Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_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: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:1765162 original size:11 final size:11
Alignment explanation
Indices: 1765146--1765185 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
1765136 AAATTTCAGG
1765146 AGCTCGATTGA
1 AGCTCGATTGA
1765157 AGCTCGATTGA
1 AGCTCGATTGA
*
1765168 AGCTCGATTCA
1 AGCTCGATTGA
1765179 AGCTCGA
1 AGCTCGA
1765186 ACTCGATTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:1765192 original size:17 final size:17
Alignment explanation
Indices: 1765170--1765206 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1765160 TCGATTGAAG
1765170 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
*
1765187 CTCGATTCGAGCTCGAA
1 CTCGATTCAAGCTCGAA
1765204 CTC
1 CTC
1765207 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:1766513 original size:24 final size:22
Alignment explanation
Indices: 1766481--1766525 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
1766471 TTAACAACTA
*
1766481 GAAAGTATAAACATAATAAAAATT
1 GAAAATATAAACA-AA-AAAAATT
*
1766505 GAAAATATACACAAAAAAAAT
1 GAAAATATAAACAAAAAAAAT
1766526 CAAAAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 2 0.11
24 11 0.58
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (22 bp):
GAAAATATAAACAAAAAAAATT
Found at i:1775145 original size:20 final size:20
Alignment explanation
Indices: 1775117--1775158 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1775107 GATACTGGGT
* *
1775117 CCTTTAGTATCGATACTGAC
1 CCTTGAGTATCGATACTAAC
*
1775137 CCTTGAGTATCGGTACTAAC
1 CCTTGAGTATCGATACTAAC
1775157 CC
1 CC
1775159 GTGGTACCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (20 bp):
CCTTGAGTATCGATACTAAC
Found at i:1793561 original size:64 final size:64
Alignment explanation
Indices: 1793482--1793620 Score: 278
Period size: 64 Copynumber: 2.2 Consensus size: 64
1793472 CTCAAATAAA
1793482 TGAACATCGAATGCCACTAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
1 TGAACATCGAATGCCACTAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
1793546 TGAACATCGAATGCCACTAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
1 TGAACATCGAATGCCACTAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
1793610 TGAACATCGAA
1 TGAACATCGAA
1793621 GGTGAATTGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 75 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (64 bp):
TGAACATCGAATGCCACTAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
Found at i:1793633 original size:64 final size:64
Alignment explanation
Indices: 1793482--1793661 Score: 254
Period size: 64 Copynumber: 2.8 Consensus size: 64
1793472 CTCAAATAAA
* *
1793482 TGAACATCGAATGCCACTAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
1 TGAACATCGAAGGCCAATAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
* *
1793546 TGAACATCGAATGCCACTAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
1 TGAACATCGAAGGCCAATAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
** * * * *
1793610 TGAACATCGAAGGTGAATTGTGTACCGATGCAT-GGAGAGTGCATCGATGCAC
1 TGAACATCGAAGGCCAATAGTGTATCGATTCATAAGA-AGTGCATCGATGCAC
1793662 ATGTTAAAGA
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 2 0.02
64 105 0.98
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (64 bp):
TGAACATCGAAGGCCAATAGTGTATCGATTCATAAGAAGTGCATCGATGCACCCCCTTAAGATT
Found at i:1793676 original size:24 final size:20
Alignment explanation
Indices: 1793635--1793706 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
1793625 AATTGTGTAC
* *
1793635 CGATGCA-TGGAGAGTGCAT
1 CGATGCACTGTAGAATGCAT
1793654 CGATGCACATGTTAAAGAATGCAT
1 CGATGCAC-TG-T--AGAATGCAT
* *
1793678 CGATACACTGTAGAATGTAT
1 CGATGCACTGTAGAATGCAT
1793698 CGATGCACT
1 CGATGCACT
1793707 TAATGGGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.16
20 16 0.37
21 2 0.05
22 1 0.02
23 2 0.05
24 15 0.35
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (20 bp):
CGATGCACTGTAGAATGCAT
Found at i:1795111 original size:32 final size:32
Alignment explanation
Indices: 1795070--1795171 Score: 122
Period size: 32 Copynumber: 3.2 Consensus size: 32
1795060 AGAGTCGAGG
1795070 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCTTTCGAGACATATGGACAGT
* *
1795102 GTTACCTATGTCCTTCGGGACATATGGACAG-
1 GTTACCTATGTCTTTCGAGACATATGGACAGT
* *
1795133 GATTACCTATGT-TCT-AAGAACATATGGACAGT
1 G-TTACCTATGTCTTTCGAG-ACATATGGACAGT
1795165 -TTACCTA
1 GTTACCTA
1795172 GGCTCTTTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
30 8 0.13
31 14 0.23
32 39 0.64
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (32 bp):
GTTACCTATGTCTTTCGAGACATATGGACAGT
Found at i:1800097 original size:32 final size:32
Alignment explanation
Indices: 1800023--1800097 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 32
1800013 AGAGTCGAGG
*
1800023 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCATTCGAGACATATGGACAGT
*
1800055 GTTACATATGTCATTCGAGACATATGGACAG-
1 GTTACCTATGTCATTCGAGACATATGGACAGT
1800086 GATTACCTATGT
1 G-TTACCTATGT
1800098 TCTAAGGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (32 bp):
GTTACCTATGTCATTCGAGACATATGGACAGT
Found at i:1801130 original size:26 final size:27
Alignment explanation
Indices: 1801046--1801135 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
1801036 AATAGTTTAG
* * *
1801046 TAAAAAT-GTTTAGGGGTTTCTTATGT
1 TAAAAATGGTTTAAGAGTTTCTTCTGT
*
1801072 GAAAAATGGTTTAA-AGATTTCTTCTGT
1 TAAAAATGGTTTAAGAG-TTTCTTCTGT
*
1801099 TGAAAATGGTTTAAGAGTTTCTTCTGT
1 TAAAAATGGTTTAAGAGTTTCTTCTGT
1801126 TAAAAATGGT
1 TAAAAATGGT
1801136 ATAGTATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
26 7 0.13
27 45 0.83
28 2 0.04
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (27 bp):
TAAAAATGGTTTAAGAGTTTCTTCTGT
Found at i:1801178 original size:25 final size:25
Alignment explanation
Indices: 1801142--1801224 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
1801132 TGGTATAGTA
* * *
1801142 TATATGACTAGATTTGTTTACTAAT
1 TATATGAATAGATTTGTTAACTGAT
** *
1801167 TATATGAATAGATTTGTCCACGGAT
1 TATATGAATAGATTTGTTAACTGAT
* *
1801192 TATATGAATAAAATTGTTAACTGAT
1 TATATGAATAGATTTGTTAACTGAT
*
1801217 TCTATGAA
1 TATATGAA
1801225 CTTGTTCTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.41
Consensus pattern (25 bp):
TATATGAATAGATTTGTTAACTGAT
Found at i:1801406 original size:20 final size:20
Alignment explanation
Indices: 1801381--1801419 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1801371 GGTCTAGAAA
1801381 TGAATGCAATGATATTTTTT
1 TGAATGCAATGATATTTTTT
1801401 TGAATGCAATGATATTTTT
1 TGAATGCAATGATATTTTT
1801420 GAATGCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (20 bp):
TGAATGCAATGATATTTTTT
Found at i:1801420 original size:18 final size:19
Alignment explanation
Indices: 1801381--1801425 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
1801371 GGTCTAGAAA
1801381 TGAATGCAATGATATTTTTT
1 TGAATGCAATGATA-TTTTT
1801401 TGAATGCAATGATA-TTTT
1 TGAATGCAATGATATTTTT
1801419 TGAATGC
1 TGAATGC
1801426 TTTCTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 11 0.44
20 14 0.56
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (19 bp):
TGAATGCAATGATATTTTT
Found at i:1802052 original size:23 final size:23
Alignment explanation
Indices: 1802020--1802092 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
1802010 GTTTTTAGAA
*
1802020 TAGGGCTACTTTAAATAATGGGT
1 TAGGGTTACTTTAAATAATGGGT
*
1802043 TAGGGTTACTTTAAATAATAGGT
1 TAGGGTTACTTTAAATAATGGGT
1802066 TAGGGTTACTTTAAATAATGGGT
1 TAGGGTTACTTTAAATAATGGGT
1802089 TAGG
1 TAGG
1802093 TTTTTTTTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (23 bp):
TAGGGTTACTTTAAATAATGGGT
Found at i:1804781 original size:31 final size:32
Alignment explanation
Indices: 1804719--1804782 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
1804709 AACAAGACCC
*
1804719 ATCAATCCCACGCTTCCACCTCCATACACCAA
1 ATCAATCCCACGCTTCCACCTCCATAAACCAA
* * *
1804751 ATCAATCCCTCTC-TCCACCTTCATAAACCAA
1 ATCAATCCCACGCTTCCACCTCCATAAACCAA
1804782 A
1 A
1804783 ACAACACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.22
Consensus pattern (32 bp):
ATCAATCCCACGCTTCCACCTCCATAAACCAA
Found at i:1805933 original size:30 final size:29
Alignment explanation
Indices: 1805891--1805956 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
1805881 TGAGTTTTTT
*
1805891 ATTATTAAATTTTTAAA-AGTTATAAAATA
1 ATTATTAAAATTTTAAATA-TTATAAAATA
*
1805920 ATTATTAAAATTTTAAATTATTATATAATA
1 ATTATTAAAATTTTAAA-TATTATAAAATA
1805950 ATTATTA
1 ATTATTA
1805957 TGATATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 16 0.48
30 16 0.48
31 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTATTAAAATTTTAAATATTATAAAATA
Found at i:1806071 original size:32 final size:32
Alignment explanation
