Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009072.1 Hibiscus syriacus cultivar Beakdansim tig00112503_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2600608
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1646970 original size:31 final size:31
Alignment explanation
Indices: 1646932--1646999 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1646922 GTAACTTTTA
1646932 ATAGTCGAGGGACTCAACAAAGTAATATCTT
1 ATAGTCGAGGGACTCAACAAAGTAATATCTT
*
1646963 ATAGTCGAGGGACTCAATAAAGTAATATCTT
1 ATAGTCGAGGGACTCAACAAAGTAATATCTT
1646994 ATAGTC
1 ATAGTC
1647000 AATGATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (31 bp):
ATAGTCGAGGGACTCAACAAAGTAATATCTT
Found at i:1651478 original size:21 final size:21
Alignment explanation
Indices: 1651454--1651494 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1651444 TGATTACGGC
*
1651454 CGTCGCGGGCGCTATTGCGGT
1 CGTCGCGGACGCTATTGCGGT
1651475 CGTCGCGGACGCTATTGCGG
1 CGTCGCGGACGCTATTGCGG
1651495 CCGTTGTGGG
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:0.07, C:0.29, G:0.41, T:0.22
Consensus pattern (21 bp):
CGTCGCGGACGCTATTGCGGT
Found at i:1652246 original size:24 final size:24
Alignment explanation
Indices: 1652219--1652265 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1652209 GAAATAAGAC
*
1652219 AAAAATGTATCACAAAAATATAAA
1 AAAAACGTATCACAAAAATATAAA
* * *
1652243 AAAAACGTGTTACAAAGATATAA
1 AAAAACGTATCACAAAAATATAA
1652266 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (24 bp):
AAAAACGTATCACAAAAATATAAA
Found at i:1652924 original size:21 final size:20
Alignment explanation
Indices: 1652901--1653040 Score: 115
Period size: 21 Copynumber: 6.7 Consensus size: 20
1652891 CATATTTGCA
1652901 TTGCGATAGTCCAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
*
1652921 ATTGCGATTTATTCCAAGTTCG-
1 -TTGCGA--TAGTCCAAGTTCGC
*
1652943 TTGCGATAGTCGAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
* *
1652963 GTTGCGATTTATTCCAAATTCG-
1 -TTGCGA--TAGTCCAAGTTCGC
*
1652985 TTGCGATAGTCGAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
* *
1653005 GTTGCGATCTATTCCAAATTCG-
1 -TTGCGA--TAGTCCAAGTTCGC
1653027 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1653041 AATCGCAACG
Statistics
Matches: 96, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
19 28 0.29
21 36 0.38
23 32 0.33
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCGC
Found at i:1652959 original size:42 final size:42
Alignment explanation
Indices: 1652901--1653037 Score: 238
Period size: 42 Copynumber: 3.3 Consensus size: 42
1652891 CATATTTGCA
* * *
1652901 TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1652943 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1652985 TTGCGATAGTCGAAGTTCGCGTTGCGATCTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1653027 TTGCGATAGTC
1 TTGCGATAGTC
1653038 CAAAATCGCA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1653150 original size:5 final size:5
Alignment explanation
Indices: 1653128--1653189 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
1653118 CACGTATTAC
* * *
1653128 CACGA CCACGA CCACGA CACGA CACGA CACGA CACGA CCCGA GACGA GACGA
1 CACGA -CACGA -CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA
* *
1653180 GACGA GACGA
1 CACGA CACGA
1653190 GACGGACGGC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 42 0.79
6 11 0.21
ACGTcount: A:0.37, C:0.37, G:0.26, T:0.00
Consensus pattern (5 bp):
CACGA
Found at i:1653190 original size:5 final size:5
Alignment explanation
Indices: 1653167--1653197 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1653157 CGACACGACC
1653167 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1653198 GCGGCGCGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:1653853 original size:21 final size:20
Alignment explanation
Indices: 1653827--1654004 Score: 175
Period size: 21 Copynumber: 8.6 Consensus size: 20
1653817 GATTTACATA
1653827 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTC-AAG
*
1653848 TTCGCATTGCGATAGTCAAC
1 TTCGCATTGCGATAGTCAAG
* *
1653868 TACCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGT-CA-AG
1653889 TTCGCATTGCGATAGTCTAAG
1 TTCGCATTGCGATAGTC-AAG
* *
1653910 TTCGCATTGCGATAGTCCAC
1 TTCGCATTGCGATAGTCAAG
*
1653930 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGT-CA-AG
1653951 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAG
1653972 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTC-AAG
*
1653993 TTCGCGTTGCGA
1 TTCGCATTGCGA
1654005 ATCTGGAAAC
Statistics
Matches: 133, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
20 34 0.26
21 97 0.73
22 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAG
Found at i:1653854 original size:41 final size:40
Alignment explanation
Indices: 1653808--1653985 Score: 161
Period size: 41 Copynumber: 4.3 Consensus size: 40
1653798 ACTTGGACTA
1653808 TCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATATTACA-ATTCGCATTGCGATAGTC-AAGT
* * *
1653849 TCGCATTGCGATAGT-CAACTACCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATATTACAA-T-TCGCATTGCGATAGT-CA-AGT
* * *
1653890 TCGCATTGCGATAGTCTA-AGTTCGCATTGCGATAGTCCACT
1 TCGCATTGCGATA-T-TACAATTCGCATTGCGATAGTCAAGT
1653931 ATCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCCAAGT
1 -TCGCATTGCGATATTACA-ATTCGCATTGCGATAGT-CAAGT
1653973 TCGCATTGCGATA
1 TCGCATTGCGATA
1653986 GTCGAAGTTC
Statistics
Matches: 111, Mismatches: 11, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
39 2 0.02
40 4 0.04
41 72 0.65
42 31 0.28
43 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
TCGCATTGCGATATTACAATTCGCATTGCGATAGTCAAGT
Found at i:1653921 original size:83 final size:83
Alignment explanation
Indices: 1653827--1654004 Score: 204
Period size: 83 Copynumber: 2.1 Consensus size: 83
1653817 GATTTACATA
* *
1653827 TTCGCATTGCGATAGTCGAAGT-TCGCATTGCGATAGTCAAC-TA-CCGCATTGCGAT-TTACAT
1 TTCGCATTGCGATAGTC-AACTATCGCATTGCGAT--T-AACATATCCGCATTGCGATAGTACA-
*
1653888 A-TTCGCATTGCGATAGTCTAAG
61 AGTTCGCATTGCGATAGTCGAAG
* * * *
1653910 TTCGCATTGCGATAGTCCACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTC
1 TTCGCATTGCGATAGTCAACTATCGCATTGCGATTAACATATCCGCATTGCGATAGTACAAGTTC
1653975 GCATTGCGATAGTCGAAG
66 GCATTGCGATAGTCGAAG
*
1653993 TTCGCGTTGCGA
1 TTCGCATTGCGA
1654005 ATCTGGAAAC
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
80 2 0.02
81 3 0.04
82 14 0.17
83 63 0.77
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (83 bp):
TTCGCATTGCGATAGTCAACTATCGCATTGCGATTAACATATCCGCATTGCGATAGTACAAGTTC
GCATTGCGATAGTCGAAG
Found at i:1654004 original size:62 final size:62
Alignment explanation
Indices: 1653804--1653988 Score: 334
Period size: 62 Copynumber: 3.0 Consensus size: 62
1653794 ACGAACTTGG
*
1653804 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCA
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCA
* * *
1653866 ACTACCGCATTGCGATTTACATATTCGCATTGCGATAGTCTAAGTTCGCATTGCGATAGTCC
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCA
1653928 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1653989 GAAGTTCGCG
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 118 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (62 bp):
ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCA
Found at i:1654844 original size:21 final size:19
Alignment explanation
Indices: 1654789--1654844 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
1654779 TGCGATCGAT
*
1654789 AATTCGCAACGCGATTTTA
1 AATTCGCAATGCGATTTTA
*
1654808 ACTATT-GCATTGCGATTTTCCA
1 A--ATTCGCAATGCGATTTT--A
1654830 AATTCGCAATGCGAT
1 AATTCGCAATGCGAT
1654845 AGTCCAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 12 0.41
22 2 0.07
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (19 bp):
AATTCGCAATGCGATTTTA
Found at i:1654850 original size:21 final size:21
Alignment explanation
Indices: 1654826--1654867 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1654816 ATTGCGATTT
* *
1654826 TCCAAATTCGCAATGCGATAG
1 TCCAAAATCCCAATGCGATAG
*
1654847 TCCAAAATCCCATTGCGATAG
1 TCCAAAATCCCAATGCGATAG
1654868 CACTGTTCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
TCCAAAATCCCAATGCGATAG
Found at i:1654883 original size:21 final size:21
Alignment explanation
Indices: 1654859--1654951 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
1654849 CAAAATCCCA
1654859 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
1654880 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
1654901 TTGCGATAGTACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
* *
1654922 TTGCGGTAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
1654943 TTGCGATAG
1 TTGCGATAG
1654952 TGATCAAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:1655656 original size:21 final size:21
Alignment explanation
Indices: 1655630--1655690 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
1655620 AATTCGCAAT
1655630 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
1655651 GTGAACAGTGCTATCGTAACG
1 GTGAACAGTGCTATCGCAACG
1655672 GTGAACAGTGCTATCGCAA
1 GTGAACAGTGCTATCGCAA
1655691 TGCGATTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:1655758 original size:21 final size:21
Alignment explanation
Indices: 1655714--1655758 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1655704 TATCGCATTA
*
1655714 CGAATTCGAAAAATCGCAACG
1 CGAATTCGAAAAATCACAACG
* *
1655735 CGAATTTGAAAAATCACAATG
