Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold295
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: 1524207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1351011 original size:7 final size:6
Alignment explanation
Indices: 1350944--1351017 Score: 54
Period size: 5 Copynumber: 13.0 Consensus size: 6
1350934 AAAGAAACAT
* *
1350944 ATAA-A ATAATA TATAAAA AT-ATA A-AATA TTAATA ATAATTA ATAATA
1 ATAATA ATAATA -ATAATA ATAATA ATAATA ATAATA ATAA-TA ATAATA
1350991 A-AA-A ATAA-A ATAATA ATTAATA A-AATA
1 ATAATA ATAATA ATAATA A-TAATA ATAATA
1351018 TTGATTAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
4 2 0.04
5 23 0.40
6 15 0.26
7 17 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAATA
Found at i:1351056 original size:9 final size:9
Alignment explanation
Indices: 1351042--1351069 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1351032 TTTTCCATTG
1351042 TATTTTTTA
1 TATTTTTTA
1351051 TATTTTTTA
1 TATTTTTTA
1351060 TATTTTTTA
1 TATTTTTTA
1351069 T
1 T
1351070 TATATTCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TATTTTTTA
Found at i:1355123 original size:83 final size:83
Alignment explanation
Indices: 1355019--1355178 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 83
1355009 AGAAATAGGT
* *
1355019 TTTTTATCTTAGCCTATTTAAACA-ATAAGGATTGTAAA-GCTTATACCTTGTATTTGAAAA-GT
1 TTTTTATCTTAGCCTACTTAAA-AGATAAGGATTGTAAATG-TTATACCTTGTACTT-AAAATGT
*
1355081 AATAATTCAAGTTAAAAAAGG
63 AACAATTCAAGTTAAAAAAGG
*
1355102 TTTTTATCTTAGCCTACTTAAAAGATAAGGATTGTAAATGTTATAGCTTGTACTTAAAATGTAAC
1 TTTTTATCTTAGCCTACTTAAAAGATAAGGATTGTAAATGTTATACCTTGTACTTAAAATGTAAC
1355167 AATTCAAGTTAA
66 AATTCAAGTTAA
1355179 TGGATTATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
82 5 0.07
83 64 0.91
84 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (83 bp):
TTTTTATCTTAGCCTACTTAAAAGATAAGGATTGTAAATGTTATACCTTGTACTTAAAATGTAAC
AATTCAAGTTAAAAAAGG
Found at i:1364863 original size:21 final size:21
Alignment explanation
Indices: 1364837--1364878 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1364827 GCATGGCGAC
1364837 GTGATGATGTTGCTCAACAAG
1 GTGATGATGTTGCTCAACAAG
1364858 GTGATGATGTTGCTCAACAAG
1 GTGATGATGTTGCTCAACAAG
1364879 ACGATGAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (21 bp):
GTGATGATGTTGCTCAACAAG
Found at i:1364884 original size:21 final size:21
Alignment explanation
Indices: 1364839--1364885 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1364829 ATGGCGACGT
**
1364839 GATGATGTTGCTCAACAAGGT
1 GATGATGTTGCTCAACAAGAC
1364860 GATGATGTTGCTCAACAAGAC
1 GATGATGTTGCTCAACAAGAC
1364881 GATGA
1 GATGA
1364886 GCATGAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.26
Consensus pattern (21 bp):
GATGATGTTGCTCAACAAGAC
Found at i:1370903 original size:69 final size:69
Alignment explanation
Indices: 1370792--1370930 Score: 226
Period size: 69 Copynumber: 2.0 Consensus size: 69
1370782 ATCCAAATGC
* *
1370792 AAATGGAGGCATTGCATAGAGAAATTCAAAAGATCAACCAAAACAAAATGAATAATCCTAGGAAG
1 AAATGGAGGCATTACATAGAGAAATTCAAAAGATAAACCAAAACAAAATGAATAATCCTAGGAAG
1370857 ACAT
66 ACAT
* *
1370861 AAATGGAGGCATTACATAGAGAAATTCGAAAA-ATAAACCAAAACAGAATGAATAATCCTAGGTA
1 AAATGGAGGCATTACATAGAGAAATTC-AAAAGATAAACCAAAACAAAATGAATAATCCTAGGAA
1370925 GACAT
65 GACAT
1370930 A
1 A
1370931 TGAGGTAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
69 61 0.94
70 4 0.06
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.18
Consensus pattern (69 bp):
AAATGGAGGCATTACATAGAGAAATTCAAAAGATAAACCAAAACAAAATGAATAATCCTAGGAAG
ACAT
Found at i:1376049 original size:78 final size:78
Alignment explanation
Indices: 1375920--1376067 Score: 197
Period size: 78 Copynumber: 1.9 Consensus size: 78
1375910 TTGCTACACT
* *
1375920 TTCCCAAAGGCTTTAACCTTCCCAAAGGTTCATATAAATTATCTCGCCTTTTCAAATGCTTGAGA
1 TTCCCAAAGACTTTAACCTTCCCAAAGGTTCATATAAATTATCTCGCCTTTTCAAAGGCTTGAGA
1375985 CTATTACTGTGCG
66 CTATTACTGTGCG
* ** ** * * *
1375998 TTCCCAAAGACTTTTACCTTTTCAAAGGTTCATATTGATTATTTCGTCTTTTTAAAGGCTTGAGA
1 TTCCCAAAGACTTTAACCTTCCCAAAGGTTCATATAAATTATCTCGCCTTTTCAAAGGCTTGAGA
*
1376063 TTATT
66 CTATT
1376068 GCTACACCTT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 59 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (78 bp):
TTCCCAAAGACTTTAACCTTCCCAAAGGTTCATATAAATTATCTCGCCTTTTCAAAGGCTTGAGA
CTATTACTGTGCG
Found at i:1382620 original size:19 final size:19
Alignment explanation
Indices: 1382593--1382641 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
1382583 GCTAGTCCAC
*
1382593 AATAGTATTTTTTAATTAA
1 AATAATATTTTTTAATTAA
*
1382612 AATAATA-TTTTTATTTAA
1 AATAATATTTTTTAATTAA
1382630 AATAATATTTTT
1 AATAATATTTTT
1382642 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATAATATTTTTTAATTAA
Found at i:1382640 original size:17 final size:18
Alignment explanation
Indices: 1382601--1382648 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1382591 ACAATAGTAT
*
1382601 TTTTTAATTAAAATAATA
1 TTTTTATTTAAAATAATA
1382619 TTTTTATTTAAAATAATA
1 TTTTTATTTAAAATAATA
1382637 TTTTTATTTAAA
1 TTTTTATTTAAA
1382649 TTTAGTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTATTTAAAATAATA
Found at i:1385080 original size:33 final size:33
Alignment explanation
Indices: 1385043--1385112 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 33
1385033 GCCATTTCGG
*
1385043 ACAATGTATCGATATAAT-T-CTTCATGTATCGAT
1 ACAATGTATCGATACAATGTGC--CATGTATCGAT
1385076 ACAATGTATCGATACAATGTGCCATGTATCGAT
1 ACAATGTATCGATACAATGTGCCATGTATCGAT