Indices: 1806004--1806107 Score: 101
Period size: 31 Copynumber: 3.4 Consensus size: 32
1805994 TGATCATTAA
** * * * *
1806004 TTTGATAAAGATTAATGAT-ATTTTCTTATAG
1 TTTGATAAATTTTAATAATAATTTTATAATAT
1806035 TTTGATAAATTTTAATAATAATTTTATAATAT
1 TTTGATAAATTTTAATAATAATTTTATAATAT
1806067 TTTGATAAA-TTTAATAATTAA-TTTATAAT-T
1 TTTGATAAATTTTAATAA-TAATTTTATAATAT
*
1806097 TTT-AAAAATTT
1 TTTGATAAATTT
1806108 AATCATTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.06
30 6 0.10
31 32 0.51
32 21 0.33
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTGATAAATTTTAATAATAATTTTATAATAT
Found at i:1806107 original size:29 final size:32
Alignment explanation
Indices: 1806035--1806116 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 32
1806025 TTTCTTATAG
*
1806035 TTTGATAAATTTTAATAA-TAATTTTATAATAT
1 TTTGA-AAAATTTAATAATTAATTTTATAATAT
*
1806067 TTTGATAAATTTAATAATTAA-TTTATAAT-T
1 TTTGAAAAATTTAATAATTAATTTTATAATAT
*
1806097 TTT-AAAAATTTAATCATTAA
1 TTTGAAAAATTTAATAATTAA
1806117 ATTGAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
29 15 0.33
30 4 0.09
31 18 0.40
32 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (32 bp):
TTTGAAAAATTTAATAATTAATTTTATAATAT
Found at i:1807735 original size:17 final size:15
Alignment explanation
Indices: 1807714--1807758 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
1807704 TATTAAATTT
1807714 TAAAAGAAATTAAATA
1 TAAAA-AAATTAAATA
*
1807730 TAAAAAAATAAAATA
1 TAAAAAAATTAAATA
1807745 TAAAAAATATTAAA
1 TAAAAAA-ATTAAA
1807759 AGGAGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
TAAAAAAATTAAATA
Found at i:1807854 original size:22 final size:22
Alignment explanation
Indices: 1807812--1807855 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1807802 TAACATGTCA
* *
1807812 AAATTAAAAGAGAATAAAAAAG
1 AAATAAAAAGAGAAAAAAAAAG
*
1807834 AAATAAAAAGAAAAAATAAAAA
1 AAATAAAAAGAGAAAA-AAAAA
1807856 TTTAAAGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (22 bp):
AAATAAAAAGAGAAAAAAAAAG
Found at i:1808914 original size:18 final size:18
Alignment explanation
Indices: 1808883--1808917 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1808873 ACCTAAACCA
1808883 AAATGAAAATAAATAAAT
1 AAATGAAAATAAATAAAT
1808901 AAAT-AAAATAAAATAAA
1 AAATGAAAAT-AAATAAA
1808918 AAGAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATGAAAATAAATAAAT
Found at i:1809117 original size:38 final size:38
Alignment explanation
Indices: 1809023--1809164 Score: 162
Period size: 36 Copynumber: 3.7 Consensus size: 38
1809013 AAATGTTTTC
* *
1809023 AAAACCATATATTATACGTTTTCAAAACTGTTTTT--T
1 AAAACTATATATTATACGTTTTCAAAACTGTTTTTAAA
* * * *
1809059 TAAACTATAAATTATACGTTTTCGAAACCGTTTTTAAA
1 AAAACTATATATTATACGTTTTCAAAACTGTTTTTAAA
* * *
1809097 AAAATTATATATTATGCGTTTTCAAAACTATTTTTAAAA
1 AAAACTATATATTATACGTTTTCAAAACTGTTTTT-AAA
1809136 AAAAGCTATATATTATACGTTTTCGAAAA
1 AAAA-CTATATATTATACGTTTTC-AAAA
1809165 AAAATACATT
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
36 30 0.35
38 28 0.33
39 7 0.08
40 17 0.20
41 4 0.05
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (38 bp):
AAAACTATATATTATACGTTTTCAAAACTGTTTTTAAA
Found at i:1809213 original size:14 final size:14
Alignment explanation
Indices: 1809190--1809219 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1809180 GAACTATATT
*
1809190 AAATATGTTTTCAA
1 AAATACGTTTTCAA
1809204 AAATACGTTTTCAA
1 AAATACGTTTTCAA
1809218 AA
1 AA
1809220 CATATACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AAATACGTTTTCAA
Found at i:1810344 original size:17 final size:18
Alignment explanation
Indices: 1810303--1810345 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1810293 GATTAGTTTT
*
1810303 TTTATAAATATAATAATA
1 TTTAAAAATATAATAATA
1810321 TTTAAAAATA-AATAA-A
1 TTTAAAAATATAATAATA
1810337 TTTCAAAAA
1 TTT-AAAAA
1810346 CACCATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 10 0.43
18 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTAAAAATATAATAATA
Found at i:1811266 original size:31 final size:31
Alignment explanation
Indices: 1811206--1811303 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
1811196 GACATTTTTT
* * *
1811206 AATTTAA-TATTTAATTTTAAATGAAATATC
1 AATTTAATTATTAAAATATAAATGAAATATC
*
1811236 AATTTAATTCTTAAAATATAAAT-AAGATATC
1 AATTTAATTATTAAAATATAAATGAA-ATATC
* ** *
1811267 AATTTCATTATTAAAAT-TTGATGAAATATT
1 AATTTAATTATTAAAATATAAATGAAATATC
1811297 AATTTAA
1 AATTTAA
1811304 CTCTTATATT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
30 22 0.40
31 33 0.60
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (31 bp):
AATTTAATTATTAAAATATAAATGAAATATC
Found at i:1811497 original size:3 final size:3
Alignment explanation
Indices: 1811489--1811518 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1811479 TTTCCTCTGA
1811489 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1811519 TTTATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1818393 original size:25 final size:26
Alignment explanation
Indices: 1818343--1818430 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 26
1818333 TTAAATGAAA
1818343 ATAAAATAT-TTTAAAATTAAGTTAAT
1 ATAAAATATATTT-AAATTAAGTTAAT
1818369 CATAAAATATATTT-AA-TAAGTTAAT
1 -ATAAAATATATTTAAATTAAGTTAAT
* *
1818394 ATAAAAATATTTTTAACTTAA--T-AT
1 AT-AAAATATATTTAAATTAAGTTAAT
1818418 ATAAAATTATATT
1 ATAAAA-TATATT
1818431 ATTTATAATC
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
23 4 0.08
24 11 0.21
25 20 0.38
26 3 0.06
27 12 0.23
28 3 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATAAAATATATTTAAATTAAGTTAAT
Found at i:1818417 original size:22 final size:23
Alignment explanation
Indices: 1818358--1818433 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 23
1818348 ATATTTTAAA
1818358 ATTAAGTTAATCATAAAATATATTT
1 ATTAAGTTAAT-ATAAAA-ATATTT
*
1818383 AATAAGTTAATATAAAAATATTT
1 ATTAAGTTAATATAAAAATATTT
*
1818406 -TTAACTTAATATATAAAATTATATT
1 ATTAAGTTAATATA-AAAA-TAT-TT
1818431 ATT
1 ATT
1818434 TATAATCCAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 11 0.25
23 10 0.23
24 9 0.20
25 12 0.27
26 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (23 bp):
ATTAAGTTAATATAAAAATATTT
Found at i:1819216 original size:31 final size:31
Alignment explanation
Indices: 1819181--1819251 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1819171 TCGGGGTGAA
* * * *
1819181 CATATCTTAATTGAATATAAACGAAAATGAT
1 CATATCTTAATTAAATAAAAACAAAAATAAT
*
1819212 CATATCTTAATTAAATAAAAATAAAAATAAT
1 CATATCTTAATTAAATAAAAACAAAAATAAT
*
1819243 TATATCTTA
1 CATATCTTA
1819252 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.35
Consensus pattern (31 bp):
CATATCTTAATTAAATAAAAACAAAAATAAT
Found at i:1820147 original size:2 final size:2
Alignment explanation
Indices: 1820140--1820197 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1820130 TGGTTCGTGC
1820140 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
1820182 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1820198 CAAAATTAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1821987 original size:19 final size:21
Alignment explanation
Indices: 1821959--1822002 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
1821949 GGTATTTTAG
1821959 TTTAAATAG-ATTTAAG-TGT
1 TTTAAATAGAATTTAAGATGT
*
1821978 TTTAATTAGAATTTAAGATGT
1 TTTAAATAGAATTTAAGATGT
1821999 TTTA
1 TTTA
1822003 GCTTGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 7 0.32
21 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
TTTAAATAGAATTTAAGATGT
Found at i:1829742 original size:32 final size:32
Alignment explanation
Indices: 1829699--1829760 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1829689 TTAAATAGGG
1829699 TTTTAGTATTTTAATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTAATTAAGTTTTAGG-TATTAT
* **
1829732 TTTTA-TATTTTATTTTTGTTTTAGGTATT
1 TTTTAGTATTTTAATTAAGTTTTAGGTATT
1829761 TTAGTTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.15
32 17 0.65
33 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (32 bp):
TTTTAGTATTTTAATTAAGTTTTAGGTATTAT
Found at i:1830444 original size:19 final size:18
Alignment explanation
Indices: 1830393--1830441 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1830383 AATCTCTTTA
1830393 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
1830412 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
1830431 ATTTTTTATTT
1 ATTTTTTATTT
1830442 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:1830591 original size:22 final size:22
Alignment explanation
Indices: 1830561--1830613 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
1830551 GAATTCTATC
*
1830561 TTTTTCTAAAATCAAGAAAGAG
1 TTTTACTAAAATCAAGAAAGAG
*
1830583 TTTTACT-AAATCACGAAAGAG
1 TTTTACTAAAATCAAGAAAGAG
1830604 TTTTACTAAA
1 TTTTACTAAA
1830614 TAACAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