1 CGAATTCGAAAAATCACAACG
1655756 CGA
1 CGA
1655759 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (21 bp):
CGAATTCGAAAAATCACAACG
Found at i:1659313 original size:16 final size:16
Alignment explanation
Indices: 1659294--1659327 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1659284 ATGCAAGTAT
*
1659294 GTCAATCCCATATAAA
1 GTCAATCCAATATAAA
1659310 GTCAATCCAATATAAA
1 GTCAATCCAATATAAA
1659326 GT
1 GT
1659328 AAATGTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (16 bp):
GTCAATCCAATATAAA
Found at i:1661990 original size:20 final size:22
Alignment explanation
Indices: 1661957--1661996 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
1661947 TCATAAATGT
*
1661957 TAAAAAATATTAATGTTTTAGG
1 TAAAAAATATTAATATTTTAGG
1661979 TAAAAAA-A-TAATATTTTA
1 TAAAAAATATTAATATTTTA
1661997 ACTAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (22 bp):
TAAAAAATATTAATATTTTAGG
Found at i:1663671 original size:3 final size:3
Alignment explanation
Indices: 1663663--1663689 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1663653 CGACATTTAC
1663663 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1663690 TTGGGTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1664809 original size:95 final size:93
Alignment explanation
Indices: 1664642--1664827 Score: 345
Period size: 94 Copynumber: 2.0 Consensus size: 93
1664632 ACAACAAATA
*
1664642 AAAAAATTGGAAAATTTTGGGGTCATTGAAACAAATCACTTCATGAAAATGATACCTTCAGACTT
1 AAAAAATTGGAAAATTTTGGGGTCATTGAAACAAATCACTTCATGAAAATGATACCTTCAGACCT
1664707 TTTCTCTATTTTGTTATATTTTCTCCAAT
66 TTTCTCTATTTTGTTATATTTT-TCCAAT
1664736 AAAAAATTGGAAAATTTTGGGGTCATTGAAACAAATCACTTCATGAAAAATGATACCTTCAGACC
1 AAAAAATTGGAAAATTTTGGGGTCATTGAAACAAATCACTTCATG-AAAATGATACCTTCAGACC
1664801 TTTTCTCTATTTTGTTATATTTTTCCA
65 TTTTCTCTATTTTGTTATATTTTTCCA
1664828 CCCTATTTGA
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
94 49 0.54
95 41 0.46
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (93 bp):
AAAAAATTGGAAAATTTTGGGGTCATTGAAACAAATCACTTCATGAAAATGATACCTTCAGACCT
TTTCTCTATTTTGTTATATTTTTCCAAT
Found at i:1667617 original size:31 final size:31
Alignment explanation
Indices: 1667570--1667640 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1667560 AGATAAGGTT
* * * *
1667570 ATTTATTATAAATCGATAATATTAGTGATTA
1 ATTTGTTACAAATCGATAACATTAGTGATCA
1667601 ATTTGTTACAAATCGATAACATTAGTGATCA
1 ATTTGTTACAAATCGATAACATTAGTGATCA
*
1667632 TTTTGTTAC
1 ATTTGTTAC
1667641 TTTTTAAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTTGTTACAAATCGATAACATTAGTGATCA
Found at i:1668832 original size:21 final size:21
Alignment explanation
Indices: 1668806--1668914 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
1668796 TAGCAAGGAT
*
1668806 CATATATGTCCCCAAGGACCA
1 CATATATGTCCCAAAGGACCA
*
1668827 CATATATGTTCCAAAGGACCA
1 CATATATGTCCCAAAGGACCA
* * * * *
1668848 AATATACGTCTCGAAGGACCT
1 CATATATGTCCCAAAGGACCA
* * * *
1668869 TATATATGTTCCAAAGAATCA
1 CATATATGTCCCAAAGGACCA
* * *
1668890 TATATATGTCCCGAAGGGCCA
1 CATATATGTCCCAAAGGACCA
1668911 CATA
1 CATA
1668915 GAACCTTCGA
Statistics
Matches: 66, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.25
Consensus pattern (21 bp):
CATATATGTCCCAAAGGACCA
Found at i:1668865 original size:42 final size:42
Alignment explanation
Indices: 1668807--1668914 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
1668797 AGCAAGGATC
* * *
1668807 ATATATGTCCCCAAGGACCACATATATGTTCCAAAGGACCAA
1 ATATACGTCCCGAAGGACCACATATATGTTCCAAAGAACCAA
* ** * *
1668849 ATATACGTCTCGAAGGACCTTATATATGTTCCAAAGAATCAT
1 ATATACGTCCCGAAGGACCACATATATGTTCCAAAGAACCAA
* *
1668891 ATATATGTCCCGAAGGGCCACATA
1 ATATACGTCCCGAAGGACCACATA
1668915 GAACCTTCGA
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (42 bp):
ATATACGTCCCGAAGGACCACATATATGTTCCAAAGAACCAA
Found at i:1674063 original size:17 final size:17
Alignment explanation
Indices: 1674021--1674084 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
1674011 AAACAACTAG
*
1674021 ATGCATAAATGAAATAC
1 ATGCTTAAATGAAATAC
* * *
1674038 TTCCCTAAATGAAATAC
1 ATGCTTAAATGAAATAC
* *
1674055 ATGCTTAAATGCAATCC
1 ATGCTTAAATGAAATAC
*
1674072 ATGCTTTAATGAA
1 ATGCTTAAATGAA
1674085 CAACATACTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (17 bp):
ATGCTTAAATGAAATAC
Found at i:1679641 original size:34 final size:34
Alignment explanation
Indices: 1679596--1679715 Score: 213
Period size: 34 Copynumber: 3.5 Consensus size: 34
1679586 CCCGAACCTG
*
1679596 AAAATACTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
*
1679630 AAAATATTATATATATAATTAATACAAACAAATAT
1 AAAATATTATATATATAATTAATATAAA-AAATAT
1679665 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
1679699 AAAATATTATATATATA
1 AAAATATTATATATATA
1679716 TAATCAGGGC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
34 49 0.60
35 33 0.40
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:1683863 original size:18 final size:18
Alignment explanation
Indices: 1683820--1683882 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
1683810 AAGTAGACAG
* *
1683820 TGAAGAAGAGGATGCCGA
1 TGAAGATGAGGATGACGA
*
1683838 TGAAGATGAGGATGACGG
1 TGAAGATGAGGATGACGA
* * *
1683856 TGACGATGAGGACGAGGA
1 TGAAGATGAGGATGACGA
*
1683874 CGAAGATGA
1 TGAAGATGA
1683883 TGAGGATGGG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.37, C:0.10, G:0.41, T:0.13
Consensus pattern (18 bp):
TGAAGATGAGGATGACGA
Found at i:1685048 original size:85 final size:83
Alignment explanation
Indices: 1684887--1685054 Score: 239
Period size: 85 Copynumber: 2.0 Consensus size: 83
1684877 TAAAACATGA
* * * * *
1684887 AAAAAGTAAAAAAGGGAAAGGATATAAAACAAAAACAAAAAACAAAAAATAGATAAGGAAAAAAT
1 AAAAAGTAAAAAAGGGAAAGCAAATAAAACAAAAAAAAAAAACAAAAAACAGATAAGAAAAAAAT
1684952 ACTTATCTTTCTAATATG
66 ACTTATCTTTCTAATATG
* *
1684970 AAAAA-TAAAAAAGGGGAAGCAAATAAAACAAAAATAACAAAAATAAAAAACAGATAAAGAAAAA
1 AAAAAGTAAAAAAGGGAAAGCAAATAAAACAAAAA-AA-AAAAACAAAAAACAGAT-AAGAAAAA
1685034 AATACTTATCTTTCTAATATG
63 AATACTTATCTTTCTAATATG
1685055 GTGGTTTCCA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 26 0.35
83 6 0.08
84 15 0.20
85 28 0.37
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.18
Consensus pattern (83 bp):
AAAAAGTAAAAAAGGGAAAGCAAATAAAACAAAAAAAAAAAACAAAAAACAGATAAGAAAAAAAT
ACTTATCTTTCTAATATG
Found at i:1687097 original size:9 final size:9
Alignment explanation
Indices: 1687065--1687089 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1687055 AAAAGGGAAA
1687065 AAATAAAAT
1 AAATAAAAT
1687074 AAATAAAAT
1 AAATAAAAT
1687083 AAATAAA
1 AAATAAA
1687090 TAAGATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1687202 original size:40 final size:42
Alignment explanation
Indices: 1687130--1687212 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
1687120 GAAAAAGGAA
*
1687130 ATATATATATATACATCAAAGTATTAATAAAATA-AATAAGCT
1 ATATATATATATACAACAAAGTATTAATAAAATAGAA-AAGCT
*
1687172 ATATATATATATACAACAAA-TATTTA-AAAATAGAAAAGCT
1 ATATATATATATACAACAAAGTATTAATAAAATAGAAAAGCT
1687212 A
1 A
1687213 CTCTCTCACT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 12 0.32
41 7 0.18
42 19 0.50
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (42 bp):
ATATATATATATACAACAAAGTATTAATAAAATAGAAAAGCT
Found at i:1687386 original size:8 final size:8
Alignment explanation
Indices: 1687373--1687540 Score: 65
Period size: 8 Copynumber: 21.1 Consensus size: 8
1687363 TTTTTTAAAA
1687373 AATAATAT
1 AATAATAT
1687381 AATAATGAAT
1 AATAAT--AT
* *
1687391 AAAAAAAT
1 AATAATAT
1687399 AATAA-A-
1 AATAATAT
1687405 AATAATAT
1 AATAATAT
1687413 -AT-ATAT
1 AATAATAT
1687419 ATATATATAT
1 A-ATA-ATAT
1687429 ATATATATAT
1 A-ATA-ATAT
1687439 ATATAA-AT
1 A-ATAATAT
*
1687447 AA-AGAAAT
1 AATA-ATAT
*
1687455 AATAAATAA
1 AAT-AATAT
1687464 AATAAT-T
1 AATAATAT
*
1687471 AAGAATAT
1 AATAATAT
1687479 -AT-ATA-
1 AATAATAT
1687484 AATATATAT
1 AATA-ATAT
*
1687493 AATAATAA
1 AATAATAT
1687501 AATAATAT
1 AATAATAT
1687509 -A-AATAT
1 AATAATAT
*
1687515 AACT-AGAT
1 AA-TAATAT
*
1687523 AATAATAC
1 AATAATAT
1687531 AATATATAT
1 AATA-ATAT
1687540 A
1 A
1687541 GTAAAATAGA
Statistics
Matches: 124, Mismatches: 14, Indels: 43
0.69 0.08 0.24
Matches are distributed among these distances:
6 20 0.16
7 15 0.12
8 49 0.40
9 14 0.11
10 26 0.21
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (8 bp):
AATAATAT
Found at i:1687414 original size:2 final size:2
Alignment explanation
Indices: 1687409--1687596 Score: 79
Period size: 2 Copynumber: 101.5 Consensus size: 2
1687399 AATAAAAATA
* * *
1687409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AA AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1687451 AA AT A- AT AA AT A- AA AT A- AT -T A- AG A- AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1687487 AT AT AT A- AT A- AT A- AA AT A- AT AT AA AT AT A- ACT AG AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
1687524 AT A- AT AC A- AT AT AT AT AGT A- AA AT AG ACT -T AT A- AG AA AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT
1687563 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1687597 AAAAATAAAT
Statistics
Matches: 143, Mismatches: 22, Indels: 42
0.69 0.11 0.20
Matches are distributed among these distances:
1 18 0.13
2 122 0.85
3 3 0.02
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (2 bp):
AT
Found at i:1695079 original size:4 final size:4
Alignment explanation
Indices: 1695065--1695100 Score: 54
