Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008721.1 Hibiscus syriacus cultivar Beakdansim tig00111779_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: 2464137
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1761401 original size:103 final size:97
Alignment explanation
Indices: 1761228--1761423 Score: 338
Period size: 103 Copynumber: 2.0 Consensus size: 97
1761218 TATAAAATAC
1761228 AACTCGAATAATTTTAAATGTTAATGGTTAGCTATTTTCAAATTTGAATCAAGTCCATTGACTTT
1 AACTCGAATAATTTTAAATGTTAATGGTTAGCTATTTTCAAATTTGAATCAAGTCCATTGACTTT
1761293 GAATGATATATGTATATTACATAAGAAATTTT
66 GAATGATATATGTATATTACATAAGAAATTTT
1761325 AACTCGAATAATTTTAAATGTTTAATGGTTAGCTGCTTGATTTTCAAATTTGAATCAAGTCCATT
1 AACTCGAATAATTTTAAATG-TTAATGGTTA---GC-T-ATTTTCAAATTTGAATCAAGTCCATT
1761390 GACTTTGAATGATATATGTATATTACATAAGAAA
60 GACTTTGAATGATATATGTATATTACATAAGAAA
1761424 AAAAATATGA
Statistics
Matches: 93, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
97 20 0.22
98 10 0.11
101 2 0.02
102 1 0.01
103 60 0.65
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (97 bp):
AACTCGAATAATTTTAAATGTTAATGGTTAGCTATTTTCAAATTTGAATCAAGTCCATTGACTTT
GAATGATATATGTATATTACATAAGAAATTTT
Found at i:1767360 original size:55 final size:55
Alignment explanation
Indices: 1767276--1767434 Score: 239
Period size: 55 Copynumber: 2.9 Consensus size: 55
1767266 ATTAGTAGTG
*
1767276 CCAACCTGAGAAGTCCAAACCAATTATTGGGAACCCTTTGCTTCGTTTAATAGCA
1 CCAACCTGAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTAATAGCA
**
1767331 CCAA-CTAGAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTAATAGTG
1 CCAACCT-GAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTAATAGCA
* * **
1767386 CCAACCTGAGAAGTCCAAACCAATTTTTGGGAACTCTTCATTTCGTTTA
1 CCAACCTGAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTA
1767435 CTGTTTAAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
54 2 0.02
55 91 0.96
56 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (55 bp):
CCAACCTGAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTAATAGCA
Found at i:1778229 original size:21 final size:21
Alignment explanation
Indices: 1778203--1778263 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 21
1778193 CGAGGTTTTC
*
1778203 ATAGGTCATTCGGGACAACTA
1 ATAGGTCCTTCGGGACAACTA
* *
1778224 ATAGGTCCTTCGGGACATATTC
1 ATAGGTCCTTCGGGACA-ACTA
*
1778246 ACAGGTCCTTCGGGACAA
1 ATAGGTCCTTCGGGACAA
1778264 ACTTCATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ATAGGTCCTTCGGGACAACTA
Found at i:1778254 original size:22 final size:21
Alignment explanation
Indices: 1778200--1778263 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
1778190 AGTCGAGGTT
*
1778200 TTCATAGGTCATTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
* *
1778221 CTAATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
1778243 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
1778264 ACTTCATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:1778871 original size:21 final size:21
Alignment explanation
Indices: 1778854--1778928 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
1778844 TATGCATATG
1778854 TGCACTGTAGCAATGCATCGA
1 TGCACTGTAGCAATGCATCGA
1778875 TGCACTGTAGCAATGCATCGA
1 TGCACTGTAGCAATGCATCGA
*
1778896 TGCACTGCAGCAATGCATCGA
1 TGCACTGTAGCAATGCATCGA
1778917 TGCACTGTAGCA
1 TGCACTGTAGCA
1778929 TTGTACACTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (21 bp):
TGCACTGTAGCAATGCATCGA
Found at i:1780238 original size:29 final size:31
Alignment explanation
Indices: 1780195--1780254 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
1780185 ATAAAATGAT
**
1780195 TTAATTGTACTTTTA-TGA-AATATAGTGAC
1 TTAATTGTAAATTTACTGATAATATAGTGAC
*
1780224 TTAATTGTAAATTTACTTATAATATAGTGAC
1 TTAATTGTAAATTTACTGATAATATAGTGAC
1780255 ATATGTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 2 0.08
31 11 0.42
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (31 bp):
TTAATTGTAAATTTACTGATAATATAGTGAC
Found at i:1780618 original size:29 final size:29
Alignment explanation
Indices: 1780576--1780631 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1780566 TTACCCTCAT
*
1780576 TCTATATTGATCCCAAAACTTTTGAATTC
1 TCTATATTCATCCCAAAACTTTTGAATTC
* *
1780605 TCTATTTTCATCCCTAAACTTTTGAAT
1 TCTATATTCATCCCAAAACTTTTGAAT
1780632 GATTAAGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (29 bp):
TCTATATTCATCCCAAAACTTTTGAATTC
Found at i:1780753 original size:59 final size:60
Alignment explanation
Indices: 1780648--1780819 Score: 181
Period size: 59 Copynumber: 2.9 Consensus size: 60
1780638 GGGGAATGTT
* ** * * * *
1780648 ATTGGAATGTTCAAATCTTTAGGGACCAAATTAGAATGAGAGTCATAGTTTGAGTATGAA
1 ATTGGGATGTTCAAAAGTTTAAGGACAAAATTAGAATGAGAGTCATAATTTGAGAATGAA
* *
1780708 ATTGGGATGTTCAAAAGTTTAAGGA-AAAATTATAATGTGAGTCATAATTTGAGAATGAA
1 ATTGGGATGTTCAAAAGTTTAAGGACAAAATTAGAATGAGAGTCATAATTTGAGAATGAA
* * * *
1780767 ATT-GGAAGTTTAAAAGTTTAATGATC-AATTTAGAATGAGAGTTC-TAATTTGAG
1 ATTGGGATGTTCAAAAGTTTAAGGA-CAAAATTAGAATGAGAG-TCATAATTTGAG
1780820 GATGTATGAT
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
58 18 0.19
59 53 0.56
60 23 0.24
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
ATTGGGATGTTCAAAAGTTTAAGGACAAAATTAGAATGAGAGTCATAATTTGAGAATGAA
Found at i:1784260 original size:26 final size:26
Alignment explanation
Indices: 1784202--1784253 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1784192 CTTATGATGC
*
1784202 ACACCTTACGTGTAAAATTTGAACTT
1 ACACTTTACGTGTAAAATTTGAACTT
1784228 ACACTTTACGTGTAAAATTTGAACTT
1 ACACTTTACGTGTAAAATTTGAACTT
1784254 GTTCTTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (26 bp):
ACACTTTACGTGTAAAATTTGAACTT
Found at i:1795556 original size:15 final size:15
Alignment explanation
Indices: 1795536--1795601 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
1795526 TTTCAGAAAA
1795536 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
1795551 TGAATTACTGGAATT
1 TGAATTACTGAAATT
*
1795566 TGAATTACTGGAAA-A
1 TGAATTACT-GAAATT
*
1795581 TGAATTACTGGAATT
1 TGAATTACTGAAATT
1795596 TGAATT
1 TGAATT
1795602 CTGGAAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
14 3 0.07
15 38 0.86
16 3 0.07
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:1795582 original size:45 final size:44
Alignment explanation
Indices: 1795531--1795617 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
1795521 TGGTTTTTCA
**
1795531 GAAAATGAATTACTGAAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGAAATTTGAATT-CTGGAAAATGAATTACTG
*
1795576 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGAAATTTGAATTCTGGAAAATGAATTAC
1795618 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGAAATTTGAATTCTGGAAAATGAATTACTG
Found at i:1795615 original size:29 final size:30
Alignment explanation
Indices: 1795536--1795617 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
1795526 TTTCAGAAAA
*
1795536 TGAATTACT-GAAATTTGAATTACTGGAATT
1 TGAATTACTGGAAA-ATGAATTACTGGAATT
1795566 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
1795596 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
1795618 ATTTCTGTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
29 16 0.32
30 30 0.60
31 4 0.08
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:1795623 original size:20 final size:20
Alignment explanation
Indices: 1795600--1795689 Score: 162
Period size: 20 Copynumber: 4.5 Consensus size: 20
1795590 GGAATTTGAA
1795600 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
1795620 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
1795640 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1795660 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1795680 TTCTGGAAAA
1 TTCTGGAAAA
1795690 CATCTGGAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:1795920 original size:28 final size:29
Alignment explanation
Indices: 1795877--1795949 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
1795867 ATAATATTTC
**
1795877 ATTATTAAATATATAATTTTTTTA-TTTAT
1 ATTATTAAA-ATATAATTTGATTATTTTAT
*
1795906 ATTATTATAATATAA-TTGATTATTTTAT
1 ATTATTAAAATATAATTTGATTATTTTAT
*
1795934 AATATTAAAATATAAT
1 ATTATTAAAATATAAT
1795950 ATTATATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 5 0.14
28 24 0.65
29 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
ATTATTAAAATATAATTTGATTATTTTAT
Found at i:1795957 original size:28 final size:27
Alignment explanation
Indices: 1795879--1795997 Score: 85
Period size: 28 Copynumber: 4.0 Consensus size: 27
1795869 AATATTTCAT
* * *
1795879 TATTAAATATATAATTTTTTTATTTATAT
1 TATTAAA-ATATAATTTATAT-TTTATAA
* *
1795908 TATTATAATATAATTGATTATTTTATAA
1 TATTAAAATATAATTTA-TATTTTATAA
*
1795936 TATTAAAATATAATATTATATTATATAAA
1 TATTAAAATATAAT-TTATATTTTAT-AA
*
1795965 TATTAATAAATATATTTTAAATATTTTAATAA
1 TATT-A-AAATATAATTT--ATATTTT-ATAA
1795997 T
1 T
1795998 TAATATTTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
28 34 0.47
29 16 0.22
30 3 0.04
31 8 0.11
32 9 0.12
33 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
TATTAAAATATAATTTATATTTTATAA
Found at i:1795965 original size:21 final size:20
Alignment explanation
Indices: 1795941--1795988 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
1795931 TATAATATTA
*
1795941 AAATATAAT-ATTATATTATAT
1 AAATATAATAAATATATT-T-T
1795962 AAATATTAATAAATATATTTT
1 AAATA-TAATAAATATATTTT
1795983 AAATAT
1 AAATAT
1795989 TTTAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 11 0.46
22 5 0.21
23 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATAATAAATATATTTT
Found at i:1796238 original size:42 final size:42
Alignment explanation
Indices: 1796179--1796298 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
1796169 ATGAATTACA
*
1796179 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1796221 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1796263 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1796299 TTCGGGGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1796507 original size:15 final size:15
