Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008166.1 Hibiscus syriacus cultivar Beakdansim tig00110747_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: 2544747
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1589946 original size:17 final size:17
Alignment explanation
Indices: 1589889--1589939 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
1589879 AATAAAGTTG
*
1589889 GTTCCTTAATTAAACTA
1 GTTCATTAATTAAACTA
*
1589906 GTTCATTCATTAAACTA
1 GTTCATTAATTAAACTA
1589923 GTTCATTAATTAAACTA
1 GTTCATTAATTAAACTA
1589940 ACTCATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (17 bp):
GTTCATTAATTAAACTA
Found at i:1598304 original size:25 final size:25
Alignment explanation
Indices: 1598276--1598324 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1598266 GAAAGGGTGA
1598276 AGGGGCAA-AGCCCCTTGCAGGGTCT
1 AGGGG-AAGAGCCCCTTGCAGGGTCT
*
1598301 AGGGGAAGAGCCCCTTGTAGGGTC
1 AGGGGAAGAGCCCCTTGCAGGGTC
1598325 AGCAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.20, C:0.24, G:0.39, T:0.16
Consensus pattern (25 bp):
AGGGGAAGAGCCCCTTGCAGGGTCT
Found at i:1598393 original size:23 final size:23
Alignment explanation
Indices: 1598362--1598414 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1598352 AACCCAAAGT
* *
1598362 TTTTCTATGGAAAAAAATAATTA
1 TTTTATATGGAAAAAAATAATGA
* *
1598385 TTTTATATGGAAAAACATCATGA
1 TTTTATATGGAAAAAAATAATGA
1598408 TTTTATA
1 TTTTATA
1598415 ATATTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (23 bp):
TTTTATATGGAAAAAAATAATGA
Found at i:1604475 original size:33 final size:33
Alignment explanation
Indices: 1604433--1604499 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1604423 CATAGTACAG
1604433 ATGGTGGACACGACCCTATGTGTCATACGGATT
1 ATGGTGGACACGACCCTATGTGTCATACGGATT
*
1604466 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCCTATGTGTCATACGGATT
1604499 A
1 A
1604500 GCACTACGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (33 bp):
ATGGTGGACACGACCCTATGTGTCATACGGATT
Found at i:1604641 original size:44 final size:44
Alignment explanation
Indices: 1604587--1604728 Score: 212
Period size: 44 Copynumber: 3.2 Consensus size: 44
1604577 GTTATGAAAT
* *
1604587 AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTACGGATA
1 AATGGTAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGATA
*
1604631 AATGGTAAGTGTATTGGTAAAATAAGCTTATGAGCTTATGGATA
1 AATGGTAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGATA
* **
1604675 AATGGTAAGTGTATTGGTAAAATAATCGCACGAGCTTATGGTATTA
1 AATGGTAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGG-A-TA
1604721 AATGGTAA
1 AATGGTAA
1604729 AATATTGCAC
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
44 78 0.88
45 1 0.01
46 10 0.11
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.31
Consensus pattern (44 bp):
AATGGTAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGATA
Found at i:1616726 original size:21 final size:21
Alignment explanation
Indices: 1616702--1616741 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1616692 ATGTTTAATG
1616702 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
1616723 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
1616742 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:1619569 original size:21 final size:22
Alignment explanation
Indices: 1619543--1619597 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
1619533 AGTGGAATAT
*
1619543 GCATGGATGTACTGCAAGAG-A
1 GCATGGATGCACTGCAAGAGTA
*
1619564 GCATGGATGCACTGCAGGAGTA
1 GCATGGATGCACTGCAAGAGTA
1619586 -CATGGATGCACT
1 GCATGGATGCACT
1619598 TTGACACCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.33, T:0.20
Consensus pattern (22 bp):
GCATGGATGCACTGCAAGAGTA
Found at i:1619910 original size:192 final size:197
Alignment explanation
Indices: 1619574--1619966 Score: 681
Period size: 192 Copynumber: 2.0 Consensus size: 197
1619564 GCATGGATGC
1619574 ACTGCAGGAGTACATGGATGCACTTTGACACCCTTTAGCATTTTTGCTCAAATATTAATTTAATG
1 ACTGCAGGAGTACATGGATGCACTTTGACACCCTTTAGCATTTTTGCTCAAATATTAA-TTAATG
*
1619639 GACTTTGAATTATTTTTGAAACCTTTTTAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACAT
65 GAC-TT-AATTA-TATTGAAACCTTTTTAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACAT
1619704 TTTTCCTTAAATTTGTTATATCGAAACATAATTCAACATTTTGCTTAAAAGCTTGGTCAACGGTG
127 TTTTCCTTAAATTTGTTATATCGAAACATAATTCAACATTTTGCTTAAAAGCTTGGTCAACGGTG
1619769 AAGCAA
192 AAGCAA
1619775 ACTGCAGGAGTACATGGATGCACTTTGACACCCTTTAGCATTTTTGCTCAAATATTTAA-TAAT-
1 ACTGCAGGAGTACATGGATGCACTTTGACACCCTTTAGCATTTTTGCTCAAATA-TTAATTAATG
*
1619838 GA-TT-CTTA-ATTGAAA-CTTTTTAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACATTTT
65 GACTTAATTATATTGAAACCTTTTTAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACATTTT
1619899 TCCTTAAATTTGTTATATCGAAACATAATTCAACATTTTGCTTAAAAGCTTGGTCAACGGTGAAG
130 TCCTTAAATTTGTTATATCGAAACATAATTCAACATTTTGCTTAAAAGCTTGGTCAACGGTGAAG
1619964 CAA
195 CAA
1619967 TCATCGATAA
Statistics
Matches: 189, Mismatches: 2, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
192 114 0.60
193 6 0.03
195 3 0.02
197 2 0.01
199 2 0.01
200 4 0.02
201 54 0.29
202 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (197 bp):
ACTGCAGGAGTACATGGATGCACTTTGACACCCTTTAGCATTTTTGCTCAAATATTAATTAATGG
ACTTAATTATATTGAAACCTTTTTAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACATTTTT
CCTTAAATTTGTTATATCGAAACATAATTCAACATTTTGCTTAAAAGCTTGGTCAACGGTGAAGC
AA
Found at i:1621439 original size:24 final size:24
Alignment explanation
Indices: 1621399--1621444 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1621389 AATCCCGAAT
* *
1621399 ATTTAATTTCAATTAATTAAATAG
1 ATTTAATTTCAAATAATAAAATAG
*
1621423 ATTTAATTTGAAATAATAAAAT
1 ATTTAATTTCAAATAATAAAAT
1621445 CCCCAATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTTAATTTCAAATAATAAAATAG
Found at i:1624869 original size:39 final size:39
Alignment explanation
Indices: 1624821--1624930 Score: 134
Period size: 38 Copynumber: 2.8 Consensus size: 39
1624811 TATTCGAGTT
* * *
1624821 GCACCAAAGTGCTTGCGCGTAAGGTTGCGTCCAACATTG
1 GCACGAAAGTGCTTACGCATAAGGTTGCGTCCAACATTG
* * * *
1624860 GCACGAAAGTGCTTATGTACAAGGTT-CGTCCACCATTG
1 GCACGAAAGTGCTTACGCATAAGGTTGCGTCCAACATTG
1624898 GCACCG-AAGTGCTTACGCATAAGGTTGCGTCCA
1 GCA-CGAAAGTGCTTACGCATAAGGTTGCGTCCA
1624931 CCATATGCAC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 31 0.53
39 28 0.47
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (39 bp):
GCACGAAAGTGCTTACGCATAAGGTTGCGTCCAACATTG
Found at i:1629368 original size:13 final size:13
Alignment explanation
Indices: 1629346--1629379 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1629336 TGGTACCATT
1629346 TATT-CTTGCTAG
1 TATTGCTTGCTAG
1629358 TATTGCTTGCTAG
1 TATTGCTTGCTAG
1629371 TATTGCTTG
1 TATTGCTTG
1629380 AAATCAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.50
Consensus pattern (13 bp):
TATTGCTTGCTAG
Found at i:1630761 original size:67 final size:63
Alignment explanation
Indices: 1630682--1630823 Score: 148
Period size: 61 Copynumber: 2.3 Consensus size: 63
1630672 TAGGTTTATT
* * *
1630682 TTAGCACT--AGTGTATAAGGACACTAAGTGCATGTGGTGAACACGACCTTATGTGTCATATTCA
1 TTAGCACTAGAGTGTATAA--AC-CT-AGTGCAGGTGGTGAACACGACCTTATGAGTCATATCCA
1630745 GA
62 GA
* ** *
1630747 TTAGCACTAGAGTG--TAAACCTAGTGTAGGTGGTGGGCACGACCTTATGAGTCATATCCGGA
1 TTAGCACTAGAGTGTATAAACCTAGTGCAGGTGGTGAACACGACCTTATGAGTCATATCCAGA
*
1630808 TTAACACTAGAGTGTA
1 TTAGCACTAGAGTGTA
1630824 AGCTTAGTGT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
61 46 0.71
62 2 0.03
63 2 0.03
65 11 0.17
67 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (63 bp):
TTAGCACTAGAGTGTATAAACCTAGTGCAGGTGGTGAACACGACCTTATGAGTCATATCCAGA
Found at i:1630787 original size:61 final size:61
Alignment explanation
Indices: 1630722--1630837 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
1630712 ATGTGGTGAA
* * *
1630722 CACGACCTTATGTGTCATATTCAGATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGG
1 CACGACCTTATGAGTCATATCCAGATTAACACTAGAGTGTAAACCTAGTGTAGGTGGTGGG
* * *
1630783 CACGACCTTATGAGTCATATCCGGATTAACACTAGAGTGTAAGCTTAGTGTAGGT
1 CACGACCTTATGAGTCATATCCAGATTAACACTAGAGTGTAAACCTAGTGTAGGT
1630838 TTAGCACTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (61 bp):
CACGACCTTATGAGTCATATCCAGATTAACACTAGAGTGTAAACCTAGTGTAGGTGGTGGG
Found at i:1631319 original size:3 final size:3
Alignment explanation
Indices: 1631313--1631344 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1631303 CATCATCATC
1631313 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1631345 AGTATTAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1631393 original size:11 final size:13
Alignment explanation
Indices: 1631365--1631396 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1631355 TAAAGGAATT
1631365 TATATTATTTTAA
1 TATATTATTTTAA
1631378 TATATT-TTTTAA
1 TATATTATTTTAA
1631390 -ATATTAT
1 TATATTAT
1631397 GCGCCAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 7 0.39
13 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATTATTTTAA
Found at i:1642647 original size:10 final size:10
Alignment explanation
Indices: 1642629--1642664 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1642619 ATGCAACAAA
1642629 AAAACAAAAT
1 AAAACAAAAT
*
1642639 AAAATAAAAT
1 AAAACAAAAT
*
1642649 AAAACAAACT
1 AAAACAAAAT
1642659 AAAACA
1 AAAACA
1642665 CGAAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAACAAAAT
Found at i:1671839 original size:39 final size:39
Alignment explanation
Indices: 1671785--1671879 Score: 145
Period size: 39 Copynumber: 2.4 Consensus size: 39
1671775 GGGTATTAAA
* *
1671785 CTGCGGTAAGGACTTACCCTGAGCAGAAAGTAGAGGAGC
1 CTGCGGTAAGGACTTACCATGAGCACAAAGTAGAGGAGC
*
1671824 CTGCGATAAGGACTTACCATGAGCACAAAGTAGAGGAGC
1 CTGCGGTAAGGACTTACCATGAGCACAAAGTAGAGGAGC
* *
1671863 ATGCGGTAAGGTCTTAC
1 CTGCGGTAAGGACTTAC
1671880 TAGTCATAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.18
Consensus pattern (39 bp):
CTGCGGTAAGGACTTACCATGAGCACAAAGTAGAGGAGC
Found at i:1678963 original size:13 final size:13
Alignment explanation
Indices: 1678945--1678973 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1678935 AAGTATCGCC
1678945 TTGGAAGAAAGTA
1 TTGGAAGAAAGTA
1678958 TTGGAAGAAAGTA
1 TTGGAAGAAAGTA
1678971 TTG
1 TTG
1678974 AGATTTGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (13 bp):
TTGGAAGAAAGTA
Found at i:1680325 original size:20 final size:21
Alignment explanation
Indices: 1680279--1680331 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1680269 TACTAAAACG
*
1680279 AGTATCGGTACCATAGTATAGA
1 AGTATCGATACCATAG-ATAGA
1680301 AGTATCGATACCATAG-TAGA
1 AGTATCGATACCATAGATAGA
* *
1680321 GGTATCAATAC
1 AGTATCGATAC
1680332 TGTTGAGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.46
22 15 0.54
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (21 bp):
AGTATCGATACCATAGATAGA
Found at i:1681035 original size:112 final size:110
Alignment explanation
Indices: 1680840--1681071 Score: 329
Period size: 112 Copynumber: 2.1 Consensus size: 110
1680830 GTTATAGGTG
* * * * * *
1680840 CATTTTGACATACTTTGTGTGTGATGTTTCGATCGATTTTGTTTAATGCATAACGGTGCATTTTC
1 CATTTTGACATACTTCGTGTATGAAGTTTCGAACGATTTTGCTTAATGCATAACCGTGCATTTTC
* *
1680905 AGCATAAAAGTTTCCACCCAAGGTATTCATAATGAGGTGAATTAC
66 AGCATAAAAGGTGCCACCCAAGGTATTCATAATGAGGTGAATTAC
*
1680950 CATTTTGACATACTTCGTGTATGAAAGTTATCGAACGATTTTGCTTAATGCTTAACCGTGCATTT
1 CATTTTGACATACTTCGTGTATG-AAGTT-TCGAACGATTTTGCTTAATGCATAACCGTGCATTT
* * *
1681015 TCGGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTCC
64 TCAGCATAAAAGGTGCCACCCAAGGTATTCATAATGAGGTGAATTAC
*
1681062 CATTTCGACA
1 CATTTTGACA
1681072 CTTCGGTGCA
