAGCTCTAAAAGGATTTCAATGGTTGGTTTTTAATTTTTGGT
1 ATTACTTTG-TTTCATCATCTCAAAGCTCTAAAAGGATTTCAATGATTGGTTTTTAATTTATAGT
12709140 TGTAACAAAATCAGGTAAGTG
65 TGTAACAAAATCAGGTAAGTG
12709161 ACTTGACATC
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
89 12 0.16
90 47 0.64
91 15 0.20
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (90 bp):
ATTACTTTGTTTCATCATCTCAAAGCTCTAAAAGGATTTCAATGATTGGTTTTTAATTTATAGTT
GTAACAAAATCAGGTAAGTGTTGCT
Found at i:12711613 original size:27 final size:27
Alignment explanation
Indices: 12711581--12711637 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
12711571 TTTTTTTCTA
*
12711581 TTGGGCCATGCCCATTTTTCTTTCTTG
1 TTGGGCCATGCCCATTTTCCTTTCTTG
12711608 TTGGGCCATGCCCATTTTCCTTTCTTG
1 TTGGGCCATGCCCATTTTCCTTTCTTG
12711635 TTG
1 TTG
12711638 CTTTCTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.07, C:0.26, G:0.19, T:0.47
Consensus pattern (27 bp):
TTGGGCCATGCCCATTTTCCTTTCTTG
Found at i:12712417 original size:22 final size:22
Alignment explanation
Indices: 12712379--12712423 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12712369 TTTATACTTA
*
12712379 TATTATTATTTCACTATTTATT
1 TATTATTATTTCACTATTAATT
*
12712401 TATT-TTATTTCTTCTATTAATT
1 TATTATTATTTC-ACTATTAATT
12712423 T
1 T
12712424 CACTACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTATTATTTCACTATTAATT
Found at i:12716177 original size:10 final size:10
Alignment explanation
Indices: 12716158--12716194 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
12716148 CAACCTAACC
12716158 TAACTTGACT
1 TAACTTGACT
*
12716168 TAATTTGACT
1 TAACTTGACT
*
12716178 TGACTTGACT
1 TAACTTGACT
12716188 TAACTTG
1 TAACTTG
12716195 GGCCACATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (10 bp):
TAACTTGACT
Found at i:12720149 original size:171 final size:170
Alignment explanation
Indices: 12719858--12720201 Score: 616
Period size: 171 Copynumber: 2.0 Consensus size: 170
12719848 CCGATTACTT
12719858 GCTTTAAATAAATTGATTTCATTTGGTTGAAATAAGTTGAAAGATGATAAATTACAGTTTGATAA
1 GCTTTAAATAAATTGATTTCATTTGGTTGAAATAAGTTGAAAGATGATAAATTACAGTTTGATAA
12719923 AATATTTTAATAGTCTCATTTTACTCGACTTTAGATATTTTGAGTAATGTTTGTTTACTCACTGG
66 AATATTTTAATAGTCTCATTTTACTCGACTTTAGATATTTTGAGTAATGTTTGTTTACTCACTGG
* *
12719988 GATTTTATAATCTCACCACCCTCATTTTCACCCATTTCAG
131 GATTTTATAATCTAACCACCCTCATTTCCACCCATTTCAG
* *
12720028 NGCTTTCAATAAATTGATTTCATTTGGTTGAAATAAGTTGAAAGATGATAAATTACAGTTTGATG
1 -GCTTTAAATAAATTGATTTCATTTGGTTGAAATAAGTTGAAAGATGATAAATTACAGTTTGATA
* * *
12720093 AAATGTTTTAATAGTCTCATTTTACTCGACTTTAGATATTTTGAGTGATGTTTGTTTACTCATTG
65 AAATATTTTAATAGTCTCATTTTACTCGACTTTAGATATTTTGAGTAATGTTTGTTTACTCACTG
12720158 GGATTTTATAATCTAACCACCCTCATTTCCACCCATTTCAG
130 GGATTTTATAATCTAACCACCCTCATTTCCACCCATTTCAG
12720199 GCT
1 GCT
12720202 CAGAATAGAT
Statistics
Matches: 166, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
170 3 0.02
171 163 0.98
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (170 bp):
GCTTTAAATAAATTGATTTCATTTGGTTGAAATAAGTTGAAAGATGATAAATTACAGTTTGATAA
AATATTTTAATAGTCTCATTTTACTCGACTTTAGATATTTTGAGTAATGTTTGTTTACTCACTGG
GATTTTATAATCTAACCACCCTCATTTCCACCCATTTCAG
Found at i:12724935 original size:19 final size:20
Alignment explanation
Indices: 12724908--12724948 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
12724898 GCCTCGAACT
12724908 AAATCAAA-TAGAGAAT-TTA
1 AAATCAAATTA-AGAATATTA
*
12724927 AAATGAAATTAAGAATATTA
1 AAATCAAATTAAGAATATTA
12724947 AA
1 AA
12724949 GTCCTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (20 bp):