Alignment explanation
Indices: 1796487--1796537 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
1796477 TTCCAGAAAA
1796487 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1796502 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
1796517 TGAATTACTGGAATT
1 TGAATTACTGGAATT
1796532 TGAATT
1 TGAATT
1796538 CTGAAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:1796516 original size:30 final size:29
Alignment explanation
Indices: 1796482--1796553 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 29
1796472 TGGTTTTCCA
1796482 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTG
1796512 GAAAATGAATTACTGGAATTTGAATTCTG
1 GAAAATGAATTACTGGAATTTGAATTCTG
*
1796541 AAAAATGAATTAC
1 GAAAATGAATTAC
1796554 ATTTCTGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (29 bp):
GAAAATGAATTACTGGAATTTGAATTCTG
Found at i:1796559 original size:20 final size:20
Alignment explanation
Indices: 1796536--1796665 Score: 224
Period size: 20 Copynumber: 6.5 Consensus size: 20
1796526 GGAATTTGAA
*
1796536 TTCTGAAAAATGAATTACAT
1 TTCTGTAAAATGAATTACAT
1796556 TTCTGTAAAATGAATTACAT
1 TTCTGTAAAATGAATTACAT
*
1796576 TTCTGGAAAATGAATTACAT
1 TTCTGTAAAATGAATTACAT
1796596 TTCTGTAAAATGAATTACAT
1 TTCTGTAAAATGAATTACAT
1796616 TTCTGTAAAATGAATTACAT
1 TTCTGTAAAATGAATTACAT
*
1796636 TTCTGGAAAATGAATTACAT
1 TTCTGTAAAATGAATTACAT
*
1796656 TTCTGGAAAA
1 TTCTGTAAAA
1796666 CATCTGAAAA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 106 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (20 bp):
TTCTGTAAAATGAATTACAT
Found at i:1796907 original size:15 final size:13
Alignment explanation
Indices: 1796877--1796950 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 13
1796867 TATAAATTTT
*
1796877 TTATTATATATTA
1 TTATAATATATTA
1796890 TTATAATATAATTGA
1 TTATAATAT-ATT-A
*
1796905 TTAT--TTTA-TA
1 TTATAATATATTA
* *
1796915 TAATATTATATTA
1 TTATAATATATTA
1796928 TTATAA-ATATTA
1 TTATAATATATTA
*
1796940 ATA-AATATATT
1 TTATAATATATT
1796951 TAAATATTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
10 4 0.08
11 3 0.06
12 17 0.35
13 16 0.33
14 3 0.06
15 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (13 bp):
TTATAATATATTA
Found at i:1796926 original size:17 final size:17
Alignment explanation
Indices: 1796883--1796939 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 17
1796873 TTTTTTATTA
1796883 TATATTATTATAATATAAT
1 TATATTATTATAA-AT-AT
1796902 TGATTATT-TTATATAATAT
1 T-A-TATTATTATA-AATAT
1796921 TATATTATTATAAATAT
1 TATATTATTATAAATAT
1796938 TA
1 TA
1796940 ATAAATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 11 0.32
18 6 0.18
19 4 0.12
20 8 0.24
21 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TATATTATTATAAATAT
Found at i:1796961 original size:21 final size:21
Alignment explanation
Indices: 1796926--1796973 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1796916 AATATTATAT
1796926 TATTATAAATATTAATAAAT-A
1 TATT-TAAATATTAATAAATAA
*
1796947 TATTTAAATATTTAATAATTAA
1 TATTTAAATA-TTAATAAATAA
1796969 TATTT
1 TATTT
1796974 TGATGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
22 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTAAATATTAATAAATAA
Found at i:1797193 original size:42 final size:42
Alignment explanation
Indices: 1797141--1797260 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
1797131 ATGAATTACA
* * *
1797141 TTCCGAAAAACGAATTACGTTAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1797183 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1797225 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1797261 TTCGGGGAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1800477 original size:182 final size:182
Alignment explanation
Indices: 1800140--1801267 Score: 1715
Period size: 182 Copynumber: 6.2 Consensus size: 182
1800130 TGGTAAAAAT
** * *
1800140 ATGAT-AAACCGGTAAACTGCTACC-GA-ATTTTGAAAGTATCGATAAATT-A-ATAAGTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
*
1800200 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTATACAAATG
66 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
* * * * *
1800265 TATCGATCCATAACAATATAACATGTAATAATATGACAAAACCGGTGTC-ATT
131 TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-A
*
1800317 ATGATAAAACCGGTAAACCA-CTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCG
1 ATGATAAAACCGGTAAA-AAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCG
1800381 ACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAAT
65 ACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAAT
*
1800446 GTATCGATCCATAGCAATATAATAGGTAATAATATGACAAAACAGGTCTCGAA
130 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* *
1800499 ATGATAAAACCGGTAAAAAGATATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
* *
1800564 CATTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATA
66 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
* *
1800629 TATCGATCCATAGCAATATAACATGTAATAATATGACAAAACATGTCTCGAA
131 TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* * *
1800681 ATGATAAAACCGATAAAAAGCTATCGGATATATTGAAAGTGTCGATAAATTAATATAATTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
*
1800746 CACTTTT-TATATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATATTTTATACAAAT
66 CACTTTTGTA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAAT
* * *
1800810 GAATCGATCCATAGCATTATAACAGGTAATAATATGACAAAACAGGTCTCAAA
130 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* * *
1800863 ATGATAAAACCGGTAAAAAGCTATCGGATATATTGAAAATGTCGATAAATTAATATAATTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
*
1800928 CACTTTT-TATATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTATCGATA-TTTATACAAAT
66 CACTTTTGTA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAAT
*
1800991 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAATAGGTCTCGAA
130 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
*
1801044 ATGATAAAATCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
* * *
1801109 CACTTTCGTAATTTAAAGAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATACTTTAT-GAAAT
66 CACTTTTGTAATTTAAA-AGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAAT
* * * * * *
1801173 GTACCGATCCATAAC-A-ATAATAGGTAAAAATATGACAAAACCGGTATCGAA
130 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* ** * *
1801224 ATGACAAAACCGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCG
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCG
1801268 GTACTTTAAT
Statistics
Matches: 882, Mismatches: 57, Indels: 21
0.92 0.06 0.02
Matches are distributed among these distances:
177 5 0.01
178 16 0.02
179 3 0.00
180 88 0.10
181 139 0.16
182 625 0.71
183 6 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
Found at i:1803089 original size:22 final size:22
Alignment explanation
Indices: 1803038--1803093 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1803028 TGTTTTTGGT
*
1803038 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
1803061 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
1803084 TTTTATTATA
1 TTTTATTATA
1803094 AATACAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:1803798 original size:22 final size:18
Alignment explanation
Indices: 1803750--1803787 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1803740 GAGAAAATTT
1803750 GAAGAAG-AAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1803767 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1803785 GAA
1 GAA
1803788 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1804114 original size:16 final size:17
Alignment explanation
Indices: 1804087--1804121 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1804077 TTTAAATATT
1804087 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
1804104 TCATG-AAAGATATTAA
1 TCATGAAAAGATATTAA
1804120 TC
1 TC
1804122 CTAATGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:1805291 original size:19 final size:19
Alignment explanation
Indices: 1805267--1805317 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1805257 AAATGTAGGG
*
1805267 TTAATTTTGTATAAGTTTT
1 TTAATTTTGTATAAGATTT
*
1805286 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
1805305 ATAATTTTGTATA
1 TTAATTTTGTATA
1805318 TGAATGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:1806227 original size:387 final size:384
Alignment explanation
Indices: 1805458--1806326 Score: 1228
Period size: 387 Copynumber: 2.2 Consensus size: 384
1805448 CATTCCAAGT
*
1805458 ATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTG--CATGGAAATGTGTTGATACATTTATAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTGACCAT---AATGTGTCGATACATTTA-AA
*
1805520 AAAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAA
62 AAA-TATCGATCC-AAAAA-A-C---A-TCATAATTATAATGTAATAGGTAAATTATCAATCTAA
* * *
1805585 CCGGTCTAAATATACCGGTTTATGAGAAAACATGTGTACATAAAGTATCGACACTTGTTTAATTT
119 CCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTGAATTT
* * *
1805650 GTGTCGATCCCGTACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTTTCGATAC
184 GTGTCGA---C-TACTTTGTGTCCAGAATGATTTCCTTACCAAGATCACCACAATGTGTCGATAC
*
1805715 CTTATAAAAGTATCGATCCCAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAAT
245 CTTATAAAAGTATCGATCCAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAAT
* * *
1805780 CTAACCGGTCTAAATACACCGGTTTATGAGAAAAAAGGTGTACATGAAGTATCGACACTTTTTGA
310 CTAACCGGTCTAAATAAACCGGTTTATGAGAAAAAAGATGTACATGAAGTATCAACACTTTTTGA
1805845 ATTTATGTCG
375 ATTTATGTCG
*
1805855 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTGACCATAATGTGTCGATACCTTTAAAAAAT
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTGACCATAATGTGTCGATACATTTAAAAAAT
1805920 ATCGATTCC-AAAAACATCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGGTCTAAAT