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
110 21 0.20
111 4 0.04
112 82 0.77
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (110 bp):
CATTTTGACATACTTCGTGTATGAAGTTTCGAACGATTTTGCTTAATGCATAACCGTGCATTTTC
AGCATAAAAGGTGCCACCCAAGGTATTCATAATGAGGTGAATTAC
Found at i:1685061 original size:59 final size:59
Alignment explanation
Indices: 1684995--1685108 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
1684985 AGTATGACTT
* ** * *
1684995 ATAAGGTCGTGTCCACCATATGTACTAGGTATGCTTAAGTACAGTCCTGAATATGACAC
1 ATAAGGTCGTGCCCACCATATACACTAGGTATACTTAAGTACAATCCTGAATATGACAC
* * * *
1685054 ATAAGGTCGTGCCCACCTTATACACTAGTTATACTTTAGTGCAATCCTGAATATG
1 ATAAGGTCGTGCCCACCATATACACTAGGTATACTTAAGTACAATCCTGAATATG
1685109 CAACCTGCTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (59 bp):
ATAAGGTCGTGCCCACCATATACACTAGGTATACTTAAGTACAATCCTGAATATGACAC
Found at i:1686715 original size:35 final size:35
Alignment explanation
Indices: 1686669--1686747 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
1686659 ATAAAACTTA
* *
1686669 TCATCTTTTGAAAAGTGAAACATTATCAAATTATT
1 TCATCTTTTGAAAAGTCAAACATGATCAAATTATT
*
1686704 TCATCTTTTGAAAAGTCAAATATGATCAAATTATT
1 TCATCTTTTGAAAAGTCAAACATGATCAAATTATT
1686739 TCATCTTTT
1 TCATCTTTT
1686748 CCAATTTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.43
Consensus pattern (35 bp):
TCATCTTTTGAAAAGTCAAACATGATCAAATTATT
Found at i:1687760 original size:13 final size:14
Alignment explanation
Indices: 1687725--1687765 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
1687715 TTCGGTATCC
*
1687725 TCATTTCCTTGTCT
1 TCATTACCTTGTCT
1687739 TCATTACCTTGTCT
1 TCATTACCTTGTCT
1687753 TC-TTACCTTGTCT
1 TCATTACCTTGTCT
1687766 CCTTCCATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.10, C:0.29, G:0.07, T:0.54
Consensus pattern (14 bp):
TCATTACCTTGTCT
Found at i:1694580 original size:15 final size:16
Alignment explanation
Indices: 1694553--1694597 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1694543 TTTAACCACT
1694553 AATTATTTAAAATATTG
1 AATTATTT-AAATATTG
1694570 -ATTATTTAAATA-TG
1 AATTATTTAAATATTG
*
1694584 AATTATATAAATAT
1 AATTATTTAAATAT
1694598 AAGTTGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 16 0.64
16 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTATTTAAATATTG
Found at i:1698196 original size:11 final size:11
Alignment explanation
Indices: 1698180--1698212 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1698170 ACAATTACTC
1698180 CATATTATATG
1 CATATTATATG
1698191 CATATTATATTG
1 CATATTATA-TG
1698203 CATA-TATATG
1 CATATTATATG
1698213 AACACCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 13 0.62
12 6 0.29
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (11 bp):
CATATTATATG
Found at i:1698343 original size:25 final size:25
Alignment explanation
Indices: 1698307--1698356 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1698297 CAAATAGAGA
* *
1698307 CTCAACTGCTAAAGTTTCCCTAAGG
1 CTCAACTACTAAAGCTTCCCTAAGG
1698332 CTCAACTACTAAAGCTTCCCTAAGG
1 CTCAACTACTAAAGCTTCCCTAAGG
1698357 TTCACTGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (25 bp):
CTCAACTACTAAAGCTTCCCTAAGG
Found at i:1698926 original size:26 final size:25
Alignment explanation
Indices: 1698897--1698949 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
1698887 TTTAAGGGGT
*
1698897 TATTCGATATTTTAAACAAATAAAAA
1 TATTCGAAATTTTAAA-AAATAAAAA
** *
1698923 TATTTTAAATTTTTAAAAATAAAAA
1 TATTCGAAATTTTAAAAAATAAAAA
1698948 TA
1 TA
1698950 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
TATTCGAAATTTTAAAAAATAAAAA
Found at i:1698953 original size:12 final size:13
Alignment explanation
Indices: 1698936--1698997 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
1698926 TTTAAATTTT
1698936 TAAAAATAAAA-A
1 TAAAAATAAAATA
1698948 TAAAAATAAAAATA
1 TAAAAAT-AAAATA
*
1698962 TAAAAATAAAATT
1 TAAAAATAAAATA
* *
1698975 TAAATTATTAAAAAA
1 TAAA--AATAAAATA
1698990 TAAAAATA
1 TAAAAATA
1698998 TATTATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
12 7 0.17
13 16 0.39
14 8 0.20
15 10 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAATAAAATA
Found at i:1698973 original size:5 final size:6
Alignment explanation
Indices: 1698936--1698972 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
1698926 TTTAAATTTT
1698936 TAAAAA TAAAAA TAAAAA TAAAAATA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA T-AAAA-A TAAAAA TAAAA
1698973 TTTAAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 19 0.66
7 8 0.28
8 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:1699002 original size:21 final size:22
Alignment explanation
Indices: 1698943--1699005 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
1698933 TTTTAAAAAT
*
1698943 AAAAATAAAA-ATAAA--AATA
1 AAAAATAAAATATAAATTATTA
*
1698962 TAAAAATAAAATTTAAATTATTA
1 -AAAAATAAAATATAAATTATTA
*
1698985 AAAAATAAAA-ATATATTATTA
1 AAAAATAAAATATAAATTATTA
1699006 TTTTTTACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.28
21 13 0.36
22 10 0.28
23 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATAAAATATAAATTATTA
Found at i:1703833 original size:13 final size:13
Alignment explanation
Indices: 1703815--1703839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1703805 AATTAAAATT
1703815 AAATATATATATC
1 AAATATATATATC
1703828 AAATATATATAT
1 AAATATATATAT
1703840 ATTAACTTTA
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATATATATC
Found at i:1704828 original size:3 final size:3
Alignment explanation
Indices: 1704820--1704892 Score: 53
Period size: 3 Copynumber: 24.7 Consensus size: 3
1704810 ATTATATATG
* * *
1704820 TTA TTA TTA TCA -TA TTA TTA TTA TTA TTAA TTA CATG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA
* * *
1704866 -TA TAA ATA -TA TTA TTA ATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1704893 TAATTGTAGC
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
2 5 0.09
3 45 0.83
4 4 0.07
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1704860 original size:23 final size:23
Alignment explanation
Indices: 1704820--1704892 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1704810 ATTATATATG
1704820 TTATTATTATCATATTATTATTA
1 TTATTATTATCATATTATTATTA
*
1704843 TTATTAATTA-CATGTTATTATTA
1 TTATT-ATTATCATATTATTATTA
* *
1704866 -TA-TA-AAT-ATATTATTAATA
1 TTATTATTATCATATTATTATTA
1704885 TTATTATT
1 TTATTATT
1704893 TAATTGTAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
19 11 0.28
20 3 0.08
21 3 0.08
22 2 0.05
23 17 0.43
24 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (23 bp):
TTATTATTATCATATTATTATTA
Found at i:1706210 original size:90 final size:89
Alignment explanation
Indices: 1706096--1706272 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
1706086 TAATCCCAAA
* * * *
1706096 TATTTAATTTTAATTAATTAAATATAGACTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
1 TATTAAATTCTAATTAATTAAATATAGACTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
1706161 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
*
1706186 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
1 TATTAAATTCTAATTAATTAAATATAGACTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
1706251 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
1706273 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 33 0.41
90 48 0.59
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTCTAATTAATTAAATATAGACTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:1715495 original size:22 final size:22
Alignment explanation
Indices: 1715470--1715526 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1715460 TTTTTTAAGG
1715470 ATGATAGATTATCTTTTAAAAA
1 ATGATAGATTATCTTTTAAAAA
* * *
1715492 ATGATAGATTTTCTTTTCAAAG
1 ATGATAGATTATCTTTTAAAAA
* *
1715514 ACGAAAGATTATC
1 ATGATAGATTATC
1715527 AGATTTCTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (22 bp):
ATGATAGATTATCTTTTAAAAA
Found at i:1716683 original size:3 final size:3
Alignment explanation
Indices: 1716675--1716750 Score: 57
Period size: 3 Copynumber: 25.0 Consensus size: 3
1716665 ATTATACATG
* * *
1716675 TTA TTA TTA TCA -TA TTA TTA TTA TTA TTAA TTA CATG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA
* * *
1716721 TTA -TA TATA TTA TTA ATA ATG TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
1716751 AATAATATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
2 3 0.05
3 48 0.83
4 7 0.12
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1716700 original size:20 final size:20
Alignment explanation
Indices: 1716675--1716735 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 20
1716665 ATTATACATG
1716675 TTATTATTATCATATTATTA
1 TTATTATTATCATATTATTA
*
1716695 TTATTATTAATTACATGTTATTA
1 TTATTATT-A-T-CATATTATTA
1716718 TTATTA-TAT-ATATTATTA
1 TTATTATTATCATATTATTA
1716736 ATAATGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 8 0.22
20 9 0.25
21 2 0.06
22 2 0.06
23 15 0.42
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (20 bp):
TTATTATTATCATATTATTA
Found at i:1716701 original size:23 final size:23
Alignment explanation
Indices: 1716675--1716724 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1716665 ATTATACATG
1716675 TTATT-ATTATCATATTATTATTA
1 TTATTAATTA-CATATTATTATTA
*
1716698 TTATTAATTACATGTTATTATTA
1 TTATTAATTACATATTATTATTA
1716721 TTAT
1 TTAT
1716725 ATATATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (23 bp):
TTATTAATTACATATTATTATTA
Found at i:1718601 original size:20 final size:20
Alignment explanation
Indices: 1718565--1718603 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1718555 AGATATGGAT
*
1718565 TCCATTGGTTGTGCAATGGC
1 TCCATTGGTTGTACAATGGC
1718585 TCCATT-GTTGTCACAATGG
1 TCCATTGGTTGT-ACAATGG
1718604 ATTTCTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TCCATTGGTTGTACAATGGC
Found at i:1719643 original size:3 final size:3
Alignment explanation
Indices: 1719628--1719699 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
1719618 CCATTTGTTT
* *
1719628 TTA TTA ATA TTA TTA TTA TTA GTA TTA TT- TTA TTTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA
1719674 TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1719700 AATAAATAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.84
4 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1724543 original size:15 final size:15
Alignment explanation
Indices: 1724523--1724554 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1724513 GATCAATACC
*
1724523 TTTTGCTTACATTCA
1 TTTTGCATACATTCA
1724538 TTTTGCATACATTCA
1 TTTTGCATACATTCA
1724553 TT
1 TT
1724555 ATTCATTGCA
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:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:1731883 original size:8 final size:9
Alignment explanation
Indices: 1731868--1731907 Score: 62
Period size: 9 Copynumber: 4.2 Consensus size: 9
1731858 TGCTTGAAGA
1731868 GAAAAAAAT
1 GAAAAAAAT
1731877 GAAAAAAAT
1 GAAAAAAAT
1731886 GAAAAACAAAT
1 G-AAAA-AAAT
1731897 GAAAAAAAT
1 GAAAAAAAT
1731906 GA
1 GA
1731908 TGAACAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 16 0.55
10 8 0.28
11 5 0.17
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:1731896 original size:11 final size:10
Alignment explanation
Indices: 1731869--1731904 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
1731859 GCTTGAAGAG
1731869 AAAAAAATG-
1 AAAAAAATGA
1731878 AAAAAAATGA
1 AAAAAAATGA
1731888 AAAACAAATGA
1 AAAA-AAATGA
1731899 AAAAAA
1 AAAAAA
1731905 TGATGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.36
10 6 0.24
11 10 0.40
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:1731916 original size:20 final size:20
Alignment explanation