TTTTACTAAAATCAAGAAAGAG
Found at i:1830593 original size:21 final size:21
Alignment explanation
Indices: 1830569--1830614 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1830559 TCTTTTTCTA
1830569 AAATCAAGAAAGAGTTTTACT
1 AAATCAAGAAAGAGTTTTACT
*
1830590 AAATCACGAAAGAGTTTTACT
1 AAATCAAGAAAGAGTTTTACT
1830611 AAAT
1 AAAT
1830615 AACAAAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (21 bp):
AAATCAAGAAAGAGTTTTACT
Found at i:1831569 original size:59 final size:59
Alignment explanation
Indices: 1831477--1831597 Score: 190
Period size: 59 Copynumber: 2.1 Consensus size: 59
1831467 AATAGATGGA
1831477 TAAGTGTACTATCGAACCATCCTAATCGCAATGAAAAGGA-AAACTCGATAATATGGCTC
1 TAAGTGTACTATCGAACCATCCTAATCGCAATGAAAA-GACAAACTCGATAATATGGCTC
* * * *
1831536 TAAGTGTCCTATCTAACCCTCCTAGTCGCAATGAAAAGACAAACTCGATAATATGGCTC
1 TAAGTGTACTATCGAACCATCCTAATCGCAATGAAAAGACAAACTCGATAATATGGCTC
1831595 TAA
1 TAA
1831598 CCAACCCTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
58 2 0.04
59 55 0.96
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (59 bp):
TAAGTGTACTATCGAACCATCCTAATCGCAATGAAAAGACAAACTCGATAATATGGCTC
Found at i:1836055 original size:59 final size:59
Alignment explanation
Indices: 1835963--1836083 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 59
1835953 AATAGATGGA
* * *
1835963 TAAGTGTCCTATCGAACCCTCCTAGTTGCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTC
1836022 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTC
1836081 TAA
1 TAA
1836084 CCAACCCTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTC
Found at i:1840002 original size:24 final size:24
Alignment explanation
Indices: 1839973--1840028 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1839963 TAGAAGTTCG
1839973 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
1839997 ATTGAAGTCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1840021 ATTGAAGC
1 ATTGAAGC
1840029 GAAAGAATAG
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:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:1840814 original size:21 final size:20
Alignment explanation
Indices: 1840788--1840826 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1840778 TGCTCATGCA
1840788 AATGCAAAGATCCAAAATGGG
1 AATGCAAA-ATCCAAAATGGG
*
1840809 AATGCAAAATGCAAAATG
1 AATGCAAAATCCAAAATG
1840827 TAAATGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (20 bp):
AATGCAAAATCCAAAATGGG
Found at i:1840818 original size:28 final size:28
Alignment explanation
Indices: 1840755--1840823 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
1840745 TGTTATATAG
* **
1840755 ATGCTAATGCAAAGATGCAAAAATGCTC
1 ATGCAAATGCAAAGATGCAAAAATGCGA
* *
1840783 ATGCAAATGCAAAGAT-CCAAAATGGGA
1 ATGCAAATGCAAAGATGCAAAAATGCGA
1840810 ATGCAAAATGCAAA
1 ATGC-AAATGCAAA
1840824 ATGTAAATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 11 0.31
28 24 0.69
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (28 bp):
ATGCAAATGCAAAGATGCAAAAATGCGA
Found at i:1840832 original size:20 final size:21
Alignment explanation
Indices: 1840787--1840832 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1840777 ATGCTCATGC
1840787 AAATGCAAAGATCCAAAATGG
1 AAATGCAAAGATCCAAAATGG
* * *
1840808 GAATGCAAA-ATGCAAAATGT
1 AAATGCAAAGATCCAAAATGG
1840828 AAATG
1 AAATG
1840833 TAATAAAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.52, C:0.11, G:0.20, T:0.17
Consensus pattern (21 bp):
AAATGCAAAGATCCAAAATGG
Found at i:1843638 original size:2 final size:2
Alignment explanation
Indices: 1843631--1843687 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1843621 TGAAACATGC
1843631 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
1843673 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1843688 ATGGACTAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1843884 original size:54 final size:53
Alignment explanation
Indices: 1843775--1843916 Score: 178
Period size: 54 Copynumber: 2.7 Consensus size: 53
1843765 CCAGAATGTA
* * * *
1843775 ATAAAACAAAAAATAGTAGCCAAATCAGAAA-CAAAAATAATGACTAAAATGC
1 ATAAAATAAAAAACAGTAGCCAAATCAGAAATAAAAAATAACGACTAAAATGC
* * *
1843827 ATAAAATAAAATAACAGTAGCCAAATAAGAAATAAAAAATAGCGACTAAAATTC
1 ATAAAATAAAA-AACAGTAGCCAAATCAGAAATAAAAAATAACGACTAAAATGC
* *
1843881 ATAAAATAAAAGAGCAGTAGTCAAATCAGAAATAAA
1 ATAAAATAAAA-AACAGTAGCCAAATCAGAAATAAA
1843917 TAATGACTGA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 10 0.13
53 18 0.23
54 49 0.64
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (53 bp):
ATAAAATAAAAAACAGTAGCCAAATCAGAAATAAAAAATAACGACTAAAATGC
Found at i:1845661 original size:29 final size:29
Alignment explanation
Indices: 1845618--1845700 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
1845608 CTCACCTAAC
*
1845618 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1845648 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1845677 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1845701 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1850430 original size:29 final size:29
Alignment explanation
Indices: 1850387--1850469 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
1850377 CTCACCTAAC
*
1850387 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1850417 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
1850446 TAAATGATGTAAGTAATCACATCA
1 TAAATGATGTAAGCAATGACATCA
1850470 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1854236 original size:45 final size:44
Alignment explanation
Indices: 1854175--1854315 Score: 142
Period size: 45 Copynumber: 3.2 Consensus size: 44
1854165 TTGCCAAAAG
* *
1854175 AATCAAAGGATTAGTTCATTTTGATTATTGGGTTGCCAAAATTAA
1 AATCAAATGATCAGTTCATTTT-ATTATTGGGTTGCCAAAATTAA
* * * * *
1854220 AATCAAATTATCAGTTCCTTTTAATTACTCGGATT--TAGAAATTAA
1 AATCAAATGATCAGTTCATTTT-ATTA-TTGGGTTGCCA-AAATTAA
* * *
1854265 AATCAAATGATTAGTTAATTTTATTATTGGGTTGCGAAAATTAA
1 AATCAAATGATCAGTTCATTTTATTATTGGGTTGCCAAAATTAA
1854309 AATCAAA
1 AATCAAA
1854316 GGATTTTTAC
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
43 5 0.06
44 19 0.25
45 48 0.62
46 5 0.06
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (44 bp):
AATCAAATGATCAGTTCATTTTATTATTGGGTTGCCAAAATTAA
Found at i:1860149 original size:20 final size:20
Alignment explanation
Indices: 1860126--1860177 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1860116 CCATGGTATT
1860126 AGTATCGATACTGATAGGTA
1 AGTATCGATACTGATAGGTA
1860146 AGTATCGATACTGATAGGTA
1 AGTATCGATACTGATAGGTA
1860166 AGTATCGATACT
1 AGTATCGATACT
1860178 CATTTAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTGATAGGTA
Found at i:1860262 original size:20 final size:20
Alignment explanation
Indices: 1860237--1860291 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1860227 CTAGGATGGT
1860237 CGGTATCGATACCAACTTTC
1 CGGTATCGATACCAACTTTC
1860257 CGGTATCGATACCAACTTTC
1 CGGTATCGATACCAACTTTC
*
1860277 CGGTATCGATGCCAA
1 CGGTATCGATACCAA
1860292 ATGTGCAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (20 bp):
CGGTATCGATACCAACTTTC
Found at i:1860869 original size:2 final size:2
Alignment explanation
Indices: 1860862--1860887 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1860852 AACCAATGTT
1860862 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
1860888 AATAAGCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1862284 original size:18 final size:17
Alignment explanation
Indices: 1862258--1862293 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1862248 TAAAATTAAT
*
1862258 TAAATAATAATTTAAAAA
1 TAAAAAATAA-TTAAAAA
1862276 TAAAAAATAATTAAAAA
1 TAAAAAATAATTAAAAA
1862293 T
1 T
1862294 GTCATGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATAATTAAAAA
Found at i:1868482 original size:3 final size:3
Alignment explanation
Indices: 1868469--1868525 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
1868459 CATTTAAATA
*
1868469 TAT TA- TAT TAT TAT TAT TAT TAT TAT ATAT TA- TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
1868513 TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TA
1868526 CAGGCCCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.12
3 39 0.81
4 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1868497 original size:27 final size:27
Alignment explanation
Indices: 1868466--1868523 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
1868456 TTTCATTTAA
*
1868466 ATATATTATATTATTATTATTATTATT
1 ATATATTATATTATAATTATTATTATT
1868493 ATATATTATATTATAATTATTATTATT
1 ATATATTATATTATAATTATTATTATT
1868520 ATAT
1 ATAT
1868524 TACAGGCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
ATATATTATATTATAATTATTATTATT
Found at i:1869535 original size:34 final size:34
Alignment explanation
Indices: 1869472--1869536 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
