Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 54
Found at i:1649771 original size:9 final size:9
Alignment explanation
Indices: 1649741--1649790 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
1649731 TTATAGCCTC
1649741 TCTTTTTTT
1 TCTTTTTTT
* *
1649750 TC-TTTCTC
1 TCTTTTTTT
1649758 T-TTTTTTT
1 TCTTTTTTT
1649766 TCTTTTTTT
1 TCTTTTTTT
*
1649775 TATTTTTTT
1 TCTTTTTTT
1649784 TCTTTTT
1 TCTTTTT
1649791 ACTATTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 10 0.30
9 23 0.70
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:1649791 original size:15 final size:14
Alignment explanation
Indices: 1649741--1649790 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1649731 TTATAGCCTC
*
1649741 TCTTTTTTTTCTTTC
1 TCTTTTTTTT-TTTT
1649756 TCTTTTTTTTTCTTT
1 TCTTTTTTTTT-TTT
*
1649771 T-TTTTATTTTTTT
1 TCTTTTTTTTTTTT
1649784 TCTTTTT
1 TCTTTTT
1649791 ACTATTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 4 0.13
14 13 0.43
15 13 0.43
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (14 bp):
TCTTTTTTTTTTTT
Found at i:1649796 original size:18 final size:17
Alignment explanation
Indices: 1649743--1649797 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
1649733 ATAGCCTCTC
*
1649743 TTTTTTTTCTTTCTCT-
1 TTTTTTTTCTTTTTCTA
*
1649759 TTTTTTTTCTTTTTTTTA
1 TTTTTTTTC-TTTTTCTA
1649777 TTTTTTTTCTTTTTACTA
1 TTTTTTTTCTTTTT-CTA
1649795 TTT
1 TTT
1649798 GAAACTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.27
17 10 0.30
18 14 0.42
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCTTTTTCTA
Found at i:1651972 original size:29 final size:30
Alignment explanation
Indices: 1651915--1651982 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1651905 TGTATTGAGC
* * * *
1651915 AATACAAATGTAATGCAAACAAAAGAAATT
1 AATAAAAATGTAATGCAAAAAAAAAAAATA
1651945 AATATAAAATGT-ATG-AAAAAAAAAAAATA
1 AATA-AAAATGTAATGCAAAAAAAAAAAATA
1651974 AATAAAAAT
1 AATAAAAAT
1651983 AAGAAGACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 5 0.15
29 15 0.45
30 7 0.21
31 6 0.18
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (30 bp):
AATAAAAATGTAATGCAAAAAAAAAAAATA
Found at i:1653331 original size:28 final size:28
Alignment explanation
Indices: 1653300--1653365 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
1653290 ATTTAAAAAT
*
1653300 ATAAATAAAAATAAA-GA-TAGAAAATTAA
1 ATAAATGAAAATAAAGGACT-G-AAATTAA
*
1653328 AT-AATGAAATTAAAGGACTGAAATTAA
1 ATAAATGAAAATAAAGGACTGAAATTAA
1653355 ATAAATGAAAA
1 ATAAATGAAAA
1653366 GATGTAAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 19 0.59
28 12 0.38
29 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.23
Consensus pattern (28 bp):
ATAAATGAAAATAAAGGACTGAAATTAA
Found at i:1653336 original size:14 final size:13
Alignment explanation
Indices: 1653321--1653364 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1653311 TAAAGATAGA
1653321 AAATTAAATAATG
1 AAATTAAATAATG
* *
1653334 AAATTAAAGGACTG
1 AAATTAAA-TAATG
1653348 AAATTAAATAAATG
1 AAATTAAAT-AATG
1653362 AAA
1 AAA
1653365 AGATGTAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.25
Consensus pattern (13 bp):
AAATTAAATAATG
Found at i:1663552 original size:16 final size:16
Alignment explanation
Indices: 1663527--1663557 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1663517 GCTTCTAAAT
*
1663527 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
1663543 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
1663558 TTTCAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:1664178 original size:54 final size:54
Alignment explanation
Indices: 1664092--1664219 Score: 188
Period size: 54 Copynumber: 2.4 Consensus size: 54
1664082 TTTGTATGTA
* *
1664092 TTTGATTATTTCTTTTAAGTTGCGATAGTAATTAAAAAAATACTTGTGGAT-ATT
1 TTTGATTATTTCTTTTAAGTTACGATAGTAATTAAAAAAATACTTGT-GATCAAT
* *
1664146 TTTGATTATTTCTTTTAAGTTATGATATTAATTAAAAAAATACTTGTGATCAAT
1 TTTGATTATTTCTTTTAAGTTACGATAGTAATTAAAAAAATACTTGTGATCAAT
*
1664200 TTT-ATTGTTTCTTTTAAGTT
1 TTTGATTATTTCTTTTAAGTT
1664220 GTATTTTTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
53 19 0.28
54 49 0.72
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (54 bp):
TTTGATTATTTCTTTTAAGTTACGATAGTAATTAAAAAAATACTTGTGATCAAT
Found at i:1669057 original size:13 final size:13
Alignment explanation
Indices: 1669039--1669113 Score: 150
Period size: 13 Copynumber: 5.8 Consensus size: 13
1669029 TTTTGATCGG
1669039 TTCTCATTTTCGC
1 TTCTCATTTTCGC
1669052 TTCTCATTTTCGC
1 TTCTCATTTTCGC
1669065 TTCTCATTTTCGC
1 TTCTCATTTTCGC
1669078 TTCTCATTTTCGC
1 TTCTCATTTTCGC
1669091 TTCTCATTTTCGC
1 TTCTCATTTTCGC
1669104 TTCTCATTTT
1 TTCTCATTTT
1669114 TTATGCTCCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 62 1.00
ACGTcount: A:0.08, C:0.29, G:0.07, T:0.56
Consensus pattern (13 bp):
TTCTCATTTTCGC
Found at i:1669534 original size:75 final size:77
Alignment explanation
Indices: 1669349--1669534 Score: 211
Period size: 75 Copynumber: 2.5 Consensus size: 77
1669339 ATGTTCATCT
* * * *
1669349 AGACTTAATATTATGGTTTAAGTCTTAAGATTTGACACTTTAATATTATAGTTTGATTATGGATT
1 AGACTTAATATTGTGGTTTGAGTCTTGAGATTTGACACTTTAATATTATAGTTCGATTATGGATT
1669414 TTATTATTCTAG
66 TTATTATTCTAG
* * * * *
1669426 AGA--TAATATTGTGGTTTGAATCTTGAGACTTGACATTTTAATATTGTTA-TTCGTTTATGGAT
1 AGACTTAATATTGTGGTTTGAGTCTTGAGATTTGACACTTTAATATT-ATAGTTCGATTATGGAT
* *
1669488 TTTATTGTT-TTG
65 TTTATTATTCTAG
* *
1669500 A-ACTTAATATTGTGGTTTGAGTTTTGATATTTGAC
1 AGACTTAATATTGTGGTTTGAGTCTTGAGATTTGAC
1669535 TTTATTTATA
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
73 1 0.01
74 3 0.03
75 82 0.90
76 2 0.02
77 3 0.03
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.49
Consensus pattern (77 bp):
AGACTTAATATTGTGGTTTGAGTCTTGAGATTTGACACTTTAATATTATAGTTCGATTATGGATT
TTATTATTCTAG
Found at i:1670856 original size:24 final size:24
Alignment explanation
Indices: 1670835--1670881 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1670825 TGCTCTCCCG
*
1670835 AATCCCTAACCCTTCTTTCTCCAA
1 AATCCCTAACCCTCCTTTCTCCAA
1670859 AATCCCTAACCCTCCTTTCTCCA
1 AATCCCTAACCCTCCTTTCTCCA
1670882 TTCCCAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (24 bp):
AATCCCTAACCCTCCTTTCTCCAA
Found at i:1681912 original size:2 final size:2
Alignment explanation
Indices: 1681905--1681971 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1681895 CGACATCATT
1681905 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1681947 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1681972 CCAATCGATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1682439 original size:13 final size:13
Alignment explanation
Indices: 1682421--1682479 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
1682411 GTCATAAATA
1682421 TATGACGCACATT
1 TATGACGCACATT
* *
1682434 TATGACACGCATT
1 TATGACGCACATT
*
1682447 TATGACACACATT
1 TATGACGCACATT
*
1682460 TATGACGTACATT
1 TATGACGCACATT
*
1682473 AATGACG
1 TATGACG
1682480 TTCATTGAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:1685160 original size:39 final size:40
Alignment explanation
Indices: 1685103--1685185 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 40
1685093 TTTCTTTCTT
* *
1685103 TTTTTCCATTTTCAGTGTCCCTTCTTCTTT-CTCCTCTTCC
1 TTTTTCCATTTGCAGTGTCCCTTCTCCTTTAC-CCTCTTCC
1685143 TTTTTCC-TTTGCAGTGTCCCTTCTCCTTTACCCTCTTCC
1 TTTTTCCATTTGCAGTGTCCCTTCTCCTTTACCCTCTTCC
1685182 TTTT
1 TTTT
1685186 CTTTCTCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
39 32 0.80
40 8 0.20
ACGTcount: A:0.05, C:0.35, G:0.06, T:0.54
Consensus pattern (40 bp):
TTTTTCCATTTGCAGTGTCCCTTCTCCTTTACCCTCTTCC
Found at i:1685218 original size:26 final size:25
Alignment explanation
Indices: 1685138--1685231 Score: 68
Period size: 26 Copynumber: 3.7 Consensus size: 25
1685128 TCTTTCTCCT
1685138 CTTC-CTTTTTCCT-TTGCAGTGTCC
1 CTTCTCTTTTTCCTCTT-CAGTGTCC
** * * *
1685162 CTTCTCCTTTACCCTCTTC-CTTTTC
1 CTTCT-CTTTTTCCTCTTCAGTGTCC
*
1685187 TTTCTCTTTTTCCATCTTCAGTGTCC
1 CTTCTCTTTTTCC-TCTTCAGTGTCC
*
1685213 CTTCTCCTTTCTCCTCTTC
1 CTTCT-CTTTTTCCTCTTC
1685232 CTTTTCAACA
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
24 10 0.20
25 12 0.24
26 20 0.39
27 9 0.18
ACGTcount: A:0.04, C:0.38, G:0.05, T:0.52
Consensus pattern (25 bp):
CTTCTCTTTTTCCTCTTCAGTGTCC
Found at i:1685223 original size:25 final size:25
Alignment explanation
Indices: 1685154--1685223 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
1685144 TTTTCCTTTG
*
1685154 CAGTGTCCCTTCTCCTTTACCCTCTT
1 CAGTGTCCCTTCTCCTTT-CCATCTT
* * * * *
1685180 C-CTTTTCTTTCTCTTTTTCCATCTT
1 CAGTGTCCCTTCTC-CTTTCCATCTT
1685205 CAGTGTCCCTTCTCCTTTC
1 CAGTGTCCCTTCTCCTTTC
1685224 TCCTCTTCCT
Statistics
Matches: 31, Mismatches: 11, Indels: 5
0.66 0.23 0.11
Matches are distributed among these distances:
25 19 0.61
26 12 0.39
ACGTcount: A:0.06, C:0.39, G:0.06, T:0.50
Consensus pattern (25 bp):
