Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 40 of 56
Found at i:9227035 original size:128 final size:128
Alignment explanation
Indices: 9226807--9227063 Score: 505
Period size: 128 Copynumber: 2.0 Consensus size: 128
9226797 TCATCGCCTT
9226807 AAGAAATGGTTTTTGTAATTGTATATCCTCCTTGACTTTGGGATTCTCATTTCTTGATACGATCA
1 AAGAAATGGTTTTTGTAATTGTATATCCTCCTTGACTTTGGGATTCTCATTTCTTGATACGATCA
9226872 TGCTATCTATGAGTTTCAATACTATGGTTATGAGTGATCATGTGGTGCTATGAACTCAACCAG
66 TGCTATCTATGAGTTTCAATACTATGGTTATGAGTGATCATGTGGTGCTATGAACTCAACCAG
*
9226935 AAGAAATGGTTTTTGTAATTGTATATCCTCCTTGACTTTGGGATTCTCCTTTCTTGATACGATCA
1 AAGAAATGGTTTTTGTAATTGTATATCCTCCTTGACTTTGGGATTCTCATTTCTTGATACGATCA
9227000 TGCTATCTATGAGTTTCAATACTATGGTTATGAGTGATCATGTGGTGCTATGAACTCAACCAG
66 TGCTATCTATGAGTTTCAATACTATGGTTATGAGTGATCATGTGGTGCTATGAACTCAACCAG
9227063 A
1 A
9227064 TCAACTCATG
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (128 bp):
AAGAAATGGTTTTTGTAATTGTATATCCTCCTTGACTTTGGGATTCTCATTTCTTGATACGATCA
TGCTATCTATGAGTTTCAATACTATGGTTATGAGTGATCATGTGGTGCTATGAACTCAACCAG
Found at i:9229010 original size:39 final size:39
Alignment explanation
Indices: 9228951--9229027 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
9228941 CAAAAAAAAA
9228951 AATATTAATAGCTCACATTGAACACAAGTGTAAGAGAGT
1 AATATTAATAGCTCACATTGAACACAAGTGTAAGAGAGT
*
9228990 AATATTAATAGCTCATATTGAACACAAGTGTAAGAGAG
1 AATATTAATAGCTCACATTGAACACAAGTGTAAGAGAG
9229028 AGTAATTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (39 bp):
AATATTAATAGCTCACATTGAACACAAGTGTAAGAGAGT
Found at i:9229601 original size:40 final size:40
Alignment explanation
Indices: 9229556--9229634 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
9229546 GATGAGAATG
**
9229556 GGGGAAGTTTTATCCTTGAAGCTTAAATGAGGGACGAGAT
1 GGGGAAGTTTTATCCCCGAAGCTTAAATGAGGGACGAGAT
*
9229596 GGGGAAGTTTTATCCCCGAAGCTTAAATGGGGGACGAGA
1 GGGGAAGTTTTATCCCCGAAGCTTAAATGAGGGACGAGA
9229635 CAGGGATTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (40 bp):
GGGGAAGTTTTATCCCCGAAGCTTAAATGAGGGACGAGAT
Found at i:9235157 original size:33 final size:33
Alignment explanation
Indices: 9235113--9235186 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 33
9235103 ATAGTGGATG
* *
9235113 GCTAAAATTTATTACTGCATAAATATCTACCTT
1 GCTAAAGTTTATTACTACATAAATATCTACCTT
9235146 GCTAAAGTTTATTACTACATAAATATCTACCTT
1 GCTAAAGTTTATTACTACATAAATATCTACCTT
9235179 -CTAGAAGT
1 GCTA-AAGT
9235187 CTTTGCACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 3 0.08
33 35 0.92
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (33 bp):
GCTAAAGTTTATTACTACATAAATATCTACCTT
Found at i:9241079 original size:49 final size:49
Alignment explanation
Indices: 9241020--9241124 Score: 201
Period size: 49 Copynumber: 2.1 Consensus size: 49
9241010 TCAGTCTGAT
*
9241020 AAACTCTATCTCATAATCCATAATAGATATCACCCTGCTCCAAACTCTG
1 AAACTCTATCTCATAATCCATAATAGACATCACCCTGCTCCAAACTCTG
9241069 AAACTCTATCTCATAATCCATAATAGACATCACCCTGCTCCAAACTCTG
1 AAACTCTATCTCATAATCCATAATAGACATCACCCTGCTCCAAACTCTG
9241118 AAACTCT
1 AAACTCT
9241125 TGATACCACT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.28
Consensus pattern (49 bp):
AAACTCTATCTCATAATCCATAATAGACATCACCCTGCTCCAAACTCTG
Found at i:9246661 original size:65 final size:65
Alignment explanation
Indices: 9246481--9246690 Score: 211
Period size: 65 Copynumber: 3.2 Consensus size: 65
9246471 TTTATCAAAG
* **
9246481 TGATGCACCGATGCACCA-ATCCATGCATCGATGCACCATGA--ATTAAATTG-AACATCGAATG
1 TGATGCATCGATGCACCATA-CCATGCATCGATGCA-C-TGAGGATTTTA-TGAAACATCGAATG
9246542 CATT
62 CATT
*
9246546 TCATGCATCGATGCA-CATACCATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACCATACCATGCATCGATGCACTGAGGATTTTATG-AAACATCGAATGCAT
9246610 T
65 T
* * * *
9246611 TGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTA-GCTATTT-TGAAACATCAAATGCA
1 TGATGCATCGATGCACCATACCATGCATCGATGCACT-GAGGAT-TTTATGAAACATCGAATGCA
*
9246673 CT
64 TT
*
9246675 TGATGCATTGATGCAC
1 TGATGCATCGATGCAC
9246691 TCTTAGTGCA
Statistics
Matches: 126, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 50 0.40
65 64 0.51
66 6 0.05
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACCATACCATGCATCGATGCACTGAGGATTTTATGAAACATCGAATGCATT
Found at i:9260728 original size:18 final size:18
Alignment explanation
Indices: 9260707--9260758 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
9260697 TTTATTGTGT
9260707 ATTAAAATAATATTATTA
1 ATTAAAATAATATTATTA
* *
9260725 ATTAATAATATTTTATTATTT
1 ATTAA-AATA--ATATTATTA
9260746 ATTAAAAATAATA
1 ATT-AAAATAATA
9260759 GATTAGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
18 5 0.19
19 6 0.22
21 14 0.52
22 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTAAAATAATATTATTA
Found at i:9260740 original size:39 final size:42
Alignment explanation
Indices: 9260696--9260802 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 42
9260686 AGGGTTGGGT
*
9260696 TTTTATTGTGTATT-AAAATAAT-ATTA-TTAATTAATAATA
1 TTTTATTATGTATTAAAAATAATAATTAGTTAATTAATAATA
* * *
9260735 TTTTATTATTTATTAAAAATAATAGATTAGTTAATTATTATTA
1 TTTTATTATGTATTAAAAATAATA-ATTAGTTAATTAATAATA
*
9260778 -TTT-TTATTTATTAATAAATTAATAA
1 TTTTATTATGTATTAA-AAA-TAATAA
9260803 GTATTATTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
39 12 0.21
40 8 0.14
41 11 0.19
42 11 0.19
43 16 0.28
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (42 bp):
TTTTATTATGTATTAAAAATAATAATTAGTTAATTAATAATA
Found at i:9260741 original size:21 final size:21
Alignment explanation
Indices: 9260717--9260801 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
9260707 ATTAAAATAA
9260717 TATTATTAATTAATAATATTT
1 TATTATTAATTAATAATATTT
* * * *
9260738 TATTATTTATTAAAAATAATA
1 TATTATTAATTAATAATATTT
* * *
9260759 GATTAGTTAATTATTATTATTTT
1 TATTA-TTAATTAATAATA-TTT
*
9260782 TATTTATTAATAAATTAATA
1 TA-TTATTAATTAA-TAATA
9260802 AGTATTATTT
Statistics
Matches: 45, Mismatches: 15, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
21 21 0.47
22 9 0.20
23 8 0.18
24 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTATTAATTAATAATATTT
Found at i:9260772 original size:25 final size:25
Alignment explanation
Indices: 9260718--9260774 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
9260708 TTAAAATAAT
* **
9260718 ATTATTAATTAATAATATTTTATTA
1 ATTATTAATAAATAATAGATTATTA
*
9260743 TTTATTAA-AAATAATAGATTAGTTA
1 ATTATTAATAAATAATAGATTA-TTA
9260768 ATTATTA
1 ATTATTA
9260775 TTATTTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTATTAATAAATAATAGATTATTA
Found at i:9265252 original size:26 final size:26
Alignment explanation
Indices: 9265222--9265280 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
9265212 AAGTTACCCA
* *
9265222 TACATTAGCAACATTAACTCCTACTT
1 TACATTAGAAACATTAACTCCTACAT
9265248 TACATTAGAAACATTAACTCCTACAT
1 TACATTAGAAACATTAACTCCTACAT
9265274 TACATTA
1 TACATTA
9265281 CAATACAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (26 bp):
TACATTAGAAACATTAACTCCTACAT
Found at i:9271560 original size:16 final size:16
Alignment explanation
Indices: 9271539--9271571 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9271529 TCGATGGGAC
9271539 ATCTAC-AGTGACATTT
1 ATCTACAAG-GACATTT
9271555 ATCTACAAGGACATTT
1 ATCTACAAGGACATTT
9271571 A
1 A
9271572 ATCCTAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (16 bp):
ATCTACAAGGACATTT
Found at i:9275709 original size:21 final size:21
Alignment explanation
Indices: 9275683--9275735 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
9275673 CTTATGTTTT
9275683 GTGATATATCACTAAAT-GAAA
1 GTGATATATCACTAAATAG-AA
9275704 GTGATATATCACTAAATAGAA
1 GTGATATATCACTAAATAGAA
9275725 GTGATATATCA
1 GTGATATATCA
9275736 TTGAAAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (21 bp):
GTGATATATCACTAAATAGAA
Found at i:9275947 original size:283 final size:283
Alignment explanation
Indices: 9275429--9275965 Score: 873
Period size: 283 Copynumber: 1.9 Consensus size: 283
9275419 GTTTGATACG
* * * *
9275429 TCACTGAATAAAAGTGATATATCATTGAAAAGTTTATGTAATGAAGTGATTGAGCACTGAAAAGA
1 TCACTAAATAAAAGTGATATATCATTGAAAAGTTTACGTAATCAAGTGATTGAGCACTAAAAAGA
* *
9275494 TTTTGTCATTGTGAATTAAATGGTCTATGAAAAAAGTATGTTTGTCACTAAAGGGAAACAAGTCA
66 TTTTATCATTGTGAATTAAATGGTCTATGAAAAAAGGATGTTTGTCACTAAAGGGAAACAAGTCA
*
9275559 AAACATCATTCAATGGTTTGATATATGATTGAATTGAACTGATATATCACTAAAAGGTTTTTGTC
131 AAACATCATTCAATGGTCTGATATATGATTGAATTGAACTGATATATCACTAAAAGGTTTTTGTC
* *
9275624 AATATGCATTAAATGTGATTGATGATAGCTCATTTTTCTTTTAAATTGGCTTATGTTTTGTGATA
196 AATATGCATTAAATGTGATTGATGATAGCTCATTTTTCTTTTAAATTAGCTTATATTTTGTGATA
9275689 TATCACTAAATGAAAGTGATATA
261 TATCACTAAATGAAAGTGATATA
* * *
9275712 TCACTAAATAGAAGTGATATATCATTGAAAAGTTTCCGTAATCAAGTGATTGGGCACTAAAAAGA
1 TCACTAAATAAAAGTGATATATCATTGAAAAGTTTACGTAATCAAGTGATTGAGCACTAAAAAGA
* * *
9275777 TTTTATCATTGTGTATTAAATGGTCTATGAAAAAAAGGAT-TTTTTCATTAAAGGGAAACAAGTC
66 TTTTATCATTGTGAATTAAATGGTCTATG-AAAAAAGGATGTTTGTCACTAAAGGGAAACAAGTC
* *
9275841 AAAACATCATTTAATGGTCTGATATATGATTGAATTGAAGTGATATATCACTGAAAA-GTTTTTG
130 AAAACATCATTCAATGGTCTGATATATGATTGAATTGAACTGATATATCACT-AAAAGGTTTTTG
9275905 TC-ATAATGCATTAAATGTGATTGATGATAGCTCATTTTTCTTTTAAATTAGCTTATATTTT
194 TCAAT-ATGCATTAAATGTGATTGATGATAGCTCATTTTTCTTTTAAATTAGCTTATATTTT
9275966 TTGAATCTTC
Statistics
Matches: 234, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
282 2 0.01
283 219 0.94
284 13 0.06
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (283 bp):