1385109 ACAA
1 ACAA
1385113 ACTATGGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 32 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTGCCATGTATCGAT
Found at i:1385084 original size:13 final size:13
Alignment explanation
Indices: 1385066--1385095 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1385056 ATAATTCTTC
1385066 ATGTATCGATACA
1 ATGTATCGATACA
1385079 ATGTATCGATACA
1 ATGTATCGATACA
1385092 ATGT
1 ATGT
1385096 GCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1385184 original size:19 final size:20
Alignment explanation
Indices: 1385141--1385195 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1385131 TTGCCAGTTT
* *
1385141 CATGTATCGATACAATTGTA
1 CATGTATCGATACAATCGAA
1385161 CATGTATCGATACAA-CGAA
1 CATGTATCGATACAATCGAA
1385180 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1385196 GTATCGATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATCGAA
Found at i:1385199 original size:13 final size:13
Alignment explanation
Indices: 1385181--1385207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1385171 TACAACGAAC
1385181 ATGTATCGATACA
1 ATGTATCGATACA
1385194 ATGTATCGATACA
1 ATGTATCGATACA
1385207 A
1 A
1385208 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1392213 original size:15 final size:15
Alignment explanation
Indices: 1392195--1392229 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1392185 CAAGTCAACT
1392195 TCATCATTATCATT-A
1 TCATCATTATC-TTCA
1392210 TCATCATTATCTTCA
1 TCATCATTATCTTCA
1392225 TCATC
1 TCATC
1392230 TTTGAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.46
Consensus pattern (15 bp):
TCATCATTATCTTCA
Found at i:1393121 original size:13 final size:13
Alignment explanation
Indices: 1393103--1393128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1393093 CAATTTTTTG
1393103 TGTATCGATACAT
1 TGTATCGATACAT
1393116 TGTATCGATACAT
1 TGTATCGATACAT
1393129 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1395695 original size:13 final size:13
Alignment explanation
Indices: 1395677--1395715 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1395667 ATAATCACCC
1395677 TGTATCGATACAA
1 TGTATCGATACAA
1395690 TGTATCGATACAA
1 TGTATCGATACAA
1395703 TGTATCGATACAA
1 TGTATCGATACAA
1395716 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1397814 original size:15 final size:15
Alignment explanation
Indices: 1397794--1397824 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1397784 ATTTCGTTTG
*
1397794 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1397809 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1397824 G
1 G
1397825 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1399657 original size:21 final size:21
Alignment explanation
Indices: 1399628--1399672 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1399618 AAGTTTTCAT
*
1399628 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1399648 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1399670 TTT
1 TTT
1399673 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1401908 original size:13 final size:13
Alignment explanation
Indices: 1401890--1401915 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1401880 CAATTTTTTG
1401890 TGTATCGATACAT
1 TGTATCGATACAT
1401903 TGTATCGATACAT
1 TGTATCGATACAT
1401916 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1403894 original size:20 final size:20
Alignment explanation
Indices: 1403861--1403915 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1403851 TTGTCTGTTT
* *
1403861 CATGTATCGGTACAATTGTA
1 CATGTATCGATACAATTGAA
*
1403881 CATTTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1403900 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1403916 ATATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1404699 original size:20 final size:19
Alignment explanation
Indices: 1404662--1404699 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1404652 TGTAAAAAGC
*
1404662 TTGATTATTTTTTTAACAG
1 TTGATTATTTTTTAAACAG
1404681 TTGATTATTTTTTGAAACA
1 TTGATTATTTTTT-AAACA
1404700 ATCTCATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (19 bp):
TTGATTATTTTTTAAACAG
Found at i:1408526 original size:13 final size:13
Alignment explanation
Indices: 1408508--1408534 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1408498 ACAATTTTCT
1408508 TTGTATCGATACA
1 TTGTATCGATACA
1408521 TTGTATCGATACA
1 TTGTATCGATACA
1408534 T
1 T
1408535 GGGTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1410960 original size:13 final size:13
Alignment explanation
Indices: 1410942--1410968 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1410932 ACATTATGCT
1410942 TTGTATCGATACA
1 TTGTATCGATACA
1410955 TTGTATCGATACA
1 TTGTATCGATACA
1410968 T
1 T
1410969 GTTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1410998 original size:20 final size:19
Alignment explanation
Indices: 1410954--1411009 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1410944 GTATCGATAC
***
1410954 ATTGTATCGATACATGTTT
1 ATTGTATCGATACATGACA
1410973 ATTGTATCGATACATGCACA
1 ATTGTATCGATACATG-ACA
*
1410993 ATTGTATTGATACATGA
1 ATTGTATCGATACATGA
1411010 AACTGGCAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.39
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:1413670 original size:18 final size:18
Alignment explanation
Indices: 1413647--1413686 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1413637 AATAAAAATG
1413647 TTATATTCATGATTCATA
1 TTATATTCATGATTCATA