CAGTGTCCCTTCTCCTTTCCATCTT
Found at i:1691561 original size:23 final size:23
Alignment explanation
Indices: 1691535--1691579 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1691525 TGAAAAGAAT
1691535 AATCCAAACAACATATAAAGCAA
1 AATCCAAACAACATATAAAGCAA
1691558 AATCCAAACAACATATAAAGCA
1 AATCCAAACAACATATAAAGCA
1691580 GAAAAAGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.60, C:0.22, G:0.04, T:0.13
Consensus pattern (23 bp):
AATCCAAACAACATATAAAGCAA
Found at i:1691585 original size:26 final size:26
Alignment explanation
Indices: 1691530--1691585 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 26
1691520 TCAAATGAAA
*
1691530 AGAATAATCCAAACAACATATAAAGC
1 AGAAAAATCCAAACAACATATAAAGC
1691556 ---AAAATCCAAACAACATATAAAGC
1 AGAAAAATCCAAACAACATATAAAGC
1691579 AGAAAAA
1 AGAAAAA
1691586 GGCAGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 22 0.85
26 4 0.15
ACGTcount: A:0.62, C:0.18, G:0.07, T:0.12
Consensus pattern (26 bp):
AGAAAAATCCAAACAACATATAAAGC
Found at i:1702635 original size:30 final size:30
Alignment explanation
Indices: 1702599--1702660 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1702589 ACATGGATAT
*
1702599 GATTGAATACAATAGAGGGTGTGAAGTGAG
1 GATTGAATACAATAGAGGGCGTGAAGTGAG
1702629 GATTGAATACAATAGAGGGCGTGAAGTGAG
1 GATTGAATACAATAGAGGGCGTGAAGTGAG
1702659 GA
1 GA
1702661 GCTTGCCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.05, G:0.37, T:0.21
Consensus pattern (30 bp):
GATTGAATACAATAGAGGGCGTGAAGTGAG
Found at i:1703466 original size:18 final size:20
Alignment explanation
Indices: 1703425--1703466 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1703415 CATCCTAAGG
*
1703425 CATGATTCTTCATTAAAAAT
1 CATGAATCTTCATTAAAAAT
1703445 CATGAATCTTCA-TAAAAA-
1 CATGAATCTTCATTAAAAAT
1703463 CATG
1 CATG
1703467 TGTTTTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 11 0.52
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (20 bp):
CATGAATCTTCATTAAAAAT
Found at i:1704997 original size:26 final size:26
Alignment explanation
Indices: 1704952--1705053 Score: 107
Period size: 26 Copynumber: 3.9 Consensus size: 26
1704942 AAGTGCTAAT
* *
1704952 ACACATAAAGG-CGTGTCCACCATAAT
1 ACACA-AAAGGTCGTGCCCACCATAAA
*
1704978 ACACAAAAGGTCATGCCCACCATAAA
1 ACACAAAAGGTCGTGCCCACCATAAA
* * * *
1705004 ATAGATAAGGTTGTGCCCACCATAAA
1 ACACAAAAGGTCGTGCCCACCATAAA
* *
1705030 ACAGATAAGGTCGTGCCCACCATA
1 ACACAAAAGGTCGTGCCCACCATA
1705054 TTCACTCCGT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
25 5 0.08
26 60 0.92
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (26 bp):
ACACAAAAGGTCGTGCCCACCATAAA
Found at i:1721033 original size:21 final size:20
Alignment explanation
Indices: 1720996--1721047 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1720986 CACTAGAAAC
1720996 CTAGCTAAGCTACCTACGTCAT
1 CTAGCT-AGCTACCTACG-CAT
* * *
1721018 CTATCTAGCTATCTACGCTT
1 CTAGCTAGCTACCTACGCAT
1721038 CTAGCTAGCT
1 CTAGCTAGCT
1721048 TACTAACCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 11 0.42
21 10 0.38
22 5 0.19
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (20 bp):
CTAGCTAGCTACCTACGCAT
Found at i:1728519 original size:21 final size:21
Alignment explanation
Indices: 1728495--1728611 Score: 225
Period size: 21 Copynumber: 5.6 Consensus size: 21
1728485 ATGGATGTTT
1728495 ACATTCATCCTAAGAATGTCC
1 ACATTCATCCTAAGAATGTCC
1728516 ACATTCATCCTAAGAATGTCC
1 ACATTCATCCTAAGAATGTCC
1728537 ACATTCATCCTAAGAATGTCC
1 ACATTCATCCTAAGAATGTCC
1728558 ACATTCATCCTAAGAATGTCC
1 ACATTCATCCTAAGAATGTCC
*
1728579 ACATTCATCCTAAGAATGTCT
1 ACATTCATCCTAAGAATGTCC
1728600 ACATTCATCCTA
1 ACATTCATCCTA
1728612 CAATTCATAT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 95 1.00
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (21 bp):
ACATTCATCCTAAGAATGTCC
Found at i:1729757 original size:7 final size:7
Alignment explanation
Indices: 1729747--1729789 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
1729737 TAATTAAGTA
1729747 TTAAATT
1 TTAAATT
1729754 TTAAAGTT
1 TTAAA-TT
*
1729762 TTAAATA
1 TTAAATT
1729769 TTAAATT
1 TTAAATT
1729776 TTAAATT
1 TTAAATT
1729783 TTAAATT
1 TTAAATT
1729790 CTAATATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (7 bp):
TTAAATT
Found at i:1729765 original size:15 final size:15
Alignment explanation
Indices: 1729742--1729787 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1729732 TTATTTAATT
*
1729742 AAGTATTAAATTTTA
1 AAGTTTTAAATTTTA
*
1729757 AAGTTTTAAATATTA
1 AAGTTTTAAATTTTA
1729772 AA-TTTTAAATTTTA
1 AAGTTTTAAATTTTA
1729786 AA
1 AA
1729788 TTCTAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (15 bp):
AAGTTTTAAATTTTA
Found at i:1729799 original size:21 final size:21
Alignment explanation
Indices: 1729740--1729788 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
1729730 TTTTATTTAA
*
1729740 TTAAGTATTAAATTTTAAAGTT
1 TTAAATATTAAATTTTAAA-TT
1729762 TTAAATATTAAATTTTAAATT
1 TTAAATATTAAATTTTAAATT
1729783 TTAAAT
1 TTAAAT
1729789 TCTAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
TTAAATATTAAATTTTAAATT
Found at i:1732917 original size:8 final size:8
Alignment explanation
Indices: 1732904--1732934 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1732894 AAACAATTCA
1732904 TCTTCTTC
1 TCTTCTTC
1732912 TCTTCTTC
1 TCTTCTTC
1732920 ATCTTCTTC
1 -TCTTCTTC
1732929 TCTTCT
1 TCTTCT
1732935 CCAACGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.61
Consensus pattern (8 bp):
TCTTCTTC
Found at i:1732932 original size:14 final size:17
Alignment explanation
Indices: 1732900--1732934 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1732890 TTCCAAACAA
1732900 TTCATCTTCTTCTCTTC
1 TTCATCTTCTTCTCTTC
1732917 TTCATCTTCTTCTCTTC
1 TTCATCTTCTTCTCTTC
1732934 T
1 T
1732935 CCAACGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (17 bp):
TTCATCTTCTTCTCTTC
Found at i:1734090 original size:22 final size:22
Alignment explanation
Indices: 1734065--1734117 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1734055 GCGGTCATTT
*
1734065 GGGACATATACAGAGGTCCTTC
1 GGGACAAATACAGAGGTCCTTC
* **
1734087 GGGACAAATACATAGGTGTTTC
1 GGGACAAATACAGAGGTCCTTC
1734109 GGGACAAAT
1 GGGACAAAT
1734118 TTCACATTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (22 bp):
GGGACAAATACAGAGGTCCTTC
Found at i:1734748 original size:12 final size:12
Alignment explanation
Indices: 1734731--1734771 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1734721 TTATAGCATT
1734731 CGGTACTGTTCA
1 CGGTACTGTTCA
*
1734743 CGGTACTATTCA
1 CGGTACTGTTCA
*
1734755 --TTACTGTTCA
1 CGGTACTGTTCA
1734765 CGGTACT
1 CGGTACT
1734772 ATTGATTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 8 0.35
12 15 0.65
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (12 bp):
CGGTACTGTTCA
Found at i:1734818 original size:22 final size:22
Alignment explanation
Indices: 1734734--1734815 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
1734724 TAGCATTCGG
1734734 TACTGTTCACGGTACTATTCAT
1 TACTGTTCACGGTACTATTCAT
*
1734756 TACTGTTCACGGTACTATTGAT
1 TACTGTTCACGGTACTATTCAT
* * *
1734778 TACTGTTCATGGTAATGTTCAT
1 TACTGTTCACGGTACTATTCAT
* *
1734800 TATTGTTCATGGTACT
1 TACTGTTCACGGTACT
1734816 GTTAATATCA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (22 bp):
TACTGTTCACGGTACTATTCAT
Found at i:1736833 original size:24 final size:24
Alignment explanation
Indices: 1736798--1736844 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1736788 CAACAAGTTG
*
1736798 ACTCGATCTGAGCTGACTCAATCT
1 ACTCGATCTGAGCTGACCCAATCT
* *
1736822 ACTCGATTTGAGTTGACCCAATC
1 ACTCGATCTGAGCTGACCCAATC
1736845 AACTAGGTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (24 bp):
ACTCGATCTGAGCTGACCCAATCT
Found at i:1736957 original size:13 final size:13
Alignment explanation
Indices: 1736939--1736966 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1736929 AACGTGTACA
1736939 ACATGCGACGGAG
1 ACATGCGACGGAG
1736952 ACATGCGACGGAG
1 ACATGCGACGGAG
1736965 AC
1 AC
1736967 GGGGATGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.25, G:0.36, T:0.07
Consensus pattern (13 bp):
ACATGCGACGGAG
Found at i:1746039 original size:14 final size:14
Alignment explanation
Indices: 1746020--1746074 Score: 101
Period size: 14 Copynumber: 3.9 Consensus size: 14
1746010 AAAATTTCTT
*
1746020 TTCAATTTCTGAGC
1 TTCAATTTTTGAGC
1746034 TTCAATTTTTGAGC
1 TTCAATTTTTGAGC
1746048 TTCAATTTTTGAGC
1 TTCAATTTTTGAGC
1746062 TTCAATTTTTGAG
1 TTCAATTTTTGAG
1746075 TAATTTCCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.49
Consensus pattern (14 bp):
TTCAATTTTTGAGC
Found at i:1748242 original size:11 final size:11
Alignment explanation
Indices: 1748226--1748250 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1748216 ATTCCCCCAC
1748226 TGATAGCGTTA
1 TGATAGCGTTA
1748237 TGATAGCGTTA
1 TGATAGCGTTA
1748248 TGA
1 TGA
1748251 AGTGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (11 bp):