66 ATCGA-TCCAAAAAACATCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGGTCTAAAT
* * * *
1805984 ACATCGGTTTATGAGAAAATAGGTGTACATGAAGTATCGACACGTT-TTGAATTTGTGTTGA-TA
130 ACACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACAC-TTGTTGAATTTGTGTCGACTA
*
1806047 CTTTGTGTCCAGAATGATTTCCTTACCAAGATCACCACAATGTGTCGATACATTTATAAAAAGTA
194 CTTTGTGTCCAGAATGATTTCCTTACCAAGATCACCACAATGTGTCGATAC-CTTAT-AAAAGTA
1806112 TCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGGTC
257 TCGATCC--AAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGGTC
* * * * *
1806177 TAAATAAACCGGTTTATGAGAAAACAGATGTACATTAAGTATTAACACTTTTTGAATTTGTGTTG
320 TAAATAAACCGGTTTATGAGAAAAAAGATGTACATGAAGTATCAACACTTTTTGAATTTATGTCG
* * * *
1806242 ATACTTTGTGTCTAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATATATTTGTAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTGACCATAATGTGTCGATACA-TT-TAAAAA
*
1806307 GTATCGATCCAAAAAACATC
64 ATATCGATCCAAAAAACATC
1806327 GAGACCCATA
Statistics
Matches: 431, Mismatches: 29, Indels: 32
0.88 0.06 0.07
Matches are distributed among these distances:
383 50 0.12
384 4 0.01
385 14 0.03
387 162 0.38
388 103 0.24
389 24 0.06
392 1 0.00
393 1 0.00
394 4 0.01
395 6 0.01
396 8 0.02
397 48 0.11
398 3 0.01
400 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (384 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTGACCATAATGTGTCGATACATTTAAAAAAT
ATCGATCCAAAAAACATCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGGTCTAAATA
CACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTGAATTTGTGTCGACTACT
TTGTGTCCAGAATGATTTCCTTACCAAGATCACCACAATGTGTCGATACCTTATAAAAGTATCGA
TCCAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGGTCTAAATA
AACCGGTTTATGAGAAAAAAGATGTACATGAAGTATCAACACTTTTTGAATTTATGTCG
Found at i:1806232 original size:198 final size:198
Alignment explanation
Indices: 1805458--1806380 Score: 1324
Period size: 198 Copynumber: 4.7 Consensus size: 198
1805448 CATTCCAAGT
** *
1805458 ATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCATGGA-AATGTGTTGATACATTTATAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-CCACAATGTGTCGATACATTTATAAA
*
1805521 AAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
64 AAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
* * *
1805586 CGGTCTAAATATACCGGTTTATGAGAAAACATGTGTACATAAAGTATCGACACTTGTTT-AATTT
129 CGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTT-TTTGAATTT
1805650 GTGTCG
193 GTGTCG
* * *
1805656 ATCCCGTACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTTTCGATAC-CTTAT
1 A-----TACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTAT
*
1805720 -AAAAGTATCGATCC--CAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
61 AAAAAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
*
1805782 AACCGGTCTAAATACACCGGTTTATGAGAAAAAAGGTGTACATGAAGTATCGACACTTTTTGAAT
126 AACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAAT
*
1805847 TTATGTCG
191 TTGTGTCG
* * *
1805855 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTGACCATAATGTGTCGATACCTTTA-AAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
1805919 -TATCGATTCC-AAAAACAT-------CATAATTATAATGTAATAGGTAAATTATCAATCTAACC
66 GTATCGA-TCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACC
* * *
1805975 GGTCTAAATACATCGGTTTATGAGAAAATAGGTGTACATGAAGTATCGACACGTTTTGAATTTGT
130 GGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGT
*
1806040 GTTG
195 GTCG
*
1806044 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGATCACCACAATGTGTCGATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
1806109 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
* * * **
1806174 GTCTAAATAAACCGGTTTATGAGAAAACAGATGTACATTAAGTATTAACACTTTTTGAATTTGTG
131 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGTG
*
1806239 TTG
196 TCG
* * *
1806242 ATACTTTGTGTCTAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATATATTTGTAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
* * *
1806307 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGT-CATTTTGCAATGTAACC
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTAT-CAATCTAACC
*
1806371 GGTATAAATA
130 GGTCTAAATA
1806381 TACCTATTTA
Statistics
Matches: 661, Mismatches: 41, Indels: 46
0.88 0.05 0.06
Matches are distributed among these distances:
189 157 0.24
190 8 0.01
191 14 0.02
194 57 0.09
195 10 0.02
196 6 0.01
197 4 0.01
198 229 0.35
199 111 0.17
201 14 0.02
202 5 0.01
203 44 0.07
204 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (198 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGTG
TCG
Found at i:1806759 original size:15 final size:15
Alignment explanation
Indices: 1806739--1806788 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
1806729 AGAATCGGGG
*
1806739 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAA
*
1806754 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAA
1806769 CTCTTCTCAACCCAA
1 CTCTTCTCAACCCAA
1806784 CTCTT
1 CTCTT
1806789 ATGAGGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.20, C:0.48, G:0.00, T:0.32
Consensus pattern (15 bp):
CTCTTCTCAACCCAA
Found at i:1809250 original size:5 final size:5
Alignment explanation
Indices: 1809240--1809281 Score: 66
Period size: 5 Copynumber: 8.0 Consensus size: 5
1809230 TTCAATCTAG
1809240 CATTT CATTT CATTTT CATTT CATTT CATTTT CATTT CATTT
1 CATTT CATTT CA-TTT CATTT CATTT CA-TTT CATTT CATTT
1809282 ATAATTAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 25 0.71
6 10 0.29
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (5 bp):
CATTT
Found at i:1809258 original size:11 final size:10
Alignment explanation
Indices: 1809240--1809281 Score: 66
Period size: 11 Copynumber: 4.0 Consensus size: 10
1809230 TTCAATCTAG
1809240 CATTTCATTT
1 CATTTCATTT
1809250 CATTTTCATTT
1 CA-TTTCATTT
1809261 CATTTCATTTT
1 CATTTCA-TTT
1809272 CATTTCATTT
1 CATTTCATTT
1809282 ATAATTAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (10 bp):
CATTTCATTT
Found at i:1809261 original size:16 final size:16
Alignment explanation
Indices: 1809240--1809281 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
1809230 TTCAATCTAG
1809240 CATTTCATTTCATTTT
1 CATTTCATTTCATTTT
1809256 CATTTCATTTCATTTT
1 CATTTCATTTCATTTT
1809272 CATTTCATTT
1 CATTTCATTT
1809282 ATAATTAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTTCATTTCATTTT
Found at i:1809335 original size:24 final size:24
Alignment explanation
Indices: 1809284--1809336 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1809274 TTTCATTTAT
* * *
1809284 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATGTA
1809308 AATTTGAGTTTGAATTTAAATGTA
1 AATTTGAGTTTGAATTTAAATGTA
1809332 AATTT
1 AATTT
1809337 CGCTCCACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATGTA
Found at i:1810228 original size:200 final size:198
Alignment explanation
Indices: 1809696--1810568 Score: 1024
Period size: 200 Copynumber: 4.4 Consensus size: 198
1809686 AATGAATTTG
* * * * * *
1809696 CTTTATTCATTTGTGTCGATACATGTTGTCCAAAATGTA-TTTCCAAACCAAGTACACAAACAAA
1 CTTTATACATTTGTGTCGATACTTGATGTCCATAATGTATTTTCCAAA-CAAGTTCACGAA-AAA
* * * *
1809760 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATA
64 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATA
* * * *
1809825 GGTAAAATAACAATGTAACCAATCTAAATATACTGGTT-TATGAGAAAAGAGGTATACATAAAGT
129 GGTAAAATAACAATGTAACCAGTCTAAATATACCGGTTAT-TAAGAAAA-AGGTATACATAATGT
1809889 ATCGACA
192 ATCGACA
1809896 CTTTATACATTTGTGTCGATACTTTG-TGTCCATAATGTATTTTCCAACCAAAACAAGTTCAC-A
1 CTTTATACATTTGTGTCGATAC-TTGATGTCCATAATGTATTTT----CC-AAACAAGTTCACGA
* * * * * * *
1809959 AATAAGTGTCGACACATTTATATCAAGTGTCGATCCCAAAAATATTGAAACCCGTAACTATAATG
60 AA-AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATG
* * ** * * * * * *
1810024 TAATAAGTCACTTTACAATGTAACCGGTTTAAATTTATCGGTT-TTATGAGAAAATAGGTCTACA
124 TAATAGGTAAAATAACAATGTAACCAGTCTAAATATACCGGTTATTA--AGAAAA-AGGTATACA
1810088 -ATATGTATCGACA
186 TA-ATGTATCGACA
* * * * *
1810101 CTTTATTCATTTGTGTCGATACATGCTGTCCAGAATGTA-TTTCCAAACCAAGTGCACGAAAAAG
1 CTTTATACATTTGTGTCGATACTTGATGTCCATAATGTATTTTCCAAA-CAAGTTCACGAAAAAG
* *
1810165 TGTCGATACATTTATAACAAGTGTCGATCCTAAAAATATCGAAACACATAATTATAATGTAATAG
65 TGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAG
* *
1810230 GTAAAATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAATGTA
130 GTAAAATAACAATGTAACCAGTCTAAATATACCGGTTATT-AAGAA-AAAGGTATACATAATGTA
*
1810295 TCGATA
193 TCGACA
* * ** *
1810301 CTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCATGAAAAAGT
1 CTTTATACATTTGTGTCGATACTTGATGTCCATAATGTATTTTCCAAACAAGTTCACGAAAAAGT
* *
1810366 GTTGATACATTTATAACAAGTGTCGATCTCAAAAACATCGAAACACATAATTATAATGTAATAGG
66 GTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGG
* *
1810431 TAACATAACAATGTAACCAGTCTAAACATACCGGTTATTAA-AAAAAGGTATACATAATGTATCG
131 TAAAATAACAATGTAACCAGTCTAAATATACCGGTTATTAAGAAAAAGGTATACATAATGTATCG
*
1810495 ATA
196 ACA
* * ** *
1810498 CTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAATT
1 CTTTATACATTTGTGTCGATACTTGATGTCCATAATGTATTTTCCAAACAAGTTCACGAAAAAGT
1810563 GTCGAT
66 GTCGAT
1810569 CCTAAAAACA
Statistics
Matches: 584, Mismatches: 70, Indels: 41
0.84 0.10 0.06
Matches are distributed among these distances:
197 92 0.16
198 2 0.00
199 5 0.01
200 297 0.51
201 21 0.04
202 1 0.00
203 2 0.00
204 94 0.16
205 67 0.11
206 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (198 bp):
CTTTATACATTTGTGTCGATACTTGATGTCCATAATGTATTTTCCAAACAAGTTCACGAAAAAGT
GTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGG
TAAAATAACAATGTAACCAGTCTAAATATACCGGTTATTAAGAAAAAGGTATACATAATGTATCG
ACA
Found at i:1810308 original size:22 final size:21
Alignment explanation
Indices: 1810282--1810327 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1810272 AAAAGAAAGG
*
1810282 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
