Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 50 of 135
Found at i:13360847 original size:16 final size:17
Alignment explanation
Indices: 13360810--13360847 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
13360800 AAACCTAGTA
13360810 TAATTTGCATTAGAGAT
1 TAATTTGCATTAGAGAT
* *
13360827 GAATTTGCATT-TAGAT
1 TAATTTGCATTAGAGAT
13360843 TAATT
1 TAATT
13360848 ACATTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (17 bp):
TAATTTGCATTAGAGAT
Found at i:13364079 original size:21 final size:21
Alignment explanation
Indices: 13364055--13364094 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13364045 TACCTTGTAC
* *
13364055 TTCTACCGATACATGTAAGAG
1 TTCTACCGAAACAAGTAAGAG
13364076 TTCTACCGAAACAAGTAAG
1 TTCTACCGAAACAAGTAAG
13364095 CAGAATTCAA
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:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (21 bp):
TTCTACCGAAACAAGTAAGAG
Found at i:13364911 original size:15 final size:15
Alignment explanation
Indices: 13364891--13364920 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13364881 TGATAACTCT
13364891 TCTTCTATGTGTCCA
1 TCTTCTATGTGTCCA
*
13364906 TCTTCTATGTTTCCA
1 TCTTCTATGTGTCCA
13364921 ATCATTACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.27, G:0.10, T:0.50
Consensus pattern (15 bp):
TCTTCTATGTGTCCA
Found at i:13366741 original size:16 final size:17
Alignment explanation
Indices: 13366707--13366747 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
13366697 TTTTGTTAGT
*
13366707 TTTTATTATTTATTTTA
1 TTTTATTATTCATTTTA
13366724 TTTTATTATTCA-TTTA
1 TTTTATTATTCATTTTA
13366740 TTTTATTA
1 TTTTATTA
13366748 ATTTTAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTCATTTTA
Found at i:13374191 original size:22 final size:23
Alignment explanation
Indices: 13374153--13374197 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
13374143 TTGCTTGTTT
*
13374153 TTTTGCTTTATTTTATTTTCTTG
1 TTTTGCTTTATTTTATTTGCTTG
*
13374176 TTTTGC-TTGTTTTATTTGCTTG
1 TTTTGCTTTATTTTATTTGCTTG
13374198 AGGAAAAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.07, C:0.09, G:0.13, T:0.71
Consensus pattern (23 bp):
TTTTGCTTTATTTTATTTGCTTG
Found at i:13387322 original size:19 final size:18
Alignment explanation
Indices: 13387291--13387353 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 18
13387281 TCAATATTTT
13387291 TTTTTAC-ATTTTTATAA
1 TTTTTACAATTTTTATAA
13387308 TTGTTTACAATTTTTTATAA
1 TT-TTTACAA-TTTTTATAA
* *
13387328 ATTTTACAGCTTTTTAATAA
1 TTTTTACA-ATTTTT-ATAA
13387348 TTTTTA
1 TTTTTA
13387354 TAATATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.05
18 5 0.13
19 12 0.32
20 19 0.50
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTTACAATTTTTATAA
Found at i:13387324 original size:20 final size:20
Alignment explanation
Indices: 13387299--13387353 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
13387289 TTTTTTTACA
13387299 TTTTTATAATTGTTTACA-AT
1 TTTTTATAATT-TTTACAGAT
* *
13387319 TTTTTATAAATTTTACAGCT
1 TTTTTATAATTTTTACAGAT
*
13387339 TTTTAATAATTTTTA
1 TTTTTATAATTTTTA
13387354 TAATATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTTATAATTTTTACAGAT
Found at i:13393290 original size:5 final size:5
Alignment explanation
Indices: 13393280--13393304 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13393270 TTAAACCCAA
13393280 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
13393305 TAGTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:13395053 original size:19 final size:19
Alignment explanation
Indices: 13395022--13395080 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
13395012 TTTTAGAATT
*
13395022 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
*
13395040 TTTTAAAAATTA-TTTCAA
1 TTTTAAAAATTATTTTGAA
* *
13395058 TTTTTGAAAATTATGTTG-A
1 -TTTTAAAAATTATTTTGAA
13395077 TTTT
1 TTTT
13395081 TTTGTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 17 0.52
19 14 0.42
20 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:13395081 original size:19 final size:18
Alignment explanation