TGATAGCGTTA
Found at i:1749847 original size:113 final size:113
Alignment explanation
Indices: 1749711--1749938 Score: 438
Period size: 113 Copynumber: 2.0 Consensus size: 113
1749701 TAAGAAGACC
1749711 CTACATTCTACAAAACATGTTTAAAGACCTTGTGTTCTAAGAAAAATGAGTTTTATGTATTTATT
1 CTACATTCTACAAAACATGTTTAAAGACCTTGTGTTCTAAGAAAAATGAGTTTTATGTATTTATT
*
1749776 GTGCCTTTATCCAAAAATTAAATGGAGTTATCTGAAAAGTTAGTGCAT
66 GTGCCTTTATCCAAAAATTAAATGGAGTTATCTGAAAAGTTAATGCAT
*
1749824 CTACATTCTACAAAACGTGTTTAAAGACCTTGTGTTCTAAGAAAAATGAGTTTTATGTATTTATT
1 CTACATTCTACAAAACATGTTTAAAGACCTTGTGTTCTAAGAAAAATGAGTTTTATGTATTTATT
1749889 GTGCCTTTATCCAAAAATTAAATGGAGTTATCTGAAAAGTTAATGCAT
66 GTGCCTTTATCCAAAAATTAAATGGAGTTATCTGAAAAGTTAATGCAT
1749937 CT
1 CT
1749939 TGTATTATGT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (113 bp):
CTACATTCTACAAAACATGTTTAAAGACCTTGTGTTCTAAGAAAAATGAGTTTTATGTATTTATT
GTGCCTTTATCCAAAAATTAAATGGAGTTATCTGAAAAGTTAATGCAT
Found at i:1750768 original size:29 final size:29
Alignment explanation
Indices: 1750726--1750814 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
1750716 CTACAGTGGT
1750726 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1750755 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1750784 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1750813 CT
1 CT
1750815 GTGGTATTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:1750871 original size:17 final size:16
Alignment explanation
Indices: 1750849--1750924 Score: 88
Period size: 15 Copynumber: 4.8 Consensus size: 16
1750839 ATGCAATCAA
1750849 CATGGGACGTGGGAATG
1 CATGGGA-GTGGGAATG
1750866 CATGGGGAG-GGG-ATG
1 CAT-GGGAGTGGGAATG
1750881 CATGGGACGTGGGAATG
1 CATGGGA-GTGGGAATG
1750898 CATGGG-GTGGGAATG
1 CATGGGAGTGGGAATG
*
1750913 CAGGGGAG-GGGA
1 CATGGGAGTGGGA
1750925 TGGTGCATTG
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
14 4 0.08
15 25 0.47
16 7 0.13
17 13 0.25
18 4 0.08
ACGTcount: A:0.22, C:0.09, G:0.54, T:0.14
Consensus pattern (16 bp):
CATGGGAGTGGGAATG
Found at i:1750883 original size:15 final size:15
Alignment explanation
Indices: 1750863--1750926 Score: 69
Period size: 14 Copynumber: 4.2 Consensus size: 15
1750853 GGACGTGGGA
1750863 ATGCATGGGGAGGGG
1 ATGCATGGGGAGGGG
1750878 ATGCAT-GGGACGTGGG
1 ATGCATGGGGA-G-GGG
* *
1750894 AATGCATGGGGTGGGA
1 -ATGCATGGGGAGGGG
1750910 ATGCA-GGGGAGGGG
1 ATGCATGGGGAGGGG
1750924 ATG
1 ATG
1750927 GTGCATTGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 14 0.34
15 12 0.29
16 5 0.12
17 7 0.17
18 3 0.07
ACGTcount: A:0.22, C:0.08, G:0.55, T:0.16
Consensus pattern (15 bp):
ATGCATGGGGAGGGG
Found at i:1750885 original size:32 final size:32
Alignment explanation
Indices: 1750849--1750919 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
1750839 ATGCAATCAA
*
1750849 CATGGGACGTGGGAATGCATGGGGAGGGGATG
1 CATGGGACGTGGGAATGCATGGGGAGGGAATG
*
1750881 CATGGGACGTGGGAATGCATGGGGTGGGAATG
1 CATGGGACGTGGGAATGCATGGGGAGGGAATG
*
1750913 CAGGGGA
1 CATGGGA
1750920 GGGGATGGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.23, C:0.10, G:0.52, T:0.15
Consensus pattern (32 bp):
CATGGGACGTGGGAATGCATGGGGAGGGAATG
Found at i:1751503 original size:41 final size:46
Alignment explanation
Indices: 1751414--1751515 Score: 133
Period size: 47 Copynumber: 2.3 Consensus size: 46
1751404 TTAAGTATAT
1751414 ATTAGTTTATTAGTTTAAGTTATATATATTATATAAAAAATTAGTTA
1 ATTAGTTTATTAGTTTAAGTTATATATA-TATATAAAAAATTAGTTA
*
1751461 ATTAGTTTCTTAGTTTAAGTTAT-TA-A-ATATAAAAAA-TA-TTA
1 ATTAGTTTATTAGTTTAAGTTATATATATATATAAAAAATTAGTTA
* *
1751502 ATTAATTTGTTAGT
1 ATTAGTTTATTAGT
1751516 GTCTTTAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
41 15 0.29
42 2 0.04
43 10 0.19
45 1 0.02
46 2 0.04
47 22 0.42
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (46 bp):
ATTAGTTTATTAGTTTAAGTTATATATATATATAAAAAATTAGTTA
Found at i:1755366 original size:16 final size:17
Alignment explanation
Indices: 1755333--1755383 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
1755323 AAATGATTTA
1755333 ATAATGATTT-A-AATAT
1 ATAATGATTTGATAAT-T
*
1755349 TTAATGATTTGATAATTT
1 ATAATGATTTGATAA-TT
1755367 AGTAATGATTTGATAAT
1 A-TAATGATTTGATAAT
1755384 AATCATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 9 0.31
17 1 0.03
18 4 0.14
19 15 0.52
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
ATAATGATTTGATAATT
Found at i:1755395 original size:26 final size:25
Alignment explanation
Indices: 1755369--1755578 Score: 185
Period size: 26 Copynumber: 8.6 Consensus size: 25
1755359 GATAATTTAG
1755369 TAATGATTTGATAATAATCATTATA
1 TAATGATTTGATAATAATCATTATA
1755394 GTAATGATTTGATAATAATCATTATAA
1 -TAATGATTTGATAATAATCATTAT-A
1755421 TAATGATTT-AGTAATAATCATTATA
1 TAATGATTTGA-TAATAATCATTATA
* *
1755446 -AA--AATT--TAATAATGATT-TA
1 TAATGATTTGATAATAATCATTATA
* * * *
1755465 -AAT-ATTTAATGATTTGATGATT-TA
1 TAATGATTTGAT-A-ATAATCATTATA
1755489 GTAATGATTTGATAATAATCATTATA
1 -TAATGATTTGATAATAATCATTATA
1755515 GTAATGATTTGATAATAATCA-T-TA
1 -TAATGATTTGATAATAATCATTATA
1755539 TAATGATTT-AGTAATAATCATTATA
1 TAATGATTTGA-TAATAATCATTATA
* *
1755564 AAATGATTTAATAAT
1 TAATGATTTGATAAT
1755579 GATTTAAATT
Statistics
Matches: 159, Mismatches: 10, Indels: 31
0.80 0.05 0.16
Matches are distributed among these distances:
19 4 0.03
20 13 0.08
22 5 0.03
23 19 0.12
24 14 0.09
25 23 0.14
26 74 0.47
27 7 0.04
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (25 bp):
TAATGATTTGATAATAATCATTATA
Found at i:1755471 original size:19 final size:20
Alignment explanation
Indices: 1755432--1755474 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1755422 AATGATTTAG
1755432 TAATAATCATTATAAAAATT
1 TAATAATCATTATAAAAATT
* *
1755452 TAATAATGATT-TAAATATT
1 TAATAATCATTATAAAAATT
1755471 TAAT
1 TAAT
1755475 GATTTGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATAATCATTATAAAAATT
Found at i:1755519 original size:121 final size:122
Alignment explanation
Indices: 1755311--1755945 Score: 939
Period size: 121 Copynumber: 5.3 Consensus size: 122
1755301 ATGTATTTAT
*
1755311 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATAATTTAGTAATGAT
1 TAATCATTAT-AAAA-GATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1755376 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
64 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1755435 TAATCATTATAAAA-ATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
1 TAATCATTATAAAAGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
1755499 GATAATAATCATTATAGTAATGATTTGATAATAATCA-T-T-ATAATGATTTAGTAA
66 GATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
1755553 TAATCATTATAAAATGATTTAATAATGATTTAAATTTTTAATGATTTGATG----A-TAATGATT
1 TAATCATTATAAAA-GATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
1755613 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TTAGTAA
65 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
1755670 TAATCATTATAAAAATGATTTAATAATGATTTAAATTTTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTAT-AAAA-GATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1755735 TTG--AATAATCATTATAGTAATGATTTGATAATAATCATTA-AATAATGATTTAGTAA
64 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1755791 TAATCATTATAAAAATGATTT-A-AAT-ATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTAT-AAAA-GATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
1755853 TTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTAA
64 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
1755911 TTAT--TTATAATAATGATTTTATACTAATGATTTAA
1 TAATCATTATAA-AA-GA-TTTA-A-TAATGATTTAA
1755946 TAATTATTAG
Statistics
Matches: 479, Mismatches: 10, Indels: 44
0.90 0.02 0.08
Matches are distributed among these distances:
115 46 0.10
116 2 0.00
117 20 0.04
118 125 0.26
119 7 0.01
120 93 0.19
121 152 0.32
122 1 0.00
123 17 0.04
124 16 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (122 bp):
TAATCATTATAAAAGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTT
GATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:1755548 original size:95 final size:104
Alignment explanation
Indices: 1755481--1755791 Score: 283
Period size: 115 Copynumber: 2.9 Consensus size: 104
1755471 TAATGATTTG
*
1755481 ATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATGAT
1 ATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAAT
1755546 TTAGTAATAATCATTATAAAATGATTTAATAATGATTTAAATTTTTA
66 TTA-TAATAATCATTATAAAATGATTT-ATAATG-----AA-TTTTA
1755593 ATGATTTGATGATAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAT
1 ATGATTT-A-G-TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAT
1755658 AATGATTAGTAATAATCATTATAAAAATGATTTAATAATG-A-TTTA
63 AAT--TTA-TAATAATCATTAT-AAAATGATTT-ATAATGAATTTTA
* *
1755703 A--ATTT-TTAATGATTTG------ATGATT-TAGTAATGATTTG--AATAATCATTATAGTAAT
1 ATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCA-T-TA-TAAT