Indices: 1731869--1731907 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1731859 GCTTGAAGAG
1731869 AAAA-AAATGAAAAAAATGA
1 AAAACAAATGAAAAAAATGA
1731888 AAAACAAATGAAAAAAATGA
1 AAAACAAATGAAAAAAATGA
1731908 TGAACAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAACAAATGAAAAAAATGA
Found at i:1733693 original size:113 final size:113
Alignment explanation
Indices: 1733495--1734573 Score: 1820
Period size: 113 Copynumber: 9.5 Consensus size: 113
1733485 ATTTCTAGAA
* *
1733495 AAGTTCATAATGAGAAGAACTCATTTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1733560 TAACCTTTTTCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
66 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
* *
1733608 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGAT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1733673 TAACCTTTTGCTTGAATTCATCACACGATGGATCAACTTTTCCAGAGG
66 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
*
1733721 AAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
1733786 TAACCTTTTGCTTGAATTCATAACTAGATGGATCAACTTTTCTAGAGG
66 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
1733834 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1733899 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
66 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
*
1733947 AAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1734012 TAACCTTTTTCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
66 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
* * * *
1734060 AAGTTCATAATTAGAAGAACTTATCTGAAGAAGGAAGAAGAAGGTCATAATAAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
1734125 TAACCTTTTGCTTGAATTCATCACTCGATTGATCAACATTTCCAGAGG
66 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
* * ** * *
1734173 AAGTTTATAATGAGAAGAACTCATCTAAAGAATAAATAAGAAGTTCATAATGAGAAGAACTTGTG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
1734238 TAATCTTTTGCTTGAATTCGTCACTCGATGGATCAACTTTTCCAGAGG
66 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
* * *
1734286 AAGTTCATAATGAGAATAACACATCTGAAGAAGGAACAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1734351 TAACCATTTT-CTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
66 TAACC-TTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
1734399 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
1734464 TAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCTAGAGG
66 TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
* * *
1734512 AAGCTCATAATGAGAAGAACTCATCT-ATAGAATGAAGAAGAATTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTCATCTGA-AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1734574 ATCTGAAGAA
Statistics
Matches: 904, Mismatches: 59, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
112 5 0.01
113 895 0.99
114 4 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
TAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
Found at i:1734589 original size:153 final size:153
Alignment explanation
Indices: 1734398--1734726 Score: 561
Period size: 153 Copynumber: 2.2 Consensus size: 153
1734388 TTTTCCAGAG
*
1734398 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
*
1734463 TTAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCTAGAGGAAGCTCATAATGAGAA
66 TTAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCCAGAGGAAGCTCATAATGAGAA
*
1734528 GAACTCATCT-ATAGAATGAAGAA
131 GAACTCATCTGA-AGAAGGAAGAA
* *
1734551 GAATTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
1734616 TTAACCTTTTGCTTGTATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAA
66 TTAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCCAGAGGAAGCTCATAATGAGAA
1734681 GAACTCATCTGAAGAAGGAAGAA
131 GAACTCATCTGAAGAAGGAAGAA
*
1734704 GAAGTTCAAAATGAGAAGAACTT
1 GAAGTTCATAATGAGAAGAACTT
1734727 GTTTAACCTT
Statistics
Matches: 165, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
153 164 0.99
154 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (153 bp):
GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TTAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCCAGAGGAAGCTCATAATGAGAA
GAACTCATCTGAAGAAGGAAGAA
Found at i:1734613 original size:40 final size:40
Alignment explanation
Indices: 1734511--1734613 Score: 163
Period size: 40 Copynumber: 2.6 Consensus size: 40
1734501 TTTTCTAGAG
* *
1734511 GAAGCTCATAATGAGAAGAACTCATCTATAGAATGAAGAA
1 GAAGTTCATAATGAGAAGAACTTATCTATAGAATGAAGAA
*
1734551 GAATTTCATAATGAGAAGAACTTATCTGA-AGAATGAAGAA
1 GAAGTTCATAATGAGAAGAACTTATCT-ATAGAATGAAGAA
1734591 GAAGTTCATAATGAGAAGAACTT
1 GAAGTTCATAATGAGAAGAACTT
1734614 GTTTAACCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 57 0.98
41 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (40 bp):
GAAGTTCATAATGAGAAGAACTTATCTATAGAATGAAGAA
Found at i:1734683 original size:113 final size:113
Alignment explanation
Indices: 1734555--1735419 Score: 1303
Period size: 113 Copynumber: 7.6 Consensus size: 113
1734545 GAAGAAGAAT
* *
1734555 TTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
*
1734620 CCTTTTGCTTGTATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
66 CCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
*
1734668 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTTTAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
*
1734733 CCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCTAGAGGAAG
66 CCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
* * *
1734781 TTCATAATGAGATGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATATA-TTGTTTA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA-ACTTGTTTA
* *
1734845 ACCTTTTGGTTGAATTCATCACTCGATGGATCAACTTTTCCAAAGGAAG
65 ACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
* *
1734894 TTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAGTGAGAAGAACTTGTTTAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
1734959 CCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
66 CCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
1735007 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
*
1735072 CCTTTTGCTTGAATTCATCACTCAATGGATCAACTTTTCCAGAGGAAG
66 CCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
* *
1735120 TTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCTTAATGAGAAGAACTTGTTTAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
* * *
1735185 CCTTTTGCTTGAATTCATCACTCGATGAATCAACTTTTCCAAAAGAAG
66 CCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
*
1735233 TTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
* *** *
1735297 CC-TTTGTTTG-ATTCTATCAGAGAAGGAGATAGATCAACATCAACATTTCCAGA-GATA-
66 CCTTTTGCTTGAATTC-ATC-----ACTCGATGGATCAAC-T-----TTTCCAGAGGA-AG
* * * *
1735354 TTCTTAATGAGAAGAACTCATCTAAAGAAGG-AGAAGAAGTTCATAATGAGAAGAAATTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
1735418 CC
66 CC
1735420 ATAGTTTGAT
Statistics
Matches: 695, Mismatches: 41, Indels: 24
0.91 0.05 0.03
Matches are distributed among these distances:
110 4 0.01
111 10 0.01
112 37 0.05
113 560 0.81
114 1 0.00
116 10 0.01
117 1 0.00
121 61 0.09
122 11 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
CCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAG
Found at i:1734951 original size:266 final size:263
Alignment explanation
Indices: 1734285--1734833 Score: 668
Period size: 266 Copynumber: 2.1 Consensus size: 263
1734275 TTTTCCAGAG
* ** * * * *
1734285 GAAGTTCATAATGAGAATAACACATCTGAAGAAGGAACAAGAAGTTCATAATGAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTTATCTGAACAATGAAGAAGAAGTTCATAATGAGAACAACTTGT
**** * * * * *** *
1734350 TTAACCATTTTCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAA
66 TT-ACC--TAAAGTGAATTCATCAATAGAAGAATCAACTAAACAAGAGGAAGTTCATAATGAGAA
*
1734415 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAA
128 GAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTTTAACCTTTTGCTTGAA
*
1734480 TTCATCACTCGATGGATAAACTTTTCTAGAGGAAGCTCATAATGAGAAGAACTCATCTATAGAAT
193 TTCATCACTCGATGGATAAACTTTTCTAGAGGAAGCTCATAATGAGAAGAACTCATCTATAGAAG
1734545 GAAGAA
258 GAAGAA
* * *
1734551 GAATTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTTATCTGAACAATGAAGAAGAAGTTCATAATGAGAACAACTTGT
*** * * * * * *** *
1734616 TTAACCTTTTGCTTGTATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAA
66 TT-ACCTAAAG--TGAATTCATCAATAGAAGAATCAACTAAACAAGAGGAAGTTCATAATGAGAA
1734681 GAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTTTAACCTTTTGCTTGAA
128 GAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTTTAACCTTTTGCTTGAA
* * * *
1734746 TTCATCACTCGATGGATCAACTTTTCTAGAGGAAGTTCATAATGAGATGAACTTATCTGA-AGAA
193 TTCATCACTCGATGGATAAACTTTTCTAGAGGAAGCTCATAATGAGAAGAACTCATCT-ATAGAA
1734810 GGAAGAA
257 GGAAGAA
1734817 GAAGTTCATAATGAGAA
1 GAAGTTCATAATGAGAA
1734834 TATATTGTTT
Statistics
Matches: 264, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
264 3 0.01
266 260 0.98
267 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (263 bp):
GAAGTTCATAATGAGAAGAACTTATCTGAACAATGAAGAAGAAGTTCATAATGAGAACAACTTGT
TTACCTAAAGTGAATTCATCAATAGAAGAATCAACTAAACAAGAGGAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTC
ATCACTCGATGGATAAACTTTTCTAGAGGAAGCTCATAATGAGAAGAACTCATCTATAGAAGGAA
GAA
Found at i:1734983 original size:605 final size:605
Alignment explanation
Indices: 1733946--1735178 Score: 2085
Period size: 605 Copynumber: 2.0 Consensus size: 605
1733936 TTTTCCAGAG
* *
1733946 GAAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* *
1734011 TTAACCTTTTTCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATTAGAA
66 TTAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAA
* *
1734076 GAACTTATCTGAAGAAGGAAGAAGAAGGTCATAATAAGAAGAACTTGTTTAACCTTTTGCTTGAA
131 GAACTCATCTGAAGAAGGAAGAAGAAGGTCAAAATAAGAAGAACTTGTTTAACCTTTTGCTTGAA
* * *
1734141 TTCATCACTCGATTGATCAACATTTCCAGAGGAAGTTTATAATGAGAAGAACTCATCTAAAGAAT
196 TTCATCACTCGATGGATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAAG
* * *
1734206 AAATAAGAAGTTCATAATGAGAAGAACTTGTGTAATCTTTTGCTTGAATTCGTCACTCGATGGAT
261 AAAGAAGAAGTTCATAATGAGAAGAACTTGTGTAACCTTTTGCTTGAATTCATCACTCGATGGAT
* * *
1734271 CAACTTTTCCAGAGGAAGTTCATAATGAGAATAACACATCTGAAGAAGGAACAAGAAGTTCATAA
326 CAACTTTTCCAAAGGAAGTTCATAATGAGAAGAACACATCTAAAGAAGGAACAAGAAGTTCATAA
1734336 TGAGAAGAACTTGTTTAACCATTTTCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAA
391 TGAGAAGAACTTGTTTAACCATTTTCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAA
1734401 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
456 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
* *
1734466 ACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCTAGAGGAAGCTCATAATGAGAAGAA
521 ACCTTTTGCTTGAATTCATCACTCAATGGATAAACTTTTCCAGAGGAAGCTCATAATGAGAAGAA
1734531 CTCATCT-ATAGAATGAAGAA
586 CTCATCTGA-AGAATGAAGAA
* *
1734551 GAATTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
*
1734616 TTAACCTTTTGCTTGTATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAA
66 TTAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAA
* *
1734681 GAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTTTAACCTTTTGCTTGAA
131 GAACTCATCTGAAGAAGGAAGAAGAAGGTCAAAATAAGAAGAACTTGTTTAACCTTTTGCTTGAA
* * * * *
1734746 TTCATCACTCGATGGATCAACTTTTCTAGAGGAAGTTCATAATGAGATGAACTTATCTGAAGAAG
196 TTCATCACTCGATGGATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAAG
* * * *
1734811 GAAGAAGAAGTTCATAATGAGAATATA-TTGTTTAACCTTTTGGTTGAATTCATCACTCGATGGA
261 AAAGAAGAAGTTCATAATGAGAAGA-ACTTGTGTAACCTTTTGCTTGAATTCATCACTCGATGGA
* *
1734875 TCAACTTTTCCAAAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATA
325 TCAACTTTTCCAAAGGAAGTTCATAATGAGAAGAACACATCTAAAGAAGGAACAAGAAGTTCATA
*
1734940 GTGAGAAGAACTTGTTTAACC-TTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
