Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 5 of 186
Found at i:1528161 original size:11 final size:11
Alignment explanation
Indices: 1528145--1528171 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1528135 TGTCCCTCTT
1528145 ATTTTAATTTA
1 ATTTTAATTTA
1528156 ATTTTAATTTA
1 ATTTTAATTTA
1528167 ATTTT
1 ATTTT
1528172 CTATTTGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTAATTTA
Found at i:1529204 original size:21 final size:21
Alignment explanation
Indices: 1529165--1529211 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1529155 ATGTTTATTG
*
1529165 TTGTTGTATATTATTTATTCA
1 TTGTTGTATATTATTTATTAA
*
1529186 TTGTTTTAT-TTATTATATTAA
1 TTGTTGTATATTATT-TATTAA
1529207 TTGTT
1 TTGTT
1529212 CTCCATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (21 bp):
TTGTTGTATATTATTTATTAA
Found at i:1529294 original size:14 final size:16
Alignment explanation
Indices: 1529263--1529294 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1529253 ATACTTGTAC
1529263 TTAATTGTTGGATTTA
1 TTAATTGTTGGATTTA
1529279 TTAATTG-TGG-TTTA
1 TTAATTGTTGGATTTA
1529293 TT
1 TT
1529295 GTACTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (16 bp):
TTAATTGTTGGATTTA
Found at i:1533663 original size:10 final size:11
Alignment explanation
Indices: 1533648--1533676 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1533638 CTGTGTGTTC
1533648 TTTATTTTA-T
1 TTTATTTTATT
1533658 TTTATTTTATT
1 TTTATTTTATT
1533669 TTTATTTT
1 TTTATTTT
1533677 CACAGTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:1534633 original size:38 final size:38
Alignment explanation
Indices: 1534582--1534661 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
1534572 ATATTGCTAG
*
1534582 TTAAAGGTTTATTTGAAATACAATAAAAATAGATGGAA
1 TTAAAGATTTATTTGAAATACAATAAAAATAGATGGAA
*
1534620 TTAAAGATTTATTTGAAATACAATAAAAATAGATGGAC
1 TTAAAGATTTATTTGAAATACAATAAAAATAGATGGAA
1534658 TTAA
1 TTAA
1534662 TTAGAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.33
Consensus pattern (38 bp):
TTAAAGATTTATTTGAAATACAATAAAAATAGATGGAA
Found at i:1538185 original size:23 final size:23
Alignment explanation
Indices: 1538159--1538205 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1538149 AAAAAAAAGG
* *
1538159 AAAAAAATAAAAATATGAAAAAA
1 AAAAAAACAAAAAAATGAAAAAA
* *
1538182 AAAATAACAAAAAAATGAATAAA
1 AAAAAAACAAAAAAATGAAAAAA
1538205 A
1 A
1538206 GATGAATTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAAAAACAAAAAAATGAAAAAA
Found at i:1539875 original size:10 final size:10
Alignment explanation
Indices: 1539860--1539886 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1539850 TAAGATCTTT
1539860 TTCCAACTTA
1 TTCCAACTTA
1539870 TTCCAACTTA
1 TTCCAACTTA
1539880 TTCCAAC
1 TTCCAAC
1539887 AACATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (10 bp):
TTCCAACTTA
Found at i:1541604 original size:33 final size:33
Alignment explanation
Indices: 1541515--1541606 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
1541505 GGTTATGTAC
*
1541515 ACTTTGTGTGTA-CACTTGGAAA-GATTAGGTAT
1 ACTTTGTGTGTACCACTTGGAAAGGA-AAGGTAT
* *
1541547 ACTTTGTGTATACCA-TATGAAAAGGAAAGGTAT
1 ACTTTGTGTGTACCACT-TGGAAAGGAAAGGTAT
1541580 ACTTTGTGTGTACCACTTGGAAAGGAA
1 ACTTTGTGTGTACCACTTGGAAAGGAA
1541607 TGTACACCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
32 12 0.24
33 36 0.71
34 3 0.06
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (33 bp):
ACTTTGTGTGTACCACTTGGAAAGGAAAGGTAT
Found at i:1549473 original size:26 final size:26
Alignment explanation
Indices: 1549444--1549551 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
1549434 TGGTACAAAT
1549444 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1549470 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1549496 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1549522 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1549548 TGAT
1 TGAT
1549552 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1556569 original size:26 final size:26
Alignment explanation
Indices: 1556540--1556647 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
1556530 TGGTACAAAT
1556540 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1556566 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1556592 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1556618 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1556644 TGAT
1 TGAT
1556648 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1559667 original size:38 final size:37
Alignment explanation
Indices: 1559616--1559689 Score: 139
Period size: 38 Copynumber: 2.0 Consensus size: 37
1559606 ATAATAAACA
1559616 CTGGAATATTAATTGATGCATAAAAATTCGTAATCAC
1 CTGGAATATTAATTGATGCATAAAAATTCGTAATCAC
1559653 NCTGGAATATTAATTGATGCATAAAAATTCGTAATCA
1 -CTGGAATATTAATTGATGCATAAAAATTCGTAATCA
1559690 AGATAATACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (37 bp):
CTGGAATATTAATTGATGCATAAAAATTCGTAATCAC
Found at i:1559961 original size:34 final size:34
Alignment explanation
Indices: 1559923--1559987 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
1559913 GATTTCTGAA
1559923 CGACTCCGGGCCAACGAAGCGGAGATCTTTAGGG
1 CGACTCCGGGCCAACGAAGCGGAGATCTTTAGGG
*
1559957 CGACTCCGGGCCAACGGAGCGGAGATCTTTA
1 CGACTCCGGGCCAACGAAGCGGAGATCTTTA
1559988 AGGGTGTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15
Consensus pattern (34 bp):
CGACTCCGGGCCAACGAAGCGGAGATCTTTAGGG
Found at i:1563698 original size:26 final size:26
Alignment explanation
Indices: 1563669--1563776 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
1563659 TGGTACAAAT
1563669 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1563695 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1563721 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1563747 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1563773 TGAT
1 TGAT
1563777 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1565483 original size:27 final size:27
Alignment explanation
Indices: 1565399--1565485 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 27
1565389 AGGAAGCGTC
* *
1565399 CTGGTGGCTATGCTACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
*
1565426 CTGATGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
1565453 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
1565480 CTGGTG
1 CTGGTG
1565486 ACTCCATCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.15
27 44 0.83
28 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:1565496 original size:27 final size:26
Alignment explanation
Indices: 1565438--1565502 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
1565428 GATGGCTCTG
* **
1565438 CCACATATATCTGTTCTGGTGGCTCTG
1 CCACA-ATATCTGTTCTGGTGACTCCA
1565465 CCACAATATCTGTATCTGGTGACTCCA
1 CCACAATATCTGT-TCTGGTGACTCCA
*
1565492 TCACAATATCT
1 CCACAATATCT
1565503 CGCAGCCTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 8 0.24
27 25 0.76
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (26 bp):
CCACAATATCTGTTCTGGTGACTCCA
Found at i:1565599 original size:21 final size:20
Alignment explanation
Indices: 1565566--1565605 Score: 55
Period size: 19 Copynumber: 1.9 Consensus size: 20
1565556 CTCCCCGCAC
1565566 GGTGTAAGGTTGG-TATGGA
1 GGTGTAAGGTTGGATATGGA
1565585 GGTGTATACGGTTGGATATGG
1 GGTGTA-A-GGTTGGATATGG
1565606 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.20, C:0.03, G:0.45, T:0.33
Consensus pattern (20 bp):
GGTGTAAGGTTGGATATGGA
Found at i:1574089 original size:46 final size:45
Alignment explanation
Indices: 1574036--1574211 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
1574026 TATTTGGGCA
1574036 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
1574082 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
1574129 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
1574175 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1574212 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:1574191 original size:93 final size:93
Alignment explanation
Indices: 1574032--1574203 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
1574022 GGGATATTTG
* *
1574032 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
1574097 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
1574125 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
1574190 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
1574204 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:1583008 original size:18 final size:17
Alignment explanation
Indices: 1582973--1583016 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
1582963 AAATGTCATG
1582973 TATATTTTTTAATATTAT
1 TATA-TTTTTAATATTAT
1582991 T-TATTTTTAATATTTTAT
1 TATATTTTTAATA--TTAT
1583009 TATATTTT
1 TATATTTT
1583017 ATGGGCACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.39
17 2 0.09
18 6 0.26
19 6 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATATTTTTAATATTAT
