Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_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: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 15
Found at i:2746600 original size:81 final size:81
Alignment explanation
Indices: 2746464--2747194 Score: 672
Period size: 81 Copynumber: 9.0 Consensus size: 81
2746454 GTGTCTTTGA
* * ** * *
2746464 GGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATTCCAGTTAGATGAACGGTTAAATATCGT
1 GGCCTAGCTGAGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGT
*
2746529 TTAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * *
2746545 GGCCTAGCTGAGCATTTGGCATAAATGTGTCAATTATGCCAGTTAGATGATCGGTTAAATATTGT
1 GGCCTAGCTGAGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGT
*** ** *
2746610 TGAAAGGCTACGTGTCT-TT
66 TG--A-G-TAAAAGAATAAT
* * * ** * * * *** *
2746629 GAGGCCCAACT-ATGTA-TTGATAGAAAGGTGTCAATTATGTCAATTAGATGAATAATTAAATAC
1 --GGCCTAGCTGA-GCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATAT
2746692 CGTTGAGTAAAAGAATAAT
63 CGTTGAGTAAAAGAATAAT
* ** * * * *
2746711 GGGCTAGCTCTGCATTTGGAAGAAA-GATGTCAATTATGCCAGTTAGATGAACGATTAAATACCC
1 GGCCTAGCTGAGCATTTGGCAGAAATG-TGTCAATTATGCCAGTTAGATGAACGGTTAAATATCG
2746775 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
* *** *
2746792 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGTTGGTTAGATGAACGGTTAAATATTGT
1 GGCCTAGCTGAGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGT
2746857 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * ** * *
2746873 GGCCTAGATGTGCATTTACCAGAAATGTGTCAATTATGCCAGTTAGAGGAACGGTTAAATACCGT
1 GGCCTAGCTGAGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGT
2746938 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* *
2746954 GGCCGAGCTTAGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-CTG
1 GGCCTAGCTGAGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATC-G
2747018 TTGAGTAAAAG-ATGAAT
65 TTGAGTAAAAGAAT-AAT
** * ** * * *
2747035 GGCCTAGCT-ATGCATTTCACAGAAAGGTGTCAATTATGATAGTTAGATGAACGATTAAACATTG
1 GGCCTAGCTGA-GCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATCG
2747099 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
* * ** * * * * *
2747116 GGACTAGTTGTA-CATTTGATAGAAA-GTGTCAAATATGCAAATTAGATGAAAGGATAAATA-CA
1 GGCCTAGCTG-AGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATC-
* *
2747178 TTTGGGTAAAAGAATAA
64 GTTGAGTAAAAGAATAA
2747195 AGGAATTATA
Statistics
Matches: 531, Mismatches: 99, Indels: 41
0.79 0.15 0.06
Matches are distributed among these distances:
80 55 0.10
81 412 0.78
82 5 0.01
83 3 0.01
84 2 0.00
85 45 0.08
86 9 0.02
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (81 bp):
GGCCTAGCTGAGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGT
TGAGTAAAAGAATAAT
Found at i:2747015 original size:243 final size:240
Alignment explanation
Indices: 2746474--2747194 Score: 815
Period size: 243 Copynumber: 3.0 Consensus size: 240
2746464 GGCCTAACTG
* * *
2746474 TGCATTT-GATAGAAAGGTGTCAATTATTCCAGTTAGATGAACGGTTAAATATCGTTTAGTAAAA
1 TGCATTTGGA-AGAAA-GTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAA
* * ** *
2746538 GAATAATGGCCTAGCTGAGCATTTGGCATAAATGTGTCAATTATGCCAGTTAGATGATCGGTTAA
64 GAATAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGATAGTTAGATGAACGGTTAA
*** ** * * * * *
2746603 ATATTGTTGAAAGGCTACGTGTCT-TTGAGGCCCA-ACTATGTATTGATAGAAAGGTGTCAATTA
129 ATATTGTTG--A-G-TAAAAGAATAAT--GGCCTAGA-TGTGCATTTATAGAAA-GTGTCAATTA
* * * *
2746666 TGTCAATTAGATGAATA-ATTAAATACCGTTGAGTAAAAGAATAATGGGCTAGCTC
186 TGCCAATTAGATGAA-AGGTTAAATACCGTTGAGTAAAAGAATAATGGCCGAGCTC
* *
2746721 TGCATTTGGAAGAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAATACCCTTGAGTAAAAG
1 TGCATTTGGAAGAAAG-TGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAG
* *
2746786 AATAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGTTGGTTAGATGAACGGTTAAA
65 AATAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGATAGTTAGATGAACGGTTAAA
* *
2746851 TATTGTTGAGTAAAAGAATAATGGCCTAGATGTGCATTTACCAGAAATGTGTCAATTATGCCAGT
130 TATTGTTGAGTAAAAGAATAATGGCCTAGATGTGCATTTA-TAGAAA-GTGTCAATTATGCCAAT
* *
2746916 TAGAGGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCCGAGCT-
193 TAGATGAAAGGTTAAATACCGTTGAGTAAAAGAATAATGGCCGAGCTC
* *
2746963 TAGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACTGTTGAGTAAAA
1 T-GCATTTGGAAGAAA-GTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAA
* ** * *
2747028 G-ATGAATGGCCTAGCTATGCATTTCACAGAAAGGTGTCAATTATGATAGTTAGATGAACGATTA
64 GAAT-AATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGATAGTTAGATGAACGGTTA
* * * * * *
2747092 AACATTGTTGAGTAAAAGAATAATGGACTAGTTGTACATTTGATAGAAAGTGTCAAATATGCAAA
128 AATATTGTTGAGTAAAAGAATAATGGCCTAGATGTGCATTT-ATAGAAAGTGTCAATTATGCCAA
* ** *
2747157 TTAGATGAAAGGATAAATACATTTGGGTAAAAGAATAA
192 TTAGATGAAAGGTTAAATACCGTTGAGTAAAAGAATAA
2747195 AGGAATTATA
Statistics
Matches: 409, Mismatches: 55, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
242 60 0.15
243 219 0.54
244 4 0.01
245 1 0.00
246 1 0.00
247 122 0.30
248 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (240 bp):
TGCATTTGGAAGAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGA
ATAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGATAGTTAGATGAACGGTTAAAT
ATTGTTGAGTAAAAGAATAATGGCCTAGATGTGCATTTATAGAAAGTGTCAATTATGCCAATTAG
ATGAAAGGTTAAATACCGTTGAGTAAAAGAATAATGGCCGAGCTC
Found at i:2749672 original size:22 final size:23
Alignment explanation
Indices: 2749625--2749674 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2749615 AAATAGTAAG
* *
2749625 TAAAAAAAATAATAAAATATATA
1 TAAAAAAAAAAAGAAAATATATA
2749648 TAAAAAAGAAAAAGAAAATA-A-A
1 TAAAAAA-AAAAAGAAAATATATA
2749670 TAAAA
1 TAAAA
2749675 CAAATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 8 0.33
24 10 0.42
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (23 bp):
TAAAAAAAAAAAGAAAATATATA
Found at i:2749700 original size:14 final size:14
Alignment explanation
Indices: 2749681--2749710 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2749671 AAAACAAATA
2749681 AACAAAGTAAGAAT
1 AACAAAGTAAGAAT
2749695 AACAAAGTAAGAAT
1 AACAAAGTAAGAAT
2749709 AA
1 AA
2749711 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (14 bp):
AACAAAGTAAGAAT
Found at i:2749741 original size:12 final size:11
Alignment explanation
Indices: 2749628--2749743 Score: 51
Period size: 11 Copynumber: 10.1 Consensus size: 11
2749618 TAGTAAGTAA
2749628 AAAAAAT-AAT
1 AAAAAATAAAT
* *
2749638 AAAATATATAT
1 AAAAAATAAAT
*
2749649 AAAAAAGAAA-
1 AAAAAATAAAT
2749659 AAGAAAATAAAT
1 AA-AAAATAAAT
*
2749671 --AAAACAAAT
1 AAAAAATAAAT
2749680 AAACAAAGTAAGAAT
1 AAA-AAA-T-A-AAT
*
2749695 AACAAAGTAAGAAT
1 AA-AAAAT-A-AAT
* * *
2749709 AATATATATAT
1 AAAAAATAAAT
2749720 AAAAAATAAAT
1 AAAAAATAAAT
2749731 AAAAAAGTAAAT
1 AAAAAA-TAAAT
2749743 A
1 A
2749744 TATATAAATT
Statistics
Matches: 79, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
9 8 0.10
10 8 0.10
11 33 0.42
12 10 0.13
13 2 0.03
14 10 0.13
15 7 0.09
16 1 0.01
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:2750258 original size:12 final size:11
Alignment explanation
Indices: 2750230--2750270 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2750220 TTACAAAATA
* *
2750230 AATAATATAAA
1 AATAATACAAG
2750241 AATAATACAAG
1 AATAATACAAG
2750252 TAATAATACAAG
1 -AATAATACAAG
2750264 AATAATA
1 AATAATA
2750271 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:2751018 original size:37 final size:37
Alignment explanation
Indices: 2750977--2751073 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
2750967 GGATCATATC
* *
2750977 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTATT
* * *
2751014 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTATT
*
2751051 TTTATGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
2751074 GACGAAAAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTATT
Found at i:2752293 original size:106 final size:106
Alignment explanation
Indices: 2751804--2752964 Score: 1524
Period size: 106 Copynumber: 11.0 Consensus size: 106
2751794 GAATTGTTCC
* * **
2751804 GAGTCCAATATTCTCCG-TCGTGAAGTTGAAATTGGCTCTTG-AACCGGGAAATT-TTTGTTGAC
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTC-TGAAATTGGGAAATTGTTTGTTGAC
* * *
2751866 AACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
64 AACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2751909 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * * *
2751968 TCAGCCG-CCCTTTCATCTTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * * *
2752010 G-GTCCAAGATCCGTCGCTGAGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTATTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
2752074 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTTTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2752115 GAGT-CAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTAAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
2752179 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2752220 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
2752285 CAAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2752326 GAGTCCAATATCCTTCGCTGTGAAGTTCAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
2752391 CCAGCGTTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2752432 GAGTCCAATATCCTTGGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
2752497 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
2752538 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGTGAAGTTGTTTGTTTACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
2752603 CCAGCGGTCCCTTTGTCGTGATGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2752644 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATT-GGAAAGTTGTTTATTAACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
* ** *
2752708 ACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGTATTATCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2752750 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
2752815 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
2752856 GAGTCCAATATCCTTCGCTGTGAATTTGAAATTGGCTCCGAAATTGGAAAATT-ATTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
2752920 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2752961 GAGT
1 GAGT