1869462 AATCCCTTAG
* *
1869472 ATTTGTAATCCTTACATTTTAGTCACTAAATCAA
1 ATTTATAATCCTTACAATTTAGTCACTAAATCAA
* * *
1869506 ATTTATAATCCTTTCAATTTGGTCTCTAAAT
1 ATTTATAATCCTTACAATTTAGTCACTAAAT
1869537 TTTATTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (34 bp):
ATTTATAATCCTTACAATTTAGTCACTAAATCAA
Found at i:1869970 original size:16 final size:17
Alignment explanation
Indices: 1869951--1869991 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1869941 ATAATAAATA
1869951 ATAATTTATTTTTTA-C
1 ATAATTTATTTTTTATC
*
1869967 ATAAATTATTTTTTATC
1 ATAATTTATTTTTTATC
*
1869984 ATATTTTA
1 ATAATTTA
1869992 ATATTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTATTTTTTATC
Found at i:1879400 original size:13 final size:13
Alignment explanation
Indices: 1879382--1879407 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1879372 CATCCAACGC
1879382 ATTGGGACGAGGA
1 ATTGGGACGAGGA
1879395 ATTGGGACGAGGA
1 ATTGGGACGAGGA
1879408 CTTGATGGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.46, T:0.15
Consensus pattern (13 bp):
ATTGGGACGAGGA
Found at i:1880533 original size:11 final size:11
Alignment explanation
Indices: 1880517--1880545 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1880507 ATTATGCTTG
1880517 AAGAAAAAAAA
1 AAGAAAAAAAA
1880528 AAG-AAAAAAA
1 AAGAAAAAAAA
1880538 AAGAAAAA
1 AAGAAAAA
1880546 GAGGGGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1880942 original size:19 final size:17
Alignment explanation
Indices: 1880900--1880948 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
1880890 TATTTTCTTT
1880900 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
1880916 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
1880934 AAAATTCAATTTATT
1 -AAATTCAATTTATT
1880949 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 1 0.04
19 13 0.46
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:1881443 original size:115 final size:115
Alignment explanation
Indices: 1881241--1881693 Score: 766
Period size: 115 Copynumber: 4.0 Consensus size: 115
1881231 TACCACGTTA
*
1881241 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
1881306 TTTGGTATGAACCCCAAAAGCCAATCATTGGATTTAAAAGATGAATTTGC
66 TTTGGTATGAACCCTAAAAGCCAATCATTGGATTTAAAAGATGAATTTGC
* *
1881356 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
1881421 TTTGGTATAAACCCTAAAAGCCAATCATTGGATTTAAAAGATGAATTTGC
66 TTTGGTATGAACCCTAAAAGCCAATCATTGGATTTAAAAGATGAATTTGC
1881471 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* *
1881536 TTTGGTATGAACCC-AAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCTAAAAGCCAATCATTGGATTTAAAAGATGAATTTGC
*
1881585 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * * * * *
1881650 TTTGGTAGGAACCATAGAA-CCAATCATTAGAATTGAAAGATGAA
66 TTTGGTATGAACCCTAAAAGCCAATCATTGGATTTAAAAGATGAA
1881694 CTGCATGATC
Statistics
Matches: 323, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
114 132 0.41
115 191 0.59
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (115 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTTGGTATGAACCCTAAAAGCCAATCATTGGATTTAAAAGATGAATTTGC
Found at i:1881643 original size:229 final size:229
Alignment explanation
Indices: 1881241--1881693 Score: 773
Period size: 229 Copynumber: 2.0 Consensus size: 229
1881231 TACCACGTTA
*
1881241 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
1881306 TTTGGTATGAACCCCAAAAGCCAATCATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAA
66 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAA
* * * *
1881371 GAAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCCT
131 GAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAGAAACCAT
* *
1881436 AAAAGCCAATCATTGGATTTAAAAGATGAATTTGC
196 AAAA-CCAATCATTAGAATTAAAAGATGAATTTGC
1881471 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
1881536 TTTGGTATGAA-CCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAA
66 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAA
* *
1881600 GGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAGGAACCAT
131 GAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAGAAACCAT
* *
1881665 AGAACCAATCATTAGAATTGAAAGATGAA
196 AAAACCAATCATTAGAATTAAAAGATGAA
1881694 CTGCATGATC
Statistics
Matches: 210, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
228 22 0.10
229 113 0.54
230 75 0.36
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (229 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTTGGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCATAGTAGAAATAA
GAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAGAAACCAT
AAAACCAATCATTAGAATTAAAAGATGAATTTGC
Found at i:1882846 original size:116 final size:110
Alignment explanation
Indices: 1882664--1882962 Score: 390
Period size: 116 Copynumber: 2.7 Consensus size: 110
1882654 TTCCAGTTCG
1882664 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAA-TTCATAATGAGAAGAATTTGTTC
* * * * * *
1882729 AACCTTTTGTTTGAATTCATCATTTGATGGATCAAC-A-TTGCCAGGGAA
64 AACCTTTTG-CTAAATCCATCACTTAATGGATC--CGATTTGCCAGAGAA
1882777 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG-AAGAAG-AATTCATAATGAGAAGAATTTG
*
1882842 TTCAACCTTTTGCTAAATCCATCACTTAATGGATCCGATTTTCCAGAGAA
61 TTCAACCTTTTGCTAAATCCATCACTTAATGGATCCGATTTGCCAGAGAA
* **
1882892 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG--TTCACAATGAGAAGAGCTTGTTCAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTCATAATGAGAAGAATTTGTTCAA
1882955 CCTTTTGC
66 CCTTTTGC
1882963 ATAATTCTAT
Statistics
Matches: 169, Mismatches: 10, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
108 30 0.18
111 6 0.04
112 13 0.08
113 20 0.12
114 1 0.01
115 47 0.28
116 50 0.30
117 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (110 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTCATAATGAGAAGAATTTGTTCAA
CCTTTTGCTAAATCCATCACTTAATGGATCCGATTTGCCAGAGAA
Found at i:1882927 original size:115 final size:115
Alignment explanation
Indices: 1882664--1882928 Score: 353
Period size: 115 Copynumber: 2.3 Consensus size: 115
1882654 TTCCAGTTCG
*
1882664 AGTTCATAATGAGAAGAACTCATCTGAAGAAG--G-AAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTG
* * * * * *
1882726 TTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGGAA
66 TTCAACCTTTTGTCTAAATCCATCACTTAATGGATC-ACATTGCCAGAGAA
* **
1882777 AGTTCATAATGAGAAGAACTCGTCAT-CTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTT
1 AGTTCATAATGAGAAGAACTCATC-TGAAGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTT
*
1882841 GTTCAACCTTTTG-CTAAATCCATCACTTAATGGATC-CGATTTTCCAGAGAA
65 GTTCAACCTTTTGTCTAAATCCATCACTTAATGGATCAC-A-TTGCCAGAGAA
1882892 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAA
1882929 GTTCACAATG
Statistics
Matches: 131, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
113 28 0.21
114 3 0.02
115 60 0.46
116 40 0.31
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (115 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTG
TTCAACCTTTTGTCTAAATCCATCACTTAATGGATCACATTGCCAGAGAA
Found at i:1883104 original size:40 final size:38
Alignment explanation
Indices: 1883008--1883106 Score: 162
Period size: 38 Copynumber: 2.6 Consensus size: 38
1882998 ACCTTTCCAG
1883008 AGAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAA
1 AGAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAA
* *
1883046 AGAAAGTTCATAATGAGAATAACTCATCTGAAAAAGAA
1 AGAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAA
1883084 AGAAGAAGTTCATAATGAGAAGA
1 AG-A-AAGTTCATAATGAGAAGA
1883107 GCTTATTCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 38 0.68
39 1 0.02
40 17 0.30
ACGTcount: A:0.54, C:0.09, G:0.19, T:0.18
Consensus pattern (38 bp):
AGAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGAA
Found at i:1883411 original size:3 final size:3
Alignment explanation
Indices: 1883347--1883398 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
1883337 TTCATTTAAA
1883347 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1883392 T-T TAT TA
1 TAT TAT TA
1883399 ATAAATATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 3 0.07
3 42 0.91
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1884922 original size:16 final size:17
Alignment explanation
Indices: 1884903--1884943 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1884893 ATAATAAATA
1884903 ATAATTTATTTTTTA-C
1 ATAATTTATTTTTTATC
*
1884919 ATAAATTATTTTTTATC
1 ATAATTTATTTTTTATC
*
1884936 ATATTTTA
1 ATAATTTA
1884944 ATATTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTATTTTTTATC
Found at i:1885193 original size:28 final size:29
Alignment explanation
Indices: 1885138--1885193 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1885128 ATATTTCTAA
1885138 ATAAATAAACATTTTATTTATAAATATAT
1 ATAAATAAACATTTTATTTATAAATATAT
* * *
1885167 ATAAATTAATATTTT-TTTATAATTATA