AAATCAAATTAAGAATATTA
Found at i:12730499 original size:25 final size:26
Alignment explanation
Indices: 12730400--12730499 Score: 98
Period size: 25 Copynumber: 4.0 Consensus size: 26
12730390 AATTATAATT
*
12730400 ATAATTTTACCACCAGAAGTGGAT-A
1 ATAATTTTACCACCAGAAGTGGATGG
* * ** *
12730425 ATAATTTTACTATCAGAA-TCTAAGG
1 ATAATTTTACCACCAGAAGTGGATGG
* * *
12730450 TTAATTTTGCCATCAGAAGTGGATGG
1 ATAATTTTACCACCAGAAGTGGATGG
12730476 ATAA-TTTACCACCAGAAGTGGATG
1 ATAATTTTACCACCAGAAGTGGATG
12730500 AATGCCATAA
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
24 2 0.03
25 49 0.84
26 7 0.12
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (26 bp):
ATAATTTTACCACCAGAAGTGGATGG
Found at i:12736325 original size:20 final size:19
Alignment explanation
Indices: 12736302--12736341 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12736292 GAGAAGAAGA
12736302 AGAAGGAGAAAAGCTGCTGG
1 AGAAGGA-AAAAGCTGCTGG
* *
12736322 AGAATGAAAAAGCTGTTGG
1 AGAAGGAAAAAGCTGCTGG
12736341 A
1 A
12736342 AGAACAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.42, C:0.07, G:0.35, T:0.15
Consensus pattern (19 bp):
AGAAGGAAAAAGCTGCTGG
Found at i:12743341 original size:9 final size:9
Alignment explanation
Indices: 12743327--12743353 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12743317 TTGGATAGAT
12743327 TCACAAACA
1 TCACAAACA
12743336 TCACAAACA
1 TCACAAACA
12743345 TCACAAACA
1 TCACAAACA
12743354 AATTAAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.11
Consensus pattern (9 bp):
TCACAAACA
Found at i:12747081 original size:19 final size:19
Alignment explanation
Indices: 12747057--12747094 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12747047 CCATTTGACT
12747057 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
12747076 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
12747095 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:12755355 original size:43 final size:43
Alignment explanation
Indices: 12755245--12755469 Score: 263
Period size: 43 Copynumber: 5.2 Consensus size: 43
12755235 AGCCAGGTCA
* *
12755245 TCATCATCGGCTTATGTGCACTCCTTACTCGCACATAGCCGGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
*
12755288 TCATCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCAGG
1 ---TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
* * *
12755334 TCATCATCGGCTTATGAGCACTCTCTACTCGCACATAGTCGGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
* **
12755377 TCATCATTGGCTTATGCGCACTCCCTACTCGCACATAGTTGGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
* * * * * * *
12755420 TTATCATCAGCTCATGTGCACT-CCGACATCGAACATAGCTGGG
1 TCATCATCGGCTTATGCGCACTCCCTAC-TCGCACATAGCCGGG
12755463 TCATCAT
1 TCATCAT
12755470 TATCATACAA
Statistics
Matches: 158, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
42 4 0.03
43 114 0.72
46 40 0.25
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.28
Consensus pattern (43 bp):
TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
Found at i:12755441 original size:86 final size:85
Alignment explanation
Indices: 12755245--12755470 Score: 292
Period size: 86 Copynumber: 2.6 Consensus size: 85
12755235 AGCCAGGTCA
12755245 TCATCATCGGCTTATGTGCACTCCTTACTCGCACATAGCCGGGTCATCATCATCGGCTTATGCGC
1 TCATCATCGGCTTATGTGCACTCC-TACTCGCACATAG-CGGGTCATCAT--TCGGCTTATGCGC
12755310 ACTCCCTACTCGCACATAGCCAGG
62 ACTCCCTACTCGCACATAGCCAGG
*
12755334 TCATCATCGGCTTATGAGCACTCTCTACTCGCACATAGTCGGGTCATCATT-GGCTTATGCGCAC
1 TCATCATCGGCTTATGTGCACTC-CTACTCGCACATAG-CGGGTCATCATTCGGCTTATGCGCAC