390 ATGAGAAGAACTTGTTTAACCATTTT-CTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGG
1735004 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
454 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
1735069 TAACCTTTTGCTTGAATTCATCACTCAATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAG
519 TAACCTTTTGCTTGAATTCATCACTCAATGGATAAACTTTTCCAGAGGAAGCTCATAATGAGAAG
1735134 AACTCATCTGAAGAATGAAGAA
584 AACTCATCTGAAGAATGAAGAA
*
1735156 GAAGTTCTTAATGAGAAGAACTT
1 GAAGTTCATAATGAGAAGAACTT
1735179 GTTTAACCTT
Statistics
Matches: 587, Mismatches: 38, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
604 4 0.01
605 581 0.99
606 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (605 bp):
GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TTAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAA
GAACTCATCTGAAGAAGGAAGAAGAAGGTCAAAATAAGAAGAACTTGTTTAACCTTTTGCTTGAA
TTCATCACTCGATGGATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAAG
AAAGAAGAAGTTCATAATGAGAAGAACTTGTGTAACCTTTTGCTTGAATTCATCACTCGATGGAT
CAACTTTTCCAAAGGAAGTTCATAATGAGAAGAACACATCTAAAGAAGGAACAAGAAGTTCATAA
TGAGAAGAACTTGTTTAACCATTTTCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGGAA
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
ACCTTTTGCTTGAATTCATCACTCAATGGATAAACTTTTCCAGAGGAAGCTCATAATGAGAAGAA
CTCATCTGAAGAATGAAGAA
Found at i:1734987 original size:492 final size:492
Alignment explanation
Indices: 1734059--1735065 Score: 1680
Period size: 492 Copynumber: 2.0 Consensus size: 492
1734049 TTTTCCAGAG
*
1734059 GAAGTTCATAATTAGAAGAACTTATCTGAAGAAGGAAGAAGAAGGTCATAATAAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGGTCATAATAAGAAGAACTTGT
* *
1734124 TTAACCTTTTGCTTGAATTCATCACTCGATTGATCAACATTTCCAGAGGAAGTTTATAATGAGAA
66 TTAACCTTTTGCTTGAATTCATCACTCGATGGATCAACATTTCCAGAGGAAGTTCATAATGAGAA
* * * *
1734189 GAACTCATCTAAAGAATAAATAAGAAGTTCATAATGAGAAGAACTTGTGTAATCTTTTGCTTGAA
131 GAACTCATCTAAAGAAGAAAGAAGAAGTTCAAAATGAGAAGAACTTGTGTAACCTTTTGCTTGAA
*
1734254 TTCGTCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAATAACACATCTGAAGAAG
196 TTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAATAACACATCTGAAGAAG
1734319 GAACAAGAAGTTCATAATGAGAAGAACTTGTTTAACCATTTTCTTGAATTCATCACTCGATGGAT
261 GAACAAGAAGTTCATAATGAGAAGAACTTGTTTAACCATTTTCTTGAATTCATCACTCGATGGAT
* *
1734384 CAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
326 CAACTTTTCCAAAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAA
*
1734449 TGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCTAGAGGAA
391 TGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCCAGAGGAA
*
1734514 GCTCATAATGAGAAGAACTCATCT-ATAGAATGAAGAA
456 GCTCATAATGAGAAGAACTCATCTGA-AGAAGGAAGAA
* * * *
1734551 GAATTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGGTCATAATAAGAAGAACTTGT
* *
1734616 TTAACCTTTTGCTTGTATTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAA
66 TTAACCTTTTGCTTGAATTCATCACTCGATGGATCAACATTTCCAGAGGAAGTTCATAATGAGAA
* * *
1734681 GAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTTTAACCTTTTGCTTGAA
131 GAACTCATCTAAAGAAGAAAGAAGAAGTTCAAAATGAGAAGAACTTGTGTAACCTTTTGCTTGAA
* **
1734746 TTCATCACTCGATGGATCAACTTTTCTAGAGGAAGTTCATAATGAG-ATGAACTTATCTGAAGAA
196 TTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAT-AACACATCTGAAGAA
* * *
1734810 GGAAGAAGAAGTTCATAATGAGAATATA-TTGTTTAACC-TTTTGGTTGAATTCATCACTCGATG
260 GGAACAAGAAGTTCATAATGAGAAGA-ACTTGTTTAACCATTTT-CTTGAATTCATCACTCGATG
1734873 GATCAACTTTTCCAAAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCA
323 GATCAACTTTTCCAAAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCA
* *
1734938 TAGTGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAG
388 TAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCCAGAG
*
1735003 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
453 GAAGCTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1735043 GAAGTTCATAATGAGAAGAACTT
1 GAAGTTCATAATGAGAAGAACTT
1735066 GTTTAACCTT
Statistics
Matches: 480, Mismatches: 31, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
491 6 0.01
492 472 0.98
493 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (492 bp):
GAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGGTCATAATAAGAAGAACTTGT
TTAACCTTTTGCTTGAATTCATCACTCGATGGATCAACATTTCCAGAGGAAGTTCATAATGAGAA
GAACTCATCTAAAGAAGAAAGAAGAAGTTCAAAATGAGAAGAACTTGTGTAACCTTTTGCTTGAA
TTCATCACTCGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAATAACACATCTGAAGAAG
GAACAAGAAGTTCATAATGAGAAGAACTTGTTTAACCATTTTCTTGAATTCATCACTCGATGGAT
CAACTTTTCCAAAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCACTCGATGGATAAACTTTTCCAGAGGAA
GCTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
Found at i:1735774 original size:3 final size:3
Alignment explanation
Indices: 1735762--1735867 Score: 126
Period size: 3 Copynumber: 35.0 Consensus size: 3
1735752 TTTTTTCCAT
* *
1735762 TTA TTT TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA GTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1735808 TTTA TATA TTA TTA TTA TAA TTA TTA TTA CATA TTA TTA TTA TTA ATA
1 -TTA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1735856 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1735868 AATAAATAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.05
3 76 0.86
4 8 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1735817 original size:28 final size:28
Alignment explanation
Indices: 1735762--1735866 Score: 121
Period size: 28 Copynumber: 3.8 Consensus size: 28
1735752 TTTTTTCCAT
1735762 TTATT-TT-TATTATTATTA-TTATTATA
1 TTATTATTATATTATTATTATTTA-TATA
1735788 TTATTATTAGTATTATT-TTATTTATATA
1 TTATTATTA-TATTATTATTATTTATATA
**
1735816 TTATTATTATAATTATTATTACATAT-TA
1 TTATTATTAT-ATTATTATTATTTATATA
1735844 TTATTATTAATATTATTATTATT
1 TTATTATT-ATATTATTATTATT
1735867 AAATAAATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
26 5 0.07
27 3 0.04
28 42 0.62
29 18 0.26
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
TTATTATTATATTATTATTATTTATATA
Found at i:1738516 original size:59 final size:59
Alignment explanation
Indices: 1738421--1738780 Score: 486
Period size: 59 Copynumber: 6.1 Consensus size: 59
1738411 TTTCTCTAAA
* * * * **
1738421 ATGAAATGTTAAATGTCTAACTGTGCATTTGACATAAAGGTTTCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * *
1738480 ATGAAAGGTTAAATGTCTAACTGTGCATTTGGCATAAATGTGCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * * **
1738539 ATGAAAGGTTAAATACCTAATTGTGCATTTGACAGAAAGGTGCCAATAACACAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * * * * *
1738598 ATAAAAGGTTAAATACCTAAATGTGCATTTGGCAGAAAGATGTCAATAATGTAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * *
1738657 ATAAAAGGTTAAATGACTAACTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * *
1738716 ATTAAAGGTTAAATGCCTAACTGTGCATTTGGAAGAAAGGTGCCACTAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
1738775 ATGAAA
1 ATGAAA
1738781 AACAATGTAT
Statistics
Matches: 268, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 268 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (59 bp):
ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
Found at i:1751910 original size:23 final size:23
Alignment explanation
Indices: 1751877--1751922 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1751867 TCCATGAAAA
1751877 ATTTAGATGATGTATCCAACCAG
1 ATTTAGATGATGTATCCAACCAG
* *
1751900 ATTTAGGTGATGTCTCCAACCAG
1 ATTTAGATGATGTATCCAACCAG
1751923 GATTATACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (23 bp):
ATTTAGATGATGTATCCAACCAG
Found at i:1756446 original size:59 final size:59
Alignment explanation
Indices: 1756374--1756733 Score: 497
Period size: 59 Copynumber: 6.1 Consensus size: 59
1756364 TTTCTCTAAA
* * * **
1756374 ATGAAAGGTTAAATGCCTAATTGTACATTTGGCATATGGGTGCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * * *
1756433 ATGAAAGGTTAAATGCCTAATTGTGCCTTTGGTAGAAAGGTGTCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* *
1756492 ATGAAAGGTTAAATGACTAATTGTGCATTT-GCTAGAAAGGTGCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGC-AGAAAGGTGCCAATAATGCAAGTTAG
* * * * *
1756551 ATGAAAGGTTAAATGCCTAACTATCCATTTGGCAGAAAGGTTCCAATACTGCAGGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* *
1756610 ATGAAAGGTTAGATGCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * * * *
1756669 ATGAAAGGTTAAATGCCTAACTATGCATTTGGTAGAAAAGTACCACTAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
1756728 ATGAAA
1 ATGAAA
1756734 AATAGTATTT
Statistics
Matches: 268, Mismatches: 31, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
58 1 0.00
59 265 0.99
60 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (59 bp):
ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
Found at i:1761176 original size:34 final size:32
Alignment explanation
Indices: 1761123--1761192 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1761113 CCTTACAAAC
* *
1761123 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCAT
1761155 TCCCTAGCTTTTACACGGGCTAAACTAGAACCAT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCAT
1761189 TCCC
1 TCCC
1761193 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.30
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCAT
Found at i:1761490 original size:21 final size:21
Alignment explanation
Indices: 1761464--1761504 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1761454 CAGAATGGGT
*
1761464 GGAATCGGTACCCCTTCATAG
1 GGAATCGATACCCCTTCATAG
1761485 GGAATCGATACCCCTTCATA
1 GGAATCGATACCCCTTCATA
1761505 ATATTCAAAT
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:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
GGAATCGATACCCCTTCATAG
Found at i:1761749 original size:30 final size:30
Alignment explanation
Indices: 1761702--1761791 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
1761692 AAATTTTGAA
1761702 TAAATTCAATT-AAGTCCAAATACATTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
* *
1761731 TAAATTTAATTCAAGTCCAAATACGTTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
*
1761761 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAATA-CATTTTG
1761792 CCTTAAATTG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 10 0.19
30 38 0.70
31 6 0.11
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAATACATTTTG
Found at i:1768735 original size:34 final size:32
Alignment explanation
Indices: 1768682--1768751 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1768672 CCTTACAAAC
* *
1768682 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAAAACCTT
*
1768714 TCCCTAGCTTTTACACGGGCTAAGCTAAAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAAAACCTT
1768748 TCCC
1 TCCC
1768752 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAAAACCTT
Found at i:1769004 original size:21 final size:20
Alignment explanation
Indices: 1768965--1769004 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1768955 TAAGTCATAT
* *
1768965 AGCCGTTGGGGATGTTTTTG
1 AGCCGTTGGGAATGATTTTG
1768985 AGCCGTTTGGGAATGATTTT
1 AGCCG-TTGGGAATGATTTT
1769005 TCTGCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.10, G:0.35, T:0.40
Consensus pattern (20 bp):
AGCCGTTGGGAATGATTTTG
Found at i:1769059 original size:21 final size:21
Alignment explanation
Indices: 1769033--1769074 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1769023 CCAGAATGGG
*
1769033 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1769054 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1769075 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1769312 original size:30 final size:30
Alignment explanation
Indices: 1769265--1769354 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