1 ATAAATAAACATTTTATTTATAAATATA
1885194 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
ATAAATAAACATTTTATTTATAAATATAT
Found at i:1887491 original size:24 final size:24
Alignment explanation
Indices: 1887448--1887501 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1887438 AATTCATGTA
1887448 ATTTT-TAAAATAAAATAAT-ATT
1 ATTTTATAAAATAAAATAATAATT
*
1887470 GATTTTATAAAAT-ATATAAATAATT
1 -ATTTTATAAAATAAAAT-AATAATT
1887495 ATTTTAT
1 ATTTTAT
1887502 TATTTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 8 0.30
24 16 0.59
25 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTTATAAAATAAAATAATAATT
Found at i:1889752 original size:118 final size:117
Alignment explanation
Indices: 1889600--1890157 Score: 541
Period size: 118 Copynumber: 4.7 Consensus size: 117
1889590 GAAAATGATG
* * * * * *
1889600 ATCCACCTCCTTTTATAATGGATTTTAGTGAAAGGTCGAAAAAATTCTTCTTATTATGAACTTTT
1 ATCCACCTCATTTTGTGATGGATTTGAGTGAAAGGTCGAAAAAATTCTTCTCATTATGAACTTCT
* *
1889665 TCTCCCTCTC-TGGATGAGTTCTTCTTAGTACGAACTCCTCATTTGAAATGTTA
66 TCTCCCTC-CATGGACGAGTTCTTCTTAGTATGAACTCC-CATTTGAAATGTTA
* ** *
1889718 ATCCACCTCATTTTGTGATGGATTAGAGTGAAAGGTCGAGCAAATTCTTCTCATTATAAAACTTC
1 ATCCACCTCATTTTGTGATGGATTTGAGTGAAAGGTCGAAAAAATTCTTCTCATTAT-GAACTTC
* * * * * *
1889783 TTATCCCTCCATTGATGAGTTCCTCTTACTATAAACTTCCCATTTGAAATGTTA
65 TTCTCCCTCCATGGACGAGTTCTTCTTAGTATGAAC-TCCCATTTGAAATGTTA
* * * * * * * * * *
1889837 ATCCACTTCCTTATGTGCTAGATTTGAGTGAAAGGTTGAACAAGTTTTTATCATTATGAACTT-T
1 ATCCACCTCATTTTGTGATGGATTTGAGTGAAAGGTCGAAAAAATTCTTCTCATTATGAACTTCT
*
1889901 TCCCCCCTCCATGGACGAGTT-TCTCTTAGTATGAACTCACCATTTGAAATGTTA
66 T-CTCCCTCCATGGACGAGTTCT-TCTTAGTATGAACTC-CCATTTGAAATGTTA
* * * *
1889955 ATCAACCTC-TTTCTGTGATGGATTTGAGTGAAAGGACGAAAAATTTATTCTCATTATGAACTTC
1 ATCCACCTCATTT-TGTGATGGATTTGAGTGAAAGGTCGAAAAAATTCTTCTCATTATGAACTTC
** * ** * *
1890019 TTCTTTCTCCGTGGACGAGTTCTTCCCATTATGAACACCTCATTTGAAATGTTA
65 TTCTCCCTCCATGGACGAGTTCTTCTTAGTATGAACTCC-CATTTGAAATGTTA
* * * ** * *
1890073 ATCTACCTCATTCTGTGATAGATTTGAGCAAAAGGTC-AAAAAAGTTCTTATTATTATGAACTTC
1 ATCCACCTCATTTTGTGATGGATTTGAGTGAAAGGTCGAAAAAA-TTCTTCTCATTATGAACTTC
* **
1890137 TTCTTCCTCTGTGGACGAGTT
65 TTCTCCCTCCATGGACGAGTT
1890158 ACATCCTTCT
Statistics
Matches: 362, Mismatches: 66, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
117 12 0.03
118 249 0.69
119 98 0.27
120 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (117 bp):
ATCCACCTCATTTTGTGATGGATTTGAGTGAAAGGTCGAAAAAATTCTTCTCATTATGAACTTCT
TCTCCCTCCATGGACGAGTTCTTCTTAGTATGAACTCCCATTTGAAATGTTA
Found at i:1890281 original size:44 final size:44
Alignment explanation
Indices: 1890224--1890355 Score: 149
Period size: 44 Copynumber: 3.0 Consensus size: 44
1890214 GGCTGCAAGA
* * *
1890224 AAAAAAGGAATGTTGATTCATCTCCTTCTGTGATGGAATCGAAT
1 AAAAAGGGAATGTTGATCCAACTCCTTCTGTGATGGAATCGAAT
* * * **
1890268 AAAATGGTG-ATGTTGATCCAACTCCTTATGTGATGGAATCTAGC
1 AAAAAGG-GAATGTTGATCCAACTCCTTCTGTGATGGAATCGAAT
* **
1890312 AAAAAGGGAATGTTGATCCACCAACTTCTGTGATGGAATCGAAT
1 AAAAAGGGAATGTTGATCCAACTCCTTCTGTGATGGAATCGAAT
1890356 CTTTTGAAAA
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
43 1 0.01
44 68 0.97
45 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (44 bp):
AAAAAGGGAATGTTGATCCAACTCCTTCTGTGATGGAATCGAAT
Found at i:1890487 original size:22 final size:22
Alignment explanation
Indices: 1890462--1890504 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1890452 CAGGATGTCT
*
1890462 TATAGATGGCTCGGAGGACTTG
1 TATAGATAGCTCGGAGGACTTG
*
1890484 TATAGATAGCTTGGAGGACTT
1 TATAGATAGCTCGGAGGACTT
1890505 ATCATCTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.30
Consensus pattern (22 bp):
TATAGATAGCTCGGAGGACTTG
Found at i:1892036 original size:20 final size:20
Alignment explanation
Indices: 1892011--1892059 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1892001 CATAAAAAGA
1892011 GTATCGATA-CTACT-GGGTTG
1 GTATCGATACCTA-TAGGG-TG
1892031 GTATCGATACCTATAGGGTG
1 GTATCGATACCTATAGGGTG
1892051 GTATCGATA
1 GTATCGATA
1892060 TCGGGATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (20 bp):
GTATCGATACCTATAGGGTG
Found at i:1896451 original size:40 final size:41
Alignment explanation
Indices: 1896404--1896482 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 41
1896394 ACAAAAACGT
*
1896404 CGCTATAGATCTTGACCTTTTG-CATTTGTATAAAAAATTC
1 CGCTATAGATCTTCACCTTTTGCCATTTGTATAAAAAATTC
1896444 CGCTATAGATCTTCACCTTTTGCCACATTTGTATAAAAA
1 CGCTATAGATCTTCACCTTTTG-C-CATTTGTATAAAAA
1896483 CGCCACTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 21 0.60
43 14 0.40
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (41 bp):
CGCTATAGATCTTCACCTTTTGCCATTTGTATAAAAAATTC
Found at i:1896500 original size:42 final size:43
Alignment explanation
Indices: 1896396--1896507 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 43
1896386 TGTTTTTAAC
* * * *
1896396 AAAAACGTCGCTATAGATCTTGACCTTTTG---CATTTGTATA
1 AAAAACGCCACTAAAGATCTTCACCTTTTGCCACATTTGTATA
** * *
1896436 AAAAATTCCGCTATAGATCTTCACCTTTTGCCACATTTGTAT-
1 AAAAACGCCACTAAAGATCTTCACCTTTTGCCACATTTGTATA
*
1896478 AAAAACGCCACTAAAGGTCTTCACCTTTTG
1 AAAAACGCCACTAAAGATCTTCACCTTTTG
1896508 TGGCGTTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
40 26 0.43
42 25 0.42
43 9 0.15
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (43 bp):
AAAAACGCCACTAAAGATCTTCACCTTTTGCCACATTTGTATA
Found at i:1898029 original size:22 final size:22
Alignment explanation
Indices: 1898003--1898051 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
1897993 TTGATCAGCA
1898003 TTGACCA-CTGTTGACCAGAACT
1 TTGACCAGCT-TTGACCAGAACT
1898025 TTGA-CAGGCTTTGACCAGAACT
1 TTGACCA-GCTTTGACCAGAACT
1898047 TTGAC
1 TTGAC
1898052 AGGCGTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.08
22 20 0.83
23 2 0.08
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (22 bp):
TTGACCAGCTTTGACCAGAACT
Found at i:1898048 original size:12 final size:12
Alignment explanation
Indices: 1898013--1898051 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1898003 TTGACCACTG
1898013 TTGACCAGAACT
1 TTGACCAGAACT
*
1898025 TTGA-CAG-GCT
1 TTGACCAGAACT
1898035 TTGACCAGAACT
1 TTGACCAGAACT
1898047 TTGAC
1 TTGAC
1898052 AGGCGTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.26
11 6 0.26
12 11 0.48
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (12 bp):
TTGACCAGAACT
Found at i:1898052 original size:22 final size:22
Alignment explanation
Indices: 1898012--1898062 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1898002 ATTGACCACT
1898012 GTTGACCAGAACTTTGACAGGC
1 GTTGACCAGAACTTTGACAGGC
*
1898034 TTTGACCAGAACTTTGACAGGC
1 GTTGACCAGAACTTTGACAGGC
1898056 GTTGACC
1 GTTGACC
1898063 GGCGTTGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (22 bp):
GTTGACCAGAACTTTGACAGGC
Found at i:1900765 original size:80 final size:78
Alignment explanation
Indices: 1900632--1900873 Score: 376
Period size: 80 Copynumber: 3.0 Consensus size: 78
1900622 GCTTATAGCA
* *
1900632 CCCAAGGCATATTTTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAATG
1 CCCAAGGTATA-TCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAA-G
1900697 GTATCCTTGGGTAGG
64 GTATCCTTGGGTAGG
* * *
1900712 CCCAAGGTATATACTTAGGTTGGTTTCTTTTGTTGTATGCTTAAGGTAACCCTACGGATCTAAGG
1 CCCAAGGTATAT-CTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGG
*
1900777 ATATCCTTGGGTAAG
65 -TATCCTTGGGTAGG
1900792 CCCAAGGTATATCGTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGG
1 CCCAAGGTATATC-TTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAA-G
1900857 GTATCCTTGGGTAGG
64 GTATCCTTGGGTAGG
1900872 CC
1 CC
1900874 TATAGGCCCC
Statistics
Matches: 148, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
79 4 0.03
80 142 0.96
81 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (78 bp):
CCCAAGGTATATCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGGT
ATCCTTGGGTAGG
Found at i:1905792 original size:80 final size:80
Alignment explanation
Indices: 1905659--1905897 Score: 392
Period size: 80 Copynumber: 3.0 Consensus size: 80
1905649 GCTTATAACC
* * * *
1905659 CCCAAGGCATATTCTTAGGTTGGTTTTCTTTGTTGTGTACTTAAGGTAACCCTATGGATCTAAGG
1 CCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGG
1905724 GTATCCTTGGGTAGG
66 GTATCCTTGGGTAGG
1905739 CCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGAT-TAAAG
1 CCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCT-AAG
*
1905803 GATATCCTTGGGTAGG
65 GGTATCCTTGGGTAGG
*
1905819 CCCAAGGTATATCCTTA-GTATGGTTTCCTTTGTTGTGTGGTTAAGGTAACCCTATGGATCTAAG
1 CCCAAGGTATATCCTTAGGT-TGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAG
1905883 GGTATCCTTGGGTAG
65 GGTATCCTTGGGTAG
1905898 ACCTATAGGC
Statistics
Matches: 149, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
79 3 0.02
80 145 0.97