*
1755756 GATTTGATAATAATCATTA-AATAATGATTTAGTAAT
63 AATTT-ATAATAATCATTATAA-AATGATTTA-TAAT
1755792 AATCATTATA
Statistics
Matches: 183, Mismatches: 4, Indels: 41
0.80 0.02 0.18
Matches are distributed among these distances:
94 3 0.02
95 20 0.11
96 15 0.08
97 16 0.09
98 11 0.06
104 10 0.05
108 4 0.02
110 5 0.03
112 8 0.04
113 1 0.01
114 1 0.01
115 55 0.30
117 17 0.09
118 17 0.09
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.44
Consensus pattern (104 bp):
ATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAAT
TTATAATAATCATTATAAAATGATTTATAATGAATTTTA
Found at i:1755634 original size:26 final size:26
Alignment explanation
Indices: 1755604--1755962 Score: 189
Period size: 26 Copynumber: 14.7 Consensus size: 26
1755594 TGATTTGATG
1755604 ATAATGATTTGATAATAATCATTATA
1 ATAATGATTTGATAATAATCATTATA
*
1755630 GTAATGATTTGATAATAATCATTATA
1 ATAATGATTTGATAATAATCATTATA
*
1755656 ATAATGATTAG-TAATAATCATTATA
1 ATAATGATTTGATAATAATCATTATA
* * *
1755681 AAAATGATTTAATAATGAT--TTA-A
1 ATAATGATTTGATAATAATCATTATA
** * * * * *
1755704 ATTTTTA-ATGAT-TTGATGATT-TA
1 ATAATGATTTGATAATAATCATTATA
* *
1755727 GTAATGATTTGAATAAT--C-ATTATA
1 ATAATGATTTG-ATAATAATCATTATA
*
1755751 GTAATGATTTGATAATAATCATTA-A
1 ATAATGATTTGATAATAATCATTATA
1755776 ATAATGATTT-AGTAATAATCATTATA
1 ATAATGATTTGA-TAATAATCATTATA
* * * *
1755802 AAAATGATTT-A-AATATTTA-AATA
1 ATAATGATTTGATAATAATCATTATA
* *
1755825 TTTAATGATTTG------ATGATT-TA
1 -ATAATGATTTGATAATAATCATTATA
*
1755845 GTAATGATTTGATAATAATCATTATA
1 ATAATGATTTGATAATAATCATTATA
* *
1755871 ATAATGATTTTATAATAATTATT-TA
1 ATAATGATTTGATAATAATCATTATA
* * * *
1755896 GTTATTATTT-AGTAATTAT--TTATA
1 ATAATGATTTGA-TAATAATCATTATA
* * *
1755920 ATAATGATTTTATACTAATGATT-TA
1 ATAATGATTTGATAATAATCATTATA
* *
1755945 ATAATTATTAG-TAATAAT
1 ATAATGATTTGATAATAAT
1755963 TATAGAATAC
Statistics
Matches: 255, Mismatches: 50, Indels: 58
0.70 0.14 0.16
Matches are distributed among these distances:
19 10 0.04
20 4 0.02
21 4 0.02
22 3 0.01
23 23 0.09
24 54 0.21
25 77 0.30
26 80 0.31
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
ATAATGATTTGATAATAATCATTATA
Found at i:1755731 original size:19 final size:19
Alignment explanation
Indices: 1755684--1755738 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
1755674 CATTATAAAA
1755684 ATGATTTAATAATGATTT-
1 ATGATTTAATAATGATTTG
* *
1755702 A-AATTT-TTAATGATTTG
1 ATGATTTAATAATGATTTG
*
1755719 ATGATTTAGTAATGATTTG
1 ATGATTTAATAATGATTTG
1755738 A
1 A
1755739 ATAATCATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 5 0.17
19 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (19 bp):
ATGATTTAATAATGATTTG
Found at i:1755758 original size:35 final size:35
Alignment explanation
Indices: 1755526--1755886 Score: 107
Period size: 37 Copynumber: 10.5 Consensus size: 35
1755516 TAATGATTTG
*
1755526 ATAATAATCA-TT-ATAATGATTTAGTAATAATCATT
1 ATAATAATGATTTAATAATGATTT-G-AATAATCATT
1755561 ATAA-AATGATTTAATAATGATTT--A-AAT--TT
1 ATAATAATGATTTAATAATGATTTGAATAATCATT
1755590 -T--TAATGATTTGATGATAATGATTTGATAATAATCATT
1 ATAATAATGATTT-A--ATAATGATTTG--AATAATCATT
* * *
1755627 ATAGTAATGATTTGATAATAATCATTAT-AATAATGATT
1 ATAATAATGA-TT--TAATAATGATT-TGAATAATCATT
* * *
1755665 AGTAATAATCATTATAAAAATGATTT-AATAATGATT
1 A-TAATAATGATT-TAATAATGATTTGAATAATCATT
*
1755701 -T-A-AAT--TTT--TAATGATTTG----ATGATT
1 ATAATAATGATTTAATAATGATTTGAATAATCATT
* * * *
1755725 -TAGTAATGATTTGAATAATCATTAT-AGTAATGATTT
1 ATAATAATGATTT-AATAATGATT-TGAATAATCA-TT
* *
1755761 GATAATAATCATTAAATAATGATTTAGTAATAATCATT
1 -ATAATAATGATTTAATAATGATTT-G-AATAATCATT
* * * * *
1755799 ATAAAAATGATTT-A-AAT-ATTTAAATATTTAATG
1 ATAATAATGATTTAATAATGATTTGAATA-ATCATT
* * *
1755832 AT-TTGATGATTTAGTAATGATTTGATAATAATCATT
1 ATAATAATGATTTAATAATGATTTG--AATAATCATT
*
1755868 ATAATAATGATTTTATAAT
1 ATAATAATGATTTAATAAT
1755887 AATTATTTAG
Statistics
Matches: 244, Mismatches: 35, Indels: 92
0.66 0.09 0.25
Matches are distributed among these distances:
24 7 0.03
26 3 0.01
27 16 0.07
28 5 0.02
29 3 0.01
30 12 0.05
31 10 0.04
32 16 0.07
33 6 0.02
34 13 0.05
35 20 0.08
36 30 0.12
37 47 0.19
38 24 0.10
39 13 0.05
40 14 0.06
41 3 0.01
42 1 0.00
43 1 0.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (35 bp):
ATAATAATGATTTAATAATGATTTGAATAATCATT
Found at i:1755891 original size:23 final size:23
Alignment explanation
Indices: 1755857--1755929 Score: 56
Period size: 25 Copynumber: 3.0 Consensus size: 23
1755847 AATGATTTGA
1755857 TAATAATCATTATAATAATGATT
1 TAATAATCATTATAATAATGATT
* * * * *
1755880 TTATAATAATTATTTAGTTATTATT
1 TAATAATCATTA--TAATAATGATT
* *
1755905 TAGTAATTATTTATAATAATGATT
1 TAATAATCA-TTATAATAATGATT
1755929 T
1 T
1755930 TATACTAATG
Statistics
Matches: 36, Mismatches: 11, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
23 10 0.28
24 9 0.25
25 14 0.39
26 3 0.08
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (23 bp):
TAATAATCATTATAATAATGATT
Found at i:1755925 original size:49 final size:48
Alignment explanation
Indices: 1755866--1755959 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 48
1755856 ATAATAATCA
* * *
1755866 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTAT
1 TTATAATAATGATTTTATAATAATGATTTAATAATTA-TTAGTAATTAT
*
1755915 TTATAATAATGATTTTATACTAATGATTTAATAATTATTAGTAAT
1 TTATAATAATGATTTTATAATAATGATTTAATAATTATTAGTAAT
1755960 AATTATAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 8 0.20
49 33 0.80
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (48 bp):
TTATAATAATGATTTTATAATAATGATTTAATAATTATTAGTAATTAT
Found at i:1755931 original size:14 final size:14
Alignment explanation
Indices: 1755914--1755949 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1755904 TTAGTAATTA
1755914 TTTATAATAATGAT
1 TTTATAATAATGAT
*
1755928 TTTATACTAATGAT
1 TTTATAATAATGAT
*
1755942 TTAATAAT
1 TTTATAAT
1755950 TATTAGTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (14 bp):
TTTATAATAATGAT
Found at i:1756182 original size:17 final size:17
Alignment explanation
Indices: 1756157--1756189 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1756147 ACTAAATATT
*
1756157 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
1756174 TAATGATTTGATACTA
1 TAATGATTTGATACTA
1756190 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:1756182 original size:25 final size:23
Alignment explanation
Indices: 1756103--1756182 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
1756093 GATTTATTGT
1756103 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
1756124 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
1756151 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
1756173 GTAATGATTT
1 -TAAT-ATTT
1756183 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:1758316 original size:15 final size:14
Alignment explanation
Indices: 1758293--1758323 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1758283 TACAACACTA
1758293 AACTTTAATATAAT
1 AACTTTAATATAAT
1758307 AACTTATAATATAAT
1 AACTT-TAATATAAT
1758322 AA
1 AA
1758324 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1758331 original size:16 final size:16
Alignment explanation
Indices: 1758298--1758344 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1758288 CACTAAACTT
*
1758298 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
1758313 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
1758329 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
1758345 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:1758583 original size:45 final size:47
Alignment explanation
Indices: 1758507--1758596 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 47
1758497 CAACAAACAA
*
1758507 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATT-AATAATTTTTTT
*
1758555 ATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAATTATTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATTAATAATTTTT
1758597 AACTATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 9 0.22
45 13 0.32
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (47 bp):
ATATAACTTAACTATTTAACTAAAACAAACTAATTAATAATTTTTTT
Found at i:1758607 original size:46 final size:47
Alignment explanation
Indices: 1758507--1758609 Score: 131
Period size: 46 Copynumber: 2.2 Consensus size: 47
1758497 CAACAAACAA
* *
1758507 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAAAACAAACTAATTAAATAATTTTTCT
*
1758555 ATATAACTAACTA-TTAAC-AAAACAAACTAATT-AATTATTTTTAACT
1 ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTT--CT
1758601 ATATAACTA
1 ATATAACTA
1758610 TCAAACTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
44 9 0.18
45 13 0.26
46 15 0.30
47 6 0.12
48 7 0.14
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.39
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTCT
Found at i:1758845 original size:27 final size:27
Alignment explanation