Period size: 4 Copynumber: 8.5 Consensus size: 4
1695055 AAAGGGAAAA
1695065 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAGAT AA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AA
1695101 GGAAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 22 0.73
5 8 0.27
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1695224 original size:38 final size:42
Alignment explanation
Indices: 1695153--1695234 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
1695143 AAAAAGGAAA
1695153 TATATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATATACATCAAAGTATTAATAAAATAGAA-AAGC
*
1695195 TATATATATATATA-A-CAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATATACATCAAAGTATTAATAAAATAGAAAAGC
1695233 TA
1 TA
1695235 CCCTCTCACT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
38 12 0.32
39 7 0.18
40 4 0.11
41 1 0.03
42 14 0.37
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.33
Consensus pattern (42 bp):
TATATATATATATACATCAAAGTATTAATAAAATAGAAAAGC
Found at i:1695325 original size:41 final size:39
Alignment explanation
Indices: 1695250--1695326 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
1695240 TCACTTCACC
* **
1695250 GAAAGTGGGGGGCTTTAGTCAGAAATAAGGCAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
*
1695289 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAATAAAACAAAAA
1695327 AATGGGCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 9 0.28
40 1 0.03
41 22 0.69
ACGTcount: A:0.47, C:0.06, G:0.30, T:0.17
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
Found at i:1695492 original size:2 final size:2
Alignment explanation
Indices: 1695448--1695476 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1695438 AATAAAAATA
1695448 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 A
1695477 AAGTTATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1695669 original size:2 final size:2
Alignment explanation
Indices: 1695662--1695686 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1695652 TGTTAAAGAA
1695662 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1695687 ATAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1695775 original size:17 final size:18
Alignment explanation
Indices: 1695742--1695777 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1695732 ATATATACGT
*
1695742 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1695760 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1695777 A
1 A
1695778 AATATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1696204 original size:35 final size:35
Alignment explanation
Indices: 1696158--1696226 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
1696148 TAAAAAACCC
1696158 TATTTTAGACTAGTATTTGAGTCCTAATCCAACTT
1 TATTTTAGACTAGTATTTGAGTCCTAATCCAACTT
1696193 TATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 TATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1696227 CTTCTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (35 bp):
TATTTTAGACTAGTATTTGAGTCCTAATCCAACTT
Found at i:1697205 original size:12 final size:12
Alignment explanation
Indices: 1697188--1697212 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1697178 AATTGTGAAG
1697188 ATTGAAATTTAA
1 ATTGAAATTTAA
1697200 ATTGAAATTTAA
1 ATTGAAATTTAA
1697212 A
1 A
1697213 AATTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTGAAATTTAA
Found at i:1700038 original size:21 final size:22
Alignment explanation
Indices: 1699995--1700048 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1699985 TTTTCCAGAA
*
1699995 TGCTACAGGGGTATCAATACCC-
1 TGCTACA-GTGTATCAATACCCT
* *
1700017 TGCTACAGTGTATCGATTCCCT
1 TGCTACAGTGTATCAATACCCT
1700039 TGCTACAGTG
1 TGCTACAGTG
1700049 ATTTCGGTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (22 bp):
TGCTACAGTGTATCAATACCCT
Found at i:1707455 original size:22 final size:22
Alignment explanation
Indices: 1707430--1707471 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1707420 TATGAAATTT
* *
1707430 TGTCCTGAAGGACCTGTGAAGG
1 TGTCCCGAAGGACCTATGAAGG
1707452 TGTCCCGAAGGACCTATGAA
1 TGTCCCGAAGGACCTATGAA
1707472 ACTCTCTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGAAGG
Found at i:1708665 original size:24 final size:24
Alignment explanation
Indices: 1708638--1708744 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1708628 AAACGGAGAT
*
1708638 ATCAGAAATCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAA
* * * *
1708662 ATCAGATATCAGAACAGAATCCAT
1 ATCAGAAATCAAAACAGAATTCAA
* * * * * * *
1708686 GTTAGGAATCAGAACATATTTCAG
1 ATCAGAAATCAAAACAGAATTCAA
**
1708710 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAA
1708734 ATCAGAAATCA
1 ATCAGAAATCA
1708745 GATAAAATAT
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAA
Found at i:1708744 original size:48 final size:48
Alignment explanation
Indices: 1708638--1708746 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
1708628 AAACGGAGAT
* * *
1708638 ATCAGAAATCAAAACATAATTCAAATCAGATATCAGAACAGAATCCAT
1 ATCAGAAATCAGAACATAATTCAAATCAGATATCAAAACAGAATCCAA
* * * * * * *
1708686 GTTAGGAATCAGAACATATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACATAATTCAAATCAGATATCAAAACAGAATCCAA
1708734 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1708747 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACATAATTCAAATCAGATATCAAAACAGAATCCAA
Found at i:1711242 original size:13 final size:13
Alignment explanation
Indices: 1711224--1711297 Score: 87
Period size: 13 Copynumber: 5.4 Consensus size: 13
1711214 AACGGTCAAC
1711224 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1711237 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1711250 GGTCAACGGGTC-
1 GGTCAACGGGTCG
*
1711262 GGTAAACGGGTCAGGTCG
1 GGTCAAC--G---GGTCG
1711280 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1711293 GGTCA
1 GGTCA
1711298 GGTTGTGACC
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.11
13 35 0.66
14 1 0.02
16 1 0.02
17 4 0.08
18 6 0.11
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1711278 original size:25 final size:26
Alignment explanation
Indices: 1711224--1711278 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
1711214 AACGGTCAAC
* *
1711224 GGTCAACGGGTCGGGTCAACGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCA
1711250 GGTCAACGGGTC-GGTAAACGGGTCA
1 GGTCAACGGGTCGGGTAAACGGGTCA
1711275 GGTC
1 GGTC
1711279 GGGTCAACGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (26 bp):
GGTCAACGGGTCGGGTAAACGGGTCA
Found at i:1713458 original size:24 final size:24
Alignment explanation
Indices: 1713430--1713535 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 24
1713420 AAACAGAGAT
1713430 ATCAGAAATCAAAACATAATTCAA
1 ATCAGAAATCAAAACATAATTCAA
* * * * *
1713454 ATCAGATATCAGAACAGAATCCAT
1 ATCAGAAATCAAAACATAATTCAA
* * * * * *
1713478 GTTAGGAATCAGAACATATTTCAG
1 ATCAGAAATCAAAACATAATTCAA
** *
1713502 ATCAGATGTCAAAACA-GATTCAA
1 ATCAGAAATCAAAACATAATTCAA
1713525 ATCAGAAATCA
1 ATCAGAAATCA
1713536 GATAAAATAT
Statistics
Matches: 58, Mismatches: 24, Indels: 1
0.70 0.29 0.01
Matches are distributed among these distances:
23 13 0.22
24 45 0.78
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACATAATTCAA
Found at i:1716027 original size:13 final size:13
Alignment explanation
Indices: 1716009--1716082 Score: 87
Period size: 13 Copynumber: 5.4 Consensus size: 13
1715999 AACGGTCAAC
1716009 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1716022 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1716035 GGTCAACGGGTC-
1 GGTCAACGGGTCG
*
1716047 GGTAAACGGGTCAGGTCG
1 GGTCAAC--G---GGTCG
1716065 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1716078 GGTCA
1 GGTCA
1716083 GGTTGTGACC
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.11
13 35 0.66
14 1 0.02
16 1 0.02
17 4 0.08
18 6 0.11
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1716063 original size:25 final size:26
Alignment explanation
Indices: 1716009--1716063 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
1715999 AACGGTCAAC
* *
1716009 GGTCAACGGGTCGGGTCAACGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCA
1716035 GGTCAACGGGTC-GGTAAACGGGTCA
1 GGTCAACGGGTCGGGTAAACGGGTCA
1716060 GGTC
1 GGTC
1716064 GGGTCAACGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (26 bp):
GGTCAACGGGTCGGGTAAACGGGTCA
Found at i:1720431 original size:21 final size:21
Alignment explanation
Indices: 1720407--1720459 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1720397 ACAAATATAA
*
1720407 TATCGATACTCATTATAGGAG
1 TATCAATACTCATTATAGGAG
1720428 TATCAATACTCATTATAGGAG
1 TATCAATACTCATTATAGGAG
1720449 TATCAATACTC
1 TATCAATACTC
1720460 CATGTACTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (21 bp):
TATCAATACTCATTATAGGAG
Found at i:1730867 original size:23 final size:22
Alignment explanation
Indices: 1730841--1730893 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1730831 TTGATCTAAT
* *
1730841 AGTATTTTAGTTAATGAAAAATA
1 AGTATTTAAATTAA-GAAAAATA
*
1730864 AGTATTTAAATTAAGAAATATA
1 AGTATTTAAATTAAGAAAAATA
*
1730886 AGAATTTA
1 AGTATTTA
1730894 TTATATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (22 bp):
AGTATTTAAATTAAGAAAAATA
Found at i:1731995 original size:2 final size:2
Alignment explanation
Indices: 1731990--1732029 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1731980 TATATTTGAC