Indices: 13395021--13395081 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
13395011 ATTTTAGAAT
*
13395021 TTTTTATAAA-TATTTTGA
1 TTTTTAAAAATTA-TTTGA
* *
13395039 ATTTTAAAAATTATTTCAA
1 TTTTTAAAAATTATTT-GA
*
13395058 TTTTTGAAAATTATGTTGA
1 TTTTTAAAAATTAT-TTGA
13395077 TTTTT
1 TTTTT
13395082 TTGTAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 11 0.32
19 21 0.62
20 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTTTAAAAATTATTTGA
Found at i:13395265 original size:23 final size:23
Alignment explanation
Indices: 13395239--13395291 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
13395229 AGTTGACTTG
*
13395239 AATAATTCGAATAATTCAATTCA
1 AATAATTCGAATAACTCAATTCA
*
13395262 AATAATTCGAATAACTCAATTCG
1 AATAATTCGAATAACTCAATTCA
13395285 AATAATT
1 AATAATT
13395292 TGAAATTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (23 bp):
AATAATTCGAATAACTCAATTCA
Found at i:13395282 original size:14 final size:13
Alignment explanation
Indices: 13395242--13395290 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
13395232 TGACTTGAAT
13395242 AATTCGAATAATTC
1 AATTCGAATAA-TC
13395256 AATTC--A-AAT-
1 AATTCGAATAATC
13395265 AATTCGAATAACTC
1 AATTCGAATAA-TC
13395279 AATTCGAATAAT
1 AATTCGAATAAT
13395291 TTGAAATTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
9 5 0.17
10 1 0.03
11 3 0.10
12 3 0.10
13 2 0.07
14 16 0.53
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (13 bp):
AATTCGAATAATC
Found at i:13403235 original size:25 final size:25
Alignment explanation
Indices: 13403202--13403258 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
13403192 AGCGAAAAAC
*
13403202 AAAG-TAAACTGGAATTGAAAATTA
1 AAAGCTAAACTGAAATTGAAAATTA
13403226 AAAGCTAAACTGAAATTGAAAATTA
1 AAAGCTAAACTGAAATTGAAAATTA
13403251 AAAGCTAA
1 AAAGCTAA
13403259 GTAATTGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (25 bp):
AAAGCTAAACTGAAATTGAAAATTA
Found at i:13406806 original size:16 final size:17
Alignment explanation
Indices: 13406773--13406806 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13406763 ATGAGGTAGA
*
13406773 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
13406790 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
13406806 A
1 A
13406807 GGGTTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:13410630 original size:24 final size:24
Alignment explanation
Indices: 13410597--13410651 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
13410587 GTTAAGAGTA
13410597 AAAATTGTCAATGCAAATGTAATAC
1 AAAA-TGTCAATGCAAATGTAATAC
* * * *
13410622 AAAATGTCAGTGTAACTGTAATAT
1 AAAATGTCAATGCAAATGTAATAC
13410646 AAAATG
1 AAAATG
13410652 AATGGATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (24 bp):
AAAATGTCAATGCAAATGTAATAC
Found at i:13412979 original size:13 final size:13
Alignment explanation
Indices: 13412961--13412987 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13412951 CTTTGGGCAC
13412961 TCTTCTTTGCTTT
1 TCTTCTTTGCTTT
13412974 TCTTCTTTGCTTT
1 TCTTCTTTGCTTT
13412987 T
1 T
13412988 TGTTTGCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.22, G:0.07, T:0.70
Consensus pattern (13 bp):
TCTTCTTTGCTTT
Found at i:13413264 original size:3 final size:3
Alignment explanation
Indices: 13413256--13413306 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
13413246 TCGAGACAAT
*
13413256 TTC TTC TTC TTC TTTC TTC TT- TTC TTT TTC TTC TTC TTC -TC TTAC
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C
13413301 TTC TTC
1 TTC TTC
13413307 GTCAGCTGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:13413281 original size:21 final size:21
Alignment explanation
Indices: 13413255--13413306 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
13413245 GTCGAGACAA
13413255 TTTCTTCTTCTTCTTTCTTCT-
1 TTTCTTCTTCTTC-TTCTTCTC
*
13413276 TTTCTTTTTCTTCTTCTTCTC
1 TTTCTTCTTCTTCTTCTTCTC
*
13413297 TTACTTCTTC
1 TTTCTTCTTC
13413307 GTCAGCTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCTTCTTCTTCTTCTTCTC
Found at i:13427161 original size:24 final size:24
Alignment explanation
Indices: 13427111--13427157 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