Found at i:1584082 original size:12 final size:12
Alignment explanation
Indices: 1584065--1584094 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1584055 TAAAATTATG
1584065 GTTGGTAGTGAA
1 GTTGGTAGTGAA
1584077 GTTGGTAGTGAA
1 GTTGGTAGTGAA
*
1584089 ATTGGT
1 GTTGGT
1584095 TACTTCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (12 bp):
GTTGGTAGTGAA
Found at i:1584254 original size:43 final size:43
Alignment explanation
Indices: 1584193--1584278 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
1584183 TCATATAAAA
* * *
1584193 GTGTCATTTTATTCATTATTTTTATTAAAAAGTTATTTTTAAT
1 GTGTCAATTTATTCATTATTTTTACTAAAAAGTTATCTTTAAT
* *
1584236 GTGTCAATTTCTTCATTATTTTTACTAAAATGTTATCTTTAAT
1 GTGTCAATTTATTCATTATTTTTACTAAAAAGTTATCTTTAAT
1584279 CCTACATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (43 bp):
GTGTCAATTTATTCATTATTTTTACTAAAAAGTTATCTTTAAT
Found at i:1590298 original size:19 final size:19
Alignment explanation
Indices: 1590253--1590299 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1590243 ATCAAATTAA
*
1590253 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
1590272 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
1590291 AATAAAAAT
1 AATAAAAAT
1590300 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:1597150 original size:96 final size:96
Alignment explanation
Indices: 1596954--1597137 Score: 316
Period size: 96 Copynumber: 1.9 Consensus size: 96
1596944 ATATTCCATT
1596954 TTTCAACTAAATCCAATGAAGAAAAAACCCTTAAATCATAAGAAAACACACACACACACACACAG
1 TTTCAACTAAATCCAATGAAGAAAAAACCCTTAAATCATAAGAAAACACACACACACACACACAG
*
1597019 AAATACCAATTGGACTGATAGTCATTCCATA
66 AAATACCAATTGGACTGATAGTCATTACATA
* *
1597050 TTTCAACTAAATCCAATGAAGAAAAAACCCTTAAATCATAA-AAAACACATACATACACACACAG
1 TTTCAACTAAATCCAATGAAGAAAAAACCCTTAAATCATAAGAAAACAC--ACACACACACACAC
1597114 AGAAATACCAATTGGACTGATAGT
64 AGAAATACCAATTGGACTGATAGT
1597138 TGATACTCTT
Statistics
Matches: 84, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
95 7 0.08
96 41 0.49
97 36 0.43
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.20
Consensus pattern (96 bp):
TTTCAACTAAATCCAATGAAGAAAAAACCCTTAAATCATAAGAAAACACACACACACACACACAG
AAATACCAATTGGACTGATAGTCATTACATA
Found at i:1598760 original size:3 final size:3
Alignment explanation
Indices: 1598754--1598779 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1598744 TTTTTCTCTT
1598754 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1598780 TACTAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1599792 original size:15 final size:14
Alignment explanation
Indices: 1599773--1599812 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1599763 CCATGGCCAT
1599773 TAAACCTTAAACCA
1 TAAACCTTAAACCA
*
1599787 TAAAACCCTAAACCA
1 T-AAACCTTAAACCA
*
1599802 TAGACCTTAAA
1 TAAACCTTAAA
1599813 TATTAAATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.20
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:1599998 original size:37 final size:38
Alignment explanation
Indices: 1599957--1600029 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
1599947 AGGTTTTAGG
* *
1599957 GGTTATAGTTTAGTATTTATGGTTTTT-AGGGTTTAAA
1 GGTTATAGATTAGTATTTATGATTTTTGAGGGTTTAAA
* *
1599994 GGTTATAGATTAGTGTTTATGATTTTTGGGGGTTTA
1 GGTTATAGATTAGTATTTATGATTTTTGAGGGTTTA
1600030 GGGTTTTAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (38 bp):
GGTTATAGATTAGTATTTATGATTTTTGAGGGTTTAAA
Found at i:1600218 original size:40 final size:41
Alignment explanation
Indices: 1600132--1600225 Score: 145
Period size: 40 Copynumber: 2.3 Consensus size: 41
1600122 ATTGCTCTGG
*
1600132 AAAAACGCCGCTATTGCTCTAGTTTTTAGCGGCATTTTACC
1 AAAAACGCCGCTATTGCTCTAGCTTTTAGCGGCATTTTACC
**
1600173 AAAAACGCCGCTATTGCTCT-GCTTTTAGCGGCATTTTTGC
1 AAAAACGCCGCTATTGCTCTAGCTTTTAGCGGCATTTTACC
*
1600213 TAAAACGCCGCTA
1 AAAAACGCCGCTA
1600226 ATGTACAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 29 0.59
41 20 0.41
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (41 bp):
AAAAACGCCGCTATTGCTCTAGCTTTTAGCGGCATTTTACC
Found at i:1601291 original size:28 final size:28
Alignment explanation
Indices: 1601258--1601314 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1601248 AACTTTTAAC
* *
1601258 TTTTAATATTTTAATATT-ATAATATATA
1 TTTTAA-ATTTAAAAATTCATAATATATA
*
1601286 TTTTAACTTTAAAAATTCATAATATATA
1 TTTTAAATTTAAAAATTCATAATATATA
1601314 T
1 T
1601315 AAACTTATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTTAAATTTAAAAATTCATAATATATA
Found at i:1606514 original size:124 final size:121
Alignment explanation
Indices: 1606236--1606616 Score: 452
Period size: 124 Copynumber: 3.1 Consensus size: 121
1606226 GGCCAAGCAG
* * *
1606236 GAACTATTGTAGAAAAAGAGTGTCAACGTGAGAGCTTTTTTCAGTAATTTTGTTGACAATGCATC
1 GAACTACTGTAGAAAAAGAGTGTCTACGTGAGAGCTTTTTTCAGTAATTTTGTTGACAGTGCATC
* * * *
1606301 CTGCTTGAAGCGTTTTTGAC-A-TATT--AACTGTTTTCTCAAAATTACTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACTATTTTTCGAACCGTCTTCTCAAAATTA-TTTTTCAA
* *
1606354 GAACTACTATAGAAAAAGAGTGTCTACGT-ATGAGCTTTTTTCACTAATTTTGTTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGTGTCTACGTGA-GAGCTTTTTTCAGTAATTTTGTTGACAGTGCAT
*
1606418 CCTGCTTGAAGTGTTTTTGACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
65 CCTGCTTGAAGCGTTTTTGACTA-TTTTTC-GAACCGTCTTCTCAAAATTA-TTTTTCAA
* * * * * * * *
1606478 GAACTACTGTATAAAAAGAGCGTCTATGTGGGAGCTTTTTTCAGTATTTTTGTTCACAGTGTATA
1 GAACTACTGTAGAAAAAGAGTGTCTACGTGAGAGCTTTTTTCAGTAATTTTGTTGACAGTGCATC
*
1606543 CTACTTGAAGCGTTTTT-ACATTATCTTTTCGGAACCGTCTTCTCAAAATTATTTTTC-A
66 CTGCTTGAAGCGTTTTTGAC--TAT-TTTTC-GAACCGTCTTCTCAAAATTATTTTTCAA
1606601 GAAACTACTGTAGAAA
1 G-AACTACTGTAGAAA
1606617 TTTTTTTTTC
Statistics
Matches: 226, Mismatches: 25, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
117 1 0.00
118 77 0.34
119 1 0.00
121 3 0.01
123 4 0.02
124 113 0.50
125 27 0.12
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (121 bp):
GAACTACTGTAGAAAAAGAGTGTCTACGTGAGAGCTTTTTTCAGTAATTTTGTTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACTATTTTTCGAACCGTCTTCTCAAAATTATTTTTCAA
Found at i:1606767 original size:35 final size:34
Alignment explanation
Indices: 1606708--1606797 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 34
1606698 ACTTATTTAA
1606708 AAAAACCTAAACCCTAATTTAATTAA-TTTTCTT
1 AAAAACCTAAACCCTAATTTAATTAATTTTTCTT
*
1606741 AAAAACACTAAACCCTAATTTAAATTAATTTTTTTT
1 AAAAAC-CTAAACCCTAATTT-AATTAATTTTTCTT
** *
1606777 AAAAATTTAAACCTTAATTTA
1 AAAAACCTAAACCCTAATTTA
1606798 TTTTTTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
33 6 0.12
34 15 0.30
35 18 0.36
36 11 0.22
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAAACCTAAACCCTAATTTAATTAATTTTTCTT
Found at i:1610662 original size:187 final size:190
Alignment explanation
Indices: 1610339--1610711 Score: 520
Period size: 187 Copynumber: 2.0 Consensus size: 190
1610329 TTTACACATT
* *
1610339 TTTTAGTAGTGCAATATTATAAAACTGGGCTGTTTGCTACATATACATGTGCTTGAAGTGTCAAT
1 TTTTAGTAGTGCAATAGTATAAAACTGGGCTGTTTGCTACATATACATGCGCTTGAAGTGTCAAT
* *
1610404 ATATGTTTGATATAGGGACAAACCAGCCGATGACAATGAAATATGGGTAATTTAATGAAAGGGTT
66 ATATGTTTGATATAGGGACAAACCAGACGATGACAATGAAATATGGGTAATTTAATGAAAGGATT
* *
1610469 ATAAATTAATCTGGGATTATAGTTGTTTGCATATTTGGCAAAAGGTGACATGATTGGCTG
131 ATAAATTAATCTGGGATTATAGTTGTTTGCATAGTTGACAAAAGGTGACATGATTGGCTG
* * * * * *
1610529 TTTTGGTAGTGCAGTAGTATAAAATTTGGCTGTTTTCTA-ATTATGCATGCG-TTGAAGTGTCAA
1 TTTTAGTAGTGCAATAGTATAAAACTGGGCTGTTTGCTACA-TATACATGCGCTTGAAGTGTCAA
* * ** *
1610592 TATATGTTTTATATA-GG-CATACTGGATGATGACAATGAAATATGGGTAATTTAATGAAAGGAT
65 TATATGTTTGATATAGGGACAAACCAGACGATGACAATGAAATATGGGTAATTTAATGAAAGGAT
* * * *
1610655 TATAAATTAATTTGGGATTATGGTTGTTTGCATAGTTGACAATAGGTGACTTGATTG
130 TATAAATTAATCTGGGATTATAGTTGTTTGCATAGTTGACAAAAGGTGACATGATTG
1610712 CAGCTAGATC
Statistics
Matches: 161, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
187 91 0.57
188 2 0.01
189 27 0.17
190 41 0.25
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (190 bp):
TTTTAGTAGTGCAATAGTATAAAACTGGGCTGTTTGCTACATATACATGCGCTTGAAGTGTCAAT
ATATGTTTGATATAGGGACAAACCAGACGATGACAATGAAATATGGGTAATTTAATGAAAGGATT
ATAAATTAATCTGGGATTATAGTTGTTTGCATAGTTGACAAAAGGTGACATGATTGGCTG
Found at i:1612995 original size:23 final size:23
Alignment explanation
Indices: 1612969--1613038 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1612959 TTCATTTAAC
*
1612969 TTAATCAAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* * *
1612992 TTAAACGAACAAGTTCATGAACA
1 TTAATCGAACATGTTCACGAACA
* *
1613015 TATAATTGAATATGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
1613039 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.27
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:1613037 original size:24 final size:23
Alignment explanation
Indices: 1612976--1613038 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
1612966 AACTTAATCA
1612976 AACATGTTCACGAACATTAAACG
1 AACATGTTCACGAACATTAAACG
* * **