81 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (80 bp):
CCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGG
GTATCCTTGGGTAGG
Found at i:1906442 original size:80 final size:80
Alignment explanation
Indices: 1906300--1906530 Score: 392
Period size: 80 Copynumber: 2.9 Consensus size: 80
1906290 CCCCCGAGGC
* *
1906300 ATATTCTTAGGTTGGTTTTCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGGGTATCCTT
1 ATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGGGTATCCTT
1906365 GGGTAGGCCCAAGGT
66 GGGTAGGCCCAAGGT
* * *
1906380 ATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTACGGATCAAAGGATATCCTT
1 ATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGGGTATCCTT
1906445 GGGTAGGCCCAAGGT
66 GGGTAGGCCCAAGGT
*
1906460 ATATCCTTA-GTATGGTTTCCTTTGTTGTGTGGTTAAGGTAACCCTATGGATCTAAGGGTATCCT
1 ATATCCTTAGGT-TGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGGGTATCCT
1906524 TGGGTAG
65 TGGGTAG
1906531 ACCTATAGGC
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
79 2 0.01
80 139 0.99
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (80 bp):
ATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCTAAGGGTATCCTT
GGGTAGGCCCAAGGT
Found at i:1908433 original size:22 final size:22
Alignment explanation
Indices: 1908405--1908446 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1908395 TAATTTATGT
1908405 TTGGGTGATA-TTTGTGTAAAAC
1 TTGGGTGATAGTTT-TGTAAAAC
*
1908427 TTGGGTGCTAGTTTTGTAAA
1 TTGGGTGATAGTTTTGTAAA
1908447 TATTGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.43
Consensus pattern (22 bp):
TTGGGTGATAGTTTTGTAAAAC
Found at i:1910027 original size:39 final size:39
Alignment explanation
Indices: 1909983--1910107 Score: 105
Period size: 39 Copynumber: 3.2 Consensus size: 39
1909973 GGGTAGGCCC
1909983 AAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTT
1 AAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTT
* * * * * **
1910022 AAGGTA-ACCCTACAGATCTAAGGATATCC-TTG-GGTAG-GCCC
1 AAGGTATATCCT-TAGGT-T--GG-TTTCCTTTGTTGT-GTGCTT
1910063 AAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTT
1 AAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTT
1910102 AAGGTA
1 AAGGTA
1910108 ACCCTATGGA
Statistics
Matches: 62, Mismatches: 14, Indels: 20
0.65 0.15 0.21
Matches are distributed among these distances:
37 4 0.06
38 10 0.16
39 19 0.31
40 2 0.03
41 13 0.21
42 10 0.16
43 4 0.06
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (39 bp):
AAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTT
Found at i:1910029 original size:80 final size:80
Alignment explanation
Indices: 1909896--1910141 Score: 420
Period size: 80 Copynumber: 3.1 Consensus size: 80
1909886 GGTAGGCTTA
* * * *
1909896 TAGGCCCAAGGCATATTCTTAGGTTGGTTTCCTTTGCTATGTGCTTAAGGTAACCCTATGGATCT
1 TAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCT
1909961 AAGGGTATCCTTGGG
66 AAGGGTATCCTTGGG
**
1909976 TAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTACAGATCT
1 TAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCT
*
1910041 AAGGATATCCTTGGG
66 AAGGGTATCCTTGGG
1910056 TAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCT
1 TAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCT
*
1910121 AAGGGTGTCCTTGGG
66 AAGGGTATCCTTGGG
1910136 TAGGCC
1 TAGGCC
1910142 TATAGGCCCC
Statistics
Matches: 155, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 155 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (80 bp):
TAGGCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGTTGTGTGCTTAAGGTAACCCTATGGATCT
AAGGGTATCCTTGGG
Found at i:1913614 original size:21 final size:21
Alignment explanation
Indices: 1913588--1913631 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1913578 TGCGTATCTC
1913588 AGCAAGACTGACTTTCGCACA
1 AGCAAGACTGACTTTCGCACA
1913609 AGCAAGACTGACTTTCGCACA
1 AGCAAGACTGACTTTCGCACA
1913630 AG
1 AG
1913632 AAGGTGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.18
Consensus pattern (21 bp):
AGCAAGACTGACTTTCGCACA
Found at i:1929466 original size:16 final size:16
Alignment explanation
Indices: 1929441--1929506 Score: 96
Period size: 16 Copynumber: 4.1 Consensus size: 16
1929431 TACCCGACCA
*
1929441 GTTTTCAACCTAACCT
1 GTTTTTAACCTAACCT
*
1929457 GTTTTTAACCTAACTT
1 GTTTTTAACCTAACCT
*
1929473 GTTTTTAACCTAACTT
1 GTTTTTAACCTAACCT
*
1929489 GTTTTTAACCTGACCT
1 GTTTTTAACCTAACCT
1929505 GT
1 GT
1929507 AAATGATCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (16 bp):
GTTTTTAACCTAACCT
Found at i:1930223 original size:19 final size:20
Alignment explanation
Indices: 1930191--1930228 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1930181 TTTTTATTCC
1930191 CTCTAAATTTCCCAATTTCT
1 CTCTAAATTTCCCAATTTCT
1930211 CTCTAAA-TTCCCAATTTC
1 CTCTAAATTTCCCAATTTC
1930229 CCTATATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (20 bp):
CTCTAAATTTCCCAATTTCT
Found at i:1930258 original size:27 final size:27
Alignment explanation
Indices: 1930196--1930258 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1930186 ATTCCCTCTA
* * *
1930196 AATTTCCCAATTTCTCTCTAAATTCCC
1 AATTTCCCTATATCTCTCAAAATTCCC
*
1930223 AATTTCCCTATAT-TCTCAAAATTTCCT
1 AATTTCCCTATATCTCTCAAAA-TTCCC
1930250 AATTTCCCT
1 AATTTCCCT
1930259 CTAAATTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTTCCCTATATCTCTCAAAATTCCC
Found at i:1930347 original size:2 final size:2
Alignment explanation
Indices: 1930340--1930412 Score: 130
Period size: 2 Copynumber: 36.5 Consensus size: 2
1930330 ACTTTAAATA
1930340 AT AT AT AT AT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
1930382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1930413 ATTAAACATA
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.01
2 67 0.97
3 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1930654 original size:20 final size:20
Alignment explanation
Indices: 1930631--1930681 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1930621 CACGGAATGG
1930631 AAGATTACCAGTGGGAATAT
1 AAGATTACCAGTGGGAATAT
*
1930651 AAGATTACCAGTGGGAATGT
1 AAGATTACCAGTGGGAATAT
1930671 AAGATTACCAG
1 AAGATTACCAG
1930682 GGAATAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAT
Found at i:1931623 original size:38 final size:38
Alignment explanation
Indices: 1931588--1931661 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
1931578 TTAGGAAATT
*
1931588 TTGAGAATATAGA-GAAATTG-GGAATTTAGAGGGAAA
1 TTGAGAATATAGAGGAAATTGAGAAATTTAGAGGGAAA
*
1931624 TTGAGAATTTAGAGGGAAATTGAGAAATTTAGAGGGAA
1 TTGAGAATATAGA-GGAAATTGAGAAATTTAGAGGGAA
1931662 TAGAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 12 0.36
38 7 0.21
39 14 0.42
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.26
Consensus pattern (38 bp):
TTGAGAATATAGAGGAAATTGAGAAATTTAGAGGGAAA
Found at i:1931654 original size:20 final size:19
Alignment explanation
Indices: 1931588--1931661 Score: 107
Period size: 19 Copynumber: 3.9 Consensus size: 19
1931578 TTAGGAAATT
*
1931588 TTGAGAATATAGA--GAAA
1 TTGAGAATTTAGAGGGAAA
*
1931605 TTGGGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGGAAA
1931624 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGGAAA
1931643 TTGAGAAATTTAGAGGGAA
1 TTGAG-AATTTAGAGGGAA
1931662 TAGAAAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.22
19 27 0.53
20 13 0.25
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.26
Consensus pattern (19 bp):
TTGAGAATTTAGAGGGAAA
Found at i:1931992 original size:20 final size:19
Alignment explanation
Indices: 1931951--1932034 Score: 77
Period size: 18 Copynumber: 4.6 Consensus size: 19
1931941 TCCTAAACCC
* *
1931951 TAAACCCTA-ATATATGTA
1 TAAACCATATATATATATA
*
1931969 TAAACCATGTATAGTATATA
1 TAAACCATATATA-TATATA
1931989 TAAA-C-TATATATATATA
1 TAAACCATATATATATATA
* *
1932006 TATA-TATATATATATATA
1 TAAACCATATATATATATA
*
1932024 TAAACTATATA
1 TAAACCATATA
1932035 AAGTAAATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.16
18 27 0.49
19 10 0.18
20 9 0.16
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (19 bp):
TAAACCATATATATATATA
Found at i:1931999 original size:35 final size:35
Alignment explanation
Indices: 1931960--1932034 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
1931950 CTAAACCCTA
* * *
1931960 ATATATGTATAAACCATGTATAGTATATATAAACTAT
1 ATATATATATATA-CATATATA-TATATATAAACTAT
*
1931997 ATATATATATATATATATATATATATATAAACTAT
1 ATATATATATATACATATATATATATATAAACTAT
1932032 ATA
1 ATA
1932035 AAGTAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 17 0.50
36 6 0.18
37 11 0.32
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (35 bp):
ATATATATATATACATATATATATATATAAACTAT
Found at i:1932034 original size:2 final size:2
Alignment explanation
Indices: 1931978--1932025 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
1931968 ATAAACCATG
*
