Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008942.1 Hibiscus syriacus cultivar Beakdansim tig00112261_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: 2383254
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1091233 original size:21 final size:20
Alignment explanation
Indices: 1091180--1091233 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
1091170 GTTTGCAAAA
1091180 AAGAAAAAGAAA-TGAGAGT
1 AAGAAAAAGAAATTGAGAGT
* *
1091199 -TGAAAAAGACATTGAGAGT
1 AAGAAAAAGAAATTGAGAGT
1091218 GAAGAAAAAGAAATTG
1 -AAGAAAAAGAAATTG
1091234 GATTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
21 12 0.43
ACGTcount: A:0.57, C:0.02, G:0.26, T:0.15
Consensus pattern (20 bp):
AAGAAAAAGAAATTGAGAGT
Found at i:1092411 original size:35 final size:35
Alignment explanation
Indices: 1092366--1092440 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
1092356 AATTAAGTAT
*
1092366 ACTATTTCATTCA-ATAAAGCTAATTCACTAATTAA
1 ACTAGTTCATTCATATAAA-CTAATTCACTAATTAA
* ** *
1092401 ACTAGTTCATTCATTTAAACTGGTTCATTAATTAA
1 ACTAGTTCATTCATATAAACTAATTCACTAATTAA
1092436 ACTAG
1 ACTAG
1092441 CTCTTTATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 30 0.88
36 4 0.12
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (35 bp):
ACTAGTTCATTCATATAAACTAATTCACTAATTAA
Found at i:1092437 original size:17 final size:17
Alignment explanation
Indices: 1092366--1092440 Score: 71
Period size: 18 Copynumber: 4.3 Consensus size: 17
1092356 AATTAAGTAT
*
1092366 ACTATTTCATTCAA-TAA
1 ACTAGTTCATT-AATTAA
* *
1092383 AGCTAATTCACTAATTAA
1 A-CTAGTTCATTAATTAA
*
1092401 ACTAGTTCATTCATTTAA
1 ACTAGTTCATT-AATTAA
*
1092419 ACTGGTTCATTAATTAA
1 ACTAGTTCATTAATTAA
1092436 ACTAG
1 ACTAG
1092441 CTCTTTATCT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 20 0.43
18 27 0.57
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (17 bp):
ACTAGTTCATTAATTAA
Found at i:1092874 original size:24 final size:25
Alignment explanation
Indices: 1092846--1092895 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1092836 AATTCAAAGC
1092846 ATTCAATGCTT-ATTTAATCA-TCAA
1 ATTCAA-GCTTGATTTAATCATTCAA
*
1092870 ATTCAAGGTTGATTTAATCATTCAA
1 ATTCAAGCTTGATTTAATCATTCAA
1092895 A
1 A
1092896 CCAAGGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 15 0.65
25 5 0.22
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (25 bp):
ATTCAAGCTTGATTTAATCATTCAA
Found at i:1098018 original size:28 final size:28
Alignment explanation
Indices: 1097978--1098062 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
1097968 TGCCACGCTG
*
1097978 GAAAGAGCGTTTCAGGGAACGCGTCTTT
1 GAAAGAGCGTTTCAGGGAACGCGCCTTT
*
1098006 GAAAGAGCGTTTCAGGGAACGCACCTTT
1 GAAAGAGCGTTTCAGGGAACGCGCCTTT
*
1098034 GAAAGAGCGTTTCAGGAAACGCGCCTTT
1 GAAAGAGCGTTTCAGGGAACGCGCCTTT
1098062 G
1 G
1098063 CTTTTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (28 bp):
GAAAGAGCGTTTCAGGGAACGCGCCTTT
Found at i:1102280 original size:139 final size:136
Alignment explanation
Indices: 1101942--1102689 Score: 750
Period size: 137 Copynumber: 5.5 Consensus size: 136
1101932 TACTATTTAC
* * * * * * * *
1101942 GTGAAAGCGCATTTCAGGGGATGCTCCATCCCTTTTTTTGTTAGATAATAGGTTATAATTTCCCT
1 GTGAAAGCGCGTTTCAGGGG-CGCGCCTTCCC-TTTTTTGTCAGAGAATAGATTATAATTGCCCT
* * * * *
1102007 ATCATGTGTGATATCCCCCGACGGGACACTATTTATGTCAGTACTATCATGTTTGAGGGGACACA
64 ATTATGTGTGATGTCCCCCGATGGGACACTATTCATGTCAGTACTATCATGTTTGAGGGGACGCA
* *
1102072 AAAAAGTG
129 ACAATGTG
* * * * *
1102080 ATGAAAGTGCGTTTCAGGGGGGCGCCTTCCCTTTTTTTATCAGAGAATAGGTTATAATTGCCCTA
1 GTGAAAGCGCGTTTCAGGGGCGCGCCTTCCC-TTTTTTGTCAGAGAATAGATTATAATTGCCCTA
* * * *
1102145 TTATGTGTGATGTCCTCCGATGGGGCACTATTCATATCAATATCTATCATGTTTGAGGGGACGCA
65 TTATGTGTGATGTCCCCCGATGGGACACTATTCATGTCAGTA-CTATCATGTTTGAGGGGACGCA
1102210 ACAATGTG
129 ACAATGTG
* *
1102218 GTGAAAGCACGTTTCAGTGGGTGCGCCTTCCCTTTTTTTGTCAGAGAATAGATTATAATTGCCCT
1 GTGAAAGCGCGTTTCAG-GGGCGCGCCTTCCC-TTTTTTGTCAGAGAATAGATTATAATTGCCCT
* * *
1102283 ATTATGTGTGATGTCCCCCGGCT-GGACACTATTAATGTCAGTACCTATCATGTTTGAGGGGAGG
64 ATTATGTGTGATGTCCCCC-GATGGGACACTATTCATGTCAGTA-CTATCATGTTTGAGGGGACG
* * *
1102347 CATCAGTGTA
127 CAACAATGTG
* * * *
1102357 GTGAAA--GCGTTACAGGGAACACGCCTTCCCTTTTTT-TCAGAGAATAGGTTATAATTGCCCTA
1 GTGAAAGCGCGTTTCAGGG-GCGCGCCTTCCCTTTTTTGTCAGAGAATAGATTATAATTGCCCTA
* * *
1102419 TTATGTGTGATATCCCCTGAT-AGACCACTATTCATGTCAGTACTTATCATGTTTGAGGGGACGC
65 TTATGTGTGATGTCCCCCGATGGGA-CACTATTCATGTCAGTAC-TATCATGTTTGAGGGGACGC
1102483 AACAATGTG
128 AACAATGTG
** * * *
1102492 GTGAAAGCGTATTTCAGGGGCGCACCTTCCCTTTTTTGTTAGAGAATA-AGTTATAATTACCCTA
1 GTGAAAGCGCGTTTCAGGGGCGCGCCTTCCCTTTTTTGTCAGAGAATAGA-TTATAATTGCCCTA
* * * ** * * *
1102556 TTATGTGTAATGTCCCCCCG-CGGGGCACTATTTTTGTCAGTACCTATCATGTTTAAAGGGACTC
65 TTATGTGTGATGT-CCCCCGATGGGACACTATTCATGTCAGTA-CTATCATGTTTGAGGGGACGC
* *
1102620 AATAATGTA
128 AACAATGTG
* * * *
1102629 ATGAAA--GCG---CA-GGGCGCGTCTTCCCCTTTTTAT-AGAGAATAGATTATAATTGCCCTAT
1 GTGAAAGCGCGTTTCAGGGGCGCGCCTTCCCTTTTTTGTCAGAGAATAGATTATAATTGCCCTAT
1102687 TAT
66 TAT
1102690 TCTTGAAATT
Statistics
Matches: 513, Mismatches: 83, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
130 25 0.05
131 19 0.04
132 2 0.00
134 5 0.01
135 89 0.17
136 23 0.04
137 173 0.34
138 65 0.13
139 110 0.21
140 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (136 bp):
GTGAAAGCGCGTTTCAGGGGCGCGCCTTCCCTTTTTTGTCAGAGAATAGATTATAATTGCCCTAT
TATGTGTGATGTCCCCCGATGGGACACTATTCATGTCAGTACTATCATGTTTGAGGGGACGCAAC
AATGTG
Found at i:1102708 original size:13 final size:13
Alignment explanation
Indices: 1102692--1102716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1102682 CCTATTATTC
1102692 TTGAAATTTATGT
1 TTGAAATTTATGT
1102705 TTGAAATTTATG
1 TTGAAATTTATG
1102717 ATAGAGTGTT
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:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTGAAATTTATGT
Found at i:1102741 original size:20 final size:19
Alignment explanation
Indices: 1102708--1102751 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1102698 TTTATGTTTG
*
1102708 AAATTTATGATAGAGTGTT
1 AAATTTATGATAGAATGTT
* *
1102727 GAATTTAATGTTAGAATGTT
1 AAATTT-ATGATAGAATGTT
1102747 AAATT
1 AAATT
1102752 GGATTATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (19 bp):
AAATTTATGATAGAATGTT
Found at i:1105622 original size:13 final size:13
Alignment explanation
Indices: 1105599--1105650 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
1105589 TAATAAAAAA
1105599 ATAAAATATTATTT
1 ATAAAA-ATTATTT
*
1105613 TTAAAAATTATTT
1 ATAAAAATTATTT
1105626 ATAAAAATTATTT
1 ATAAAAATTATTT
1105639 A-AAAAATATATT
1 ATAAAAAT-TATT
1105651 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
12 6 0.17
13 24 0.69
14 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAAAATTATTT
Found at i:1105650 original size:26 final size:27
Alignment explanation
Indices: 1105599--1105650 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
1105589 TAATAAAAAA
*
1105599 ATAAAATATTATTTTTAAAAATTATTT
1 ATAAAATATTATTTTAAAAAATTATTT
1105626 ATAAAA-ATTA-TTTAAAAAATATATT
1 ATAAAATATTATTTTAAAAAAT-TATT
1105651 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 9 0.39
26 8 0.35
27 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAAATATTATTTTAAAAAATTATTT
Found at i:1106366 original size:27 final size:24
Alignment explanation
Indices: 1106312--1106357 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1106302 TTAAAATAAT
1106312 ATTTATATAATTATTATTTATTTAA
1 ATTTAT-TAATTATTATTTATTTAA
1106337 ATTTATTAATTATTA-TTATTT
1 ATTTATTAATTATTATTTATTT
1106358 GTACTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 9 0.43
25 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTATTAATTATTATTTATTTAA
Found at i:1108066 original size:42 final size:41
Alignment explanation
Indices: 1107975--1108055 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 41
1107965 AGTACGTGCC
* * *
1107975 CAACCCACTAGTTCATATGTCATCACCGCAAGGGTATATGT
1 CAACCCACCAGCTCATATGTCATCACCGCAAGGGTACATGT
* * *
1108016 CAAGCCCACCAGCTCATATGTCATCTCCGTAAGGTTACAT
1 CAA-CCCACCAGCTCATATGTCATCACCGCAAGGGTACAT
1108056 TCCTAACCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 3 0.09
42 30 0.91
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (41 bp):
CAACCCACCAGCTCATATGTCATCACCGCAAGGGTACATGT
Found at i:1108653 original size:24 final size:24
Alignment explanation
Indices: 1108626--1108672 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1108616 TTAAATATTT
*
1108626 TTAAAATTCAAATTCAAATTTAAC
1 TTAAAATTCAAATTAAAATTTAAC
* *
1108650 TTAATATTCCAATTAAAATTTAA
1 TTAAAATTCAAATTAAAATTTAA
1108673 AATTATATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (24 bp):
TTAAAATTCAAATTAAAATTTAAC
Found at i:1108666 original size:46 final size:45
Alignment explanation
Indices: 1108573--1108706 Score: 127
Period size: 46 Copynumber: 3.0 Consensus size: 45
1108563 TTGTTACAAC
***
1108573 AATATTTTTAAAATTTAAATTCAAATTCAACATTAA-ATGT-TTGTTA
1 AATATTTTTAAAA-TTAAATTCAAATTCAAC-TTAATAT-TCCAATTA
*
1108619 AATATTTTTAAAATTCAAATTCAAATTTAACTTAATATTCCAATTA
1 AATATTTTTAAAATT-AAATTCAAATTCAACTTAATATTCCAATTA
* *
1108665 AA-A--TTTAAAATTATATTCGAAATTCAAGTTAAT-TTCCAATTA
1 AATATTTTTAAAATTAAATTC-AAATTCAACTTAATATTCCAATTA
1108707 TAGTTCACCA
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
42 14 0.18
43 21 0.27
45 8 0.10
46 34 0.44
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (45 bp):
AATATTTTTAAAATTAAATTCAAATTCAACTTAATATTCCAATTA
Found at i:1108680 original size:24 final size:24
Alignment explanation
Indices: 1108626--1108688 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
1108616 TTAAATATTT
* * *
1108626 TTAAAATTCAAATTCAAATTTAAC
1 TTAATATTCAAATTAAAATTTAAA
*
1108650 TTAATATTCCAATTAAAATTTAAAA
1 TTAATATTCAAATTAAAATTT-AAA