1731990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1732030 TCTCTAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1732941 original size:12 final size:12
Alignment explanation
Indices: 1732924--1732949 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1732914 TTTCTTATTT
1732924 CTTCAATTTCTC
1 CTTCAATTTCTC
1732936 CTTCAATTTCTC
1 CTTCAATTTCTC
1732948 CT
1 CT
1732950 AAATCATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (12 bp):
CTTCAATTTCTC
Found at i:1739610 original size:31 final size:31
Alignment explanation
Indices: 1739575--1739636 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1739565 CCAACATGTG
1739575 AGGGTAGGATTATTTAACAAATTATTATCCC
1 AGGGTAGGATTATTTAACAAATTATTATCCC
*
1739606 AGGGTAGGATTCTTTAACAAATTATTATCCC
1 AGGGTAGGATTATTTAACAAATTATTATCCC
1739637 TGATTAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (31 bp):
AGGGTAGGATTATTTAACAAATTATTATCCC
Found at i:1740275 original size:20 final size:22
Alignment explanation
Indices: 1740235--1740276 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1740225 CACTCTGCAT
1740235 TTTGCATATGCATCATTTTATTA
1 TTTGCATATGCAT-ATTTTATTA
1740258 TTTGCA-ATGCAT-TTTTATT
1 TTTGCATATGCATATTTTATT
1740277 TTTCTTACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (22 bp):
TTTGCATATGCATATTTTATTA
Found at i:1743921 original size:36 final size:36
Alignment explanation
Indices: 1743881--1744395 Score: 288
Period size: 39 Copynumber: 14.1 Consensus size: 36
1743871 TTTAAAAAAG
* *
1743881 ATTTTATCTCACTTGAGATAGTTTCCCTCGAAACAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
** *
1743917 ATTTTTTTATCTCGCTTGAGATAGTTTCCCTCAAAATAGAA
1 A---TTTTATCTCGCTTGAGATAGTTTCCCT-TGAA-ACAA
*
1743958 GATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC--AA
* * *
1743997 GATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAACAGAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC--AA
* * *
1744036 GATTTTGTCTCGCTTGAGATAGTTT-TCTCGAAACTGAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC--AA
* *
1744074 GATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
* * *
1744111 ATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA-A
* **
1744148 A---AATCT---TTGA-ATATGTTTCTATTGAAACAA
1 ATTTTATCTCGCTTGAGATA-GTTTCCCTTGAAACAA
* * * *
1744178 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
* *
1744214 A---AATCT---TTAAGACT-GTTTCCCTTGAAACAA
1 ATTTTATCTCGCTTGAGA-TAGTTTCCCTTGAAACAA
* * *
1744244 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-A-A
* * * * ** * *
1744282 AATGTATCTCACTTGAGATGGTTTTTCTTAAAACCA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
** * * *
1744318 ATTTCGTCTCGTTTGAGACAATTTCCCTTGAAACAAGAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC---AA
* * * * *
1744357 ATTTTATCTCACTCGAGAGAGCTTCTCTT-AAACAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1744392 ATTT
1 ATTT
1744396 CTTATACATT
Statistics
Matches: 385, Mismatches: 63, Indels: 63
0.75 0.12 0.12
Matches are distributed among these distances:
30 25 0.06
31 18 0.05
33 9 0.02
34 3 0.01
35 6 0.02
36 97 0.25
37 8 0.02
38 68 0.18
39 145 0.38
40 2 0.01
41 3 0.01
42 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (36 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
Found at i:1743935 original size:39 final size:39
Alignment explanation
Indices: 1743878--1744145 Score: 348
Period size: 39 Copynumber: 7.0 Consensus size: 39
1743868 GTTTTTAAAA
* *
1743878 AAGATTTTATCTCACTTGAGATAGTTTCCCTCGAAACA-
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAG
** * * *
1743916 AATTTTTTTATCTCGCTTGAGATAGTTTCCCTCAAAATAG
1 AA-GATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAG
*
1743956 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAG
*
1743995 AAGATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAG
* *
1744034 AAGATTTTGTCTCGCTTGAGATAGTTT-TCTCGAAACTG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAG
* *
1744072 AAGATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAAC--
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAG
* * *
1744109 AA-ATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACA
1744146 TAAAATCTTT
Statistics
Matches: 210, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
36 33 0.16
37 2 0.01
38 38 0.18
39 135 0.64
40 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (39 bp):
AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAG
Found at i:1744061 original size:20 final size:20
Alignment explanation
Indices: 1743999--1744061 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1743989 AAACAGAAGA
1743999 TTTTGTCTCGCTTGAGATAG
1 TTTTGTCTCGCTTGAGATAG
* ****
1744019 -TTTCTCTCGAAACAGA-AG
1 TTTTGTCTCGCTTGAGATAG
1744037 ATTTTGTCTCGCTTGAGATAG
1 -TTTTGTCTCGCTTGAGATAG
1744058 TTTT
1 TTTT
1744062 CTCGAAACTG
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 15 0.50
21 2 0.07
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.43
Consensus pattern (20 bp):
TTTTGTCTCGCTTGAGATAG
Found at i:1744253 original size:66 final size:67
Alignment explanation
Indices: 1744090--1744284 Score: 295
Period size: 66 Copynumber: 2.9 Consensus size: 67
1744080 GTCTCGCTTG
* *
1744090 AGACAGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAATCTT
1 AGACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAAATCTT
1744155 TGA
65 TGA
* **
1744158 ATA-TGTTTCTATTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTT
1 AGACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTT
1744222 -A
66 GA
* *
1744223 AGACTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGAAAT
1 AGACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA-AAAT
1744285 GTATCTCACT
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
65 3 0.03
66 58 0.50
67 52 0.45
68 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (67 bp):
AGACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTT
GA
Found at i:1744395 original size:74 final size:74
Alignment explanation
Indices: 1744238--1744396 Score: 207
Period size: 74 Copynumber: 2.1 Consensus size: 74
1744228 GTTTCCCTTG
* * *
1744238 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGAAATGTATCTCACTTGAGATGG
1 AAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAACAAGAAATGTATCTCACTCGAGATGG
* *
1744303 TTTTTCTTA
66 CTTCTCTTA
* *
1744312 AAACCAATTTCGTCTCGT-TTGAGACAATTTCCCTTGAAACAAGAAATTTTATCTCACTCGAGA-
1 AAACAAATTTCGTCTC-TCTTGAGACAATTTCCCTTGAAACAAGAAA-TGTATCTCACTCGAGAT
1744375 GAGCTTCTCTT-
64 G-GCTTCTCTTA
1744386 AAACAAATTTC
1 AAACAAATTTC
1744397 TTATACATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
74 52 0.70
75 22 0.30
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (74 bp):
AAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAACAAGAAATGTATCTCACTCGAGATGG
CTTCTCTTA
Found at i:1744892 original size:105 final size:105
Alignment explanation
Indices: 1744710--1745098 Score: 514
Period size: 105 Copynumber: 3.7 Consensus size: 105
1744700 AGGGATCGAT
* * *
1744710 ATTTCCAGAAGAGTTTATAATGAGAAGAACTCATCCTAAAGGAGAAATTTCATAATGAGAAGAAC
1 ATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAAC
* *
1744775 TTCTTCCTTTCAAATTCACCAAAGAAGGAGGTGAATCAAC
66 TTGTTCCTTTCAAATTCACCAAAGAAGGAGGTGAACCAAC
* * *
1744815 ATTTCCAGAAGAGTTCATACTGAAAAGAACTCGTCCTAAAGGAGAAAGTTCATACTGAGAAGAAC
1 ATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAAC
* *
1744880 TTGTTCCTTTCAAATTCACCACAGAA-TAGGGTGAACCAAC
66 TTGTTCCTTTCAAATTCACCAAAGAAGGA-GGTGAACCAAC
* * * * * *
1744920 ATTTCTAGAAGAGTTCATAACGAGAAGAACTCTTCCTAAAGGAGAAAGTTCATAACGATAAGAAC
1 ATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAAC
1744985 TTGTTCCTTTCAAATTCACCACAA-AAGGAGGTGAACCAAC
66 TTGTTCCTTTCAAATTCACCA-AAGAAGGAGGTGAACCAAC
* * * * *
1745025 ATTTACAAAAGAGTTCATAAT-AAGAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAC
1 ATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCCTAA-AGG-AG-A-AAGTTCATAATGAGAA
1745089 GAACTTGTTC
62 GAACTTGTTC
1745099 AACTTTGCAT
Statistics
Matches: 246, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
104 14 0.06
105 204 0.83
106 4 0.02
107 1 0.00
108 23 0.09
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (105 bp):
ATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAAC
TTGTTCCTTTCAAATTCACCAAAGAAGGAGGTGAACCAAC
Found at i:1745147 original size:91 final size:91
Alignment explanation
Indices: 1745021--1745389 Score: 487
Period size: 91 Copynumber: 4.1 Consensus size: 91
1745011 GGAGGTGAAC
* * *
1745021 CAACATTTACAA--AAGAGTTCATAATAAG-AGAACTCATCCAAAGAGGAAGAAGAAGTTCATAA
1 CAACATTTTCAACGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAA
* *
1745083 TGAGACGAACTTGTTCAA-CTTTGCAT
66 TGAGAAGAACTTGTTCAACCTTAGC-T
** ** *
1745109 CAATGTTTTCATTGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGAAAGAAGAAGTTCATAA
1 CAACATTTTCAACGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAA
1745174 TGAGAAGAACTTGTTCAACCTTAGCT
66 TGAGAAGAACTTGTTCAACCTTAGCT
* * *
1745200 CAGCATTTCCAACGGAGAGTTCATAATGAGAAGAACTCATCCAACGA-GAGAGAAGAAGTTCATA
1 CAACATTTTCAACGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGA-AGAAGAAGTTCATA
1745264 ATGAGAAGAACTTGTTCAACCTTAGCT
65 ATGAGAAGAACTTGTTCAACCTTAGCT
* * * * * *
1745291 CAACATTTTCAACGGAGAGTTCATAATGAGAAGAATTCGTCCAGCGAGGGAGAAGAATTTCATAA
1 CAACATTTTCAACGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAA
* *
1745356 TGAGAATAACTTGTTCAACCTTAGAT
66 TGAGAAGAACTTGTTCAACCTTAGCT
*
1745382 CAATATTT
1 CAACATTT