Indices: 1758788--1758845 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
1758778 AAAAAATTTA
*
1758788 CCTTATCTCCCTTTCTTCTTCTTACTTT
1 CCTTATCTCCCTTTCTTCTTCTTA-TCT
1758816 CCTT-TCTCCCTTTCTTTCTTCCTT-TCT
1 CCTTATCTCCCTTTC-TTCTT-CTTATCT
1758843 CCT
1 CCT
1758846 CTTTTCTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 15 0.56
28 9 0.33
29 3 0.11
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (27 bp):
CCTTATCTCCCTTTCTTCTTCTTATCT
Found at i:1758853 original size:18 final size:19
Alignment explanation
Indices: 1758814--1758863 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
1758804 TCTTCTTACT
*
1758814 TTCCTTTCTCCCTTTCTTTC
1 TTCCTTTCT-CCTCTCTTTC
1758834 TTCCTTTCTCCTCT-TTTC
1 TTCCTTTCTCCTCTCTTTC
*
1758852 TTTCTTTCTCCT
1 TTCCTTTCTCCT
1758864 GCAATCTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.54
19 4 0.14
20 9 0.32
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCCTTTCTCCTCTCTTTC
Found at i:1758916 original size:8 final size:9
Alignment explanation
Indices: 1758891--1758923 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
1758881 TTCTGCAATC
1758891 TCTTCTCCTT
1 TCTTCT-CTT
1758901 TCTTCTCTT
1 TCTTCTCTT
1758910 T-TTCTCTT
1 TCTTCTCTT
1758918 TCTTCT
1 TCTTCT
1758924 TTCTATAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 8 0.36
10 6 0.27
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (9 bp):
TCTTCTCTT
Found at i:1758958 original size:25 final size:25
Alignment explanation
Indices: 1758930--1758981 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1758920 TTCTTTCTAT
1758930 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
1758955 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
1758980 AA
1 AA
1758982 TAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (25 bp):
AACCGGCTGCCTCAATTATTTCACC
Found at i:1759200 original size:29 final size:29
Alignment explanation
Indices: 1759168--1759247 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
1759158 ATGGGAATGG
1759168 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
1759197 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* * *
1759226 TGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1759248 CTCTATTCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 45 0.96
30 2 0.04
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.16
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:1759329 original size:12 final size:12
Alignment explanation
Indices: 1759312--1759343 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1759302 TCGTATGGCT
1759312 CGTATGTCACCC
1 CGTATGTCACCC
1759324 CGTATGTCACCC
1 CGTATGTCACCC
*
1759336 TGTATGTC
1 CGTATGTC
1759344 GCCTGGATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.34, G:0.19, T:0.31
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:1759386 original size:29 final size:29
Alignment explanation
Indices: 1759341--1759399 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1759331 CACCCTGTAT
* *
1759341 GTCGCCTGGATTGCATGGCGTCCTACAAG
1 GTCGCCCGGATTGCATGGCGACCTACAAG
*
1759370 GTCGCCCGGA-TGCCATGGCGACCTCCAAG
1 GTCGCCCGGATTG-CATGGCGACCTACAAG
1759399 G
1 G
1759400 CCACTGTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.17, C:0.32, G:0.32, T:0.19
Consensus pattern (29 bp):
GTCGCCCGGATTGCATGGCGACCTACAAG
Found at i:1760983 original size:16 final size:17
Alignment explanation
Indices: 1760952--1760983 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1760942 ATTATTTTTT
1760952 AATATTTTTTAGTTAAA
1 AATATTTTTTAGTTAAA
1760969 AATATTTTTTA-TTAA
1 AATATTTTTTAGTTAA
1760984 CAATCGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
AATATTTTTTAGTTAAA
Found at i:1762219 original size:25 final size:24
Alignment explanation
Indices: 1762191--1762259 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
1762181 GAACTTAAAA
* * *
1762191 AAAATTAGAAGTTCGATTGAAGCTT
1 AAAATTAG-AGCTCAATTGAAGCCT
*
1762216 AAAATTTGAGCTCAATTGAAGCCT
1 AAAATTAGAGCTCAATTGAAGCCT
*
1762240 AAAATTTGAGCTCAATTGAA
1 AAAATTAGAGCTCAATTGAA
1762260 ACGAAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 33 0.82
25 7 0.17
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAGCCT
Found at i:1762235 original size:24 final size:24
Alignment explanation
Indices: 1762206--1762259 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1762196 TAGAAGTTCG
*
1762206 ATTGAAGCTTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1762230 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1762254 ATTGAA
1 ATTGAA
1762260 ACGAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:1763056 original size:10 final size:10
Alignment explanation
Indices: 1763017--1763056 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1763007 TTCATCACAC
1763017 CAAATTCTCT
1 CAAATTCTCT
*
1763027 CAATTTCTCT
1 CAAATTCTCT
*
1763037 CAACTTCTCT
1 CAAATTCTCT
*
1763047 CAAATACTCT
1 CAAATTCTCT
1763057 TATAATCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1763114 original size:9 final size:9
Alignment explanation
Indices: 1763102--1763153 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
1763092 TAATATTTTG
1763102 TATTTAATT
1 TATTTAATT
*
1763111 TATTTAA-G
1 TATTTAATT
1763119 TATTTAATT
1 TATTTAATT
1763128 TATTTAA--
1 TATTTAATT
* *
1763135 TATTTTACT
1 TATTTAATT
1763144 TATTTAATT
1 TATTTAATT
1763153 T
1 T
1763154 TTTTTGCAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:1763123 original size:17 final size:17
Alignment explanation
Indices: 1763101--1763150 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1763091 TTAATATTTT
1763101 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1763118 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
1763135 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
1763151 TTTTTTTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1763146 original size:16 final size:16
Alignment explanation
Indices: 1763110--1763155 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1763100 TGTATTTAAT
* *
1763110 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
1763127 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
1763143 TTATTTAAT-TTTT
1 TTATTTAATATTTT
1763156 TTTGCAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:1769352 original size:17 final size:18
Alignment explanation
Indices: 1769316--1769357 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1769306 TTAGTTCACG
*
1769316 AAAAAATTATTAATCGAT
1 AAAAAATTATTAATCAAT
*
1769334 AAAAATTTATT-ATCAAT
1 AAAAAATTATTAATCAAT
1769351 AATAAAA
1 AA-AAAA
1769358 AATAGTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAAATTATTAATCAAT
Found at i:1770191 original size:15 final size:16
Alignment explanation
Indices: 1770152--1770192 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
1770142 ATTTAGACAA
1770152 AAATATAAACTTTTATT
1 AAAT-TAAACTTTTATT
1770169 ATAATTAAA-TTTTATT
1 A-AATTAAACTTTTATT
1770185 AAATTAAA
1 AAATTAAA
1770193 ATAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 8 0.35
17 5 0.22
18 3 0.13
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTAAACTTTTATT
Found at i:1770509 original size:22 final size:22
Alignment explanation
Indices: 1770483--1770554 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
1770473 ATGTTTATGT
1770483 TTATTTATTTTTTAAAATGTTC
1 TTATTTATTTTTTAAAATGTTC
* * **
1770505 TTATTTAATTTATATTTATG-T-
1 TTATTTATTTTTTA-AAATGTTC
* *
1770526 TTGTTTATTTTTTAAAATATTC
1 TTATTTATTTTTTAAAATGTTC
*
1770548 TTTTTTA
1 TTATTTA
1770555 ATTTATATTT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
20 2 0.06
21 12 0.33
22 19 0.53
23 3 0.08
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTTATTTTTTAAAATGTTC
Found at i:1770537 original size:43 final size:43
Alignment explanation
Indices: 1770471--1770578 Score: 166
Period size: 43 Copynumber: 2.6 Consensus size: 43
1770461 ATGAATAAAA
* *
1770471 TTATGTTTATGTTTATTTATTTTTTAAAATGTTCTTATTTAAT
1 TTATATTTATGTTTATTTATTTTTTAAAATATTCTTATTTAAT
* *
1770514 TTATATTTATGTTTGTTTATTTTTTAAAATATTCTTTTTTAAT
1 TTATATTTATGTTTATTTATTTTTTAAAATATTCTTATTTAAT
1770557 TTATATTTA--TTTATTTATTTTT
1 TTATATTTATGTTTATTTATTTTT
1770579 AAGGTGTTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 12 0.20
43 48 0.80
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.69
Consensus pattern (43 bp):
TTATATTTATGTTTATTTATTTTTTAAAATATTCTTATTTAAT
Found at i:1771621 original size:21 final size:21
Alignment explanation
Indices: 1771583--1771622 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1771573 ATTGTTGATA
*
1771583 TTTCTTATTCTTTTTATTTAT
1 TTTCTTATTCTTTATATTTAT
1771604 TTTCTTATGT-TTTATATTT
1 TTTCTTAT-TCTTTATATTT
1771623 TTTATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTCTTATTCTTTATATTTAT
Found at i:1772081 original size:2 final size:2
Alignment explanation
Indices: 1772074--1772144 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