1413665 TTATATTCATGATTCATA
1 TTATATTCATGATTCATA
1413683 TTAT
1 TTAT
1413687 GTATCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATATTCATGATTCATA
Found at i:1414562 original size:19 final size:18
Alignment explanation
Indices: 1414538--1414573 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1414528 TAAAGGCATT
1414538 AAATATGATATTATATTAA
1 AAATATGATATT-TATTAA
*
1414557 AAATATTATATTTATTA
1 AAATATGATATTTATTA
1414574 TTTTTAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATATGATATTTATTAA
Found at i:1419473 original size:5 final size:5
Alignment explanation
Indices: 1419463--1419501 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
1419453 AGTATGTATC
1419463 ATATT ATATT ATATT ATATT A-ATT ATA-T ATATAT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATAT-T ATATT
1419502 TATAAAAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 8 0.26
5 18 0.58
6 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:1419489 original size:19 final size:19
Alignment explanation
Indices: 1419465--1419501 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1419455 TATGTATCAT
1419465 ATTATAT-TATATTATATTA
1 ATTATATATATA-TATATTA
1419484 ATTATATATATATATATT
1 ATTATATATATATATATT
1419502 TATAAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATATATATATATATTA
Found at i:1424007 original size:31 final size:31
Alignment explanation
Indices: 1423966--1424024 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
1423956 GAAATCAAAT
1423966 ACAAAGAGC-TTAGAAAAATAATAACAATATGA
1 ACAAAGAGCTTTAGAAAAAT-ATAA-AATATGA
*
1423998 ACAAA-AGCTTTTGAAAAATATAAAATA
1 ACAAAGAGCTTTAGAAAAATATAAAATA
1424025 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 7 0.28
32 14 0.56
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.22
Consensus pattern (31 bp):
ACAAAGAGCTTTAGAAAAATATAAAATATGA
Found at i:1424321 original size:13 final size:13
Alignment explanation
Indices: 1424303--1424328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1424293 CAATTTTTGG
1424303 TGTATCGATACAT
1 TGTATCGATACAT
1424316 TGTATCGATACAT
1 TGTATCGATACAT
1424329 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1424340 original size:32 final size:33
Alignment explanation
Indices: 1424283--1424346 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1424273 TACAAGCCAA
**
1424283 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1424316 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1424347 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1424353 original size:19 final size:18
Alignment explanation
Indices: 1424283--1424353 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
1424273 TACAAGCCAA
1424283 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
1424303 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
1424316 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1424335 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1424354 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1426885 original size:13 final size:13
Alignment explanation
Indices: 1426867--1426930 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
1426857 ATAATCCCCC
1426867 TGTATCGATACAG
1 TGTATCGATACAG
*
1426880 TGTATCGATACAT
1 TGTATCGATACAG
1426893 TGTATCGATACAG
1 TGTATCGATACAG
*
1426906 TGTATCGATACAT
1 TGTATCGATACAG
1426919 TGTATCGATACA
1 TGTATCGATACA
1426931 AAGAAAAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1426896 original size:26 final size:26
Alignment explanation
Indices: 1426867--1426930 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
1426857 ATAATCCCCC
1426867 TGTATCGATACAGTGTATCGATACAT
1 TGTATCGATACAGTGTATCGATACAT
1426893 TGTATCGATACAGTGTATCGATACAT
1 TGTATCGATACAGTGTATCGATACAT
1426919 TGTATCGATACA
1 TGTATCGATACA
1426931 AAGAAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (26 bp):
TGTATCGATACAGTGTATCGATACAT
Found at i:1429033 original size:15 final size:15
Alignment explanation
Indices: 1429013--1429044 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1429003 ATTTCGTTTG
*
1429013 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1429028 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1429043 GA
1 GA
1429045 ACACTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1430890 original size:21 final size:21
Alignment explanation
Indices: 1430845--1430892 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1430835 CAAGTTTTTA
*
1430845 TTTTTC-TTAGCTAACTCATT
1 TTTTTCATTAGCCAACTCATT
*
1430865 ATTTTCATTAGCCAACTTC-TT
1 TTTTTCATTAGCCAAC-TCATT
1430886 TTTTTCA
1 TTTTTCA
1430893 ACTTGCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 16 0.70
22 2 0.09
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTTTCATTAGCCAACTCATT
Found at i:1433154 original size:32 final size:33
Alignment explanation
Indices: 1433097--1433161 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1433087 TACAAGCCAA
** *
1433097 TGTATCGATACAATTTTTGGTGTATCTATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1433130 TGTATCGATAC-ATACTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1433162 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1435391 original size:2 final size:2
Alignment explanation
Indices: 1435386--1435416 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1435376 ATATCATTAT
1435386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1435417 TTCTAAGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1437969 original size:20 final size:20
Alignment explanation