1108675 TT-ATATTCGAAATT
1 TTAATATTC-AAATT
1108689 CAAGTTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.41
Consensus pattern (24 bp):
TTAATATTCAAATTAAAATTTAAA
Found at i:1110393 original size:19 final size:19
Alignment explanation
Indices: 1110367--1110410 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1110357 TCAAGTAATT
1110367 AACATTTTCAATTTAATCG
1 AACATTTTCAATTTAATCG
*
1110386 AGCATTTTCAATTTAATCG
1 AACATTTTCAATTTAATCG
1110405 AACATT
1 AACATT
1110411 ACCCTAAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (19 bp):
AACATTTTCAATTTAATCG
Found at i:1116541 original size:20 final size:20
Alignment explanation
Indices: 1116516--1116567 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1116506 GCGAAATAAA
1116516 AATCGCAACGC-GATCTCCAG
1 AATCGCAACGCAGATC-CCAG
** *
1116536 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGCAGATCCCAG
1116556 AATCGCAACGCA
1 AATCGCAACGCA
1116568 ATTATGAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.35, C:0.33, G:0.17, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCAGATCCCAG
Found at i:1116644 original size:20 final size:20
Alignment explanation
Indices: 1116619--1116890 Score: 156
Period size: 20 Copynumber: 13.4 Consensus size: 20
1116609 GATTTTCTAG
*
1116619 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
1116639 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
1116659 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
1116679 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
1116700 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* **
1116720 AATCGCAATGATAATACGTAA
1 AATCGCAACGCGAATACG-AA
* * *
1116741 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
1116761 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
1116781 AATCGAAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
1116801 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
1116821 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
1116841 AATCGCAACGAC-AATACATAA
1 AATCGCAACG-CGAATAC-GAA
* * *
1116862 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
1116882 AATCGCAAC
1 AATCGCAAC
1116891 ACGATTTTTA
Statistics
Matches: 194, Mismatches: 47, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
19 3 0.02
20 140 0.72
21 51 0.26
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:1116711 original size:41 final size:40
Alignment explanation
Indices: 1116619--1116890 Score: 314
Period size: 40 Copynumber: 6.7 Consensus size: 40
1116609 GATTTTCTAG
* ** * * * **
1116619 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
1116659 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
* *
1116700 AATCGCAACGCGTATCCGTAAATCGCAATGATAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
1116741 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* *
1116781 AATCGAAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * *
1116821 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
1116862 AATCGCAACGCGTATCCGTAAATCGCAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
1116891 ACGATTTTTA
Statistics
Matches: 200, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.01
40 97 0.49
41 95 0.47
42 4 0.02
43 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:1116795 original size:40 final size:41
Alignment explanation
Indices: 1116680--1116890 Score: 327
Period size: 41 Copynumber: 5.2 Consensus size: 41
1116670 GATTCTGACT
* *
1116680 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
1116721 ATCGCAATGATAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
1116762 ATCGCAACGAGAATACGT-AAATCGAAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1116802 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
1116842 ATCGCAACGACAATACATAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
1116883 ATCGCAAC
1 ATCGCAAC
1116891 ACGATTTTTA
Statistics
Matches: 155, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 73 0.47
41 82 0.53
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:1117454 original size:20 final size:19
Alignment explanation
Indices: 1117429--1117539 Score: 90
Period size: 20 Copynumber: 5.8 Consensus size: 19
1117419 TTCTAAACTT
1117429 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
*
1117449 AAAATCGCAATACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
1117469 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
1117490 AAAATCGCAAC-G---A-G
1 AAAATCGCAACAGAAAATG
*
1117504 AGAATCGCAACACG-AAATG
1 AAAATCGCAACA-GAAAATG
1117523 AAAATCGCAACGAGAAA
1 AAAATCGCAAC-AGAAA
1117540 CCAAAATCGC
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
14 11 0.15
15 1 0.01
16 1 0.01
18 1 0.01
19 13 0.18
20 31 0.42
21 15 0.21
ACGTcount: A:0.51, C:0.18, G:0.19, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:1117568 original size:19 final size:19
Alignment explanation
Indices: 1117546--1117691 Score: 89
Period size: 19 Copynumber: 8.1 Consensus size: 19
1117536 GAAACCAAAA
*
1117546 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1117565 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
* *
1117581 T--CGTTGCAATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
1117598 TCGCGTTGCGATTTTCAAT
1 TCGCGTTGCGATTTTCATT
1117617 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1117631 TCTCGTTGCGATAGTT-ATT
1 TCGCGTTGCGAT-TTTCATT
* **
1117650 TCCGCATTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
1117670 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1117690 TC
1 TC
1117692 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
14 17 0.18
16 4 0.04
17 10 0.10
19 38 0.40
20 26 0.27
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1117651 original size:52 final size:52
Alignment explanation
Indices: 1117546--1117662 Score: 164
Period size: 52 Copynumber: 2.2 Consensus size: 52
1117536 GAAACCAAAA
* * *
1117546 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTGTCGTTGCAATTTTAATT
1 TCGCATTGCGATTTTCAATTCGCGTTGCGATTCTCTCGTTGCAATGTTAATT
* *
1117598 TCGCGTTGCGATTTTCAATTCGCGTTGCGATTCTCTCGTTGCGATAGTT-ATT
1 TCGCATTGCGATTTTCAATTCGCGTTGCGATTCTCTCGTTGCAAT-GTTAATT
1117650 TCCGCATTGCGAT
1 T-CGCATTGCGAT
1117663 AGTCATTCTC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 45 0.79
53 12 0.21
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCAATTCGCGTTGCGATTCTCTCGTTGCAATGTTAATT
Found at i:1117679 original size:20 final size:20
Alignment explanation
Indices: 1117627--1117682 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1117617 TCGCGTTGCG
*
1117627 ATTCTCTCGTTGCGATAGTT
1 ATTCTCTCGTTGCGATAGTC
1117647 ATT-TC-CGCATTGCGATAGTC
1 ATTCTCTCG--TTGCGATAGTC
1117667 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1117683 TTTCATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 23 0.74
21 2 0.06
22 2 0.06
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1117688 original size:20 final size:20
Alignment explanation
Indices: 1117627--1117689 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
1117617 TCGCGTTGCG
1117627 ATTCTCTCGTTGCGATAGTT-
1 ATTCTCTCGTTGCGATA-TTC
*
1117647 ATT-TC-CGCATTGCGATAGTC
1 ATTCTCTCG--TTGCGATATTC
*
1117667 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATATTC
1117687 ATT
1 ATT
1117690 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 26 0.74
21 2 0.06
22 2 0.06
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATATTC
Found at i:1119540 original size:94 final size:94
Alignment explanation
Indices: 1119379--1119852 Score: 844
Period size: 94 Copynumber: 5.1 Consensus size: 94
1119369 TAGATTGCTT
* * *
1119379 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1119444 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1119473 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1119538 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1119567 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1119632 ATTTGTCTTTTTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1119661 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1119726 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1119755 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1119820 ATTTGTCTTTGTTTTATCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1119848 AGTAA
1 AGTAA
1119853 TGCAATCCAT
Statistics
Matches: 369, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
93 26 0.07
94 343 0.93
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1119956 original size:19 final size:17
Alignment explanation
Indices: 1119940--1120017 Score: 81
Period size: 17 Copynumber: 4.5 Consensus size: 17
1119930 AAAAATGACT
1119940 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
1119957 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
* *
1119976 ATCACAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
1119990 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
1120009 ATCGCAACG
1 ATCGCAACG
1120018 ACAAAATCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 21 0.42
19 17 0.34
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.10
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:1119962 original size:17 final size:18
Alignment explanation
Indices: 1119917--1120017 Score: 86
Period size: 19 Copynumber: 5.6 Consensus size: 18
1119907 ACGAAACTTA
*
1119917 AAATCGCAACGTGAAAAATG
1 AAATCGCAACGCG--AAATG
*
1119937 ACTATCGCAACGCGAAATG
1 A-AATCGCAACGCGAAATG
1119956 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
* *
1119973 AAAATCACAA--CGAGA-G
1 -AAATCGCAACGCGAAATG
1119989 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
1120006 AAAATCGCAACG
1 -AAATCGCAACG
1120018 ACAAAATCGC
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
14 7 0.11
16 5 0.08
17 21 0.32
19 22 0.33