TCACTAAATAAAAGTGATATATCATTGAAAAGTTTACGTAATCAAGTGATTGAGCACTAAAAAGA
TTTTATCATTGTGAATTAAATGGTCTATGAAAAAAGGATGTTTGTCACTAAAGGGAAACAAGTCA
AAACATCATTCAATGGTCTGATATATGATTGAATTGAACTGATATATCACTAAAAGGTTTTTGTC
AATATGCATTAAATGTGATTGATGATAGCTCATTTTTCTTTTAAATTAGCTTATATTTTGTGATA
TATCACTAAATGAAAGTGATATA
Found at i:9276462 original size:197 final size:197
Alignment explanation
Indices: 9276120--9276486 Score: 522
Period size: 197 Copynumber: 1.9 Consensus size: 197
9276110 ACAGAGGAAT
* * *
9276120 GTAAACATGATGTTCGCTGTAGATGTATCACACCTCCAAATGAAGTAGAAAATTGAAAGAAAACT
1 GTAAACATGATGTTCGCTATAGATGTATCACACCACCAAATGAAGCAGAAAATTGAAAGAAAACT
* * * *
9276185 TAGAGCATATGTTACATGTTTCAGTTAACGATACATAATTTTAGATACTCTACTCAAATATGGAA
66 TAGACCATATGTTACATGTTTCAGTTAACGACACATAATTTCAGACACTCTACTCAAATATGGAA
* * *
9276250 CATTCCAATTTGAGGATGATGATGATATTGTTGTGATGGTGATGATGTGTTTATGTCACAAAGGC
131 CAATCAAACTTGAGGATGATGATGATATTGTTGTGATGGTGATGATGTGTTTATGTCACAAAGGC
9276315 CC
196 CC
*
9276317 GTAAACATGATGTTC-CTTATAGATGTATCACATCACCAAATGAAGCAGAAAATTGAAAGAAAAC
1 GTAAACATGATGTTCGC-TATAGATGTATCACACCACCAAATGAAGCAGAAAATTGAAAGAAAAC
* * * ** *
9276381 TTAGACCGTATGTTTCATGTTTTAGTTATTGACACATAATTTCAGACACT-TCACTCATATATGG
65 TTAGACCATATGTTACATGTTTCAGTTAACGACACATAATTTCAGACACTCT-ACTCAAATATGG
** *
9276445 AGTAATCAAACTTGAGGATGATGATGATGTTGTTGTGATGGT
129 AACAATCAAACTTGAGGATGATGATGATATTGTTGTGATGGT
9276487 TGGATTGAAT
Statistics
Matches: 148, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
196 2 0.01
197 146 0.99
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (197 bp):
GTAAACATGATGTTCGCTATAGATGTATCACACCACCAAATGAAGCAGAAAATTGAAAGAAAACT
TAGACCATATGTTACATGTTTCAGTTAACGACACATAATTTCAGACACTCTACTCAAATATGGAA
CAATCAAACTTGAGGATGATGATGATATTGTTGTGATGGTGATGATGTGTTTATGTCACAAAGGC
CC
Found at i:9278013 original size:13 final size:13
Alignment explanation
Indices: 9277981--9278013 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
9277971 TGTTTTTTTG
9277981 TCATTTATGTTAT
1 TCATTTATGTTAT
*
9277994 TCA-TTATGTTCT
1 TCATTTATGTTAT
9278006 TCATTTAT
1 TCATTTAT
9278014 TATTCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (13 bp):
TCATTTATGTTAT
Found at i:9282263 original size:21 final size:21
Alignment explanation
Indices: 9282239--9282287 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
9282229 CACTAGATGA
9282239 CTAGCTAGCTACCTACA-CTAC
1 CTAGCTAGCTACCTA-ATCTAC
* * *
9282260 CTAGCGAGTTACTTAATCTAC
1 CTAGCTAGCTACCTAATCTAC
9282281 CTAGCTA
1 CTAGCTA
9282288 CACTAGTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.29
Consensus pattern (21 bp):
CTAGCTAGCTACCTAATCTAC
Found at i:9287253 original size:19 final size:20
Alignment explanation
Indices: 9287211--9287255 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
9287201 ACTATACTAA
* *
9287211 AAATTAATGTTAGAGTGTTG
1 AAATTGATGTTAGAATGTTG
9287231 AAATTGATGTTAGAATG-TG
1 AAATTGATGTTAGAATGTTG
9287250 AAATTG
1 AAATTG
9287256 GGTCATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (20 bp):
AAATTGATGTTAGAATGTTG
Found at i:9291837 original size:61 final size:60
Alignment explanation
Indices: 9291740--9291986 Score: 318
Period size: 61 Copynumber: 4.0 Consensus size: 60
9291730 TAGTGCTAAC
* *
9291740 ATGACACATAAGGTTGTACCCACCTCCTACACTAAGTTTACACTCTAGTGT-TGATCCGACT
1 ATGACACATAAGGTCGTGCCCACCTCCTACACTAAGTTTACACTCTAGT-TATGATCCGA-T
* *
9291801 ATGACACATAAGGTCGTGCCCACCTCCTGCAATAAGTTTACACTCTAGTTATGATCCGGAT
1 ATGACACATAAGGTCGTGCCCACCTCCTACACTAAGTTTACACTCTAGTTATGATCC-GAT
* * * *
9291862 ATGACACATAAGGTCGTGCCCACCTCCTATACTAAGTCTACACTCTAGTGT-TAATCCATAT
1 ATGACACATAAGGTCGTGCCCACCTCCTACACTAAGTTTACACTCTAGT-TATGATCC-GAT
* * * *
9291923 ATGAAACATAAGGTCGTGCCCACCTCCTGCACTAAGTTTACACTGTAGTTCTGATCCGGAT
1 ATGACACATAAGGTCGTGCCCACCTCCTACACTAAGTTTACACTCTAGTTATGATCC-GAT
9291984 ATG
1 ATG
9291987 CAGCCCTACT
Statistics
Matches: 163, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
60 2 0.01
61 158 0.97
62 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (60 bp):
ATGACACATAAGGTCGTGCCCACCTCCTACACTAAGTTTACACTCTAGTTATGATCCGAT
Found at i:9291959 original size:122 final size:122
Alignment explanation
Indices: 9291740--9291986 Score: 388
Period size: 122 Copynumber: 2.0 Consensus size: 122
9291730 TAGTGCTAAC
* * * *
9291740 ATGACACATAAGGTTGTACCCACCTCCTACACTAAGTTTACACTCTAGTGTTGATCCGACTATGA
1 ATGACACATAAGGTCGTACCCACCTCCTACACTAAGTCTACACTCTAGTGTTAATCCGAATATGA
*
9291805 CACATAAGGTCGTGCCCACCTCCTGCAATAAGTTTACACTCTAGTTATGATCCGGAT
66 AACATAAGGTCGTGCCCACCTCCTGCAATAAGTTTACACTCTAGTTATGATCCGGAT
* *
9291862 ATGACACATAAGGTCGTGCCCACCTCCTATACTAAGTCTACACTCTAGTGTTAATCC-ATATATG
1 ATGACACATAAGGTCGTACCCACCTCCTACACTAAGTCTACACTCTAGTGTTAATCCGA-ATATG
* * *
9291926 AAACATAAGGTCGTGCCCACCTCCTGCACTAAGTTTACACTGTAGTTCTGATCCGGAT
65 AAACATAAGGTCGTGCCCACCTCCTGCAATAAGTTTACACTCTAGTTATGATCCGGAT
9291984 ATG
1 ATG
9291987 CAGCCCTACT
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
121 1 0.01
122 113 0.99
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (122 bp):
ATGACACATAAGGTCGTACCCACCTCCTACACTAAGTCTACACTCTAGTGTTAATCCGAATATGA
AACATAAGGTCGTGCCCACCTCCTGCAATAAGTTTACACTCTAGTTATGATCCGGAT
Found at i:9292153 original size:22 final size:22
Alignment explanation
Indices: 9292127--9292173 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
9292117 ACCCAAAATA
* *
9292127 ATATTCGTAATAAACATCATAT
1 ATATTCATAATAAACACCATAT
*
9292149 ATATTCATGATAAACACCATAT
1 ATATTCATAATAAACACCATAT
9292171 ATA
1 ATA
9292174 ATAACCAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATTCATAATAAACACCATAT
Found at i:9293339 original size:20 final size:19
Alignment explanation
Indices: 9293296--9293340 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
9293286 AAAAATGGCC
* *
9293296 CAATTTCACATTCTAACAT
1 CAATTTCACACTCAAACAT
9293315 CAATTTCAACACTCAAACAT
1 CAATTTC-ACACTCAAACAT
*
9293335 TAATTT
1 CAATTT
9293341 TTAGTGTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTTCACACTCAAACAT
Found at i:9294549 original size:29 final size:29
Alignment explanation
Indices: 9294509--9294565 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
9294499 CCTTAAACTT
* *
9294509 TTTCAAACTTTATACTTTTGA-CACTAAAC
1 TTTCAAAATTTACA-TTTTGATCACTAAAC
9294538 TTTCAAAATTTACATTTTGATCACTAAA
1 TTTCAAAATTTACATTTTGATCACTAAA
9294566 TAAAATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTCAAAATTTACATTTTGATCACTAAAC
Found at i:9297331 original size:19 final size:19
Alignment explanation
Indices: 9297289--9297349 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
9297279 TGAAGTCTCC
*
9297289 CATTTCTAT-CTTCTCTTATT
1 CATTTCT-TCCTTCT-TTCTT
9297309 CATTTCTTCCTTCTTTCTT
1 CATTTCTTCCTTCTTTCTT
* *
9297328 CATTTATTCATTCTTTCTT
1 CATTTCTTCCTTCTTTCTT
9297347 CAT
1 CAT
9297350 CTCCCTCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 25 0.68
20 12 0.32
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (19 bp):
CATTTCTTCCTTCTTTCTT
Found at i:9297904 original size:15 final size:15
Alignment explanation
Indices: 9297884--9297942 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
9297874 GTATTGACAT
9297884 TGTGAGTACCAATAC
1 TGTGAGTACCAATAC
* * ** *
9297899 TATGAGTCCCGGTAT
1 TGTGAGTACCAATAC
*
9297914 TGTGAGTATCAATAC
1 TGTGAGTACCAATAC
*
9297929 TGCGAGTACCAATA
1 TGTGAGTACCAATA
9297943 TTCTTCTTAT
Statistics
Matches: 31, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (15 bp):
TGTGAGTACCAATAC
Found at i:9299434 original size:13 final size:13
Alignment explanation
Indices: 9299416--9299443 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9299406 TCTCATATAG
9299416 ACTCTATCAACTC
1 ACTCTATCAACTC
9299429 ACTCTATCAACTC
1 ACTCTATCAACTC
9299442 AC
1 AC
9299444 CCAACTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (13 bp):
ACTCTATCAACTC
Found at i:9302234 original size:24 final size:24
Alignment explanation
Indices: 9302207--9302252 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
9302197 TTTGATAATT
9302207 TAATT-TTACTCTATTTC-ATTTCAC
1 TAATTATT-CTCT-TTTCAATTTCAC
9302231 TAATTATTCTCTTTTCAATTTC
1 TAATTATTCTCTTTTCAATTTC
9302253 TTCACTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 14 0.70
25 2 0.10
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATTATTCTCTTTTCAATTTCAC
Found at i:9302710 original size:17 final size:17
Alignment explanation
Indices: 9302690--9302726 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
9302680 TACAAATTCA
9302690 AAAAATATTTTTATTTT
1 AAAAATATTTTTATTTT
9302707 AAAAATATTTTTATTTT
1 AAAAATATTTTTATTTT
9302724 AAA
1 AAA
9302727 TAAATTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAAATATTTTTATTTT
Found at i:9306681 original size:8 final size:8
Alignment explanation
Indices: 9306618--9306693 Score: 52
Period size: 8 Copynumber: 9.9 Consensus size: 8
9306608 CTTATATGTC
9306618 TATGTG-A
1 TATGTGAA
9306625 TAT-TGAA
1 TATGTGAA
* *
9306632 CTACGTGAT
1 -TATGTGAA
*
9306641 TATATGAA
1 TATGTGAA
9306649 TATGTGAA
1 TATGTGAA
9306657 -ATGTGAA
1 TATGTGAA
* *
9306664 AATG-GTA
1 TATGTGAA
9306671 TATGTGAA
1 TATGTGAA
* *
9306679 TATATGAC
1 TATGTGAA
9306687 TATGTGA
1 TATGTGA
9306694 TAAACTATAT
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
6 2 0.04
7 16 0.31
8 31 0.60
9 3 0.06
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (8 bp):
TATGTGAA
Found at i:9306817 original size:23 final size:23
Alignment explanation
Indices: 9306782--9306883 Score: 105
Period size: 23 Copynumber: 4.4 Consensus size: 23
9306772 GAGTCGAGGG