2752965 GGCACGATAT
Statistics
Matches: 928, Mismatches: 113, Indels: 30
0.87 0.11 0.03
Matches are distributed among these distances:
99 4 0.00
100 73 0.08
101 8 0.01
102 1 0.00
104 7 0.01
105 178 0.19
106 649 0.70
107 8 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2753580 original size:23 final size:22
Alignment explanation
Indices: 2753522--2753584 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
2753512 TTTTATTTTC
*
2753522 AAAGTTCTGAAAATA-TCAATA
1 AAAGTTTTGAAAATATTCAATA
* *
2753543 AAGAGTTTCGAAAAATATTTAATCA
1 AA-AGTTTTG-AAAATATTCAAT-A
2753568 AAAGTTTTGAAAATATT
1 AAAGTTTTGAAAATATT
2753585 GTCTCTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.06
22 5 0.15
23 14 0.41
24 10 0.29
25 3 0.09
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.33
Consensus pattern (22 bp):
AAAGTTTTGAAAATATTCAATA
Found at i:2753796 original size:22 final size:22
Alignment explanation
Indices: 2753770--2753845 Score: 152
Period size: 22 Copynumber: 3.5 Consensus size: 22
2753760 TTGTGTTTGG
2753770 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
2753792 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
2753814 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
2753836 TCAAAGGTTT
1 TCAAAGGTTT
2753846 TATGGGGTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:2754480 original size:14 final size:14
Alignment explanation
Indices: 2754463--2754513 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
2754453 TTCTTTTTGA
2754463 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
*
2754477 TTTTTTTTC-TTCT
1 TTTTTGTTCTTTCT
2754490 TTTTTGTTTCTTTTCT
1 TTTTTG-TTC-TTTCT
2754506 TTTTTGTT
1 TTTTTGTT
2754514 TTTGCCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 9 0.28
14 11 0.34
15 2 0.06
16 10 0.31
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:2754507 original size:16 final size:15
Alignment explanation
Indices: 2754463--2754514 Score: 74
Period size: 16 Copynumber: 3.6 Consensus size: 15
2754453 TTCTTTTTGA
2754463 TTTTTG-TTCTTTCT
1 TTTTTGTTTCTTTCT
2754477 TTTTT-TTTC-TTCT
1 TTTTTGTTTCTTTCT
2754490 TTTTTGTTTCTTTTCT
1 TTTTTGTTTC-TTTCT
2754506 TTTTTGTTT
1 TTTTTGTTT
2754515 TTGCCCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.26
14 12 0.35
16 13 0.38
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.83
Consensus pattern (15 bp):
TTTTTGTTTCTTTCT
Found at i:2759606 original size:27 final size:28
Alignment explanation
Indices: 2759576--2759628 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
2759566 AAGAGAAAGT
2759576 AAAAATATATAATA-ATAATA-AAATATA
1 AAAAATATA-AATATATAATATAAATATA
*
2759603 AAAAATATACATATATAATATAAATA
1 AAAAATATAAATATATAATATAAATA
2759629 AGTAGAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 15 0.65
28 5 0.22
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAATATAAATATATAATATAAATATA
Found at i:2760297 original size:37 final size:37
Alignment explanation
Indices: 2760256--2760358 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
2760246 GTGCTTGTGG
* * * * *
2760256 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGTAAAACTCT
* *
2760293 ATCCTATTTTTAAGAGTTTGAATCCTAGGAAAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGTAAAACTCT
*
2760330 AT-CTATTTTTATGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAAGAGTTTGAATCCTAGTA
2760359 TGACGAAAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
36 25 0.44
37 32 0.56
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTGAATCCTAGTAAAACTCT
Found at i:2762432 original size:24 final size:21
Alignment explanation
Indices: 2762398--2762440 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2762388 TCCACAAGAC
*
2762398 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
2762420 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
2762441 AGAATATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:2765983 original size:16 final size:16
Alignment explanation
Indices: 2765951--2765995 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2765941 AAAAAGAAGT
2765951 ATTGAAAGAAATGGAA
1 ATTGAAAGAAATGGAA
*
2765967 ATTGATAAGGAAT-GAA
1 ATTGA-AAGAAATGGAA
*
2765983 ATGGAAAGAAATG
1 ATTGAAAGAAATG
2765996 ATATCAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (16 bp):
ATTGAAAGAAATGGAA
Found at i:2766232 original size:35 final size:34
Alignment explanation
Indices: 2766129--2766232 Score: 147
Period size: 34 Copynumber: 3.0 Consensus size: 34
2766119 TGGTAAGGGA
* *
2766129 ATGGTGATTATATTGCCGTGAATGGTGATAGAAG
1 ATGGTGATTATATAGGCGTGAATGGTGATAGAAG
*
2766163 ATGGTGATTATATAGGCATGAATGGTGATAGAAG
1 ATGGTGATTATATAGGCGTGAATGGTGATAGAAG
*
2766197 ATGGTGATGT-TATAGGCGTGAAATGGTGATGGAAG
1 ATGGTGAT-TATATAGGCGTG-AATGGTGATAGAAG
2766232 A
1 A
2766233 CGGCGATGGA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 48 0.76
35 15 0.24
ACGTcount: A:0.32, C:0.04, G:0.35, T:0.30
Consensus pattern (34 bp):
ATGGTGATTATATAGGCGTGAATGGTGATAGAAG
Found at i:2777416 original size:26 final size:26
Alignment explanation
Indices: 2777380--2777439 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
2777370 CCTTGTTGTC
2777380 ATGTTTGATTTATAGTAATGTGAGCT
1 ATGTTTGATTTATAGTAATGTGAGCT
2777406 ATGTTTGATTTATAGTAATGTGAGCT
1 ATGTTTGATTTATAGTAATGTGAGCT
*
2777432 AAGTTTGA
1 ATGTTTGA
2777440 AGGCCATGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.45
Consensus pattern (26 bp):
ATGTTTGATTTATAGTAATGTGAGCT
Found at i:2789219 original size:2 final size:2
Alignment explanation
Indices: 2789212--2789236 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2789202 TTAGAAAACA
2789212 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2789237 AAAGAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2796490 original size:14 final size:14
Alignment explanation
Indices: 2796471--2796498 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2796461 TAAGATACTA
2796471 TTTCCATCACCATC
1 TTTCCATCACCATC
2796485 TTTCCATCACCATC
1 TTTCCATCACCATC
2796499 AATCCTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:2806452 original size:76 final size:74
Alignment explanation
Indices: 2806349--2806851 Score: 593
Period size: 76 Copynumber: 6.7 Consensus size: 74
2806339 TCGGTTTCTT
*
2806349 AAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAACTGATATAATATATAGTTTTTTT
1 AAAA-ATATATATAATATATAGTTTTTAAAACATTTTGAAAA-TTATATAATATATAG-TTTTTT
2806414 AAAACA-TTTTG
63 AAAACATTTTTG
2806425 AAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTTTA
1 -AAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAA-TTATATAATATATAGTTTTTTA
2806490 AAACATTTTTG
64 AAACATTTTTG
*
2806501 AAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATTTAATATATAG-TTTTTA
1 -AAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAA-TTATATAATATATAGTTTTTTA
2806565 AAA-ATATTTTG
64 AAACAT-TTTTG
*
2806576 -AATATATATATAATATATA-TAATTTTAAAACATTTTGAAAAAATATATATAATATATAG-TTT
1 AAAAATATATATAATATATAGT--TTTTAAAACATTTTG--AAAAT-TATATAATATATAGTTTT
2806638 TTAAAACA-TTTTG
61 TTAAAACATTTTTG
* *
2806651 AAAACT-TATATAATATATAGTTTTTAAAATATTTTGAAAATATATATATATAATATA-TAGTTT
1 AAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAAT-TATATA-AT-ATATAGT--TTT
2806714 TTAAAACATTTTTG
61 TTAAAACATTTTTG
* * ** *
2806728 -AAAATATATATAATATATAGTTTTAAAAACATTTTTAAAAAAATATAATAAATAG--TTTTAAA
1 AAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAATTATATAATATATAGTTTTTTAAA
*
2806790 ATATTTTTG
66 ACATTTTTG
* ** * *
2806799 -AAAATATATATATTATATAGTTTTGGAAATATTTTTGAAAA-TGTATAATATAT
1 AAAAATATATATAATATATAGTTTTTAAAACA-TTTTGAAAATTATATAATATAT
2806852 TATTATTATT
Statistics
Matches: 384, Mismatches: 23, Indels: 44
0.85 0.05 0.10
Matches are distributed among these distances:
71 51 0.13
72 21 0.05
73 20 0.05
74 40 0.10
75 47 0.12
76 164 0.43
77 41 0.11
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (74 bp):
AAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAATTATATAATATATAGTTTTTTAAA
ACATTTTTG
Found at i:2806473 original size:112 final size:109
Alignment explanation
Indices: 2806354--2806845 Score: 629
Period size: 112 Copynumber: 4.4 Consensus size: 109
2806344 TTCTTAAAAT
*
2806354 ATATATATAATATATAGTTTTTAAAACA-TTTTGAAAACT-GATATAATATATAGTTTTTTTAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTGAAAA-TATATATAATATATAG--TTTTTAAA
*
2806417 ACATTTTGAAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAA
63 ACATTTTG-AAAAAT-TATATAATATATAGTTTTTAAAATATTTTGAAA
2806466 ACT-TATATAATATATAGTTTTTTAAAACATTTTTGAAAAAATATATATAATATATAGTTTTTAA
1 A-TATATATAATATATAG-TTTTTAAAACATTTTTG--AAAATATATATAATATATAGTTTTTAA
* * *
2806530 AACATTTTGAAAACTTATTTAATATATAGTTTTTAAAAATATTTTGAAT
62 AACATTTTGAAAAATTATATAATATATAGTTTTT-AAAATATTTTGAAA
2806579 ATATATATAATATATA-TAATTTTAAAACA-TTTTGAAAAAATATATATAATATATAGTTTTTAA
1 ATATATATAATATATAGT--TTTTAAAACATTTTTG--AAAATATATATAATATATAGTTTTTAA
*
2806642 AACATTTTGAAAACTTATATAATATATAGTTTTTAAAATATTTTGAAAATA
62 AACATTTTGAAAAATTATATAATATATAGTTTTTAAAATATTTTG--AA-A
*
2806693 TATATATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATAATATATAGTTTTAAAAAC
1 -ATATATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATAATATATAGTTTTTAAAAC
* * *
2806758 ATTTTTAAAAA-AATATAATAAATAG-TTTTAAAATATTTTTGAAA
65 ATTTTGAAAAATTATATAATATATAGTTTTTAAAATA-TTTTGAAA
* ** * *
2806802 ATATATATATTATATAGTTTTGGAAATATTTTTGAAAATGTATA
1 ATATATATAATATATAGTTTTTAAAACATTTTTGAAAATATATA
2806846 ATATATTATT
Statistics
Matches: 346, Mismatches: 17, Indels: 38
0.86 0.04 0.09
Matches are distributed among these distances:
108 39 0.11
109 1 0.00
110 2 0.01
111 22 0.06
112 118 0.34
113 93 0.27
114 31 0.09
115 22 0.06
116 18 0.05
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (109 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATAATATATAGTTTTTAAAACA
TTTTGAAAAATTATATAATATATAGTTTTTAAAATATTTTGAAA
Found at i:2806604 original size:188 final size:187
Alignment explanation
Indices: 2806354--2806822 Score: 688
Period size: 188 Copynumber: 2.5 Consensus size: 187
2806344 TTCTTAAAAT
**
2806354 ATATATATAATATATAGTTTTT-AAAACATTTTGAAAACTGATATAATATATAGTTTTTTTAAAA
1 ATATATATAATATATAGTTTTTAAAAACATTTTGAAAA-T-ATATAATATATA-TAATTTTAAAA
2806418 CATTTTGAAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAG
63 CATTTTGAAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAG
2806483 TTTTTTAAAACATTTTTGAAAA-A-ATATATATAATATATAGTTTTTAAAACA-TTTTGAAA
128 -TTTTTAAAACA-TTTTGAAAATATATATATATAATATATAGTTTTTAAAACATTTTTGAAA
* *
2806542 ACT-TATTTAATATATAGTTTTTAAAAATATTTTGAATATATATATAATATATATAATTTTAAAA
1 A-TATATATAATATATAGTTTTTAAAAACATTTTGAA-A-ATATATAATATATATAATTTTAAAA
2806606 CATTTTGAAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAG
63 CATTTTGAAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAG
*
2806671 TTTTTAAAATATTTTGAAAATATATATATATAATATATAGTTTTTAAAACATTTTTGAAA
128 TTTTTAAAACATTTTGAAAATATATATATATAATATATAGTTTTTAAAACATTTTTGAAA
* * * *
2806731 ATATATATAATATATAG-TTTTAAAAACATTTTTAAAAAAATATAATA-A-ATAGTTTTAAAATA
1 ATATATATAATATATAGTTTTTAAAAACA-TTTTGAAAATATATAATATATATAATTTTAAAACA
*
2806793 TTTTTG--AAAATATATATATTATATAGTTTT
65 -TTTTGAAAAAATATATATAATATATAGTTTT
2806823 GGAAATATTT
Statistics
Matches: 259, Mismatches: 12, Indels: 24
0.88 0.04 0.08
Matches are distributed among these distances:
184 23 0.09
185 12 0.05
186 15 0.06
187 20 0.08
188 133 0.51
189 53 0.20
190 2 0.01
191 1 0.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (187 bp):
ATATATATAATATATAGTTTTTAAAAACATTTTGAAAATATATAATATATATAATTTTAAAACAT
TTTGAAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTT
TTAAAACATTTTGAAAATATATATATATAATATATAGTTTTTAAAACATTTTTGAAA
Found at i:2806888 original size:27 final size:28
Alignment explanation
Indices: 2806857--2806910 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
2806847 TATATTATTA
*
2806857 TTATTATTATTCATTTTT-TTTTATTTT
1 TTATTATTATTAATTTTTATTTTATTTT
*
2806884 TTATTTTTATTAATTTTTATTTTATTT
1 TTATTATTATTAATTTTTATTTTATTT
2806911 ATTTTCAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (28 bp):
TTATTATTATTAATTTTTATTTTATTTT
Found at i:2806900 original size:16 final size:16
Alignment explanation
Indices: 2806871--2806915 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
2806861 TATTATTCAT
* *
2806871 TTTTTTTTATTTTTTA
1 TTTTTATTAATTTTTA
2806887 TTTTTATTAATTTTTA
1 TTTTTATTAATTTTTA
*
2806903 -TTTTATTTATTTT
1 TTTTTATTAATTTT
2806916 CAGGTCCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTATTAATTTTTA
Found at i:2806906 original size:33 final size:32
Alignment explanation
Indices: 2806851--2806915 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
2806841 GTATAATATA
*
2806851 TTATTATTATTATTATTCATTTTTTTTTATTTT
1 TTATTATTATTATTATTCA-TTTTATTTATTTT
* *
2806884 TTATTTTTATTAATT-TTTATTTTATTTATTTT
1 TTATTATTATT-ATTATTCATTTTATTTATTTT
2806916 CAGGTCCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 12 0.43
33 13 0.46
34 3 0.11
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (32 bp):
TTATTATTATTATTATTCATTTTATTTATTTT
Found at i:2807176 original size:21 final size:21
Alignment explanation
Indices: 2807150--2807190 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2807140 CAGAAAGACC
*
2807150 TCGAAATATCCGGGATCGACG
1 TCGAAATATCCAGGATCGACG
2807171 TCGAAATATCCAGGATCGAC
1 TCGAAATATCCAGGATCGAC
2807191 CCCCAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
TCGAAATATCCAGGATCGACG
Found at i:2810727 original size:17 final size:17
Alignment explanation
Indices: 2810686--2810731 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
2810676 TGGTCAAAGT
2810686 AACGGTCAACGGTGGTC
1 AACGGTCAACGGTGGTC
** *
2810703 AATAGTCAATGGTGGTC
1 AACGGTCAACGGTGGTC
2810720 AACGGTCAACGG
1 AACGGTCAACGG
2810732 CTCATTCAGC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (17 bp):
AACGGTCAACGGTGGTC
Found at i:2810823 original size:10 final size:10
Alignment explanation
Indices: 2810791--2810829 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2810781 GTGGCTCGGC
2810791 TCAGACCGGT
1 TCAGACCGGT
* *
2810801 CCAG-CCGGC
1 TCAGACCGGT
2810810 TCAGACCGGT
1 TCAGACCGGT
2810820 TCAGACCGGT
1 TCAGACCGGT
2810830 CCTACCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:2814963 original size:18 final size:18
Alignment explanation
Indices: 2814940--2814996 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
2814930 CATTCGGATT
*
2814940 GGCACGGTTCGATGACTC
1 GGCACGGTGCGATGACTC
* *
2814958 GGCACGGCGCGGTGACTC
1 GGCACGGTGCGATGACTC
* *
2814976 GGCTCGGTAGC-TTGACTC
1 GGCACGGT-GCGATGACTC
2814994 GGC
1 GGC
2814997 GGCTCGACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 30 0.94
19 2 0.06
ACGTcount: A:0.12, C:0.30, G:0.39, T:0.19
Consensus pattern (18 bp):
GGCACGGTGCGATGACTC
Found at i:2818093 original size:65 final size:64
Alignment explanation
Indices: 2818015--2818174 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 64
2818005 GAATAAATTG
*
2818015 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCAATGCACTCAGGAT-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACA-AGCCATGCATCAATGCACTCAGGATATTT-TG
2818078 AA
64 -A
* * * *
2818080 AACATC-AAGTGCATTTGATGCATCGATGCACAAGCCATGTATCAATGCACTCTGGCTATTTTGA
1 AACATCGAA-TGCATTTCATGCATCGATGCACAAGCCATGCATCAATGCACTCAGGATATTTTGA
*
2818144 AACGTCGAATGCATTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
2818175 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
64 30 0.35
65 52 0.61
66 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCAATGCACTCAGGATATTTTGA
Found at i:2828738 original size:3 final size:3
Alignment explanation
Indices: 2828732--2828797 Score: 107
Period size: 3 Copynumber: 21.7 Consensus size: 3
2828722 TTTTTCATCA
2828732 TAT TAT TAT TAT TAT TAT TAT TAT ATAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT TAT
2828779 TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
2828798 AATAAAAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 52 0.85
4 7 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2828766 original size:20 final size:19
Alignment explanation
Indices: 2828732--2828797 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 19
2828722 TTTTTCATCA
2828732 TATTATTAT-TATTATTAT
1 TATTATTATATATTATTAT
2828750 TATTATATATATATTATTAT
1 TATTAT-TATATATTATTAT
2828770 TATTATTATTATATTATTAT
1 TATTATTA-TATATTATTAT
2828790 TATTATTA
1 TATTATTA
2828798 AATAAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.13
19 5 0.11
20 34 0.76
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTATTATATATTATTAT
Found at i:2829309 original size:14 final size:14
Alignment explanation
Indices: 2829290--2829316 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2829280 TGTGATGTGG
2829290 TATATTATATATAA
1 TATATTATATATAA
2829304 TATATTATATATA
1 TATATTATATATA
2829317 TTAAACTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTATATATAA
Found at i:2832721 original size:22 final size:23
Alignment explanation
Indices: 2832696--2832760 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 23
2832686 TGCATTCGTA
2832696 TTTTTTTCATTACATTTGCATTT
1 TTTTTTTCATTACATTTGCATTT
* *
2832719 TTTTATGT--TTGCATTTGCATTT
1 TTTT-TTTCATTACATTTGCATTT
2832741 TTATATTTTCATTTACATTT
1 TT-T-TTTTCA-TTACATTT
2832761 TATATTTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
22 15 0.47
23 7 0.22
24 3 0.09
26 7 0.22
ACGTcount: A:0.18, C:0.11, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTTTTTCATTACATTTGCATTT
Found at i:2832741 original size:20 final size:20
Alignment explanation
Indices: 2832708--2832768 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
2832698 TTTTTCATTA
*
2832708 CATTTGCATTTTTTTATGTTTG
1 CATTTGCA--TTTTTATATTTG
*
2832730 CATTTGCATTTTTATATTTT
1 CATTTGCATTTTTATATTTG
*
2832750 CATTTACA-TTTTATATTTG
1 CATTTGCATTTTTATATTTG
2832769 TATCTTTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.29
20 17 0.49
22 8 0.23
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.62
Consensus pattern (20 bp):
CATTTGCATTTTTATATTTG
Found at i:2832814 original size:22 final size:22
Alignment explanation
Indices: 2832789--2832830 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2832779 TTGCACAGTT
* *
2832789 TGCATTCTTATTTTTTCATTTA
1 TGCATTCTTATATTTACATTTA
*
2832811 TGCATTTTTATATTTACATT
1 TGCATTCTTATATTTACATT
2832831 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.62
Consensus pattern (22 bp):
TGCATTCTTATATTTACATTTA
Found at i:2833785 original size:19 final size:18
Alignment explanation
Indices: 2833761--2833797 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2833751 GAAGGAAGTC
*
2833761 GAGAATTTATTGATAAATG
1 GAGAATTAATTGA-AAATG
2833780 GAGAATTAATTGAAAATG
1 GAGAATTAATTGAAAATG
2833798 TGATCAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (18 bp):
GAGAATTAATTGAAAATG
Found at i:2834985 original size:71 final size:72
Alignment explanation
Indices: 2834894--2835027 Score: 243
Period size: 71 Copynumber: 1.9 Consensus size: 72
2834884 ATACAATAAA
2834894 GCTTGAGTTATCCCCCTAAAGAAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTAAT
1 GCTTGAGTTATCCCCCTAAAGAAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTAAT
2834959 CTATTAT
66 CTATTAT
* *
2834966 GCTTGAGTTA-CCCCCTAAAGCAATTGGTTAATCGCCCCGGCTTTATGGATAATATTCAGCTA
1 GCTTGAGTTATCCCCCTAAAGAAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTA
2835028 GCATGTTATA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
71 50 0.83
72 10 0.17
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAGAAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTAAT
CTATTAT
Found at i:2838657 original size:22 final size:22
Alignment explanation
Indices: 2838629--2838705 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
2838619 ACATCTATAT
2838629 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
2838651 TCTTCAAAGATGAT--ATTTTC
1 TCTTCAAAGATGATAGATTCTC
2838671 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
2838693 TTTTCAAAGATGA
1 TCTTCAAAGATGA
2838706 AAACTTTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 19 0.38
22 31 0.62
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:2839437 original size:45 final size:45
Alignment explanation
Indices: 2839368--2839798 Score: 632
Period size: 45 Copynumber: 9.6 Consensus size: 45
2839358 CTATTTCCCA
* *
2839368 CATCTGTAAGCCCTTCAGTTCATGATGTTTTCAAAACATTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
2839413 CATCTGTAGGCCCTTCAGTGCATGATATTTTCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
2839458 CATCTGTAAGCCCTTCAGTGCATGATGTTTT-ACAAGCCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCA-AAACCTTCGGGT