Indices: 1437943--1437996 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1437933 AACCCTGAAA
1437943 AGTATCGATACACATTTAAAT
1 AGTATCGATACACA-TTAAAT
* **
1437964 -GTATCGATACAGATTGCAT
1 AGTATCGATACACATTAAAT
1437983 AGTATCGATACACA
1 AGTATCGATACACA
1437997 CAATATGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
AGTATCGATACACATTAAAT
Found at i:1438120 original size:53 final size:53
Alignment explanation
Indices: 1437984--1438120 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1437974 AGATTGCATA
* *
1437984 GTATCGATACACACAATATGTATCAATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACATGACATTGGCAGTAGCCAAATTT
*
1438037 GTATCGATACACACAATATGTATCGATACATGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACATGACATTGGCAGTAGCCAAATTT
1438090 GTATCGATACACACAATATGTATCGATACAT
1 GTATCGATACACACAATATGTATCGATACAT
1438121 TGGAAGTAGC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 81 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACATGACATTGGCAGTAGCCAAATTT
Found at i:1438775 original size:34 final size:35
Alignment explanation
Indices: 1438712--1438778 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1438702 CTAAGTGATT
1438712 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1438748 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1438779 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1439493 original size:6 final size:6
Alignment explanation
Indices: 1439478--1439515 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1439468 AATAAAATAA
*
1439478 AAAATCT AAAATT -AAATG AAAATT AAAATT AAAATT AA
1 AAAAT-T AAAATT AAAATT AAAATT AAAATT AAAATT AA
1439516 TAATCATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 4 0.14
6 19 0.68
7 5 0.18
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:1441154 original size:32 final size:32
Alignment explanation
Indices: 1441108--1441171 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1441098 GGCAGAACTT
1441108 AAGTCGAAAAAAGGTTGGCCAGGATGAAACCA
1 AAGTCGAAAAAAGGTTGGCCAGGATGAAACCA
* ***
1441140 AAGTGGAAAAAAGGTTGGTTGGGATGAAACCA
1 AAGTCGAAAAAAGGTTGGCCAGGATGAAACCA
1441172 TATAAACCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.16
Consensus pattern (32 bp):
AAGTCGAAAAAAGGTTGGCCAGGATGAAACCA
Found at i:1444027 original size:26 final size:23
Alignment explanation
Indices: 1443997--1444051 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 23
1443987 TGTATAATAA
1443997 ATAAATTTAAATATTATATAAAATT
1 ATAAATTTAAATATT-T-TAAAATT
1444022 ATTAAATTTAAATATTTTAAAATT
1 A-TAAATTTAAATATTTTAAAATT
1444046 ATAAAT
1 ATAAAT
1444052 ATCTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 2 0.07
26 14 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAAATTTAAATATTTTAAAATT
Found at i:1444621 original size:20 final size:20
Alignment explanation
Indices: 1444592--1444645 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1444582 TACCCAGATC
*
1444592 TATCGATACATTTTTCAATG
1 TATCGATACATTCTTCAATG
*
1444612 TATGGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
1444632 TATCGATACATTCT
1 TATCGATACATTCT
1444646 GTCTTTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:1448344 original size:26 final size:26
Alignment explanation
Indices: 1448285--1448347 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
1448275 ATAAATAACA
1448285 TAAAAT-ATACTT-AAAAATTTATATT
1 TAAAATAATA-TTCAAAAATTTATATT
*
1448310 TAAATTAATATTCAAAAA-TTATATT
1 TAAAATAATATTCAAAAATTTATATT
1448335 TCAAAATAATATT
1 T-AAAATAATATT
1448348 GATATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 15 0.45
26 18 0.55
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAAATAATATTCAAAAATTTATATT
Found at i:1448445 original size:13 final size:13
Alignment explanation
Indices: 1448427--1448451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1448417 TTATATTTAT
1448427 TATATTTAAAATA
1 TATATTTAAAATA
1448440 TATATTTAAAAT
1 TATATTTAAAAT
1448452 TATCCCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATTTAAAATA
Found at i:1448970 original size:22 final size:22
Alignment explanation
Indices: 1448945--1449021 Score: 55
Period size: 25 Copynumber: 3.2 Consensus size: 22
1448935 GATAAAATAT
1448945 ATAATAAATATTTTAAGAAAAG
1 ATAATAAATATTTTAAGAAAAG
* ** * *
1448967 ATAATTTCAATTATTGAAAAATATATAT
1 ATAA--T-AAATATTTTAAGA-A-A-AG
1448995 ATAATAAATATTTTAAGAAAAG
1 ATAATAAATATTTTAAGAAAAG
1449017 ATAAT
1 ATAAT
1449022 TTCAATTATT
Statistics
Matches: 39, Mismatches: 10, Indels: 12
0.64 0.16 0.20
Matches are distributed among these distances:
22 10 0.26
23 1 0.03
24 2 0.05
25 18 0.46
26 2 0.05
27 1 0.03
28 5 0.13
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (22 bp):
ATAATAAATATTTTAAGAAAAG
Found at i:1449000 original size:50 final size:50
Alignment explanation
Indices: 1448941--1449037 Score: 194
Period size: 50 Copynumber: 1.9 Consensus size: 50
1448931 ATAAGATAAA
1448941 ATATATAATAAATATTTTAAGAAAAGATAATTTCAATTATTGAAAAATAT
1 ATATATAATAAATATTTTAAGAAAAGATAATTTCAATTATTGAAAAATAT
1448991 ATATATAATAAATATTTTAAGAAAAGATAATTTCAATTATTGAAAAA
1 ATATATAATAAATATTTTAAGAAAAGATAATTTCAATTATTGAAAAA
1449038 AAAATCATCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (50 bp):
ATATATAATAAATATTTTAAGAAAAGATAATTTCAATTATTGAAAAATAT
Found at i:1449037 original size:22 final size:22
Alignment explanation
Indices: 1448962--1449037 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
1448952 ATATTTTAAG
1448962 AAAAGATAATTTCAATTATTGA
1 AAAAGATAATTTCAATTATTGA