** *
9306782 TTCTACGCAGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
9306805 TTCTACGTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
9306828 TTCTACGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* ** * *
9306851 TACTATATGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
9306874 TTCTATGTGG
1 TTCTACGTGG
9306884 CACTTCAGTG
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:9306834 original size:46 final size:46
Alignment explanation
Indices: 9306782--9306878 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
9306772 GAGTCGAGGG
* * *
9306782 TTCTACGCAGTCCTTCGGGATAATTCTACGTGGTCCTTTGGGACAT
1 TTCTACGCAGTCCTTCGGGACAATACTACATGGTCCTTTGGGACAT
** *
9306828 TTCTACGTGGTCCTTCGGGACAATACTATATGGTCCTTTGGGACAT
1 TTCTACGCAGTCCTTCGGGACAATACTACATGGTCCTTTGGGACAT
9306874 TTCTA
1 TTCTA
9306879 TGTGGCACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (46 bp):
TTCTACGCAGTCCTTCGGGACAATACTACATGGTCCTTTGGGACAT
Found at i:9306899 original size:24 final size:24
Alignment explanation
Indices: 9306872--9306930 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
9306862 CCTTTGGGAC
*
9306872 ATTTCTATGTGGCACTTC-AGTGCA
1 ATTTCTATGAGGCACTTCGA-TGCA
* *
9306896 ATTTCTACGAGGCGCTTCGATGCA
1 ATTTCTATGAGGCACTTCGATGCA
*
9306920 ATTTATATGAG
1 ATTTCTATGAG
9306931 CTGTGGTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.36
Consensus pattern (24 bp):
ATTTCTATGAGGCACTTCGATGCA
Found at i:9308127 original size:21 final size:20
Alignment explanation
Indices: 9308102--9308141 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
9308092 TTAAATAATA
*
9308102 AAAAATGATGAATCTATTTAG
1 AAAAATAATGAATCT-TTTAG
9308123 AAAAATAATGAATCTTTTA
1 AAAAATAATGAATCTTTTA
9308142 TTTAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
AAAAATAATGAATCTTTTAG
Found at i:9324491 original size:19 final size:19
Alignment explanation
Indices: 9324467--9324539 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
9324457 TAGATTACTA
9324467 AAAAGTATCAAAACTATTG
1 AAAAGTATCAAAACTATTG
* *
9324486 AAAAGT-TTAGAAACTATAG
1 AAAAGTATCA-AAACTATTG
* *
9324505 TAAAAGTTTCAAAACTCTTG
1 -AAAAGTATCAAAACTATTG
** *
9324525 AGGAGTATCGAAACT
1 AAAAGTATCAAAACT
9324540 TGTCACGCGA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
18 2 0.05
19 25 0.60
20 13 0.31
21 2 0.05
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (19 bp):
AAAAGTATCAAAACTATTG
Found at i:9324519 original size:20 final size:19
Alignment explanation
Indices: 9324467--9324520 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
9324457 TAGATTACTA
* *
9324467 AAAAGTATCAAAACTATTG
1 AAAAGTTTCAAAACTATAG
9324486 AAAAGTTT-AGAAACTATAG
1 AAAAGTTTCA-AAACTATAG
9324505 TAAAAGTTTCAAAACT
1 -AAAAGTTTCAAAACT
9324521 CTTGAGGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 13 0.43
21 1 0.03
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (19 bp):
AAAAGTTTCAAAACTATAG
Found at i:9326826 original size:19 final size:20
Alignment explanation
Indices: 9326782--9326818 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
9326772 ATATTTTTTG
*
9326782 TAAAATTATTTTTAAATCCC
1 TAAAATTATTTTCAAATCCC
9326802 TAAAATT-TTTTCAAATC
1 TAAAATTATTTTCAAATC
9326819 TTTAAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATTATTTTCAAATCCC
Found at i:9328636 original size:24 final size:23
Alignment explanation
Indices: 9328607--9328653 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
9328597 TGTTTAGTTA
9328607 AAAATAA-AAAATAATTTAATAATT
1 AAAATAATAAAA-AATTTAA-AATT
9328631 AAAATAATAAAAAATTTAAAATT
1 AAAATAATAAAAAATTTAAAATT
9328654 TAGTAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 14 0.64
25 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAATAATAAAAAATTTAAAATT
Found at i:9328879 original size:8 final size:8
Alignment explanation
Indices: 9328868--9328903 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
9328858 GTTTTATATT
9328868 TTTTAAAA
1 TTTTAAAA
*
9328876 TTTTATAA
1 TTTTAAAA
*
9328884 TTTTATAA
1 TTTTAAAA
9328892 TTTTAAAA
1 TTTTAAAA
9328900 TTTT
1 TTTT
9328904 TCAATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTTAAAA
Found at i:9328919 original size:24 final size:24
Alignment explanation
Indices: 9328866--9328922 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
9328856 TAGTTTTATA
* *
9328866 TTTTTTAAAATTTTATAATTTTAT
1 TTTTTTAAAATTTTATAATATAAT
**
9328890 AATTTTAAAATTTT-TCAATATAAT
1 TTTTTTAAAATTTTAT-AATATAAT
9328914 TTTTTTAAA
1 TTTTTTAAA
9328923 TCCAGATTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTTAAAATTTTATAATATAAT
Found at i:9329358 original size:97 final size:93
Alignment explanation
Indices: 9329233--9329420 Score: 322
Period size: 97 Copynumber: 2.0 Consensus size: 93
9329223 AAATTTTGTG
9329233 TCCATCAAATAATATTTCATACCAAGATTTTAACCTCGTTTTACCAAAAAAAAAAAAAACACATT
1 TCCATCAAATAATATTTCATACCAAGATTTTAACCTCGTTTTACC---AAAAAAAAAAA-ACATT
9329298 TAAACAATCAATAATTACCTCTCAGATATCGT
62 TAAACAATCAATAATTACCTCTCAGATATCGT
**
9329330 TCCATCAAATAATATTTCATACCAAGATTTTAACCTCGTTTTACCCCAAAAAAAAAACATTTAAA
1 TCCATCAAATAATATTTCATACCAAGATTTTAACCTCGTTTTACCAAAAAAAAAAAACATTTAAA
9329395 CAATCAATAATTACCTCTCAGATATC
66 CAATCAATAATTACCTCTCAGATATC
9329421 TATCAAATAT
Statistics
Matches: 89, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
93 35 0.39
94 9 0.10
97 45 0.51
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (93 bp):
TCCATCAAATAATATTTCATACCAAGATTTTAACCTCGTTTTACCAAAAAAAAAAAACATTTAAA
CAATCAATAATTACCTCTCAGATATCGT
Found at i:9334012 original size:21 final size:21
Alignment explanation
Indices: 9333986--9334025 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9333976 CAGAACCCCA
*
9333986 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
9334007 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
9334026 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:9334054 original size:19 final size:20
Alignment explanation
Indices: 9334008--9334067 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
9333998 TTCCCCTGTG
9334008 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
9334031 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
9334050 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
9334068 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:9343865 original size:21 final size:20
Alignment explanation
Indices: 9343841--9343880 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
9343831 ATTTTAAAAA
*
9343841 TATTTATTATATCATTATTTT
1 TATTTATAATAT-ATTATTTT
9343862 TATTTATAATATATTATTT
1 TATTTATAATATATTATTT
9343881 AATGAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTATAATATATTATTTT
Found at i:9349852 original size:64 final size:66
Alignment explanation
Indices: 9349759--9349915 Score: 167
Period size: 66 Copynumber: 2.4 Consensus size: 66
9349749 GGTACTAGGG
* * * * * * * ** *
9349759 GTGCATCGGTACACTAATTACTTTCGATGTTTCAAAGA-GCT-AGGAGTGCATTGATGCAT-GGT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAATACTCAAGAGTGCATCAATGCATAGCT
9349821 AT
66 -T
* *
9349823 GTGCATCGGTACACAAAATGCATTGGATGTTTCAAAAATATTCAAGAGTGCATCAATGCATAGCT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAATACTCAAGAGTGCATCAATGCATAGCT
9349888 T
66 T
*
9349889 GTGCATCGGTACACAAAATGAATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
9349916 AATGGGTGTG
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 32 0.42
65 1 0.01
66 41 0.54
67 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (66 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAATACTCAAGAGTGCATCAATGCATAGCT
T
Found at i:9350336 original size:17 final size:17
Alignment explanation
Indices: 9350299--9350340 Score: 77
Period size: 16 Copynumber: 2.5 Consensus size: 17
9350289 ATAAAAATTA
9350299 CTCCCCCTTACTATATT
1 CTCCCCCTTACTATATT
9350316 -TCCCCCTTACTATATT
1 CTCCCCCTTACTATATT
9350332 CTCCCCCTT
1 CTCCCCCTT
9350341 TTTGTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.14, C:0.45, G:0.00, T:0.40
Consensus pattern (17 bp):
CTCCCCCTTACTATATT
Found at i:9352589 original size:23 final size:21
Alignment explanation
Indices: 9352552--9352605 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
9352542 AGCAGAGTGC
* *
9352552 ATCGATGAACATTCAAGGAATGT
1 ATCGATGCACCTTCAAGG--TGT
* *
9352575 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACCTTCAAGGTGT
9352596 ATCGATGCAC
1 ATCGATGCAC
9352606 ATTAAAGGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 12 0.46
23 14 0.54
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (21 bp):
ATCGATGCACCTTCAAGGTGT
Found at i:9352608 original size:44 final size:43
Alignment explanation
Indices: 9352547--9352690 Score: 166
Period size: 43 Copynumber: 3.3 Consensus size: 43
9352537 TGCACAGCAG
* * * *
9352547 AGTGCATCGATGAACATTCAAGGAATGTATCGGTGCAC-CTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTC-TC-T
* * * *
9352591 GGTGTATCGATGCACATTAAAGGGATGCATTGGTACACTCTCT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTCTCT
*
9352634 AGTGTATCGATGCACATTCAAAGG-ATGCATTGGTACACTCTCT
1 AGTGTATCGATGCACATTC-AAGGAATGCATCGGTACACTCTCT
9352677 AGTGTATCGATGCA
1 AGTGTATCGATGCA
9352691 TGAAGCACAA
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
43 51 0.58
44 36 0.41
45 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGTACACTCTCT
Found at i:9352646 original size:43 final size:43
Alignment explanation
Indices: 9352592--9352690 Score: 182
Period size: 43 Copynumber: 2.3 Consensus size: 43