1772064 ATCAAGTTCG
1772074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1772116 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1772145 TAAGTTAAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1778029 original size:31 final size:31
Alignment explanation
Indices: 1777989--1778047 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1777979 GTGTGATTAT
*
1777989 ATCATATCTTAATTAAATAAAAATGAAAGTG
1 ATCACATCTTAATTAAATAAAAATGAAAGTG
*
1778020 ATCACATCTTAATTAAATTAAAATGAAA
1 ATCACATCTTAATTAAATAAAAATGAAA
1778048 ATAAACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (31 bp):
ATCACATCTTAATTAAATAAAAATGAAAGTG
Found at i:1778510 original size:13 final size:13
Alignment explanation
Indices: 1778473--1778514 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1778463 TGGTTGTTGG
*
1778473 TTATAATTAA-AT
1 TTATAATTAATAA
1778485 TTATTAATCTAATAA
1 TTA-TAAT-TAATAA
1778500 TTATAATTAATAA
1 TTATAATTAATAA
1778513 TT
1 TT
1778515 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.12
13 12 0.46
14 7 0.27
15 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATAATTAATAA
Found at i:1779485 original size:95 final size:94
Alignment explanation
Indices: 1779364--1779561 Score: 272
Period size: 95 Copynumber: 2.1 Consensus size: 94
1779354 CGACGATGTG
** *
1779364 GTATCGATACCATGGTAAGGGTATCGATAGTAGATAACATCGAACCTAATTTTAGTATCGATACC
1 GTATCGATACCATGGTAAGGGTATCGATACCAGACAACATCGAACCTAATTTTAGTATCGATACC
* *
1779429 AGAAGGGGGTATC-AGTACCATAGTATAGTA
66 AGAA-AGGGTATCGA-TACCATAGTAGAGTA
* * * *
1779459 GTATCGATACCATGGTAAGGGTATCGATACCAGGCCACATCGAATCTAATTTTGGTATCGATACC
1 GTATCGATACCATGGTAAGGGTATCGATACCAGACAACATCGAACCTAATTTTAGTATCGATACC
* *
1779524 GGAAAGGGTATCGATACCATAGTAGGGTA
66 AGAAAGGGTATCGATACCATAGTAGAGTA
1779553 GTATCGATA
1 GTATCGATA
1779562 TTGAAGAACT
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
94 29 0.32
95 62 0.68
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (94 bp):
GTATCGATACCATGGTAAGGGTATCGATACCAGACAACATCGAACCTAATTTTAGTATCGATACC
AGAAAGGGTATCGATACCATAGTAGAGTA
Found at i:1779978 original size:60 final size:59
Alignment explanation
Indices: 1779895--1780350 Score: 672
Period size: 59 Copynumber: 7.8 Consensus size: 59
1779885 ATGGCACTAA
1779895 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
1779954 ATATGATAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
1780014 GTGTGCTAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTCCGTATAGGGCACTCC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
1780073 GTGTGCTAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAAGACACTTC
1 GTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* *
1780133 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAA--T--ATATAGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
*
1780188 GTGTAG-TAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTCCGTATAGGGCACTTC
1 GTGT-GCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* ** *
1780247 GTGTGCTAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCTATATTGGGCACCTT-
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCA-CTTC
* *
1780306 GTGTGATAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC
1780351 ATATGAGAAA
Statistics
Matches: 357, Mismatches: 31, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
55 47 0.13
56 1 0.00
57 2 0.01
58 1 0.00
59 194 0.54
60 112 0.31
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:1780032 original size:119 final size:118
Alignment explanation
Indices: 1779895--1780350 Score: 674
Period size: 119 Copynumber: 3.9 Consensus size: 118
1779885 ATGGCACTAA
* * *
1779895 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCATATGA
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTT-GTGTGA
*
1779960 TAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
65 TAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * * *
1780014 GTGTGCTAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTCCGTATAGGGCACTCCGTGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT-TGTGTGA
* * *
1780079 TAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATAAGACACTTC
65 TAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
1780133 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAA--T--ATATAGGGCACTT-TGTG-T
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTGTGTGAT
* *
1780192 AGTAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTCCGTATAGGGCACTTC
66 A--AAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
* * *
1780247 GTGTGCTAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCTATATTGGGCACCTTGTGTGA
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA-CTTGTGTGA
1780312 T-AAAATGATAAGAAATTCATACTAAGTGTATGAATTTCC
65 TAAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCC
1780351 ATATGAGAAA
Statistics
Matches: 306, Mismatches: 21, Indels: 21
0.88 0.06 0.06
Matches are distributed among these distances:
112 2 0.01
113 4 0.01
114 86 0.28
115 11 0.04
116 1 0.00
117 1 0.00
118 45 0.15
119 151 0.49
120 4 0.01
121 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (118 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTGTGTGAT
AAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTC
Found at i:1786981 original size:59 final size:59
Alignment explanation
Indices: 1786926--1787322 Score: 638
Period size: 59 Copynumber: 6.7 Consensus size: 59
1786916 ATGGCACTAA
* *
1786926 GTGTGCTAAAATGTTAAGAAATTCATACGAAGTGTATGAATTTTCGTATAGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
* * *
1786985 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGAACTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
*
1787044 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATG-AGTTTCTGTATAGGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTC-GTATA-GGGCACTTC
*
1787104 GTGTGCTAAAATGTTAAG-AATTCATACTAAGTGTATGAATTTTCGTATAGGCCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
1787162 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
* * * *
1787221 GTGTGCTAAAATATTAATAAATTCATACTAAGTGTATGAA-TTTCAGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTC-GTATAGGGCACTTC
*
1787280 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT
1787323 CTGTATGGGA
Statistics
Matches: 313, Mismatches: 19, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
58 34 0.11
59 247 0.79
60 32 0.10
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
Found at i:1791293 original size:16 final size:17
Alignment explanation
Indices: 1791257--1791298 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1791247 AATAATTAAA
1791257 ATTATTTT-AAATATAT
1 ATTATTTTAAAATATAT
1791273 ATTATTTTAAAAT-TAT
1 ATTATTTTAAAATATAT
* *
1791289 TTTATATTAA
1 ATTATTTTAA
1791299 TACAAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTTTAAAATATAT
Found at i:1799388 original size:30 final size:31
Alignment explanation
Indices: 1799346--1799414 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1799336 AAAAGCCTTA
* *
1799346 GAAAA-TTTGGGGACC-ATTATG-TAATTTTT
1 GAAAAGTTAGGGGACCAATT-TGATAATTTTG
1799375 GAAAAGTTAGGGGACCAATTTGATAATTTTG
1 GAAAAGTTAGGGGACCAATTTGATAATTTTG
1799406 GAAAAGTTA
1 GAAAAGTTA
1799415 TGAATAATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 5 0.14
30 11 0.31
31 19 0.54
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (31 bp):
GAAAAGTTAGGGGACCAATTTGATAATTTTG
Found at i:1800738 original size:25 final size:25
Alignment explanation
Indices: 1800710--1800796 Score: 165
Period size: 25 Copynumber: 3.5 Consensus size: 25
1800700 ATATAAATAA
1800710 TGTGAGATAAGTGATTATGTAAAAC
1 TGTGAGATAAGTGATTATGTAAAAC
*
1800735 TGTGCGATAAGTGATTATGTAAAAC
1 TGTGAGATAAGTGATTATGTAAAAC
1800760 TGTGAGATAAGTGATTATGTAAAAC
1 TGTGAGATAAGTGATTATGTAAAAC
1800785 TGTGAGATAAGT
1 TGTGAGATAAGT
1800797 TATAGGGCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (25 bp):
TGTGAGATAAGTGATTATGTAAAAC
Found at i:1803258 original size:4 final size:4
Alignment explanation
Indices: 1803249--1803275 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1803239 TAATACATGT
1803249 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1803276 CAGTTGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1803780 original size:17 final size:17
Alignment explanation
Indices: 1803727--1803780 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 17
1803717 AGATTAAGAA
1803727 ATTCTTAAAAAATTATT
1 ATTCTTAAAAAATTATT
*
1803744 ATCCTCTTCAAAAAAATATT
1 AT--TCTT-AAAAAATTATT
*
1803764 ATTCTTAAAAAGTTATT
1 ATTCTTAAAAAATTATT
1803781 CAAACGGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 11 0.35
18 4 0.13
19 4 0.13
20 12 0.39
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTCTTAAAAAATTATT
Found at i:1811821 original size:18 final size:19
Alignment explanation
Indices: 1811783--1811842 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 19