* * * *
1448984 AAAATATATATATAATAAATATTTTAA
1 AAAAGATA-AT-T--TCAAT-TATTGA
1449011 GAAAAGATAATTTCAATTATTGA
1 -AAAAGATAATTTCAATTATTGA
1449034 AAAA
1 AAAA
1449038 AAAATCATCC
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
22 11 0.28
23 6 0.15
24 5 0.12
26 5 0.12
27 6 0.15
28 7 0.17
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAAGATAATTTCAATTATTGA
Found at i:1452117 original size:14 final size:14
Alignment explanation
Indices: 1452065--1452117 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
1452055 ATTTTATATT
*
1452065 TAATAATATTTAAA
1 TAATAATATTAAAA
*
1452079 TAAAAATATTAAAAA
1 TAATAATATT-AAAA
*
1452094 TTATAATATTAAAA
1 TAATAATATTAAAA
*
1452108 TAATATTATT
1 TAATAATATT
1452118 TTATATTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATAATATTAAAA
Found at i:1452129 original size:29 final size:29
Alignment explanation
Indices: 1452045--1452132 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
1452035 TGATATGTTA
1452045 TAAAA-AAAAA-ATTTTATATTTAATAATAT
1 TAAAATAAAAATATTTTATATTT--TAATAT
* ** * *
1452074 TTAAATAAAAATATTAAAAATTATAATAT
1 TAAAATAAAAATATTTTATATTTTAATAT
* *
1452103 TAAAATAATATTATTTTATATTTTAATAT
1 TAAAATAAAAATATTTTATATTTTAATAT
1452132 T
1 T
1452133 TTTAATTATT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
29 33 0.73
30 5 0.11
31 7 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAAATAAAAATATTTTATATTTTAATAT
Found at i:1452442 original size:3 final size:3
Alignment explanation
Indices: 1452436--1452474 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1452426 TAAAAAAAAT
1452436 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1452475 CTCGAAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1453308 original size:16 final size:16
Alignment explanation
Indices: 1453289--1453335 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
1453279 AATTGTGTTA
1453289 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
*
1453305 ATTTTAAATATAAATT
1 ATTTTAAATTTAAATT
1453321 ATTTT-AATTTAAATT
1 ATTTTAAATTTAAATT
1453336 TTAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 9 0.31
16 20 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:1453333 original size:21 final size:20
Alignment explanation
Indices: 1453307--1453362 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 20
1453297 TTTAAATTAT
1453307 TTTAAATATAAATTATTTTAA
1 TTTAAAT-TAAATTATTTTAA
*
1453328 TTTAAATTTTAATTATTTTAA
1 TTTAAA-TTAAATTATTTTAA
1453349 TTTAAATTAAATTA
1 TTTAAATTAAATTA
1453363 AATTTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 7 0.22
21 24 0.75
22 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAATTAAATTATTTTAA
Found at i:1453345 original size:15 final size:16
Alignment explanation
Indices: 1453286--1453424 Score: 64
Period size: 15 Copynumber: 8.8 Consensus size: 16
1453276 AAAAATTGTG
1453286 TTAATTTTAAATTTAAA
1 TTAA-TTTAAATTTAAA
* *
1453303 TTATTTTAAATATAAA
1 TTAATTTAAATTTAAA
*
1453319 TT-ATTTTAATTTAAA
1 TTAATTTAAATTTAAA
*
1453334 TTTTAATTATTTTAATTTAAA
1 --TT-A--ATTTAAATTTAAA
*
1453355 TTAAATTAAATTT--A
1 TTAATTTAAATTTAAA
*
1453369 TTAATTTTAAAATT-AA
1 TTAA-TTTAAATTTAAA
1453385 -TAGA-TTAAATTTAAA
1 TTA-ATTTAAATTTAAA
*
1453400 -TAA-TT-CATTT-AA
1 TTAATTTAAATTTAAA
*
1453412 TTAAATTAAATTT
1 TTAATTTAAATTT
1453425 TATTAAAATT
Statistics
Matches: 97, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
12 2 0.02
13 7 0.07
14 17 0.18
15 27 0.28
16 23 0.24
17 5 0.05
18 1 0.01
19 2 0.02
21 13 0.13
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.53
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:1453368 original size:21 final size:20
Alignment explanation
Indices: 1453292--1453423 Score: 76
Period size: 21 Copynumber: 6.3 Consensus size: 20
1453282 TGTGTTAATT
* *
1453292 TTAAATTTAAATTATTTTAAA
1 TTAAA-TTAATTTAATTTAAA
*
1453313 TATAAATTATTTTAATTTAAA
1 T-TAAATTAATTTAATTTAAA
* *
1453334 TTTTAATTATTTTAATTTAAA
1 -TTAAATTAATTTAATTTAAA
1453355 TTAAATTAAATTTATTAATTTTAAAA
1 TTAAATT-AA--T-TTAA-TTT-AAA
*
1453381 TT-AA-TAGATTAAATTTAAA
1 TTAAATTA-ATTTAATTTAAA
*
1453400 -T-AATTCATTTAA-TTAAA
1 TTAAATTAATTTAATTTAAA
1453417 TTAAATT
1 TTAAATT
1453424 TTATTAAAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
17 5 0.06
18 9 0.10
19 8 0.09
20 9 0.10
21 35 0.39
22 6 0.07
23 2 0.02
24 6 0.07
25 5 0.06
26 5 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
TTAAATTAATTTAATTTAAA
Found at i:1455285 original size:20 final size:20
Alignment explanation
Indices: 1455248--1455286 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1455238 AAGATGGATA
* *
1455248 AATTAAATATTTATATAATT
1 AATTAAATATCTAAATAATT
*
1455268 AATTTAATATCTAAATAAT
1 AATTAAATATCTAAATAAT
1455287 CTTGTTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTAAATATCTAAATAATT
Found at i:1456544 original size:14 final size:14
Alignment explanation
Indices: 1456525--1456579 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1456515 GCAGTTATTC
1456525 TGGCACATGTACTT
1 TGGCACATGTACTT
**
1456539 TGGCACAAATACCTT
1 TGGCACATGTA-CTT
* * *
1456554 TGGTATAGGTACTT
1 TGGCACATGTACTT
1456568 TGGCACATGTAC
1 TGGCACATGTAC
1456580 CTTCAACACA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (14 bp):
TGGCACATGTACTT
Found at i:1456692 original size:88 final size:88
Alignment explanation
Indices: 1456526--1456693 Score: 205
Period size: 88 Copynumber: 1.9 Consensus size: 88
1456516 CAGTTATTCT
* * * *
1456526 GGCACATGTACTTTGGCACAAATACCTTTGGTATAGGTACTTTGGCACATGTACCTTCAACACAG