20 1 0.02
21 10 0.15
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:1119997 original size:33 final size:33
Alignment explanation
Indices: 1119955--1120036 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
1119945 AACGCGAAAT
*
1119955 GAATCGCAACGCGAAATGAAAATCACAACGAGA
1 GAATCGCAACGCGAAATGAAAATCACAACGACA
*
1119988 GAATCGCAACGCGAAATGAAAATCGCAACGACA
1 GAATCGCAACGCGAAATGAAAATCACAACGACA
* *
1120021 AAATCGCAAAGCGAAA
1 GAATCGCAACGCGAAA
1120037 CTATAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.49, C:0.22, G:0.21, T:0.09
Consensus pattern (33 bp):
GAATCGCAACGCGAAATGAAAATCACAACGACA
Found at i:1120068 original size:19 final size:19
Alignment explanation
Indices: 1120046--1120180 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
1120036 ACTATAATCG
1120046 CGTTGCGATTTTCATTTCT
1 CGTTGCGATTTTCATTTCT
*
1120065 CGTTGTGA--TTC---TCT
1 CGTTGCGATTTTCATTTCT
*
1120079 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCT
*
1120098 CGTTGCGATTTTCATTTCA
1 CGTTGCGATTTTCATTTCT
1120117 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCT
*
1120131 CGTTGCGA--TTCATTTCG
1 CGTTGCGATTTTCATTTCT
** *
1120148 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCT
1120169 CGTTGCGATTTT
1 CGTTGCGATTTT
1120181 AAGTTCCATA
Statistics
Matches: 94, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
14 23 0.24
16 3 0.03
17 16 0.17
19 38 0.40
21 14 0.15
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCT
Found at i:1120121 original size:52 final size:50
Alignment explanation
Indices: 1120043--1120178 Score: 200
Period size: 52 Copynumber: 2.6 Consensus size: 50
1120033 GAAACTATAA
* *
1120043 TCGCGTTGCGATTTTCATTTCTCGTTGTGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCACGTTGCGATTCTCTCGTTGCGA--TTCATT
1120095 TCGCGTTGCGATTTTCATTTCACGTTGCGATTCTCTCGTTGCGATTCATT
1 TCGCGTTGCGATTTTCATTTCACGTTGCGATTCTCTCGTTGCGATTCATT
**
1120145 TCGCGTTGCGATAGTCATTTTTCACGTTGCGATT
1 TCGCGTTGCGATTTTCA--TTTCACGTTGCGATT
1120179 TTAAGTTCCA
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
50 21 0.27
52 57 0.73
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (50 bp):
TCGCGTTGCGATTTTCATTTCACGTTGCGATTCTCTCGTTGCGATTCATT
Found at i:1120656 original size:41 final size:40
Alignment explanation
Indices: 1120581--1120700 Score: 98
Period size: 41 Copynumber: 2.9 Consensus size: 40
1120571 GACTCGCCTG
* * * * * *
1120581 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGCCCCTA
1 TCATTCCTCGAGAGTCC-CTCCCACCGTTCAAGAGCCACTA
*
1120622 TCATTCCTCGAGAGTCCTCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCC-CTCCCACCGTTCAAGA-GCCACTA
* * *
1120664 TCA-TCGTTGAAGAGGTCCCTCCCACCATTCAAGAGCC
1 TCATTCCTCG-AGA-GTCCCTCCCACCGTTCAAGAGCC
1120701 TGATTCACAT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
41 35 0.54
42 26 0.40
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (40 bp):
TCATTCCTCGAGAGTCCCTCCCACCGTTCAAGAGCCACTA
Found at i:1122060 original size:14 final size:14
Alignment explanation
Indices: 1122041--1122076 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1122031 ATTGTTTAAT
1122041 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1122055 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1122069 TGATTTGT
1 TGATTTGT
1122077 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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1122199 original size:19 final size:19
Alignment explanation
Indices: 1122183--1122267 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
1122173 AAAAATGACT
1122183 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1122202 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1122216 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1122235 ATCGCAACGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
1122254 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1122268 CTAAATTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.70
20 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1122284 original size:19 final size:19
Alignment explanation
Indices: 1122215--1122277 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
1122205 GCAACGAGAG
1122215 AATCGCAATGCGAAA-TGAA
1 AATCGCAATGCGAAACT-AA
*
1122234 AATCGCAACGCGAAACTAA
1 AATCGCAATGCGAAACTAA
1122253 AATCGCAATGCGAAACTAA
1 AATCGCAATGCGAAACTAA
*
1122272 ATTCGC
1 AATCGC
1122278 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 39 0.98
20 1 0.03
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAACTAA
Found at i:1122295 original size:19 final size:19
Alignment explanation
Indices: 1122273--1122377 Score: 94
Period size: 19 Copynumber: 5.7 Consensus size: 19
1122263 CGAAACTAAA
1122273 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1122292 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1122307 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * **
1122325 TTCGCATTGTGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
1122344 TTCCGCGTTGCGATTTTTAT
1 TT-CGCGTTGCGATTTTCAT
*
1122364 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
1122378 CTCTCGTTGC
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
14 9 0.14
16 3 0.05
17 3 0.05
19 37 0.56
20 14 0.21
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1122319 original size:33 final size:33
Alignment explanation
Indices: 1122277--1122390 Score: 138
Period size: 33 Copynumber: 3.3 Consensus size: 33
1122267 ACTAAATTCG
*
1122277 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1122310 CGTTGCGATTTTCATTTCGCATTGTGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
*
1122349 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1122382 CGTTGCGAT
1 CGTTGCGAT
1122391 AGTAATTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
33 36 0.52
34 1 0.01
35 2 0.03
37 2 0.03
38 1 0.01
39 27 0.39
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1124950 original size:24 final size:24
Alignment explanation
Indices: 1124923--1124969 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1124913 ATCATAAAAA
1124923 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
1124947 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
1124970 TTTTGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:1126322 original size:20 final size:20
Alignment explanation
Indices: 1126293--1126441 Score: 131
Period size: 20 Copynumber: 7.3 Consensus size: 20
1126283 CAAAATCGCA
*
1126293 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATACTCG
* *
1126313 TTGTGATTTACAG-ATACGCG
1 TTGCGATTTAC-GTATACTCG
* *
1126333 TTGCGATTTACCTATTCTCG
1 TTGCGATTTACGTATACTCG
* * *
1126353 TTGCGATTTACGGATACGCT
1 TTGCGATTTACGTATACTCG
**
1126373 TTGCGATTTTACGTATTGTCG
1 TTGCGA-TTTACGTATACTCG
*
1126394 TTGCGATTTACAG-ATACGCG
1 TTGCGATTTAC-GTATACTCG
* *
1126414 TTGTGATTTTACGGATACTCG
1 TTGCGA-TTTACGTATACTCG
1126435 TTGCGAT
1 TTGCGAT
1126442 AGTCAGAATC
Statistics
Matches: 100, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
20 67 0.67
21 33 0.33
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTATACTCG
Found at i:1126396 original size:41 final size:40
Alignment explanation
Indices: 1126293--1126502 Score: 217
Period size: 40 Copynumber: 5.2 Consensus size: 40
1126283 CAAAATCGCA
*
1126293 TTGCGATTTACGTATTCTCGTTGTGATTTACAGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
* * *
1126333 TTGCGATTTACCTATTCTCGTTGCGATTTACGGATACGCT
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
*
1126373 TTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCG
1 TTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACGCG
* * * *
1126414 TTGTGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCG
1 TTGCGA-TTTACGTATTCTCGTTGCGAT-TTACAGATA-CGCG
* ** * * * * *
1126455 TCGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
1126495 TTGCGATT
1 TTGCGATT
1126503 CTGGAAAATC
Statistics
Matches: 140, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 72 0.51
41 66 0.47
42 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (40 bp):
TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
Found at i:1126473 original size:20 final size:20
Alignment explanation
Indices: 1126450--1126502 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1126440 ATAGTCAGAA
* *
1126450 TCGCGTCGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1126470 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1126490 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1126503 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1126520 original size:21 final size:21
Alignment explanation
Indices: 1126496--1126548 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1126486 ATATTCGCGT
1126496 TGCGATTCTGGAAAATCGCAA
1 TGCGATTCTGGAAAATCGCAA
* ** *
1126517 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGGAAAATCGCAA
1126538 TGCGATTCTGG
1 TGCGATTCTGG
1126549 GAACTGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCGATTCTGGAAAATCGCAA
Found at i:1126580 original size:20 final size:20
Alignment explanation
Indices: 1126490--1126584 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
1126480 ATTTTCATAT
* *
1126490 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGG-AGA
* * *
1126511 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGA-GA
1126532 TCGCATTGCGATTCTGG-GA
1 TCGCATTGCGATTCTGGAGA
*
1126551 ACTG-ATTTGCGATTCTGGAGA
1 TC-GCA-TTGCGATTCTGGAGA
*
1126572 TCGCGTTGCGATT
1 TCGCATTGCGATT
1126585 TTTATTTCGC
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.05
20 26 0.46
21 25 0.44
22 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATTCTGGAGA
Found at i:1131545 original size:82 final size:80
Alignment explanation
Indices: 1131325--1131546 Score: 252
Period size: 81 Copynumber: 2.7 Consensus size: 80