1769255 AAATTTTGAA
1769265 TAAATTCAATT-AAGTCCAAATACATTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
* *
1769294 TAAATTTAATTCAAGTCCAAATACGTTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
*
1769324 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAATA-CATTTTG
1769355 CCTTAAATTG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 10 0.19
30 38 0.70
31 6 0.11
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAATACATTTTG
Found at i:1772021 original size:17 final size:16
Alignment explanation
Indices: 1771982--1772014 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1771972 GACTAGAGGA
1771982 TGATTTTTATACCATT
1 TGATTTTTATACCATT
*
1771998 TGATTTTTATATCATT
1 TGATTTTTATACCATT
1772014 T
1 T
1772015 TAGTTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (16 bp):
TGATTTTTATACCATT
Found at i:1777977 original size:29 final size:29
Alignment explanation
Indices: 1777922--1778004 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
1777912 AGTTTAGTGG
*
1777922 CCAAAGTATAAAGTATGGAAAAGTTCAAAGA
1 CCAAAGTAT-AA-TTTGGAAAAGTTCAAAGA
1777953 CCAAAGTATAATTTGGAAAAGTTCAAAGA
1 CCAAAGTATAATTTGGAAAAGTTCAAAGA
* *
1777982 CCAAAGTTTAATTTGAAAAAGTT
1 CCAAAGTATAATTTGGAAAAGTT
1778005 AGTATTTAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
29 38 0.78
30 2 0.04
31 9 0.18
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (29 bp):
CCAAAGTATAATTTGGAAAAGTTCAAAGA
Found at i:1778509 original size:22 final size:22
Alignment explanation
Indices: 1778462--1778507 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1778452 CATTTAAGTT
1778462 AAATAAATGAAAAATGTACATG
1 AAATAAATGAAAAATGTACATG
* *
1778484 AAATTAATGAAAAAT-TTCATG
1 AAATAAATGAAAAATGTACATG
1778505 AAA
1 AAA
1778508 ATATAGCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.59, C:0.04, G:0.11, T:0.26
Consensus pattern (22 bp):
AAATAAATGAAAAATGTACATG
Found at i:1779501 original size:38 final size:39
Alignment explanation
Indices: 1779459--1779533 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
1779449 TTCAGATATG
*
1779459 AATTTTGAGCAGTTTGCAAAAAGATATG-AATTTTAACT
1 AATTTTGAGCAGTTTGCAAAAAGATACGAAATTTTAACT
*
1779497 AATTTTGAGTAGTTTGCAAAAAGATACGAAATTTTAA
1 AATTTTGAGCAGTTTGCAAAAAGATACGAAATTTTAA
1779534 TCGAGGTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (39 bp):
AATTTTGAGCAGTTTGCAAAAAGATACGAAATTTTAACT
Found at i:1780200 original size:24 final size:24
Alignment explanation
Indices: 1780168--1780223 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
1780158 ACTAGTGCAT
*
1780168 TTGTTGCACTCTTATTTTAGTTCC
1 TTGTTGCACTCTTATCTTAGTTCC
*
1780192 TTGTTGCACTCTTGTCTTAGTTCC
1 TTGTTGCACTCTTATCTTAGTTCC
1780216 TTGTTGCA
1 TTGTTGCA
1780224 ATCCATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.11, C:0.21, G:0.16, T:0.52
Consensus pattern (24 bp):
TTGTTGCACTCTTATCTTAGTTCC
Found at i:1780260 original size:24 final size:24
Alignment explanation
Indices: 1780233--1780298 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
1780223 AATCCATTAA
*
1780233 TAGTGCATTTGTGTACTCCTGTAT
1 TAGTACATTTGTGTACTCCTGTAT
* * *
1780257 TAGTAC-TTTTTGGTACTCTTGTGT
1 TAGTACATTTGT-GTACTCCTGTAT
1780281 TAGTACATTTGTGTACTC
1 TAGTACATTTGTGTACTC
1780299 GTGGCACTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.11
24 27 0.77
25 4 0.11
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (24 bp):
TAGTACATTTGTGTACTCCTGTAT
Found at i:1783424 original size:46 final size:46
Alignment explanation
Indices: 1783353--1783604 Score: 280
Period size: 46 Copynumber: 5.8 Consensus size: 46
1783343 ATTGCTCTAA
* *
1783353 AACGAAT-CCATAACTAAAATACATGAAAGGATGCATTAAGGTATG
1 AACGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATG
* *
1783398 AACGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAGTCACG
1 AACGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATG
*
1783444 AACGGATGCC---A-T--AA---ATG-AA--ATGCATTAAGGCATG
1 AACGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATG
* *
1783478 AACGAATGCCATAACTGAAATGCATGAAAGAATGCATTAAGGCATGG
1 AACGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCAT-G
* * *
1783525 AA-GGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCACG
1 AACGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATG
* * *
1783570 AACGGATGCCATAACTAAAATGTATGAATGGATGC
1 AACGAATGCCATAACTAAAATGCATGAAAGGATGC
1783605 CATAACTAAA
Statistics
Matches: 176, Mismatches: 16, Indels: 29
0.80 0.07 0.13
Matches are distributed among these distances:
34 22 0.12
36 2 0.01
37 4 0.02
38 1 0.01
40 4 0.02
42 1 0.01
43 4 0.02
44 2 0.01
45 10 0.06
46 123 0.70
47 3 0.02
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (46 bp):
AACGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATG
Found at i:1783468 original size:34 final size:34
Alignment explanation
Indices: 1783429--1783502 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
1783419 GCATGAAAGG
* *
1783429 ATGCATTAAGTCACGAACGGATGCCATAAATGAA
1 ATGCATTAAGGCACGAACGAATGCCATAAATGAA
* *
1783463 ATGCATTAAGGCATGAACGAATGCCATAACTGAA
1 ATGCATTAAGGCACGAACGAATGCCATAAATGAA
1783497 ATGCAT
1 ATGCAT
1783503 GAAAGAATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (34 bp):
ATGCATTAAGGCACGAACGAATGCCATAAATGAA
Found at i:1783479 original size:80 final size:80
Alignment explanation
Indices: 1783383--1783548 Score: 253
Period size: 80 Copynumber: 2.1 Consensus size: 80
1783373 ACATGAAAGG
* * *
1783383 ATGCATTAAGGTATGAACGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAGTCA-CGAAC
1 ATGCATTAAGGCATGAACGAATGCCATAACTAAAATGCATGAAAGAATGCATTAAGGCATCGAA-
*
1783447 GGATGCCATAAATGAA
65 GGATGCCATAAATAAA
* *
1783463 ATGCATTAAGGCATGAACGAATGCCATAACTGAAATGCATGAAAGAATGCATTAAGGCATGGAAG
1 ATGCATTAAGGCATGAACGAATGCCATAACTAAAATGCATGAAAGAATGCATTAAGGCATCGAAG
*
1783528 GATGCCATAACTAAA
66 GATGCCATAAATAAA
1783543 ATGCAT
1 ATGCAT
1783549 GAAATGATGC
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
80 75 0.96
81 3 0.04
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (80 bp):
ATGCATTAAGGCATGAACGAATGCCATAACTAAAATGCATGAAAGAATGCATTAAGGCATCGAAG
GATGCCATAAATAAA
Found at i:1783557 original size:26 final size:26
Alignment explanation
Indices: 1783473--1783630 Score: 115
Period size: 26 Copynumber: 6.5 Consensus size: 26
1783463 ATGCATTAAG
* * *
1783473 GCATGAACGAATGCCATAACTGAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
* *
1783499 GCATGAAAGAATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAACTAAAAT
*
1783519 GCATGGAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
* *
1783545 GCATGAAATGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAACTAAAAT
* *
1783565 GCACGAACGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
* *
1783591 GTATGAATGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
*
1783617 ACATGAAAGGATGC
1 GCATGAAAGGATGC
1783631 ATTAAGGCAC
Statistics
Matches: 102, Mismatches: 18, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
20 25 0.25
21 6 0.06
22 2 0.02
24 2 0.02
25 6 0.06
26 61 0.60
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.20
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAACTAAAAT
Found at i:1783611 original size:72 final size:72
Alignment explanation
Indices: 1783519--1783675 Score: 242
Period size: 72 Copynumber: 2.2 Consensus size: 72
1783509 ATGCATTAAG
* * * *
1783519 GCATGGAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCACGAACGGATGCCATAA
1 GCATGAAAGGATGCCATAACTAAAATACATGAAAGGATGCATTAAGGCACGAAAGGATGCCATAA
1783584 CTAAAAT
66 CTAAAAT
* * **
1783591 GTATGAATGGATGCCATAACTAAAATACATGAAAGGATGCATTAAGGCACGAAATTATGCCATAA
1 GCATGAAAGGATGCCATAACTAAAATACATGAAAGGATGCATTAAGGCACGAAAGGATGCCATAA
1783656 CTAAAAT
66 CTAAAAT
1783663 GCATGAAAGGATG
1 GCATGAAAGGATG
1783676 TATTAAGGTA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (72 bp):
GCATGAAAGGATGCCATAACTAAAATACATGAAAGGATGCATTAAGGCACGAAAGGATGCCATAA
CTAAAAT
Found at i:1783697 original size:46 final size:46
Alignment explanation
Indices: 1783591--1783705 Score: 158
Period size: 46 Copynumber: 2.5 Consensus size: 46
1783581 TAACTAAAAT
*
1783591 GTATGAATGGATGCCATAACTAAAATACATGAAAGGATGCATTAAG
1 GTATGAAAGGATGCCATAACTAAAATACATGAAAGGATGCATTAAG
* * ** * *
1783637 GCACGAAATTATGCCATAACTAAAATGCATGAAAGGATGTATTAAG
1 GTATGAAAGGATGCCATAACTAAAATACATGAAAGGATGCATTAAG
*
1783683 GTATGAAAGGATGCCACAACTAA
1 GTATGAAAGGATGCCATAACTAA
1783706 GATTAATGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (46 bp):
GTATGAAAGGATGCCATAACTAAAATACATGAAAGGATGCATTAAG
Found at i:1783716 original size:118 final size:118
Alignment explanation
Indices: 1783483--1783705 Score: 329
Period size: 118 Copynumber: 1.9 Consensus size: 118
1783473 GCATGAACGA
* * * *
1783483 ATGCCATAACTGAAATGCATGAAAGAATGCATTAAGGCATGGAAGGATGCCATAACTAAAATGCA
1 ATGCCATAACTAAAATACATGAAAGAATGCATTAAGGCACGAAAGGATGCCATAACTAAAATGCA
* * *
1783548 TGAAATGATGCATTAAGGCACGAACGGATGCCATAACTAAAATGTATGAATGG
66 TGAAAGGATGCATTAAGGCACGAAAGGATGCCACAACTAAAATGTATGAATGG
* **
1783601 ATGCCATAACTAAAATACATGAAAGGATGCATTAAGGCACGAAATTATGCCATAACTAAAATGCA
1 ATGCCATAACTAAAATACATGAAAGAATGCATTAAGGCACGAAAGGATGCCATAACTAAAATGCA
* * *
1783666 TGAAAGGATGTATTAAGGTATGAAAGGATGCCACAACTAA
66 TGAAAGGATGCATTAAGGCACGAAAGGATGCCACAACTAA
1783706 GATTAATGAA
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
118 92 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (118 bp):
ATGCCATAACTAAAATACATGAAAGAATGCATTAAGGCACGAAAGGATGCCATAACTAAAATGCA
TGAAAGGATGCATTAAGGCACGAAAGGATGCCACAACTAAAATGTATGAATGG
Found at i:1787236 original size:3 final size:3
Alignment explanation
Indices: 1787219--1787281 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
1787209 GTCCGGGTCT
1787219 TTA TTA TT- TTA -TA 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 TTA TTA TTA
1787265 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
1787282 CTCTTATTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 54 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1788880 original size:29 final size:30
Alignment explanation
Indices: 1788846--1788976 Score: 124
Period size: 30 Copynumber: 4.4 Consensus size: 30
1788836 ATAATTATTG
*
1788846 TTTTAGTCCTTTTAGTTTCTATTTTTACTA
1 TTTTAGTCCTTTAAGTTTCTATTTTTACTA
* * *
1788876 -TTTAGCCCTTTAAGATTCTATTTTT-GTGA
1 TTTTAGTCCTTTAAGTTTCTATTTTTACT-A
* * *
1788905 TTTTAGTTCC-TGAAATATCTATTTTTACTA
1 TTTTAG-TCCTTTAAGTTTCTATTTTTACTA
* * *
1788935 TTTTAGTCCTTCAAGTTTCTTTTTTTGCTA
1 TTTTAGTCCTTTAAGTTTCTATTTTTACTA
*
1788965 TTTTGGTCCTTT
1 TTTTAGTCCTTT
1788977 TAAATAGAAT
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
28 1 0.01
29 26 0.33
30 49 0.62
31 3 0.04
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.58
Consensus pattern (30 bp):
TTTTAGTCCTTTAAGTTTCTATTTTTACTA
Found at i:1788911 original size:59 final size:60
Alignment explanation
Indices: 1788846--1788979 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
1788836 ATAATTATTG
* * *
1788846 TTTTAGTCCTTTTAGTTTCTATTTTTACTA-TTTAGCCCTTTAAGATTCTATTTTTG-TGA
1 TTTTAGTCCTTTTAATATCTATTTTTACTATTTTAGCCCTTCAAGATTCTATTTTTGCT-A
** * * *
1788905 TTTTAGTTCC-TGAAATATCTATTTTTACTATTTTAGTCCTTCAAGTTTCTTTTTTTGCTA
1 TTTTAG-TCCTTTTAATATCTATTTTTACTATTTTAGCCCTTCAAGATTCTATTTTTGCTA
*
1788965 TTTTGGTCCTTTTAA
1 TTTTAGTCCTTTTAA
1788980 ATAGAATACG
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
59 25 0.42
60 34 0.57
61 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (60 bp):
TTTTAGTCCTTTTAATATCTATTTTTACTATTTTAGCCCTTCAAGATTCTATTTTTGCTA
Found at i:1789272 original size:5 final size:5
Alignment explanation
Indices: 1789255--1789289 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1789245 CGCTTTTCAT
*