1 GGCACATGTACTTTGGCACAAATACCTTTAGTATAGGTACATTGGCACATATACCTTCAAAACAG
* * *
1456591 GTATTTTGGCATAGGGTACCTTC
66 ATACTTTGACATAGGGTACCTTC
** * *
1456614 GGCACATGTACTTTCGTTACAAGTA-CTTTAGTATAGGTATCATTGGCACATATA-CTTTAAAAC
1 GGCACATGTACTTT-GGCACAAATACCTTTAGTATAGGTA-CATTGGCACATATACCTTCAAAAC
1456677 AGATACTTTGACATAGG
64 AGATACTTTGACATAGG
1456694 TATCTCCGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
88 48 0.72
89 19 0.28
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (88 bp):
GGCACATGTACTTTGGCACAAATACCTTTAGTATAGGTACATTGGCACATATACCTTCAAAACAG
ATACTTTGACATAGGGTACCTTC
Found at i:1457594 original size:25 final size:25
Alignment explanation
Indices: 1457560--1457609 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1457550 AAGATGATGA
1457560 AAGCCAACGAAGAGAGAATAAAAAT
1 AAGCCAACGAAGAGAGAATAAAAAT
1457585 AAGCCAACGAAGAGAGAATAAAAAT
1 AAGCCAACGAAGAGAGAATAAAAAT
1457610 GCTTGAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.20, T:0.08
Consensus pattern (25 bp):
AAGCCAACGAAGAGAGAATAAAAAT
Found at i:1461293 original size:48 final size:48
Alignment explanation
Indices: 1461241--1461376 Score: 184
Period size: 48 Copynumber: 2.8 Consensus size: 48
1461231 AGTAAATAAT
* * * *
1461241 CCAAAGGTTGTTCCAGGAGTTGTGCCAAAGGATGTT-TCAGGAGTTATG
1 CCAAAGGTTGTTCCAGAAGTCGTGCCAAAAGATGTTCT-AGGACTTATG
*
1461289 CCAAAGGTTGTTCTAGAAGTCGTGCCAAAAGATGTTCTAGGACTTATG
1 CCAAAGGTTGTTCCAGAAGTCGTGCCAAAAGATGTTCTAGGACTTATG
* * *
1461337 CCAAAGGTTGTTCTAGAAGTCATGCTAAAAGATGTTCTAG
1 CCAAAGGTTGTTCCAGAAGTCGTGCCAAAAGATGTTCTAG
1461377 CAGTTGTGCT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 79 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (48 bp):
CCAAAGGTTGTTCCAGAAGTCGTGCCAAAAGATGTTCTAGGACTTATG
Found at i:1461325 original size:72 final size:72
Alignment explanation
Indices: 1461249--1461405 Score: 172
Period size: 72 Copynumber: 2.2 Consensus size: 72
1461239 ATCCAAAGGT
* * * * *
1461249 TGTTCCAGGAGTTGTGCCAAAGGATGTT-TCAGGAGTTATGCCAAAGGTTGTTCTAGAAGTCGTG
1 TGTTCCAGGAGTTATGCCAAAGGATGTTCT-AGAAGTCATGCCAAAAGATGTTCTAGAAGTCGTG
1461313 CCAAAAGA
65 CCAAAAGA
* * * * * *
1461321 TGTTCTAGGACTTATGCCAAAGGTTGTTCTAGAAGTCATGCTAAAAGATGTTCTAGCAGTTGTGC
1 TGTTCCAGGAGTTATGCCAAAGGATGTTCTAGAAGTCATGCCAAAAGATGTTCTAGAAGTCGTGC
* *
1461386 TAAATGA
66 CAAAAGA
*
1461393 TGTGCCAGGAGTT
1 TGTTCCAGGAGTT
1461406 TTGCTGAAAG
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
72 67 0.99
73 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (72 bp):
TGTTCCAGGAGTTATGCCAAAGGATGTTCTAGAAGTCATGCCAAAAGATGTTCTAGAAGTCGTGC
CAAAAGA
Found at i:1461350 original size:24 final size:24
Alignment explanation
Indices: 1461241--1461381 Score: 131
Period size: 24 Copynumber: 5.9 Consensus size: 24
1461231 AGTAAATAAT
* *
1461241 CCAAAGGTTGTTCCAGGAGTTGTG
1 CCAAAGGTTGTTCTAGGAGTTATG
*
1461265 CCAAAGGATGTT-TCAGGAGTTATG
1 CCAAAGGTTGTTCT-AGGAGTTATG
* **
1461289 CCAAAGGTTGTTCTAGAAGTCGTG
1 CCAAAGGTTGTTCTAGGAGTTATG
* * *
1461313 CCAAAAGATGTTCTAGGACTTATG
1 CCAAAGGTTGTTCTAGGAGTTATG
* *
1461337 CCAAAGGTTGTTCTAGAAGTCATG
1 CCAAAGGTTGTTCTAGGAGTTATG
* * * *
1461361 CTAAAAGATGTTCTAGCAGTT
1 CCAAAGGTTGTTCTAGGAGTT
1461382 GTGCTAAATG
Statistics
Matches: 92, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
24 91 0.99
25 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (24 bp):
CCAAAGGTTGTTCTAGGAGTTATG
Found at i:1461405 original size:24 final size:24
Alignment explanation
Indices: 1461359--1461415 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
1461349 CTAGAAGTCA
* *
1461359 TGCTAAAAGATGTTCTAGCAGTTG
1 TGCTAAAAGATGTGCCAGCAGTTG
* * *
1461383 TGCTAAATGATGTGCCAGGAGTTT
1 TGCTAAAAGATGTGCCAGCAGTTG
*
1461407 TGCTGAAAG
1 TGCTAAAAG
1461416 TACTAGGAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (24 bp):
TGCTAAAAGATGTGCCAGCAGTTG
Found at i:1464305 original size:32 final size:33
Alignment explanation
Indices: 1464235--1464306 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
1464225 TTGCAAATAG
* *
1464235 ACAAGTAGTATCTACTAGGTACTACTAGCATCT
1 ACAAGTAGCATCTACTAGGTACTACTAGCATAT
* * *
1464268 ACAAGTAGCA-CTACTATGTACTAGTTGCATAT
1 ACAAGTAGCATCTACTAGGTACTACTAGCATAT
*
1464300 GCAAGTA
1 ACAAGTA
1464307 ATACCTACTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 24 0.73
33 9 0.27
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (33 bp):
ACAAGTAGCATCTACTAGGTACTACTAGCATAT
Found at i:1465180 original size:21 final size:20
Alignment explanation
Indices: 1465156--1465208 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1465146 TTCTACAAAT
1465156 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAA-AGTAAA
* *
1465177 TGTATCGATACATAAGTGAA
1 TGTATCGATACAAAAGTAAA
1465197 TGTATCGATACA
1 TGTATCGATACA
1465209 TGTTTGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:1465221 original size:21 final size:21
Alignment explanation
Indices: 1465156--1465226 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
1465146 TTCTACAAAT
*
1465156 TGTATCGATACAAATAGT-AAA
1 TGTATCGATACATA-AGTGAAA
1465177 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAGTGAAA
***
1465197 TGTATCGATACATGTTTGAAA
1 TGTATCGATACATAAGTGAAA
1465218 TGTATCGAT
1 TGTATCGAT
1465227 GCAAAACCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.45
21 24 0.55
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:1469252 original size:29 final size:29
Alignment explanation
Indices: 1469219--1469281 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1469209 TGATACTTCA