1131315 CTAAAATGAG
* * * *
1131325 AGGTTAAATGCCTAACTATGCATTTGGTAGAAATGTGACAATAAT-CAAGTTAGATGAAAGGTTA
1 AGGTTAAATGACTAACTGTGCATTTGG-AGAAAGGTGACAATAATGCAAGTTAGATGAAAGATTA
1131389 AATACCTTTAGATAAA
65 AATACCTTTAGATAAA
* * * * *
1131405 AGGTTAATTGTCTAACTGTGCATTTGGATGAAAGGTGTCAATAATGCAAATTAGATGAAATATTA
1 AGGTTAAATGACTAACTGTGCATTTGGA-GAAAGGTGACAATAATGCAAGTTAGATGAAAGATTA
*
1131470 AATGCCTTTAGA-AGAA
65 AATACCTTTAGATA-AA
* * *
1131486 AGAG-TAAATGACTAACTGTACATTTTGGCAGAAAGGTGCCATTAATGCAAGTTAGATGAAA
1 AG-GTTAAATGACTAACTGTGCA-TTTGG-AGAAAGGTGACAATAATGCAAGTTAGATGAAA
1131547 AACATTGTAT
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
79 1 0.01
80 39 0.32
81 46 0.38
82 34 0.28
83 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (80 bp):
AGGTTAAATGACTAACTGTGCATTTGGAGAAAGGTGACAATAATGCAAGTTAGATGAAAGATTAA
ATACCTTTAGATAAA
Found at i:1138252 original size:22 final size:22
Alignment explanation
Indices: 1138226--1138269 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1138216 ATAATGCAGA
*
1138226 TTAGATGAAAGGTTAAATGCCT
1 TTAGACGAAAGGTTAAATGCCT
*
1138248 TTAGACGAAAGGTTAATTGCCT
1 TTAGACGAAAGGTTAAATGCCT
1138270 AACTGTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (22 bp):
TTAGACGAAAGGTTAAATGCCT
Found at i:1138311 original size:81 final size:81
Alignment explanation
Indices: 1138176--1138398 Score: 315
Period size: 81 Copynumber: 2.7 Consensus size: 81
1138166 CTAAAATGAG
* * *
1138176 AGGTTAATTGCCTAAATGTGCATTTGGCAAAAAGGTGTCAATAATGC-AGATTAGATGAAAGGTT
1 AGGTTAATTGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAG-TTAGATGAAAGGTT
1138240 AAATGCCTTTAGACGAA
65 AAATGCCTTTAGACGAA
*
1138257 AGGTTAATTGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATTCAAGTTAGATGAAAGGTTA
1 AGGTTAATTGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTA
* *
1138322 AATGTCTTTAGATGAA
66 AATGCCTTTAGACGAA
* * * *
1138338 AGAG-TAAATACCTAACTGTGCATTTTGGCAGAAATGTGCCACTAATGCAAGTTAGATGAAA
1 AG-GTTAATTGCCTAACTGTGCA-TTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
1138399 AACGTTGCAT
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
81 90 0.70
82 38 0.30
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (81 bp):
AGGTTAATTGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTA
AATGCCTTTAGACGAA
Found at i:1143212 original size:54 final size:54
Alignment explanation
Indices: 1142775--1143196 Score: 637
Period size: 54 Copynumber: 7.8 Consensus size: 54
1142765 TGTACTATAG
* * * * *
1142775 GCACTATGTGTGCAACTCAAGGAAATCATCATATGTTGATGAACAACCATACAG
1 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAA
* *
1142829 GCACTATGTGTGCAACTCACGTAATTCATCATATGTTGATGAACAACCGTACAA
1 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAA
* *
1142883 GAACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAT
1 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAA
* * *
1142937 GCACTATGTGTGCAACTCACGAAATTCATGATATGTTGATGAACAACCGTACAA
1 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAA
* * * *
1142991 GCGCTATGTGTGCAACCCATGGAATTCATCATATGTTGATAAACAACCGTACAT
1 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAA
*
1143045 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAT
1 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAA
*
1143099 GCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTACAA
1 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAA
* * * * *
1143153 GCACTATGTGTACAACCCACAGAATTCATAATAAGTTCATGAAC
1 GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAAC
1143197 GACTGTATAG
Statistics
Matches: 336, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 336 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (54 bp):
GCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAA
Found at i:1146554 original size:18 final size:19
Alignment explanation
Indices: 1146531--1146577 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1146521 AGCTGAACAA
**
1146531 TATCGATAC-TGAGGTGGG
1 TATCGATACTTGAGGAAGG
1146549 TATCGATACTTTGAGGAAGG
1 TATCGATAC-TTGAGGAAGG
1146569 TATCGATAC
1 TATCGATAC
1146578 CATTGATTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (19 bp):
TATCGATACTTGAGGAAGG
Found at i:1147062 original size:54 final size:54
Alignment explanation
Indices: 1147003--1147531 Score: 589
Period size: 54 Copynumber: 9.8 Consensus size: 54
1146993 GTACTATAGG
* * *
1147003 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTATAGA
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
* * ** * * * * * *
1147057 CACTATGTATACAATTCAAGGAATTCGTCATATGTTGATGAACAACCATAGAGC
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
* * ** *
1147111 CACTATATTTGCAAGTCACGAAATTCATCATATGTTAATGAACAACCGTACAGA
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
* * *
1147165 CACTATGTGTGCAACCCACGGAATCCATCATATGTTGATGAACAACCATACATG-
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACA-GA
* * *
1147219 CACTATGTATGCAACCCACGAAATTCATCATATGTTGATGAACAATCGTA-AAA
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
* * *
1147272 GCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATGCAGG
1 -CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
*
1147327 CACTATGCGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACA-A
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
* * * * *
1147380 GCACTATGTGTACAACTCACGAAATTCATCATATGTTGATGAAAAACCGTACCGG
1 -CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
* * * * * * * * **
1147435 TACTATGTATGCAACTCATGGAATTCATCTTATGCTGATGAACAACCTTACATT
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
* *
1147489 CACTATGTGTGCAACCCA-TAGAATTCATCATAGGTTGATGAAC
1 CACTATGTGTGCAACCCACGA-AATTCATCATATGTTGATGAAC
1147532 GACTGTATAT
Statistics
Matches: 399, Mismatches: 69, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.00
54 396 0.99
55 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (54 bp):
CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAGA
Found at i:1147196 original size:108 final size:108
Alignment explanation
Indices: 1147000--1147531 Score: 654
Period size: 108 Copynumber: 4.9 Consensus size: 108
1146990 ACTGTACTAT
* * *
1147000 AGGCACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTATAGACACTATGT
1 AGGCACTATGTATGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTACAGACACTATGT
* * ** * * *
1147065 ATACAATTCAAGGAATTCGTCATATGTTGATGAACAACCATAG
66 GTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATAC
* * * * *
1147108 AGCCACTATATTTGCAAGTCACGAAATTCATCATATGTTAATGAACAACCGTACAGACACTATGT
1 AGGCACTATGTATGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTACAGACACTATGT
*
1147173 GTGCAACCCACGGAATCCATCATATGTTGATGAACAACCATAC
66 GTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATAC
* * * *
1147216 ATGCACTATGTATGCAACCCACGAAATTCATCATATGTTGATGAACAATCGTA-AAAGCACTATG
1 AGGCACTATGTATGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTACAGA-CACTATG
* *
1147280 TGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATGC
65 TGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATAC
** *
1147324 AGGCACTATGCGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACA-AGCACTATG
1 AGGCACTATGTATGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTACAGA-CACTATG
* * * * *
1147388 TGTACAACTCACGAAATTCATCATATGTTGATGAAAAACCGTAC
65 TGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATAC
* * * * * * * **
1147432 CGGTACTATGTATGCAACTCATGGAATTCATCTTATGCTGATGAACAACCTTACATTCACTATGT
1 AGGCACTATGTATGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTACAGACACTATGT
** *
1147497 GTGCAACCCATAGAATTCATCATAGGTTGATGAAC
66 GTGCAACCCACGGAATTCATCATATGTTGATGAAC
1147532 GACTGTATAT
Statistics
Matches: 367, Mismatches: 54, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
107 2 0.01
108 364 0.99
109 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (108 bp):
AGGCACTATGTATGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTACAGACACTATGT
GTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATAC
Found at i:1147252 original size:27 final size:27
Alignment explanation
Indices: 1147222--1147307 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
1147212 ATACATGCAC
1147222 TATGTATGCAACCCACGAAATTCATCA
1 TATGTATGCAACCCACGAAATTCATCA
* **
1147249 TATGTTGATG-AA-CAATCGTAAAAGCA-C-
1 TATG-T-ATGCAACCCA-CG-AAATTCATCA
*
1147276 TATGTGTGCAACCCACGAAATTCATCA
1 TATGTATGCAACCCACGAAATTCATCA
1147303 TATGT
1 TATGT
1147308 TGATGAACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 7 0.16
26 6 0.14
27 17 0.39
28 6 0.14
29 8 0.18
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (27 bp):
TATGTATGCAACCCACGAAATTCATCA
Found at i:1147295 original size:162 final size:161
Alignment explanation
Indices: 1147003--1147531 Score: 655
Period size: 162 Copynumber: 3.3 Consensus size: 161
1146993 GTACTATAGG
* *
1147003 CACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCGTATAGACACTATGTATA
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAG-CACTATGTATA
* * * * * * * * *
1147068 CAATTCAAGGAATTCGTCATATGTTGATGAACAACCAT-AGAGCCACTATATTTGCAAGTCACGA
65 CAACTCACGAAATTCATCATATGTTGATGAACAACCGTAAAAG-CACTATGTATGCAACTCACGA
* *
1147132 AATTCATCATATGTTAATGAACAACCGTACAGA
129 AATTCATCATATGTTGATGAACAACCATACAGA
* * *
1147165 CACTATGTGTGCAACCCACGGAATCCATCATATGTTGATGAACAACCATACATGCACTATGTATG
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACA-GCACTATGTATA
* * * *
1147230 CAACCCACGAAATTCATCATATGTTGATGAACAATCGTAAAAGCACTATGTGTGCAACCCACGAA
65 CAACTCACGAAATTCATCATATGTTGATGAACAACCGTAAAAGCACTATGTATGCAACTCACGAA
* *
1147295 ATTCATCATATGTTGATGAACAACCATGCAGG
130 ATTCATCATATGTTGATGAACAACCATACAGA
* * *
1147327 CACTATGCGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTACAAGCACTATGTGTA
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTAC-AGCACTATGTATA