***
12755398 TCCCTACTCGCACATAGTTGGG
64 TCCCTACTCGCACATAGCCAGG
* * * * *
12755420 TTATCATCAGCTCATGTGCACTCCGACATCGAACATAGCTGGGTCATCATT
1 TCATCATCGGCTTATGTGCACTCCTAC-TCGCACATAGC-GGGTCATCATT
12755471 ATCATACAAC
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
85 4 0.03
86 71 0.58
87 1 0.01
89 46 0.37
90 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.28
Consensus pattern (85 bp):
TCATCATCGGCTTATGTGCACTCCTACTCGCACATAGCGGGTCATCATTCGGCTTATGCGCACTC
CCTACTCGCACATAGCCAGG
Found at i:12759618 original size:21 final size:22
Alignment explanation
Indices: 12759577--12759618 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12759567 CCCATTGGTC
*
12759577 TGTTTTTAAAATTTCATCCATT
1 TGTTTTCAAAATTTCATCCATT
*
12759599 TGTTTTCAAATTTTCA-CCAT
1 TGTTTTCAAAATTTCATCCAT
12759619 ACACTTGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (22 bp):
TGTTTTCAAAATTTCATCCATT
Found at i:12769843 original size:15 final size:15
Alignment explanation
Indices: 12769819--12769848 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12769809 AAATTGTTTT
*
12769819 AAAATTGAATAATTG
1 AAAATAGAATAATTG
12769834 AAAATAGAATAATTG
1 AAAATAGAATAATTG
12769849 GATACCATTT
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:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (15 bp):
AAAATAGAATAATTG
Found at i:12778151 original size:11 final size:11
Alignment explanation
Indices: 12778118--12778152 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
12778108 CCTAGGGGTC
12778118 TTGTTCTTCCT
1 TTGTTCTTCCT
12778129 TT-TTCTTCCT
1 TTGTTCTTCCT
*
12778139 TTGTTCTTGCT
1 TTGTTCTTCCT
12778150 TTG
1 TTG
12778153 GCCGACCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.00, C:0.23, G:0.11, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:12791265 original size:20 final size:22
Alignment explanation
Indices: 12791240--12791281 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
12791230 CAAAGTCACA
12791240 TTCTTTTC-CATTA-TTTTCTT
1 TTCTTTTCTCATTACTTTTCTT
*
12791260 TTCTTTTCTCTTTACTTTTCTT
1 TTCTTTTCTCATTACTTTTCTT
12791282 GCATGGGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (22 bp):
TTCTTTTCTCATTACTTTTCTT
Found at i:12794237 original size:27 final size:27
Alignment explanation
Indices: 12794206--12794285 Score: 142
Period size: 27 Copynumber: 3.0 Consensus size: 27
12794196 CTTATTTCTA
*
12794206 TTGGGCCATGCCCATTTTTCTTTCTTG
1 TTGGGCCATGCCCATTTTCCTTTCTTG
12794233 TTGGGCCATGCCCATTTTCCTTTCTTG
1 TTGGGCCATGCCCATTTTCCTTTCTTG
*
12794260 TTGGGTCATGCCCATTTTCCTTTCTT
1 TTGGGCCATGCCCATTTTCCTTTCTT
12794286 ATTACTTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.07, C:0.28, G:0.17, T:0.47
Consensus pattern (27 bp):
TTGGGCCATGCCCATTTTCCTTTCTTG
Found at i:12794672 original size:34 final size:34
Alignment explanation
Indices: 12794612--12794712 Score: 96
Period size: 34 Copynumber: 3.0 Consensus size: 34
12794602 ATTCTACTGC
* *
12794612 AAAAATCTACACTTTTCAGTCC-CCAAAACCAACA
1 AAAAAACTACACTTTTCA-ACCTCCAAAACCAACA
* * * ** * *
12794646 ACAAAGCTGCACTTTTTGACCTCCAAAATCAGCA
1 AAAAAACTACACTTTTCAACCTCCAAAACCAACA
*
12794680 AAAAAATTACACTTTTCAACCTCCAAAACCAAC
1 AAAAAACTACACTTTTCAACCTCCAAAACCAAC
12794713 CCTTAAATGG
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
33 2 0.04
34 48 0.96
ACGTcount: A:0.43, C:0.31, G:0.05, T:0.22
Consensus pattern (34 bp):
AAAAAACTACACTTTTCAACCTCCAAAACCAACA
Found at i:12797983 original size:16 final size:16
Alignment explanation
Indices: 12797948--12797981 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12797938 GTTGGTCTTC