1931978 TA TA GTA TA TA TA AA CTA 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
1932022 TA TA
1 TA TA
1932026 AACTATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 39 0.93
3 3 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1932051 original size:35 final size:36
Alignment explanation
Indices: 1931978--1932059 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
1931968 ATAAACCATG
* *
1931978 TATAGTATATATAAACTATATATATATATATATATA
1 TATAGTATATATAAACTATATAAATAAATATATATA
1932014 TATA-TATATATAAACTATATAAAGTAAAT-TACT-TA
1 TATAGTATATATAAACTATATAAA-TAAATATA-TATA
*
1932049 TATAGTTTATA
1 TATAGTATATA
1932060 GAAATACTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 26 0.65
36 14 0.35
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (36 bp):
TATAGTATATATAAACTATATAAATAAATATATATA
Found at i:1932201 original size:18 final size:18
Alignment explanation
Indices: 1932180--1932273 Score: 63
Period size: 18 Copynumber: 5.2 Consensus size: 18
1932170 ACATATAAAC
1932180 TATATATTTTATATAGTA
1 TATATATTTTATATAGTA
1932198 TATATACTATATTA-ATA-TA
1 TATATA-T-T-TTATATAGTA
* *
1932217 AATAATATTTTATAAAGTA
1 TAT-ATATTTTATATAGTA
* *
1932236 TATA-CTTTT-TATAGTT
1 TATATATTTTATATAGTA
*
1932252 TATATACTTTT-TATAGTT
1 TATATA-TTTTATATAGTA
1932270 TATA
1 TATA
1932274 CATATAGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
16 9 0.15
17 7 0.11
18 25 0.41
19 10 0.16
20 7 0.11
21 3 0.05
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.53
Consensus pattern (18 bp):
TATATATTTTATATAGTA
Found at i:1932218 original size:54 final size:54
Alignment explanation
Indices: 1932142--1932259 Score: 166
Period size: 54 Copynumber: 2.2 Consensus size: 54
1932132 AATGCATACA
*
1932142 TATATATACTATATTAATATAAATTATAACATATAAACTATATA-TTTTATATAG
1 TATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTT-TATAG
*** *
1932196 TATATATACTATATTAATATAAATAATATTTTATAAAGTATATACTTTTTATAG
1 TATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTTTATAG
*
1932250 TTTATATACT
1 TATATATACT
1932260 TTTTATAGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 53 0.93
55 4 0.07
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (54 bp):
TATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTTTATAG
Found at i:1932365 original size:18 final size:18
Alignment explanation
Indices: 1932317--1932499 Score: 115
Period size: 18 Copynumber: 9.8 Consensus size: 18
1932307 CCACATAAAC
* *
1932317 ATAATTTATATATAGCTT
1 ATAATATATATATAGTTT
1932335 ATAATA-ATTATATAGTTT
1 ATAATATA-TATATAGTTT
* *
1932353 ATAATATAAATATAATTT
1 ATAATATATATATAGTTT
*
1932371 ATAATTTTATATACATAGTTT
1 ATAA---TATATATATAGTTT
* **
1932392 AT-ATATAGTTCACATA-AAT
1 ATAATATA--T-ATATAGTTT
*
1932411 ATAATTTATATATAGTTT
1 ATAATATATATATAGTTT
1932429 ATAATA-ATTATATAGTTT
1 ATAATATA-TATATAGTTT
*
1932447 ATAATATAAATATAGTTT
1 ATAATATATATATAGTTT
* *
1932465 ATATATAATTTTATATA-TAT
1 ATA-AT-A-TATATATAGTTT
1932485 ATATATATATATATA
1 ATA-ATATATATATA
1932500 TATTATATTT
Statistics
Matches: 131, Mismatches: 19, Indels: 30
0.73 0.11 0.17
Matches are distributed among these distances:
17 10 0.08
18 74 0.56
19 9 0.07
20 19 0.15
21 19 0.15
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (18 bp):
ATAATATATATATAGTTT
Found at i:1932369 original size:47 final size:47
Alignment explanation
Indices: 1932311--1932471 Score: 186
Period size: 47 Copynumber: 3.4 Consensus size: 47
1932301 TGTAGTCCAC
* *
1932311 ATAAACATAATTTATATATAGCTTATAATAATTATATAGTTTATAAT
1 ATAAATATAATTTATATATAGTTTATAATAATTATATAGTTTATAAT
* * * * *
1932358 ATAAATATAATTTATA-AT-TTTATATACATAGTT-TATA-TATAGTTCAC
1 ATAAATATAATTTATATATAGTT-TATA-ATAATTATATAGTTTA--TAAT
1932405 ATAAATATAATTTATATATAGTTTATAATAATTATATAGTTTATAAT
1 ATAAATATAATTTATATATAGTTTATAATAATTATATAGTTTATAAT
*
1932452 ATAAATATAGTTTATATATA
1 ATAAATATAATTTATATATA
1932472 ATTTTATATA
Statistics
Matches: 93, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
45 4 0.04
46 10 0.11
47 64 0.69
48 10 0.11
49 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (47 bp):
ATAAATATAATTTATATATAGTTTATAATAATTATATAGTTTATAAT
Found at i:1932415 original size:94 final size:95
Alignment explanation
Indices: 1932281--1932467 Score: 322
Period size: 94 Copynumber: 2.0 Consensus size: 95
1932271 ATACATATAG
*
1932281 TTTATATACATAGTTATATATGTAGTCCACATAAACATAATTTATATATAGCTTATAATAATTAT
1 TTTATATACATAGTTATATATATAGTCCACATAAACATAATTTATATATAGCTTATAATAATTAT
1932346 ATAGTTTATAATATAAATATAATTTATAAT
66 ATAGTTTATAATATAAATATAATTTATAAT
* * *
1932376 TTTATATACATAGTT-TATATATAGTTCACATAAATATAATTTATATATAGTTTATAATAATTAT
1 TTTATATACATAGTTATATATATAGTCCACATAAACATAATTTATATATAGCTTATAATAATTAT
*
1932440 ATAGTTTATAATATAAATATAGTTTATA
66 ATAGTTTATAATATAAATATAATTTATA
1932468 TATAATTTTA
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
94 72 0.83
95 15 0.17
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (95 bp):
TTTATATACATAGTTATATATATAGTCCACATAAACATAATTTATATATAGCTTATAATAATTAT
ATAGTTTATAATATAAATATAATTTATAAT
Found at i:1932424 original size:2 final size:2
Alignment explanation
Indices: 1932417--1932507 Score: 61
Period size: 2 Copynumber: 47.5 Consensus size: 2
1932407 AAATATAATT
* * *
1932417 TA TA TA TA GTT TA TA -A TA -A T- TA TA TA GTT TA TA -A TA TA AA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
1932457 TA TA GTT TA TA TA TA -A T- TT 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
1932498 TA TA T- TA TA T
1 TA TA TA TA TA T
1932508 TTTTTCAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
1 7 0.10
2 60 0.86
3 3 0.04
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1932479 original size:12 final size:13
Alignment explanation
Indices: 1932451--1932507 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
1932441 TAGTTTATAA
* *
1932451 TATAAATATAGTT
1 TATATATATATTT
1932464 TATATATA-ATTT
1 TATATATATATTT
*
1932476 TATATATATATATA
1 TATATATATAT-TT
*
1932490 TATATATATATAT
1 TATATATATATTT
1932503 TATAT
1 TATAT
1932508 TTTTTCAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 11 0.30
13 14 0.38
14 12 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TATATATATATTT
Found at i:1932488 original size:47 final size:46
Alignment explanation
Indices: 1932311--1932489 Score: 159
Period size: 47 Copynumber: 3.8 Consensus size: 46
1932301 TGTAGTCCAC
* ** *
1932311 ATAAACATAATTTATATATAGCTTATAATAATTATATAGTTTATAAT
1 ATAAATATAATTTATATATATTTTATAAT-AGTATATAGTTTATAAT
* * * *
1932358 ATAAATATAATTTATA-AT-TTTATATACATAGTTTATA-TATAGTTCAC
1 ATAAATATAATTTATATATATTT-TATA-ATAGTATATAGTTTA--TAAT
* *
1932405 ATAAATATAATTTATATATAGTTTATAATAATTATATAGTTTATAAT
1 ATAAATATAATTTATATATATTTTATAAT-AGTATATAGTTTATAAT
*
1932452 ATAAATATAGTTTATATATAATTTTATATATA-TATATA
1 ATAAATATAATTTATATAT-ATTTTATA-ATAGTATATA
1932490 TATATATATA
Statistics
Matches: 106, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
45 4 0.04
46 12 0.11
47 63 0.59
48 20 0.19
49 7 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (46 bp):
ATAAATATAATTTATATATATTTTATAATAGTATATAGTTTATAAT
Found at i:1935021 original size:21 final size:21
Alignment explanation
Indices: 1934995--1935050 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1934985 ATGTGAGAGC
*
1934995 TATTCCACTTAAGAAATTGGA
1 TATTCCACTCAAGAAATTGGA
1935016 TATTCCACTCAAGAAATTGGA
1 TATTCCACTCAAGAAATTGGA
1935037 TATTCCACTCAAGA
1 TATTCCACTCAAGA
1935051 GATAATGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (21 bp):
TATTCCACTCAAGAAATTGGA
Found at i:1938049 original size:29 final size:30
Alignment explanation
Indices: 1938004--1938067 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
1937994 AGATTTTATG
*
1938004 TTTAGATGATCGAATTTGAA-TTTATAAAAT
1 TTTAGAGGATCGAATTT-AAGTTTATAAAAT
1938034 TTTAGAGGAT-GAATTTAAGTTTATAAAAT
1 TTTAGAGGATCGAATTTAAGTTTATAAAAT
1938063 TTTAG
1 TTTAG
1938068 GGTGAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 2 0.06
29 21 0.66
30 9 0.28
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.44
Consensus pattern (30 bp):
TTTAGAGGATCGAATTTAAGTTTATAAAAT
Found at i:1939684 original size:20 final size:20
Alignment explanation
Indices: 1939655--1939724 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1939645 AGACTGTCTG
* **
1939655 GTCTCTATACCGAAGGACTA
1 GTCTCCATACCGAAAAACTA
* *
1939675 GTCTCCATACTGAAAAACTG
1 GTCTCCATACCGAAAAACTA
*
1939695 GTCTCCATACCGAATAAACGA
1 GTCTCCATACCGAA-AAACTA
*
1939716 GTATCCATA
1 GTCTCCATA
1939725 ATGAAGGCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 28 0.70
21 12 0.30
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (20 bp):
GTCTCCATACCGAAAAACTA
Found at i:1943521 original size:14 final size:14
Alignment explanation
Indices: 1943499--1943539 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1943489 GTCAAAGTCA
1943499 ACGGGTTGACTCAG