2839503 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
2839548 CATCTATAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
2839593 CATCTGTAACCCCTTCAATGCATGATGCTTTCAAAGCCTTC-GGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
2839637 CATCTATAAGCCCTTCAATGCATGATGTTTTCAAAACATTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
2839682 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
2839727 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
2839772 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGCCCTTCAGTGCATGATG
2839799 ATAAGACCTC
Statistics
Matches: 347, Mismatches: 36, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
44 39 0.11
45 307 0.88
46 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:2839710 original size:179 final size:180
Alignment explanation
Indices: 2839368--2839780 Score: 632
Period size: 179 Copynumber: 2.3 Consensus size: 180
2839358 CTATTTCCCA
* * ** *
2839368 CATCTGTAAGCCCTTCAGTTCATGATGTTTTCAAAACATTCGGGTCATCTGTAGGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAACCCCTTCAATG
* * * * *
2839433 CATGATATTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTACAAGCCTT
66 CATGATACTTTCAAAACCTTCGAGTCATCTATAAGCCCTTCAATGCATGATGTTTTACAAACATT
*
2839498 CAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
131 CAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
* *
2839548 CATCTATAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAACCCCTTCAATG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAACCCCTTCAATG
* *
2839613 CATGATGCTTTCAAAGCCTTCG-GTCATCTATAAGCCCTTCAATGCATGATGTTTT-CAAAACAT
66 CATGATACTTTCAAAACCTTCGAGTCATCTATAAGCCCTTCAATGCATGATGTTTTAC-AAACAT
**
2839676 TTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
130 TCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
* *
2839727 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTTCGGGTCATCTGTAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAA
2839781 GACCTACAGT
Statistics
Matches: 211, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
178 1 0.00
179 133 0.63
180 77 0.36
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (180 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAACCCCTTCAATG
CATGATACTTTCAAAACCTTCGAGTCATCTATAAGCCCTTCAATGCATGATGTTTTACAAACATT
CAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
Found at i:2839975 original size:3 final size:3
Alignment explanation
Indices: 2839969--2840049 Score: 83
Period size: 3 Copynumber: 24.7 Consensus size: 3
2839959 TTTTTCATCA
2839969 TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA- TAT ATAT ATAT ATAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT -TAT -TAT -TAT
2840018 ATAT TAT TAT TAT TAT ATAT ATAT TAT TAT TA
1 -TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TA
2840050 AATAAAAAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.03
3 43 0.58
4 29 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2840002 original size:2 final size:2
Alignment explanation
Indices: 2839990--2840041 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
2839980 TTATTATTAT
2839990 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2840028 TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2840042 TATTATTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 5 0.11
2 40 0.89
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2844901 original size:22 final size:19
Alignment explanation
Indices: 2844854--2844920 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 19
2844844 AAAATGGTAC
2844854 CGATACCATAGTAGAGTAT
1 CGATACCATAGTAGAGTAT
2844873 C-AGTACCATAGTATAGAAGTAT
1 CGA-TACCATAG--TAG-AGTAT
* *
2844895 CGATACCATGGTAGGGGTAT
1 CGATACCATAGTA-GAGTAT
2844915 CGATAC
1 CGATAC
2844921 TATGGAGTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 1 0.03
19 9 0.22
20 12 0.30
21 4 0.10
22 13 0.32
23 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (19 bp):
CGATACCATAGTAGAGTAT
Found at i:2850248 original size:21 final size:21
Alignment explanation
Indices: 2850182--2850253 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
2850172 ACTAGCATAG
** *
2850182 TATCGATGTTGCTTCAATGAA
1 TATCGATACTGCTTCAACGAA
*
2850203 TATCGATACT-ATTCTTAAC-AA
1 TATCGATACTGCTTC--AACGAA
*
2850224 TATCGATACTGCTTCAACGAG
1 TATCGATACTGCTTCAACGAA
2850245 TATCGATAC
1 TATCGATAC
2850254 CCTTGTATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 6 0.15
21 30 0.73
22 5 0.12
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
TATCGATACTGCTTCAACGAA
Found at i:2856434 original size:45 final size:45
Alignment explanation
Indices: 2856363--2856450 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
2856353 AAACACAAAG
* * * *
2856363 ATGATTAAAAGCACAAGCTCATATAAAATGGGTTCGAACATAAGC
1 ATGATTAAAACCACAAGCTCACATAAAATGAGTTCAAACATAAGC
*
2856408 ATGATTAAAACCACAAGTTCACATAAAATGAGTTCAAACATAA
1 ATGATTAAAACCACAAGCTCACATAAAATGAGTTCAAACATAA
2856451 AATTAAAGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (45 bp):
ATGATTAAAACCACAAGCTCACATAAAATGAGTTCAAACATAAGC
Found at i:2864693 original size:18 final size:18
Alignment explanation
Indices: 2864670--2864704 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2864660 AATAAAAATA
2864670 TTGTTTTTGATTTAATTG
1 TTGTTTTTGATTTAATTG
2864688 TTGTTTTTGATTTAATT
1 TTGTTTTTGATTTAATT
2864705 ATATTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (18 bp):
TTGTTTTTGATTTAATTG
Found at i:2866623 original size:16 final size:17
Alignment explanation
Indices: 2866602--2866637 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2866592 GAATTTAAAG
2866602 ATTT-TATTCGATTCAA
1 ATTTATATTCGATTCAA
2866618 ATTTTATATTCGATTCAA
1 A-TTTATATTCGATTCAA
2866636 AT
1 AT
2866638 ATTACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.06
17 4 0.22
18 13 0.72
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTATATTCGATTCAA
Found at i:2869624 original size:32 final size:32
Alignment explanation
Indices: 2869525--2869623 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 32
2869515 ATTCAATATG
2869525 AATTCAAATTTATATGAAACATTTTGAATCAC
1 AATTCAAATTTATATGAAACATTTTGAATCAC
* * * * * * *
2869557 AATTCAAAATCA-AAGCATCCTTTTG-A--AG
1 AATTCAAATTTATATGAAACATTTTGAATCAC
* *
2869585 AATTCAACTTTATATGTAACATTTTGAATCAC
1 AATTCAAATTTATATGAAACATTTTGAATCAC
2869617 AATTCAA
1 AATTCAA
2869624 CACTCTTAAT
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
28 10 0.21
29 9 0.19
30 2 0.04
31 9 0.19
32 18 0.38
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (32 bp):
AATTCAAATTTATATGAAACATTTTGAATCAC
Found at i:2869819 original size:44 final size:45
Alignment explanation
Indices: 2869749--2869835 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
2869739 AAACACAAAG
* *
2869749 ATGATTAAAAGCACAAGCTCATATAAAATGGGTTC-AACATAAGC
1 ATGATTAAAAGCACAAGCTCACATAAAATGAGTTCAAACATAAGC
*
2869793 ATGATTAAAA-CTACAAGTTCACATAAAATGAGTTCAAACATAA
1 ATGATTAAAAGC-ACAAGCTCACATAAAATGAGTTCAAACATAA
2869836 AATTAAAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 1 0.03
44 30 0.79
45 7 0.18
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (45 bp):
ATGATTAAAAGCACAAGCTCACATAAAATGAGTTCAAACATAAGC
Found at i:2870938 original size:17 final size:17
Alignment explanation
Indices: 2870913--2870947 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2870903 CTTTGTCTCA
* *
2870913 TTCTTCTTCCTTTTCTT
1 TTCTCCTTCATTTTCTT
2870930 TTCTCCTTCATTTTCTT
1 TTCTCCTTCATTTTCTT
2870947 T
1 T
2870948 ACCATTCCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTCCTTCATTTTCTT
Found at i:2875734 original size:22 final size:22
Alignment explanation
Indices: 2875704--2875745 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2875694 CAGTTCTAAG
2875704 GCACATTAGTATTAATGCAAAT
1 GCACATTAGTATTAATGCAAAT
* *
2875726 GCACTTTAGTATTAGTGCAA
1 GCACATTAGTATTAATGCAA
2875746 GGCACTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (22 bp):
GCACATTAGTATTAATGCAAAT
Found at i:2881439 original size:22 final size:21
Alignment explanation
Indices: 2881414--2881462 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2881404 AGGCACATTA
* *
2881414 GTATTAATGCAAATGCACTTTT
1 GTATTAATGC-AAGGCACTTCT
*
2881436 GTATTAGTGCAAGGCACTTCT
1 GTATTAATGCAAGGCACTTCT
2881457 GTATTA
1 GTATTA
2881463 CTTTTAAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (21 bp):
GTATTAATGCAAGGCACTTCT
Found at i:2881454 original size:21 final size:22
Alignment explanation
Indices: 2881403--2881462 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
2881393 AATCAGTTAT
* *
2881403 AAGGCACATTAGTATTAATGCA
1 AAGGCACTTTTGTATTAATGCA
* *
2881425 AATGCACTTTTGTATTAGTGC-
1 AAGGCACTTTTGTATTAATGCA
*
2881446 AAGGCACTTCTGTATTA
1 AAGGCACTTTTGTATTA
2881463 CTTTTAAGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (22 bp):
AAGGCACTTTTGTATTAATGCA
Found at i:2888104 original size:22 final size:21
Alignment explanation
Indices: 2888067--2888124 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
2888057 TATTTTTTTT
2888067 AAAAAAAAAAGCAAAAAAAGC
1 AAAAAAAAAAGCAAAAAAAGC
*
2888088 AAAACAAAAAA-CAAAAAAA-A
1 AAAA-AAAAAAGCAAAAAAAGC
*
2888108 AAAAAAAAAAGCCAAAA
1 AAAAAAAAAAGCAAAAA
2888125 TTTCAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 12 0.36
22 6 0.18
ACGTcount: A:0.84, C:0.10, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAGCAAAAAAAGC
Found at i:2892790 original size:15 final size:15
Alignment explanation
Indices: 2892770--2892801 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2892760 TCAAAAAAAC
*
2892770 AAAAAAAAAAGGCAA
1 AAAAAAAAAAGCCAA
2892785 AAAAAAAAAAGCCAA
1 AAAAAAAAAAGCCAA
2892800 AA
1 AA
2892802 TTTCAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGCCAA
Found at i:2897616 original size:22 final size:22
Alignment explanation
Indices: 2897586--2897627 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2897576 CAGTTCTAAG
2897586 GCACATTAGTATTAATGCAAAT
1 GCACATTAGTATTAATGCAAAT
* *
2897608 GCACTTTAGTATTAGTGCAA
1 GCACATTAGTATTAATGCAA
2897628 GGCACTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (22 bp):
GCACATTAGTATTAATGCAAAT
Found at i:2903300 original size:22 final size:22
Alignment explanation
Indices: 2903270--2903311 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2903260 CAGTTCTAAG
2903270 GCACATTAGTATTAATGCAAAT