1745390 CTAGAAGAAC
Statistics
Matches: 248, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
88 8 0.03
90 16 0.06
91 218 0.88
92 6 0.02
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (91 bp):
CAACATTTTCAACGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTAGCT
Found at i:1748251 original size:16 final size:16
Alignment explanation
Indices: 1748225--1748266 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1748215 GCAGACCAAC
1748225 TTTTGTCTTAAAAATGA
1 TTTT-TCTTAAAAATGA
*
1748242 TTTTTCTT-AAAATTA
1 TTTTTCTTAAAAATGA
1748257 TTTTT-TTAAA
1 TTTTTCTTAAA
1748267 GACATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 13 0.57
16 4 0.17
17 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTTTCTTAAAAATGA
Found at i:1751786 original size:11 final size:11
Alignment explanation
Indices: 1751770--1751795 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1751760 CATCAAGAAA
1751770 AAAATAAAAAT
1 AAAATAAAAAT
1751781 AAAATAAAAAT
1 AAAATAAAAAT
1751792 AAAA
1 AAAA
1751796 AGAATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:1763664 original size:2 final size:2
Alignment explanation
Indices: 1763657--1763713 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1763647 TTATGAAAAC
1763657 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1763699 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1763714 TGTTTCTAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1773056 original size:29 final size:29
Alignment explanation
Indices: 1773013--1773092 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
1773003 AAACTAAATT
1773013 GATGTCATTGCTTACATCAATTAGATGAA
1 GATGTCATTGCTTACATCAATTAGATGAA
* *
1773042 GATGTTATTGTTTACATCAATTAGATGAA
1 GATGTCATTGCTTACATCAATTAGATGAA
1773071 GAT-TGCATTGCTTACATCAATT
1 GATGT-CATTGCTTACATCAATT
1773093 TAGTTAGGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 1 0.02
29 45 0.98
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (29 bp):
GATGTCATTGCTTACATCAATTAGATGAA
Found at i:1777775 original size:29 final size:29
Alignment explanation
Indices: 1777733--1777812 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
1777723 AAACTAAATT
1777733 GATGTCATTGCTTACATCAATTAGATGAA
1 GATGTCATTGCTTACATCAATTAGATGAA
*
1777762 GATGTTATTGCTTACATCAATTAGATGAA
1 GATGTCATTGCTTACATCAATTAGATGAA
1777791 GAT-TGCATTGCTTACATCAATT
1 GATGT-CATTGCTTACATCAATT
1777813 TAGTTAGGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 1 0.02
29 47 0.98
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (29 bp):
GATGTCATTGCTTACATCAATTAGATGAA
Found at i:1783730 original size:16 final size:16
Alignment explanation
Indices: 1783709--1783751 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1783699 TCTTCCTCGT
*
1783709 CTTTTTTATATTTCAA
1 CTTTTTCATATTTCAA
1783725 CTTTTTCATATTTC-A
1 CTTTTTCATATTTCAA
*
1783740 -TATTTCATATTT
1 CTTTTTCATATTT
1783752 TCATCCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 13 0.52
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (16 bp):
CTTTTTCATATTTCAA
Found at i:1789132 original size:16 final size:16
Alignment explanation
Indices: 1789110--1789196 Score: 120
Period size: 16 Copynumber: 5.4 Consensus size: 16
1789100 GGTATTACCC
1789110 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1789126 AACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1789142 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
* * *
1789158 GACTTATTTTTAACCT
1 GACCTGTTTTCAACCT
*
1789174 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1789190 GACCTGT
1 GACCTGT
1789197 AAATGATCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 63 1.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.40
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:1789419 original size:11 final size:11
Alignment explanation
Indices: 1789389--1789421 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1789379 CATATTATAT
1789389 AAATTATTTAA
1 AAATTATTTAA
1789400 AAA--ATTTAA
1 AAATTATTTAA
1789409 AAATTATTTAA
1 AAATTATTTAA
1789420 AA
1 AA
1789422 GTAAATTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTATTTAA
Found at i:1789481 original size:14 final size:14
Alignment explanation
Indices: 1789459--1789505 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1789449 TGCAAAGGAA
*
1789459 AATTAATATAGTTT
1 AATTTATATAGTTT
1789473 AATTTATATA----
1 AATTTATATAGTTT
1789483 AA-TTATATAGTTT
1 AATTTATATAGTTT
1789496 AATTTATATA
1 AATTTATATA
1789506 AAGACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:1789492 original size:23 final size:24
Alignment explanation
Indices: 1789458--1789507 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1789448 ATGCAAAGGA
1789458 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1789482 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1789505 AAA
1 AAA
1789508 GACAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1789689 original size:14 final size:14
Alignment explanation
Indices: 1789667--1789731 Score: 69
Period size: 14 Copynumber: 4.7 Consensus size: 14
1789657 TCTATTTAAA
1789667 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
1789681 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
** **
1789695 TTAAAGTTTA-GAA
1 TTAGGGTTTATGGT
*
1789708 TTAGGGTTTATGAT
1 TTAGGGTTTATGGT
1789722 TTAGGGTTTA
1 TTAGGGTTTA
1789732 GGATTTCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
13 9 0.21
14 33 0.79
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:1789828 original size:11 final size:11
Alignment explanation
Indices: 1789812--1789837 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1789802 TAATTTACTT
1789812 TATAGTTTATA
1 TATAGTTTATA
1789823 TATAGTTTATA
1 TATAGTTTATA
1789834 TATA
1 TATA
1789838 CTATACATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TATAGTTTATA
Found at i:1789842 original size:20 final size:21
Alignment explanation
Indices: 1789819--1789868 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1789809 CTTTATAGTT
*
1789819 TATATATAGTTTATATATAC-
1 TATATATAGTTTATACATACA
* *
1789839 TATACATGGTTTATACATACA
1 TATATATAGTTTATACATACA
1789860 TATTATATA
1 TA-TATATA
1789869 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATATAGTTTATACATACA
Found at i:1790267 original size:41 final size:40
Alignment explanation
Indices: 1790203--1790279 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
1790193 TGCTAGTCCA
* * * *
1790203 TTTAAATTAGGGTTTATGGTTTAGTATTTATGGTTTAAAG
1 TTTAAATTAAGGTTTATGATTTAGGATTTAGGGTTTAAAG
1790243 TTTAGAATTAAGGTTTATGATTTAGGATTTAGGGTTT
1 TTTA-AATTAAGGTTTATGATTTAGGATTTAGGGTTT
1790280 CTATAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 4 0.12
41 28 0.88
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.49
Consensus pattern (40 bp):
TTTAAATTAAGGTTTATGATTTAGGATTTAGGGTTTAAAG
Found at i:1790370 original size:11 final size:11
Alignment explanation
Indices: 1790354--1790381 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1790344 TAATTTACTT
1790354 TATATAGTTTA
1 TATATAGTTTA
1790365 TATATAGTTTA
1 TATATAGTTTA
1790376 TATATA
1 TATATA
1790382 CTATACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:1790372 original size:49 final size:48
Alignment explanation
Indices: 1790276--1790372 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 48
1790266 AGGATTTAGG
** * *
1790276 GTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGT
1 GTTTCTATAAACTATATAAGTAATTACTTTATATAGTTTATACATAGT
*
1790324 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATAGT
1 GTTTCTATAAACTATATAAGTAA-TTACTTTATATAGTTTATACATAGT
1790373 TTATATATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (48 bp):
GTTTCTATAAACTATATAAGTAATTACTTTATATAGTTTATACATAGT
Found at i:1790386 original size:20 final size:21
Alignment explanation
Indices: 1790363--1790412 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1790353 TTATATAGTT
*
1790363 TATATATAGTTTATATATAC-
1 TATATATAGTTTATACATACA
* *
1790383 TATACATGGTTTATACATACA
1 TATATATAGTTTATACATACA
1790404 TATTATATA
1 TA-TATATA
1790413 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATATAGTTTATACATACA
Found at i:1790637 original size:542 final size:541
Alignment explanation
Indices: 1789589--1792621 Score: 4546
Period size: 542 Copynumber: 5.8 Consensus size: 541
1789579 TTTTGGCAAT
* *
1789589 ACATTAGTTTACAAAGG-CCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
1 ACATTAGTTTACATAGGCCCAATGC--AAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
* * * *
1789653 CTAGTCTATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTA
64 CTAGTCCATTTAAATTAGGGTTTATGATTTAGTATTTATGGTTTAAAGTTTAGAATTAAGGTTTA
* *
1789718 TGATTTAGGGTTTAGGATTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTG
129 TGATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTG
1789783 TTTCTATAAACTATATAAGTAATTTACTTTATAGTTTATATATAGTTTATATATACTATACATGG
194 TTTCTATAAACTATATAAGTAATTTACTTTATA-TTTATATATAGTTTATATATACTATACATGG
1789848 TTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTAT
258 TTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTAT
*
1789913 ATAAAACATGATTAATTAGGTATTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAA
323 ATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAA
1789978 ATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAAT
388 ATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAAT
*