9352582 CACCTTCATG
9352592 GTGTATCGATGCACATT-AAAGGGATGCATTGGTACACTCTCTA
1 GTGTATCGATGCACATTCAAA-GGATGCATTGGTACACTCTCTA
9352635 GTGTATCGATGCACATTCAAAGGATGCATTGGTACACTCTCTA
1 GTGTATCGATGCACATTCAAAGGATGCATTGGTACACTCTCTA
9352678 GTGTATCGATGCA
1 GTGTATCGATGCA
9352691 TGAAGCACAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 52 0.95
44 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (43 bp):
GTGTATCGATGCACATTCAAAGGATGCATTGGTACACTCTCTA
Found at i:9354655 original size:15 final size:15
Alignment explanation
Indices: 9354637--9354671 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
9354627 AGCATCATGA
9354637 GTTTCCTCATCTTTC
1 GTTTCCTCATCTTTC
*
9354652 GTTTCCTCGTCTTTC
1 GTTTCCTCATCTTTC
9354667 GTTTC
1 GTTTC
9354672 TTCCTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.31, G:0.11, T:0.54
Consensus pattern (15 bp):
GTTTCCTCATCTTTC
Found at i:9356532 original size:21 final size:20
Alignment explanation
Indices: 9356506--9356552 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
9356496 GAGATTATTT
9356506 TCATTTTTTAATTTTAAAATA
1 TCATTTTTTAATTTTAAAA-A
*
9356527 TCATTTTTTTATTTTAAAAA
1 TCATTTTTTAATTTTAAAAA
9356547 T-ATTTT
1 TCATTTT
9356553 CTCATAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 5 0.20
20 2 0.08
21 18 0.72
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TCATTTTTTAATTTTAAAAA
Found at i:9359317 original size:272 final size:272
Alignment explanation
Indices: 9358826--9359367 Score: 1012
Period size: 272 Copynumber: 2.0 Consensus size: 272
9358816 GAATATTCTT
9358826 TAAAAATGATTGTGAAATCTTAAAATTCAATAACCCTTAATTTGTTATATCAAAACATCAAAATG
1 TAAAAATGATTGTGAAATCTTAAAATTCAATAACCCTTAATTTGTTATATCAAAACATCAAAATG
9358891 TTTTCAACAAAGTCTTCTTAACATTTAATACCCTATCTCTTAGCTTTCCAACGCAGTTTGAATCA
66 TTTTCAACAAAGTCTTCTTAACATTTAATACCCTATCTCTTAGCTTTCCAACGCAGTTTGAATCA
* *
9358956 TATCAATTTGATATCGTGTTCTCGAGATATTTCCAAATTACTGAAGATAATGCAGGCTGGAAATT
131 CATCAATTTGATATCGTGTTCTCGAGATATTTCCAAATTACTGAAGACAATGCAGGCTGGAAATT
* * * *
9359021 AATATGGGATTTGAAACTATTCATCTCATTCAATGGGCTTATTCATGAGAAGTATTAATGGAGAC
196 AATATGGGATTTGAAACCATTCATCTCATTCAATGGACTTATGCATGAGAAGCATTAATGGAGAC
9359086 ATGCATGGACTG
261 ATGCATGGACTG
9359098 TAAAAATGATTGTGAAATCTTAAAATTCAATAACCCTTAATTTGTTATATCAAAACATCAAAATG
1 TAAAAATGATTGTGAAATCTTAAAATTCAATAACCCTTAATTTGTTATATCAAAACATCAAAATG
*
9359163 TTTTCAACTAAGTCTTCTTAACATTTAATACCCTATCTCTTAGCTTTCCAACGCAGTTTGAATCA
66 TTTTCAACAAAGTCTTCTTAACATTTAATACCCTATCTCTTAGCTTTCCAACGCAGTTTGAATCA
*
9359228 CATCAATTTTATATCGTGTTCTCGAGATATTTCCAAATTACTGAAGACAATGCAGGCTGGAAATT
131 CATCAATTTGATATCGTGTTCTCGAGATATTTCCAAATTACTGAAGACAATGCAGGCTGGAAATT
9359293 AATATGGGATTTGAAACCATTCATCTCATTCAATGGACTTATGCATGAGAAGCATTAATGGAGAC
196 AATATGGGATTTGAAACCATTCATCTCATTCAATGGACTTATGCATGAGAAGCATTAATGGAGAC
9359358 ATGCATGGAC
261 ATGCATGGAC
9359368 GAGAAAATAA
Statistics
Matches: 262, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
272 262 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (272 bp):
TAAAAATGATTGTGAAATCTTAAAATTCAATAACCCTTAATTTGTTATATCAAAACATCAAAATG
TTTTCAACAAAGTCTTCTTAACATTTAATACCCTATCTCTTAGCTTTCCAACGCAGTTTGAATCA
CATCAATTTGATATCGTGTTCTCGAGATATTTCCAAATTACTGAAGACAATGCAGGCTGGAAATT
AATATGGGATTTGAAACCATTCATCTCATTCAATGGACTTATGCATGAGAAGCATTAATGGAGAC
ATGCATGGACTG
Found at i:9359630 original size:34 final size:34
Alignment explanation
Indices: 9359587--9359663 Score: 145
Period size: 34 Copynumber: 2.3 Consensus size: 34
9359577 GGCTATGAAG
*
9359587 ATACATTCATGAAGATTTATTCATTTAATTCATT
1 ATACATTCATGAAGATTTATTCATTTAATTCATC
9359621 ATACATTCATGAAGATTTATTCATTTAATTCATC
1 ATACATTCATGAAGATTTATTCATTTAATTCATC
9359655 ATACATTCA
1 ATACATTCA
9359664 CCATTGGTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.44
Consensus pattern (34 bp):
ATACATTCATGAAGATTTATTCATTTAATTCATC
Found at i:9361944 original size:18 final size:18
Alignment explanation
Indices: 9361921--9361967 Score: 71
Period size: 16 Copynumber: 2.7 Consensus size: 18
9361911 TGAAAAAATC
*
9361921 TTTAATTAAAAAATAACA
1 TTTAATTAAAAAATAAAA
9361939 TTTAATT--AAAATAAAA
1 TTTAATTAAAAAATAAAA
9361955 TTTAATTAAAAAA
1 TTTAATTAAAAAA
9361968 GTTTCGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 15 0.58
18 11 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAATTAAAAAATAAAA
Found at i:9362150 original size:24 final size:21
Alignment explanation
Indices: 9362106--9362165 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 21
9362096 TGTAGTATAT
9362106 AAAAT-TTGATTTTTTATTAA-A
1 AAAATGTT-ATTTTTT-TTAATA
9362127 AAATATGTTATTTTTTTTAATA
1 AAA-ATGTTATTTTTTTTAATA
9362149 AAAATGTTATTTTTTTT
1 AAAATGTTATTTTTTTT
9362166 TGAAATTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 21 0.58
22 13 0.36
23 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (21 bp):
AAAATGTTATTTTTTTTAATA
Found at i:9362204 original size:32 final size:33
Alignment explanation
Indices: 9362162--9362237 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 33
9362152 ATGTTATTTT
* *
9362162 TTTTTGAAATTTGAAATTAAAGAATATGTTA-A
1 TTTTAGAAATTTGAAATTAAAAAATATGTTATA
* *
9362194 TTTTAGAAATTTGTATTTAAAAAATATGTTATA
1 TTTTAGAAATTTGAAATTAAAAAATATGTTATA
9362227 TTTTA-AAATTT
1 TTTTAGAAATTT
9362238 TAATTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 33 0.85
33 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (33 bp):
TTTTAGAAATTTGAAATTAAAAAATATGTTATA
Found at i:9369849 original size:28 final size:28
Alignment explanation
Indices: 9369809--9369865 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
9369799 AACAATTGCT
*
9369809 TTCCACCGAAAGTGCAAGTGGGAGATAG
1 TTCCACCGAAAGTGCAAGTGGGAAATAG
9369837 TTCCACCGAAAGTGCAAGTGGGAAATAG
1 TTCCACCGAAAGTGCAAGTGGGAAATAG
9369865 T
1 T
9369866 CAAATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.19
Consensus pattern (28 bp):
TTCCACCGAAAGTGCAAGTGGGAAATAG
Found at i:9375983 original size:41 final size:42
Alignment explanation
Indices: 9375922--9376025 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 42
9375912 TCAAAAAGGA
** *
9375922 AAAAAAAGTAACTTACTCCTCCATCTTGAGGTTTTGACACTTT
1 AAAAAAA-TAACTTGTTCCTCCATCTTGAGGTCTTGACACTTT
* *
9375965 -GAAAAATAACTTGTTCCTCCATCTTGAGGTCTTGACAGTTT
1 AAAAAAATAACTTGTTCCTCCATCTTGAGGTCTTGACACTTT
*
9376006 AAAAAAATAATTTGTTCCTC
1 AAAAAAATAACTTGTTCCTC
9376026 TATTTTAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.58
42 22 0.42
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (42 bp):
AAAAAAATAACTTGTTCCTCCATCTTGAGGTCTTGACACTTT
Found at i:9376551 original size:3 final size:3
Alignment explanation
Indices: 9376543--9376602 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
9376533 TTTTTCATTC
* *
9376543 TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
9376589 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
9376603 AACAAATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:9387159 original size:54 final size:53
Alignment explanation
Indices: 9387084--9387346 Score: 323
Period size: 54 Copynumber: 4.9 Consensus size: 53
9387074 AACATATGTT
* * *
9387084 CAGAAGCCATAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTG
1 CAGAAGCCACATGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTG-G
* *
9387138 CATAAGCCACGTGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGG
1 CAGAAGCCACATGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCT-GG
* * *
9387192 CAGAAGCCACAAG-AAAGAATGAATGCGTTGTCAAATATTTTACGAACATCTGGG
1 CAGAAGCCACATGAAAAG-ATGAATGTGTTGTCAAATGTTTTACGAACATCT-GG
* * * *
9387246 AAGAAGCCACA-GGAAAGAATGAACGTGTTATCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACATGAAAAG-ATGAATGTGTTGTCAAATGTTTTACGAACATCTG-G
* * *
9387300 CAGAAACCACATGAGATGATGAATGTGTTGTCAAATGTTTTACGAAC
1 CAGAAGCCACATGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
9387347 CAGTTATTCT
Statistics
Matches: 181, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
53 6 0.03
54 171 0.94
55 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (53 bp):
CAGAAGCCACATGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGG
Found at i:9387734 original size:22 final size:22
Alignment explanation
Indices: 9387706--9387810 Score: 169
Period size: 22 Copynumber: 4.8 Consensus size: 22
9387696 CATATATACA
9387706 TCTCTCTTCAAAGATGATAGA-T
1 TCTCTCTTCAAAGATGATA-ACT
9387728 TCTCTCTTCAAAGATGATAACT
1 TCTCTCTTCAAAGATGATAACT
9387750 TCTCTCTTCAAAGATGATAACT
1 TCTCTCTTCAAAGATGATAACT
9387772 TCTCTCTTCAAAGATGATAGA-T
1 TCTCTCTTCAAAGATGATA-ACT
*
9387794 TCTCTTTTCAAAGATGA
1 TCTCTCTTCAAAGATGA
9387811 AAGCTTTATT
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
21 1 0.01
22 78 0.98
23 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (22 bp):
TCTCTCTTCAAAGATGATAACT
Found at i:9388446 original size:45 final size:45
Alignment explanation
Indices: 9388386--9388900 Score: 737
Period size: 45 Copynumber: 11.4 Consensus size: 45
9388376 CCATTTCTCA
* * * *
9388386 CATCCGTAAGTCCTTCACTGCATGATGTTTTCAAAACCTTAGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
9388431 CATGTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
9388476 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGA-CTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA-ACCTTCGGGT
* * * *
9388521 CACCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAGCCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
9388566 CATGTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