1789255 TTTTA TTTT- TTTTA TTTTA TTGTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1789290 CTTGACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1790520 original size:88 final size:89
Alignment explanation
Indices: 1790370--1790545 Score: 329
Period size: 88 Copynumber: 2.0 Consensus size: 89
1790360 TAACGGAATG
1790370 CTGATGTTGCCTGTTAATTAACTCTTTTTTTGGCATTATTTGACCAAGTTCATTATTCAAAATTG
1 CTGATGTTGCCTGTTAATTAACTCTTTTTTTGGCATTATTTGACCAAGTTCATTATTCAAAATTG
1790435 A-CCTTTTCTCTTTCATCTTCACTT
66 ACCCTTTT-TCTTTCATCTTCACTT
1790459 CTGATGTTGCCTGTTAATTAACT-TTTTTTTGGCATTATTTGACCAAGTTCATTATTCAAAATTG
1 CTGATGTTGCCTGTTAATTAACTCTTTTTTTGGCATTATTTGACCAAGTTCATTATTCAAAATTG
1790523 ACCCTTTTTCTTTCATCTTCACT
66 ACCCTTTTTCTTTCATCTTCACT
1790546 CTCTCCACGC
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
88 57 0.66
89 29 0.34
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (89 bp):
CTGATGTTGCCTGTTAATTAACTCTTTTTTTGGCATTATTTGACCAAGTTCATTATTCAAAATTG
ACCCTTTTTCTTTCATCTTCACTT
Found at i:1792158 original size:3 final size:3
Alignment explanation
Indices: 1792150--1792198 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
1792140 ATTTTTCCAT
* *
1792150 TTA TTA TTA TTA TTA TTA TTA TTA TATA ATA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
1792196 TTA
1 TTA
1792199 AAATTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1794309 original size:24 final size:23
Alignment explanation
Indices: 1794251--1794310 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1794241 AAATCCAGCA
*
1794251 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
1794274 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATGAAAGCACTC-AAAAG
*
1794298 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
1794311 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:1797080 original size:11 final size:13
Alignment explanation
Indices: 1797048--1797077 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1797038 TGGCCAAAGA
1797048 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1797061 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1797073 TGAAA
1 TGAAA
1797078 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1800834 original size:12 final size:11
Alignment explanation
Indices: 1800797--1800879 Score: 73
Period size: 12 Copynumber: 7.4 Consensus size: 11
1800787 TTTTAATTTC
*
1800797 TTTTATCATTA
1 TTTTATTATTA
1800808 -TTTATT-TTCAA
1 TTTTATTATT--A
1800819 TTTTATTATTA
1 TTTTATTATTA
*
1800830 CTTTTAATA-TA
1 -TTTTATTATTA
1800841 TTTTAATTATTA
1 TTTT-ATTATTA
*
1800853 CTTTAATTATTA
1 -TTTTATTATTA
1800865 TTTTATTATTA
1 TTTTATTATTA
1800876 TTTT
1 TTTT
1800880 TTCTTAGTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
9 2 0.03
10 9 0.15
11 21 0.36
12 22 0.37
13 5 0.08
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:1800851 original size:23 final size:24
Alignment explanation
Indices: 1800818--1800880 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
1800808 TTTATTTTCA
1800818 ATTTTATTATTACTTTTAA-TA-T
1 ATTTTATTATTACTTTTAATTATT
1800840 ATTTTAATTATTAC-TTTAATTATT
1 ATTTT-ATTATTACTTTTAATTATT
*
1800864 ATTTTATTATTATTTTT
1 ATTTTATTATTACTTTT
1800881 TCTTAGTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 10 0.28
23 17 0.47
24 9 0.25
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTATTATTACTTTTAATTATT
Found at i:1800880 original size:12 final size:12
Alignment explanation
Indices: 1800819--1800879 Score: 67
Period size: 11 Copynumber: 5.3 Consensus size: 12
1800809 TTATTTTCAA
1800819 TTTTATTATTAC
1 TTTTATTATTAC
*
1800831 TTTTAATA-TA-
1 TTTTATTATTAC
1800841 TTTTAATTATTAC
1 TTTT-ATTATTAC
*
1800854 TTTAATTATTA-
1 TTTTATTATTAC
1800865 TTTTATTATTA-
1 TTTTATTATTAC
1800876 TTTT
1 TTTT
1800880 TTCTTAGTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 4 0.10
11 19 0.45
12 16 0.38
13 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTATTATTAC
Found at i:1801282 original size:148 final size:150
Alignment explanation
Indices: 1800925--1801341 Score: 461
Period size: 147 Copynumber: 2.7 Consensus size: 150
1800915 GTTTAAATAA
* * * *
1800925 TAATATTTATTTGTTTCTAATATCAAAGAAAATGA-CAGTCTTAAAGCAACTAGATGTCCTATTC
1 TAATATTTATTTATTTTTAATAT-TAAG-AAATGAGCAGTCTTAAAGCAACTAGATGTCCTTTTC
** * * **
1800989 TGGTATTTTAAATAAATAAATATCTTACTTATAAAAATCATAAAATACATATTGTTTTATTTAAA
64 TAATATTTTAAATAAATAAATATCTTATTTATAAAAAT-AT---ATATATATTAATTTATTTAAA
*
1801054 TTATTTTCTTAGAAAAATAATCATATTT
125 TTATTTTCATAG-AAAATAAT-ATATTT
* *
1801082 TAATATTTATTTATTTTTCAATATTAAGAAA-GGGAAGTCTTAAAGCAACTAGATGTCCATTTTC
1 TAATATTTATTTATTTTT-AATATTAAGAAATGAGCAGTCTTAAAGCAACTAGATGTCC-TTTTC
* * * *
1801146 TAATATTCTTAAATAAATAAATATCTTATTTTTATAAAT-TATATATATTAATTTCTTTTAATTA
64 TAATATT-TTAAATAAATAAATATCTTATTTATAAAAATATATATATATTAATTTATTTAAATTA
*
1801210 TTTTCATAG-AAAT-GT-T-TTAT
128 TTTTCATAGAAAATAATATATT-T
* * *
1801230 TAATATTTATTTATTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTA
1 TAATATTTATTTATTTTTAATATTAAGAAATGAGCAGTCTTAAAGCAACTAGATGTCCTTTTCTA
* *
1801295 ATATTTCTAAGTAAATAAATATCTTATTTATAAAAATAAATATATAT
66 ATATTT-TAAATAAATAAATATCTTATTTATAAAAATATATATATAT
1801342 ATATATATAT
Statistics
Matches: 225, Mismatches: 27, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
146 1 0.00
147 53 0.24
148 50 0.22
150 1 0.00
151 4 0.02
153 27 0.12
155 1 0.00
156 27 0.12
157 28 0.12
158 33 0.15
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (150 bp):
TAATATTTATTTATTTTTAATATTAAGAAATGAGCAGTCTTAAAGCAACTAGATGTCCTTTTCTA
ATATTTTAAATAAATAAATATCTTATTTATAAAAATATATATATATTAATTTATTTAAATTATTT
TCATAGAAAATAATATATTT
Found at i:1805693 original size:36 final size:36
Alignment explanation
Indices: 1805611--1805696 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 36
1805601 TTGAATCTGT
*
1805611 TTTCCTTTAAAC-AAATTTCGTCTCTCTTGAGACAG
1 TTTCCTTAAAACAAAATTTCGTCTCTCTTGAGACAG
**
1805646 TTT-CTTAAAACAAAATTT-GTCTCTCTTGAGATGG
1 TTTCCTTAAAACAAAATTTCGTCTCTCTTGAGACAG
*
1805680 TTTCCCTTGAAACAAAA
1 TTT-CCTTAAAACAAAA
1805697 ACTTTGAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
34 24 0.55
35 9 0.20
36 11 0.25
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
TTTCCTTAAAACAAAATTTCGTCTCTCTTGAGACAG
Found at i:1805703 original size:99 final size:101
Alignment explanation
Indices: 1805529--1805722 Score: 284
Period size: 99 Copynumber: 1.9 Consensus size: 101
1805519 AAGTTTTGTC
* * *
1805529 TCTCTCTTGAGAAAATTTCTTTTAGAACTAAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 TCTCTCTTGAGAAAATTTC-TTTAAAACTAAAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
* *
1805594 AAAATCTTTGAATCTGTTTTCCTTTAAACAAATTTCG
65 AAAAACTTTGAATCTGTTTTCCTTGAAACAAATTTCG
* * *
1805631 TCTCTCTTGAGACAGTTTC-TTAAAAC-AAAATTTGTCTCTCTTGAGATGGTTTCCCTTGAAACA
1 TCTCTCTTGAGAAAATTTCTTTAAAACTAAAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
*
1805694 AAAACTTTGAATTTGTTTTCCTTGAAACA
66 AAAACTTTGAATCTGTTTTCCTTGAAACA
1805723 GAGACAGTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
99 60 0.72
100 6 0.07
102 17 0.20
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (101 bp):
TCTCTCTTGAGAAAATTTCTTTAAAACTAAAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
AAAACTTTGAATCTGTTTTCCTTGAAACAAATTTCG
Found at i:1805884 original size:36 final size:36
Alignment explanation
Indices: 1805788--1805911 Score: 169
Period size: 36 Copynumber: 3.4 Consensus size: 36
1805778 CAAAATCTTT
* *
1805788 TTTC-CTTTAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * *
1805823 TTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACAG
*
1805860 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
*
1805896 TTTCTCTTGAAACAAA
1 TTTCTCTTAAAACAAA
1805912 ATCTTTTAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
35 4 0.05
36 41 0.54
37 31 0.41
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.42
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1809635 original size:7 final size:7
Alignment explanation
Indices: 1809621--1809696 Score: 59
Period size: 7 Copynumber: 11.3 Consensus size: 7
1809611 AAATATCTAA
1809621 ATTATAT
1 ATTATAT
*
1809628 AGTATAT
1 ATTATAT
1809635 ATTATAT
1 ATTATAT
1809642 ATTATAT
1 ATTATAT
* *
1809649 TTTA-AA
1 ATTATAT
*
1809655 AATATAT
1 ATTATAT
*
1809662 A-TATCT
1 ATTATAT
* *
1809668 -TTTTAA
1 ATTATAT
*
1809674 AATATAT
1 ATTATAT
1809681 ATTATAT
1 ATTATAT
1809688 ATTATAT
1 ATTATAT
1809695 AT
1 AT
1809697 AGAAAGAATA
Statistics
Matches: 51, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
6 9 0.18
7 42 0.82
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (7 bp):
ATTATAT
Found at i:1809668 original size:60 final size:60
Alignment explanation
Indices: 1809571--1809696 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
1809561 GTAATATATA
* * *
1809571 ATATAATATATAGTATTTTTAAAAATATGTATAATC-TTTTAAATATCTAAATTATATAGT
1 ATATATTATATAGTATTTTTAAAAATATATATAATCTTTTTAAA-ATATAAATTATATAGT
* * *
1809631 ATATATTATATATTATATTTTAAAAATATATAT-ATCTTTTTAAAATATATATTATATATT
1 ATATATTATATAGTAT-TTTTAAAAATATATATAATCTTTTTAAAATATAAATTATATAGT
1809691 ATATAT
1 ATATAT
1809697 AGAAAGAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 36 0.62
61 22 0.38
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (60 bp):
ATATATTATATAGTATTTTTAAAAATATATATAATCTTTTTAAAATATAAATTATATAGT
Found at i:1809675 original size:19 final size:19
Alignment explanation
Indices: 1809637--1809687 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1809627 TAGTATATAT
1809637 TATATATTATATTTTAAAAA
1 TATATA-TATATTTTAAAAA
* *
1809657 TATATATATCTTTTTAAAA
1 TATATATATATTTTAAAAA
1809676 TATATATTATAT
1 TATATA-TATAT
1809688 ATTATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATATATATTTTAAAAA
Found at i:1809681 original size:46 final size:48
Alignment explanation
Indices: 1809630--1809730 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 48
1809620 AATTATATAG
*
1809630 TATATATTATATATTATATTTTA-AAA-ATATATATA-TCTTTTTAAAA-
1 TATATATTATATATTATA-TATAGAAAGA-ATATATAGTCTTTTTAAAAC
*
1809676 TATATATTATATATTATATATAGAAAGAATATATAGTTTTTTTAAAAC
1 TATATATTATATATTATATATAGAAAGAATATATAGTCTTTTTAAAAC
1809724 TATATAT
1 TATATAT
1809731 GTAATTGTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
45 3 0.06
46 28 0.57
47 11 0.22
48 7 0.14
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.50
Consensus pattern (48 bp):
TATATATTATATATTATATATAGAAAGAATATATAGTCTTTTTAAAAC
Found at i:1809682 original size:21 final size:21
Alignment explanation
Indices: 1809648--1809687 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
1809638 ATATATTATA
1809648 TTTTAAAAATATA-TATATCT
1 TTTTAAAAATATATTATATCT
1809668 TTTTAAAATATATATTATAT
1 TTTTAAAA-ATATATTATAT
1809688 ATTATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTAAAAATATATTATATCT
Found at i:1809779 original size:20 final size:18
Alignment explanation
Indices: 1809756--1809805 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
1809746 ATAAGTAAAT
*
1809756 TATATTATATTATACTATTA
1 TATATTATATT-GA-TATTA
1809776 TATATTGTATATTGATATTA
1 TATA-T-TATATTGATATTA
1809796 TATATTATAT
1 TATATTATAT
1809806 ATTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 13 0.48
21 2 0.07
22 6 0.22
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
TATATTATATTGATATTA
Found at i:1809786 original size:7 final size:7
Alignment explanation
Indices: 1809761--1809808 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
1809751 TAAATTATAT
1809761 TATATTA
1 TATATTA
1809768 TACTATTA
1 TA-TATTA
*
1809776 TATATTG
1 TATATTA
1809783 TATATT-
1 TATATTA
*
1809789 GATATTA
1 TATATTA
1809796 TATATTA
1 TATATTA
1809803 TATATT
1 TATATT
1809809 TTTAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 5 0.14