* *** * * *
1147392 CAACTCACGAAATTCATCATATGTTGATGAAAAACCGTACCGGTACTATGTATGCAACTCATGGA
65 CAACTCACGAAATTCATCATATGTTGATGAACAACCGTAAAAGCACTATGTATGCAACTCACGAA
* * * **
1147457 ATTCATCTTATGCTGATGAACAACCTTACATT
130 ATTCATCATATGTTGATGAACAACCATACAGA
** *
1147489 CACTATGTGTGCAACCCATAGAATTCATCATAGGTTGATGAAC
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAAC
1147532 GACTGTATAT
Statistics
Matches: 315, Mismatches: 49, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
162 310 0.98
163 5 0.02
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (161 bp):
CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTACAGCACTATGTATAC
AACTCACGAAATTCATCATATGTTGATGAACAACCGTAAAAGCACTATGTATGCAACTCACGAAA
TTCATCATATGTTGATGAACAACCATACAGA
Found at i:1151129 original size:18 final size:19
Alignment explanation
Indices: 1151108--1151143 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1151098 TCCTTTGGCT
1151108 GTGCTTGTTCCTC-TGCTC
1 GTGCTTGTTCCTCGTGCTC
1151126 GTGCTTGTTCCTCGTGCT
1 GTGCTTGTTCCTCGTGCT
1151144 GTTCTGGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (19 bp):
GTGCTTGTTCCTCGTGCTC
Found at i:1151153 original size:18 final size:19
Alignment explanation
Indices: 1151108--1151158 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
1151098 TCCTTTGGCT
*
1151108 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
1151126 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
1151144 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
1151159 CGGAGTCGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:1152783 original size:22 final size:23
Alignment explanation
Indices: 1152736--1152796 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
1152726 GATTCCCTAT
1152736 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
1152759 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
1152781 AGGGGGTATCGATTCC
1 AGGGGGAATCGGTTCC
1152797 TCTGCAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 15 0.42
23 21 0.58
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:1156623 original size:22 final size:21
Alignment explanation
Indices: 1156581--1156620 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1156571 GAATTTGTTT
*
1156581 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1156602 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1156621 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1164442 original size:20 final size:20
Alignment explanation
Indices: 1164419--1164461 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1164409 GAGAAAAGGT
*
1164419 AAAATTTAA-AATGAAAGAG
1 AAAAATTAATAATGAAAGAG
*
1164438 AAAAATTAATAATGAAAGAT
1 AAAAATTAATAATGAAAGAG
1164458 AAAA
1 AAAA
1164462 GAAAAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (20 bp):
AAAAATTAATAATGAAAGAG
Found at i:1171294 original size:24 final size:24
Alignment explanation
Indices: 1171250--1171296 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1171240 TTAAAGAACC
*
1171250 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1171274 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
1171297 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1177692 original size:54 final size:54
Alignment explanation
Indices: 1177581--1177685 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
1177571 ATTGCACCGA
* *
1177581 AGTGCCGAAATGGAAATTCACAAACTCATTATGAATTCCATGGATTGCACACAT
1 AGTGCCGAAATGGAAATTCACAAACGCATTATGAATACCATGGATTGCACACAT
* ** * * *
1177635 AGTGTCGAAATGGTCATTCATAAACGCGTTATGAATACCATGGGTTGCACA
1 AGTGCCGAAATGGAAATTCACAAACGCATTATGAATACCATGGATTGCACA
1177686 TTTAGTGCTG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (54 bp):
AGTGCCGAAATGGAAATTCACAAACGCATTATGAATACCATGGATTGCACACAT
Found at i:1180252 original size:18 final size:18
Alignment explanation
Indices: 1180229--1180264 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1180219 ATTCAAATAA
1180229 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
1180247 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
1180265 CTTAAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:1180758 original size:26 final size:25
Alignment explanation
Indices: 1180702--1180754 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1180692 CAAAATATCC
*
1180702 AAACAACCAAATATTCAAATTTGTT
1 AAACAACCAAATATTCAAATATGTT
1180727 AAACAACCAAAT-TCATCAAA-ATGTT
1 AAACAACCAAATAT--TCAAATATGTT
1180752 AAA
1 AAA
1180755 ACAATGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 1 0.04
25 19 0.76
26 5 0.20
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (25 bp):
AAACAACCAAATATTCAAATATGTT
Found at i:1183275 original size:11 final size:11
Alignment explanation
Indices: 1183259--1183321 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
1183249 GTATTATAGA
1183259 ATTTTTAATAT
1 ATTTTTAATAT
1183270 ATTTTTAA-A-
1 ATTTTTAATAT
1183279 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
1183290 ATAAATAGTGT
1 ATTTTTAATAT
1183301 ATTTTTAATAT
1 ATTTTTAATAT
1183312 ATTTTTAATA
1 ATTTTTAATA
1183322 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:1184632 original size:13 final size:13
Alignment explanation
Indices: 1184616--1184640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184606 TGAAAACTAT
1184616 TTTGAAAAATAAG
1 TTTGAAAAATAAG
1184629 TTTGAAAAATAA
1 TTTGAAAAATAA
1184641 TAGTATGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TTTGAAAAATAAG
Found at i:1185227 original size:21 final size:21
Alignment explanation
Indices: 1185202--1185254 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1185192 TTAAGAACAA
1185202 TATCGATACCTATTAAAGAAG
1 TATCGATACCTATTAAAGAAG
** *
1185223 TATCGATA-CTATTCTAGTAG
1 TATCGATACCTATTAAAGAAG
1185243 TATCGATACCTA
1 TATCGATACCTA
1185255 GCAAGAGGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (21 bp):
TATCGATACCTATTAAAGAAG
Found at i:1191452 original size:18 final size:18
Alignment explanation
Indices: 1191429--1191482 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
1191419 ATTCGAATAA
1191429 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
1191447 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
*
1191465 TTGAATCAAATATAAAAT
1 TTGAATCGAATATAAAAT
1191483 CTTAAAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:1193421 original size:51 final size:50
Alignment explanation
Indices: 1193346--1193531 Score: 142
Period size: 51 Copynumber: 3.9 Consensus size: 50
1193336 GATGTAAGTG
* *
1193346 AATAAAAAATATATCATTTAACACATACTTACACCAATGTAAGTAAATAA
1 AATAAAAAATATAGCACTTAACACATACTTACACCAATGTAAGTAAATAA
* *
1193396 AATAAAAAAGTGTAGCACTTAACACATACTT------ATG-AATTAAAT--
1 AATAAAAAA-TATAGCACTTAACACATACTTACACCAATGTAAGTAAATAA
** * * * *
1193438 -A-AAAAAATGCAGCACTTAACATATATTTACACTAGTGTAAGTAAATAA
1 AATAAAAAATATAGCACTTAACACATACTTACACCAATGTAAGTAAATAA
* * * **
1193486 AATAAAAAACTAAAACACTTAACACATAATTACACCGGTGTAAGTA
1 AATAAAAAA-TATAGCACTTAACACATACTTACACCAATGTAAGTA
1193532 CTAAGTAATA
Statistics
Matches: 107, Mismatches: 16, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
39 18 0.17
40 6 0.06
41 1 0.01
44 7 0.07
45 5 0.05
46 7 0.07
49 1 0.01
50 15 0.14
51 47 0.44
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.26
Consensus pattern (50 bp):
AATAAAAAATATAGCACTTAACACATACTTACACCAATGTAAGTAAATAA
Found at i:1197284 original size:17 final size:18
Alignment explanation
Indices: 1197259--1197296 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1197249 TAAGAAAATC
1197259 TATTAATTTATATA-AAA
1 TATTAATTTATATAGAAA
* *
1197276 TATTTATTTATTTAGAAA
1 TATTAATTTATATAGAAA
1197294 TAT
1 TAT
1197297 CAAAAAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTAATTTATATAGAAA
Found at i:1197518 original size:2 final size:2
Alignment explanation
Indices: 1197511--1197536 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1197501 ATCTAAACAA
1197511 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
1197537 GACTAATATA
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):
AT
Found at i:1199342 original size:3 final size:3
Alignment explanation
Indices: 1199336--1199391 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
1199326 ATTATTTATT
* *
1199336 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1199380 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1199392 ATAAAACAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1199358 original size:19 final size:19
Alignment explanation
Indices: 1199336--1199388 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
1199326 ATTATTTATT
* *
1199336 TAATAATAATAATATAATA
1 TAATAATAATAATAAAACA
*
1199355 TAATAATAATATTAAAACA
1 TAATAATAATAATAAAACA
*
1199374 AAATAATAATAATAA
1 TAATAATAATAATAA
1199389 TAAATAAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAATAATAATAAAACA
Found at i:1199361 original size:22 final size:21
Alignment explanation
Indices: 1199314--1199395 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
1199304 TGTAAAAATG
* * *
1199314 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
1199336 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
* * *
1199358 TAATAATATTAAAACAAAATAA
1 TAATAATAAT-AAATAATATAA
1199380 TAATAATAATAAATAA
1 TAATAATAATAAATAA
1199396 AACAAATGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 5 0.10
22 37 0.74
23 8 0.16
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:1199395 original size:16 final size:15
Alignment explanation
Indices: 1199336--1199391 Score: 66
Period size: 14 Copynumber: 4.0 Consensus size: 15
1199326 ATTATTTATT
1199336 TAATAATAATAAT-A
1 TAATAATAATAATAA
1199350 TAAT-ATAATAATAA
1 TAATAATAATAATAA
* *
1199364 TATTAA-AACAA-AA
1 TAATAATAATAATAA
1199377 TAATAATAATAATAA
1 TAATAATAATAATAA