1810304 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
1810325 TAT
1 TAT
1810328 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:1810504 original size:22 final size:21
Alignment explanation
Indices: 1810479--1810524 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1810469 TAAAAAAAGG
*
1810479 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
1810501 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
1810522 TAT
1 TAT
1810525 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:1813515 original size:198 final size:197
Alignment explanation
Indices: 1813110--1813632 Score: 538
Period size: 198 Copynumber: 2.6 Consensus size: 197
1813100 ATTAGATTTT
* * * *
1813110 GTGTCGATACATTTATAACAA-GTATCGATCCCAAAATCAAAGAGACCGATAATTATAATGTAAT
1 GTGTCGATACATTT-TAA-AATGTATCGATCCCGAAA-CATAGAAACCGATAATTATAATGTAAC
* *
1813174 AGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGGTTCATGAGAGAATAGGTCAACATAAAG
63 AGGTAAATTTACAATGTAACCGGTAGAAATATACCGGGTTAATGAGAGAATAGGTCAACATAAAG
* * * * * * *
1813239 TATCGACACTTTTTTAATTTGTGTCGATATATTTTTCCAAAATGAATGGCAAACGAGGTGTACGC
128 TATCGACACTCTTTAAATATGAGTCGATATATTTTTCCAAAATGAAAGACAAACGAGGTGCACGC
1813304 ATAAA
193 ATAAA
* * *
1813309 GTGTCGATACATTTGTAAAATGTATCGATCCTCGAAACATTGAAATCGATAATTATTATGTAACA
1 GTGTCGATACATTT-TAAAATGTATCGATCC-CGAAACATAGAAACCGATAATTATAATGTAACA
* * * * * * *
1813374 TGTAATTTTACAATGTAATCGGTTA-AAATATACC-GGTTAATTAGCA-AATAGGTCTACATTAT
64 GGTAAATTTACAATGTAACCGG-TAGAAATATACCGGGTTAATGAG-AGAATAGGTCAACATAAA
* * *
1813436 GTATCGACACTCTTTAAATATGAGTCGATATTTTTTTCTAAAAT-AAAGCACAAACGAGTTGCAC
127 GTATCGACACTCTTTAAATATGAGTCGATATATTTTTCCAAAATGAAAG-ACAAACGAGGTGCAC
1813500 GCATAAA
191 GCATAAA
* * *
1813507 GTGTCGATACA-TTTAAAATTGTATCGATCCCGAAAACATCGAAACCGAT-ATACATAATGTAAT
1 GTGTCGATACATTTTAAAA-TGTATCGATCCCG-AAACATAGAAACCGATAAT-TATAATGTAAC
* * * ** * ** * * *
1813570 AGGTTAATTTATAATGTAACTGGTTTAAATTTACCGCTTTTATGAGAAAATAGGTCAATATAA
63 AGGTAAATTTACAATGTAACCGGTAGAAATATACCGGGTTAATGAGAGAATAGGTCAACATAA
1813633 GCGCTACCTA
Statistics
Matches: 266, Mismatches: 47, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
196 10 0.04
197 64 0.24
198 109 0.41
199 77 0.29
200 6 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (197 bp):
GTGTCGATACATTTTAAAATGTATCGATCCCGAAACATAGAAACCGATAATTATAATGTAACAGG
TAAATTTACAATGTAACCGGTAGAAATATACCGGGTTAATGAGAGAATAGGTCAACATAAAGTAT
CGACACTCTTTAAATATGAGTCGATATATTTTTCCAAAATGAAAGACAAACGAGGTGCACGCATA
AA
Found at i:1813706 original size:23 final size:23
Alignment explanation
Indices: 1813680--1813738 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1813670 CGGTTAAATG
*
1813680 CCTATTTTATTATATAAACGCTA
1 CCTATTATATTATATAAACGCTA
* **
1813703 CCTATTACATTATATAAGTGCTA
1 CCTATTATATTATATAAACGCTA
*
1813726 CCTAATATATTAT
1 CCTATTATATTAT
1813739 TGTGCTTGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (23 bp):
CCTATTATATTATATAAACGCTA
Found at i:1813773 original size:87 final size:87
Alignment explanation
Indices: 1813627--1813853 Score: 400
Period size: 87 Copynumber: 2.6 Consensus size: 87
1813617 AAATAGGTCA
* * * *
1813627 ATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
1 ATATAAGTGCTACCTAATATATTATTGTGCTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
1813692 TATAAACGCTACCTATTACATT
66 TATAAACGCTACCTATTACATT
1813714 ATATAAGTGCTACCTAATATATTATTGTGCTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
1 ATATAAGTGCTACCTAATATATTATTGTGCTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
*
1813779 TATAAGCGCTACCTATTACATT
66 TATAAACGCTACCTATTACATT
*
1813801 ATATAAGTGCTACCTAATATATTATTGTGCTTGATAATATTTCCAGTTAAATG
1 ATATAAGTGCTACCTAATATATTATTGTGCTTGATAATATTTCCGGTTAAATG
1813854 ATATAATATA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 134 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (87 bp):
ATATAAGTGCTACCTAATATATTATTGTGCTTGATAATATTTCCGGTTAAATGCCTATTTTATTA
TATAAACGCTACCTATTACATT
Found at i:1813793 original size:23 final size:23
Alignment explanation
Indices: 1813767--1813825 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1813757 CGGTTAAATG
*
1813767 CCTATTTTATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
* *
1813790 CCTATTACATTATATAAGTGCTA
1 CCTATTATATTATATAAGCGCTA
*
1813813 CCTAATATATTAT
1 CCTATTATATTAT
1813826 TGTGCTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (23 bp):
CCTATTATATTATATAAGCGCTA
Found at i:1814510 original size:2 final size:2
Alignment explanation
Indices: 1814503--1814535 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1814493 ATTGTAATTT
1814503 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1814536 TAATAAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1815136 original size:13 final size:13
Alignment explanation
Indices: 1815118--1815143 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1815108 ATGAAATTGA
1815118 AATACTCAAAGTT
1 AATACTCAAAGTT
1815131 AATACTCAAAGTT
1 AATACTCAAAGTT
1815144 TAAGCACCAG
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
AATACTCAAAGTT
Found at i:1819389 original size:16 final size:16
Alignment explanation
Indices: 1819336--1819390 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1819326 TATAATGATC
*
1819336 AAATGTCGAATGATTT
1 AAATGTTGAATGATTT
* *
1819352 AAACGTTAAATGATTT
1 AAATGTTGAATGATTT
1819368 AAATGTTGAATGATTT
1 AAATGTTGAATGATTT
*
1819384 AGATGTT
1 AAATGTT
1819391 TTATATGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (16 bp):
AAATGTTGAATGATTT
Found at i:1819419 original size:24 final size:22
Alignment explanation
Indices: 1819374--1819419 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1819364 ATTTAAATGT
**
1819374 TGAATGATTTAGATGTTTTATA
1 TGAATGATTTAGATGTGATATA
1819396 TGAATGAATTATAGATGTGATATA
1 TGAATG-ATT-TAGATGTGATATA
1819420 CTGTTTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (22 bp):
TGAATGATTTAGATGTGATATA
Found at i:1819705 original size:18 final size:19
Alignment explanation
Indices: 1819671--1819710 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1819661 CCTTTCGCTA
*
1819671 AAAATACCATTTAAATATC
1 AAAATACCATATAAATATC
1819690 AAAATA-CATATAAATATC
1 AAAATACCATATAAATATC
1819708 AAA
1 AAA
1819711 CATTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATACCATATAAATATC
Found at i:1820483 original size:24 final size:24
Alignment explanation
Indices: 1820455--1820503 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1820445 TTGAGTAATG
1820455 TCAGAGGTTCGAATCCTGACATTA
1 TCAGAGGTTCGAATCCTGACATTA
1820479 TCAGAGGTTCGAATCCTGACATTA
1 TCAGAGGTTCGAATCCTGACATTA
1820503 T
1 T
1820504 GAATGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (24 bp):
TCAGAGGTTCGAATCCTGACATTA
Found at i:1827075 original size:18 final size:18
Alignment explanation
Indices: 1827052--1827098 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1827042 ATATAGAGTA
1827052 GTATCAGTACCCCTTTGG
1 GTATCAGTACCCCTTTGG
1827070 GTATCAGTACCCCTTTGG
1 GTATCAGTACCCCTTTGG
*
1827088 GTATCGGTACC
1 GTATCAGTACC
1827099 AATTTTGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (18 bp):
GTATCAGTACCCCTTTGG
Found at i:1836313 original size:25 final size:27
Alignment explanation
Indices: 1836285--1836348 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 27
1836275 TATGAATAAG
*
1836285 ATAATAAAAAATAATA-AT-GAAAGTA
1 ATAATAAAAAATAATATATCAAAAGTA
**
1836310 ATAAT-TTAAAT-ATATATCAAAAGTA
1 ATAATAAAAAATAATATATCAAAAGTA
1836335 ATAATAAAATAATA
1 ATAATAAAA-AATA
1836349 TTACAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
23 3 0.10
24 6 0.21
25 16 0.55
26 1 0.03
27 3 0.10
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (27 bp):
ATAATAAAAAATAATATATCAAAAGTA
Found at i:1836355 original size:25 final size:25
Alignment explanation
Indices: 1836304--1836349 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1836294 AATAATAATG
*
1836304 AAAGTAATAATTTAAATATATATCA
1 AAAGTAATAATTAAAATATATATCA
1836329 AAAGTAATAA-TAAAATA-ATAT
1 AAAGTAATAATTAAAATATATAT
1836350 TACAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 6 0.30
25 10 0.50
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (25 bp):
AAAGTAATAATTAAAATATATATCA
Found at i:1836359 original size:17 final size:17
Alignment explanation
Indices: 1836337--1836376 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1836327 CAAAAGTAAT
1836337 AATAAAATAAT-ATTACA
1 AATAAAATAATGATTA-A
1836354 AAT-AAATAATGATTAA
1 AATAAAATAATGATTAA
1836370 AATAAAA
1 AATAAAA
1836377 GAAATTGCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
AATAAAATAATGATTAA
Found at i:1837272 original size:2 final size:2
Alignment explanation
Indices: 1837265--1837363 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
1837255 TTTATCCTAA
1837265 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
1837307 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
1837349 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1837364 GGACTAAAAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1838451 original size:12 final size:13
Alignment explanation
Indices: 1838436--1838496 Score: 76
Period size: 12 Copynumber: 5.0 Consensus size: 13
1838426 TTTGGGCCTG
*
1838436 TAATAATATAT-T
1 TAATAATATATAA
1838448 TAATAATA-ATAA
1 TAATAATATATAA
1838460 TAATAATATATAA
1 TAATAATATATAA
*
1838473 TTATAATA-ATAA
1 TAATAATATATAA
1838485 TAATAATA-ATAA
1 TAATAATATATAA
1838497 AAGTAAACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 2 0.05
12 31 0.70
13 11 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:1838454 original size:3 final size:3
Alignment explanation
Indices: 1838448--1838496 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
1838438 ATAATATATT
*
1838448 TAA TAA TAA TAA TAA TAA TATA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1838494 TAA
1 TAA
1838497 AAGTAAACTG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1838763 original size:44 final size:45