12797948 TTATATATATATATAT
1 TTATATATATATATAT
*
12797964 TTATATTTATATACTAT
1 TTATATATATATA-TAT
12797981 T
1 T
12797982 ATTACTGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATATATATATATAT
Found at i:12801429 original size:43 final size:43
Alignment explanation
Indices: 12801359--12801477 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
12801349 GTAATTATGT
* *
12801359 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
12801402 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
12801445 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
12801478 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:12801487 original size:43 final size:43
Alignment explanation
Indices: 12801369--12801490 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
12801359 TGACTCGGCT
* **
12801369 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
12801412 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
12801455 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
12801491 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:12801501 original size:20 final size:20
Alignment explanation
Indices: 12801476--12801538 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
12801466 GGGAGTGCGC
12801476 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
*
12801496 ATGAGCTGGTGATGATGATA
1 ATGAGCTGGTGATGATGATG
* *
12801516 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
12801535 ATGA
1 ATGA
12801539 TGGGTATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.27, C:0.03, G:0.40, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:12801550 original size:2 final size:2
Alignment explanation
Indices: 12801543--12801577 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12801533 TGATGATGGG
*
12801543 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12801578 GTAAATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12804821 original size:4 final size:4
Alignment explanation
Indices: 12804812--12804841 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
12804802 ATTTATATAA
*
12804812 GTAT GTAT GTAT GTAT GTAT GTTT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
12804842 GGTGTTCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (4 bp):
GTAT
Found at i:12807115 original size:35 final size:34
Alignment explanation
Indices: 12807075--12807157 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 34
12807065 TGGTTGGAGA
*
12807075 AACAGATCACATGCA-TGCCAAAGCAGTGGACGAAG
1 AACAGATCAC--GCAGTGCCAAAGCAATGGACGAAG
** *
12807110 AACAGATCACGCATGTGCCAAAGCAATGGGTGGAG
1 AACAGATCACGCA-GTGCCAAAGCAATGGACGAAG
12807145 AACAGATCACGCA
1 AACAGATCACGCA
12807158 CAACGTCGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 3 0.07
35 39 0.93
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.12
Consensus pattern (34 bp):
AACAGATCACGCAGTGCCAAAGCAATGGACGAAG
Found at i:12810467 original size:20 final size:20
Alignment explanation
Indices: 12810442--12810480 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12810432 CTATAAATAT
12810442 CTCATTTCTCTAGCAGTTTC
1 CTCATTTCTCTAGCAGTTTC
*
12810462 CTCATTTTTCTAGCAGTTT
1 CTCATTTCTCTAGCAGTTT
12810481 TTTGTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.26, G:0.10, T:0.49
Consensus pattern (20 bp):
CTCATTTCTCTAGCAGTTTC
Found at i:12814784 original size:42 final size:43
Alignment explanation
Indices: 12814703--12814787 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
12814693 TCATCATCAT
* * * *