7 24 0.67
8 7 0.19
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:1809806 original size:20 final size:20
Alignment explanation
Indices: 1809771--1809808 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1809761 TATATTATAC
*
1809771 TATTATATATTGTATATTGA
1 TATTATATATTATATATTGA
1809791 TATTATATATTATATATT
1 TATTATATATTATATATT
1809809 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTATATATTATATATTGA
Found at i:1809845 original size:11 final size:12
Alignment explanation
Indices: 1809806--1809839 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1809796 TATATTATAT
1809806 ATTTTTAATTTTA
1 ATTTTT-ATTTTA
1809819 A-TTTTATTTTA
1 ATTTTTATTTTA
1809830 ATTTTTATTT
1 ATTTTTATTT
1809840 AGTTTTCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.35
12 12 0.60
13 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:1812637 original size:21 final size:21
Alignment explanation
Indices: 1812611--1812676 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1812601 AACCGAAAAA
1812611 ATCGGATATCCAAAAATTTGG
1 ATCGGATATCCAAAAATTTGG
* ***
1812632 ATCGGATATCCGAAAATTCAT
1 ATCGGATATCCAAAAATTTGG
* *
1812653 ATCGGATATCCAAATATCTGG
1 ATCGGATATCCAAAAATTTGG
1812674 ATC
1 ATC
1812677 CGAATCTGAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (21 bp):
ATCGGATATCCAAAAATTTGG
Found at i:1816351 original size:21 final size:20
Alignment explanation
Indices: 1816321--1816392 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 20
1816311 AATGCATCAG
1816321 TGCATCTTCATGATGTATCGA
1 TGCAT-TTCATGATGTATCGA
* *
1816342 TGCATATTCAAAGGGATGCATCGA
1 TGCAT-TTC--A-TGATGTATCGA
1816366 TGCACTTTCAT-AGTGTATCGA
1 TGCA-TTTCATGA-TGTATCGA
1816387 TGCATT
1 TGCATT
1816393 ATGAACAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
20 3 0.07
21 19 0.46
22 1 0.02
23 1 0.02
24 16 0.39
25 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (20 bp):
TGCATTTCATGATGTATCGA
Found at i:1816352 original size:44 final size:45
Alignment explanation
Indices: 1816293--1816391 Score: 125
Period size: 45 Copynumber: 2.2 Consensus size: 45
1816283 GGCCTTGTGC
*
1816293 ATCGATGCATGTTC-AAGGAATGCATC-AGTGCA-TCTTCAT-GATGT
1 ATCGATGCATATTCAAAGGAATGCATCGA-TGCACT-TTCATAG-TGT
*
1816337 ATCGATGCATATTCAAAGGGATGCATCGATGCACTTTCATAGTGT
1 ATCGATGCATATTCAAAGGAATGCATCGATGCACTTTCATAGTGT
1816382 ATCGATGCAT
1 ATCGATGCAT
1816392 TATGAACAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
44 13 0.27
45 33 0.67
46 3 0.06
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (45 bp):
ATCGATGCATATTCAAAGGAATGCATCGATGCACTTTCATAGTGT
Found at i:1820710 original size:17 final size:17
Alignment explanation
Indices: 1820688--1820727 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
1820678 TCTTCTTCTC
1820688 CGTCTCCTTCTTTGGCT
1 CGTCTCCTTCTTTGGCT
1820705 CGTCTCCTTCTTTGGCT
1 CGTCTCCTTCTTTGGCT
1820722 CGTCTC
1 CGTCTC
1820728 TTTTCTCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.00, C:0.38, G:0.17, T:0.45
Consensus pattern (17 bp):
CGTCTCCTTCTTTGGCT
Found at i:1822363 original size:64 final size:63
Alignment explanation
Indices: 1822229--1822372 Score: 150
Period size: 64 Copynumber: 2.3 Consensus size: 63
1822219 GAAAAAGCCT
* * * * * *
1822229 GGGTGCATCGATGCATGGCTTGTTCATCGGTGCATAAAATCAATTCGATGTTTTAATATATAT
1 GGGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAAGCAATTCGATGTTTTAATATACAA
*
1822292 GGAGTGCATCGATGCATGG-TATGTGCATCGGTACACAAAAGCCATTCGATGTTCAATTAA-A-A
1 GG-GTGCATCGATGCATGGCT-TGTGCATCGGTACACAAAAGCAATTCGATGTT---TTAATATA
1822354 CAA
61 CAA
*
1822357 GGGTGCATCAATGCAT
1 GGGTGCATCGATGCAT
1822373 TGATTCATGC
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
63 3 0.04
64 56 0.82
65 4 0.06
66 1 0.01
67 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (63 bp):
GGGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAAGCAATTCGATGTTTTAATATACAA
Found at i:1835497 original size:17 final size:17
Alignment explanation
Indices: 1835475--1835510 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1835465 GATATCGACA
*
1835475 TTCCATAATAACCTCCG
1 TTCCATAATAAACTCCG
1835492 TTCCATAATAAACTCCG
1 TTCCATAATAAACTCCG
1835509 TT
1 TT
1835511 TTTGCCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.33
Consensus pattern (17 bp):
TTCCATAATAAACTCCG
Found at i:1838590 original size:42 final size:42
Alignment explanation
Indices: 1838469--1839850 Score: 332
Period size: 42 Copynumber: 32.1 Consensus size: 42
1838459 AGGTCTTATG
** * * *
1838469 GATGACCCGAAGGATTT-ATCATTTTTCTCGAAAGACTCACA
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * * * *
1838510 AATGACCTGAAGGATTTAATCATTATACTCAAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
*
1838552 GATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
*** * ** * *
1838594 GATGGTACTTATTAATGGATTTACTTCA-CTACT-CTTCGGTGGAGCCTTACA
1 GAT-G-AC--CCGAA-GGATTT-CATCATC-A-TGC-TC-G-AAAGACTTACT
* * * * *
1838645 AATTACCCGAACGATTTAATCATCATGCTCAAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * *
1838687 GATGTCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACA
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* *
1838729 AATGACTCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * ** * * *
1838771 GATAGAACTTACTGATGGATTTGTTTCA-CTACT-CTTCAGTGAAGGCTTACA
1 GAT-G-AC---CCGAAGGATTT-CATCATC-A-TGC-TC-G-AAAGACTTACT
* * * ** * *
1838822 AATTACTCGAATAATTTAATCATCATGCTCGAAAGACTTATT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * * *
1838864 GATGGCCCAAAGGACTCCATCATCATGCTCGAAAGACTTAAT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* *
1838906 GACGACCCAAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * * * * * *
1838948 GATGGCACTTACTGAGGGATTTGCTTCA-CTACTCCTTGGTGAAGGCTTACA
1 GAT-G-AC---CCGAAGGATTT-CATCATC-A-TGC-TCG-AAAGACTTACT
* * * * *
1838999 AATTACCTGAAGGATTTAATCATCTTGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * **
1839041 GATGACCCGAAGGACTTAATCATCACACTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
** * * * * *
1839083 GAT-A---GATTTG-CTTCA-CTACTCTTTGGT-G-AAGGCTTACA
1 GATGACCCGA-AGGATTTCATC-A-TC-ATGCTCGAAAGACTTACT
* * * * *
1839121 AATTACCCGAAGGATTTAATCATCATTCTCGAAAGACTTAAT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
*
1839163 GATGGCCCGAAGGACTTATTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGA--T-TTCATCATCATGCTCGAAAGACTTACT
* *** * * * * *
1839208 GATG---GGTTTG-CTTCA-CAAC-T-CTTCCGTGAAGGCTTACA
1 GATGACCCGAAGGATTTCATCATCATGC-T-CG-AAAGACTTACT
* * * * *
1839246 AACT-ACCTGAAGGATTTAATCATCATGCTCGTAAGACTTATT
1 GA-TGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
*
1839288 GATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
**** * * * *
1839330 GATG----GGTTTATTTCA-CTACTC-TTCT-GTGAAGGCTTACA
1 GATGACCCGAAGGATTTCATC-A-TCATGCTCG-AAAGACTTACT
* * ** * *
1839368 AATTACTTGAAGGATTTAATCATCATGCTTGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * *
1839410 AATGGA-CCAAAGGACTTCATCATCATGCTCGAAAGACTTACT
1 GAT-GACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * * *
1839452 GAT-----G--GGTTTTCTTCATTACT-CTTTCGTGAAGGCTTA-T
1 GATGACCCGAAGGATTTCATCATCA-TGC--TCG-AAAGACTTACT
* * * *
1839489 AAACT-ACCCGAAGGATTTAATCATCATGCTTGAAAGACTTAAT
1 -GA-TGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * *
1839532 GATGGCTCGAAGGACTTATTCATCATCATGCTCGAAAGACTTATT
1 GATGACCCGAAGGA--T-TTCATCATCATGCTCGAAAGACTTACT
* * ** * ** * * *
1839577 GATGACACTTACTGATGGGTTTGTTTCACTACTTTTTCGTGAAGTCTTACA
1 GATGAC-C---C-GAAGGATTT-CATCA-T-CATGCTCG-AAAGACTTACT
* * * *
1839628 AACT-ACCTGAAGGATTTAATTATCATGCTCGAAAGACTTACT
1 GA-TGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * *
1839670 GATGGCCGGAAGGACTTCATCATTATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * * * * * * *
1839712 GCTGGCACTTACTGATGGGTTTGCTTCACTACTAT-TTTGTGAAGGCTTACAT
1 GAT-G-AC---CCGAAGGATTT-CATCA-T-C-ATGCTCG-AAAGACTTAC-T
* *
1839764 -ATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
* * * *
1839805 GATGGA-CCAAAAGACTTCATCATCATGCTCGAAATACTTACT
1 GAT-GACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1839847 GATG
1 GATG
1839851 GCACTTACTG
Statistics
Matches: 944, Mismatches: 278, Indels: 238
0.65 0.19 0.16
Matches are distributed among these distances:
35 12 0.01
36 3 0.00
37 12 0.01
38 59 0.06
39 9 0.01
40 3 0.00
41 29 0.03
42 492 0.52
43 29 0.03
44 21 0.02
45 87 0.09
46 41 0.04
47 36 0.04
48 24 0.03
49 19 0.02
50 16 0.02
51 50 0.05
52 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (42 bp):
GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
Found at i:1838724 original size:22 final size:21
Alignment explanation
Indices: 1838663--1838768 Score: 85
Period size: 22 Copynumber: 5.0 Consensus size: 21
1838653 GAACGATTTA
*
1838663 ATCATCATGCTCAAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
1838684 A-C-TGATGTCCCGAAGGACTT
1 ATCATCATG-CTCGAAAGACTT
1838704 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
* * *
1838726 A-CA-AATGACTCGAAGGATTT
1 ATCATCATG-CTCGAAAGACTT
1838746 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1838768 A
1 A
1838769 CTGATAGAAC
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
19 7 0.11
20 22 0.34
21 5 0.08
22 23 0.36
23 7 0.11
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1838801 original size:177 final size:177
Alignment explanation
Indices: 1838473--1839081 Score: 774
Period size: 177 Copynumber: 3.4 Consensus size: 177
1838463 CTTATGGATG
* ** * * ** * * *
1838473 ACCCGAAGGATTT-ATCATTTTTCTCGAAAGACTCACAAATGACCTGAAGGATTTAATCATTATA
1 ACCCGAACGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTAATCATCATA
* * * *
1838537 CTCAAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGTAC
66 CTCGAAAGACTTACAGATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGAAC
* * * * *
1838602 TTATTAATGGATTTACTTCACTACTCTTCGGTGGAGCCTTACAAATT
131 TTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATT
* * * *
1838649 ACCCGAACGATTTAATCATCATGCTCAAAAGACTTACTGATGTCCCGAAGGACTTCATCATCATG
1 ACCCGAACGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTAATCATCATA
* * *
1838714 CTCGAAAGACTTACAAATGACTCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATAGAAC
66 CTCGAAAGACTTACAGATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGAAC
* *
1838779 TTACTGATGGATTTGTTTCACTACTCTTCAGTGAAGGCTTACAAATT
131 TTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATT
* ** * * * ** *
1838826 ACTCGAATAATTTAATCATCATGCTCGAAAGACTTATTGATGGCCCAAAGGACTCCATCATCATG
1 ACCCGAACGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTAATCATCATA
* * *
1838891 CTCGAAAGACTTA-ATGACGACCCAAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCA
66 CTCGAAAGACTTACA-GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGAA
*
1838955 CTTACTGAGGGATTTGCTTCACTACTCCTT-GGTGAAGGCTTACAAATT
130 CTTACTGATGGATTTGCTTCACTACT-CTTCGGTGAAGGCTTACAAATT
* * * *
1839003 ACCTGAAGGATTTAATCATCTTGCTCGAAAGACTTACTGATGACCCGAAGGACTTAATCATCACA
1 ACCCGAACGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTAATCATCATA
1839068 CTCGAAAGACTTAC
66 CTCGAAAGACTTAC
1839082 TGATAGATTT
Statistics
Matches: 372, Mismatches: 57, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
176 13 0.03
177 356 0.96
178 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (177 bp):
ACCCGAACGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTAATCATCATA
CTCGAAAGACTTACAGATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGAAC
TTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATT
Found at i:1839021 original size:135 final size:129
Alignment explanation
Indices: 1838882--1839984 Score: 1077
Period size: 135 Copynumber: 8.5 Consensus size: 129
1838872 AAAGGACTCC
* * * *