1790043 TCACATTAATGACTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCC
453 TCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCC
1790108 ATTTGCAATAGTGCTAGTCCATTA
518 ATTTGCAATAGTGCTAGTCCATTA
* *
1790132 ACATTAGTTTGCATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCTTTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
*
1790197 AGTCCATTTAAATTAGGGTTTATGGTTTAGTATTTATGGTTTAAAGTTTAGAATTAAGGTTTATG
66 AGTCCATTTAAATTAGGGTTTATGATTTAGTATTTATGGTTTAAAGTTTAGAATTAAGGTTTATG
1790262 ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
131 ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
1790327 TCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATAGTTTATATATACTATACATGG
196 TCTATAAACTATATAAGTAATTTAC-TT-TATA-TTTATATATAGTTTATATATACTATACATGG
1790392 TTTATACATACATATTATATAAAATTATTTAAT-AAATTAATAAAATTATTTAAATGTAAATTAT
258 TTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTAT
1790456 AT-AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAA
323 ATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAA
*
1790520 ATAGTAGTACATGTCATATTAATTTAGATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAAT
388 ATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAAT
*
1790585 TCACATTAATGGCTCATTTATTTTTTTGTTATGAATAAGTAATAATAAAACCC-AAAATAAGTCC
453 TCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCC
1790649 ATTTGCAATAGTGCTAGTCCATTA
518 ATTTGCAATAGTGCTAGTCCATTA
*
1790673 ACATTAGTTTACATAGGCCCAATGTAAGCCCACTCTTTTATTAC--A-ATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* * * *
1790735 AGTTCATTTACATTAGGGTTTATGGTTTAGTATTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
66 AGTCCATTTAAATTAGGGTTTATGATTTAGTATTTATGGTTTAAAGTTTAGAATTAAGGTTTATG
1790800 A-TTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGC---GTGTT
131 ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
1790861 TCTATAAACTATATAAGTAATTTAC-------TT-TATATAG-TT-TATATACTATACATGGTTT
196 TCTATAAACTATATAAGTAATTTACTTTATATTTATATATAGTTTATATATACTATACATGGTTT
* *
1790916 ATGCATACATA-TATATAAAATTATTTAATAAATTTAATAAAATTATTTAAATGTAAATTATATA
261 ATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATA
1790980 AAACATGATTAATTAGGTGTT-AATAATTAGTATGTCACATTGCATA-T-TATGGTTCAT-AATA
326 AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATA
1791041 GTAGTACATGTCATA-TAATTTAAATTGCATAATTTGTA-TTTAGTTGCATGTTAGGTTAATTCA
391 GTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCA
* *
1791104 CATTAATGTCTCATTTATTTTGTTGTTATGAATAAGTAATAACAAAACCCAAAAATAAGTCCATT
456 CATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATT
1791169 TGCAATAGTGCTAGTCCATTA
521 TGCAATAGTGCTAGTCCATTA
* *
1791190 ACATTAGTTTGCATAGGCGCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* *
1791255 AGTTCATTTAAATTAGGGTTTATGATTTAGTGTTTATGGTTTAAAGTTTAGAATTAAGGTTTATG
66 AGTCCATTTAAATTAGGGTTTATGATTTAGTATTTATGGTTTAAAGTTTAGAATTAAGGTTTATG
*
1791320 ATTTAGGATTTAAGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
131 ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
1791385 TCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATAGTTTATATATACTATACATGG
196 TCTATAAACTATATAAGTAATTTAC-TT-TATA-TTTATATATAGTTTATATATACTATACATGG
*
1791450 TTTATACATACATATTATAT-AAATTATTTATTAAAATTAATAAAATTATTTAAATGTAAATTAT
258 TTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTAT
1791514 ATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCAT-A
323 ATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAA
1791578 ATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTA-TTGCATGTTAGGTTAAT
388 ATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAAT
*
1791642 TCACATTAAT-GCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCC-AAAATAAGTCT
453 TCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCC
1791705 ATTTGCAATAGTGCTAGTCCATTA
518 ATTTGCAATAGTGCTAGTCCATTA
* * *
1791729 ACATTAGTTTACATAGGCCCAGTGCAAGTCCACTCTTTCATTAC-AA-ATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* * ** *** * *
1791792 AGTTCATTTACATTAGAATTTATGATTTAGTATTTA-GTGTTTGTGGTTTA-AAGTTTAGGATTA
66 AGTCCATTTAAATTAGGGTTTATGATTTAGTATTTATG-GTTTAAAGTTTAGAA-TTAAGGTTTA
* * * * * * *
1791855 GGGTTTATGATTTAAGGTTTCTATAAACGATATATTTTACTAC----TATAGTTTATGTATAGTG
129 TGATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTG
1791916 TTTCTATAAACTATATAAG----------TA-A--T-T-TATA-TTTATATATACTATACATGGT
194 TTTCTATAAACTATATAAGTAATTTACTTTATATTTATATATAGTTTATATATACTATACATGGT
1791965 TTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAA-TATTTAAATGTAAATTATA
259 TTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATA
1792029 T-AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATT-CTATATTATATGGTTCATAA
324 TAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGC-ATATTATATGGTTCATAA
* * *
1792092 ATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGCT-TTTTAGTTGCATGTTAGGTT-A
388 ATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTG-TATTTTAGTTGCATGTTAGGTTAA
* *
1792155 TTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAG---TAATAAAACCCAAAAATAAGTC
452 TTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTC
**
1792217 CATTTATAATAGTGCTAGTCCATTA
517 CATTTGCAATAGTGCTAGTCCATTA
* * * * *
1792242 ACATTAATTTAGATATGCCCAATGCAAGCCTACTCTTTTATTACAAATATATATGCATTAGTGAT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* * * * *
1792307 AGTCTATTTACATTA-GGTTTATGATTTAGTGTTTA-GTGTTT---G--T-GATTTAAAGTTTAT
66 AGTCCATTTAAATTAGGGTTTATGATTTAGTATTTATG-GTTTAAAGTTTAGAATTAAGGTTTAT
* * * *
1792364 GGTTTATGATTTAGGATTTCTATAAACTATATATTTTATTAC-TTATATAGTTTAT--ATA-TAT
130 GATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGT
* * * * * * *
1792425 ATATATATA-TATAT-A-T-ATATA-TATATATATATATAATA-TATATATATACTATACATGGT
195 TTCTATAAACTATATAAGTAATTTACTTTATATTTATAT-ATAGTTTATATATACTATACATGGT
*
1792484 TTATACACACATA-T-TAT-AAA--A--T--T---ATTAATAAAATTATTTAAATGTAAATTATA
259 TTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATA
*
1792537 TAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATATGGTTCATAAA
324 TAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAA
1792602 TAGTAGTACATGTCATATTA
389 TAGTAGTACATGTCATATTA
1792622 GTGTTTGTCC
Statistics
Matches: 2331, Mismatches: 95, Indels: 162
0.90 0.04 0.06
Matches are distributed among these distances:
506 1 0.00
507 15 0.01
508 73 0.03
509 86 0.04
510 2 0.00
511 11 0.00
512 13 0.01
513 129 0.06
514 142 0.06
515 99 0.04
516 77 0.03
517 103 0.04
518 21 0.01
519 46 0.02
520 99 0.04
521 142 0.06
522 23 0.01
523 7 0.00
524 32 0.01
533 36 0.02
534 32 0.01
535 7 0.00
536 5 0.00
537 254 0.11
538 111 0.05
539 75 0.03
540 69 0.03
541 127 0.05
542 369 0.16
543 50 0.02
544 75 0.03
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (541 bp):
ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
AGTCCATTTAAATTAGGGTTTATGATTTAGTATTTATGGTTTAAAGTTTAGAATTAAGGTTTATG
ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
TCTATAAACTATATAAGTAATTTACTTTATATTTATATATAGTTTATATATACTATACATGGTTT
ATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATA
AAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATA
GTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCA
CATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATT
TGCAATAGTGCTAGTCCATTA
Found at i:1790811 original size:20 final size:20
Alignment explanation
Indices: 1790747--1790816 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1790737 TTCATTTACA
*
1790747 TTAGGGTTTATGGTTTAGTAT
1 TTAGGGTTTAT-GTTTAGGAT
* * *
1790768 TTATGGTTTAAAGTTTA-GAA
1 TTAGGGTTT-ATGTTTAGGAT
*
1790788 TTAGGGTTTATGATTAGGAT
1 TTAGGGTTTATGTTTAGGAT
1790808 TTAGGGTTT
1 TTAGGGTTT
1790817 CTATAAACTA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 5 0.13
20 20 0.51
21 13 0.33
22 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (20 bp):
TTAGGGTTTATGTTTAGGAT
Found at i:1790864 original size:45 final size:46
Alignment explanation
Indices: 1790813--1790899 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
1790803 AGGATTTAGG
** *
1790813 GTTTCTATAAACTATATATTTTA-TTACTTTATATAGTTTATGCGT
1 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGCGT
1790858 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTAT
1 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTAT
1790900 ATACTATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (46 bp):
GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGCGT
Found at i:1791289 original size:14 final size:13
Alignment explanation
Indices: 1791271--1791331 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
1791261 TTTAAATTAG
1791271 GGTTTATGATTTA
1 GGTTTATGATTTA
*
1791284 GTGTTTATGGTTTAA
1 G-GTTTATGATTT-A
* *
1791299 AGTTTA-GAATTAA
1 GGTTTATG-ATTTA
1791312 GGTTTATGATTTA
1 GGTTTATGATTTA
1791325 GGATTTA
1 GG-TTTA
1791332 AGGTTTCTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
13 14 0.38
14 22 0.59
15 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (13 bp):
GGTTTATGATTTA
Found at i:1791337 original size:41 final size:40
Alignment explanation
Indices: 1791261--1791337 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
1791251 TGCTAGTTCA
* *
1791261 TTTAAATTAGGGTTTATGATTTAGTGTTTATGGTTTAAAG
1 TTTAAATTAAGGTTTATGATTTAGTGTTTAAGGTTTAAAG
1791301 TTTAGAATTAAGGTTTATGATTTAG-GATTTAAGGTTT
1 TTTA-AATTAAGGTTTATGATTTAGTG-TTTAAGGTTT
1791338 CTATAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (40 bp):
TTTAAATTAAGGTTTATGATTTAGTGTTTAAGGTTTAAAG