1 GCACATTAGTATTAATGCAAAT
* *
2903292 GCACTTTAGTATTAGTGCAA
1 GCACATTAGTATTAATGCAA
2903312 GGCACTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (22 bp):
GCACATTAGTATTAATGCAAAT
Found at i:2918522 original size:22 final size:22
Alignment explanation
Indices: 2918464--2918523 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2918454 AAATCCAAGC
* *
2918464 AGTGCTAAGGCACTTTAGTATT
1 AGTGCTAAGGCACTTCAGTATA
* * *
2918486 AGTGCAAATGCACTTCATTATA
1 AGTGCTAAGGCACTTCAGTATA
*
2918508 AGTGCTAAGGAACTTC
1 AGTGCTAAGGCACTTC
2918524 TGTACTAGTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (22 bp):
AGTGCTAAGGCACTTCAGTATA
Found at i:2921204 original size:24 final size:24
Alignment explanation
Indices: 2921187--2921305 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 24
2921177 ATCAAAACAT
2921187 AAAT-CAGGTCAAGTATCATATCA
1 AAATCCAGGTCAAGTATCATATCA
2921210 AAATCCAGGTCAAGTATCATATCA
1 AAATCCAGGTCAAGTATCATATCA
* *
2921234 AAATCCAAGTCAAGTATCAGATCA
1 AAATCCAGGTCAAGTATCATATCA
* **
2921258 GAATCCATCTC-AGATATCATATCA
1 AAATCCAGGTCAAG-TATCATATCA
* **
2921282 TAATCCATATCAAGTATCATATCA
1 AAATCCAGGTCAAGTATCATATCA
2921306 GAATTCAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
23 6 0.07
24 77 0.91
25 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (24 bp):
AAATCCAGGTCAAGTATCATATCA
Found at i:2923133 original size:36 final size:36
Alignment explanation
Indices: 2923086--2923158 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
2923076 GATAAGTTAT
*
2923086 AATCTACATATCCGTGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
*
2923122 AATCTATATATCCATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
2923158 A
1 A
2923159 TTCCAGAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (36 bp):
AATCTACATATCCATGGTTGATTCTTTTATCACTTA
Found at i:2925030 original size:13 final size:13
Alignment explanation
Indices: 2925012--2925036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2925002 TACTCACTAG
2925012 AAATATAGTTTCC
1 AAATATAGTTTCC
2925025 AAATATAGTTTC
1 AAATATAGTTTC
2925037 ATTACTCACT
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:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
AAATATAGTTTCC
Found at i:2925038 original size:37 final size:36
Alignment explanation
Indices: 2924996--2925065 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
2924986 TTAAATTTAT
2924996 TTTCATTACTCACTAGAAATATAGTTTCCAAATATAG
1 TTTCATTACTCACTAGAAATATA-TTTCCAAATATAG
* *
2925033 TTTCATTACTCACTGGAAATATATTTCCCAATA
1 TTTCATTACTCACTAGAAATATATTTCCAAATA
2925066 ATTTTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (36 bp):
TTTCATTACTCACTAGAAATATATTTCCAAATATAG
Found at i:2930553 original size:35 final size:35
Alignment explanation
Indices: 2930503--2930570 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2930493 ACCTTGTTTC
*
2930503 TGTAGAAATAGAGTTTTTCGATTCTGGTAAACAAA
1 TGTAGAAATAGAGTTTTTCGATTCTAGTAAACAAA
* *
2930538 TGTAGAAATCA-AGTTTTTTGATTTTAGTAAACA
1 TGTAGAAAT-AGAGTTTTTCGATTCTAGTAAACA
2930571 CAGTTTTCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (35 bp):
TGTAGAAATAGAGTTTTTCGATTCTAGTAAACAAA
Found at i:2934208 original size:35 final size:35
Alignment explanation
Indices: 2934168--2934255 Score: 149
Period size: 35 Copynumber: 2.5 Consensus size: 35
2934158 GACTTATACC
*
2934168 ATGTAGAAATAGAGTTTTCCGGTTCTTATAAACAG
1 ATGTAGAAATAGAGTTTTCCGGTTCTGATAAACAG
* *
2934203 ATGTAGAAATAGAGTTTTCTGGTTCTGGTAAACAG
1 ATGTAGAAATAGAGTTTTCCGGTTCTGATAAACAG
2934238 ATGTAGAAATAGAGTTTT
1 ATGTAGAAATAGAGTTTT
2934256 TTTAGTTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (35 bp):
ATGTAGAAATAGAGTTTTCCGGTTCTGATAAACAG
Found at i:2937577 original size:37 final size:37
Alignment explanation
Indices: 2937511--2937596 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
2937501 CCTTTTATAT
* * **
2937511 TTTTTCTCTTTTTTCTTTGGTTTGAATCTCTCTAGGTA
1 TTTTTCTCTTTGTTCTGTGGTTCAAATCTCT-TAGGTA
*
2937549 TTTTTCTCTTTGTT-TGTGGTTCAAATCTCTTTGGTA
1 TTTTTCTCTTTGTTCTGTGGTTCAAATCTCTTAGGTA
*
2937585 TTTTTTTCTTTG
1 TTTTTCTCTTTG
2937597 ATTTCCCCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 16 0.38
37 13 0.31
38 13 0.31
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (37 bp):
TTTTTCTCTTTGTTCTGTGGTTCAAATCTCTTAGGTA
Found at i:2938169 original size:13 final size:13
Alignment explanation
Indices: 2938146--2938178 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2938136 TTTAGGTCAG
2938146 CTTGT-ATTGGGT
1 CTTGTAATTGGGT
2938158 CTTGTAATTGGGT
1 CTTGTAATTGGGT
2938171 CTATGTAA
1 CT-TGTAA
2938179 CCTGGGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 9 0.47
14 5 0.26
ACGTcount: A:0.18, C:0.09, G:0.27, T:0.45
Consensus pattern (13 bp):
CTTGTAATTGGGT
Found at i:2938778 original size:131 final size:131
Alignment explanation
Indices: 2938443--2938787 Score: 363
Period size: 131 Copynumber: 2.6 Consensus size: 131
2938433 AGGGTGACAT
* *
2938443 GGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATAACATGGTTTCTACACGATGAGGACAGCTG
1 GGCTCCTACGTGATAAGGAGATCTGGTCGGTGGATGACATGGTTTCTACACGATGAGGACAGCTG
* * *
2938508 GCCATCTTTAGGGATGTTGATAACACAGTTCCTATACAATGAGGATGGATGGTTATCTACGGGTA
66 GCCATCTTTAGGGA---TGATAACACAGTTCCTATACAATGAGGATCGATGGTTATCTAAGCGTA
2938573 AAGC
128 AAGC
* * * * * * * * *
2938577 GGCTCCTACGTGATAAGAAGATCTGGTCGGGGGATGACATTGTTCCTACATGATTATGATAACTG
1 GGCTCCTACGTGATAAGGAGATCTGGTCGGTGGATGACATGGTTTCTACACGATGAGGACAGCTG
** * *
2938642 GCCATCTTTAGGGATGATAACATGGTT-C-ATACATGATGAGG-TCGACTGGTTATCTAAGCTTG
66 GCCATCTTTAGGGATGATAACACAGTTCCTATACA--ATGAGGATCGA-TGGTTATCTAAGCGTA
**
2938704 TCGC
128 AAGC
* * * * * *
2938708 GGCTTCTATGTGCTAAGGAGATCTGGTCGGTGGATGACATGGTTTCTACGCAATGAGGACGGCTG
1 GGCTCCTACGTGATAAGGAGATCTGGTCGGTGGATGACATGGTTTCTACACGATGAGGACAGCTG
* *
2938773 ACCATCTTTATGGAT
66 GCCATCTTTAGGGAT
2938788 AATGTTTCAA
Statistics
Matches: 171, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
129 5 0.03
130 4 0.02
131 94 0.55
134 68 0.40
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (131 bp):
GGCTCCTACGTGATAAGGAGATCTGGTCGGTGGATGACATGGTTTCTACACGATGAGGACAGCTG
GCCATCTTTAGGGATGATAACACAGTTCCTATACAATGAGGATCGATGGTTATCTAAGCGTAAAG
C
Found at i:2939086 original size:66 final size:65
Alignment explanation
Indices: 2938789--2939114 Score: 435
Period size: 65 Copynumber: 5.0 Consensus size: 65
2938779 TTTATGGATA
* * *
2938789 ATGTTTCAAGAGAAAAC-GTCTCAAGATAGACAAAATTTGTTTCAAGGGAAACGGA-CTCAAAAA
1 ATGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA-AGATCTCAAAGA
2938852 TG
64 TG
** *
2938854 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTT-ATAGGGAAATGATCTCAAAGAT
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCA-AGGGAAAAGATCTCAAAGAT
2938918 G
65 G
* ** *
2938919 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTTAAGGGAAAAGATCTCAAAGATG
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAAGATCTCAAAGATG
* *
2938984 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTTAAAGATT
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAAGATCTCAAAGA-T
*
2939049 T
65 G
* *
2939050 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAATTTTGTTTCAAGGGAAATAGA-CTCAAAGA
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTCAAGGGAAA-AGATCTCAAAGA
2939114 T
64 T
2939115 TTTTCTTTTG
Statistics
Matches: 236, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
64 7 0.03
65 168 0.71
66 33 0.14
67 26 0.11
68 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (65 bp):
ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAAGATCTCAAAGATG
Found at i:2939189 original size:39 final size:39
Alignment explanation
Indices: 2939146--2939250 Score: 101
Period size: 38 Copynumber: 2.7 Consensus size: 39
2939136 ACAACTTCAG
* **
2939146 AATTTGTATTTTAAAGAAAAATTGTCTCTAA-TAAGATGA
1 AATTTGT-TTTTAAAGAAAAATTGTCTCTAAGCAAGACAA
* * *
2939185 AATTTGTTTTCAATAG-AAACTTGTCTC-AAGCGAGACAA
1 AATTTGTTTTTAA-AGAAAAATTGTCTCTAAGCAAGACAA
*
2939223 AATTTGTTTTT-AAGAAAAACTGTCTCTA
1 AATTTGTTTTTAAAGAAAAATTGTCTCTA
2939251 GCGAGACGAC
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
36 2 0.04
37 12 0.23
38 30 0.57
39 9 0.17
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTGTTTTTAAAGAAAAATTGTCTCTAAGCAAGACAA
Found at i:2939256 original size:37 final size:37
Alignment explanation
Indices: 2939184--2939279 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 37
2939174 TAATAAGATG
* * *
2939184 AAATTTGTTTTCAATAGAAACTTGTCTCAAGCGAGACA
1 AAATTTGTTTTCAAGAAAAAC-TGTCTCTAGCGAGACA
*
2939222 AAATTTGTTTTTAAGAAAAACTGTCTCTAGCGAGACGA
1 AAATTTGTTTTCAAGAAAAACTGTCTCTAGCGAGAC-A
* *
2939260 CACTTTG-TTTCAAGAAAAAC
1 AAATTTGTTTTCAAGAAAAAC
2939280 ACCCCAAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 26 0.52
38 24 0.48
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (37 bp):
AAATTTGTTTTCAAGAAAAACTGTCTCTAGCGAGACA
Found at i:2940453 original size:25 final size:25
Alignment explanation
Indices: 2940402--2940454 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2940392 TCTTGTCCTC
* *
2940402 TTTTTTTCTTTGCTTTTATTTATTA
1 TTTTTTTCTTTGCTTTGATTGATTA
2940427 TTTTTTTCTTTGCTTTGATGTGA-TA
1 TTTTTTTCTTTGCTTTGAT-TGATTA
2940452 TTT
1 TTT
2940455 GCACTTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.11, C:0.08, G:0.09, T:0.72
Consensus pattern (25 bp):
TTTTTTTCTTTGCTTTGATTGATTA
Found at i:2944318 original size:15 final size:14
Alignment explanation
Indices: 2944293--2944322 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2944283 AGTCAAATAT
2944293 TAACAATAATAACA
1 TAACAATAATAACA
2944307 TAACATATAATAACA
1 TAACA-ATAATAACA
2944322 T
1 T
2944323 GACTAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (14 bp):
TAACAATAATAACA
Found at i:2944894 original size:37 final size:38
Alignment explanation
Indices: 2944828--2944911 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
2944818 CTCTCTTTTA
* *
2944828 TATTTTTCTCTTTATTCTTTGGTCTGAATCTCTATGGG
1 TATTTTTCTCTTTATTCTGTGGTCTGAATCTCTATGCG
* * *
2944866 TATTTTTCTCTTTGTT-TGTGGT-TCGAATCTCTCTGCT
1 TATTTTTCTCTTTATTCTGTGGTCT-GAATCTCTATGCG
2944903 TATTTTTCT
1 TATTTTTCT
2944912 TTGATTTCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 1 0.03
37 24 0.60
38 15 0.38
ACGTcount: A:0.11, C:0.17, G:0.14, T:0.58
Consensus pattern (38 bp):
TATTTTTCTCTTTATTCTGTGGTCTGAATCTCTATGCG