Alignment explanation
Indices: 1838650--1838788 Score: 183
Period size: 45 Copynumber: 3.1 Consensus size: 45
1838640 GAAGTCCTAT
* * *
1838650 CATCTTGCACTGTAGGTCTTAAAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
** *
1838695 CATCATTTACTGAAGG-CATTACAGATGACCCGAAGTTTTTGAAAA
1 CATCATGCACTGAAGGTC-TTACAGATGACCCGAAGGTTTTGAAAA
*
1838740 CATCATGCACTG-AGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
*
1838784 TATCA
1 CATCA
1838789 AAAATCTCCT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
44 33 0.41
45 48 0.59
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (45 bp):
CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:1838969 original size:76 final size:76
Alignment explanation
Indices: 1838723--1838999 Score: 395
Period size: 75 Copynumber: 3.7 Consensus size: 76
1838713 TTACAGATGA
*
1838723 CCCGAA-G-TTTTTGAAAACATCATGCACTG-AGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
*
1838785 ATCAAAAATCT
66 ATCAAAAAGCT
* * * ** * *
1838796 CCTGAAGACTTTTTGAAAACATCCTGCACTATAGGTCTTATGGATGACCTG-AGGTTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
1838860 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1838871 TCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTAAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
1838936 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1838947 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC--ACAGATGTCTCGAAGG
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGG
1839000 TCTTAAGGCA
Statistics
Matches: 179, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
73 5 0.03
74 14 0.08
75 86 0.48
76 74 0.41
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
ATCAAAAAGCT
Found at i:1839066 original size:45 final size:45
Alignment explanation
Indices: 1838947--1839084 Score: 145
Period size: 45 Copynumber: 3.0 Consensus size: 45
1838937 TCAAAAAGCT
* *
1838947 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTC--ACAGATGT
1 CCCGAAGGC--TTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* * *
1838992 CTCGAAGGTCTTAAGGCAAAACATCATGCATTGTAGGTCTTACAGATGA
1 CCCGAAGG-CTT--TG-AAAACATCATGCACTGTAGGTCTTACAGATGA
* *
1839041 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGCTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
1839085 TGGGAAATAG
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
44 2 0.03
45 35 0.45
46 3 0.04
47 20 0.26
48 3 0.04
49 14 0.18
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (45 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
Found at i:1840252 original size:54 final size:54
Alignment explanation
Indices: 1840156--1840259 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
1840146 TAACTGGTTT
* *
1840156 GTAAAACATTTGACAACACATTCATCATCTCATATGGTTTCTGCTCAGATGCTC
1 GTAAAACATTTGACAACACATTCATCATCTCATATGGCTTCTGCCCAGATGCTC
* * * *
1840210 GTAAAACCTTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGAT
1 GTAAAACATTTGACAACACATTCATCATCTCATATGGCTTCTGCCCAGAT
1840260 TTCTCAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATATGGCTTCTGCCCAGATGCTC
Found at i:1841242 original size:42 final size:41
Alignment explanation
Indices: 1841195--1841308 Score: 106
Period size: 41 Copynumber: 2.7 Consensus size: 41
1841185 GGCTTTCAGC
*
1841195 ATGCCCCACATGAATCATTTCTGTTTGAATTAGACATTCAAA
1 ATGCCCCACATG-ATCATTTCTGTTTGAAATAGACATTCAAA
* * * * *
1841237 ATGCCCGAACAT--TCTATTTCTGGTTGAAATGGACTTTCAAG
1 ATGCCC-CACATGATC-ATTTCTGTTTGAAATAGACATTCAAA
* *
1841278 ATGTCCCACATGGATCATTTCTGTCTGAAAT
1 ATGCCCCACAT-GATCATTTCTGTTTGAAAT
1841309 GGGCTTTCGA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
40 6 0.11
41 26 0.46
42 19 0.33
43 6 0.11
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (41 bp):
ATGCCCCACATGATCATTTCTGTTTGAAATAGACATTCAAA
Found at i:1841309 original size:42 final size:40
Alignment explanation
Indices: 1841177--1841325 Score: 110
Period size: 42 Copynumber: 3.6 Consensus size: 40
1841167 TCGATTCTTA
* *
1841177 TTGAAATGGGCTTTC-AGCATGCCCCACATGAATCATTTCTG
1 TTGAAATGGACTTTCAAG-ATGTCCCACATG-ATCATTTCTG
* * * *
1841218 TTTGAATTAGACATTCAAAATG-CCCGAACAT--TCTATTTCTGG
1 -TTGAAATGGACTTTCAAGATGTCCC--ACATGATC-ATTTCT-G
1841260 TTGAAATGGACTTTCAAGATGTCCCACATGGATCATTTCTG
1 TTGAAATGGACTTTCAAGATGTCCCACAT-GATCATTTCTG
* *
1841301 TCTGAAATGGGCTTTCGAGAT-TCCC
1 T-TGAAATGGACTTTCAAGATGTCCC
1841326 CAATATTTGC
Statistics
Matches: 86, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
40 6 0.07
41 32 0.37
42 41 0.48
43 7 0.08
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (40 bp):
TTGAAATGGACTTTCAAGATGTCCCACATGATCATTTCTG
Found at i:1841427 original size:118 final size:118
Alignment explanation
Indices: 1841272--1841687 Score: 706
Period size: 118 Copynumber: 3.5 Consensus size: 118
1841262 GAAATGGACT
* * * *
1841272 TTCAAGATGTCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCGAGATTCCCCAATATTTGCT
1 TTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTGCT
* *
1841337 TCTTGCTAATATGAGCTTTCAAAAATACCCAAATATTCATACTGACGTGGGCC
66 TCTTGCTAATATGAGCTTTCAAAAATGCTCAAATATTCATACTGACGTGGGCC
* * *
1841390 TTCAAAATGCCTCTCATGAATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTGCT
1 TTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTGCT
*
1841455 TCTTGCTAATATAAGCTTTCAAAAATGCTCAAATATTCATACTGACGTGGGCC
66 TCTTGCTAATATGAGCTTTCAAAAATGCTCAAATATTCATACTGACGTGGGCC
1841508 TTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTGCT
1 TTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTGCT
* *
1841573 TCTTGATAATATGAGCTTTCAAAAATGCTCAAATATTCATACCGACGTGGGCC
66 TCTTGCTAATATGAGCTTTCAAAAATGCTCAAATATTCATACTGACGTGGGCC
* *
1841626 TTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGAGCTTTCGAGATGCCCCAACATTT
1 TTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTT
1841688 TAAACTGTAA
Statistics
Matches: 280, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 280 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (118 bp):
TTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTGCT
TCTTGCTAATATGAGCTTTCAAAAATGCTCAAATATTCATACTGACGTGGGCC
Found at i:1842481 original size:34 final size:32
Alignment explanation
Indices: 1842419--1842488 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1842409 ACCTTACAAC
* * *
1842419 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
*
1842451 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
1842485 TCCC
1 TCCC
1842489 ATTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:1844931 original size:19 final size:20
Alignment explanation
Indices: 1844888--1844935 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1844878 TCTAAATCCT
*
1844888 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1844908 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1844927 TTTTCAAAA
1 TTTTCAAAA
1844936 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1846171 original size:21 final size:21
Alignment explanation
Indices: 1846145--1846197 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1846135 TGGAACGTGG
1846145 GGGGAATCGGTACCCCATCGT
1 GGGGAATCGGTACCCCATCGT
1846166 GGGGAATCGGTACCCCATCGT
1 GGGGAATCGGTACCCCATCGT
1846187 GGGGAATCGGT
1 GGGGAATCGGT
1846198 TCCCTAAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (21 bp):
GGGGAATCGGTACCCCATCGT
Found at i:1849930 original size:14 final size:15
Alignment explanation
Indices: 1849913--1849949 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1849903 CAAAAATAAG
*
1849913 AATGCAAACTGTGC-
1 AATGCAAACTATGCA
1849927 AATGCAAA-TATGCA
1 AATGCAAACTATGCA
1849941 AATGCAAAC
1 AATGCAAAC
1849950 ATAAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (15 bp):
AATGCAAACTATGCA
Found at i:1853301 original size:25 final size:26
Alignment explanation
Indices: 1853273--1853337 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
1853263 TATGACTAAG
*
1853273 ATAATAATAAATAATA-AT-GAAAGTA
1 ATAAT-ATAAATAATATATCAAAAGTA
*
1853298 ATAATTTAAAT-ATATATCAAAAGTA
1 ATAATATAAATAATATATCAAAAGTA
1853323 ATAATA-AAATAATAT
1 ATAATATAAATAATAT
1853338 TACAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 3 0.09
24 11 0.32
25 20 0.59
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (26 bp):
ATAATATAAATAATATATCAAAAGTA
Found at i:1853347 original size:17 final size:17
Alignment explanation
Indices: 1853325--1853364 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1853315 CAAAAGTAAT
1853325 AATAAAATAAT-ATTACA
1 AATAAAATAATGATTA-A
1853342 AAT-AAATAATGATTAA
1 AATAAAATAATGATTAA
1853358 AATAAAA
1 AATAAAA
1853365 GAAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
AATAAAATAATGATTAA
Found at i:1855173 original size:73 final size:73
Alignment explanation
Indices: 1855091--1855344 Score: 349
Period size: 73 Copynumber: 3.5 Consensus size: 73
1855081 TTAAAAATTG
* * * *
1855091 TTTTCGAAAATATATATATTATATAGTTTTGGAAA-ATTTTGAAATCATATATAATATATAGTTT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTAAAT-ATATATAATATATAGTTT
1855155 TTGAAAACA
65 TTGAAAACA
1855164 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTAATATATATATATAATATATAG
1 TTTTTGAAAATATATATAATATATAG-TTTTGAAAACATTTTT-A-A-ATATATATAATATATAG
1855229 TTTTT-AAAACA
62 TTTTTGAAAACA
*
1855240 -TTTTAAAAATATATAT-A-ATATAGTTCTTGAAAACATTTTTAAA-ATATATAATATATAGTTT
1 TTTTTGAAAATATATATAATATATAGTT-TTGAAAACATTTTTAAATATATATAATATATAGTTT
*
1855301 TTGAAAATA
65 TTGAAAACA
*
1855310 TTTTTGAAAATATATATAATATATATTTTTGAAAA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAA
1855345 TATATATTAA
Statistics
Matches: 163, Mismatches: 8, Indels: 21
0.85 0.04 0.11
Matches are distributed among these distances:
69 20 0.12
70 6 0.04
71 16 0.10
72 11 0.07
73 51 0.31
74 9 0.06
75 20 0.12
76 7 0.04
77 21 0.13
78 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (73 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTAAATATATATAATATATAGTTTT
TGAAAACA
Found at i:1855179 original size:38 final size:38
Alignment explanation
Indices: 1855091--1855344 Score: 336
Period size: 38 Copynumber: 6.9 Consensus size: 38
1855081 TTAAAAATTG
* * *
1855091 TTTTCGAAAATATATATATTATATAG-TTTTGGAAA-A
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1855127 -TTTTG-AAATCATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAAT-ATATATAATATATAGTTTTTGAAAACA
1855164 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1855202 TTTTT-AATATATATATATAATATATAGTTTTT-AAAACA
1 TTTTTGAA-A-ATATATATAATATATAGTTTTTGAAAACA
* *
1855240 -TTTTAAAAATATATAT-A-ATATAGTTCTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
1855275 TTTTT--AAA-ATATATAATATATAGTTTTTGAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1855310 TTTTTGAAAATATATATAATATATA-TTTTTGAAAA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAA
1855345 TATATATTAA
Statistics
Matches: 197, Mismatches: 6, Indels: 29
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.03
34 18 0.09
35 46 0.23
36 20 0.10
37 21 0.11
38 60 0.30
39 26 0.13
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (38 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:1855198 original size:26 final size:26
Alignment explanation
Indices: 1855164--1855214 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1855154 TTTGAAAACA
*
1855164 TTTTTGAAAATATATATAATATATAG
1 TTTTTGAAAACATATATAATATATAG
* *
1855190 TTTTTGAAAACATTTTTAATATATA
1 TTTTTGAAAACATATATAATATATA
1855215 TATATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (26 bp):
TTTTTGAAAACATATATAATATATAG
Found at i:1855362 original size:23 final size:24
Alignment explanation
Indices: 1855305--1855366 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
1855295 TAGTTTTTGA
*
1855305 AAATATTTTTGAAAATATATATAAT
1 AAATAGTTTTGAAAATATATAT-AT
* *
1855330 ATATATTTTTGAAAATATATAT-T
1 AAATAGTTTTGAAAATATATATAT
*
1855353 AAATGGTTTT-AAAA
1 AAATAGTTTTGAAAA
1855367 CAATTTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 4 0.12
23 8 0.24
25 21 0.64
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
AAATAGTTTTGAAAATATATATAT
Found at i:1855377 original size:60 final size:61
Alignment explanation
Indices: 1855274--1855404 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 61
1855264 TCTTGAAAAC
* * *
1855274 ATTTTT-AAAATATATAATATATAGTTTTTGAAAATATTTTTGAAAATATATATAATATAT
1 ATTTTTGAAAATATATAATAAATAGGTTTTAAAAATATTTTTGAAAATATATATAATATAT
* *
1855334 ATTTTTGAAAATATATATTAAAT-GGTTTTAAAACA-ATTTTTGAAAATATATATATTATAT
1 ATTTTTGAAAATATATAATAAATAGGTTTTAAAA-ATATTTTTGAAAATATATATAATATAT
**
1855394 GGTTTTGAAAA
1 ATTTTTGAAAA
1855405 CAATTTTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 47 0.76
61 15 0.24
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.47
Consensus pattern (61 bp):
ATTTTTGAAAATATATAATAAATAGGTTTTAAAAATATTTTTGAAAATATATATAATATAT
Found at i:1855380 original size:35 final size:35
Alignment explanation
Indices: 1855334--1855438 Score: 133
Period size: 35 Copynumber: 2.9 Consensus size: 35
1855324 TATAATATAT
*
1855334 ATTTTTGAAAATATATATTAAATGGTTTTAAAACA
1 ATTTTTGAAAATATATATTATATGGTTTTAAAACA
1855369 ATTTTTGAAAATATATATATTATATGGTTTTGAAAACA
1 ATTTTTG-AAA-ATATATATTATATGGTTTT-AAAACA
* *
1855407 ATTTTT-AAAAGCATATA-TATATAGTTTTAAAA
1 ATTTTTGAAAA-TATATATTATATGGTTTTAAAA
1855439 ATGATTTATA
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
34 4 0.06
35 18 0.29
36 11 0.17
37 18 0.29
38 12 0.19
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (35 bp):
ATTTTTGAAAATATATATTATATGGTTTTAAAACA
Found at i:1855396 original size:37 final size:36
Alignment explanation
Indices: 1855334--1855438 Score: 135
Period size: 37 Copynumber: 2.9 Consensus size: 36
1855324 TATAATATAT
*
1855334 ATTTTTG-AAAATATATATTAAATGGTTTTAAAACA
1 ATTTTTGAAAAATATATATTATATGGTTTTAAAACA
1855369 ATTTTTGAAAATATATATATTATATGGTTTTGAAAACA
1 ATTTTTGAAAA-ATATATATTATATGGTTTT-AAAACA
** *
1855407 ATTTTT-AAAAGCATATA-TATATAGTTTTAAAA
1 ATTTTTGAAAAATATATATTATATGGTTTTAAAA
1855439 ATGATTTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
34 4 0.06
35 17 0.27
36 8 0.13
37 22 0.35
38 12 0.19
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (36 bp):
ATTTTTGAAAAATATATATTATATGGTTTTAAAACA
Found at i:1855480 original size:10 final size:10
Alignment explanation
Indices: 1855473--1855500 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1855463 TTAATATTAT
1855473 TTATTATTTA
1 TTATTATTTA
1855483 TTATTATTTA
1 TTATTATTTA
1855493 TTATTATT
1 TTATTATT
1855501 CATTTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTATTATTTA
Found at i:1856571 original size:21 final size:21
Alignment explanation
Indices: 1856547--1856620 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
1856537 GTTATTCATT
1856547 TTTTTCTTTTTAATTTTAGCA
1 TTTTTCTTTTTAATTTTAGCA
* *
1856568 TTTTTTTATTTTAGTTATT--CA
1 TTTTTCT-TTTTAATT-TTAGCA
* * *
1856589 TTTTCCCTTTTAATTTTAGTA
1 TTTTTCTTTTTAATTTTAGCA
*
1856610 TGTTT-TTTTTA
1 TTTTTCTTTTTA
1856621 CTTCTTATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 9
0.67 0.17 0.16
Matches are distributed among these distances:
19 2 0.05
20 12 0.31
21 16 0.41
22 7 0.18
23 2 0.05
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTCTTTTTAATTTTAGCA
Found at i:1856618 original size:44 final size:43
Alignment explanation
Indices: 1856531--1856617 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 43
1856521 AACCTTTAAA
* *
1856531 ATTTTAGTTATTCATTTTTTTCTTTTTAATTTTAGCATTTTTTT
1 ATTTTAGTTATTCA-TTTTTCCCTTTTAATTTTAGCATTTTTTT
*
1856575 ATTTTAGTTATTCA-TTTTCCCTTTTAATTTTAGTATGTTTTTT
1 ATTTTAGTTATTCATTTTTCCCTTTTAATTTTAGCAT-TTTTTT
1856618 TTACTTCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 19 0.49
43 6 0.15
44 14 0.36
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (43 bp):
ATTTTAGTTATTCATTTTTCCCTTTTAATTTTAGCATTTTTTT
Found at i:1856715 original size:32 final size:33
Alignment explanation
Indices: 1856663--1856742 Score: 108
Period size: 32 Copynumber: 2.4 Consensus size: 33
1856653 ATTTAACATT
1856663 TTTTATTTTATTTTTCCCTTTGATTTATTTAATA
1 TTTTATTTTA-TTTTCCCTTTGATTTATTTAATA
* * *
1856697 TTTTATTTTATTTT-CCTTTGATTTTTTTTATT
1 TTTTATTTTATTTTCCCTTTGATTTATTTAATA
1856729 TTTTATTTTGATTT
1 TTTTATTTT-ATTT
1856743 ATTTAATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 24 0.57
33 8 0.19
34 10 0.24
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (33 bp):
TTTTATTTTATTTTCCCTTTGATTTATTTAATA
Found at i:1856747 original size:21 final size:22
Alignment explanation
Indices: 1856696--1856757 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
1856686 TTTATTTAAT
* **
1856696 ATTTTATTTTAT-TTTCCTTTG
1 ATTTTATTTAATATTTATTTTG
* * *
1856717 ATTTTTTTTATTTTTTATTTTG
1 ATTTTATTTAATATTTATTTTG
1856739 A-TTTATTTAATATTTATTT
1 ATTTTATTTAATATTTATTT
1856758 CTTATTTCTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (22 bp):
ATTTTATTTAATATTTATTTTG
Found at i:1857690 original size:14 final size:14
Alignment explanation
Indices: 1857671--1857697 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1857661 AATTTACCCT
1857671 GATTTATAAATTTG
1 GATTTATAAATTTG
1857685 GATTTATAAATTT
1 GATTTATAAATTT
1857698 ATAGTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (14 bp):
GATTTATAAATTTG
Found at i:1858203 original size:153 final size:154
Alignment explanation
Indices: 1858001--1858309 Score: 611
Period size: 153 Copynumber: 2.0 Consensus size: 154
1857991 TGATTTTAAA
1858001 ATTGAAATTTTGAGGTATAGGGGAAAAGAAAATTGGCCAAGAAATTCCATTTTGATATAAGTTAA
1 ATTGAAATTTTGAGGTATAGGGGAAAAGAAAATTGGCCAAGAAATTCCATTTTGATATAAGTTAA
1858066 CTTAAGGGTAAATTAGTATTCAGTCCCTAAAATTTATAATTTTCTCAATTTAATTCTTAATTTTT
66 CTTAAGGGTAAATTAGTATTCAGTCCCTAAAATTTATAATTTTCTCAATTTAATTCTTAATTTTT
1858131 TATTCATGTTAGTCTTTAG-CTTG
131 TATTCATGTTAGTCTTTAGACTTG
1858154 ATTGAAATTTTGAGGTATAGGGGAAAAGAAAATTGGCCAAGAAATTCCATTTTGATATAAGTTAA
1 ATTGAAATTTTGAGGTATAGGGGAAAAGAAAATTGGCCAAGAAATTCCATTTTGATATAAGTTAA
1858219 CTTAAGGGTAAATTAGTATTCAGTCCCTAAAATTTATAATTTTCTCAATTTAATTCTTAATTTTT
66 CTTAAGGGTAAATTAGTATTCAGTCCCTAAAATTTATAATTTTCTCAATTTAATTCTTAATTTTT
1858284 TATTCATGTTAGTCTTTAGACTTG
131 TATTCATGTTAGTCTTTAGACTTG
1858308 AT
1 AT
1858310 CTTTGAATCT
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 149 0.96
154 6 0.04
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (154 bp):
ATTGAAATTTTGAGGTATAGGGGAAAAGAAAATTGGCCAAGAAATTCCATTTTGATATAAGTTAA
CTTAAGGGTAAATTAGTATTCAGTCCCTAAAATTTATAATTTTCTCAATTTAATTCTTAATTTTT
TATTCATGTTAGTCTTTAGACTTG
Found at i:1858679 original size:32 final size:33
Alignment explanation
Indices: 1858615--1858699 Score: 111
Period size: 32 Copynumber: 2.6 Consensus size: 33
1858605 AAAAATTGGG
* * *
1858615 TTCGGGTCGGG-TCGAGTTTTTTTATGTTTGATA
1 TTCGGGTCGGGTTCG-GGTTTTTTAAGTGTGATA
*
1858648 TTCGGGTCGTGTT-GGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTCGGGTTTTTTAAGTGTGATA
1858680 TTCGGGTCGGGTTCGGGTTT
1 TTCGGGTCGGGTTCGGGTTT
1858700 AGGGTAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
32 27 0.60
33 17 0.38
34 1 0.02
ACGTcount: A:0.09, C:0.09, G:0.35, T:0.46
Consensus pattern (33 bp):
TTCGGGTCGGGTTCGGGTTTTTTAAGTGTGATA
Found at i:1859618 original size:13 final size:13
Alignment explanation
Indices: 1859600--1859624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1859590 ATTTTCAAAG
1859600 ATTATCTTTTAAT
1 ATTATCTTTTAAT
1859613 ATTATCTTTTAA
1 ATTATCTTTTAA
1859625 AGATAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTATCTTTTAAT
Found at i:1859897 original size:2 final size:2
Alignment explanation
Indices: 1859890--1859925 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1859880 AAATCATCCA
*
1859890 AT AT AT AT AT AT AT AT AT AT AG 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