9388611 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAGCCTTTAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
9388656 CATCTGTAAGTCCC-TCAGTGCATGATGTTTTCAAAGCCTTTGGGT
1 CATCTGTAAG-CCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
9388701 CATTTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
9388746 CATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
9388791 CATCTGTAAGCCCTTCAGTGCAAGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
9388836 CATCTGTAAGCCATTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
9388881 TATCTGTAAGACCTACAGTG
1 CATCTGTAAGCCCTTCAGTG
9388901 TAAGATAACA
Statistics
Matches: 425, Mismatches: 41, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
44 2 0.00
45 420 0.99
46 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:9388454 original size:20 final size:20
Alignment explanation
Indices: 9388431--9388499 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
9388421 ACCTTAGGGT
9388431 CATGTGTAAGCCCTTCAGTG
1 CATGTGTAAGCCCTTCAGTG
**
9388451 CATGATGTTATCAAAACCTTCGAGT-
1 CATG-TG---T-AAGCCCTTC-AGTG
*
9388476 CATCTGTAAGCCCTTCAGTG
1 CATGTGTAAGCCCTTCAGTG
9388496 CATG
1 CATG
9388500 ATGTTTTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.08
20 14 0.39
21 3 0.08
24 3 0.08
25 10 0.28
26 3 0.08
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (20 bp):
CATGTGTAAGCCCTTCAGTG
Found at i:9389084 original size:3 final size:3
Alignment explanation
Indices: 9389076--9389137 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
9389066 TTTTTCATTC
* *
9389076 TAT TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9389124 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
9389138 AACAAATATT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:9390639 original size:8 final size:8
Alignment explanation
Indices: 9390626--9390655 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9390616 ATTACTTTAA
9390626 TTATTATT
1 TTATTATT
9390634 TTATTATT
1 TTATTATT
9390642 TTATTATT
1 TTATTATT
*
9390650 ATATTA
1 TTATTA
9390656 GTCATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTATTATT
Found at i:9392787 original size:70 final size:64
Alignment explanation
Indices: 9392657--9392794 Score: 152
Period size: 67 Copynumber: 2.1 Consensus size: 64
9392647 GGTCGAAAGC
* *
9392657 CAACTTCCCCTCCCCTTCCCCAACCTTTCATTGTCTGAAATAAAAAAAAAATTGCTTTCACCCT
1 CAACTTCCCCTCCCCTTCCCCAACCTTTCATTGTCTAAAACAAAAAAAAAATTGCTTTCACCCT
* * *
9392721 CAACTCTCCCCTCCCCTTTCCTCC-CCCATTTCATTGTTTAAAACAAAAATAAAATTTCTGCTTT
1 CAACT-TCCCCTCCCC-TTCC-CCAACC-TTTCATTGTCTAAAACAAAAA-AAAA-AT-TGCTTT
*
9392785 CACTCT
59 CACCCT
9392791 CAAC
1 CAAC
9392795 ACCCCCAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
64 5 0.08
65 10 0.16
66 6 0.10
67 20 0.33
68 4 0.07
69 1 0.02
70 15 0.25
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (64 bp):
CAACTTCCCCTCCCCTTCCCCAACCTTTCATTGTCTAAAACAAAAAAAAAATTGCTTTCACCCT
Found at i:9396777 original size:29 final size:29
Alignment explanation
Indices: 9396701--9396777 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
9396691 GTAAAAGAGT
* *
9396701 TTAATTGATTTTTTATT-AAGTTTGAGGGC
1 TTAATTAATTTTTT-TTAAAGTTTGAGGAC
* *
9396730 TTAATTAATATTTTATAAAGTTTGAGGAC
1 TTAATTAATTTTTTTTAAAGTTTGAGGAC
*
9396759 TTATTTAATTTTTTTTAAA
1 TTAATTAATTTTTTTTAAA
9396778 AATAAAGGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.53
Consensus pattern (29 bp):
TTAATTAATTTTTTTTAAAGTTTGAGGAC
Found at i:9399444 original size:12 final size:12
Alignment explanation
Indices: 9399406--9399449 Score: 67
Period size: 11 Copynumber: 3.9 Consensus size: 12
9399396 TATTTATCTA
9399406 TAAAAAAAA--T
1 TAAAAAAAATTT
9399416 TAAAAAAAATTT
1 TAAAAAAAATTT
9399428 T-AAAAAAATTT
1 TAAAAAAAATTT
9399439 TAAAAAAAATT
1 TAAAAAAAATT
9399450 CTGGATATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.29
11 11 0.35
12 11 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TAAAAAAAATTT
Found at i:9399518 original size:15 final size:16
Alignment explanation
Indices: 9399477--9399518 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
9399467 CTACATACGA
9399477 GTACCCGCAAAATCCGG
1 GTACCCG-AAAATCCGG
* *
9399494 GTTCCTGAAAA-CCGG
1 GTACCCGAAAATCCGG
9399509 GTACCCGAAA
1 GTACCCGAAA
9399519 CACCCGGCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 4 0.19
17 5 0.24
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (16 bp):
GTACCCGAAAATCCGG
Found at i:9399762 original size:35 final size:35
Alignment explanation
Indices: 9399710--9399797 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
9399700 AAAATTGAAA
* * *
9399710 CAAACTTAAATACTTAAAAATCCGAATTACATAATT
1 CAAACATAAA-ACTTAAAAATCCAAATTACATAATC
* * * *
9399746 CAAACATAAAATTTAAACATTCAAATTGCATAATC
1 CAAACATAAAACTTAAAAATCCAAATTACATAATC
*
9399781 CAAATATAAAACTTAAA
1 CAAACATAAAACTTAAA
9399798 TGATAAAAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 34 0.79
36 9 0.21
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.28
Consensus pattern (35 bp):
CAAACATAAAACTTAAAAATCCAAATTACATAATC
Found at i:9400824 original size:3 final size:3
Alignment explanation
Indices: 9400806--9400853 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
9400796 GATTAAAAAA
*
9400806 TAT TAT TAGT TA- TAT TAT TAT TAT TAT TAT TAT TAAT AAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
9400852 TA
1 TA
9400854 ATTTACATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:9402121 original size:2 final size:2
Alignment explanation
Indices: 9402114--9402160 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
9402104 ATTAATTTGA
9402114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9402156 AT AT A
1 AT AT A
9402161 ACATTAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9413359 original size:10 final size:10
Alignment explanation
Indices: 9413330--9413363 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
9413320 GTTGAAGAAG
9413330 AAGAAAAAGAA
1 AAGAAAAAG-A
*
9413341 AAGAGAAAGA
1 AAGAAAAAGA
9413351 AAGAAAAAGA
1 AAGAAAAAGA
9413361 AAG
1 AAG
9413364 GAGGGTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:9414989 original size:3 final size:3
Alignment explanation
Indices: 9414971--9415003 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
9414961 GATTGAAAAA
9414971 TAT TAT TAGT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
9415004 CAATTTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:9416325 original size:2 final size:2
Alignment explanation
Indices: 9416318--9416352 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9416308 AATTGAATAC
9416318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9416353 ATTTAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9436057 original size:19 final size:19
Alignment explanation
Indices: 9436033--9436072 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9436023 TTTATATCTC
9436033 TCATTTCATCTTCTTCCTT
1 TCATTTCATCTTCTTCCTT
** *
9436052 TCATTTTTTCTTTTTCCTT
1 TCATTTCATCTTCTTCCTT
9436071 TC
1 TC
9436073 TCTATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (19 bp):
TCATTTCATCTTCTTCCTT
Found at i:9436094 original size:21 final size:22
Alignment explanation
Indices: 9436054--9436095 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
9436044 TCTTCCTTTC
* *
9436054 ATTTTTTCTTTTTCCTTTCTCT
1 ATTTTTTCTTTCTCCATTCTCT
9436076 ATTTTTTC-TTCTCCATTCTC
1 ATTTTTTCTTTCTCCATTCTC
9436096 CACCCAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTTTCTTTCTCCATTCTCT
Found at i:9436670 original size:20 final size:20
Alignment explanation
Indices: 9436607--9436678 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
9436597 TTATGTAGGG
*
9436607 AGTATTGATACTCTTGCCAA
1 AGTATGGATACTCTTGCCAA
* **
9436627 AGTATGGAAACTCTTATCAA
1 AGTATGGATACTCTTGCCAA
**
9436647 AGTATGGATACTCTTGCCCT
1 AGTATGGATACTCTTGCCAA
*
9436667 AGTATCGATACT
1 AGTATGGATACT
9436679 AATTTTGGTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (20 bp):
AGTATGGATACTCTTGCCAA
Found at i:9439813 original size:111 final size:111
Alignment explanation
Indices: 9439616--9439824 Score: 310
Period size: 111 Copynumber: 1.9 Consensus size: 111
9439606 GGTGCCACTA
*
9439616 ATGAAAGTTATCGATCGATTTTGATTAATGCATAACGATGCATTATTGACATAAAAGGTGCCACT
1 ATGAAAGCTATCGATCGATTTTGATTAATGCATAACGATGCATTATTGACATAAAAGGTGCCACT
* * * **
9439681 CATGGTGTTCATAAAAGGTGAATTACCATTTCGACATAGTTCGTGT
66 AATGGTATTCATAAAAAGTGAAAGACCATTTCGACATAGTTCGTGT
* * * * * *
9439727 ATGAAAGCTATCGATCGATTTTGTTTAATGCATAATGGTGTATTATTGGCATAAAAGGTTCCACT
1 ATGAAAGCTATCGATCGATTTTGATTAATGCATAACGATGCATTATTGACATAAAAGGTGCCACT
9439792 AATGGTATTCATAAAAAGTGAAAGACCATTTCG
66 AATGGTATTCATAAAAAGTGAAAGACCATTTCG
9439825 GCACTTCGGT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
111 86 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (111 bp):
ATGAAAGCTATCGATCGATTTTGATTAATGCATAACGATGCATTATTGACATAAAAGGTGCCACT
AATGGTATTCATAAAAAGTGAAAGACCATTTCGACATAGTTCGTGT
Found at i:9446260 original size:20 final size:18
Alignment explanation
Indices: 9446235--9446271 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
9446225 ATGTTACAAC
9446235 AAATGTTTTAGTTTATATTA
1 AAATGTTTT-GTTT-TATTA
9446255 AAATGTTTTGTTTTATT
1 AAATGTTTTGTTTTATT
9446272 TTCGAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (18 bp):
AAATGTTTTGTTTTATTA
Found at i:9447010 original size:111 final size:111
Alignment explanation
Indices: 9446814--9447014 Score: 312