Found at i:2951491 original size:160 final size:159
Alignment explanation
Indices: 2951225--2951701 Score: 656
Period size: 160 Copynumber: 3.0 Consensus size: 159
2951215 CGGGGTAAAA
* * * *
2951225 TATGTGTTCTCGATGATGATGAGTTGAGGTAGGAACTCCTTACAGAGGCACGTTGCAATCCTTTG
1 TATGTGTTCTTGATGATGATGAGTTGAGGCAGGAACTCCTTACAGAGGCACATTGCAAACCTTTG
* * *
2951290 ATGATGCATCCTAGTGATAA-GAAAATGTATCAAGATGTTAAAAGCAAATATTGGTGGTCAGGTA
66 ATGATGCATCTTAGTGGTAACG-AAATGTATCAAGATGTTAAAAGCATATATTGGTGGTC-GGTA
*
2951354 TGAAAAGAGCGAAATCATAAAGTAGAAGATG
129 TGAAAAGAGCGAAATCATAAAGTAGAAGACG
* * * * *
2951385 TGTGTGTTCTTGATGATGATGAGTTGAGGCGGGAACTACTTACAAAGGCACATTGCAAACTTTTG
1 TATGTGTTCTTGATGATGATGAGTTGAGGCAGGAACTCCTTACAGAGGCACATTGCAAACCTTTG
* * *
2951450 AAGAAGCATCTTGGTGGTAACGAAATGTATCAAGATGTTAAAAGCATATATTGGTGGTCGGTATG
66 ATGATGCATCTTAGTGGTAACGAAATGTATCAAGATGTTAAAAGCATATATTGGTGGTCGGTATG
*
2951515 AAAAGAGAGAAATCATAAAGTAGAAGACG
131 AAAAGAGCGAAATCATAAAGTAGAAGACG
* *
2951544 TATGTCTT-TTGACGATGATGAGTTGAGGCAGGAACTCCTTACAGAGGCACATTGCAAACCTTTG
1 TATGTGTTCTTGATGATGATGAGTTGAGGCAGGAACTCCTTACAGAGGCACATTGCAAACCTTTG
* * * * *
2951608 ATGATGTAT-TCTAGTAGTAACAAAATATATCTAAAAT-TTAAAAGCATATATTGGTGGTCGAGT
66 ATGATGCATCT-TAGTGGTAACGAAATGTATC-AAGATGTTAAAAGCATATATTGGTGGTCG-GT
*
2951671 ATGAAAAGAGCGAAATCATAAAGTAAAAGAC
128 ATGAAAAGAGCGAAATCATAAAGTAGAAGAC
2951702 ATCACTTGAG
Statistics
Matches: 279, Mismatches: 34, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
157 1 0.00
158 96 0.34
159 74 0.27
160 107 0.38
161 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (159 bp):
TATGTGTTCTTGATGATGATGAGTTGAGGCAGGAACTCCTTACAGAGGCACATTGCAAACCTTTG
ATGATGCATCTTAGTGGTAACGAAATGTATCAAGATGTTAAAAGCATATATTGGTGGTCGGTATG
AAAAGAGCGAAATCATAAAGTAGAAGACG
Found at i:2956914 original size:2 final size:2
Alignment explanation
Indices: 2956907--2956934 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2956897 GTCCTTATTC
2956907 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
2956935 GTAGCTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2966563 original size:77 final size:76
Alignment explanation
Indices: 2966456--2966606 Score: 241
Period size: 77 Copynumber: 2.0 Consensus size: 76
2966446 AGGATATCCT
* * * *
2966456 GTTCTATCAGGATTGCTTCAACCTATCTAGATTTTATAGTGGAAGTGAGATAGAGTGACCATAG-
1 GTTCTATCAGGATTACTTCAACCTACCTAGATTTCATAGTGGAAATGAGATAGAGTGACCA-AGT
2966520 ATTTTATGATGGG
65 ATTTTA-GATGGG
2966533 GTTCTATCAGGATTACTTCAACCTACCTAGATTTCATAGTGGAAATGAGATAGAGTGACCAAGTA
1 GTTCTATCAGGATTACTTCAACCTACCTAGATTTCATAGTGGAAATGAGATAGAGTGACCAAGTA
2966598 TTTTAGATG
66 TTTTAGATG
2966607 ACATGCTTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
76 6 0.09
77 63 0.91
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (76 bp):
GTTCTATCAGGATTACTTCAACCTACCTAGATTTCATAGTGGAAATGAGATAGAGTGACCAAGTA
TTTTAGATGGG
Found at i:2968261 original size:34 final size:34
Alignment explanation
Indices: 2968223--2968293 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
2968213 AGTGCTAACG
2968223 TTAGAAACAAAAATATGCACTCCAGGTGCAATCA
1 TTAGAAACAAAAATATGCACTCCAGGTGCAATCA
* *
2968257 TTAGATACAAAAATATGCACTCCATGTGCAATCA
1 TTAGAAACAAAAATATGCACTCCAGGTGCAATCA
2968291 TTA
1 TTA
2968294 AATGTACACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (34 bp):
TTAGAAACAAAAATATGCACTCCAGGTGCAATCA
Found at i:2972125 original size:17 final size:17
Alignment explanation
Indices: 2972103--2972135 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2972093 TGGTTCGACT
2972103 TCTCAACTAAGTCTACC
1 TCTCAACTAAGTCTACC
2972120 TCTCAACTAAGTCTAC
1 TCTCAACTAAGTCTAC
2972136 AGATAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (17 bp):
TCTCAACTAAGTCTACC
Found at i:2972665 original size:20 final size:20
Alignment explanation
Indices: 2972619--2972674 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2972609 GCAATGTTGG
* *
2972619 TAGTATCGATACTACCTAGT
1 TAGTATTGATACTTCCTAGT
2972639 TAGTATTGATACTTCCTAGT
1 TAGTATTGATACTTCCTAGT
*
2972659 TAGTATTGATTCTTCC
1 TAGTATTGATACTTCC
2972675 CTTACCTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (20 bp):
TAGTATTGATACTTCCTAGT
Found at i:2979013 original size:34 final size:34
Alignment explanation
Indices: 2978960--2979034 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
2978950 GTGCAATAAC
2978960 CACTCCAAGTGCTAACATCAGAAACAAAAATATG
1 CACTCCAAGTGCTAACATCAGAAACAAAAATATG
* * *
2978994 CACTCCAATTGC-AATCATCAGATACAGAAATATG
1 CACTCCAAGTGCTAA-CATCAGAAACAAAAATATG
2979028 CACTCCA
1 CACTCCA
2979035 TGTACAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 2 0.05
34 35 0.95
ACGTcount: A:0.43, C:0.27, G:0.11, T:0.20
Consensus pattern (34 bp):
CACTCCAAGTGCTAACATCAGAAACAAAAATATG
Found at i:2979043 original size:34 final size:34
Alignment explanation
Indices: 2978975--2979045 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
2978965 CAAGTGCTAA
*
2978975 CATCAGAAACAAAAATATGCACTCCAATTGCAAT
1 CATCAGAAACAAAAATATGCACTCCAATTACAAT
* *
2979009 CATCAGATACAGAAATATGCACTCC-ATGTACAAT
1 CATCAGAAACAAAAATATGCACTCCAAT-TACAAT
2979043 CAT
1 CAT
2979046 TAAATGTACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.23
Consensus pattern (34 bp):
CATCAGAAACAAAAATATGCACTCCAATTACAAT
Found at i:2989518 original size:67 final size:66
Alignment explanation
Indices: 2989404--2989630 Score: 233
Period size: 67 Copynumber: 3.4 Consensus size: 66
2989394 CAGATTTGTT
* *
2989404 TCACTCGAGACAGTTTCCCTTGAAATACAAACCTTTGAGATCATTTCTCTTGAAACAAAATTTCA
1 TCACTCGAGATAGTTTCCCTTGAAATACAAA-CTTTGAGATTATTTCTCTTGAAACAAAATTTCA
2989469 TC
65 TC
* * *
2989471 TCACTCGAGATAGTTTCCCTTGAAACACAAACATTTGAGATTGTTTCTCTTGAAACAAAA-TTCT
1 TCACTCGAGATAGTTTCCCTTGAAATACAAAC-TTTGAGATTATTTCTCTTGAAACAAAATTTCA
2989535 TC
65 TC
* * * * * * * *
2989537 TCGCCCGAGACAATTA-TTTCTCTTGAAATATAAACTTTGAAAATTACTTCCCCTGAAACAAAAT
1 TCACTCGAG---A-TAGTTTCCCTTGAAATACAAACTTTG-AGATTATTTCTCTTGAAACAAAAT
*
2989601 TTTATC
61 TTCATC
* *
2989607 TCACTCGATATAGTTTCCCATGAA
1 TCACTCGAGATAGTTTCCCTTGAA
2989631 CGTAAACGTC
Statistics
Matches: 130, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
66 15 0.12
67 64 0.49
68 4 0.03
69 35 0.27
70 12 0.09
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (66 bp):
TCACTCGAGATAGTTTCCCTTGAAATACAAACTTTGAGATTATTTCTCTTGAAACAAAATTTCAT
C
Found at i:2998728 original size:111 final size:112
Alignment explanation
Indices: 2998540--2998759 Score: 309
Period size: 111 Copynumber: 2.0 Consensus size: 112
2998530 GGCTTACTTA
* * *
2998540 GCAGTGAGGAGCCATCTATCAGTTAAATTTTTCAAAGCCAATTTGAAATTCACGATGGAGGATAT
1 GCAGCGAGGAGCCATCTATCAGTTAAATTTTTCAAAGCCAATTTCAAATTCACGATAGAGGATAT
* * *
2998605 TGGGTCAGAAAGATAATTCATAATTAACTATAATTTAGCTTAACTCT
66 TGGGTCAGAAAGACAATTCAGAATTAACTATAATCTAGCTTAACTCT
* * * *
2998652 GCAGCGAGGATCCATCTTTTAGTTAAATTTTTCAAAGCCAA-TTCAACTTCACGATAGAGGATAT
1 GCAGCGAGGAGCCATCTATCAGTTAAATTTTTCAAAGCCAATTTCAAATTCACGATAGAGGATAT
* *
2998716 TGGATTCA-AAAGACAATTCAGAATTAACTGTAATCTAGCTTAAC
66 TGG-GTCAGAAAGACAATTCAGAATTAACTATAATCTAGCTTAAC
2998760 ATGAAGGCGT
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
111 55 0.58
112 40 0.42
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (112 bp):
GCAGCGAGGAGCCATCTATCAGTTAAATTTTTCAAAGCCAATTTCAAATTCACGATAGAGGATAT
TGGGTCAGAAAGACAATTCAGAATTAACTATAATCTAGCTTAACTCT
Found at i:2998788 original size:111 final size:112
Alignment explanation
Indices: 2998545--2998789 Score: 273
Period size: 111 Copynumber: 2.2 Consensus size: 112
2998535 ACTTAGCAGT
* * *
2998545 GAGGAGCCATCTAT-CAGTTAAATTTTTCAAAGCCAATTTGAAATTCACGATGGAGGATATTGGG
1 GAGGAGCCAGCT-TCCAGTTAAATTTTTCAAAGCCAATTTCAAATTCACGATAGAGGATATTGGG
* * * * *
2998609 TCAGAAAGATAATTCATAATTAACTATAATTTAGCTTAACTCTGCAGC
65 TCAGAAAGACAATTCAGAATTAACTATAATCTAGCTTAACTATGAAGC
* * ** * *
2998657 GAGGATCCATCTTTTAGTTAAATTTTTCAAAGCCAA-TTCAACTTCACGATAGAGGATATTGGAT
1 GAGGAGCCAGCTTCCAGTTAAATTTTTCAAAGCCAATTTCAAATTCACGATAGAGGATATTGG-G
*
2998721 TCA-AAAGACAATTCAGAATTAACTGTAATCTAGCTTAAC-ATGAAGGC
65 TCAGAAAGACAATTCAGAATTAACTATAATCTAGCTTAACTATGAA-GC
* * *
2998768 GTGGAGCTAGCTTCCGGTTAAA
1 GAGGAGCCAGCTTCCAGTTAAA
2998790 ATCATCAAAC
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
110 3 0.03
111 73 0.66
112 35 0.32
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (112 bp):
GAGGAGCCAGCTTCCAGTTAAATTTTTCAAAGCCAATTTCAAATTCACGATAGAGGATATTGGGT
CAGAAAGACAATTCAGAATTAACTATAATCTAGCTTAACTATGAAGC
Found at i:2999736 original size:19 final size:17
Alignment explanation
Indices: 2999714--2999771 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 17
2999704 TATACAATTT
2999714 TATATTATATAAGCATATA
1 TATATTATATAA--ATATA
* *
2999733 TATATTTTTTAAATATA
1 TATATTATATAAATATA
2999750 TATA-TATAT--ATATA
1 TATATTATATAAATATA
2999764 TATATTAT
1 TATATTAT
2999772 TGAAAATATG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.26
15 3 0.09
16 3 0.09
17 9 0.26
19 10 0.29
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TATATTATATAAATATA
Found at i:2999785 original size:22 final size:20
Alignment explanation
Indices: 2999755--2999917 Score: 79
Period size: 24 Copynumber: 7.7 Consensus size: 20
2999745 ATATATATAT
2999755 ATATATATATATATTATTGAAA
1 ATAT-TATATATATT-TTGAAA
**
2999777 ATATGTATATAGGTTTTGAAA
1 ATAT-TATATATATTTTGAAA
*
2999798 CATATTATATAT-TTTTTAAA
1 -ATATTATATATATTTTGAAA
*
2999818 A-A-TATATA-GTTTTGAAA
1 ATATTATATATATTTTGAAA
*
2999835 TATATATGTTATATATTTT-AAA
1 -ATAT-T-ATATATATTTTGAAA
*
2999857 ATA-TATATAGT-TTTATTAAA
1 ATATTATATA-TATTT-TGAAA
2999877 ATTATATATTATATATTTTAGAAA
1 A-TAT-TA-TATATATTTT-GAAA
2999901 TATATGTATTATATATT
1 -ATAT-TA-TATATATT
2999918 AAATATATTA
Statistics
Matches: 112, Mismatches: 11, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
17 13 0.12
18 9 0.08
19 5 0.04
20 11 0.10
21 18 0.16
22 23 0.21
23 8 0.07
24 24 0.21
25 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.50
Consensus pattern (20 bp):
ATATTATATATATTTTGAAA
Found at i:2999797 original size:21 final size:20
Alignment explanation
Indices: 2999771--2999839 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 20
2999761 ATATATATTA
2999771 TTGAAAATATGTATATAGGTT
1 TTGAAAATAT-TATATAGGTT
*
2999792 TTGAAACATATTATATA-TTT
1 TTGAAA-ATATTATATAGGTT
*
2999812 TTTAAAA-A-TATATA-GTT
1 TTGAAAATATTATATAGGTT