1859926 TGTAACCCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1861325 original size:19 final size:18
Alignment explanation
Indices: 1861274--1861325 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
1861264 CGGTTAACGA
1861274 TCGGGTCA-ACGGTCGGG
1 TCGGGTCAGACGGTCGGG
*
1861291 TCGGGTCAGTAGGGTCGGG
1 TCGGGTCAG-ACGGTCGGG
1861310 TCGGGTCAGACCGGTC
1 TCGGGTCAGA-CGGTC
1861326 AAATCGGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 8 0.27
18 1 0.03
19 21 0.70
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.19
Consensus pattern (18 bp):
TCGGGTCAGACGGTCGGG
Found at i:1866362 original size:79 final size:79
Alignment explanation
Indices: 1866269--1866425 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
1866259 TGTCAACTTA
1866269 AATAACTAATTTTTTTCACTTAACTCGACTCGATCGAATCCTCACCCTTAATTTTATACTTTGTT
1 AATAACTAATTTTTTTCACTTAACTCGACTCGATCGAATCCTCACCCTTAATTTTATACTTTGTT
1866334 GTTATAAATTATTT
66 GTTATAAATTATTT
1866348 AATAACTTAA-TTTTTTCACTTAACTCGACTCGATCGAATCCTCACCCTTAATTTTATACTTTGT
1 AATAAC-TAATTTTTTTCACTTAACTCGACTCGATCGAATCCTCACCCTTAATTTTATACTTTGT
1866412 TGTTATAAATTATT
65 TGTTATAAATTATT
1866426 GAATTAAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
79 74 0.96
80 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (79 bp):
AATAACTAATTTTTTTCACTTAACTCGACTCGATCGAATCCTCACCCTTAATTTTATACTTTGTT
GTTATAAATTATTT
Found at i:1866717 original size:44 final size:44
Alignment explanation
Indices: 1866667--1866799 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
1866657 AAATTTAATA
1866667 AATGATTAAATCATTGGTTTTTACTAATTTCTTACATATAACTT
1 AATGATTAAATCATTGGTTTTTACTAATTTCTTACATATAACTT
* * * *
1866711 AATGATT-TATCGAATTGTTGCTTTTA-AAAATT-TT--A-AT-A---
1 AATGATTAAATC--ATTG--GTTTTTACTAATTTCTTACATATAACTT
1866749 AATGATTAAATCATTGGTTTTTACTAATTTCTTACATATAACTT
1 AATGATTAAATCATTGGTTTTTACTAATTTCTTACATATAACTT
1866793 AATGATT
1 AATGATT
1866800 TATCGATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 28
0.65 0.08 0.27
Matches are distributed among these distances:
35 6 0.09
36 4 0.06
37 6 0.09
38 7 0.10
39 4 0.06
40 2 0.03
41 2 0.03
42 2 0.03
43 4 0.06
44 14 0.21
45 6 0.09
46 4 0.06
47 6 0.09
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.47
Consensus pattern (44 bp):
AATGATTAAATCATTGGTTTTTACTAATTTCTTACATATAACTT
Found at i:1866777 original size:82 final size:82
Alignment explanation
Indices: 1866640--1866805 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 82
1866630 ATAAATTTTT
1866640 GAATTGTTGCTTTTAAAAAATTTAATAAATGATTAAATCATTGGTTTTTACTAATTTCTTACATA
1 GAATTGTTGCTTTTAAAAAATTTAATAAATGATTAAATCATTGGTTTTTACTAATTTCTTACATA
1866705 TAACTTAATGATTTATC
66 TAACTTAATGATTTATC
*
1866722 GAATTGTTGCTTTTAAAAATTTTAATAAATGATTAAATCATTGGTTTTTACTAATTTCTTACATA
1 GAATTGTTGCTTTTAAAAAATTTAATAAATGATTAAATCATTGGTTTTTACTAATTTCTTACATA
1866787 TAACTTAATGATTTATC
66 TAACTTAATGATTTATC
1866804 GA
1 GA
1866806 TTTTCATTAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.46
Consensus pattern (82 bp):
GAATTGTTGCTTTTAAAAAATTTAATAAATGATTAAATCATTGGTTTTTACTAATTTCTTACATA
TAACTTAATGATTTATC
Found at i:1867229 original size:2 final size:2
Alignment explanation
Indices: 1867217--1867252 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1867207 TTTGATTATC
* *
1867217 GA GA AA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1867253 AAATGGAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1876244 original size:29 final size:29
Alignment explanation
Indices: 1876211--1876269 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1876201 TTTTAGGTGA
1876211 TGTGACATTAACTCTCGTTAACCCCTTCT
1 TGTGACATTAACTCTCGTTAACCCCTTCT
1876240 TGTGACATTAACTCTCGTTAACCCCTTCT
1 TGTGACATTAACTCTCGTTAACCCCTTCT
1876269 T
1 T
1876270 CTTATTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.31, G:0.10, T:0.39
Consensus pattern (29 bp):
TGTGACATTAACTCTCGTTAACCCCTTCT
Found at i:1876645 original size:153 final size:153
Alignment explanation
Indices: 1876432--1876735 Score: 599
Period size: 153 Copynumber: 2.0 Consensus size: 153
1876422 ATAAAAATGA
1876432 GGCGATGGGTTTTTCTGATGAGATTCGAGGGCCTCTCCACGGCGAACGGTTGTGAGTCTCTGCCA
1 GGCGATGGGTTTTTCTGATGAGATTCGAGGGCCTCTCCACGGCGAACGGTTGTGAGTCTCTGCCA
*
1876497 ATGGCTAGCGGGGTTTTGGTCGGAATGGGGTGGCACTCCTACTGGTACCGATGTTGATGGTTACT
66 ATGGCTAGCGGGGTTTTGGTCGGAATGGGGTGGCACTCCTACTGGTACCGATGTTGACGGTTACT
1876562 GGCGATTGATGAAGGAGATCAGT
131 GGCGATTGATGAAGGAGATCAGT
1876585 GGCGATGGGTTTTTCTGATGAGATTCGAGGGCCTCTCCACGGCGAACGGTTGTGAGTCTCTGCCA
1 GGCGATGGGTTTTTCTGATGAGATTCGAGGGCCTCTCCACGGCGAACGGTTGTGAGTCTCTGCCA
1876650 ATGGCTAGCGGGGTTTTGGTCGGAATGGGGTGGCACTCCTACTGGTACCGATGTTGACGGTTACT
66 ATGGCTAGCGGGGTTTTGGTCGGAATGGGGTGGCACTCCTACTGGTACCGATGTTGACGGTTACT
1876715 GGCGATTGATGAAGGAGATCA
131 GGCGATTGATGAAGGAGATCA
1876736 TGATGGGTGT
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 150 1.00
ACGTcount: A:0.18, C:0.19, G:0.36, T:0.28
Consensus pattern (153 bp):
GGCGATGGGTTTTTCTGATGAGATTCGAGGGCCTCTCCACGGCGAACGGTTGTGAGTCTCTGCCA
ATGGCTAGCGGGGTTTTGGTCGGAATGGGGTGGCACTCCTACTGGTACCGATGTTGACGGTTACT
GGCGATTGATGAAGGAGATCAGT
Found at i:1877869 original size:20 final size:20
Alignment explanation
Indices: 1877844--1877916 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1877834 ACTGTAGACT
1877844 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1877864 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
1877885 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1877905 ATCGTAACGCGA
1 ATCGCAACGCGA
1877917 TTTTCAACTA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1877889 original size:41 final size:41
Alignment explanation
Indices: 1877841--1877941 Score: 193
Period size: 41 Copynumber: 2.5 Consensus size: 41
1877831 ACAACTGTAG
1877841 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1877882 ACTATCGCAACGCGAAATGGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1877923 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
1877942 CAACGCGAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1877945 original size:21 final size:21
Alignment explanation
Indices: 1877841--1877945 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 21
1877831 ACAACTGTAG
*
1877841 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
1877862 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
1877882 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
1877903 A-AATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
1877923 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
1877944 AC
1 AC
1877946 GCGAATTTGC
Statistics
Matches: 61, Mismatches: 21, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:1880954 original size:12 final size:12
Alignment explanation
Indices: 1880945--1880978 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1880935 CCTAATTATG
1880945 AGCATAATTAAA
1 AGCATAATTAAA
1880957 AGCATAATTAAA
1 AGCATAATTAAA
*
1880969 AACATAATTA
1 AGCATAATTA
1880979 CTATGTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (12 bp):
AGCATAATTAAA
Found at i:1886418 original size:8 final size:9
Alignment explanation
Indices: 1886400--1886426 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1886390 ATCTGATTAC
1886400 TTTATTTTT
1 TTTATTTTT
1886409 TTTATTTTT
1 TTTATTTTT
1886418 TTTATTTTT
1 TTTATTTTT
1886427 AATATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTATTTTT
Found at i:1887272 original size:50 final size:50
Alignment explanation
Indices: 1887188--1887286 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
1887178 TTGAACCTCG
* ** *
1887188 AATTAGTAGTTCAATCGATTCGACCAGTGATATAAAATCAAGTATAATAA
1 AATTAGTAGTTCAACCGATTCGACCAAAGATATAAAATAAAGTATAATAA
* * *
1887238 AATTAGTAGTTCAACCTATTCGGCCAAAGGTATAAAATAAAGTATAATA
1 AATTAGTAGTTCAACCGATTCGACCAAAGATATAAAATAAAGTATAATA
1887287 CGAACTGTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (50 bp):
AATTAGTAGTTCAACCGATTCGACCAAAGATATAAAATAAAGTATAATAA
Found at i:1889019 original size:3 final size:3
Alignment explanation
Indices: 1888978--1889007 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1888968 CACTTTCATA
1888978 TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
1889008 CCGTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1890407 original size:22 final size:22
Alignment explanation
Indices: 1890382--1890430 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1890372 ATTATTTATT
*
1890382 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
1890404 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
1890426 TATTA
1 TATTA
1890431 GTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:1890429 original size:11 final size:10
Alignment explanation
Indices: 1890361--1890430 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 10
1890351 GCTTTTTAAT
1890361 TTATTTTAATCA
1 TTATTTT-AT-A
*
1890373 TTATTTATTTA
1 TTATTT-TATA
*
1890384 TTATTTTGTTA
1 TTATTTT-ATA
1890395 TTACTTTTATA
1 TTA-TTTTATA
1890406 TTATTTTATTA
1 TTATTTTA-TA
1890417 TTATTTTCATA
1 TTATTTT-ATA
1890428 TTA
1 TTA
1890431 GTCACATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
10 6 0.12
11 32 0.63
12 12 0.24
13 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (10 bp):
TTATTTTATA
Found at i:1890740 original size:115 final size:115
Alignment explanation
Indices: 1890610--1890816 Score: 272
Period size: 115 Copynumber: 1.8 Consensus size: 115
1890600 CATATTTTAA
** * * * *
1890610 TATTTATTTATTAATATTGAAGGAAAGAGTTATTTTAAAGCAACTAGAA-ACATTTTTCTAATAT
1 TATTTATTTATTAATATCAAAAGAAAGAGCTATCTTAAAGCAACTAGAAGAC-CTTTTCTAATAT
* *
1890674 TTTTAAATAAATAAATATCTTACTATATTAAAATAGTTTTTTATTATTATT
65 TTCTAAATAAATAAATATATTACTATATTAAAATAGTTTTTTATTATTATT
* * * * *
1890725 TATTTATTTTTTAATATCAAAAGAAAGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATATT
1 TATTTATTTATTAATATCAAAAGAAAGAGCTATCTTAAAGCAACTAGAAGACCTTTTCTAATATT
*
1890790 TCTAAATAAATAAATATATTATTATAT