1612999 AACAAGTTCATGAACATATAATTG
1 AACATGTTCACGAACAT-TAAACG
*
1613023 AATATGTTCACGAACA
1 AACATGTTCACGAACA
1613039 ATGTTAATGA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (23 bp):
AACATGTTCACGAACATTAAACG
Found at i:1621365 original size:23 final size:22
Alignment explanation
Indices: 1621339--1621417 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 22
1621329 CCAACGACAT
1621339 AATCACTATTTTACTCAAATTTC
1 AATCA-TATTTTACTCAAATTTC
* ** * *
1621362 AATCATAAAACTATCCCTCTAATTTA
1 AATCAT---A-TTTTACTCAAATTTC
1621388 AATCAATATTTTACTCAAATTTC
1 AATC-ATATTTTACTCAAATTTC
1621411 AATCATA
1 AATCATA
1621418 AAACTATCGC
Statistics
Matches: 41, Mismatches: 10, Indels: 11
0.66 0.16 0.18
Matches are distributed among these distances:
22 4 0.10
23 19 0.46
24 1 0.02
25 1 0.02
26 14 0.34
27 2 0.05
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (22 bp):
AATCATATTTTACTCAAATTTC
Found at i:1621386 original size:26 final size:26
Alignment explanation
Indices: 1621351--1621439 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 26
1621341 TCACTATTTT
*
1621351 ACTCAAATTTCAATCATAAAACTATC
1 ACTCTAATTTCAATCATAAAACTATC
* * * * *
1621377 CCTCTAATTTAAATC--AATA-TTTT
1 ACTCTAATTTCAATCATAAAACTATC
*
1621400 ACTCAAATTTCAATCATAAAACTATC
1 ACTCTAATTTCAATCATAAAACTATC
*
1621426 GCTCTAATTT-AATC
1 ACTCTAATTTCAATC
1621440 TAACTTCATT
Statistics
Matches: 46, Mismatches: 14, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
23 14 0.30
24 3 0.07
25 7 0.15
26 22 0.48
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.37
Consensus pattern (26 bp):
ACTCTAATTTCAATCATAAAACTATC
Found at i:1621411 original size:49 final size:49
Alignment explanation
Indices: 1621339--1621437 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
1621329 CCAACGACAT
*
1621339 AATCACTATTTTACTCAAATTTCAATCATAAAACTATCCCTCTAATTTA
1 AATCAATATTTTACTCAAATTTCAATCATAAAACTATCCCTCTAATTTA
*
1621388 AATCAATATTTTACTCAAATTTCAATCATAAAACTATCGCTCTAATTTA
1 AATCAATATTTTACTCAAATTTCAATCATAAAACTATCCCTCTAATTTA
1621437 A
1 A
1621438 TCTAACTTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.38
Consensus pattern (49 bp):
AATCAATATTTTACTCAAATTTCAATCATAAAACTATCCCTCTAATTTA
Found at i:1622034 original size:45 final size:45
Alignment explanation
Indices: 1621970--1622060 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
1621960 ATTTGAAAAC
1621970 ATTGACATGAAAGATGTTATAAAATATCTGACACAAGGCAGCAGT
1 ATTGACATGAAAGATGTTATAAAATATCTGACACAAGGCAGCAGT
*
1622015 ATTGACATGGAAGATGTTATAAAATATCTGACACAAGGCAGCAGT
1 ATTGACATGAAAGATGTTATAAAATATCTGACACAAGGCAGCAGT
1622060 A
1 A
1622061 GTTGGAATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (45 bp):
ATTGACATGAAAGATGTTATAAAATATCTGACACAAGGCAGCAGT
Found at i:1622925 original size:33 final size:32
Alignment explanation
Indices: 1622876--1622943 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
1622866 AGAGAAGAGG
*
1622876 CTTGTATTTTTATTGGATGATTTTAATTTAGA
1 CTTGTATTATTATTGGATGATTTTAATTTAGA
1622908 CTTGTATTAATTATTGGATGATTTTAATTTAGA
1 CTTGTATT-ATTATTGGATGATTTTAATTTAGA
1622941 CTT
1 CTT
1622944 TGTAGGAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.54
Consensus pattern (32 bp):
CTTGTATTATTATTGGATGATTTTAATTTAGA
Found at i:1623640 original size:30 final size:30
Alignment explanation
Indices: 1623604--1623663 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1623594 TATTTTATTA
1623604 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
1623634 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
1623664 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:1629200 original size:14 final size:14
Alignment explanation
Indices: 1629181--1629220 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1629171 TTGATTGCCA
1629181 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
1629195 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
1629209 GGAAAATGTTTT
1 GTAAAATGTTTT
1629221 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:1629229 original size:20 final size:20
Alignment explanation
Indices: 1629204--1629243 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1629194 CGTAAAATGA
*
1629204 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1629224 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1629244 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1629233 original size:34 final size:35
Alignment explanation
Indices: 1629189--1629255 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1629179 CAGTAAAATG
*
1629189 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
1629223 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1629256 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1629259 original size:14 final size:15
Alignment explanation
Indices: 1629183--1629259 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1629173 GATTGCCAGT
* *
1629183 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
1629197 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
1629211 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
1629231 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
1629246 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
1629260 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:1641939 original size:13 final size:14
Alignment explanation
Indices: 1641922--1641958 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1641912 ATTCACTTAA
1641922 CATTT-AATATATT
1 CATTTCAATATATT
*
1641935 TATTTCAA-ATATT
1 CATTTCAATATATT
1641948 CATTTCAATAT
1 CATTTCAATAT
1641959 CCTTTTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (14 bp):
CATTTCAATATATT
Found at i:1642667 original size:26 final size:26
Alignment explanation
Indices: 1642638--1642700 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
1642628 ATGTTCACAA
*
1642638 ACTCAAATCCTGCTAAATAAACACCG
1 ACTCAAAGCCTGCTAAATAAACACCG
*
1642664 ACTCAAGGCCTGCTAAATAAACACCG
1 ACTCAAAGCCTGCTAAATAAACACCG
*
1642690 ACTCAAGGCCT
1 ACTCAAAGCCT
1642701 ACTATTCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.38, C:0.32, G:0.13, T:0.17
Consensus pattern (26 bp):
ACTCAAAGCCTGCTAAATAAACACCG
Found at i:1643550 original size:5 final size:5
Alignment explanation
Indices: 1643542--1643571 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1643532 TTAACTTAAA
1643542 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1643572 TATTAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:1646773 original size:20 final size:20
Alignment explanation
Indices: 1646748--1646796 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1646738 TACCGAGCAA
*
1646748 AACAGAACATTTAACTTTAC
1 AACAGAACATTTAACTTCAC
*
1646768 AACAGAACATTTAACTTCAT
1 AACAGAACATTTAACTTCAC
1646788 AACAGAACA
1 AACAGAACA
1646797 ACTATACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.24
Consensus pattern (20 bp):
AACAGAACATTTAACTTCAC
Found at i:1649848 original size:55 final size:57
Alignment explanation
Indices: 1649754--1649859 Score: 128
Period size: 55 Copynumber: 1.9 Consensus size: 57
1649744 AACTATTTAA
* * * **
1649754 AAAATTTTATAATCTTTATCAAAAATTTAGAACATTATAATTTGTTTAAAATTTATT
1 AAAACTTTATAATCGTTATCAAAAATTTAAAACATTATAACATGTTTAAAATTTATT
*
1649811 AAAACTTTATAAT-GTT-TCAAAATTTTAAAATCA-TATAACATGTTTAAAA
1 AAAACTTTATAATCGTTATCAAAAATTTAAAA-CATTATAACATGTTTAAAA
1649860 ATAATTATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
55 26 0.62
56 4 0.10
57 12 0.29
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (57 bp):
AAAACTTTATAATCGTTATCAAAAATTTAAAACATTATAACATGTTTAAAATTTATT
Found at i:1649870 original size:21 final size:22
Alignment explanation
Indices: 1649844--1649884 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1649834 TTTAAAATCA
1649844 TATAACATGTTT-AAAAATAAT
1 TATAACATGTTTGAAAAATAAT
* *
1649865 TATAACGTTTTTGAAAAATA
1 TATAACATGTTTGAAAAATA
1649885 TGTTAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (22 bp):
TATAACATGTTTGAAAAATAAT
Found at i:1660387 original size:45 final size:44
Alignment explanation
Indices: 1660323--1660450 Score: 193
Period size: 45 Copynumber: 2.9 Consensus size: 44
1660313 ATATGTCAAT
1660323 ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATAAA
1 ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATAAA
* * * *
1660367 GATGAGTAAGGCCACAGCTGAAAGATGCTATGGCATCAAGATAAA
1 -ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATAAA
* *
1660412 ATAAGTAAGACCATAACTGAAAGATGTTATGGCATCATG
1 ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATG
1660451 TGAAAGCACG
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
44 33 0.45
45 40 0.55
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (44 bp):
ATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATAAA
Found at i:1669274 original size:9 final size:8
Alignment explanation
Indices: 1669260--1669316 Score: 60
Period size: 9 Copynumber: 6.5 Consensus size: 8
1669250 AATAATTTAT
1669260 TGTTACATG
1 TGTTA-ATG