1811773 CTTTGCAAAA
* *
1811783 TTTAAAAAT-AAAAAACA-
1 TTTAAAAATGACAAAATAT
*
1811800 TTTAAACAT-ACAAAATAT
1 TTTAAAAATGACAAAATAT
*
1811818 TTTAAAAATGATAAAATAT
1 TTTAAAAATGACAAAATAT
*
1811837 TATAAA
1 TTTAAA
1811843 TGTAGAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 14 0.40
18 8 0.23
19 13 0.37
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (19 bp):
TTTAAAAATGACAAAATAT
Found at i:1811971 original size:21 final size:22
Alignment explanation
Indices: 1811914--1811956 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1811904 AAAATATATG
*
1811914 AAAATTTATATAAAAATAATTAT
1 AAAATATAT-TAAAAATAATTAT
1811937 AAAATATATT-AAAATAATTA
1 AAAATATATTAAAAATAATTA
1811957 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATATATTAAAAATAATTAT
Found at i:1814353 original size:21 final size:22
Alignment explanation
Indices: 1814303--1814355 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1814293 ATAGGTATCC
* *
1814303 ATACCACATTAACTGGTATCAAT
1 ATACCAGATGAACTGGTAT-AAT
1814326 ATA--AGATGAACTGGTAT-AT
1 ATACCAGATGAACTGGTATAAT
1814345 ATACCAGATGA
1 ATACCAGATGA
1814356 GTTATATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 5 0.19
21 18 0.69
23 3 0.12
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (22 bp):
ATACCAGATGAACTGGTATAAT
Found at i:1830983 original size:21 final size:21
Alignment explanation
Indices: 1830959--1831012 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1830949 TCCATACCAC
1830959 ATGAACTGGTATCAATATCAG
1 ATGAACTGGTATCAATATCAG
1830980 ATGAACTGGTATCAATATCAG
1 ATGAACTGGTATCAATATCAG
1831001 ATGAACTGGTAT
1 ATGAACTGGTAT
1831013 ATATACCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (21 bp):
ATGAACTGGTATCAATATCAG
Found at i:1831022 original size:21 final size:21
Alignment explanation
Indices: 1830947--1831023 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1830937 GAATAATATA
* *
1830947 TATCCATACCACATGAACTGG
1 TATCAATACCAGATGAACTGG
*
1830968 TATCAATATCAGATGAACTGG
1 TATCAATACCAGATGAACTGG
*
1830989 TATCAATATCAGATGAACTGG
1 TATCAATACCAGATGAACTGG
1831010 TAT-ATATACCAGAT
1 TATCA-ATACCAGAT
1831024 AAGTTGTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (21 bp):
TATCAATACCAGATGAACTGG
Found at i:1831101 original size:41 final size:40
Alignment explanation
Indices: 1831015--1831102 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 40
1831005 ACTGGTATAT
* *
1831015 ATACCAGATAAGTTGTATTCATATCTGACATGTTGATATCT
1 ATACCAGATAAGCTGTATTCATATC-GACATGTTGATATCC
*
1831056 ATACCAGATGAGCTGATATTCATATC-A-ATGATTGAGTATCC
1 ATACCAGATAAGCTG-TATTCATATCGACATG-TTGA-TATCC
1831097 ATACCA
1 ATACCA
1831103 AAGGCTTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 3 0.07
40 5 0.12
41 23 0.56
42 10 0.24
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (40 bp):
ATACCAGATAAGCTGTATTCATATCGACATGTTGATATCC
Found at i:1833527 original size:3 final size:3
Alignment explanation
Indices: 1833519--1833571 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
1833509 TTGTTTTTAA
* *
1833519 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
1833564 TAT TAT TA
1 TAT TAT TA
1833572 AATAATTACA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1833550 original size:25 final size:27
Alignment explanation
Indices: 1833516--1833569 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
1833506 CATTTGTTTT
1833516 TAATATTA-TTATTA-ATATATTATTA
1 TAATATTATTTATTATATATATTATTA
*
1833541 TAATTTTATTTATTATTATATATTATTA
1 TAATATTATTTATTA-TATATATTATTA
1833569 T
1 T
1833570 TAAATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
28 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATATTATTTATTATATATATTATTA
Found at i:1833564 original size:10 final size:10
Alignment explanation
Indices: 1833522--1833569 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
1833512 TTTTTAATAT
1833522 TATTATTAATA
1 TATTATT-ATA
1833533 TATTATTATA
1 TATTATTATA
*
1833543 -ATT-TTATT
1 TATTATTATA
1833551 TATTATTATA
1 TATTATTATA
1833561 TATTATTAT
1 TATTATTAT
1833570 TAAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 16 0.48
11 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTATA
Found at i:1835137 original size:20 final size:19
Alignment explanation
Indices: 1835112--1835153 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1835102 CTATTTTATA
1835112 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
1835132 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1835151 AAT
1 AAT
1835154 ATCTAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1835237 original size:116 final size:115
Alignment explanation
Indices: 1835011--1835225 Score: 256
Period size: 116 Copynumber: 1.9 Consensus size: 115
1835001 ATTTTAATCA
* * * *
1835011 TGTTTTAATATTTATTTATTTTTCAATATTAAGAAATGACAGTCTTAAAACAACTGGATGTCCAT
1 TGTTTTAATATTTATTTATTTTTCAATATTAAGAAAAGACAGTCTGAAAACAACTAGAAGTCCAT
* ** *
1835076 TTTCTGATATTTTTAAAATAAATATCCTATTTTATAAATTATATATTAAT
66 TTTCTGATATTTCTAAAATAAATATAATATTTTATAAATAATATATTAAT
* * ** * *
1835126 TGTTTTAATTATTTATTTATTTTTTAATATCTAAGAAAAGAGCTGTCTGAAGGCACCTATAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATAT-TAAGAAAAGA-CAGTCTGAAAACAACTAGAAGTC
1835191 C-TTTTCTGATATTTCT-AAATAAATA-AATATTTTAT
63 CATTTTCTGATATTTCTAAAATAAATATAATATTTTAT
1835226 TTATAAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
115 16 0.19
116 29 0.35
117 23 0.27
118 16 0.19
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (115 bp):
TGTTTTAATATTTATTTATTTTTCAATATTAAGAAAAGACAGTCTGAAAACAACTAGAAGTCCAT
TTTCTGATATTTCTAAAATAAATATAATATTTTATAAATAATATATTAAT
Found at i:1835241 original size:29 final size:28
Alignment explanation
Indices: 1835209--1835264 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
1835199 ATATTTCTAA
1835209 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTT-TTTATAAATATAT
* *
1835238 ATAAATTAATATTTTTTTATAATTATA
1 ATAAATAAATATTTTTTTATAAATATA
1835265 ATTTTGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAAATAAATATTTTTTTATAAATATAT
Found at i:1835765 original size:26 final size:24
Alignment explanation
Indices: 1835734--1835787 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
1835724 TAATTCTTTC
*
1835734 TTTTCAAAATTTTTATATACTTATTA
1 TTTTCAAAATATTTATATA--TATTA
* *
1835760 TTTTCATAGTATTTATATATATTA
1 TTTTCAAAATATTTATATATATTA
1835784 TTTT
1 TTTT
1835788 ATTATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.36
26 16 0.64
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTCAAAATATTTATATATATTA
Found at i:1835795 original size:11 final size:11
Alignment explanation
Indices: 1835754--1835807 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
1835744 TTTTATATAC
1835754 TTATTATTTTCA
1 TTATTATTTT-A
*
1835766 -TAGTATTTATA
1 TTATTATTT-TA
1835777 TATATTATTTTA
1 T-TATTATTTTA
1835789 TTATTATTTTA
1 TTATTATTTTA
1835800 TT-TTATTT
1 TTATTATTT
1835808 GCAAGTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 6 0.16
11 20 0.54
12 4 0.11
13 7 0.19
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:1835806 original size:24 final size:24
Alignment explanation
Indices: 1835749--1835825 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 24
1835739 AAAATTTTTA
*
1835749 TATACTTATTATTTTCATAGTATT
1 TATATTTATTATTTTCATAGTATT
* *
1835773 TATATATATTATTTT-ATTATTATT
1 TATATTTATTATTTTCA-TAGTATT
*
1835797 T-TA-TT-TTATTTGCA-AGTATT
1 TATATTTATTATTTTCATAGTATT
1835817 T-TATTTATT
1 TATATTTATT
1835826 TTTCTGTCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 8 0.19
21 8 0.19
22 4 0.09
23 3 0.07
24 20 0.47
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (24 bp):
TATATTTATTATTTTCATAGTATT
Found at i:1839103 original size:15 final size:15
Alignment explanation
Indices: 1839083--1839114 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1839073 GATCAATACC
1839083 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1839098 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1839113 TT
1 TT
1839115 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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1846855 original size:19 final size:18
Alignment explanation
Indices: 1846813--1846861 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
1846803 TATTTTCTCT
1846813 AAATTCAATTTA--TTTG
1 AAATTCAATTTATTTTTG
*
1846829 AGATTCAATTTATTTTTG
1 AAATTCAATTTATTTTTG
1846847 AAAATTCAATTTATT
1 -AAATTCAATTTATT
1846862 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
18 4 0.14
19 13 0.46
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Found at i:1848194 original size:113 final size:113
Alignment explanation
Indices: 1847996--1848672 Score: 1068
Period size: 113 Copynumber: 6.0 Consensus size: 113
1847986 TAGAAAAGAT
*
1847996 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1848061 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