2999829 TTGAAATATAT
1 TTGAAA-ATAT
2999840 ATGTTATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 13 0.32
18 2 0.05
19 2 0.05
20 7 0.17
21 12 0.30
22 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.46
Consensus pattern (20 bp):
TTGAAAATATTATATAGGTT
Found at i:2999910 original size:24 final size:23
Alignment explanation
Indices: 2999820--2999935 Score: 108
Period size: 24 Copynumber: 5.3 Consensus size: 23
2999810 TTTTTAAAAA
* *
2999820 TATATAGTTTTGAAATATATATGT
1 TATATA-TTTTAAAATATATATAT
2999844 TATATATTTTAAAATATATATAGT
1 TATATATTTTAAAATATATATA-T
2999868 T-T-TA--TTAAAAT-TATATAT
1 TATATATTTTAAAATATATATAT
*
2999886 TATATATTTTAGAAATATATGTAT
1 TATATATTTTA-AAATATATATAT
2999910 TATATA--TT-AAATATAT-TAT
1 TATATATTTTAAAATATATATAT
2999929 TAT-TATT
1 TATATATT
2999936 ATTTTCCTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
18 4 0.05
19 13 0.16
20 17 0.21
22 7 0.09
23 19 0.24
24 20 0.25
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
TATATATTTTAAAATATATATAT
Found at i:2999925 original size:42 final size:41
Alignment explanation
Indices: 2999753--2999935 Score: 141
Period size: 42 Copynumber: 4.4 Consensus size: 41
2999743 AAATATATAT
* *
2999753 ATATATATATATATATTATTGAAAATATGTATATAGGTTT-TGAAA
1 ATATATAT-TATATATT-TT-AAAATA--TATATAGTTTTATTAAA
* *
2999798 CATAT-TA-TATATTTTTTAAAA-ATATATAGTTTTGA--AAT
1 -ATATATATTATATATTTTAAAATATATATAGTTTT-ATTAAA
*
2999836 ATATATGTTATATATTTTAAAATATATATAGTTTTATTAAA
1 ATATATATTATATATTTTAAAATATATATAGTTTTATTAAA
*
2999877 ATTATATATTATATATTTTAGAAATATATGTA-TTATATATT-AA
1 A-TATATATTATATATTTTA-AAATATATATAGTT-T-TATTAAA
2999920 ATATATTATTAT-TATT
1 ATATA-TATTATATATT
2999936 ATTTTCCTTT
Statistics
Matches: 117, Mismatches: 8, Indels: 28
0.76 0.05 0.18
Matches are distributed among these distances:
37 4 0.03
38 13 0.11
39 14 0.12
40 13 0.11
41 7 0.06
42 29 0.25
43 27 0.23
44 4 0.03
45 2 0.02
46 4 0.03
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (41 bp):
ATATATATTATATATTTTAAAATATATATAGTTTTATTAAA
Found at i:3006394 original size:40 final size:40
Alignment explanation
Indices: 3006340--3006470 Score: 117
Period size: 40 Copynumber: 3.4 Consensus size: 40
3006330 TTTTTTAAAC
*
3006340 AAGATTTGTCTCACTTGAGACAATTTTTACTCGAAACAAG
1 AAGATTTATCTCACTTGAGACAATTTTTACTCGAAACAAG
* ** *** * **
3006380 AAGATTTATTTCACTCAAGATTGTTTTT-TTTTAAAC---
1 AAGATTTATCTCACTTGAGACAATTTTTACTCGAAACAAG
* *
3006416 AAGATTTGTCTCACTTGAGACAATTTGTACTCGAAACAAG
1 AAGATTTATCTCACTTGAGACAATTTTTACTCGAAACAAG
*
3006456 AAGATTTATTTCACT
1 AAGATTTATCTCACT
3006471 CAAGATTGTT
Statistics
Matches: 64, Mismatches: 23, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
36 20 0.31
37 5 0.08
39 5 0.08
40 34 0.53
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (40 bp):
AAGATTTATCTCACTTGAGACAATTTTTACTCGAAACAAG
Found at i:3006401 original size:76 final size:75
Alignment explanation
Indices: 3006231--3006559 Score: 405
Period size: 76 Copynumber: 4.3 Consensus size: 75
3006221 TAATACAGAG
* ** * *
3006231 GATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AGACTTTGTATCACTTTAGAC--TGTTTTA
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACAAT-TTTTA
* *
3006293 CTTGAAAGAAGA
64 CTCGAAACAAGA
* * * *
3006305 CATTTCATTTGACTCAAGATTGTTTTTTTTTAAACAAGATTTGTCTCACTTGAGACAATTTTTAC
1 GATTT-ATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTTAC
3006370 TCGAAACAAGAA
65 TCGAAACAAG-A
* * *
3006382 GATTTATTTCACTCAAGATTGTTTTTTTTTAAACAAGATTTGTCTCACTTGAGACAATTTGTACT
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTTACT
3006447 CGAAACAAGAA
66 CGAAACAAG-A
* **
3006458 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACGGTTTTTACT
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTTACT
*
3006523 CGAAAGAAG-
66 CGAAACAAGA
3006532 GCATTTCATTTCACTCAAGATTGTTTTT
1 G-ATTT-ATTTCACTCAAGATTGTTTTT
3006560 AAAGAAGATT
Statistics
Matches: 227, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
74 5 0.02
75 42 0.19
76 174 0.77
77 6 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (75 bp):
GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAATTTTTACT
CGAAACAAGA
Found at i:3006430 original size:36 final size:36
Alignment explanation
Indices: 3006316--3006430 Score: 104
Period size: 36 Copynumber: 3.1 Consensus size: 36
3006306 ATTTCATTTG
3006316 ACTCAAGATTGTTTTTTTTTAAACAAGATTTGTCTC
1 ACTCAAGATTGTTTTTTTTTAAACAAGATTTGTCTC
** *** * ** * *
3006352 ACTTGAGACAATTTTTACTCGAAACAAGAAGATTTATTTC
1 ACTCAAGATTGTTTTT-TTTTAAAC---AAGATTTGTCTC
3006392 ACTCAAGATTGTTTTTTTTTAAACAAGATTTGTCTC
1 ACTCAAGATTGTTTTTTTTTAAACAAGATTTGTCTC
3006428 ACT
1 ACT
3006431 TGAGACAATT
Statistics
Matches: 55, Mismatches: 20, Indels: 8
0.66 0.24 0.10
Matches are distributed among these distances:
36 24 0.44
37 5 0.09
39 5 0.09
40 21 0.38
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (36 bp):
ACTCAAGATTGTTTTTTTTTAAACAAGATTTGTCTC
Found at i:3006621 original size:39 final size:39
Alignment explanation
Indices: 3006562--3006765 Score: 261
Period size: 39 Copynumber: 5.5 Consensus size: 39
3006552 TTGTTTTTAA
* *
3006562 AGAAGATTTTATCTCTCTTGACATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
3006601 ATAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
3006640 ATAAAATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
3006679 AGAAG-----AT-T---TT---ATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
3006706 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
3006745 AGAAGATTTTATCTCGCTTGA
1 AGAAGATTTTATCTCGCTTGA
3006766 TAAAAGCTCT
Statistics
Matches: 144, Mismatches: 9, Indels: 24
0.81 0.05 0.14
Matches are distributed among these distances:
27 22 0.15
30 2 0.01
32 2 0.01
33 2 0.01
34 2 0.01
36 2 0.01
39 112 0.78
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:3006700 original size:27 final size:27
Alignment explanation
Indices: 3006662--3006717 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3006652 CTCGCTTGAG
3006662 ATAGTTTCCCTCGAAACAGAAGATTTT
1 ATAGTTTCCCTCGAAACAGAAGATTTT
3006689 ATAGTTTCCCTCGAAACAGAAGATTTT
1 ATAGTTTCCCTCGAAACAGAAGATTTT
3006716 AT
1 AT
3006718 CTCGCTTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (27 bp):
ATAGTTTCCCTCGAAACAGAAGATTTT
Found at i:3006729 original size:66 final size:66
Alignment explanation
Indices: 3006623--3006756 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
3006613 CTCACTTGAG
*
3006623 ATAGTTTCCCTCGAAACATAAAATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTT
1 ATAGTTTCCCTCGAAACAGAAAATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTT
3006688 T
66 T
*
3006689 ATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTT
1 ATAGTTTCCCTCGAAACAGAAAATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTT
3006754 T
66 T
3006755 AT
1 AT
3006757 CTCGCTTGAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (66 bp):
ATAGTTTCCCTCGAAACAGAAAATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTT
T
Found at i:3007441 original size:30 final size:31
Alignment explanation
Indices: 3007385--3007444 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3007375 AATCTGTGGA
*
3007385 GGCATGGGCACGGGATGGGATTTGATTAAAG
1 GGCATGGGCAAGGGATGGGATTTGATTAAAG
*
3007416 GGCATGGGCAAGGGATGTG-TTTGATTAAA
1 GGCATGGGCAAGGGATGGGATTTGATTAAA
3007445 AAATGGTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.27, C:0.08, G:0.40, T:0.25
Consensus pattern (31 bp):
GGCATGGGCAAGGGATGGGATTTGATTAAAG
Found at i:3010949 original size:17 final size:17
Alignment explanation
Indices: 3010908--3010979 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
3010898 ATTCATGCAT
3010908 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
3010925 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
3010943 CTAGTTCATTCATAAAA
1 CTAGTTCATTAATTAAA
*
3010960 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
3010977 CTA
1 CTA
3010980 ACTCTTAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 34 0.72
18 13 0.28
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:3010965 original size:34 final size:35
Alignment explanation
Indices: 3010908--3010979 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
3010898 ATTCATGCAT
**
3010908 CTAGTTCATTGAATAAAGTTAGTTCATTAATTAAA
1 CTAGTTCATTGAATAAAACTAGTTCATTAATTAAA
* *
3010943 CTAGTTCATT-CATAAAACTAGTTCATTTATTAAA
1 CTAGTTCATTGAATAAAACTAGTTCATTAATTAAA
3010977 CTA
1 CTA
3010980 ACTCTTAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 23 0.70
35 10 0.30
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (35 bp):
CTAGTTCATTGAATAAAACTAGTTCATTAATTAAA
Found at i:3022403 original size:12 final size:12
Alignment explanation
Indices: 3022386--3022413 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3022376 TCTAGACCGG
3022386 GTCAGGTATCGA
1 GTCAGGTATCGA
3022398 GTCAGGTATCGA
1 GTCAGGTATCGA
3022410 GTCA
1 GTCA
3022414 ACACGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (12 bp):
GTCAGGTATCGA
Found at i:3022551 original size:12 final size:12
Alignment explanation
Indices: 3022518--3022575 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
3022508 TTTGGGCCTA
3022518 TAATAATATTAT
1 TAATAATATTAT
* *
3022530 TATTATTATTAT
1 TAATAATATTAT
*
3022542 TAATAATATTAA
1 TAATAATATTAT
3022554 TAA-AATAATTA-
1 TAATAAT-ATTAT
*
3022565 AAATAATATTA
1 TAATAATATTA
3022576 AAATAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:3022577 original size:20 final size:21
Alignment explanation
Indices: 3022540--3022581 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3022530 TATTATTATT
*
3022540 ATTAATAATATTAATAAAATA
1 ATTAATAATAATAATAAAATA
*
3022561 ATTAA-AATAATATTAAAATA
1 ATTAATAATAATAATAAAATA
3022581 A
1 A
3022582 AAAAGGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTAATAATAATAATAAAATA
Found at i:3023058 original size:123 final size:123
Alignment explanation
Indices: 3022706--3023396 Score: 984
Period size: 123 Copynumber: 5.7 Consensus size: 123
3022696 GGATATGAAT
* * ** * * *
3022706 GTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTCTT-TGAATGAGTTCTTCTCATTATGA
1 GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAG-ATGAGTTCTTCTTATTACGA
* * * * * * *
3022770 ACCCCTTCTGTAATTATTGATGTTGTTCTATCTCCTTCTGCGATAGAGTTGAGCAAAAG
65 ACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAG
*