1669269 TGTTACATG
1 TGTTA-ATG
1669278 TGTTTAATG
1 TG-TTAATG
*
1669287 TGTTAGTG
1 TGTTAATG
1669295 TGTTTAATG
1 TG-TTAATG
1669304 TGTTTAATG
1 TG-TTAATG
1669313 TGTT
1 TGTT
1669317 TGTTAAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
8 9 0.20
9 32 0.73
10 3 0.07
ACGTcount: A:0.19, C:0.04, G:0.25, T:0.53
Consensus pattern (8 bp):
TGTTAATG
Found at i:1669297 original size:26 final size:26
Alignment explanation
Indices: 1669267--1669316 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
1669257 TATTGTTACA
1669267 TGTG-TTACATGTGTTTAATGTGTTAG
1 TGTGTTTA-ATGTGTTTAATGTGTTAG
1669293 TGTGTTTAATGTGTTTAATGTGTT
1 TGTGTTTAATGTGTTTAATGTGTT
1669317 TGTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.18, C:0.02, G:0.26, T:0.54
Consensus pattern (26 bp):
TGTGTTTAATGTGTTTAATGTGTTAG
Found at i:1669317 original size:9 final size:9
Alignment explanation
Indices: 1669266--1669317 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
1669256 TTATTGTTAC
1669266 ATGTG-TTA
1 ATGTGTTTA
1669274 CATGTGTTTA
1 -ATGTGTTTA
1669284 ATGTG-TTA
1 ATGTGTTTA
*
1669292 GTGTGTTTA
1 ATGTGTTTA
1669301 ATGTGTTTA
1 ATGTGTTTA
1669310 ATGTGTTT
1 ATGTGTTT
1669318 GTTAAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 7 0.18
9 29 0.74
10 3 0.08
ACGTcount: A:0.19, C:0.02, G:0.25, T:0.54
Consensus pattern (9 bp):
ATGTGTTTA
Found at i:1670617 original size:66 final size:66
Alignment explanation
Indices: 1670540--1670666 Score: 191
Period size: 66 Copynumber: 1.9 Consensus size: 66
1670530 CTAATGAAAT
* * * *
1670540 AAGTGAGCTATAAGAGTATTTTCTAGTTAATATGGAATTAAAATTAACTTTTTAATAAAAACAAA
1 AAGTGAACTATAAGAGTATTCTCTAATAAATATGGAATTAAAATTAACTTTTTAATAAAAACAAA
1670605 G
66 G
* * *
1670606 AAGTGAACTATAAGAGTGTTCTCTAATAAATGTGGGATTAAAATTAACTTTTTAATAAAAA
1 AAGTGAACTATAAGAGTATTCTCTAATAAATATGGAATTAAAATTAACTTTTTAATAAAAA
1670667 TAGTAAAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (66 bp):
AAGTGAACTATAAGAGTATTCTCTAATAAATATGGAATTAAAATTAACTTTTTAATAAAAACAAA
G
Found at i:1671611 original size:21 final size:22
Alignment explanation
Indices: 1671569--1671612 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1671559 TATGGGATTA
*
1671569 AAATTAACTTTTTAAAGGAATT
1 AAATTAACTTTTTAAAGAAATT
*
1671591 AAATTAA-TTTTTAATGAAATT
1 AAATTAACTTTTTAAAGAAATT
1671612 A
1 A
1671613 GTGAAGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATTAACTTTTTAAAGAAATT
Found at i:1673818 original size:23 final size:24
Alignment explanation
Indices: 1673783--1673831 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
1673773 TTTTATAATT
1673783 TTTTAAAAATTTAAAATAATTTTA
1 TTTTAAAAATTTAAAATAATTTTA
**
1673807 TTTT-AAAATTTAAAATGTTTTTA
1 TTTTAAAAATTTAAAATAATTTTA
1673830 TT
1 TT
1673832 CTTTTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTTAAAAATTTAAAATAATTTTA
Found at i:1675397 original size:22 final size:23
Alignment explanation
Indices: 1675350--1675397 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
1675340 TAATTTTTTG
*
1675350 AAATATTTATGAAAAATACTTTA
1 AAATATTTATGAAAAATACTTAA
*
1675373 AAAT-TTTATTAAATAATA-TTAA
1 AAATATTTATGAAA-AATACTTAA
1675395 AAA
1 AAA
1675398 AATATCCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATATTTATGAAAAATACTTAA
Found at i:1690274 original size:16 final size:16
Alignment explanation
Indices: 1690255--1690285 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1690245 GTCCTTAATT
1690255 TTTATTATTAATTATC
1 TTTATTATTAATTATC
1690271 TTTATTATTAATTAT
1 TTTATTATTAATTAT
1690286 TGTAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATTAATTATC
Found at i:1698951 original size:17 final size:18
Alignment explanation
Indices: 1698917--1698951 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1698907 ATACTTTTCT
1698917 TAAGGTATCGATATATTCC
1 TAAGGTATCGA-ATATTCC
1698936 TAAGGTATCG-ATATTC
1 TAAGGTATCGAATATTC
1698952 TCACTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (18 bp):
TAAGGTATCGAATATTCC
Found at i:1699934 original size:43 final size:42
Alignment explanation
Indices: 1699869--1700138 Score: 324
Period size: 43 Copynumber: 6.3 Consensus size: 42
1699859 CGCTATATGC
*
1699869 AACGCCGCTAAAGACCATGACCTTTAGCGGCGCCTTTTTCGCA
1 AACGCCGCTAAAGACCATGACCTTTAGCGGC-ACTTTTTCGCA
* * * * *
1699912 AACGCCTCTAAAGATCAGGACCTTTAGCGGCGCTTTTTTCACA
1 AACGCCGCTAAAGACCATGACCTTTAGCGGCAC-TTTTTCGCA
* * * *
1699955 AACGCCGCTAAAGACAATAACCTTTAGCGACGCTTTTTTCGCA
1 AACGCCGCTAAAGACCATGACCTTTAGCGGCAC-TTTTTCGCA
* * *
1699998 AACGTCGCTAAAGACCACGACCTTTAGCGGCACTTTTTAGCA
1 AACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTCGCA
* * *
1700040 AATGCCGCTAAAGACCACGACCTTTAGCGGCACTTTTTTGACA
1 AACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTCG-CA
* * *
1700083 AACGCCGCTAAAGATCATAACCTTTAGCGGCACTTTTTCCCCA
1 AACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTT-CGCA
1700126 AACGCCGCTAAAG
1 AACGCCGCTAAAG
1700139 GTCATCAAAT
Statistics
Matches: 196, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 46 0.23
43 150 0.77
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (42 bp):
AACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTCGCA
Found at i:1700069 original size:128 final size:129
Alignment explanation
Indices: 1699869--1700138 Score: 391
Period size: 128 Copynumber: 2.1 Consensus size: 129
1699859 CGCTATATGC
* * * * * *
1699869 AACGCCGCTAAAGACCATGACCTTTAGCGGCGCCTTTTTCGCAAACGCCTCTAAAGATCAGGACC
1 AACGCCGCTAAAGACCACGACCTTTAGCGGCGACTTTTTAGCAAACGCCGCTAAAGACCACGACC
* * * *
1699934 TTTAGCGGCGCTTTTTTCACAAACGCCGCTAAAGA-CAATAACCTTTAGCGACGCTTTTTTCGCA
66 TTTAGCGGCACTTTTTTCACAAACGCCGCTAAAGATC-ATAACCTTTAGCGACACTTTTTCCCCA
* *
1699998 AACGTCGCTAAAGACCACGACCTTTAGCGGC-ACTTTTTAGCAAATGCCGCTAAAGACCACGACC
1 AACGCCGCTAAAGACCACGACCTTTAGCGGCGACTTTTTAGCAAACGCCGCTAAAGACCACGACC
* *
1700062 TTTAGCGGCACTTTTTTGACAAACGCCGCTAAAGATCATAACCTTTAGCGGCACTTTTTCCCCA
66 TTTAGCGGCACTTTTTTCACAAACGCCGCTAAAGATCATAACCTTTAGCGACACTTTTTCCCCA
1700126 AACGCCGCTAAAG
1 AACGCCGCTAAAG
1700139 GTCATCAAAT
Statistics
Matches: 125, Mismatches: 15, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
128 95 0.76
129 30 0.24
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (129 bp):
AACGCCGCTAAAGACCACGACCTTTAGCGGCGACTTTTTAGCAAACGCCGCTAAAGACCACGACC
TTTAGCGGCACTTTTTTCACAAACGCCGCTAAAGATCATAACCTTTAGCGACACTTTTTCCCCA
Found at i:1700452 original size:19 final size:19
Alignment explanation
Indices: 1700407--1700453 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1700397 TAAATATTAA
*
1700407 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
1700426 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
1700445 AATAAAAAT
1 AATAAAAAT
1700454 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:1705599 original size:41 final size:41
Alignment explanation
Indices: 1705554--1705813 Score: 384
Period size: 41 Copynumber: 6.4 Consensus size: 41
1705544 GTTATATGAC
1705554 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* *
1705595 TTTTAGCGGCGTTTTACAGAAAGCGCCGCTAATTCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1705636 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1705677 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
1705718 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGAC-CT-GT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATG-CTCTGGT
* ** * * *
1705758 TTTTAGCGGCATTTT-TTGTTAAAACGCCGCTATTGCTCT-AT
1 TTTTAGCGGCGTTTTACCG--AAAGCGCCGCTAATGCTCTGGT
1705799 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
1705814 TGGTAAAACG
Statistics
Matches: 204, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
39 1 0.00
40 17 0.08
41 185 0.91
42 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:1705844 original size:41 final size:41
Alignment explanation
Indices: 1705554--1705843 Score: 376
Period size: 41 Copynumber: 7.1 Consensus size: 41
1705544 GTTATATGAC
*
1705554 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCTGGT
*
1705595 TTTTAGCGGCGTTTTACAGAAAGCGCCGCTAATT-CTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCT-ATTGCTCTGGT
*
1705636 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCTGGT
*
1705677 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCTGGT
1705718 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGAC-CT-GT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTG-CTCTGGT
* ** * *
1705758 TTTTAGCGGCATTTT-TTGTTAAAACGCCGCTATTGCTCT-AT
1 TTTTAGCGGCGTTTTACCG--AAAGCGCCGCTATTGCTCTGGT
** *
1705799 TTTTAGCGGCGTTTT-TGGTAAAACGCCGCTATTGCTCTGTGT
1 TTTTAGCGGCGTTTTACCG-AAAGCGCCGCTATTGCTCTG-GT
1705841 TTT
1 TTT
1705844 ACAATTTTTG
Statistics
Matches: 228, Mismatches: 13, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
39 1 0.00
40 39 0.17
41 181 0.79
42 7 0.03
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTCTGGT
Found at i:1706950 original size:18 final size:18
Alignment explanation
Indices: 1706924--1706958 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1706914 TAAACATAAA