1848109 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1848174 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * *
1848222 TCAAATCCATCACTTGATGGATCAGCTTTTCCAAAGGAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1848287 AGAAGGAAAAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
1848335 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCCGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1848400 ATAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTTTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * **
1848448 TCAAATCCATCACTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGGGCTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* ** *
1848513 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * * * * **
1848561 TTGAATTCATCATTTGATGGATCATCATTGCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
1848625 AGAAGGAAGAGGAAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
1848673 ATAACTCTAT
Statistics
Matches: 523, Mismatches: 41, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
112 68 0.13
113 455 0.87
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:1848791 original size:120 final size:123
Alignment explanation
Indices: 1848581--1848816 Score: 295
Period size: 120 Copynumber: 1.9 Consensus size: 123
1848571 CATTTGATGG
* * *
1848581 ATCATCATTGCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATA
1 ATCAGCATTGCCAGAAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAGGAAGTTCATA
* *
1848646 ATGAAAAGAACTTGTTCAACCTTTTGCATA-ACT-CTATCACAAAAGGAGATATATCATC
66 AGGAAAAGAACTTATTCAACCTTTTGC-TAGACTAC-ATCACAAAAGGAGATATATCATC
* *
1848704 ATCAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATATGAAGAA-G-A-A-GAATTTCAT
1 ATCAGCATTGCCAGAA-GAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAGGAAGTTCAT
** * * *
1848765 AAGGAGGAGAATTTATTCAACTTTTTGCTAGATTACATCACAAAAGGAGATA
65 AAGGAAAAGAACTTATTCAACCTTTTGCTAGACTACATCACAAAAGGAGATA
1848817 AATTGTCATC
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
119 2 0.02
120 48 0.49
121 2 0.02
122 1 0.01
123 15 0.15
124 30 0.31
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (123 bp):
ATCAGCATTGCCAGAAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAGGAAGTTCATA
AGGAAAAGAACTTATTCAACCTTTTGCTAGACTACATCACAAAAGGAGATATATCATC
Found at i:1849048 original size:25 final size:25
Alignment explanation
Indices: 1849014--1849064 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1849004 CATTTGTTTT
1849014 TAATATTA-TTATTAATATAATATTA
1 TAATATTATTTATTAATAT-ATATTA
* *
1849039 TAATTTTATTTATTATTATATATTA
1 TAATATTATTTATTAATATATATTA
1849064 T
1 T
1849065 TATTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TAATATTATTTATTAATATATATTA
Found at i:1849067 original size:20 final size:20
Alignment explanation
Indices: 1849012--1849073 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 20
1849002 CCCATTTGTT
1849012 TTTAATATTAT-TATTA--A
1 TTTAATATTATATATTATTA
*
1849029 TATAATATTATA-ATT-TTA
1 TTTAATATTATATATTATTA
*
1849047 TTTATTATTATATATTATTA
1 TTTAATATTATATATTATTA
*
1849067 TTAAATA
1 TTTAATA
1849074 ATTACAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 13 0.37
18 11 0.31
19 3 0.09
20 8 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATATTATATATTATTA
Found at i:1850649 original size:20 final size:19
Alignment explanation
Indices: 1850624--1850665 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1850614 CTATTTTATA
1850624 AATTATATATTAATTATTTT
1 AATTATATATTAATT-TTTT
* *
1850644 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1850663 AAT
1 AAT
1850666 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1850749 original size:116 final size:115
Alignment explanation
Indices: 1850525--1850737 Score: 261
Period size: 116 Copynumber: 1.9 Consensus size: 115
1850515 TTTAATCCTG
* * * *
1850525 TTTTAATATTTATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAACAACTGGATGTCCATTT
1 TTTTAATATTTATTTATTTTTCAATATGAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCATTT
* ** *
1850590 TCTGATATTTTTAAAATAAATATCCTATTTTATAAATTATATATTAATTA
66 TCTGATATTTCTAAAATAAATATAATATTTTATAAATAATATATTAATTA
* * ** *
1850640 TTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCC-
1 TTTTAA-TATTTATTTATTTTTCAATAT-GAAG-AAAGAGCAGTCTTAAAACAACTAGAAGTCCA
1850704 TTTTCTGATATTTCT-AAATAAATA-AATATTTTAT
63 TTTTCTGATATTTCTAAAATAAATATAATATTTTAT
1850738 TTATAAATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
115 14 0.17
116 29 0.35
117 17 0.20
118 23 0.28
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (115 bp):
TTTTAATATTTATTTATTTTTCAATATGAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCATTT
TCTGATATTTCTAAAATAAATATAATATTTTATAAATAATATATTAATTA
Found at i:1850778 original size:25 final size:29
Alignment explanation
Indices: 1850721--1850777 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1850711 ATATTTCTAA
1850721 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTATTTATAAATATAT
* * *
1850750 ATAAATTAATATTTTTTTTATAATTATA
1 ATAAATAAATATTTTATTTATAAATATA
1850778 ATTTTGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATAAATAAATATTTTATTTATAAATATAT
Found at i:1853986 original size:25 final size:25
Alignment explanation
Indices: 1853958--1854028 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
1853948 ACTAATATAC
1853958 TTAGTATCGATATCATCTTAGTGAG
1 TTAGTATCGATATCATCTTAGTGAG
*
1853983 TTAG----G--AT-A-CTAAGATGA-
1 TTAGTATCGATATCATCTTAG-TGAG
1854000 TTAGTATCGATATCATCTTAGTGAG
1 TTAGTATCGATATCATCTTAGTGAG
1854025 TTAG
1 TTAG
1854029 GAAATAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 20
0.61 0.04 0.36
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
21 2 0.06
23 2 0.06
24 4 0.12
25 12 0.35
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (25 bp):
TTAGTATCGATATCATCTTAGTGAG
Found at i:1853991 original size:42 final size:42
Alignment explanation
Indices: 1853945--1854030 Score: 147
Period size: 42 Copynumber: 2.0 Consensus size: 42
1853935 GGTTAGTATC
*
1853945 GATACTAATAT-ACTTAGTATCGATATCATCTTAGTGAGTTAG
1 GATACTAAGATGA-TTAGTATCGATATCATCTTAGTGAGTTAG
1853987 GATACTAAGATGATTAGTATCGATATCATCTTAGTGAGTTAG
1 GATACTAAGATGATTAGTATCGATATCATCTTAGTGAGTTAG
1854029 GA
1 GA
1854031 AATAAACTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (42 bp):
GATACTAAGATGATTAGTATCGATATCATCTTAGTGAGTTAG
Found at i:1871039 original size:21 final size:21
Alignment explanation
Indices: 1871014--1871088 Score: 98
Period size: 21 Copynumber: 3.5 Consensus size: 21
1871004 TTTTCGTAAG
1871014 AGTACTTTGTGTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
1871035 AGTACTTTGTGTACTATGGCAAG-
1 AGTACTTTGTGTACT-TGG--AGT
* *
1871058 ATTACTTTGTGTACTTGTAGT
1 AGTACTTTGTGTACTTGGAGT
1871079 AGTACTTTGT
1 AGTACTTTGT
1871089 AAACTATGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 2 0.04
21 24 0.51
22 5 0.11
23 14 0.30
24 2 0.04
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.44
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:1871095 original size:44 final size:44
Alignment explanation
Indices: 1871011--1871096 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
1871001 GCATTTTCGT
**
1871011 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTACTATGGC
1 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTAAACTATGGC
* *
1871055 AAGATTACTTTGTGTACTTGTAGTAGTACTTTGTAAACTATG
1 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTAAACTATG
1871097 ACACTTTGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (44 bp):
AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTAAACTATGGC
Found at i:1872977 original size:22 final size:24
Alignment explanation
Indices: 1872952--1872995 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
1872942 TCATATTGGC
1872952 ATGGGTTG-GTTG-TCTTCGCATT
1 ATGGGTTGCGTTGATCTTCGCATT
* *
1872974 ATGGTTTGCGTTGATTTTCGCA
1 ATGGGTTGCGTTGATCTTCGCA
1872996 ATAGGCGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 4 0.22
24 7 0.39
ACGTcount: A:0.11, C:0.14, G:0.30, T:0.45
Consensus pattern (24 bp):
ATGGGTTGCGTTGATCTTCGCATT
Found at i:1878037 original size:21 final size:21
Alignment explanation
Indices: 1878013--1878055 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1878003 TATTGTAATT
1878013 TTGTAAAAGTACTTTGTGTAC
1 TTGTAAAAGTACTTTGTGTAC
**
1878034 TTGTAGTAGTACTTTGTGTAC
1 TTGTAAAAGTACTTTGTGTAC
1878055 T
1 T
1878056 ATGGCACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (21 bp):
TTGTAAAAGTACTTTGTGTAC
Found at i:1882045 original size:2 final size:2
Alignment explanation
Indices: 1882038--1882122 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
1882028 TTGTATTTTG
1882038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1882080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1882122 A
1 A
1882123 CGAGTCTGAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.