Found at i:1791428 original size:11 final size:11
Alignment explanation
Indices: 1791412--1791439 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1791402 TAATTTACTT
1791412 TATATAGTTTA
1 TATATAGTTTA
1791423 TATATAGTTTA
1 TATATAGTTTA
1791434 TATATA
1 TATATA
1791440 CTATACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:1791430 original size:49 final size:48
Alignment explanation
Indices: 1791334--1791430 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 48
1791324 AGGATTTAAG
** * *
1791334 GTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGT
1 GTTTCTATAAACTATATAAGTAATTACTTTATATAGTTTATACATAGT
*
1791382 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATAGT
1 GTTTCTATAAACTATATAAGTAA-TTACTTTATATAGTTTATACATAGT
1791431 TTATATATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (48 bp):
GTTTCTATAAACTATATAAGTAATTACTTTATATAGTTTATACATAGT
Found at i:1791444 original size:20 final size:21
Alignment explanation
Indices: 1791421--1791470 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1791411 TTATATAGTT
*
1791421 TATATATAGTTTATATATAC-
1 TATATATAGTTTATACATACA
* *
1791441 TATACATGGTTTATACATACA
1 TATATATAGTTTATACATACA
1791462 TATTATATA
1 TA-TATATA
1791471 AATTATTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATATAGTTTATACATACA
Found at i:1792352 original size:21 final size:21
Alignment explanation
Indices: 1792319--1792377 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1792309 TCTATTTACA
*
1792319 TTAG-GTTTATGATTTAGTGT
1 TTAGTGTTTATGATTTAGAGT
* *
1792339 TTAGTGTTTGTGATTTAAAGT
1 TTAGTGTTTATGATTTAGAGT
1792360 TTA-TGGTTTATGATTTAG
1 TTAGT-GTTTATGATTTAG
1792378 GATTTCTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (21 bp):
TTAGTGTTTATGATTTAGAGT
Found at i:1792421 original size:2 final size:2
Alignment explanation
Indices: 1792416--1792477 Score: 108
Period size: 2 Copynumber: 31.0 Consensus size: 2
1792406 TTATATAGTT
1792416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1792458 TA -A TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA -TA TA
1792478 CATGGTTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1792695 original size:7 final size:7
Alignment explanation
Indices: 1792641--1792708 Score: 50
Period size: 7 Copynumber: 10.0 Consensus size: 7
1792631 CATTTATATC
1792641 AGGGTTT
1 AGGGTTT
*
1792648 ATGGTTT
1 AGGGTTT
*
1792655 AGTGTTT
1 AGGGTTT
*
1792662 ATGG-TT
1 AGGGTTT
**
1792668 AAAG-TT
1 AGGGTTT
*
1792674 AGGGTGT
1 AGGGTTT
*
1792681 ATGGTTT
1 AGGGTTT
1792688 AGGGTTT
1 AGGGTTT
*
1792695 AGAGTTT
1 AGGGTTT
1792702 AGGGTTT
1 AGGGTTT
1792709 CTATAAACTA
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
6 8 0.18
7 37 0.82
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:1792881 original size:23 final size:23
Alignment explanation
Indices: 1792855--1792933 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
1792845 ATGCATATTA
1792855 CATTAATATACATATCATACATG
1 CATTAATATACATATCATACATG
*
1792878 CATTAATA-A-ATTATACATATATG
1 CATTAATATACA-TAT-CATACATG
* *
1792901 CATACATATTATACATA-CATGCATG
1 CAT---TAATATACATATCATACATG
1792926 CATTAATA
1 CATTAATA
1792934 AATTATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
21 1 0.02
22 8 0.18
23 18 0.41
25 9 0.20
26 4 0.09
27 3 0.07
28 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.35
Consensus pattern (23 bp):
CATTAATATACATATCATACATG
Found at i:1793233 original size:23 final size:24
Alignment explanation
Indices: 1793206--1793261 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 24
1793196 ATATACATAC
*
1793206 ATATATAAAATTATTT-AAT-AAA
1 ATATATAAAATCATTTAAATGAAA
1793228 AT-TATAAAATCATTTAAATGTAAA
1 ATATATAAAATCATTTAAATG-AAA
*
1793252 TTATATAAAA
1 ATATATAAAA
1793262 CATGATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 12 0.43
22 5 0.18
24 4 0.14
25 7 0.25
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATATATAAAATCATTTAAATGAAA
Found at i:1807105 original size:33 final size:32
Alignment explanation
Indices: 1807047--1807119 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
1807037 ATTATTATAT
1807047 ATATATAATATTAATAATTTAATTTAATTTAAA
1 ATATAT-ATATTAATAATTTAATTTAATTTAAA
* *
1807080 ATATATATA-TAATATTTATATATTTAATTTAAT
1 ATATATATATTAATAATT-TA-ATTTAATTTAAA
1807113 ATATATA
1 ATATATA
1807120 CCGCCCGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 7 0.19
32 5 0.14
33 24 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATATATATTAATAATTTAATTTAATTTAAA
Found at i:1807994 original size:20 final size:21
Alignment explanation
Indices: 1807951--1808003 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
1807941 AGGGTGTCAA
*
1807951 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCATGT
*
1807972 AGTGCATCGATGCA-CCATGT
1 AGTGCATCCATGCACCCATGT
1807992 AGTGCATCCATG
1 AGTGCATCCATG
1808004 AACTCCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGT
Found at i:1811002 original size:21 final size:21
Alignment explanation
Indices: 1810976--1811015 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1810966 AAACAATTGG
1810976 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
1810997 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
1811016 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1811260 original size:21 final size:22
Alignment explanation
Indices: 1811234--1811292 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
1811224 AGGGTGTCAA
1811234 AGTGCATCCATGCACC-CCTAC-
1 AGTGCATCCATGCACCGCC-ACT
1811255 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACC-GCCACT
*
1811278 AGTGCATCGATGCAC
1 AGTGCATCCATGCAC
1811293 ACATTCTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (22 bp):
AGTGCATCCATGCACCGCCACT
Found at i:1811341 original size:20 final size:19
Alignment explanation
Indices: 1811316--1811390 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 19
1811306 AATGCAATTA
*
1811316 GTGCATCGATGCACTCTGCT
1 GTGCATCCATGCAC-CTGCT
*
1811336 GTGCATCCATGCACCCTGTT
1 GTGCATCCATGCA-CCTGCT
1811356 GTGCATCCATGCACCTTGCT
1 GTGCATCCATGCACC-TGCT
1811376 GTGCATCCATGCACC
1 GTGCATCCATGCACC
1811391 AGAGCTGCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 2 0.04
20 47 0.94
21 1 0.02
ACGTcount: A:0.16, C:0.35, G:0.21, T:0.28
Consensus pattern (19 bp):
GTGCATCCATGCACCTGCT
Found at i:1814753 original size:15 final size:15
Alignment explanation
Indices: 1814733--1814762 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1814723 TCTACTTTAG
1814733 TTTTTTTTTGTCTGT
1 TTTTTTTTTGTCTGT
1814748 TTTTTTTTTGTCTGT
1 TTTTTTTTTGTCTGT
1814763 GTGTGTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTGTCTGT
Found at i:1815673 original size:31 final size:33
Alignment explanation
Indices: 1815635--1815699 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
1815625 TTTTATTTTT
* *
1815635 TAATTTAATTACT-TAACTTTCAAA-TTACTCA
1 TAATTTAATCACTCTAACTTTCAAACTTAATCA
*
1815666 TAATTTAATCACTCTATCTTTCAAACTTAATCA
1 TAATTTAATCACTCTAACTTTCAAACTTAATCA
1815699 T
1 T
1815700 TTTTATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 12 0.41
32 10 0.34
33 7 0.24
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (33 bp):
TAATTTAATCACTCTAACTTTCAAACTTAATCA
Found at i:1818522 original size:95 final size:95
Alignment explanation
Indices: 1818317--1818511 Score: 322
Period size: 95 Copynumber: 2.1 Consensus size: 95
1818307 CATTAGTCTC
* * *
1818317 TCTTTTTTATCTTTATAATCGATGCCGGCATAAACATTGGTACGGATCACCAACTGTCAGTATTC
1 TCTTTTTTATCTTTATGAGCGATGCCGACATAAACATTGGTACGGATCACCAACTGTCAGTATTC
1818382 ATTTCTTTTATTTTATTTTATTATATCACA
66 ATTTCTTTTATTTTATTTTATTATATCACA
*
1818412 TCTTTTTTATCTTTATGAGCGATGCCGACATAAACATTGGTACTGG-TCACCAGCTGTCAGTATT
1 TCTTTTTTATCTTTATGAGCGATGCCGACATAAACATTGGTAC-GGATCACCAACTGTCAGTATT
1818476 CATTGT-TTTTATTTTATTTTATTATATCACA
65 CATT-TCTTTTATTTTATTTTATTATATCACA
1818507 TCTTT
1 TCTTT
1818512 ATTTTTTTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
95 91 0.97
96 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (95 bp):
TCTTTTTTATCTTTATGAGCGATGCCGACATAAACATTGGTACGGATCACCAACTGTCAGTATTC
ATTTCTTTTATTTTATTTTATTATATCACA
Found at i:1823385 original size:39 final size:39
Alignment explanation
Indices: 1823298--1823433 Score: 168
Period size: 39 Copynumber: 3.5 Consensus size: 39
1823288 TATTACATAT
**
1823298 AAAGAGCAGAATGCAAGAGTCCCCTACAA-TTGAGATAC
1 AAAGAGCAGAATGCAATTGTCCCCTACAATTTGAGATAC
* *
1823336 AAAGAACAGAATG-AACTTGTCCCCTGCAATTTGAGATAC
1 AAAGAGCAGAATGCAA-TTGTCCCCTACAATTTGAGATAC
* * * *
1823375 AAAGAGCAGAATGCAATCGTCCCCTACAATATCAAATAC
1 AAAGAGCAGAATGCAATTGTCCCCTACAATTTGAGATAC
*
1823414 AAAGAGCAGAATGCACTTGT
1 AAAGAGCAGAATGCAATTGT
1823434 ACTCTATAGG
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
37 2 0.02
38 22 0.27
39 57 0.69
40 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.19
Consensus pattern (39 bp):
AAAGAGCAGAATGCAATTGTCCCCTACAATTTGAGATAC
Found at i:1825493 original size:69 final size:69
Alignment explanation
Indices: 1825380--1825522 Score: 241
Period size: 69 Copynumber: 2.1 Consensus size: 69
1825370 AATGCAAGAG
* * *
1825380 TCAAACTTGTATACAAACAACTCTTCATCTAATGAGGAGCTCAATCGGATGAATGCCAGCAGTTT
1 TCAAACTTGTATACAAACAACTCTTCATCTAATGAGGAGATCAATCAGATGAATGCCAGCAGTTC
1825445 AAAA
66 AAAA
* *
1825449 TCAAACTTGTATACAAACAACTCTTCATCTGATGAGGATATCAATCAGATGAATGCCAGCAGTTC
1 TCAAACTTGTATACAAACAACTCTTCATCTAATGAGGAGATCAATCAGATGAATGCCAGCAGTTC