Period size: 111 Copynumber: 1.8 Consensus size: 111
9446804 TAGTGAAAGT
* * * *
9446814 TATTTATCAATTTTGATTAATGCATAACGGTGCATTATCGGCATAAAATGTGCCACTCATGGTAT
1 TATTGATCAATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGGTAT
* * *
9446879 TCATAATAGGTTAATTACCATTTCGACATACTTCGTTTATGAAAAC
66 TCATAAAAGGTGAATGACCATTTCGACATACTTCGTTTATGAAAAC
* * *
9446925 TATTGATCGATTTTGTTTAATGCATAACAGTTCATTATCGGCATAAAAGGTGCCACTAATGGTAT
1 TATTGATCAATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGGTAT
9446990 TCATAAAAGGTGAATGACCATTTCG
66 TCATAAAAGGTGAATGACCATTTCG
9447015 GCACTTCGGT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 80 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (111 bp):
TATTGATCAATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAATGGTAT
TCATAAAAGGTGAATGACCATTTCGACATACTTCGTTTATGAAAAC
Found at i:9447507 original size:20 final size:18
Alignment explanation
Indices: 9447482--9447518 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
9447472 ATGTTACAAC
9447482 AAATGTTTTAGTTTATATTA
1 AAATGTTTT-GTTT-TATTA
9447502 AAATGTTTTGTTTTATT
1 AAATGTTTTGTTTTATT
9447519 TTCGAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (18 bp):
AAATGTTTTGTTTTATTA
Found at i:9459477 original size:23 final size:22
Alignment explanation
Indices: 9459451--9459507 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
9459441 GGTTTGCATT
*
9459451 GAAGTGACACATAGGTTTGTCCC
1 GAAG-GACACATAGGATTGTCCC
9459474 GAAGGACCACATA-GATTGTCCC
1 GAAGGA-CACATAGGATTGTCCC
9459496 GAAGGAC-CATAG
1 GAAGGACACATAG
9459508 AACCCTCGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 4 0.13
21 1 0.03
22 16 0.52
23 10 0.32
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (22 bp):
GAAGGACACATAGGATTGTCCC
Found at i:9459495 original size:22 final size:23
Alignment explanation
Indices: 9459458--9459504 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
9459448 ATTGAAGTGA
*
9459458 CACATAGGTTTGTCCCGAAGGAC
1 CACATAGGATTGTCCCGAAGGAC
9459481 CACATA-GATTGTCCCGAAGGAC
1 CACATAGGATTGTCCCGAAGGAC
9459503 CA
1 CA
9459505 TAGAACCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (23 bp):
CACATAGGATTGTCCCGAAGGAC
Found at i:9459737 original size:16 final size:15
Alignment explanation
Indices: 9459712--9459751 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
9459702 ATACATATAT
*
9459712 AACATTTTCAGATAG
1 AACATTTTCACATAG
9459727 AACACTTTTCACATAG
1 AACA-TTTTCACATAG
9459743 AACCATTTT
1 AA-CATTTT
9459752 ATGAAACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 16 0.73
17 2 0.09
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (15 bp):
AACATTTTCACATAG
Found at i:9460724 original size:19 final size:19
Alignment explanation
Indices: 9460697--9460735 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9460687 TTAATTAAAC
9460697 CCTTGAGAAGTCAAATATT
1 CCTTGAGAAGTCAAATATT
* *
9460716 CCTTTAGAATTCAAATATT
1 CCTTGAGAAGTCAAATATT
9460735 C
1 C
9460736 ATCATTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (19 bp):
CCTTGAGAAGTCAAATATT
Found at i:9463364 original size:31 final size:32
Alignment explanation
Indices: 9463329--9463413 Score: 129
Period size: 31 Copynumber: 2.7 Consensus size: 32
9463319 AGTATTGCTG
*
9463329 AGCTCGACTCGACTTGAAAACTCTGAAAT-GA
1 AGCTCGACTCGACTCGAAAACTCTGAAATAGA
*
9463360 AGCTCGACTCAACTCGAAAACTCTGAAATAGA
1 AGCTCGACTCGACTCGAAAACTCTGAAATAGA
*
9463392 A-CTCGACTCGACACGAAAACTC
1 AGCTCGACTCGACTCGAAAACTC
9463414 ATGAGCTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 46 0.94
32 3 0.06
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (32 bp):
AGCTCGACTCGACTCGAAAACTCTGAAATAGA
Found at i:9483265 original size:18 final size:20
Alignment explanation
Indices: 9483227--9483267 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
9483217 TTATTCTGTG
9483227 AATGAATAGTTTATCCCCAA
1 AATGAATAGTTTATCCCCAA
9483247 AATGAATAGTTT-T-CCCAA
1 AATGAATAGTTTATCCCCAA
9483265 AAT
1 AAT
9483268 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
19 1 0.05
20 12 0.57
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (20 bp):
AATGAATAGTTTATCCCCAA
Found at i:9483959 original size:14 final size:14
Alignment explanation
Indices: 9483939--9483979 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9483929 AATAACAAGT
9483939 AAATTAAATAAAAA
1 AAATTAAATAAAAA
* *
9483953 TAATTAAAGAAAAA
1 AAATTAAATAAAAA
*
9483967 AAATGAAATAAAA
1 AAATTAAATAAAA
9483980 GACATAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (14 bp):
AAATTAAATAAAAA
Found at i:9484006 original size:21 final size:22
Alignment explanation
Indices: 9483967--9484023 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
9483957 TAAAGAAAAA
9483967 AAATGAAATAAAAGACATAAAT
1 AAATGAAATAAAAGACATAAAT
** *
9483989 AAAT-AAATAAAATCCATAAAAGC
1 AAATGAAATAAAAGACAT-AAA-T
9484012 AAATGAAATAAA
1 AAATGAAATAAA
9484024 TAAAATACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
22 7 0.24
23 4 0.14
24 7 0.24
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
AAATGAAATAAAAGACATAAAT
Found at i:9485628 original size:95 final size:98
Alignment explanation
Indices: 9485522--9485844 Score: 323
Period size: 102 Copynumber: 3.3 Consensus size: 98
9485512 AACTTCCAAA
* * * * **
9485522 AGAAACTGTCTCAAGGGAGACGAGATTTGTTTAACGTAAAA-TA-T-AT-TCA-AAGATTTTGTT
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACTACTCATGTCACAA-ATTTCATT
9485582 TCAAAGGAAATTGTTTTCAAAGTTTATGCTTCAAG
65 TCAAAGGAAA-TGTTTTCAAAGTTTATGCTTCAAG
*
9485617 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACTATCTCATGAGTGACAAATTTCA
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACTA-CTCAT--GTCACAAATTTCA
* *
9485682 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAG
63 TTTCAAAGGAAATGTTTTCAAAGTTTATGCTTCAAG
* * * * ** * *
9485718 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCTCAAGAGAGAAAAAATTC
1 AGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTAAAGGAAAACTA-CTC-A-TGTCACAAATTTC
* * * *
9485783 ATTTCAAGGGAAATGTTTTCGATGTTTATGTTTCAAG
62 ATTTCAAAGGAAATGTTTTCAAAGTTTATGCTTCAAG
* *
9485820 AGAAACTATCTCAAGAGAGACAAAA
1 AGAAACTGTCTCAAGGGAGACAAAA
9485845 CTTAGTTCCA
Statistics
Matches: 197, Mismatches: 20, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
95 37 0.19
96 2 0.01
98 1 0.01
99 2 0.01
101 47 0.24
102 105 0.53
103 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (98 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACTACTCATGTCACAAATTTCATTT
CAAAGGAAATGTTTTCAAAGTTTATGCTTCAAG
Found at i:9485767 original size:37 final size:36
Alignment explanation
Indices: 9485709--9486019 Score: 134
Period size: 37 Copynumber: 8.9 Consensus size: 36
9485699 TCAATGTTTA
* * * *
9485709 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAAATT
*
9485746 TGTTTCAAGGGAACCTATCTCAAGAGAGAAAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATT
** * * * *
9485782 CATTTCAAGGGAAA-TGTTTTC--GA-TG-----TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGAGAGAAAAAATT
* *
9485810 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAAATT
* * ** * * * **
9485848 AGTTCCAAAAGAAAATGTCTCAAGGGAGATGAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATT
* *
9485884 TGTTTCAAGGGAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAAC-TATCTCAAGAGAGAAAAAATT
* * *
9485913 TGTTTCAAGAGAAACTATCTCAAGATAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATT
** * * *
9485949 CATTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAAATT
* * *
9485986 TGTTTTAAGGGAAACTGTCTCAAGAGAGGAAAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAA
9486020 CTTGGAAATT
Statistics
Matches: 198, Mismatches: 54, Indels: 45
0.67 0.18 0.15
Matches are distributed among these distances:
28 4 0.02
29 33 0.17
30 2 0.01
31 3 0.02
32 3 0.02
33 3 0.02
34 2 0.01
35 2 0.01
36 66 0.33
37 78 0.39
38 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATT
Found at i:9485795 original size:102 final size:102
Alignment explanation
Indices: 9485580--9485977 Score: 426
Period size: 102 Copynumber: 3.9 Consensus size: 102
9485570 AAAGATTTTG
* * * *
9485580 TTTCAAAGGAAATTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAAGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* * * * * *
9485645 GTTTAAAGGAAAACTATCTCATGAGTGACAAATTTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATTCA
* * *
9485682 TTTCAAAGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAAGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
*
9485746 TGTTTCAAGGGAACCTATCTCAAGAGAGAAAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATTCA
* * *
9485784 TTTCAAGGGAAA-TGTTTTCGATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TTTCAAAGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* * ** * * * ** **
9485848 AGTTCCAAAAGAAAATGTCTCAAGGGAGATGAAATTTG
65 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATTCA
* * * *
9485886 TTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGATAGACAAAATT
1 TTTCAAAGGAAACTGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
** *
9485949 CATTTCAAGGGAAACTGTCTCAAGAGAGA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGA
9485978 CAAGATTTTG
Statistics
Matches: 255, Mismatches: 38, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
101 71 0.28
102 180 0.71
103 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (102 bp):
TTTCAAAGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
GTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATTCA
Found at i:9486555 original size:106 final size:106
Alignment explanation
Indices: 9486247--9486899 Score: 799
Period size: 106 Copynumber: 6.2 Consensus size: 106
9486237 GTTCTCCAAC
* * * * * * *
9486247 GTGATGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTATTGACAGCCAGCCGCCCCTTCGCTGT
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGTCGCCCCTTCGTTGT
* *
9486312 GAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCT
66 GAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* * * ** *
9486353 GTGAAGTTGAAATTGACTCTGAATGAAGCTGAGAAGTTGTTTGTTGATAGTCAGTCGCCCCTTCA
1 GTGAAGTTGAAATTGGCTCTG-A--AA-CTGGGAAGTTGTTTGTTGACAACCAGTCGCCCCTTCG
* *
9486418 TTGTGAAGTTGAGCTTGTGTTGTCT-GAAGTCCAATATCCTTTGTT
62 TTGTGAAGTTGAGCTTGTGTTGTCTCG-AGTCCAATATCCTTCGCT
* *
9486463 ATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGCCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGTCGCCCCTTCGTTGT
* *
9486528 GAAGTTGAGCTTGTGTTGCCTCGAGTCCAATATCCTTCGTT
66 GAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* *
9486569 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAATCAATCGCCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGTCGCCCCTTCGTTGT
*
9486634 GAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCGCT
66 GAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* * *
9486675 GTGAAGTTGAAATTGGCTCTGAAAATGGGATGTTGTTTGTTGACAACCAGTCACCCCTTCG-T-T
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGTCGCCCCTTCGTTGT
*
9486738 ---GTT-A-----TGTTGTCTTGAGTCCAATATCCTTCGCT
66 GAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
* * * * * ** *
9486770 GTGAAGTTGAAATTGACTCTGAATGAAATTGAAATGTTGTTTGCTGACAGTCAGTCACCCCTTCG
1 GTGAAGTTGAAATTGGCTCTG-A--AACTGGGAA-GTTGTTTGTTGACAACCAGTCGCCCCTTCG
* *
9486835 CTGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAATATCCTTCGCT
62 TTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
9486880 GTGAAGTTGAAATTGGCTCT
1 GTGAAGTTGAAATTGGCTCT
9486900 AAAGCTACAT
Statistics
Matches: 479, Mismatches: 47, Indels: 38
0.85 0.08 0.07
Matches are distributed among these distances:
95 48 0.10
96 1 0.00
98 6 0.01
99 27 0.06
100 2 0.00
101 4 0.01
104 4 0.01
105 2 0.00
106 246 0.51
107 3 0.01
109 4 0.01
110 132 0.28
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGTCGCCCCTTCGTTGT
GAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
Found at i:9486821 original size:95 final size:93
Alignment explanation
Indices: 9486647--9486899 Score: 263
Period size: 95 Copynumber: 2.5 Consensus size: 93
9486637 GTTGAGCTTG
* **
9486647 TGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAAATGGGATGTTGTT
1 TGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAAATGAAATGTTGTT
*
9486712 TGTTGACAACCAGTCACCCCTTCGTTGTTA
66 TGCTG--AACCAGTCACCCCTTCGTTGTTA
9486742 TGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAATGT
1 TGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-A--AAA-TGAAATGT
*
9486807 TGTTTGCTGACAGTCAGTCACCCCTTCGCTGTGAAGTTGA
62 TGTTTGCTGA-A-CCAGTCACCCCTTCG-T-T---GTT-A
** *
9486847 GCTTGTGTTGTCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
1 -----TGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
9486900 AAAGCTACAT
Statistics
Matches: 133, Mismatches: 8, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
95 48 0.36
96 1 0.01
97 1 0.01
98 4 0.03
99 28 0.21
100 1 0.01
101 1 0.01
104 3 0.02
105 1 0.01
110 45 0.34
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (93 bp):
TGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAAATGAAATGTTGTT
TGCTGAACCAGTCACCCCTTCGTTGTTA
Found at i:9487147 original size:33 final size:33
Alignment explanation
Indices: 9487075--9487170 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
9487065 ATTCCCAAAG
* * * *
9487075 ATGCCTCAATATTCGATGTTGAATCTC-ACAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAAA
*
9487107 ATACCCCAACATTTGATGTTGAATCTCAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAAA
9487140 ATGCCCCAACATTTGATGTTGAATCTACAAA
1 ATGCCCCAACATTTGATGTTGAATCT-CAAA
9487171 GACGCCCTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.41
33 29 0.52
34 4 0.07
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (33 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAAA
Found at i:9488219 original size:69 final size:69
Alignment explanation
Indices: 9488104--9488241 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
9488094 TGTCTCTCTC
*
9488104 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
9488169 TCAT
66 TCAT
* * *
9488173 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTTCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
9488238 TCAT
66 TCAT
9488242 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:9488342 original size:13 final size:14
Alignment explanation
Indices: 9488313--9488363 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
9488303 TTTTTCTTCA
9488313 ATTTTC-CTTTGTT
1 ATTTTCTCTTTGTT
9488326 -TTTTCTCTTT-TT
1 ATTTTCTCTTTGTT
9488338 ATTTTCTCTTTGCTT
1 ATTTTCTCTTTG-TT
*
9488353 TTTTTCTCTTT
1 ATTTTCTCTTT
9488364 TTGTTCTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
15 12 0.36
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (14 bp):
ATTTTCTCTTTGTT
Found at i:9488355 original size:26 final size:26
Alignment explanation
Indices: 9488313--9488365 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
9488303 TTTTTCTTCA
9488313 ATTTTCCTTTG-TTTTTTCTCTTTTT
1 ATTTTCCTTTGCTTTTTTCTCTTTTT
9488338 ATTTTCTCTTTGCTTTTTTTCTCTTTTT
1 ATTTTC-CTTTGC-TTTTTTCTCTTTTT
9488366 GTTCTAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
28 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (26 bp):
ATTTTCCTTTGCTTTTTTCTCTTTTT
Found at i:9491852 original size:22 final size:22
Alignment explanation
Indices: 9491827--9491869 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9491817 ATATACTAAA
9491827 GTAAAAAGA-AAATACATAAAAT
1 GTAAAAA-ACAAATACATAAAAT
*
9491849 GTAAAAAACAATTACATAAAA
1 GTAAAAAACAAATACATAAAA
9491870 AAATGTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (22 bp):
GTAAAAAACAAATACATAAAAT
Found at i:9496798 original size:2 final size:2
Alignment explanation
Indices: 9496791--9496827 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9496781 CATGAAAAAC
9496791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9496828 ATAACCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9499505 original size:54 final size:53
Alignment explanation
Indices: 9499441--9499843 Score: 522
Period size: 54 Copynumber: 7.5 Consensus size: 53
9499431 TATAAGTTCG
* ** *
9499441 TTGGGGTGCACAAGTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTC
1 TTGGGTTGCACACTTAGTGC-GATACGGTCGTTCATAAACATATTATGAATTTC
* * *
9499495 TTGGGTTGCACACTTACTGCTGATACAGTCATTCATAAACATATTATGAA-TTC
1 TTGGGTTGCACACTTAGTGC-GATACGGTCGTTCATAAACATATTATGAATTTC
*
9499548 TTTGGGTTGCACACTTAGTGCTGATACGGTAGTTCATAAACATATTATGAA-TTC
1 -TTGGGTTGCACACTTAGTGC-GATACGGTCGTTCATAAACATATTATGAATTTC
* * * *
9499602 TGTGGGTTGCACAATTAGTGTCGATATGGTCGTTCTTAAACATATTATGAATTCC
1 T-TGGGTTGCACACTTAGTG-CGATACGGTCGTTCATAAACATATTATGAATTTC
* *
9499657 ATGGGTTGCACACTTAGTGTCGATGCGGTCGTTCATAAACATATTATGAATTTC
1 TTGGGTTGCACACTTAGTG-CGATACGGTCGTTCATAAACATATTATGAATTTC
* * * *
9499711 GTGGGTTGCACACTTAGTTCTGATAAGGTCGTTCATAAACATATTATGAATTCC
1 TTGGGTTGCACACTTAGTGC-GATACGGTCGTTCATAAACATATTATGAATTTC
*
9499765 TTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCC
1 TTGGGTTGCACACTTAGTG-CGATACGGTCGTTCATAAACATATTATGAATTTC
*
9499819 GTGGGTTGCACACTTAGTGCCGATA
1 TTGGGTTGCACACTTAGTG-CGATA
9499844 GTACACATAG
Statistics
Matches: 310, Mismatches: 33, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
53 5 0.02
54 301 0.97
55 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (53 bp):
TTGGGTTGCACACTTAGTGCGATACGGTCGTTCATAAACATATTATGAATTTC
Found at i:9499718 original size:162 final size:161
Alignment explanation
Indices: 9499441--9499843 Score: 578
Period size: 162 Copynumber: 2.5 Consensus size: 161
9499431 TATAAGTTCG
* * * * *
9499441 TTGGGGTGCACAAGTAGTG-CAGATACGGTCGTTCATAAACTTATTATGAATTTCTTGGGTTGCA
1 TTGGGTTGCACAATTAGTGTC-GATACGGTCGTTCATAAACATATTATGAATTCCATGGGTTGCA
* *
9499505 CACTTACTGCTGATACAGTCATTCATAAACATATTATGAATTCTTTGGGTTGCACACTTAGTGCT
65 CACTTAGTGC-GATACAGTCATTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGCT
*
9499570 GATACGGTAGTTCATAAACATATTATGAATT-C
129 GATAAGGTAGTTCATAAACATATTATGAATTCC
* *
9499602 TGTGGGTTGCACAATTAGTGTCGATATGGTCGTTCTTAAACATATTATGAATTCCATGGGTTGCA
1 T-TGGGTTGCACAATTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGTTGCA
* * * *
9499667 CACTTAGTGTCGATGCGGTCGTTCATAAACATATTATGAATT-TCGTGGGTTGCACACTTAGTTC
65 CACTTAGTG-CGATACAGTCATTCATAAACATATTATGAATTCT-GTGGGTTGCACACTTAGTGC
*
9499731 TGATAAGGTCGTTCATAAACATATTATGAATTCC
128 TGATAAGGTAGTTCATAAACATATTATGAATTCC
* *
9499765 TTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTGCAC
1 TTGGGTTGCACAATTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGTTGCAC
9499830 ACTTAGTGCCGATA
66 ACTTAGTG-CGATA
9499844 GTACACATAG
Statistics
Matches: 216, Mismatches: 21, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
161 2 0.01
162 210 0.97
163 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (161 bp):
TTGGGTTGCACAATTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGTTGCAC
ACTTAGTGCGATACAGTCATTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGCTGA
TAAGGTAGTTCATAAACATATTATGAATTCC