1706924 TATTAATATTTAATTATT
1 TATTAATATTTAATTATT
* *
1706942 TATTTATATTTAGTTAT
1 TATTAATATTTAATTAT
1706959 ATAATAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTAATATTTAATTATT
Found at i:1707079 original size:15 final size:15
Alignment explanation
Indices: 1707059--1707111 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1707049 ATTCAATATT
1707059 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1707074 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
1707093 AATATATTAATAATA
1 AATATTTTAATAATA
1707108 AATA
1 AATA
1707112 GTTTGTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.45
16 2 0.06
17 4 0.13
18 1 0.03
19 10 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1708409 original size:19 final size:19
Alignment explanation
Indices: 1708387--1708425 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1708377 TAATTAGTTA
* *
1708387 TGATTTTTTTATATTTAAT
1 TGATATTTTTAAATTTAAT
1708406 TGATATTTTTAAATTTAAT
1 TGATATTTTTAAATTTAAT
1708425 T
1 T
1708426 TGTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TGATATTTTTAAATTTAAT
Found at i:1710248 original size:14 final size:14
Alignment explanation
Indices: 1710229--1710257 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1710219 ATAAATGTAA
1710229 ACACGAGTAGGCAT
1 ACACGAGTAGGCAT
1710243 ACACGAGTAGGCAT
1 ACACGAGTAGGCAT
1710257 A
1 A
1710258 GATGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.28, T:0.14
Consensus pattern (14 bp):
ACACGAGTAGGCAT
Found at i:1719233 original size:6 final size:6
Alignment explanation
Indices: 1719222--1719256 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1719212 TGGACATGAT
*
1719222 TCTGTA TCTGTA TCTGTA TCTGCA TCTGTA TCTGT
1 TCTGTA TCTGTA TCTGTA TCTGTA TCTGTA TCTGT
1719257 TCCTGATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (6 bp):
TCTGTA
Found at i:1720089 original size:86 final size:88
Alignment explanation
Indices: 1719938--1720178 Score: 310
Period size: 89 Copynumber: 2.7 Consensus size: 88
1719928 CTTGTAACTT
* *
1719938 TTTCAAAAAAAGTAATTAAGCCCTTACTTTTTTTTTGCACTCAATTGGGTACTTAAAACTTTCAA
1 TTTCAAAAAAAGTAATTAAGCCCTTGCTTTTTTTTTGCACTCAATTGGGTACTT-GAACTTTCAA
*
1720003 AATGTATAAAAAAGACCCTCAAAC
65 AATGGATAAAAAAGACCCTCAAAC
* * *
1720027 -TT-AAAAAAA-AAATTAAGCCCCTTGCTTTTTTTTTTCACTCAATTGGGTACTTGAGCTTTCAA
1 TTTCAAAAAAAGTAATTAAG-CCCTTGCTTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAA
*
1720089 AATGGATTAAAAAGACCCTCAAAC
65 AATGGATAAAAAAGACCCTCAAAC
* * * * *
1720113 TTTTCAAAAAAAGTAATCAAG-TCTCTGATTTTTTTTTGCACTCAATTGGTTACTTGAACTATCA
1 -TTTCAAAAAAAGTAATTAAGCCCT-TGCTTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCA
1720177 AA
64 AA
1720179 TGCAAAAAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
86 37 0.28
87 39 0.30
88 6 0.05
89 43 0.33
90 6 0.05
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (88 bp):
TTTCAAAAAAAGTAATTAAGCCCTTGCTTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAA
ATGGATAAAAAAGACCCTCAAAC
Found at i:1720187 original size:86 final size:86
Alignment explanation
Indices: 1719937--1720187 Score: 278
Period size: 86 Copynumber: 2.9 Consensus size: 86
1719927 TCTTGTAACT
* *
1719937 TTTTCAAAAAAAGTAATTAAGCCCTTACTTTTTTTTTGCACTCAATTGGGTACTTAAAACTTTCA
1 TTTTCAAAAAAAGTAATTAAGCCCTGA-TTTTTTTTTGCACTCAATTGGGTACTT-GAACTTTCA
*
1720002 AAATGTATAAAAAAGACCCTCAAAC
64 AAATG--CAAAAAAGACCCTCAAAC
* * * *
1720027 --TT-AAAAAAA-AAATTAAGCCCCTTGCTTTTTTTTTTCACTCAATTGGGTACTTGAGCTTTCA
1 TTTTCAAAAAAAGTAATTAAG-CCC-TGATTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCA
*
1720088 AAATGGATTAAAAAGACCCTCAAAC
64 AAATGCA--AAAAAGACCCTCAAAC
* * * *
1720113 TTTTCAAAAAAAGTAATCAAGTCTCTGATTTTTTTTTGCACTCAATTGGTTACTTGAACTATC-A
1 TTTTCAAAAAAAGTAATTAAG-CCCTGATTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAA
1720177 AATGCAAAAAA
65 AATGCAAAAAA
1720188 AAAAATTATT
Statistics
Matches: 136, Mismatches: 17, Indels: 20
0.79 0.10 0.12
Matches are distributed among these distances:
84 1 0.01
86 40 0.29
87 36 0.26
88 11 0.08
89 40 0.29
90 8 0.06
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.35
Consensus pattern (86 bp):
TTTTCAAAAAAAGTAATTAAGCCCTGATTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAA
ATGCAAAAAAGACCCTCAAAC
Found at i:1720307 original size:10 final size:10
Alignment explanation
Indices: 1720284--1720401 Score: 59
Period size: 10 Copynumber: 11.8 Consensus size: 10
1720274 ATAAAAAAAA
* *
1720284 TAAAAATCAA
1 TAAAAATTAT
1720294 TAAAAATTAT
1 TAAAAATTAT
1720304 T-AAAATTAT
1 TAAAAATTAT
1720313 T--AAATTAT
1 TAAAAATTAT
1720321 AATAAAAA-TA-
1 --TAAAAATTAT
*
1720331 TAAAAACTA-
1 TAAAAATTAT
*
1720340 TAAAAAATAT
1 TAAAAATTAT
*
1720350 TAAAATTTTAT
1 TAAAA-ATTAT
*
1720361 TAAAAATAAGTT
1 TAAAAATTA--T
*
1720373 ATAAAAATAAT
1 -TAAAAATTAT
*
1720384 AAAAAATTAT
1 TAAAAATTAT
*
1720394 AAAAAATT
1 TAAAAATT
1720402 GTAAAATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
8 13 0.15
9 19 0.21
10 33 0.37
11 11 0.12
12 4 0.04
13 9 0.10
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:1720319 original size:8 final size:9
Alignment explanation
Indices: 1720296--1720356 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
1720286 AAAATCAATA
1720296 AAAATTATT
1 AAAATTATT
1720305 AAAATTATT
1 AAAATTATT
1720314 -AAATTATAAT
1 AAAATTAT--T
* *
1720324 AAAAATATA
1 AAAATTATT
* *
1720333 AAAACTATA
1 AAAATTATT
*
1720342 AAAAATATT
1 AAAATTATT
1720351 AAAATT
1 AAAATT
1720357 TTATTAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 7 0.16
9 29 0.67
10 1 0.02
11 6 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAATTATT
Found at i:1720341 original size:20 final size:20
Alignment explanation
Indices: 1720318--1720368 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
1720308 ATTATTAAAT
1720318 TATAATAAAAATATAAAAAC
1 TATAATAAAAATATAAAAAC
* *
1720338 TAT-A-AAAAATATTAAAAT
1 TATAATAAAAATATAAAAAC
* *
1720356 TTTATTAAAAATA
1 TATAATAAAAATA
1720369 AGTTATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 14 0.56
19 1 0.04
20 10 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAATAAAAATATAAAAAC
Found at i:1720351 original size:37 final size:38
Alignment explanation
Indices: 1720282--1720368 Score: 104
Period size: 37 Copynumber: 2.3 Consensus size: 38
1720272 ATATAAAAAA
* * *
1720282 AATAAAAATCAATAAAAATTATTAAAATTATT-AAATTAT
1 AATAAAAAT--ATAAAAACTATAAAAAATATTAAAATTAT
*
1720321 AATAAAAATATAAAAACTATAAAAAATATTAAAATTTT
1 AATAAAAATATAAAAACTATAAAAAATATTAAAATTAT
*
1720359 ATTAAAAATA
1 AATAAAAATA
1720369 AGTTATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 18 0.43
38 15 0.36
39 9 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (38 bp):
AATAAAAATATAAAAACTATAAAAAATATTAAAATTAT
Found at i:1720395 original size:19 final size:18
Alignment explanation
Indices: 1720270--1720398 Score: 63
Period size: 19 Copynumber: 7.2 Consensus size: 18
1720260 TGTGGCAAAT
**
1720270 AAAT-ATAAAAAAAATAA
1 AAATAATAAAAATTATAA
*
1720287 AAATCAATAAAAATTATTA
1 AAAT-AATAAAAATTATAA
* *
1720306 AAATTAT-TAAATTATAA
1 AAATAATAAAAATTATAA
* *
1720323 TAAAAATATAAAAACTATAA
1 -AAATA-ATAAAAATTATAA
* * *
1720343 AAA-ATATTAAAATTTTATT
1 AAATA-ATAAAAATTATA-A
*
1720362 AAA-AAT--AAGTTATAA
1 AAATAATAAAAATTATAA
1720377 AAATAATAAAAAATTATAA
1 AAATAAT-AAAAATTATAA
1720396 AAA
1 AAA
1720399 ATTGTAAAAT
Statistics
Matches: 84, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
15 3 0.04
16 9 0.11
17 12 0.14
18 18 0.21
19 34 0.40
20 8 0.10
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (18 bp):
AAATAATAAAAATTATAA
Found at i:1720407 original size:9 final size:10
Alignment explanation
Indices: 1720314--1720418 Score: 63
Period size: 10 Copynumber: 10.2 Consensus size: 10
1720304 TAAAATTATT
1720314 AAATTATAATA
1 AAATTATAA-A
*
1720325 AAAATAT-AA
1 AAATTATAAA
*
1720334 AAACTATAAA
1 AAATTATAAA
1720344 AAA-TATTAAA
1 AAATTA-TAAA
**
1720354 ATTTTATTAAAA
1 AAATTA-T-AAA
1720366 ATAAGTTAT-AA
1 A-AA-TTATAAA
*
1720377 AAATAATAAA
1 AAATTATAAA
1720387 AAATTATAAA
1 AAATTATAAA
*
1720397 AAATTGTAAA
1 AAATTATAAA
**
1720407 ATTTTATAAA
1 AAATTATAAA
1720417 AA
1 AA
1720419 TCATAATATA
Statistics
Matches: 74, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
9 12 0.16
10 41 0.55
11 13 0.18
12 4 0.05
13 1 0.01
14 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (10 bp):
AAATTATAAA
Found at i:1720407 original size:53 final size:50
Alignment explanation
Indices: 1720322--1720419 Score: 144
Period size: 53 Copynumber: 1.9 Consensus size: 50
1720312 TTAAATTATA
1720322 ATAAAAATATAAAAACTATAAAAAATATTAAAATTTTATTAAAAATAAGTT
1 ATAAAAATATAAAAACTATAAAAAATATTAAAATTTTA-TAAAAATAAGTT
*
1720373 ATAAAAATAATAAAAAATTATAAAAAAT-TGTAAAATTTTATAAAAAT
1 ATAAAAAT-AT-AAAAACTATAAAAAATAT-TAAAATTTTATAAAAAT
1720420 CATAATATAC
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
51 8 0.19
52 10 0.23
53 25 0.58