1825514 AAAA
66 AAAA
1825518 TCAAA
1 TCAAA
1825523 AGGCAGAAGC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (69 bp):
TCAAACTTGTATACAAACAACTCTTCATCTAATGAGGAGATCAATCAGATGAATGCCAGCAGTTC
AAAA
Found at i:1830837 original size:3 final size:3
Alignment explanation
Indices: 1830831--1830855 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1830821 GATTTTTTTG
1830831 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
1830856 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1853915 original size:14 final size:14
Alignment explanation
Indices: 1853896--1853922 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1853886 ATTGCTGCCA
1853896 AAATCCCTAAATCT
1 AAATCCCTAAATCT
1853910 AAATCCCTAAATC
1 AAATCCCTAAATC
1853923 CCTAAATCAA
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:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATCCCTAAATCT
Found at i:1853919 original size:8 final size:8
Alignment explanation
Indices: 1853896--1853930 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
1853886 ATTGCTGCCA
1853896 AAATCCCT
1 AAATCCCT
1853904 AAAT--CT
1 AAATCCCT
1853910 AAATCCCT
1 AAATCCCT
1853918 AAATCCCT
1 AAATCCCT
1853926 AAATC
1 AAATC
1853931 AAAACCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
8 19 0.76
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (8 bp):
AAATCCCT
Found at i:1854170 original size:17 final size:17
Alignment explanation
Indices: 1854143--1854184 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1854133 GTGGGGGAAT
1854143 TTTTTTCAAAAAAAAATA
1 TTTTTT-AAAAAAAAATA
* *
1854161 TTTTTTAAAAAATAATT
1 TTTTTTAAAAAAAAATA
1854178 TTTTTTA
1 TTTTTTA
1854185 TTTTTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTTTAAAAAAAAATA
Found at i:1854172 original size:15 final size:15
Alignment explanation
Indices: 1854153--1854181 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1854143 TTTTTTCAAA
1854153 AAAAAAT-ATTTTTT
1 AAAAAATAATTTTTT
1854167 AAAAAATAATTTTTT
1 AAAAAATAATTTTTT
1854182 TTATTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAAATAATTTTTT
Found at i:1854222 original size:19 final size:21
Alignment explanation
Indices: 1854185--1854224 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1854175 ATTTTTTTTA
1854185 TTTTTCAAATAAAAAATAAAC
1 TTTTTCAAATAAAAAATAAAC
*
1854206 TTTTT-AAA-AAAATATAAAC
1 TTTTTCAAATAAAAAATAAAC
1854225 ATGACACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
TTTTTCAAATAAAAAATAAAC
Found at i:1854676 original size:82 final size:84
Alignment explanation
Indices: 1854575--1854739 Score: 275
Period size: 82 Copynumber: 2.0 Consensus size: 84
1854565 TAAAAAATTC
1854575 TTAGCACCTAAAATTAACTTTATATATAATTTAAACACTT-CTTTTACATT-AACCCATAAAAT-
1 TTAGCACCTAAAATTAAC-TTATATATAATTTAAACACTTACTTTTACATTAAACCCATAAAATA
1854637 ATCAT-ATTATTATTACAACT
65 AT-ATAATTATTATTACAACT
1854657 TTAGCACCTAAAATTAACTTATATATAATTTAAACACTTACTTTTACATTAAAACCCATAAAATA
1 TTAGCACCTAAAATTAACTTATATATAATTTAAACACTTACTTTTACATT-AAACCCATAAAATA
1854722 ATATAATTATTATTACAA
65 ATATAATTATTATTACAA
1854740 AATAAAAATA
Statistics
Matches: 78, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
81 21 0.27
82 28 0.36
84 14 0.18
85 15 0.19
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.39
Consensus pattern (84 bp):
TTAGCACCTAAAATTAACTTATATATAATTTAAACACTTACTTTTACATTAAACCCATAAAATAA
TATAATTATTATTACAACT
Found at i:1857470 original size:61 final size:61
Alignment explanation
Indices: 1857401--1857522 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1857391 ACTGAAAAAT
1857401 GGCCAGCTGAGGAATTTCCTTTTGATAATCCAAGCACTCAGAATCAAGCTGCACAGCTAGA
1 GGCCAGCTGAGGAATTTCCTTTTGATAATCCAAGCACTCAGAATCAAGCTGCACAGCTAGA
1857462 GGCCAGCTGAGGAATTTCCTTTTGATAATCCAAGCACTCAGAATCAAGCTGCACAGCTAGA
1 GGCCAGCTGAGGAATTTCCTTTTGATAATCCAAGCACTCAGAATCAAGCTGCACAGCTAGA
1857523 AGATAAAAGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (61 bp):
GGCCAGCTGAGGAATTTCCTTTTGATAATCCAAGCACTCAGAATCAAGCTGCACAGCTAGA
Found at i:1861043 original size:30 final size:31
Alignment explanation
Indices: 1861009--1861083 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1860999 GACTGAATAT
*
1861009 AAATTTTAAAAGTTT-AGAGACT-AAAGTGTA
1 AAATTTTAAAAGTTTAAG-GACTAAAAATGTA
* *
1861039 AAATTGTAAAACTTTAAGGACTAAAAATGTA
1 AAATTTTAAAAGTTTAAGGACTAAAAATGTA
*
1861070 AAATTTCAAAAGTT
1 AAATTTTAAAAGTT
1861084 AAATTTTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 17 0.46
31 20 0.54
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.32
Consensus pattern (31 bp):
AAATTTTAAAAGTTTAAGGACTAAAAATGTA
Found at i:1862619 original size:18 final size:18
Alignment explanation
Indices: 1862593--1862658 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
1862583 TAAATGTTTA
1862593 CAGTTATCAGATGATTTT
1 CAGTTATCAGATGATTTT
* *
1862611 CAGTGATCATATGATTTT
1 CAGTTATCAGATGATTTT
*
1862629 CAGTTATCAGATGATTTA
1 CAGTTATCAGATGATTTT
*
1862647 CAGTTATTAGAT
1 CAGTTATCAGAT
1862659 AATTATAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (18 bp):
CAGTTATCAGATGATTTT
Found at i:1862850 original size:41 final size:41
Alignment explanation
Indices: 1862788--1862868 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
1862778 AAGTGAGTGC
* *
1862788 TTATCAGTTCAGTTTTAGTACATTTGTGTATCAATGTTCAA
1 TTATCAGTTCAGCTTTAGTACATTCGTGTATCAATGTTCAA
* *
1862829 TTATCAGTTCAGCTTTGGTACATTCGTGTATCAGTGTTCA
1 TTATCAGTTCAGCTTTAGTACATTCGTGTATCAATGTTCA
1862869 GCATCGTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.44
Consensus pattern (41 bp):
TTATCAGTTCAGCTTTAGTACATTCGTGTATCAATGTTCAA
Found at i:1862995 original size:3 final size:3
Alignment explanation
Indices: 1862987--1863014 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1862977 ACCTTATATT
1862987 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1863015 AACCCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1866430 original size:30 final size:30
Alignment explanation
Indices: 1866394--1866459 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
1866384 TTAATTGTAC
* * *
1866394 TAAAAAAATTTCAATATAT-AATTACACAAT
1 TAAAAAAAATTAAATAT-TCAATCACACAAT
1866424 TAAAAAAAATTAAATATTCAATCACACAAT
1 TAAAAAAAATTAAATATTCAATCACACAAT
1866454 TAAAAA
1 TAAAAA
1866460 TTATTCTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (30 bp):
TAAAAAAAATTAAATATTCAATCACACAAT
Found at i:1868341 original size:25 final size:25
Alignment explanation
Indices: 1868313--1868400 Score: 151
Period size: 25 Copynumber: 3.5 Consensus size: 25
1868303 TTATTTAATT
1868313 AAGTT-AATGATGTATTATAAAACAA
1 AAGTTCAA-GATGTATTATAAAACAA
1868338 AAGTTCAAGATGTATTATAAAACAA
1 AAGTTCAAGATGTATTATAAAACAA
1868363 AAGTTCAAGATGTATTATAAAACAA
1 AAGTTCAAGATGTATTATAAAACAA
*
1868388 AAGTTCATGATGT
1 AAGTTCAAGATGT
1868401 CTTGCAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
25 59 0.97
26 2 0.03
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.31
Consensus pattern (25 bp):
AAGTTCAAGATGTATTATAAAACAA
Found at i:1868862 original size:19 final size:20
Alignment explanation
Indices: 1868829--1868873 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1868819 ATTCTTTTTT
*
1868829 TAAAAGTTATAAAA-TGTTA
1 TAAAATTTATAAAATTGTTA
* *
1868848 TTAAATTTATCAAATTGTTA
1 TAAAATTTATAAAATTGTTA
1868868 TAAAAT
1 TAAAAT
1868874 AGAGTCATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (20 bp):
TAAAATTTATAAAATTGTTA
Found at i:1868963 original size:32 final size:31
Alignment explanation
Indices: 1868911--1868994 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 31
1868901 TAAATTTTTG
*
1868911 ATAAATTTAATGA-TATTTTTAAAACAATTCG
1 ATAAATTTAATGATTA-TTTTAAAACAATTCA
* * *
1868942 ATAAAATTTAATGATTATTTTATAATAATTTA
1 AT-AAATTTAATGATTATTTTAAAACAATTCA
* *
1868974 ATATATTTAATAATTATTTTA
1 ATAAATTTAATGATTATTTTA
1868995 TAATTTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 19 0.42
32 24 0.53
33 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (31 bp):
ATAAATTTAATGATTATTTTAAAACAATTCA
Found at i:1868986 original size:20 final size:22
Alignment explanation
Indices: 1868942--1868992 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
1868932 AAACAATTCG
*
1868942 ATAA-AATTTAATGATTATTTT
1 ATAATAATTTAATGATTATTTA
1868963 ATAATAATTTAAT-A-TATTTA
1 ATAATAATTTAATGATTATTTA
*
1868983 ATAATTATTT
1 ATAATAATTT
1868993 TATAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 14 0.52
21 5 0.19
22 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATAATAATTTAATGATTATTTA
Found at i:1868990 original size:26 final size:25
Alignment explanation
Indices: 1868964--1869015 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
1868954 GATTATTTTA
*
1868964 TAATAATTTAATATATTTAATAATTATT
1 TAATAATTT--TAAATTTAATAATTA-T
*
1868992 TTATAATTTTAAATTTAATAATTA
1 TAATAATTTTAAATTTAATAATTA
1869016 AAATCACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
28 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATAATTTTAAATTTAATAATTAT
Found at i:1869002 original size:20 final size:19
Alignment explanation
Indices: 1868957--1869003 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1868947 ATTTAATGAT
1868957 TATTTT-ATAATAATTTAA
1 TATTTTAATAATAATTTAA
* *
1868975 TATATTTAATAATTATTTTA
1 TAT-TTTAATAATAATTTAA
1868995 TAATTTTAA
1 T-ATTTTAA
1869004 ATTTAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 16 0.67
21 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTAATAATAATTTAA
Done.