3022829 GTTGAATAAGTTCTTCAGATTACGAACTTCTTCTTCCTCTTCAGATGAG---TTCTTATTACGAA
1 GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
* * *
3022891 CTCCTTCTGGAAATGTTGATGTTGTTCTATCTCATTCTGCGATAGAGTCGAGCAAAAG
66 CTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAG
* * *
3022949 GTTGAATAAGTTCTTCAGATTATAAACTTCTTCTTCCTCTTCATATGAGTTCTTCTTATTATGAA
1 GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
* *
3023014 CTCCTTCTGGAAATGTTGATGCTACTCTATCTCATTCTGCGATAGAGTCGAGCAAAAG
66 CTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAG
* *
3023072 TTTGAATAAGTTCGTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
1 GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
* * * * *
3023137 CTCCTTCTGGAAATGTTGATCCTACTCTATCTCCTTATGTGATAGATTCGAGCAAAAG
66 CTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAG
* * * *
3023195 GTTGAATAAGTTTTTC-GATTATGAACTTTTTCTTCCTCTTCAAATGATTTCTTCTTATTACGAA
1 GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
* *
3023259 CTCCTTCTGGAAATGTTGATTCTGCTCTATCTCCTTCTGC-ATAGAGTCGA-TATAAAG
66 CTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCA-AAAG
3023316 GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACG-A
1 GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
3023380 CTCCTTCTGGAAATGTT
66 CTCCTTCTGGAAATGTT
3023397 TATCCATCGA
Statistics
Matches: 515, Mismatches: 47, Indels: 14
0.89 0.08 0.02
Matches are distributed among these distances:
120 110 0.21
121 46 0.09
122 124 0.24
123 234 0.45
124 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (123 bp):
GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
CTCCTTCTGGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAG
Found at i:3024320 original size:7 final size:7
Alignment explanation
Indices: 3024305--3024341 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
3024295 TCCTTTTTTA
3024305 TTTTC-T
1 TTTTCTT
3024311 TTTTCTT
1 TTTTCTT
3024318 TTTTC-T
1 TTTTCTT
*
3024324 TCTTCTT
1 TTTTCTT
3024331 TTTTCTT
1 TTTTCTT
3024338 TTTT
1 TTTT
3024342 TCTTCAAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 10 0.37
7 17 0.63
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:3024321 original size:13 final size:13
Alignment explanation
Indices: 3024305--3024340 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
3024295 TCCTTTTTTA
3024305 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
*
3024318 TTTTCTTCTTCTT
1 TTTTCTTTTTCTT
3024331 TTTTCTTTTT
1 TTTTCTTTTT
3024341 TTCTTCAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:3024344 original size:18 final size:17
Alignment explanation
Indices: 3024297--3024346 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
3024287 CTTGACCCTC
*
3024297 CTTTTTTATTTTCTTTTT
1 CTTTTTT-TCTTCTTTTT
3024315 CTTTTTTCTTCTTCTTTTTT
1 C-TTTTT-TTCTTC-TTTTT
3024335 CTTTTTTTCTTC
1 CTTTTTTTCTTC
3024347 AAGCATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 7 0.25
19 14 0.50
20 7 0.25
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTTTTTCTTCTTTTT
Found at i:3031495 original size:15 final size:14
Alignment explanation
Indices: 3031457--3031501 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
3031447 ATACATAAAT
*
3031457 AAAATAAATGTAATG
1 AAAATGAATGT-ATG
3031472 AATAATGAATGTATG
1 AA-AATGAATGTATG
3031487 CAAAATGAATGTATG
1 -AAAATGAATGTATG
3031502 TAAGAGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.51, C:0.02, G:0.18, T:0.29
Consensus pattern (14 bp):
AAAATGAATGTATG
Found at i:3034848 original size:10 final size:10
Alignment explanation
Indices: 3034833--3034858 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3034823 TAAATAATTG
3034833 AAAGAAATCA
1 AAAGAAATCA
3034843 AAAGAAATCA
1 AAAGAAATCA
3034853 AAAGAA
1 AAAGAA
3034859 TTATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.08, G:0.12, T:0.08
Consensus pattern (10 bp):
AAAGAAATCA
Found at i:3035481 original size:18 final size:20
Alignment explanation
Indices: 3035458--3035496 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
3035448 CCCTTTCTTT
3035458 AATATTAA-AAAATA-AATA
1 AATATTAATAAAATATAATA
3035476 AATATTAATAAAATATAATA
1 AATATTAATAAAATATAATA
3035496 A
1 A
3035497 TTTTCTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATATTAATAAAATATAATA
Found at i:3036958 original size:11 final size:11
Alignment explanation
Indices: 3036918--3036963 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
3036908 TTAATATTAT
3036918 TAATATTAATAA
1 TAATATTAA-AA
3036930 T-ATAATTAAAA
1 TAAT-ATTAAAA
3036941 T-AT-TTAAAA
1 TAATATTAAAA
3036950 TAATATTAAAA
1 TAATATTAAAA
3036961 TAA
1 TAA
3036964 AAAAAGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 7 0.23
10 2 0.06
11 16 0.52
12 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:3041151 original size:60 final size:59
Alignment explanation
Indices: 3041082--3041256 Score: 287
Period size: 60 Copynumber: 2.9 Consensus size: 59
3041072 TTTAAATTGT
*
3041082 AGTGATCAAAATATAAATAAGAAAAAATGAATGATGAAATTTGAAATTAACCATTTTTTA
1 AGTGATCAAAATATAAATGAGAAAAAATGAATGATGAAATTTGAAATTAACC-TTTTTTA
*
3041142 AGTGATCAAAATATAAGTGAGAAAAAATGAATGATGAAATTTGAAATTAACCTTTTTTAA
1 AGTGATCAAAATATAAATGAGAAAAAATGAATGATGAAATTTGAAATTAACCTTTTTT-A
* * *
3041202 AGTGATCAAAATATAACTGAGAAAAAATGAATTATGAAACTTGAAATTAACCTTT
1 AGTGATCAAAATATAAATGAGAAAAAATGAATGATGAAATTTGAAATTAACCTTT
3041257 ATTTTAAAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
59 6 0.06
60 103 0.94
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (59 bp):
AGTGATCAAAATATAAATGAGAAAAAATGAATGATGAAATTTGAAATTAACCTTTTTTA
Found at i:3052507 original size:12 final size:13
Alignment explanation
Indices: 3052481--3052517 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
3052471 CTATTTACAA
3052481 CAAGTGGTCATTG
1 CAAGTGGTCATTG
3052494 CAAGTGGT-ATTG
1 CAAGTGGTCATTG
*
3052506 CAAGTGGGCATT
1 CAAGTGGTCATT
3052518 ATCTCTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (13 bp):
CAAGTGGTCATTG
Found at i:3054239 original size:21 final size:21
Alignment explanation
Indices: 3054215--3054275 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3054205 CCAACTTTGA
3054215 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
3054236 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
3054250 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
3054271 AAATG
1 AAATG
3054276 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:3054296 original size:36 final size:35
Alignment explanation
Indices: 3054209--3054313 Score: 185
Period size: 35 Copynumber: 3.0 Consensus size: 35
3054199 TGGCAACCAA
3054209 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
3054244 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
3054279 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
3054314 GGTAGATGTT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 44 0.65
36 24 0.35
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:3058852 original size:21 final size:21
Alignment explanation
Indices: 3058828--3058888 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3058818 CCAACTTTGA
3058828 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
3058849 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
3058863 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
3058884 AAATG
1 AAATG
3058889 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:3058909 original size:36 final size:35
Alignment explanation
Indices: 3058822--3058936 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
3058812 TGGCAACCAA
3058822 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
3058857 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
3058892 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
3058928 -GTTGAAAAT
1 CTTTGAAAAT
3058937 AGGAATGGGT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
34 5 0.07
35 43 0.57
36 28 0.37
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:3062488 original size:16 final size:16
Alignment explanation
Indices: 3062467--3062528 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 16
3062457 AATTTTAATT
*
3062467 ATTAAAGTAAAACAAA
1 ATTAAAGTAAAAGAAA
*
3062483 ATTAAA-T-TAAGAAA
1 ATTAAAGTAAAAGAAA
3062497 ATATAAAGTAAAAGAAA
1 AT-TAAAGTAAAAGAAA
*
3062514 ACTTTAAATTAAAAG
1 A--TTAAAGTAAAAG
3062529 GGTTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 7 0.19
17 7 0.19
18 10 0.27
19 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (16 bp):
ATTAAAGTAAAAGAAA
Found at i:3063820 original size:35 final size:35
Alignment explanation
Indices: 3063753--3063942 Score: 197
Period size: 35 Copynumber: 5.4 Consensus size: 35
3063743 TTTTTTAAAA
* *
3063753 TATACGTTTTCAAAATCC-TTTAAAAAACCATATAT
1 TATACGTTTTCAAAA-CCATTTTAAAAACTATATAT
* *
3063788 TATATGTTTTCAAAACCATTTCGAAAAAC-ATAT-T
1 TATACGTTTTCAAAACCATTT-TAAAAACTATATAT
* * * *
3063822 ATATATGTTTTCAAAACCATTTTTAAAACTATACAC
1 -TATACGTTTTCAAAACCATTTTAAAAACTATATAT
** *
3063858 TATACGTTTTCAAAATTATTTTAAAAACTATATAC
1 TATACGTTTTCAAAACCATTTTAAAAACTATATAT
* * *
3063893 TATATGTTTTCAAATCCGTTTTAAAAACTATATAT
1 TATACGTTTTCAAAACCATTTTAAAAACTATATAT
*
3063928 TATACGTTTTTAAAA
1 TATACGTTTTCAAAA
3063943 ATAAGTTTCC
Statistics
Matches: 130, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
34 8 0.06
35 116 0.89
36 6 0.05
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (35 bp):
TATACGTTTTCAAAACCATTTTAAAAACTATATAT
Found at i:3063826 original size:70 final size:70
Alignment explanation
Indices: 3063752--3063942 Score: 219
Period size: 70 Copynumber: 2.7 Consensus size: 70
3063742 TTTTTTTAAA
* * * *
3063752 ATATACGTTTTCAAAATCC-TTTAAAAAACCATATATTATATGTTTTCAAAACCATTTCGAAAAA
1 ATATATGTTTTCAAAATCCATTTTAAAAACTATATATTATACGTTTTCAAAACCATTT-GAAAAA
3063816 C-ATATT
65 CTATA-T
* * * ** *
3063822 ATATATGTTTTCAAAA-CCATTTTTAAAACTATACACTATACGTTTTCAAAATTATTTTAAAAAC
1 ATATATGTTTTCAAAATCCATTTTAAAAACTATATATTATACGTTTTCAAAACCATTTGAAAAAC
3063886 TATAT
66 TATAT
* *
3063891 ACTATATGTTTTC-AAATCCGTTTTAAAAACTATATATTATACGTTTTTAAAA
1 A-TATATGTTTTCAAAATCCATTTTAAAAACTATATATTATACGTTTTCAAAA
3063943 ATAAGTTTCC
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
69 13 0.13
70 89 0.87
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (70 bp):
ATATATGTTTTCAAAATCCATTTTAAAAACTATATATTATACGTTTTCAAAACCATTTGAAAAAC
TATAT
Done.