1838882 ATCATCATGCTCGAAAGACTTAATGACGACCCAAAGGATTTCATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
* * *
1838947 TGATGGCACTTACTGAGGGATTTGCTTCACTACTCCTTGGTGAAGGCTTACAAATTACCTGAAGG
66 TGATGG--CTTA-T-AGGG-TTTGCTTCACTACT-CTTCGTGAAGGCTTACAAACTACCCGAAGG
1839012 ATTTA
125 ATTTA
* * **
1839017 ATCATCTTGCTCGAAAGACTTACTGATGACCCGAAGGACTTAATCATCACACTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
* * *
1839082 ---T-G---ATA-GATTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTACCCGAAGGATTTA
66 TGATGGCTTATAGGGTTTGCTTCACTACTC-TTCGTGAAGGCTTACAAACTACCCGAAGGATTTA
* * *
1839139 ATCATCATTCTCGAAAGACTTAATGATGGCCCGAAGGACTTATTCATCATCATGCTCGAAAGACT
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGAC---TTCATCATCATGCTCGAAAGACT
* *
1839204 TAC---T-G---AT-GGGTTTGCTTCACAACTCTTCCGTGAAGGCTTACAAACTACCTGAAGGAT
63 TACTGATGGCTTATAGGGTTTGCTTCACTACTCTT-CGTGAAGGCTTACAAACTACCCGAAGGAT
1839261 TTA
127 TTA
* * * *
1839264 ATCATCATGCTCGTAAGACTTATTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
* * **
1839329 TGATGGGTT-TA-----T--TTCACTACTCTTCTGTGAAGGCTTACAAATTACTTGAAGGATTTA
66 TGATGGCTTATAGGGTTTGCTTCACTACTCTTC-GTGAAGGCTTACAAACTACCCGAAGGATTTA
* * *
1839386 ATCATCATGCTTGAAAGACTTACTAATGGA-CCAAAGGACTTCATCATCATGCTCGAAAGACTTA
1 ATCATCATGCTCGAAAGACTTACTGAT-GACCCGAAGGACTTCATCATCATGCTCGAAAGACTTA
* * *
1839450 C---T-G---AT-GGGTTTTCTTCATTACTCTTTCGTGAAGGCTTATAAACTACCCGAAGGATTT
65 CTGATGGCTTATAGGGTTTGCTTCACTACTC-TTCGTGAAGGCTTACAAACTACCCGAAGGATTT
1839507 A
129 A
* * * *
1839508 ATCATCATGCTTGAAAGACTTAATGATGGCTCGAAGGACTTATTCATCATCATGCTCGAAAGACT
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGAC---TTCATCATCATGCTCGAAAGACT
* * * * * *
1839573 TATTGATGACACTTACTGATGGGTTTGTTTCACTACTTTTTCGTGAAGTCTTACAAACTACCTGA
63 TACTGATG--GCTTA-T-A-GGGTTTGCTTCACTAC-TCTTCGTGAAGGCTTACAAACTACCCGA
1839638 AGGATTTA
122 AGGATTTA
* * * *
1839646 ATTATCATGCTCGAAAGACTTACTGATGGCCGGAAGGACTTCATCATTATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
* * * * *
1839711 TGCTGGCACTTACTGATGGGTTTGCTTCACTACTATTTTGTGAAGGCTTACATATTACCCGAAGG
66 TGATGG--CTTA-T-A-GGGTTTGCTTCACTACT-CTTCGTGAAGGCTTACAAACTACCCGAAGG
1839776 ATTTA
125 ATTTA
* * *
1839781 ATCATCATGCTCGAAAGACTTACTGATGGA-CCAAAAGACTTCATCATCATGCTCGAAATACTTA
1 ATCATCATGCTCGAAAGACTTACTGAT-GACCCGAAGGACTTCATCATCATGCTCGAAAGACTTA
1839845 CTGATGGCACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAACTACCCGAAG
65 CTGATGG--CTTA-T-A-GGGTTTGCTTCACTACTCTT-CGTGAAGGCTTACAAACTACCCGAAG
1839910 GATTTA
124 GATTTA
* * * * * * * *
1839916 ATCATCATGTTGGAAAGACTTCCTGATGTCCCAAACGACTTCATCATCATGATCAAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
1839981 TGAT
66 TGAT
1839985 AGGTTTGCTT
Statistics
Matches: 829, Mismatches: 90, Indels: 98
0.82 0.09 0.10
Matches are distributed among these distances:
116 1 0.00
118 1 0.00
119 1 0.00
120 1 0.00
121 3 0.00
122 272 0.33
123 5 0.01
124 4 0.00
125 133 0.16
126 2 0.00
128 2 0.00
131 1 0.00
132 1 0.00
134 5 0.01
135 317 0.38
136 1 0.00
138 78 0.09
139 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (129 bp):
ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
TGATGGCTTATAGGGTTTGCTTCACTACTCTTCGTGAAGGCTTACAAACTACCCGAAGGATTTA
Found at i:1839078 original size:22 final size:21
Alignment explanation
Indices: 1839026--1839080 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
1839016 AATCATCTTG
* * *
1839026 CTCGAAAGACTTACTGATGAC
1 CTCGAAAGACTTAATCATCAC
*
1839047 C-CGAAGGACTTAATCATCAC
1 CTCGAAAGACTTAATCATCAC
1839067 ACTCGAAAGACTTA
1 -CTCGAAAGACTTA
1839081 CTGATAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 15 0.56
21 2 0.07
22 10 0.37
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (21 bp):
CTCGAAAGACTTAATCATCAC
Found at i:1839172 original size:122 final size:122
Alignment explanation
Indices: 1838954--1840013 Score: 1017
Period size: 122 Copynumber: 8.3 Consensus size: 122
1838944 TACTGATGGC
** * * * *
1838954 ACTTACTGAGGGATTTGCTTCACTACTCCTTGGTGAAGGCTTACAAATTACCTGAAGGATTTAAT
1 ACTTACTGATAGATTTGCTTCACTACTCTTTCGTGAAGGCTTACAAACTACCCGAAGGATTTAAT
* * * *
1839019 CATCTTGCTCGAAAGACTTACTGATGACCCGAAGGACTTAATCATCACACTCGAAAG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATACTCGAAAG
* *
1839076 ACTTACTGATAGATTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATAGATTTGCTTCACTACTCTTTCGTGAAGGCTTACAAACTACCCGAAGGATTTAAT
* * *
1839141 CATCATTCTCGAAAGACTTAATGATGGCCCGAAGGACTTATTCATCATCATGCTCGAAAG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC---TTCATCATCATACTCGAAAG
* * * * *
1839201 ACTTACTGATGGGTTTGCTTCACAACTCTTCCGTGAAGGCTTACAAACTACCTGAAGGATTTAAT
1 ACTTACTGATAGATTTGCTTCACTACTCTTTCGTGAAGGCTTACAAACTACCCGAAGGATTTAAT
* * * *
1839266 CATCATGCTCGTAAGACTTATTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATACTCGAAAG
* * ** * **
1839323 ACTTACTGATGGGTTTATTTCACTACTC-TTCTGTGAAGGCTTACAAATTACTTGAAGGATTTAA
1 ACTTACTGATAGATTTGCTTCACTACTCTTTC-GTGAAGGCTTACAAACTACCCGAAGGATTTAA
* * * * *
1839387 TCATCATGCTTGAAAGACTTACTAATGGACCAAAGGACTTCATCATCATGCTCGAAAG
65 TCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATACTCGAAAG
* * * * *
1839445 ACTTACTGATGGGTTTTCTTCATTACTCTTTCGTGAAGGCTTATAAACTACCCGAAGGATTTAAT
1 ACTTACTGATAGATTTGCTTCACTACTCTTTCGTGAAGGCTTACAAACTACCCGAAGGATTTAAT
* * * *
1839510 CATCATGCTTGAAAGACTTAATGATGGCTCGAAGGACTTATTCATCATCATGCTCGAAAG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC---TTCATCATCATACTCGAAAG
* * * *
1839570 ACTTATTGATGACACTTACTGATGGGTTTGTTTCACTACTTTTTCGTGAAGTCTTACAAACTACC
1 ACTTA---CTG--A--TA--GA----TTTGCTTCACTACTCTTTCGTGAAGGCTTACAAACTACC
* * * * *
1839635 TGAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCGGAAGGACTTCATCATTATGCTC
53 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATACTC
1839700 GAAAG
118 GAAAG
* * * *
1839705 ACTTACTGCTGGCACTTACTGATGGGTTTGCTTCACTACTATTTTGTGAAGGCTTACATATTACC
1 ACTTA---CT-G-A--TA--GA----TTTGCTTCACTACTCTTTCGTGAAGGCTTACAAACTACC
* * * *
1839770 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCAAAAGACTTCATCATCATGCTC
53 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATACTC
*
1839835 GAAAT
118 GAAAG
*
1839840 ACTTACTGATGGCACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAACTACC
1 ACTTAC---T-G-A--TA--GA----TTTGCTTCACTACTCTTTCGTGAAGGCTTACAAACTACC
* * * * * *
1839905 CGAAGGATTTAATCATCATGTTGGAAAGACTTCCTGATGTCCCAAACGACTTCATCATCATGA-T
53 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCAT-ACT
*
1839969 CAAAAG
117 CGAAAG
* * *
1839975 ACTTACTGATAGGTTTGCTTCACCACTCTTCCGTGAAGG
1 ACTTACTGATAGATTTGCTTCACTACTCTTTCGTGAAGG
1840014 ATTTAATCAT
Statistics
Matches: 817, Mismatches: 95, Indels: 52
0.85 0.10 0.05
Matches are distributed among these distances:
121 2 0.00
122 331 0.41
123 3 0.00
125 133 0.16
126 1 0.00
128 4 0.00
130 2 0.00
131 1 0.00
132 3 0.00
134 1 0.00
135 258 0.32
136 1 0.00
138 77 0.09
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (122 bp):
ACTTACTGATAGATTTGCTTCACTACTCTTTCGTGAAGGCTTACAAACTACCCGAAGGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATACTCGAAAG
Found at i:1839858 original size:13 final size:13
Alignment explanation
Indices: 1839840--1839864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1839830 TGCTCGAAAT
1839840 ACTTACTGATGGC
1 ACTTACTGATGGC
1839853 ACTTACTGATGG
1 ACTTACTGATGG
1839865 GTTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:1840236 original size:37 final size:37
Alignment explanation
Indices: 1840195--1840276 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
1840185 TCTTGCTCTA
* *
1840195 AAGGCTTTAGATGGATTTGCTTCACTACTCTTTGGTG
1 AAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTG
1840232 AAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTG
1 AAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTG
1840269 AAGGCTTA
1 AAGGCTTA
1840277 GGATTAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (37 bp):
AAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTG
Found at i:1840292 original size:37 final size:37
Alignment explanation
Indices: 1840195--1840292 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
1840185 TCTTGCTCTA
* * *
1840195 AAGGCTTTAGATGGATTTGCTTCACTACTCTTTGGTG
1 AAGGCTTAAGATGAATTTGCTTCACTACTCTTCGGTG
*
1840232 AAGGCTTAAGATGGATTTGCTTCACTACTCTTCGGTG
1 AAGGCTTAAGATGAATTTGCTTCACTACTCTTCGGTG
* * *
1840269 AAGGCTTAGGATTAATTTACTTCA
1 AAGGCTTAAGATGAATTTGCTTCA
1840293 TTCAAGAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.38
Consensus pattern (37 bp):
AAGGCTTAAGATGAATTTGCTTCACTACTCTTCGGTG
Found at i:1841794 original size:125 final size:124
Alignment explanation
Indices: 1841571--1841807 Score: 359
Period size: 125 Copynumber: 1.9 Consensus size: 124
1841561 CCTTCACTAG
** * *
1841571 TGCCCCAACATTATCTTATACTGGTACGGACCTTCAAAATGCCCCAACACCTCAAATTGTAAGGC
1 TGCCCCAACATTATCTTATACTAATACGGA-CTTCAAAATGCCCCAACACCACAAATTGTAAGGA
* *
1841636 TCATTCTCAATGCCTTCTTTGTCTAAATGTTGTCATCTCAACATGATGTGGGTTCAGTCA
65 TCATTCTCAATGCCTTCTTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCA
1841696 TGCCCCAACATTATCTTATACTAATACGAGTA-TTCAAAATGCCCCAACACCACAAATTGTAAGG
1 TGCCCCAACATTATCTTATACTAATACG-G-ACTTCAAAATGCCCCAACACCACAAATTGTAAGG
* * *
1841760 ATCATTCTCAATTCCTTCTTGGTCTGAATCTTGTCATCTCATCATGAT
64 ATCATTCTCAATGCCTTCTTGGTCTAAATCTTGTCATCTCAACATGAT
1841808 TTAGGTTTTT
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
125 99 0.98
126 1 0.01
127 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (124 bp):
TGCCCCAACATTATCTTATACTAATACGGACTTCAAAATGCCCCAACACCACAAATTGTAAGGAT
CATTCTCAATGCCTTCTTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCA
Found at i:1851233 original size:3 final size:3
Alignment explanation
Indices: 1851225--1851263 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
1851215 TTTATCCATA
*
1851225 TAT TAT TAT TAT TAT TAT TAT TAAC TATT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T-AT TA-T TAT TAT TAT T
1851264 GTGTTTTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 28 0.88
4 4 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1862716 original size:83 final size:83
Alignment explanation
Indices: 1862577--1862742 Score: 287
Period size: 83 Copynumber: 2.0 Consensus size: 83
1862567 AATATACTCT
* *
1862577 TATAGAAATTATGTTCGAACTTAAGACCTCAAGCGATAACAACAATCATTTAACCATTGAAGTGT
1 TATAGAAATTATGTTCAAACTTAAGACCTCAAACGATAACAACAATCATTTAACCATTGAAGTGT
1862642 TTGATTCATGTGATAATC
66 TTGATTCATGTGATAATC
* * *
1862660 TATAGAAGTTATGTTCAAACTTAAGACCTCAAACGATAACAACAATCCTTTAACCATTGAATTGT
1 TATAGAAATTATGTTCAAACTTAAGACCTCAAACGATAACAACAATCATTTAACCATTGAAGTGT
1862725 TTGATTCATGTGATAATC
66 TTGATTCATGTGATAATC
1862743 ATACTTTGAA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (83 bp):
TATAGAAATTATGTTCAAACTTAAGACCTCAAACGATAACAACAATCATTTAACCATTGAAGTGT
TTGATTCATGTGATAATC
Found at i:1865631 original size:21 final size:21
Alignment explanation
Indices: 1865607--1865650 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1865597 CAAATCTGTT
1865607 TTGT-TAATATAATAAATAAAA
1 TTGTCTAATATAA-AAATAAAA
* *
1865628 TTGTCTGATTTAAAAATAAAA
1 TTGTCTAATATAAAAATAAAA
1865649 TT
1 TT
1865651 TAATTAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (21 bp):
TTGTCTAATATAAAAATAAAA
Found at i:1865717 original size:18 final size:19
Alignment explanation
Indices: 1865664--1865717 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
1865654 TTAACAATTA
1865664 AAATTTAATTTAATA-TAGT
1 AAATTT-ATTTAATACTAGT
1865683 AATATTTATTT-ATACTA-T
1 AA-ATTTATTTAATACTAGT
1865701 AAATTTATTTAATACTA
1 AAATTTATTTAATACTA
1865718 ATTATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.25
18 12 0.38
19 8 0.25
20 4 0.12
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (19 bp):
AAATTTATTTAATACTAGT
Done.