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (50 bp):
ATAAAAATATAAAAACTATAAAAAATATTAAAATTTTATAAAAATAAGTT
Found at i:1720639 original size:28 final size:27
Alignment explanation
Indices: 1720607--1720661 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1720597 CTTTAGTACG
1720607 ATATTTATATATC-TTTTTTATGAATTTT
1 ATATTTATATA-CATTTTTTAT-AATTTT
* *
1720635 ATATTTCTTTACATTTTTTATAATTTT
1 ATATTTATATACATTTTTTATAATTTT
1720662 CTTACGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (27 bp):
ATATTTATATACATTTTTTATAATTTT
Found at i:1720692 original size:19 final size:19
Alignment explanation
Indices: 1720670--1720730 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
1720660 TTCTTACGAC
1720670 TTTATAAAATTTTATGATT
1 TTTATAAAATTTTATGATT
* *
1720689 TTTATAAAACTTTATAATT
1 TTTATAAAATTTTATGATT
*
1720708 TTTATAAATTTTTTATGATT
1 TTTATAAA-ATTTTATGATT
1720728 TTT
1 TTT
1720731 GTAATTTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 25 0.69
20 11 0.31
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTATAAAATTTTATGATT
Found at i:1720693 original size:9 final size:9
Alignment explanation
Indices: 1720679--1720816 Score: 64
Period size: 9 Copynumber: 14.4 Consensus size: 9
1720669 CTTTATAAAA
*
1720679 TTTTATGAT
1 TTTTATAAT
*
1720688 TTTTATAAAA
1 TTTTAT-AAT
*
1720698 CTTTATAAT
1 TTTTATAAT
1720707 TTTTATAAATT
1 TTTTAT-AA-T
*
1720718 TTTTATGAT
1 TTTTATAAT
*
1720727 TTTTGTAAT
1 TTTTATAAT
1720736 TTTGTACTAAT
1 TTT-TA-TAAT
* *
1720747 TTTAAATAAA
1 TTT-TATAAT
* *
1720757 ATTTAAATAT
1 TTTTATA-AT
1720767 TTTTAT-AT
1 TTTTATAAT
*
1720775 TTTTATTAAA
1 TTTTA-TAAT
*
1720785 ATTTA-ATAT
1 TTTTATA-AT
*
1720794 TTTTATAAA
1 TTTTATAAT
1720803 TTTTATTAAT
1 TTTTA-TAAT
1720813 TTTT
1 TTTT
1720817 TATTACCATT
Statistics
Matches: 94, Mismatches: 24, Indels: 21
0.68 0.17 0.15
Matches are distributed among these distances:
8 8 0.09
9 38 0.40
10 33 0.35
11 15 0.16
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1720718 original size:29 final size:28
Alignment explanation
Indices: 1720686--1720806 Score: 88
Period size: 29 Copynumber: 4.2 Consensus size: 28
1720676 AAATTTTATG
1720686 ATTTTTATAAAACTTTATAATTTTTATAA
1 ATTTTTATAAAA-TTTATAATTTTTATAA
* ** *
1720715 ATTTTTTATGATTTTTGTAATTTTGTACT-A
1 A-TTTTTATAAAATTTATAATTTT-TA-TAA
* *
1720745 ATTTTAAATAAAATTTA-AATATTTT-TAT
1 ATTTT-TATAAAATTTATAAT-TTTTATAA
1720773 ATTTTTATTAAAATTTA-ATATTTTTATAA
1 ATTTTTA-TAAAATTTATA-ATTTTTATAA
1720802 ATTTT
1 ATTTT
1720807 ATTAATTTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
27 2 0.03
28 19 0.27
29 28 0.39
30 21 0.30
31 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (28 bp):
ATTTTTATAAAATTTATAATTTTTATAA
Found at i:1720736 original size:19 final size:19
Alignment explanation
Indices: 1720620--1720738 Score: 82
Period size: 19 Copynumber: 6.2 Consensus size: 19
1720610 TTTATATATC
*
1720620 TTTTTTATGAATTTTAT-A
1 TTTTTTATGATTTTTATAA
*
1720638 TTTCTTTA-CATTTTTTATAA
1 TTT-TTTATGA-TTTTTATAA
* *
1720658 TTTTCTTACGA-CTTTATAA
1 TTTT-TTATGATTTTTATAA
**
1720677 AATTTTATGATTTTTATAA
1 TTTTTTATGATTTTTATAA
*** *
1720696 AACTTTATAATTTTTATAAA
1 TTTTTTATGATTTTTAT-AA
*
1720716 TTTTTTATGATTTTTGTAA
1 TTTTTTATGATTTTTATAA
1720735 TTTT
1 TTTT
1720739 GTACTAATTT
Statistics
Matches: 79, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
18 9 0.11
19 48 0.61
20 21 0.27
21 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTTATGATTTTTATAA
Found at i:1720748 original size:20 final size:20
Alignment explanation
Indices: 1720670--1720749 Score: 67
Period size: 19 Copynumber: 4.1 Consensus size: 20
1720660 TTCTTACGAC
* *
1720670 TTTATAAAATTT-TATGATT
1 TTTATAAATTTTGTATAATT
**
1720689 TTTATAAAACTT-TATAATT
1 TTTATAAATTTTGTATAATT
* *
1720708 TTTATAAATTTTTTATGATT
1 TTTATAAATTTTGTATAATT
*
1720728 TTTGT-AATTTTGTACTAATT
1 TTTATAAATTTTGTA-TAATT
1720748 TT
1 TT
1720750 AAATAAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 35 0.69
20 16 0.31
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTATAAATTTTGTATAATT
Found at i:1720805 original size:17 final size:19
Alignment explanation
Indices: 1720771--1720821 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1720761 AAATATTTTT
1720771 ATATTTTTATTAAAATTTA
1 ATATTTTTATTAAAATTTA
*
1720790 ATATTTTTA-TAAATTTTA
1 ATATTTTTATTAAAATTTA
*
1720808 TTAATTTTTTATTA
1 AT-A-TTTTTATTA
1720822 CCATTTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.33
19 10 0.37
20 6 0.22
21 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATTTTTATTAAAATTTA
Found at i:1720809 original size:28 final size:28
Alignment explanation
Indices: 1720734--1720811 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 28
1720724 GATTTTTGTA
*
1720734 ATTTTGTACTAATTTTAAATAAAATTTAAAT
1 ATTTT-TA-TAATTTT-ATTAAAATTTAAAT
*
1720765 ATTTTTATATTTTTATTAAAATTT-AAT
1 ATTTTTATAATTTTATTAAAATTTAAAT
1720792 ATTTTTATAAATTTTATTAA
1 ATTTTTAT-AATTTTATTAA
1720812 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 11 0.26
28 19 0.44
29 6 0.14
30 2 0.05
31 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
ATTTTTATAATTTTATTAAAATTTAAAT
Found at i:1727092 original size:66 final size:67
Alignment explanation
Indices: 1726963--1727092 Score: 174
Period size: 66 Copynumber: 1.9 Consensus size: 67
1726953 GGGATGTATC
*
1726963 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
1727028 AGGACA
62 AGGACA
* *
1727034 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
1727093 TTCACCATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.16
68 1 0.02
71 21 0.38
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:1728775 original size:30 final size:30
Alignment explanation
Indices: 1728739--1728821 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 30
1728729 AATGAGCTTA
*
1728739 AAAAAACCTTCTAATTAGTTCAATTGAGTT
1 AAAAAACCTTCTAATTAGTTAAATTGAGTT
* *
1728769 AAAAAACCTTCTAATGATTTGTTAAATTTAGTT
1 AAAAAACCTTCT-A--ATTAGTTAAATTGAGTT
1728802 AAAAAACCTTCTAATTAGTT
1 AAAAAACCTTCTAATTAGTT
1728822 TAAAATGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 18 0.39
31 1 0.02
32 1 0.02
33 26 0.57
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (30 bp):
AAAAAACCTTCTAATTAGTTAAATTGAGTT
Found at i:1733187 original size:18 final size:17
Alignment explanation
Indices: 1733112--1733187 Score: 64
Period size: 17 Copynumber: 4.3 Consensus size: 17
1733102 AATATAGTTC
* *
1733112 AAAATATAAAAGTAAAA
1 AAAATCTAAAAATAAAA
*
1733129 AAAGTCTAAAAA-AACAA
1 AAAATCTAAAAATAA-AA
*
1733146 AAAAACATAAAAATAGAAA
1 AAAATC-TAAAAATA-AAA
*
1733165 TAAATCTAAAAATAAAA
1 AAAATCTAAAAATAAAA
1733182 TAAAAT
1 -AAAAT
1733188 AAAATAAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
16 2 0.04
17 18 0.39
18 18 0.39
19 7 0.15
20 1 0.02
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAATCTAAAAATAAAA
Found at i:1742562 original size:28 final size:26
Alignment explanation
Indices: 1742487--1742559 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 26
1742477 TGAATCGTTG
1742487 TTATTTCATAAAATCACAATTTTATA
1 TTATTTCATAAAATCACAATTTTATA
* * *
1742513 TTATTTCATATTATTCACAATTTTGTTA
1 TTATTTCATA-AAATCACAATTTT-ATA
1742541 TTATTTCATAAAATCACAA
1 TTATTTCATAAAATCACAA
1742560 ATTAATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 10 0.25
27 18 0.45
28 12 0.30
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.48
Consensus pattern (26 bp):
TTATTTCATAAAATCACAATTTTATA
Found at i:1746106 original size:32 final size:32
Alignment explanation
Indices: 1746069--1746145 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
1746059 CACACACTCT
* *
1746069 TGTGGCCCACATGACATACTTGGCCCAGTCTG
1 TGTGGCCCACATGACATACCTGGCCCAGTCCG
* * *
1746101 TGTGGCCCACACGACTTACCTGGCCTAGTCCG
1 TGTGGCCCACATGACATACCTGGCCCAGTCCG
*
1746133 TGTGGCTCACATG
1 TGTGGCCCACATG
1746146 GCCTAGCATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.17, C:0.32, G:0.26, T:0.25
Consensus pattern (32 bp):
TGTGGCCCACATGACATACCTGGCCCAGTCCG
Found at i:1749122 original size:33 final size:33
Alignment explanation
Indices: 1749085--1749147 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
1749075 ATTAAATAAT
1749085 TTAATTTTGATTACATAGATCAAGAAAAGCGAA
1 TTAATTTTGATTACATAGATCAAGAAAAGCGAA
1749118 TTAATTTTGATTACATAGATCAAGAAAAGC
1 TTAATTTTGATTACATAGATCAAGAAAAGC
1749148 AAAATTCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (33 bp):
TTAATTTTGATTACATAGATCAAGAAAAGCGAA
Found at i:1754313 original size:46 final size:46
Alignment explanation
Indices: 1754263--1754483 Score: 354
Period size: 46 Copynumber: 4.8 Consensus size: 46
1754253 TGGTTGAGCA
*
1754263 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
1754309 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1754355 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
1754401 CCCGAGA-TCATTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACG
1 TCCGA-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