1 ACGGGTTGACTCAG
*
1943513 ACGGTTTGACTCAG
1 ACGGGTTGACTCAG
*
1943527 ACCGAGTTGACTC
1 A-CGGGTTGACTC
1943540 GGTGAGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (14 bp):
ACGGGTTGACTCAG
Found at i:1944980 original size:21 final size:21
Alignment explanation
Indices: 1944929--1944981 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1944919 ATTATGACTA
1944929 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1944950 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1944971 TCGCAATGCGA
1 TCGCAATGCGA
1944982 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1944996 original size:20 final size:21
Alignment explanation
Indices: 1944971--1945022 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1944961 TTTTCCCAAT
*
1944971 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1944991 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1945012 TCGCAATGCGA
1 TCGCAATGCGA
1945023 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1945001 original size:41 final size:41
Alignment explanation
Indices: 1944956--1945147 Score: 113
Period size: 41 Copynumber: 4.7 Consensus size: 41
1944946 AATTTCGCGT
*
1944956 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
1944997 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
1945038 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* * *
1945079 TGCGATTTTCATAATTCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * * *
1945121 CGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAATTCGCAATGCGAAT
1945148 CTTACTATCG
Statistics
Matches: 109, Mismatches: 35, Indels: 15
0.69 0.22 0.09
Matches are distributed among these distances:
39 2 0.02
40 4 0.04
41 92 0.84
42 9 0.08
43 1 0.01
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:1945066 original size:21 final size:21
Alignment explanation
Indices: 1945032--1945104 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
1945022 ATACTGACTA
* *
1945032 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
1945053 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
1945073 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
1945094 TCGCAATGCGA
1 TCGCAATGCGA
1945105 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:1945098 original size:103 final size:103
Alignment explanation
Indices: 1944909--1945125 Score: 262
Period size: 103 Copynumber: 2.1 Consensus size: 103
1944899 GTTTCCAGAT
* * *
1944909 TCGCAACGCGATTATGACTATCGCAATGCGATTTTCCAATTTCGCGTTGCGATTTTCCCAATTCG
1 TCGCAACGCGATTATGACTATCGCAATGCAATTTTCCAATTTCGCATTGCGATTTTACCAATTCG
*
1944974 CAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
66 CAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAA
* **
1945012 TCGCAATGCGA-TACTGACTATCGCAATGCAATTTTCCTAA-TTCGCATTGCGA-TTTACGTATT
1 TCGCAACGCGATTA-TGACTATCGCAATGCAATTTTCC-AATTTCGCATTGCGATTTTACCAATT
** * * *
1945074 CGCGTTGCGATTTTCA-TAATTCGCAATGCGAATTAGGAAAA
64 CGCAATGCGA--ATAAGTAAATCGCAATGCGAATTAGGAAAA
1945115 TCGCAACGCGA
1 TCGCAACGCGA
1945126 ATACGTAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
102 17 0.18
103 76 0.78
104 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (103 bp):
TCGCAACGCGATTATGACTATCGCAATGCAATTTTCCAATTTCGCATTGCGATTTTACCAATTCG
CAATGCGAATAAGTAAATCGCAATGCGAATTAGGAAAA
Found at i:1945118 original size:21 final size:21
Alignment explanation
Indices: 1945094--1945147 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1945084 TTTTCATAAT
*
1945094 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
1945115 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
1945135 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1945148 CTTACTATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:1945196 original size:123 final size:123
Alignment explanation
Indices: 1944949--1945173 Score: 292
Period size: 123 Copynumber: 1.8 Consensus size: 123
1944939 ATTTTCCAAT
* * * **
1944949 TTCGCGTTGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATC
1 TTCGCGTTGCGATTTTCACAATTCGCAATGCGAATAAGAAAATCGCAACGCGAATTACGAAAATC
* * *
1945014 GCAATGCGATACTGACTATCGCAATGCAATTTTCCTAATTCGCATTGCGATTTACGTA
66 GCAATGCGATACTGACTATCGCAATGCAATTTACATAATGCGCATTGCGATTTACGTA
* * *
1945072 TTCGCGTTGCGATTTTCATAATTCGCAATGCGAATTAGGAAAATCGCAACGCGAA-TACGTAAAT
1 TTCGCGTTGCGATTTTCACAATTCGCAATGCGAA-TAAGAAAATCGCAACGCGAATTACGAAAAT
* * *
1945136 CGCAATGCGA-ATCTTACTATCGTAATGCGATTTACATA
65 CGCAATGCGATA-CTGACTATCGCAATGCAATTTACATA
1945174 GCGCCATTCG
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
122 1 0.01
123 69 0.79
124 17 0.20
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (123 bp):
TTCGCGTTGCGATTTTCACAATTCGCAATGCGAATAAGAAAATCGCAACGCGAATTACGAAAATC
GCAATGCGATACTGACTATCGCAATGCAATTTACATAATGCGCATTGCGATTTACGTA
Found at i:1945713 original size:20 final size:20
Alignment explanation
Indices: 1945685--1945752 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1945675 TTCGAGAATG
1945685 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGCGGAAATA
**
1945705 ACTATCGCAACGCGGAAATA
1 AAAATCGCAACGCGGAAATA
**
1945725 AAAATCGCAACGC-GAAACC
1 AAAATCGCAACGCGGAAATA
1945744 AAAATCGCA
1 AAAATCGCA
1945753 TTGCGATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 13 0.31
20 29 0.69
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAATA
Found at i:1945770 original size:19 final size:19
Alignment explanation
Indices: 1945748--1945812 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1945738 GAAACCAAAA
1945748 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1945767 TCGCGTTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1945783 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1945800 TCGCATTGCGATT
1 TCGCATTGCGATT
1945813 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
16 7 0.18
17 7 0.18
19 18 0.47
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1945789 original size:14 final size:14
Alignment explanation
Indices: 1945770--1945825 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1945760 TTTCATTTCG
1945770 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1945784 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
1945801 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
1945817 CGTTGCGAT
1 CGTTGCGAT
1945826 AGTCATTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 15 0.43
16 7 0.20
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1945795 original size:33 final size:33
Alignment explanation
Indices: 1945753--1945882 Score: 188
Period size: 33 Copynumber: 3.9 Consensus size: 33
1945743 CAAAATCGCA
**
1945753 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
** *
1945786 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
*
1945819 TTGCGATAGTCATTTCGCGTTGCAATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
*
1945852 TTGAGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
1945883 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 75 0.84
34 14 0.16
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:1945884 original size:20 final size:20
Alignment explanation
Indices: 1945861--1945907 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1945851 GTTGAGATAG
1945861 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
1945881 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
1945901 TCATTTC
1 TCATTTC
1945908 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:1947206 original size:21 final size:20
Alignment explanation
Indices: 1947135--1947207 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1947125 CTCCACTTCG
1947135 AGAGCCATCACCTCAC--CC
1 AGAGCCATCACCTCACAACC
*
1947153 AGAGCCATCACCTGATCAACC
1 AGAGCCATCACCTCA-CAACC
* * *
1947174 CGA-CTATACACCTCTACAACG
1 AGAGCCAT-CACCTC-ACAACC
1947195 AGAGCCATCACCT
1 AGAGCCATCACCT
1947208 ATCCCGTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 3 0.07
21 20 0.48
22 4 0.10
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (20 bp):
AGAGCCATCACCTCACAACC
Found at i:1947954 original size:42 final size:42
Alignment explanation
Indices: 1947908--1947996 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
1947898 CCTATCGTTG
*
1947908 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * * *
1947950 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCTACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
1947992 AAGAG
1 AAGAG
1947997 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:1949370 original size:14 final size:14
Alignment explanation
Indices: 1949351--1949386 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1949341 ATTGTTTAAT
1949351 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1949365 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1949379 TGATTTGT
1 TGATTTGT
1949387 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Done.