* *
1469219 GCACATATA-CTTCGGCGTAGGTACCTTTG
1 GCACATATACCTTCGACATAGGTA-CTTTG
* *
1469248 GCACATGTACCTTTGACATAGGTACTTTG
1 GCACATATACCTTCGACATAGGTACTTTG
1469277 GCACA
1 GCACA
1469282 AGTATTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (29 bp):
GCACATATACCTTCGACATAGGTACTTTG
Found at i:1469259 original size:15 final size:15
Alignment explanation
Indices: 1469239--1469297 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
1469229 TTCGGCGTAG
*
1469239 GTACCTTTGGCACAT
1 GTACCTTTGGCACAA
* * *
1469254 GTACCTTTGACATAG
1 GTACCTTTGGCACAA
1469269 GTA-CTTTGGCACAA
1 GTACCTTTGGCACAA
**
1469283 GTATTTTTGGCACAA
1 GTACCTTTGGCACAA
1469298 ATATTTTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 11 0.31
15 25 0.69
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (15 bp):
GTACCTTTGGCACAA
Found at i:1469302 original size:15 final size:15
Alignment explanation
Indices: 1469273--1469306 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1469263 ACATAGGTAC
*
1469273 TTTGGCACAAGTATT
1 TTTGGCACAAATATT
1469288 TTTGGCACAAATATT
1 TTTGGCACAAATATT
1469303 TTTG
1 TTTG
1469307 ACATATGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (15 bp):
TTTGGCACAAATATT
Found at i:1469413 original size:29 final size:29
Alignment explanation
Indices: 1469381--1469436 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1469371 ATAACCTTAG
1469381 CATAAGTACTTT-AACACAAGTACCTTTGA
1 CATAAGTA-TTTCAACACAAGTACCTTTGA
* * *
1469410 CATAGGTATTTCAGCATAAGTACCTTT
1 CATAAGTATTTCAACACAAGTACCTTT
1469437 AAGCAGTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (29 bp):
CATAAGTATTTCAACACAAGTACCTTTGA
Found at i:1482278 original size:3 final size:3
Alignment explanation
Indices: 1482270--1482309 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1482260 CGAGTCAACT
*
1482270 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1482310 TGATGGTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:1484009 original size:33 final size:32
Alignment explanation
Indices: 1483949--1484010 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1483939 CATTTCAAGG
1483949 TGTATCGATACAATGAACATGTATCGATAGAA
1 TGTATCGATACAATGAACATGTATCGATAGAA
*
1483981 TGTATCGATACTAA-GCAATATGTATCGATA
1 TGTATCGATAC-AATG-AACATGTATCGATA
1484011 CATCTGCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAATGAACATGTATCGATAGAA
Found at i:1488138 original size:20 final size:21
Alignment explanation
Indices: 1488111--1488167 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
1488101 TCAAAAACCT
1488111 AGAATGTATTGATACAATG-A
1 AGAATGTATTGATACAATGCA
* ** *
1488131 ATAATGTATCAATACATTGCA
1 AGAATGTATTGATACAATGCA
*
1488152 AGCATGTATTGATACA
1 AGAATGTATTGATACA
1488168 TTCATACATG
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (21 bp):
AGAATGTATTGATACAATGCA
Found at i:1488273 original size:20 final size:21
Alignment explanation
Indices: 1488248--1488298 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
1488238 TGCAAGCATT
*
1488248 TATCGATACATTCACTTA-TG
1 TATCGATACATTAACTTATTG
1488268 TATCGATACATTAACTTATTG
1 TATCGATACATTAACTTATTG
*
1488289 TATCAATACA
1 TATCGATACA
1488299 AATTATAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (21 bp):
TATCGATACATTAACTTATTG
Found at i:1491969 original size:44 final size:44
Alignment explanation
Indices: 1491906--1491995 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
1491896 TGTGAAAGAT
1491906 AGAGATGGCCAAGGTGACAAGATGAAGAAAACTGGGAAGTCTTC
1 AGAGATGGCCAAGGTGACAAGATGAAGAAAACTGGGAAGTCTTC
1491950 AGAGATGGCCAAGGTGACAAGATGAAGAAAACTGGGAAGTCTTC
1 AGAGATGGCCAAGGTGACAAGATGAAGAAAACTGGGAAGTCTTC
1491994 AG
1 AG
1491996 TTTTAATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.39, C:0.13, G:0.32, T:0.16
Consensus pattern (44 bp):
AGAGATGGCCAAGGTGACAAGATGAAGAAAACTGGGAAGTCTTC
Found at i:1496869 original size:11 final size:11
Alignment explanation
Indices: 1496833--1496872 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1496823 CTATTTTTTG
1496833 CTTTTTTCTTT
1 CTTTTTTCTTT
*
1496844 CATTTTTTATTT
1 C-TTTTTTCTTT
*
1496856 CTTTTTTCTCT
1 CTTTTTTCTTT
1496867 CTTTTT
1 CTTTTT
1496873 ATTTTTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:1496871 original size:21 final size:22
Alignment explanation
Indices: 1496833--1496881 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
1496823 CTATTTTTTG
*
1496833 CTTTTTTCTTTCATTTTTTATTT
1 CTTTTTTCTCTCA-TTTTTATTT
1496856 CTTTTTTCTCTC-TTTTTATTT
1 CTTTTTTCTCTCATTTTTATTT
1496877 -TTTTT
1 CTTTTT
1496882 CAACATCACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
23 11 0.44
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (22 bp):
CTTTTTTCTCTCATTTTTATTT
Found at i:1497024 original size:2 final size:2
Alignment explanation
Indices: 1497017--1497052 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1497007 AATCAAAATA
1497017 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
1497053 CAATCAGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1500162 original size:13 final size:13
Alignment explanation
Indices: 1500144--1500169 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1500134 TACACCAAGT
1500144 ATGTATCGATACA
1 ATGTATCGATACA
1500157 ATGTATCGATACA
1 ATGTATCGATACA
1500170 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1500167 original size:32 final size:33
Alignment explanation
Indices: 1500126--1500189 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1500116 TAGCCAAACT