1199392 ATAAAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 15 0.44
14 16 0.47
15 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATAATAATAATAA
Found at i:1199402 original size:25 final size:27
Alignment explanation
Indices: 1199349--1199401 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
1199339 TAATAATAAT
1199349 ATAATATAATAATAATATTAAAACAAA
1 ATAATATAATAATAATATTAAAACAAA
1199376 ATAATAATAATAATAA-A-TAAAACAAA
1 ATAAT-ATAATAATAATATTAAAACAAA
1199402 TGAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 9 0.36
27 6 0.24
28 10 0.40
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (27 bp):
ATAATATAATAATAATATTAAAACAAA
Found at i:1199932 original size:113 final size:112
Alignment explanation
Indices: 1199738--1200360 Score: 894
Period size: 113 Copynumber: 5.5 Consensus size: 112
1199728 ATTGAACAAG
* * *
1199738 TTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTCT-CTCTGGAAAAGTTGATCCATCAAG
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGCTGATCCATCAAG
* *
1199802 TGATGAATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
65 TGATGAATT-AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
1199851 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGTAATGATGATCCATCGAA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGCTGATCCATC-AA
1199915 -TGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
64 GTGATGAATT-AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* * **
1199964 TTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTGACT-TGGCAATGCTGATCCATCGGG
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT-ACTCTGGAAATGCTGATCCATCAAG
* *
1200028 TGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTC
65 TGATGAATTAAA-CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* * **
1200077 TTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATTTTGATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATCCATCAAGT
* *
1200142 GATGAATTAAAGAAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTC
66 GATGAATTAAACAAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTC
*
1200190 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATCCATCAAGT
* * * * *
1200255 GATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
66 GAT-GAATTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
1200303 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCC
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATCC
1200361 TGAAGATACT
Statistics
Matches: 467, Mismatches: 34, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
112 10 0.02
113 445 0.95
114 12 0.03
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATCCATCAAGT
GATGAATTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:1200403 original size:3 final size:3
Alignment explanation
Indices: 1200395--1200466 Score: 108
Period size: 3 Copynumber: 24.0 Consensus size: 3
1200385 ATTGATTTAT
* * * *
1200395 TTA TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1200443 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1200467 AATATATTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1200474 original size:12 final size:11
Alignment explanation
Indices: 1200399--1200475 Score: 53
Period size: 9 Copynumber: 7.5 Consensus size: 11
1200389 ATTTATTTAT
*
1200399 TATTATTATTA
1 TATTATTAATA
1200410 TAATTA-TAAT-
1 T-ATTATTAATA
1200420 TATTATT-AT-
1 TATTATTAATA
1200429 TATTA-TAA-A
1 TATTATTAATA
1200438 TATTATT-AT-
1 TATTATTAATA
*
1200447 TATTATTATTA
1 TATTATTAATA
1200458 TTATTATTAAATA
1 -TATTATT-AATA
1200471 TATTA
1 TATTA
1200476 AATATATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
8 1 0.02
9 25 0.47
10 4 0.08
11 4 0.08
12 16 0.30
13 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTATTAATA
Found at i:1200936 original size:15 final size:15
Alignment explanation
Indices: 1200916--1200957 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1200906 ACAACGCAGC
1200916 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1200931 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1200946 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1200958 CTTACCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1200941 original size:20 final size:20
Alignment explanation
Indices: 1200916--1200957 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1200906 ACAACGCAGC
*
1200916 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
1200936 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
1200956 AA
1 AA
1200958 CTTACCGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:1201164 original size:16 final size:16
Alignment explanation
Indices: 1201145--1201182 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1201135 GGCCGGCGGT
1201145 GACGGTCACGGCGGCA
1 GACGGTCACGGCGGCA
1201161 GACGGTCACGGCGGCA
1 GACGGTCACGGCGGCA
1201177 GACGGT
1 GACGGT
1201183 TGCCGTCCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.45, T:0.08
Consensus pattern (16 bp):
GACGGTCACGGCGGCA
Found at i:1202578 original size:28 final size:27
Alignment explanation
Indices: 1202536--1202622 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 27
1202526 TTTTTTTTTC
*
1202536 TTTTCAAAATTTTTATATTT-ACTTATTA
1 TTTTC-AAATATTTATATTTCA-TTATTA
1202564 TTTTCATAATATTTATATGTTTCATT-TTA
1 TTTTCA-AATATTTATA--TTTCATTATTA
* *
1202593 TTTGCAAGTATTT-TATTTCATTATTA
1 TTTTCAAATATTTATATTTCATTATTA
1202619 TTTT
1 TTTT
1202623 TTCTGTCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
25 7 0.14
26 6 0.12
27 3 0.06
28 20 0.40
29 8 0.16
30 5 0.10
31 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTTCAAATATTTATATTTCATTATTA
Found at i:1205983 original size:14 final size:15
Alignment explanation
Indices: 1205953--1205985 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1205943 TTTTTATTTT
1205953 ATTTATTAAGATAAA
1 ATTTATTAAGATAAA
*
1205968 ATTTATTAA-TTAAA
1 ATTTATTAAGATAAA
1205982 ATTT
1 ATTT
1205986 GGAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTATTAAGATAAA
Found at i:1213262 original size:11 final size:11
Alignment explanation
Indices: 1213246--1213287 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
1213236 TATTATGCTT
1213246 AAAAAAAAG-A
1 AAAAAAAAGAA
1213256 AAAAAAAAGAA
1 AAAAAAAAGAA
*
1213267 GAAAAAAAGAA
1 AAAAAAAAGAA
*
1213278 AAGAAAAAGA
1 AAAAAAAAGA
1213288 GGGGTCAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1213268 original size:13 final size:12
Alignment explanation
Indices: 1213246--1213285 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
1213236 TATTATGCTT
1213246 AAAAAAAAGAAA
1 AAAAAAAAGAAA
1213258 AAAAAAGAAGAAA
1 AAAAAA-AAGAAA
1213271 AAAAGAAAAGAAA
1 AAAA-AAAAGAAA
1213284 AA
1 AA
1213286 GAGGGGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.23
13 18 0.69
14 2 0.08
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:1213273 original size:21 final size:22
Alignment explanation
Indices: 1213247--1213287 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1213237 ATTATGCTTA
1213247 AAAAAAAGAAAA-AAAAAGAAG
1 AAAAAAAGAAAAGAAAAAGAAG
1213268 AAAAAAAGAAAAGAAAAAGA
1 AAAAAAAGAAAAGAAAAAGA
1213288 GGGGTCAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAAAGAAAAAGAAG
Found at i:1213624 original size:16 final size:16
Alignment explanation
Indices: 1213598--1213642 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1213588 TTTGAATACA
*
1213598 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
1213615 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
1213630 ATTCAATTTATTT
1 ATTCAATTTATTT
1213643 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:1214577 original size:83 final size:83
Alignment explanation
Indices: 1214439--1214820 Score: 633
Period size: 83 Copynumber: 4.6 Consensus size: 83
1214429 ATGCAATGTA
*
1214439 CTCATAGCATCTTCTGGAAGT-TTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGA
1214503 ATTTGGAAGATGAATATG
66 ATTTGGAAGATGAATATG
*
1214521 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGA
*
1214586 AATTGGAAGATGAATATG
66 ATTTGGAAGATGAATATG
*
1214604 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGA
1214669 ATTTGGAAGA-GTAATATG
66 ATTTGGAAGATG-AATATG
* * * *
1214687 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAGTTATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGA
*
1214752 ATTTGGAAAGATGAATGTG
66 ATTTGG-AAGATGAATATG
*
1214771 CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1214821 TATGAACCCC
Statistics
Matches: 284, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
82 22 0.08
83 204 0.72
84 11 0.04
85 47 0.17
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGA
ATTTGGAAGATGAATATG
Found at i:1215847 original size:113 final size:113
Alignment explanation
Indices: 1215650--1216614 Score: 1409
Period size: 113 Copynumber: 8.5 Consensus size: 113
1215640 TAGCAAAGAT
* * *
1215650 TTAAATCCATCA-TTCAATGGATCGGCTTTTCCAGATAAAGTTCATAATAAGAAGAACTCATCTG
1 TTAAATCCATCACTT-GATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTG
* * * * *
1215714 AAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTTTTCAACCTTATGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
1215763 TTAAATCCATCA-TTCAATGGATCGGCTTTTCCAGATAAAGTTCATAATAAGAAGAACTCATCTG
1 TTAAATCCATCACTT-GATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTG
* * * * *
1215827 AAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTATGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
1215876 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
1215941 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * **
1215989 TTAAATCCATTACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
**
1216054 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAAATTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * **
1216102 TTAAATCCATTACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
*
1216167 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAACTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * **
1216215 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
*
1216280 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
1216328 TCAAATCTATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
*
1216393 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
1216441 TCAAATCTATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
*
1216506 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
1216554 TCAAATCCATCACTTGATGGGTCAG-TTTTCCCA-A-AGAAGTTCATAATGAGAAGAACTCATC
1 TTAAATCCATCACTTGATGGATCAGCTTTT-CCAGATA-AAGTTCATAATGAGAAGAACTCATC
1216615 AAGAGCTTAT
Statistics
Matches: 812, Mismatches: 37, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
111 1 0.00
112 30 0.04
113 779 0.96
114 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
TTAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1216880 original size:3 final size:3
Alignment explanation
Indices: 1216872--1216967 Score: 183
Period size: 3 Copynumber: 32.0 Consensus size: 3
1216862 ATTGATTTAT
1216872 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1216920 TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1216968 AATATATTAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1217437 original size:15 final size:15
Alignment explanation
Indices: 1217417--1217452 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1217407 ACAACGCAGC
1217417 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1217432 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
1217447 AAAGAA
1 AAAGAA
1217453 GATAAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1218618 original size:19 final size:19
Alignment explanation
Indices: 1218594--1218641 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1218584 GAATTTTTAA
1218594 AATTTTTAATAATAGAGAC
1 AATTTTTAATAATAGAGAC
1218613 AATTTTTAATAATAGAGAC
1 AATTTTTAATAATAGAGAC
*
1218632 AATTTATAAT
1 AATTTTTAAT
1218642 TAAAAAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (19 bp):
AATTTTTAATAATAGAGAC
Found at i:1227783 original size:24 final size:22
Alignment explanation
Indices: 1227740--1227795 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1227730 TTTAATACTT
1227740 GAAAATAA-AATAAAACATTAA
1 GAAAATAATAATAAAACATTAA
* * *
1227761 TAAAATAATATATATAAATATTAG
1 GAAAATAATA-ATA-AAACATTAA
1227785 GAAAATAATAA
1 GAAAATAATAA
1227796 GTATATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.25
22 1 0.04
23 4 0.14
24 16 0.57
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (22 bp):
GAAAATAATAATAAAACATTAA
Found at i:1228343 original size:17 final size:18
Alignment explanation
Indices: 1228318--1228355 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1228308 TAAGAAAATC
1228318 TATTAATTTATATA-AAA
1 TATTAATTTATATAGAAA
* *
1228335 TATTTATTTATTTAGAAA
1 TATTAATTTATATAGAAA
1228353 TAT
1 TAT
1228356 CAGAAAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTAATTTATATAGAAA
Found at i:1230432 original size:3 final size:3
Alignment explanation
Indices: 1230426--1230478 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
1230416 ATTATTTATT
* *
1230426 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1230470 TAA TAA TAA
1 TAA TAA TAA
1230479 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1230448 original size:19 final size:18
Alignment explanation
Indices: 1230426--1230481 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
1230416 ATTATTTATT
1230426 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
1230445 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
1230464 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
1230482 AAACAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:1230451 original size:22 final size:21
Alignment explanation
Indices: 1230404--1230482 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
1230394 TGTAAAAATG
* * *
1230404 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
1230426 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
1230448 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
1230467 TAATAATAATAAATAA
1 TAATAATAATAAATAA
1230483 AACAAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:1230489 original size:22 final size:22
Alignment explanation
Indices: 1230426--1230489 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
1230416 ATTATTTATT
* *
1230426 TAATAAT-AATAATATAATATAA
1 TAATAATAAATAAAACAA-ATAA
*
1230448 TAATAATA-TTAAAACAAAATAA
1 TAATAATAAATAAAAC-AAATAA
1230470 TAATAATAAATAAAACAAAT
1 TAATAATAAATAAAACAAAT
1230490 GAAATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAAATAAAACAAATAA
Found at i:1237359 original size:43 final size:39
Alignment explanation
Indices: 1237311--1237421 Score: 163
Period size: 38 Copynumber: 2.8 Consensus size: 39
1237301 TTCTATCTCG
*
1237311 TTCGTTGGACTTTACAAAATTGAATTATTTACTCACTCAATTA
1 TTCGTTTGACTTTAC-AAATTG-A--ATTTACTCACTCAATTA
1237354 TTCGTTTGACTTTACAAATTG-ATTTACTCACTCAATTA
1 TTCGTTTGACTTTACAAATTGAATTTACTCACTCAATTA
1237392 TTCGTTTGACTTTACAAATTG-ATTTACTCA
1 TTCGTTTGACTTTACAAATTGAATTTACTCA
1237422 ATCGTTCACT
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
38 47 0.70
42 6 0.09
43 14 0.21
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (39 bp):
TTCGTTTGACTTTACAAATTGAATTTACTCACTCAATTA
Found at i:1237382 original size:38 final size:38
Alignment explanation
Indices: 1237333--1237421 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
1237323 TACAAAATTG
1237333 AATT-ATTTACTCACTCAATTATTCGTTTGACTTTACA
1 AATTGATTTACTCACTCAATTATTCGTTTGACTTTACA
1237370 AATTGATTTACTCACTCAATTATTCGTTTGACTTTACA
1 AATTGATTTACTCACTCAATTATTCGTTTGACTTTACA
1237408 AATTGATTTACTCA
1 AATTGATTTACTCA
1237422 ATCGTTCACT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 4 0.08
38 47 0.92
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (38 bp):
AATTGATTTACTCACTCAATTATTCGTTTGACTTTACA
Found at i:1237547 original size:11 final size:13
Alignment explanation
Indices: 1237522--1237572 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1237512 TTTTTATTAA
1237522 ATAATATAATAATT
1 ATAATAT-ATAATT
1237536 AT-ATATAT-ATT
1 ATAATATATAATT
1237547 ATTAATATATAATT
1 A-TAATATATAATT
* *
1237561 ATGACATATAAT
1 ATAATATATAAT
1237573 ATTTAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 4 0.12
12 3 0.09
13 19 0.59
14 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (13 bp):
ATAATATATAATT
Found at i:1237569 original size:26 final size:26
Alignment explanation
Indices: 1237523--1237575 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1237513 TTTTATTAAA
* *
1237523 TAATATAATAATTATATATATATTAT
1 TAATATAATAATTATACATATAATAT
1237549 TAATAT-ATAATTATGACATATAATAT
1 TAATATAATAATTAT-ACATATAATAT
1237575 T
1 T
1237576 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
TAATATAATAATTATACATATAATAT
Found at i:1238845 original size:15 final size:16
Alignment explanation
Indices: 1238811--1238849 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
1238801 AAAAATGAAA
1238811 AAAAT-TAAAAAAAGTC
1 AAAATATAAAAAAAG-C
1238827 AAAATATAAAAAAAG-
1 AAAATATAAAAAAAGC
1238842 AAAATATA
1 AAAATATA
1238850 TTTTTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 9 0.41
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAATATAAAAAAAGC
Found at i:1239785 original size:27 final size:27
Alignment explanation
Indices: 1239755--1239807 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1239745 TGATCAAACA
*
1239755 TATTTTCTAATTTATAAAAAAT-GAAAT
1 TATTTTCTAATATA-AAAAAATAGAAAT
*
1239782 TATTTTTTAATATAAAAAAATAGAAA
1 TATTTTCTAATATAAAAAAATAGAAA
1239808 CCAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (27 bp):
TATTTTCTAATATAAAAAAATAGAAAT
Found at i:1242624 original size:17 final size:17
Alignment explanation
Indices: 1242604--1242646 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1242594 AGGGAAGTAG
1242604 TTCATTAAACTAGTTCA
1 TTCATTAAACTAGTTCA
* *
1242621 TTCATCAAACTAGTTCG
1 TTCATTAAACTAGTTCA
*
1242638 TTTATTAAA
1 TTCATTAAA
1242647 TTAACTCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (17 bp):
TTCATTAAACTAGTTCA
Found at i:1245344 original size:31 final size:31
Alignment explanation
Indices: 1245304--1245373 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
1245294 CTGATATTCT
*
1245304 TGCATCTATTGAAACCGTTCAACTTCTCTCA
1 TGCACCTATTGAAACCGTTCAACTTCTCTCA
1245335 TGCACCTATTGAAACCGTTCAACTTCTCTCA
1 TGCACCTATTGAAACCGTTCAACTTCTCTCA
1245366 TGCACCTA
1 TGCACCTA
1245374 GACACAAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (31 bp):
TGCACCTATTGAAACCGTTCAACTTCTCTCA
Found at i:1245456 original size:17 final size:17
Alignment explanation
Indices: 1245434--1245495 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
1245424 AATTAAGATA
*
1245434 AATGAACTAGTTTGATG
1 AATGAACTAGTTTAATG
*
1245451 AATGAACTAGTTTAATT
1 AATGAACTAGTTTAATG
* * *
1245468 AATGAACTAACTTTATTC
1 AATGAACT-AGTTTAATG
1245486 AATGAACTAG
1 AATGAACTAG
1245496 ATGCATGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 24 0.63
18 14 0.37
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (17 bp):
AATGAACTAGTTTAATG
Found at i:1245489 original size:18 final size:18
Alignment explanation
Indices: 1245451--1245494 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1245441 TAGTTTGATG
*
1245451 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
1245468 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
1245485 CAATGAACTA
1 -AATGAACTA
1245495 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:1249170 original size:17 final size:17
Alignment explanation