Found at i:9522372 original size:21 final size:21
Alignment explanation
Indices: 9522309--9522372 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
9522299 CATTCAAAGT
* **
9522309 GTATCGATACCTAGAGAGGGAG
1 GTATCGATACCT-GAGTGACAG
* *
9522331 GTATCGGTACCTGGGTGACAG
1 GTATCGATACCTGAGTGACAG
9522352 GTATCGATACCT-AGTGCACAG
1 GTATCGATACCTGAGTG-ACAG
9522373 AATGGTCAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 3 0.09
21 20 0.59
22 11 0.32
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.22
Consensus pattern (21 bp):
GTATCGATACCTGAGTGACAG
Found at i:9522777 original size:15 final size:15
Alignment explanation
Indices: 9522759--9522789 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9522749 TCTCCTTTTG
9522759 TGACATGATCTCTAA
1 TGACATGATCTCTAA
*
9522774 TGACATGATGTCTAA
1 TGACATGATCTCTAA
9522789 T
1 T
9522790 TTCAATGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (15 bp):
TGACATGATCTCTAA
Found at i:9562073 original size:24 final size:26
Alignment explanation
Indices: 9562026--9562076 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
9562016 CATATTTTTT
*
9562026 AAAAATAATATGCATCAAATAAATAC
1 AAAAATAATATGAATCAAATAAATAC
9562052 AAAAATAA-ATGAAT-AAATAAATAC
1 AAAAATAATATGAATCAAATAAATAC
9562076 A
1 A
9562077 TATAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.46
25 5 0.21
26 8 0.33
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.22
Consensus pattern (26 bp):
AAAAATAATATGAATCAAATAAATAC
Found at i:9562902 original size:25 final size:25
Alignment explanation
Indices: 9562874--9562928 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
9562864 AGAATATATA
*
9562874 GTAAATTTCGACTAATCTAAAATTT
1 GTAAATCTCGACTAATCTAAAATTT
* * *
9562899 GTAAGTCTCGACTAATTTAAATTTT
1 GTAAATCTCGACTAATCTAAAATTT
*
9562924 TTAAA
1 GTAAA
9562929 ATTTTCAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (25 bp):
GTAAATCTCGACTAATCTAAAATTT
Found at i:9563115 original size:27 final size:28
Alignment explanation
Indices: 9563074--9563129 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
9563064 ATATTCAATT
* *
9563074 TTTTTAATTTTAATAAT-AGTTTTATAA
1 TTTTTAATATGAATAATCAGTTTTATAA
* *
9563101 TTTTTAATATGAATATTCAGTTTTTTAA
1 TTTTTAATATGAATAATCAGTTTTATAA
9563129 T
1 T
9563130 AATTTAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (28 bp):
TTTTTAATATGAATAATCAGTTTTATAA
Found at i:9563146 original size:22 final size:23
Alignment explanation
Indices: 9563112--9563183 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 23
9563102 TTTTAATATG
* *
9563112 AATATTCAGTTTTTTAATAATTT
1 AATATTTACTTTTTTAATAATTT
* *
9563135 AATTTTTA--TTTTTAATACTTT
1 AATATTTACTTTTTTAATAATTT
*
9563156 TATATTTACTTTTTTGAAT-ATTT
1 AATATTTACTTTTTT-AATAATTT
9563179 GAATA
1 -AATA
9563184 ATTTTATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
21 18 0.47
23 14 0.37
24 6 0.16
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
AATATTTACTTTTTTAATAATTT
Found at i:9565188 original size:15 final size:15
Alignment explanation
Indices: 9565168--9565255 Score: 79
Period size: 15 Copynumber: 5.9 Consensus size: 15
9565158 TTAATTTCTC
9565168 GAAAAATGAATTACT
1 GAAAAATGAATTACT
* *
9565183 GAAAAATTAATTAAT
1 GAAAAATGAATTACT
* **
9565198 GGAATTTGAATTACT
1 GAAAAATGAATTACT
*
9565213 AAAAAATGAATTACT
1 GAAAAATGAATTACT
* **
9565228 GGAATTTGAATT-CT
1 GAAAAATGAATTACT
*
9565242 GAAAAATAAATTAC
1 GAAAAATGAATTAC
9565256 ATTTTTGGAA
Statistics
Matches: 53, Mismatches: 19, Indels: 2
0.72 0.26 0.03
Matches are distributed among these distances:
14 10 0.19
15 43 0.81
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (15 bp):
GAAAAATGAATTACT
Found at i:9565210 original size:30 final size:30
Alignment explanation
Indices: 9565174--9565254 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
9565164 TCTCGAAAAA
*
9565174 TGAATTACTGAAAAATTAATTAATGGAATT
1 TGAATTACTGAAAAATAAATTAATGGAATT
* * *
9565204 TGAATTACTAAAAAATGAATTACTGGAATT
1 TGAATTACTGAAAAATAAATTAATGGAATT
9565234 TGAATT-CTGAAAAATAAATTA
1 TGAATTACTGAAAAATAAATTA
9565255 CATTTTTGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 13 0.28
30 33 0.72
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (30 bp):
TGAATTACTGAAAAATAAATTAATGGAATT
Found at i:9565439 original size:19 final size:19
Alignment explanation
Indices: 9565417--9565469 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 19
9565407 ATTAAATACA
9565417 ATAAATAATATTATTTATC
1 ATAAATAATATTATTTATC
*
9565436 AT-AA-AAT-TTATTTATT
1 ATAAATAATATTATTTATC
*
9565452 ATTAAATAGTATT-TTTAT
1 A-TAAATAATATTATTTAT
9565470 AATTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 9 0.32
17 4 0.14
18 4 0.14
19 9 0.32
20 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATAAATAATATTATTTATC
Found at i:9565616 original size:23 final size:23
Alignment explanation
Indices: 9565567--9565629 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
9565557 GTATTATATT
* **
9565567 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
9565590 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
9565613 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
9565630 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:9565676 original size:27 final size:28
Alignment explanation
Indices: 9565615--9565677 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
9565605 TTATTAAAAT
* *
9565615 ATTATTTAAATATATAAATAATATTATTC
1 ATTA-TTAAATATATAAAAAAAATTATTC
9565644 ATTATTAAATATA-AAAAAAAATTATT-
1 ATTATTAAATATATAAAAAAAATTATTC
9565670 ATATATTA
1 AT-TATTA
9565678 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
27 16 0.52
28 9 0.29
29 4 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTATTAAATATATAAAAAAAATTATTC
Found at i:9565688 original size:24 final size:24
Alignment explanation
Indices: 9565655--9565702 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9565645 TTATTAAATA
* *
9565655 TAAAAAAAAATTATTATATATTAT
1 TAAAAAAAAAATATAATATATTAT
* *
9565679 TAAAATAAAAATATAATATCTTAT
1 TAAAAAAAAAATATAATATATTAT
9565703 ATTATTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAAAAAAAATATAATATATTAT
Found at i:9565703 original size:29 final size:29
Alignment explanation
Indices: 9565613--9565714 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 29
9565603 CTTTATTAAA
* * *
9565613 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTATTAAAATA-AAAAAAAATTATTAT
9565642 -TCATTATTAAATATAAAAAAAAATTATTAT
1 AT-ATTATTAAA-ATAAAAAAAAATTATTAT
*
9565672 ATATTATTAAAATAAAAATATAA-TATCT-T
1 ATATTATTAAAATAAAAA-AAAATTAT-TAT
*
9565701 ATATTATTATAATA
1 ATATTATTAAAATA
9565715 TAATTGATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
28 1 0.02
29 38 0.61
30 22 0.35
31 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTATTAAAATAAAAAAAAATTATTAT
Found at i:9565755 original size:22 final size:23
Alignment explanation
Indices: 9565730--9565773 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
9565720 GATTATTTTA
9565730 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
9565752 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
9565774 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:9565787 original size:30 final size:29
Alignment explanation
Indices: 9565605--9565787 Score: 86
Period size: 30 Copynumber: 6.1 Consensus size: 29
9565595 TTAAATATCT
* *
9565605 TTATTA-AAATATTATTTAAATATATAAATA
1 TTATTATAAATATTA--AAAATAAATAAATA
* * * * * *
9565635 ATATTATTCATTATTAAATATAAAAAAAAA
1 TTATTA-TAAATATTAAAAATAAATAAATA
* *
9565665 TTATTATATATTATTAAAATAAAAATATAATA
1 TTATTATA-AATATTAAAA-ATAAATA-AATA
* * * * * *
9565697 -TCTTAT-ATTATTATAATATAATTGATTA
1 TTATTATAAATATTA-AAAATAAATAAATA
*
9565725 TT-TTATATAATATTAAAAATATAATATTATA
1 TTATTATA-AATATTAAAAATA-AATA-AATA
9565756 TTATTATAAATATTAATAAATAAATAAATA
1 TTATTATAAATATTAA-AAATAAATAAATA
9565786 TT
1 TT
9565788 TTGATGAAAA
Statistics
Matches: 113, Mismatches: 27, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
28 7 0.06
29 18 0.16
30 43 0.38
31 26 0.23
32 19 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
TTATTATAAATATTAAAAATAAATAAATA
Found at i:9565994 original size:42 final size:42
Alignment explanation
Indices: 9565947--9566066 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 42
9565937 ATGAATTACG
*
9565947 TTCCGGAAAACAAATTATGTGAAACAAACACTGG-AAAACATT
1 TTCCGGAAAACAAATTACGTGAAACAAACAC-GGAAAAACATT
* *
9565989 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAATATT
1 TTCCGGAAAACAAATTACGTGAAACAAACACGGAAAAACATT
** * *
9566031 TTTTGGAAAACTAATTACGTGAAACAAATAC-GAAAA
1 TTCCGGAAAACAAATTACGTGAAACAAACACGGAAAA
9566067 TTCAGGAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
41 7 0.10
42 63 0.90
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (42 bp):
TTCCGGAAAACAAATTACGTGAAACAAACACGGAAAAACATT
Found at i:9568683 original size:5 final size:6
Alignment explanation
Indices: 9568668--9568692 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9568658 TTCCAAATTC
9568668 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
9568693 ATATTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:9574107 original size:10 final size:10
Alignment explanation
Indices: 9574092--9574123 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
9574082 TGATCACATA
9574092 TAGTATATAG
1 TAGTATATAG
9574102 TAGTATATAG
1 TAGTATATAG
9574112 TAGTATATAG
1 TAGTATATAG
9574122 TA
1 TA
9574124 TTGATTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTATATAG
Done.