12814703 CATCGGCTTATGCTCACTCCTTACTCGCACATAGTCGGGTCAA
1 CATCGACTTATGCGCACTCCTCACTCGCACATAGCCGGGTCAA
12814746 CATCGACTTATGCGCACTCC-CACTCGCACATAGCCGGGTCAA
1 CATCGACTTATGCGCACTCCTCACTCGCACATAGCCGGGTCAA
12814788 TATCATTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 20 0.53
43 18 0.47
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (43 bp):
CATCGACTTATGCGCACTCCTCACTCGCACATAGCCGGGTCAA
Found at i:12818853 original size:20 final size:20
Alignment explanation
Indices: 12818828--12818867 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12818818 TTATAAACAT
12818828 CTCATTTCTCTAGCAGCTTC
1 CTCATTTCTCTAGCAGCTTC
*
12818848 CTCATTTTTCTAGCAGCTTC
1 CTCATTTCTCTAGCAGCTTC
12818868 TTGTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.33, G:0.10, T:0.42
Consensus pattern (20 bp):
CTCATTTCTCTAGCAGCTTC
Found at i:12824795 original size:19 final size:19
Alignment explanation
Indices: 12824771--12824808 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12824761 ACTTCTAAAC
12824771 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
12824790 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
12824809 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:12826063 original size:52 final size:52
Alignment explanation
Indices: 12825970--12826124 Score: 238
Period size: 52 Copynumber: 3.0 Consensus size: 52
12825960 TTCCACCTCA
*
12825970 CACATGGCATATATCATCAGTGTGTGCACTCAGACAGCACACCACTATCACG
1 CACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACG
* * *
12826022 CACTTGGCATATATCATCAGTGTGTGCGCTCACACAACACACCACTATCACG
1 CACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACG
* * * *
12826074 CGCATAGCATATATCATCAGTGTGTGCACTCACATAGCACACTACTATCAC
1 CACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCAC
12826125 CGACATGTGC
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.23
Consensus pattern (52 bp):
CACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACG
Found at i:12827364 original size:2 final size:2
Alignment explanation
Indices: 12827357--12827387 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12827347 ATGGAGAATA
12827357 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
12827388 ATTGAATAAG
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:12827661 original size:35 final size:35
Alignment explanation
Indices: 12827613--12827719 Score: 133
Period size: 35 Copynumber: 3.1 Consensus size: 35
12827603 GAGGAGAAGC
* *
12827613 TTTTGCTGCTGATTTTGAAGGCTGAAAAGTGCAGT
1 TTTTGCTGTTGATTTTGAAGGCTGAAAAGTGCGGT
** **
12827648 TTTTGCTGTTGATTTTGAAGGCTGAACGGTATGGT
1 TTTTGCTGTTGATTTTGAAGGCTGAAAAGTGCGGT
* * *
12827683 TTTAGTTATTGATTTTGAAGGCTGAAAAGTGCGGT
1 TTTTGCTGTTGATTTTGAAGGCTGAAAAGTGCGGT
12827718 TT
1 TT
12827720 AGCTGTTAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 59 1.00
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.41
Consensus pattern (35 bp):
TTTTGCTGTTGATTTTGAAGGCTGAAAAGTGCGGT
Found at i:12827815 original size:34 final size:35
Alignment explanation
Indices: 12827737--12827818 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 35
12827727 AATCTTTGTG
*
12827737 GCTTTGGCTACTGATTTTTGAGGAGAAATAGAGCA
1 GCTTTGGCTACTGATTTTTGAGAAGAAATAGAGCA
* **
12827772 GC-TTAGCTACTGA-TTTTGA-AATCAATATGAGCA
1 GCTTTGGCTACTGATTTTTGAGAAGAAATA-GAGCA
12827805 GCTTTGGCTACTGA
1 GCTTTGGCTACTGA
12827819 AAATTATTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 5 0.12
33 13 0.32
34 20 0.50
35 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (35 bp):
GCTTTGGCTACTGATTTTTGAGAAGAAATAGAGCA
Done.