Indices: 1249145--1249189 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1249135 AACAATTAAG
*
1249145 ATAAATGAACTAGTTTG
1 ATAAATGAACTAGTTTA
*
1249162 ATGAATGAACTAGTTTA
1 ATAAATGAACTAGTTTA
1249179 ATAAATGAACT
1 ATAAATGAACT
1249190 TTATTCAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (17 bp):
ATAAATGAACTAGTTTA
Found at i:1250608 original size:9 final size:8
Alignment explanation
Indices: 1250593--1250630 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
1250583 CCCATGTTAG
1250593 TAAAAAAA
1 TAAAAAAA
1250601 TGAAAAAAA
1 T-AAAAAAA
1250610 TAAAAAAA
1 TAAAAAAA
1250618 TAAATAAAA
1 TAAA-AAAA
1250627 -AAAA
1 TAAAA
1250631 GTTTAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.04
8 15 0.54
9 12 0.43
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1250702 original size:8 final size:8
Alignment explanation
Indices: 1250689--1250713 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1250679 TTCATCTTTA
1250689 TATTCAAT
1 TATTCAAT
1250697 TATTCAAT
1 TATTCAAT
1250705 TATTCAAT
1 TATTCAAT
1250713 T
1 T
1250714 TTGTTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (8 bp):
TATTCAAT
Found at i:1253853 original size:42 final size:41
Alignment explanation
Indices: 1253807--1253900 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
1253797 GGCTTTTTAA
* * *
1253807 ACAAACGCCGCAAAAGGTCCAGATCTATAGCGACATTTTTCC
1 ACAAACGCCGCAAAAGAT-CAGATCTATAACGACATATTTCC
** * *
1253849 ACAAATACTGCAAAAGATGAGATCTATAACGACATATTTCC
1 ACAAACGCCGCAAAAGATCAGATCTATAACGACATATTTCC
1253890 ACAAACGCCGC
1 ACAAACGCCGC
1253901 TAATAGTCAT
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 28 0.67
42 14 0.33
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (41 bp):
ACAAACGCCGCAAAAGATCAGATCTATAACGACATATTTCC
Found at i:1256114 original size:14 final size:14
Alignment explanation
Indices: 1256092--1256130 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1256082 CTGCGGTTGT
1256092 GGTGATGGCTGCAC
1 GGTGATGGCTGCAC
* *
1256106 GGTGGTGGCTTCAC
1 GGTGATGGCTGCAC
*
1256120 TGTGATGGCTG
1 GGTGATGGCTG
1256131 GGCGTTAGAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.10, C:0.18, G:0.44, T:0.28
Consensus pattern (14 bp):
GGTGATGGCTGCAC
Found at i:1256291 original size:42 final size:42
Alignment explanation
Indices: 1256236--1256366 Score: 147
Period size: 42 Copynumber: 3.1 Consensus size: 42
1256226 AAAAGCGACG
* * *
1256236 CTAAGGTGTATGACTATCGCATCATTTATTACAAAAATGTCA
1 CTAAAGTGCATGACTATCGCATCATTTATTACAAAAATGCCA
** * * *
1256278 CTAGGGTTCATGACTATCACATCATTTATTACAAAAATGCCG
1 CTAAAGTGCATGACTATCGCATCATTTATTACAAAAATGCCA
* * *
1256320 CTAAAGTGCATGATTATCGCGA-CGTTTATTACAAAAATGCCG
1 CTAAAGTGCATGACTATCGC-ATCATTTATTACAAAAATGCCA
1256362 CTAAA
1 CTAAA
1256367 CTACATTATT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
42 75 0.99
43 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (42 bp):
CTAAAGTGCATGACTATCGCATCATTTATTACAAAAATGCCA
Found at i:1257733 original size:27 final size:26
Alignment explanation
Indices: 1257674--1257726 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1257664 ACTCCGGTTA
*
1257674 GGTAAAATTACGAAAATACTCTTATG
1 GGTAAAATTACGAAAATACCCTTATG
* *
1257700 GGATAAACTTATGAAAATACCCTTATG
1 GG-TAAAATTACGAAAATACCCTTATG
1257727 TTGTAAAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (26 bp):
GGTAAAATTACGAAAATACCCTTATG
Found at i:1260940 original size:19 final size:19
Alignment explanation
Indices: 1260913--1260965 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
1260903 ACTGGTCATT
*
1260913 TCGACCCGTCTGACCCAAC
1 TCGAACCGTCTGACCCAAC
1260932 TCGAACCGTCTGACCCAAC
1 TCGAACCGTCTGACCCAAC
*
1260951 TCGAACCGCCTGACC
1 TCGAACCGTCTGACC
1260966 GACCCAGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.45, G:0.17, T:0.15
Consensus pattern (19 bp):
TCGAACCGTCTGACCCAAC
Found at i:1261680 original size:27 final size:27
Alignment explanation
Indices: 1261650--1261710 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
1261640 ACTCTAGTTA
* * *
1261650 GGTAAAATTTTTAAAATACCCTTATGT
1 GGTAAAATTATGAAAATACCCGTATGT
1261677 GGTAAAATTATGAAAATACCCGTATGT
1 GGTAAAATTATGAAAATACCCGTATGT
*
1261704 TGTAAAA
1 GGTAAAA
1261711 AGATAAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (27 bp):
GGTAAAATTATGAAAATACCCGTATGT
Found at i:1262609 original size:19 final size:19
Alignment explanation
Indices: 1262560--1262609 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1262550 GAAATATAGG
*
1262560 TTGATCTCTGATTTATGTT
1 TTGATCTCTGATATATGTT
* * * *
1262579 CTAAACTTTGATATATGTT
1 TTGATCTCTGATATATGTT
1262598 TTGATCTCTGAT
1 TTGATCTCTGAT
1262610 TTCTGATCTG
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (19 bp):
TTGATCTCTGATATATGTT
Found at i:1263835 original size:41 final size:41
Alignment explanation
Indices: 1263704--1263898 Score: 153
Period size: 40 Copynumber: 4.8 Consensus size: 41
1263694 TGCAACTAAG
* * * * * *
1263704 GTGCATGACTATTGCGA--TATATATATAAAATACCACTAAG
1 GTGCATGACTATTGCGACGTTTAT-TAAAAAACAACACAAAA
*
1263744 GTGCATGACTATTGCGACGTTTATTGCAAAAACAACACAAAA
1 GTGCATGACTATTGCGACGTTTATT-AAAAAACAACACAAAA
** * ** *
1263786 GTATATGACTATTGCGACGTTTATTTAAAAACATTACGAAA
1 GTGCATGACTATTGCGACGTTTATTAAAAAACAACACAAAA
* * * ** * *
1263827 GTGCATGACTGTTGTGGCGTTTA-TAAAAAACGCCACTAAG
1 GTGCATGACTATTGCGACGTTTATTAAAAAACAACACAAAA
*
1263867 GTGCATGACTATTGCGAAGTTTATTACAAAAA
1 GTGCATGACTATTGCGACGTTTATTA-AAAAA
1263899 TGTCGTTAAG
Statistics
Matches: 122, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
40 47 0.39
41 33 0.27
42 42 0.34
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (41 bp):
GTGCATGACTATTGCGACGTTTATTAAAAAACAACACAAAA
Found at i:1263911 original size:42 final size:41
Alignment explanation
Indices: 1263699--1264022 Score: 189
Period size: 42 Copynumber: 7.9 Consensus size: 41
1263689 GGGGTTGCAA
* * * *
1263699 CTAAGGTGCATGACTATTGCG-ATATATATA-TAAAATACCA
1 CTAAGGTGCATGACTATTGCGAATTTAT-TACAAAAATGCCG
* * *** *
1263739 CTAAGGTGCATGACTATTGCGACGTTTATTGCAAAAACAACA
1 CTAAGGTGCATGACTATTGCGA-ATTTATTACAAAAATGCCG
* * ** * **
1263781 CAAAAGTATATGACTATTGCGACGTTTATTTA-AAAACATTACG
1 CTAAGGTGCATGACTATTGCGA-ATTTA-TTACAAAA-ATGCCG
* * * ** * *
1263824 --AAAGTGCATGACTGTTGTGGCGTTTA-TA-AAAAACGCCA
1 CTAAGGTGCATGACTATTG-CGAATTTATTACAAAAATGCCG
*
1263862 CTAAGGTGCATGACTATTGCGAAGTTTATTACAAAAATGTCG
1 CTAAGGTGCATGACTATTGCGAA-TTTATTACAAAAATGCCG
* * * * *
1263904 TTAAGGTGCATGATTGTTGAGAAGTTTATTACAAAAATGCCA
1 CTAAGGTGCATGACTATTGCGAA-TTTATTACAAAAATGCCG
* **
1263946 CTAAGGTGCATGACTGTTTTGACATTTA-TA-AAAAATGCCG
1 CTAAGGTGCATGACTATTGCGA-ATTTATTACAAAAATGCCG
*
1263986 CTAAGGTGCATGACTATTGCGGCATTTATTACAAAAA
1 CTAAGGTGCATGACTATTGC-GAATTTATTACAAAAA
1264023 CATCACCTAA
Statistics
Matches: 223, Mismatches: 46, Indels: 28
0.75 0.15 0.09
Matches are distributed among these distances:
38 2 0.01
39 7 0.03
40 71 0.32
41 27 0.12
42 110 0.49
43 6 0.03
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (41 bp):
CTAAGGTGCATGACTATTGCGAATTTATTACAAAAATGCCG
Found at i:1263931 original size:123 final size:123
Alignment explanation
Indices: 1263704--1264024 Score: 306
Period size: 123 Copynumber: 2.6 Consensus size: 123
1263694 TGCAACTAAG
* * * * * ** *
1263704 GTGCATGACTATTGCGATATATATATAAAATACCACTAAGGTGCATGACTATTGCGACGTTTATT
1 GTGCATGACTGTTGTGACATTTATAAAAAACGCCACTAAGGTGCATGACTATTGCGAAGTTTATT
* * * * *
1263769 GCAAAAACAACACAAAAGTATATGACTATTGCGACGTTTATTTA-AAAACAT-TACGAAA
66 ACAAAAACAACACAAAAGTACATGACTATTGAGAAGTTTA-TTACAAAA-ATCCACGAAA
* *
1263827 GTGCATGACTGTTGTGGCGTTTATAAAAAACGCCACTAAGGTGCATGACTATTGCGAAGTTTATT
1 GTGCATGACTGTTGTGACATTTATAAAAAACGCCACTAAGGTGCATGACTATTGCGAAGTTTATT
*** *** * * * * * *
1263892 ACAAAAATGTCGTTAAGGTGCATGATTGTTGAGAAGTTTATTACAAAAATGCCACTAAG
66 ACAAAAACAACACAAAAGTACATGACTATTGAGAAGTTTATTACAAAAAT-CCACGAAA
* * * *
1263951 GTGCATGACTGTTTTGACATTTATAAAAAATGCCGCTAAGGTGCATGACTATTGCGGCA-TTTAT
1 GTGCATGACTGTTGTGACATTTATAAAAAACGCCACTAAGGTGCATGACTATTGC-GAAGTTTAT
1264015 TACAAAAACA
65 TACAAAAACA
1264025 TCACCTAATA
Statistics
Matches: 159, Mismatches: 35, Indels: 7
0.79 0.17 0.03
Matches are distributed among these distances:
122 5 0.03
123 85 0.53
124 67 0.42
125 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (123 bp):
GTGCATGACTGTTGTGACATTTATAAAAAACGCCACTAAGGTGCATGACTATTGCGAAGTTTATT
ACAAAAACAACACAAAAGTACATGACTATTGAGAAGTTTATTACAAAAATCCACGAAA
Found at i:1264019 original size:82 final size:83
Alignment explanation
Indices: 1263698--1264023 Score: 242
Period size: 82 Copynumber: 4.0 Consensus size: 83
1263688 GGGGGTTGCA
* * * * *
1263698 ACTAAGGTGCATGACTATTGCG-A-TATATATA-TAAAATACCACTAAGGTGCATGACTATTGCG
1 ACTAAGGTGCATGACTATTGCGAAGTTTAT-TACAAAAATGCCGCTAAGGTGCATGACTGTTG-G
* * * **
1263760 ACGTTTATTGCAAAAACAAC
64 GCATTTATTACAAAAACGCC
* * ** * ** *
1263780 ACAAAAGTATATGACTATTGCGACGTTTATTTA-AAAACATTACG--AAAGTGCATGACTGTTGT
1 ACTAAGGTGCATGACTATTGCGAAGTTTA-TTACAAAA-ATGCCGCTAAGGTGCATGACTGTTG-
*
1263842 GGCGTTTA-TA-AAAAACGCC
63 GGCATTTATTACAAAAACGCC
* * * * *
1263861 ACTAAGGTGCATGACTATTGCGAAGTTTATTACAAAAATGTCGTTAAGGTGCATGATTGTTGAGA
1 ACTAAGGTGCATGACTATTGCGAAGTTTATTACAAAAATGCCGCTAAGGTGCATGACTGTTGGGC
*
1263926 AGTTTATTACAAAAATGCC
66 A-TTTATTACAAAAACGCC
* ** *
1263945 ACTAAGGTGCATGACTGTTTTGACA-TTTA-TA-AAAAATGCCGCTAAGGTGCATGACTATTGCG
1 ACTAAGGTGCATGACTATTGCGA-AGTTTATTACAAAAATGCCGCTAAGGTGCATGACTGTTG-G
1264007 GCATTTATTACAAAAAC
64 GCATTTATTACAAAAAC
1264024 ATCACCTAAT
Statistics
Matches: 192, Mismatches: 40, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
80 7 0.04
81 36 0.19
82 76 0.40
83 28 0.15
84 40 0.21
85 5 0.03
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (83 bp):
ACTAAGGTGCATGACTATTGCGAAGTTTATTACAAAAATGCCGCTAAGGTGCATGACTGTTGGGC
ATTTATTACAAAAACGCC
Done.