**
1500126 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1500158 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1500190 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1505216 original size:13 final size:13
Alignment explanation
Indices: 1505198--1505223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1505188 TACACCAAGT
1505198 ATGTATCGATACA
1 ATGTATCGATACA
1505211 ATGTATCGATACA
1 ATGTATCGATACA
1505224 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1505221 original size:32 final size:33
Alignment explanation
Indices: 1505180--1505243 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1505170 TAGCCAAACT
**
1505180 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1505212 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1505244 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1508848 original size:42 final size:42
Alignment explanation
Indices: 1508793--1508911 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1508783 TTCTTCTCTC
* *
1508793 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
**
1508835 CTCCTCCTATCATCCCTCCTAACTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1508877 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1508912 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.09, C:0.46, G:0.03, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1508853 original size:24 final size:24
Alignment explanation
Indices: 1508817--1508902 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
1508807 CCTCCTCTCT
* *
1508817 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
** *
1508841 CTATCATCCCTCC--TAACT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1508862 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1508883 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1508903 TCTTTCTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 4 0.09
20 4 0.09
21 14 0.30
22 4 0.09
24 21 0.45
ACGTcount: A:0.12, C:0.45, G:0.02, T:0.41
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1508886 original size:21 final size:21
Alignment explanation
Indices: 1508821--1508887 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1508811 CTCTCTCTAT
1508821 TATCTCTCCTGTCTCTCCTCC
1 TATCTCTCCTGTCTCTCCTCC
* *
1508842 TATCATC-CCT-CCTAACT-CTAC
1 TATC-TCTCCTGTCT--CTCCTCC
1508863 TATCTCTCCTGTCTCTCCTCC
1 TATCTCTCCTGTCTCTCCTCC
1508884 TATC
1 TATC
1508888 ATCCCTCCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
20 6 0.17
21 24 0.67
22 6 0.17
ACGTcount: A:0.12, C:0.45, G:0.03, T:0.40
Consensus pattern (21 bp):
TATCTCTCCTGTCTCTCCTCC
Found at i:1511271 original size:13 final size:13
Alignment explanation
Indices: 1511253--1511278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1511243 CAATTTTTTG
1511253 TGTATCGATACAT
1 TGTATCGATACAT
1511266 TGTATCGATACAT
1 TGTATCGATACAT
1511279 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1511290 original size:32 final size:33
Alignment explanation
Indices: 1511230--1511296 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
1511220 CGTTACAAGC
**
1511230 CATTGTATCGATACAATTTTTTGTGTATCGATA
1 CATTGTATCGATACAATACTTTGTGTATCGATA
1511263 CATTGTATCGATAC-ATACTTTGTGTATCGATA
1 CATTGTATCGATACAATACTTTGTGTATCGATA
1511295 CA
1 CA
1511297 AGTTTGGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
CATTGTATCGATACAATACTTTGTGTATCGATA
Found at i:1513866 original size:13 final size:13
Alignment explanation
Indices: 1513848--1513877 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1513838 ATCCCCCTGT
1513848 TCGATACAGTGTA
1 TCGATACAGTGTA
*
1513861 TCGATACATTGTA
1 TCGATACAGTGTA
1513874 TCGA
1 TCGA
1513878 AACAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (13 bp):
TCGATACAGTGTA
Found at i:1517824 original size:21 final size:22
Alignment explanation
Indices: 1517798--1517845 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
1517788 TATGCAAGTT
*
1517798 TTATTTTTC-TTAGCTAACTCA
1 TTATTTTTCATTAGCCAACTCA
1517819 TTA-TTTTCATTAGCCAACTCA
1 TTATTTTTCATTAGCCAACTCA
1517840 TTATTT
1 TTATTT
1517846 CAACTTGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 17 0.71
22 2 0.08
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (22 bp):
TTATTTTTCATTAGCCAACTCA
Found at i:1519376 original size:19 final size:19
Alignment explanation
Indices: 1519352--1519390 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1519342 TCCCGTGTGA
*
1519352 ATGTATCGATACATTTTTG
1 ATGTATCGATACATATTTG
1519371 ATGTATCGATACATATTTG
1 ATGTATCGATACATATTTG
1519390 A
1 A
1519391 AAATATAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (19 bp):
ATGTATCGATACATATTTG
Found at i:1519467 original size:18 final size:19
Alignment explanation
Indices: 1519441--1519478 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1519431 TTGTGTATCG
1519441 ATACATTGT-AATCGATAC
1 ATACATTGTGAATCGATAC
* *
1519459 ATACTTTGTGTATCGATAC
1 ATACATTGTGAATCGATAC
1519478 A
1 A
1519479 AGTTTGGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
ATACATTGTGAATCGATAC
Found at i:1519467 original size:33 final size:33
Alignment explanation
Indices: 1519411--1519478 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1519401 CGTTACAAGC
**
1519411 CATTGTATCGATACAATTTTTTGTGTATCGATA
1 CATTGTATCGATACAATACTTTGTGTATCGATA
1519444 CATTGTAATCGATAC-ATACTTTGTGTATCGATA
1 CATTGT-ATCGATACAATACTTTGTGTATCGATA
1519477 CA
1 CA
1519479 AGTTTGGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (33 bp):
CATTGTATCGATACAATACTTTGTGTATCGATA
Done.