66 TCTAAATAAATAAATATATTACTATAT
1890817 ATATATATAT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
115 76 0.99
116 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (115 bp):
TATTTATTTATTAATATCAAAAGAAAGAGCTATCTTAAAGCAACTAGAAGACCTTTTCTAATATT
TCTAAATAAATAAATATATTACTATATTAAAATAGTTTTTTATTATTATT
Found at i:1893307 original size:21 final size:21
Alignment explanation
Indices: 1893287--1893325 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1893277 TCTATCTCTA
*
1893287 AACCTTAAAC-CTTAATTTCT
1 AACCTTAAACTCTCAATTTCT
*
1893307 AACTTTAAACTCTCAATTT
1 AACCTTAAACTCTCAATTT
1893326 AGAGTTCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (21 bp):
AACCTTAAACTCTCAATTTCT
Found at i:1895113 original size:2 final size:2
Alignment explanation
Indices: 1895106--1895140 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1895096 TTAAAGCTTT
1895106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1895141 TTAAAAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1896283 original size:27 final size:27
Alignment explanation
Indices: 1896251--1896332 Score: 164
Period size: 27 Copynumber: 3.0 Consensus size: 27
1896241 GAATAATGTC
1896251 ATGAAACCAGTAGTTAGAAAGGAAACT
1 ATGAAACCAGTAGTTAGAAAGGAAACT
1896278 ATGAAACCAGTAGTTAGAAAGGAAACT
1 ATGAAACCAGTAGTTAGAAAGGAAACT
1896305 ATGAAACCAGTAGTTAGAAAGGAAACT
1 ATGAAACCAGTAGTTAGAAAGGAAACT
1896332 A
1 A
1896333 AGTATAGTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (27 bp):
ATGAAACCAGTAGTTAGAAAGGAAACT
Found at i:1899387 original size:142 final size:142
Alignment explanation
Indices: 1899021--1899404 Score: 520
Period size: 144 Copynumber: 2.7 Consensus size: 142
1899011 TAAAAGGTTT
* *
1899021 GGAGCTGGCCTCCGGCAGCAAGGCAGGTGTCAGCCAGCCGATCTACCGAAACAAAGCTTATTCAT
1 GGAGCTGGCCTCCGGCAACAAGGCAGGTGTC-GCCAGCCGATCTACCGAAAGAAAGCTTATTCAT
* *
1899086 GAATACAGTTCCAGCATTCTAGACAGGTCCAACTTCATAAAGATACATAAATAAATACGACCTAG
65 GAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAATAAATACGACCTAG
*
1899151 TAAGAGGGGGGCAG
130 TAAGAGAGGGG-AG
* * * * * * *
1899165 GGAGCCGGCCTTC-GAAACCAAGGCTAGTTTTCGCCAGCTGATCTACCGAAAGGAAGCTTATTCA
1 GGAGCTGGCCTCCGGCAA-CAAGGC-AGGTGTCGCCAGCCGATCTACCGAAAGAAAGCTTATTCA
** * * *
1899229 CAAATACAGTTACAGCATTCTTGGCAAGTCCAACTTCATAAAGATCCATAAATAAATACGACCTA
64 TGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAATAAATACGACCTA
1899294 GTAAGAGAGGGG-G
129 GTAAGAGAGGGGAG
* * *
1899307 GGAGCTGACCTCCGGCAACAAGGCCGGTGTCGGCCAGCCAATCTACCGAAAGAAAGCTTATTCAT
1 GGAGCTGGCCTCCGGCAACAAGGCAGGTGTC-GCCAGCCGATCTACCGAAAGAAAGCTTATTCAT
*
1899372 GAATACAGTTCCAGCATTCCTGGCAGGTCCAAC
65 GAATACAGTTCCAGCATTCTTGGCAGGTCCAAC
1899405 ATGATAAGAC
Statistics
Matches: 204, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
141 4 0.02
142 75 0.37
143 5 0.02
144 115 0.56
145 5 0.02
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (142 bp):
GGAGCTGGCCTCCGGCAACAAGGCAGGTGTCGCCAGCCGATCTACCGAAAGAAAGCTTATTCATG
AATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAATAAATACGACCTAGT
AAGAGAGGGGAG
Found at i:1905276 original size:30 final size:30
Alignment explanation
Indices: 1905240--1905303 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1905230 GAAGGACCTG
* *
1905240 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1905270 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1905300 TCCA
1 TCCA
1905304 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1905492 original size:17 final size:19
Alignment explanation
Indices: 1905460--1905495 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1905450 CATATATCTC
1905460 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
1905479 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
1905496 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:1906090 original size:64 final size:65
Alignment explanation
Indices: 1905979--1906129 Score: 191
Period size: 64 Copynumber: 2.3 Consensus size: 65
1905969 TCTTTCAATG
* * * * * *
1905979 AAGGTATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTATTATTTT-
1906043 A
65 A
* *
1906044 AAGG-ATGCATCGATGCATTATC-TATGCATCGATGCATCAAAGGCATTCGATGTTATTCTTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTATTATTTTA
1906107 AAGGAATGCATCGATGCACTTAT
1 AAGGAATGCATCGATGCA-TTAT
1906130 GAATGTGCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 5 0.07
64 62 0.82
65 9 0.12
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (65 bp):
AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTATTATTTTA
Found at i:1909666 original size:17 final size:19
Alignment explanation
Indices: 1909639--1909680 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1909629 ATCTCATATC
1909639 ATATCACATGTATT-ATGT
1 ATATCACATGTATTCATGT
1909657 ATAT-ACATGTATTCATGT
1 ATATCACATGTATTCATGT
*
1909675 AAATCA
1 ATATCA
1909681 TTTCATGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 11 0.52
19 1 0.05
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (19 bp):
ATATCACATGTATTCATGT
Found at i:1910246 original size:19 final size:19
Alignment explanation
Indices: 1910222--1910273 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1910212 TTTTAAAAGG
1910222 ATGCATCGATGCATTATCT
1 ATGCATCGATGCATTATCT
1910241 ATGCATCGATGCATTATCT
1 ATGCATCGATGCATTATCT
1910260 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1910274 CAAAGGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (19 bp):
ATGCATCGATGCATTATCT
Found at i:1910299 original size:83 final size:84
Alignment explanation
Indices: 1910157--1910340 Score: 230
Period size: 83 Copynumber: 2.2 Consensus size: 84
1910147 TCAATGAAGG
* * * *
1910157 TATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTAAAAGG
1 TATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTT-AAAGG
1910222 -ATGCATCGATGCA-TTATC
65 AATGCATCGATGCACTTATC
* * *
1910240 TATGCATCGATGCATTA-TCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTAAAGG
1 TATGCATCGATGCACTACT-TATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAGG
*
1910304 AATGCATCGATGCACTTATGAA
65 AATGCATCGATGCACTTAT--C
*
1910326 TGTGCATCGATGCAC
1 TATGCATCGATGCAC
1910341 CTTGTCCAGA
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
82 6 0.07
83 63 0.73
84 4 0.05
86 13 0.15
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (84 bp):
TATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAGGA
ATGCATCGATGCACTTATC
Found at i:1914347 original size:57 final size:57
Alignment explanation
Indices: 1914259--1914370 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
1914249 GGCAATTCTT
*
1914259 GATTTTCTCGCGAAATTAGTTTGGTGTATCCAACCAGACTGACGTTCTGATGCAGTC
1 GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGATGCAGTC
*
1914316 GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGTTGCAG
1 GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGATGCAG
1914371 CCGTGAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.33
Consensus pattern (57 bp):
GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGATGCAGTC
Found at i:1915416 original size:2 final size:2
Alignment explanation
Indices: 1915411--1915458 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1915401 CTAATAAAAA
1915411 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
1915453 AT AT AT
1 AT AT AT
1915459 GATTGAATCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1920462 original size:28 final size:29
Alignment explanation
Indices: 1920421--1920480 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1920411 ATTCGTTTTT
*
1920421 TAAAAAATAAATAAAATTTGAATAAAAA-A
1 TAAAAAATAAATAAAA-TTCAATAAAAATA
*
1920450 TAAAAAA-GAATAAAATTCAATAAAAATA
1 TAAAAAATAAATAAAATTCAATAAAAATA
1920478 TAA
1 TAA
1920481 TGTAAAGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.36
28 11 0.39
29 7 0.25
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (29 bp):
TAAAAAATAAATAAAATTCAATAAAAATA
Found at i:1921642 original size:22 final size:22
Alignment explanation
Indices: 1921584--1921655 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
1921574 TAATAAATTG
* *
1921584 TTTTTATATTACTAAATAATTA
1 TTTTTATATTAATAAATAACTA
* *
1921606 CTTTTTAAATGAATAAATAACTA
1 -TTTTTATATTAATAAATAACTA
*
1921629 TTTTTGTATTAATAAAATAAACTA
1 TTTTTATATTAAT-AAAT-AACTA
1921653 TTT
1 TTT
1921656 AAGCATTCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 10 0.25
23 22 0.55
24 8 0.20
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (22 bp):
TTTTTATATTAATAAATAACTA
Found at i:1923514 original size:18 final size:18
Alignment explanation
Indices: 1923491--1923565 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 18
1923481 GTTCTTAAGG
1923491 AGTGGTATTTCGGGACAT
1 AGTGGTATTTCGGGACAT
1923509 AGTGGT-TATTCGGGACATAT
1 AGTGGTAT-TTCGGGAC--AT
1923529 ACAGTGGTCA-TTCGGGACAT
1 --AGTGGT-ATTTCGGGACAT
**
1923549 AGTGGTCCTTCGGGACA
1 AGTGGTATTTCGGGACA
1923566 AATATTCAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
17 1 0.02
18 29 0.60
20 4 0.08
22 14 0.29
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTATTTCGGGACAT
Found at i:1924166 original size:22 final size:22
Alignment explanation
Indices: 1924138--1924185 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1924128 TGTGGCAGTA
*
1924138 CTGTAGCAGGGGTATCGATTCC
1 CTGTAGCAGGGGAATCGATTCC
*
1924160 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGATTCC
1924182 CTGT
1 CTGT
1924186 TAACAATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGATTCC
Found at i:1924746 original size:17 final size:18
Alignment explanation
Indices: 1924702--1924753 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1924692 TTGAAATGTC
* *
1924702 TGTGAGGGAATTAGAATA
1 TGTGAAGGAATTGGAATA
1924720 TGTGAAGGAATTGGAATA
1 TGTGAAGGAATTGGAATA
1924738 TGT-AAGGAATTGGAAT
1 TGTGAAGGAATTGGAAT
1924754 CCAATTCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (18 bp):
TGTGAAGGAATTGGAATA
Done.