1754447 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1754484 GCGGGTTACA
Statistics
Matches: 167, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
46 166 0.99
47 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:1766530 original size:42 final size:43
Alignment explanation
Indices: 1766418--1766574 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 43
1766408 TGTGTTTTCG
* * * *
1766418 TGTAAGACCACGT-TAGGGACGTTTGTATCGACT-TATGATTTACG
1 TGTAAGACCACGTCTA-GGACGTTGGCATCGA-TATTTGA-TTACA
** * * *
1766462 TGTAAGACCGTGTTTGGGACGTTGGCATC-ATATTTGATTTCA
1 TGTAAGACCACGTCTAGGACGTTGGCATCGATATTTGATTACA
*
1766504 TGTAAGACCCCGTCTAGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCACGTCTAGGAC-GTTGGCATCGATATTTGATTACA
*
1766547 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTAGGACGTTGGCAT
1766575 TGTACGAGCT
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 28 0.30
43 42 0.45
44 22 0.24
45 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTAGGACGTTGGCATCGATATTTGATTACA
Found at i:1770579 original size:16 final size:16
Alignment explanation
Indices: 1770558--1770589 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1770548 TAATTGGTTG
*
1770558 ATTTTTAGTTTAATTA
1 ATTTTTAGGTTAATTA
1770574 ATTTTTAGGTTAATTA
1 ATTTTTAGGTTAATTA
1770590 GATTAATTGA
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:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATTTTTAGGTTAATTA
Found at i:1772977 original size:57 final size:57
Alignment explanation
Indices: 1772876--1773007 Score: 174
Period size: 57 Copynumber: 2.3 Consensus size: 57
1772866 GGAGCAATTG
* * * * **
1772876 CACATGCTGCTGCTGATAGAGCAGCTGCTGTCCGTTCTGCTTTTCATAAAGCAGCTT
1 CACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGCTT
* *
1772933 CACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGGTTTTCGTAAAGCAGCTT
1 CACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGCTT
* *
1772990 CACAAGTTGCTTCTGATG
1 CACAAGCTGCTGCTGATG
1773008 TAGCTGCTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (57 bp):
CACAAGCTGCTGCTGATGGAACAGCTGCTGCCCAATCTGCTTTTCATAAAGCAGCTT
Found at i:1773076 original size:24 final size:24
Alignment explanation
Indices: 1773046--1773126 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
1773036 AGGTGGCATT
1773046 GGTGGAGGTAGTTTAAGAGGTGGA
1 GGTGGAGGTAGTTTAAGAGGTGGA
* * *
1773070 GGAGGAGGCAGTTTAATAGGTGGA
1 GGTGGAGGTAGTTTAAGAGGTGGA
* *
1773094 GGTGGAAGTAGTTTTAGAGGTGGA
1 GGTGGAGGTAGTTTAAGAGGTGGA
1773118 GGTGGAGGT
1 GGTGGAGGT
1773127 GGAAGCAGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.01, G:0.49, T:0.25
Consensus pattern (24 bp):
GGTGGAGGTAGTTTAAGAGGTGGA
Found at i:1773121 original size:30 final size:30
Alignment explanation
Indices: 1773087--1773144 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1773077 GCAGTTTAAT
*
1773087 AGGTGGAGGTGGAAGTAGTTTTAGAGGTGG
1 AGGTGGAGGTGGAAGCAGTTTTAGAGGTGG
*
1773117 AGGTGGAGGTGGAAGCAGTTTTGGAGGT
1 AGGTGGAGGTGGAAGCAGTTTTAGAGGT
1773145 AGTGCTACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.02, G:0.50, T:0.26
Consensus pattern (30 bp):
AGGTGGAGGTGGAAGCAGTTTTAGAGGTGG
Found at i:1773189 original size:66 final size:66
Alignment explanation
Indices: 1773118--1773282 Score: 267
Period size: 66 Copynumber: 2.5 Consensus size: 66
1773108 TAGAGGTGGA
* *
1773118 GGTGGAGGTGGAAGCAGTTTTGGAGGTAGTGCTACCGGTTCCGTTGGTGGACGTGGTGCTACCGT
1 GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCTACCGGTTCCCTTGGTGGACGTGGTGCTACCGT
1773183 T
66 T
* *
1773184 GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCTACCGGTTCCCTTGGTGGACGTGGTGCTGCTGT
1 GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCTACCGGTTCCCTTGGTGGACGTGGTGCTACCGT
1773249 T
66 T
* * *
1773250 GGTGGAGGTGGAGGTAGTGTTGGAGGTAGTGCT
1 GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCT
1773283 GGCGGTAGTT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 92 1.00
ACGTcount: A:0.14, C:0.13, G:0.45, T:0.28
Consensus pattern (66 bp):
GGTGGAGGTGGAAGCAGTATTGGAGGTAGTGCTACCGGTTCCCTTGGTGGACGTGGTGCTACCGT
T
Found at i:1773275 original size:12 final size:12
Alignment explanation
Indices: 1773258--1773291 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1773248 TTGGTGGAGG
*
1773258 TGGAGGTAGTGT
1 TGGAGGTAGTGC
1773270 TGGAGGTAGTGC
1 TGGAGGTAGTGC
*
1773282 TGGCGGTAGT
1 TGGAGGTAGT
1773292 TTAAAGGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.06, G:0.50, T:0.29
Consensus pattern (12 bp):
TGGAGGTAGTGC
Found at i:1773310 original size:36 final size:36
Alignment explanation
Indices: 1773270--1773345 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
1773260 GAGGTAGTGT
**
1773270 TGGAGGTAGTGCTGGCGGTAGTTTAAAGGGTGGAGG
1 TGGAGGTAGTGCTGGAAGTAGTTTAAAGGGTGGAGG
* * *
1773306 TGGAGGTAGTGTTGGAAGTGGTTTAAGGGGTGGAGG
1 TGGAGGTAGTGCTGGAAGTAGTTTAAAGGGTGGAGG
1773342 TGGA
1 TGGA
1773346 TATGGAGGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.20, C:0.03, G:0.51, T:0.26
Consensus pattern (36 bp):
TGGAGGTAGTGCTGGAAGTAGTTTAAAGGGTGGAGG
Found at i:1773313 original size:24 final size:24
Alignment explanation
Indices: 1773250--1773318 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
1773240 TGCTGCTGTT
**
1773250 GGTGGAGGTGGAGGTAGTGTTGGA
1 GGTGGAGGTGGAGGTAGTGTTAAA
* * * *
1773274 GGTAGTGCTGGCGGTAGT-TTAAA
1 GGTGGAGGTGGAGGTAGTGTTAAA
1773297 GGGTGGAGGTGGAGGTAGTGTT
1 -GGTGGAGGTGGAGGTAGTGTT
1773319 GGAAGTGGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
23 3 0.09
24 28 0.85
25 2 0.06
ACGTcount: A:0.17, C:0.03, G:0.52, T:0.28
Consensus pattern (24 bp):
GGTGGAGGTGGAGGTAGTGTTAAA
Found at i:1773326 original size:24 final size:24
Alignment explanation
Indices: 1773251--1773326 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1773241 GCTGCTGTTG
*
1773251 GTGGAGGTGGAGGTAGTGTTGGAG
1 GTGGAGGTGGAGGTAGTGTTGGAA
* * * * *
1773275 GTAGTGCTGGCGGTAGT-TT-AAA
1 GTGGAGGTGGAGGTAGTGTTGGAA
1773297 GGGTGGAGGTGGAGGTAGTGTTGGAA
1 --GTGGAGGTGGAGGTAGTGTTGGAA
1773323 GTGG
1 GTGG
1773327 TTTAAGGGGT
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
22 1 0.03
23 2 0.05
24 30 0.81
25 2 0.05
26 2 0.05
ACGTcount: A:0.18, C:0.03, G:0.53, T:0.26
Consensus pattern (24 bp):
GTGGAGGTGGAGGTAGTGTTGGAA
Found at i:1773817 original size:18 final size:18
Alignment explanation
Indices: 1773794--1773830 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1773784 ATCGTAAACT
1773794 ACTAACATGAATTGTAAA
1 ACTAACATGAATTGTAAA
1773812 ACTAACATGAATTGTAAA
1 ACTAACATGAATTGTAAA
1773830 A
1 A
1773831 TTAATACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (18 bp):
ACTAACATGAATTGTAAA
Found at i:1778018 original size:10 final size:10
Alignment explanation
Indices: 1778003--1778032 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1777993 TGTTGGCATT
1778003 TATGCTTGTG
1 TATGCTTGTG
1778013 TATGCTTGTG
1 TATGCTTGTG
*
1778023 TATGCATGTG
1 TATGCTTGTG
1778033 ACAATAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.30, T:0.47
Consensus pattern (10 bp):
TATGCTTGTG
Found at i:1780062 original size:54 final size:54
Alignment explanation
Indices: 1780003--1780184 Score: 222
Period size: 54 Copynumber: 3.4 Consensus size: 54
1779993 CACACCAAAA
* * * * * *
1780003 TAAGGAATAGCCGTTGTGGAAATCTCTGGAAAAGAATGCCTTCGTGGCACATTC
1 TAAGGAATAGCCTTTGTGGCAATCTCTAGAAAGGAACGCCTTCGTGGCACACTC
* ** *
1780057 TAAGGAACATTCTTTGTGGCAATCTCTAGAAAGGAACGTCTTCGTGGCACACTC
1 TAAGGAATAGCCTTTGTGGCAATCTCTAGAAAGGAACGCCTTCGTGGCACACTC
* * *
1780111 TGAA-GAATAGCCTTTTGTGTCAATCTCTAGAAAGGAACGCCTTCATGGCGCACTC
1 T-AAGGAATAGCC-TTTGTGGCAATCTCTAGAAAGGAACGCCTTCGTGGCACACTC
1780166 TAAGGAATAGCCTTTGTGG
1 TAAGGAATAGCCTTTGTGG
1780185 TGTAATGTGA
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
54 58 0.54
55 49 0.46
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (54 bp):
TAAGGAATAGCCTTTGTGGCAATCTCTAGAAAGGAACGCCTTCGTGGCACACTC
Found at i:1780111 original size:28 final size:26
Alignment explanation
Indices: 1780042--1780111 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 26
1780032 AAAAGAATGC
* *
1780042 CTTCGTGGCACATTCTAAGGAACATT
1 CTTCGTGGCACACTCTAAGGAACAGT
*
1780068 CTTTGTGGCA-ATCTCTAGAAAGGAAC-GT
1 CTTCGTGGCACA-CTCT---AAGGAACAGT
1780096 CTTCGTGGCACACTCT
1 CTTCGTGGCACACTCT
1780112 GAAGAATAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
25 1 0.03
26 12 0.34
28 14 0.40
29 8 0.23
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (26 bp):
CTTCGTGGCACACTCTAAGGAACAGT
Found at i:1790552 original size:31 final size:31
Alignment explanation
Indices: 1790514--1790591 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
1790504 TTTAACGGTT
1790514 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1790545 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
**
1790576 ACTGGGATGAAGCCTT
1 ACTGGGCCGAAGCCTT
1790592 CACTGTAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:1791700 original size:27 final size:27
Alignment explanation
Indices: 1791670--1791734 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1791660 GGGCATATTC
1791670 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
1791697 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
1791724 GTCTTTTTACC
1 GTCATTTTACC
1791735 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:1791818 original size:27 final size:27
Alignment explanation
Indices: 1791788--1791895 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
1791778 GTAAATCTAC
1791788 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
1791815 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
1791841 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
1791871 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
1791896 ACAAATTGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 41 0.60
28 7 0.10
29 18 0.26
30 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:1791901 original size:27 final size:26
Alignment explanation
Indices: 1791851--1792034 Score: 172
Period size: 27 Copynumber: 6.8 Consensus size: 26
1791841 AGAAAGTCAA
**
1791851 GGGTATTTCT-GTAATTTTGTAAATCAG
1 GGGTATTT-TGGTAATTTTACAAA-CAG
**
1791878 GGGTATTTTGGTAATTTTACAAATTG
1 GGGTATTTTGGTAATTTTACAAACAG
* * *
1791904 AAGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAA-CAG
* *
1791932 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAAC-AG
1791959 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAAC-AG
* **
1791986 GGGTATTTTGGTAATTCTATCCTACAG
1 GGGTATTTTGGTAATTTTA-CAAACAG
* *
1792013 GGGTATTTTAGTAATTTCACAA
1 GGGTATTTTGGTAATTTTACAA
1792035 TCGAGGGTAA
Statistics
Matches: 131, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
26 4 0.03
27 123 0.94
28 4 0.03
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTACAAACAG
Found at i:1791991 original size:81 final size:81
Alignment explanation
Indices: 1791852--1792001 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 81
1791842 GAAAGTCAAG
* ** *
1791852 GGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAAGGTATTTCGGT
1 GGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAAGGTATTTCGGT
1791917 AATTTCACAAACCAGT
66 AATTTCACAAACCAGT
* *
1791933 GGTATTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTG
1 GGTATTTCGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACAAA-TAGAAGGTATTTCG
1791996 GTAATT
64 GTAATT
1792002 CTATCCTACA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
80 1 0.02
81 58 0.95
82 2 0.03
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (81 bp):
GGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAAGGTATTTCGGT
AATTTCACAAACCAGT
Found at i:1792067 original size:27 final size:27
Alignment explanation
Indices: 1792033--1792124 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
1792023 GTAATTTCAC
1792033 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGATAATTTTGTA
* * *
1792060 AA-CTGAGGGTAAAATGGTAATTTTTTA
1 AATC-GAGGGTAAAACGATAATTTTGTA
* * *
1792087 AATCGAAGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGATAATTTTGTA
*
1792114 AATCGAAGGTA
1 AATCGAGGGTA
1792125 CTTTGGTAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 53 0.96
28 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACGATAATTTTGTA
Found at i:1797518 original size:16 final size:17
Alignment explanation
Indices: 1797497--1797528 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1797487 GTGCCATTGA
1797497 TGAATGCTTGA-GATGT
1 TGAATGCTTGATGATGT
1797513 TGAATGCTTGATGATG
1 TGAATGCTTGATGATG
1797529 GAAAATGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (17 bp):
TGAATGCTTGATGATGT
Found at i:1814632 original size:307 final size:307
Alignment explanation
Indices: 1814078--1814692 Score: 1221
Period size: 307 Copynumber: 2.0 Consensus size: 307
1814068 GGTGGAGATG
1814078 TGATTTTCATGCAAGCCTATGGTAATAACTTTTCATATTGACTGATGAGTGCTACTTATATTGTC
1 TGATTTTCATGCAAGCCTATGGTAATAACTTTTCATATTGACTGATGAGTGCTACTTATATTGTC
1814143 CTTAAACACTTTGAGTGATTTGAGTGAATCTTTAGTAAGGATGTTAAACTCTGTGAGATTTTGAA
66 CTTAAACACTTTGAGTGATTTGAGTGAATCTTTAGTAAGGATGTTAAACTCTGTGAGATTTTGAA
*
1814208 TCGAGGTAACCACTTAGATAAGGGGAGATGCCTAAAGTTTTGCATGATTAAATACTCAACTTGGA
131 TCAAGGTAACCACTTAGATAAGGGGAGATGCCTAAAGTTTTGCATGATTAAATACTCAACTTGGA
1814273 ATGTTTGAAACTTTGATGTTCTTTCAGTTGAATTTTCAATGTATGATTACCTATGGATTATTTTG
196 ATGTTTGAAACTTTGATGTTCTTTCAGTTGAATTTTCAATGTATGATTACCTATGGATTATTTTG
1814338 AGATATTATCAATAGAAATTATAAGTTGAGAAGAATTTATTTTGAAT
261 AGATATTATCAATAGAAATTATAAGTTGAGAAGAATTTATTTTGAAT
1814385 TGATTTTCATGCAAGCCTATGGTAATAACTTTTCATATTGACTGATGAGTGCTACTTATATTGTC
1 TGATTTTCATGCAAGCCTATGGTAATAACTTTTCATATTGACTGATGAGTGCTACTTATATTGTC
1814450 CTTAAACACTTTGAGTGATTTGAGTGAATCTTTAGTAAGGATGTTAAACTCTGTGAGATTTTGAA
66 CTTAAACACTTTGAGTGATTTGAGTGAATCTTTAGTAAGGATGTTAAACTCTGTGAGATTTTGAA
1814515 TCAAGGTAACCACTTAGATAAGGGGAGATGCCTAAAGTTTTGCATGATTAAATACTCAACTTGGA
131 TCAAGGTAACCACTTAGATAAGGGGAGATGCCTAAAGTTTTGCATGATTAAATACTCAACTTGGA
1814580 ATGTTTGAAACTTTGATGTTCTTTCAGTTGAATTTTCAATGTATGATTACCTATGGATTATTTTG
196 ATGTTTGAAACTTTGATGTTCTTTCAGTTGAATTTTCAATGTATGATTACCTATGGATTATTTTG
1814645 AGATATTATCAATAGAAATTATAAGTTGAGAAGAATTTATTTTGAAT
261 AGATATTATCAATAGAAATTATAAGTTGAGAAGAATTTATTTTGAAT
1814692 T
1 T
1814693 TGAGTTGAGA
Statistics
Matches: 307, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
307 307 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (307 bp):
TGATTTTCATGCAAGCCTATGGTAATAACTTTTCATATTGACTGATGAGTGCTACTTATATTGTC
CTTAAACACTTTGAGTGATTTGAGTGAATCTTTAGTAAGGATGTTAAACTCTGTGAGATTTTGAA
TCAAGGTAACCACTTAGATAAGGGGAGATGCCTAAAGTTTTGCATGATTAAATACTCAACTTGGA
ATGTTTGAAACTTTGATGTTCTTTCAGTTGAATTTTCAATGTATGATTACCTATGGATTATTTTG
AGATATTATCAATAGAAATTATAAGTTGAGAAGAATTTATTTTGAAT
Found at i:1829876 original size:21 final size:21
Alignment explanation
Indices: 1829851--1829891 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1829841 CAAGATTCTG
1829851 TTTTTAGGTATTAGTGGTCTA
1 TTTTTAGGTATTAGTGGTCTA
*
1829872 TTTTTAGGTATTGGTGGTCT
1 TTTTTAGGTATTAGTGGTCT
1829892 CCGAAGCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.27, T:0.54
Consensus pattern (21 bp):
TTTTTAGGTATTAGTGGTCTA
Found at i:1832731 original size:39 final size:40
Alignment explanation
Indices: 1832636--1832897 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
1832626 TTGAATGATG
*
1832636 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
1832674 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
1832715 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
1832754 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1832793 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
1832832 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
1832871 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
1832898 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:1840747 original size:39 final size:40
Alignment explanation
Indices: 1840652--1840874 Score: 273
Period size: 39 Copynumber: 5.7 Consensus size: 40
1840642 TTGAATGATG
*
1840652 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
1840690 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
1840731 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1840770 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1840809 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1840848 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
1840875 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
39 93 0.56
40 61 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:1840838 original size:79 final size:81
Alignment explanation
Indices: 1840652--1840874 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
1840642 TTGAATGATG
* * *
1840652 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATATCCGGGCTAAGACCCGAAGGCA
*
1840713 TTTGTGCGAGATACTAAT
64 TTTGTGCGAGATACTAAA
1840731 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
*
1840793 TGTGCGAGTTACTAAA
66 TGTGCGAGATACTAAA
* * * * *
1840809 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
1840873 TG
66 TG
1840875 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:1840896 original size:79 final size:79
Alignment explanation
Indices: 1840652--1840907 Score: 224
Period size: 79 Copynumber: 3.3 Consensus size: 79
1840642 TTGAATGATG
* * * *
1840652 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
1840713 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
1840731 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
1840795 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
1840809 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
*
1840873 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
1840889 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
1840908 TACGTGATTT
Statistics
Matches: 153, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
77 1 0.01
78 45 0.29
79 70 0.46
80 36 0.24
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Done.