13427101 AAGAATTAAT
13427111 TTGTCAATGCAAATATAAAATAAA
1 TTGTCAATGCAAATATAAAATAAA
*
13427135 TTGTC-ATAGCAAAT-TAAGATAAA
1 TTGTCAAT-GCAAATATAAAATAAA
13427158 ATTGAGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (24 bp):
TTGTCAATGCAAATATAAAATAAA
Found at i:13428739 original size:15 final size:16
Alignment explanation
Indices: 13428700--13428739 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
13428690 TTTTCTGCTT
13428700 TTCTCTTTTTCTTTGC
1 TTCTCTTTTTCTTTGC
13428716 TT-TCTTTTTC-TT-C
1 TTCTCTTTTTCTTTGC
13428729 TTCTCTATTTT
1 TTCTCT-TTTT
13428740 TTTATACGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 5 0.23
15 12 0.55
16 2 0.09
ACGTcount: A:0.03, C:0.23, G:0.03, T:0.72
Consensus pattern (16 bp):
TTCTCTTTTTCTTTGC
Found at i:13428739 original size:16 final size:16
Alignment explanation
Indices: 13428689--13428740 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
13428679 AGCAATATAT
* *
13428689 TTTTTCTGCTTTTCTC
1 TTTTTCTTCTTCTCTC
* *
13428705 TTTTTCTT-TGCTTTC
1 TTTTTCTTCTTCTCTC
*
13428720 TTTTTCTTCTTCTCTA
1 TTTTTCTTCTTCTCTC
13428736 TTTTT
1 TTTTT
13428741 TTATACGTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTTTCTTCTTCTCTC
Found at i:13429346 original size:17 final size:17
Alignment explanation
Indices: 13429326--13429368 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
13429316 AAATGAACTA
* *
13429326 ACAAGTAAAATGCAATG
1 ACAACTAAAATACAATG
13429343 ACAACTAAAATACAATG
1 ACAACTAAAATACAATG
*
13429360 ACAATTAAA
1 ACAACTAAA
13429369 TGAGATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.58, C:0.14, G:0.09, T:0.19
Consensus pattern (17 bp):
ACAACTAAAATACAATG
Found at i:13429801 original size:21 final size:21
Alignment explanation
Indices: 13429768--13429810 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
13429758 GGCATCTTTG
* * *
13429768 TCCTCTTCATCCTTTTTCTCT
1 TCCTCCTCATCCTCTTCCTCT
*
13429789 TCCTCCTCTTCCTCTTCCTCT
1 TCCTCCTCATCCTCTTCCTCT
13429810 T
1 T
13429811 TAGTTCATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.53
Consensus pattern (21 bp):
TCCTCCTCATCCTCTTCCTCT
Found at i:13429806 original size:15 final size:15
Alignment explanation
Indices: 13429768--13429808 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
13429758 GGCATCTTTG
* *
13429768 TCCTCTTCATCCTTT
1 TCCTCTTCCTCCTCT
*
13429783 TTCTCTTCCTCCTCT
1 TCCTCTTCCTCCTCT
13429798 TCCTCTTCCTC
1 TCCTCTTCCTC
13429809 TTTAGTTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.51
Consensus pattern (15 bp):
TCCTCTTCCTCCTCT
Found at i:13437654 original size:24 final size:23
Alignment explanation
Indices: 13437624--13437670 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
13437614 AAGAATTAAT
*
13437624 TTGTCAATGCAAATATAAAATAAA
1 TTGTCAAAGCAAAT-TAAAATAAA
*
13437648 TTGTCAAAGCAAATTAAGATAAA
1 TTGTCAAAGCAAATTAAAATAAA
13437671 AATGAGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (23 bp):
TTGTCAAAGCAAATTAAAATAAA
Found at i:13439123 original size:25 final size:26
Alignment explanation
Indices: 13439093--13439173 Score: 123
Period size: 25 Copynumber: 3.2 Consensus size: 26
13439083 TGTGCATATC
13439093 AGAGAGCACTGACGTGCTAATAAT-T
1 AGAGAGCACTGACGTGCTAATAATCT
13439118 AGAGAGCACTGACGTGCTAATAATCT
1 AGAGAGCACTGACGTGCTAATAATCT
* *
13439144 A-AGACCACTAACGTGCTAATAATCT
1 AGAGAGCACTGACGTGCTAATAATCT
13439169 A-AGAG
1 AGAGAG
13439174 TGAGCTAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
25 50 0.96
26 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (26 bp):
AGAGAGCACTGACGTGCTAATAATCT
Found at i:13441361 original size:2 final size:2
Alignment explanation
Indices: 13441354--13441387 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13441344 TATTAATTTC
13441354 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
13441388 TCATTTAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13441768 original size:87 final size:87
Alignment explanation
Indices: 13441620--13441926 Score: 391
Period size: 87 Copynumber: 3.5 Consensus size: 87
13441610 ACTTAAGTCT
* * *
13441620 AGAACGTTTACGCTCATCAGCTAATCAGAATCAGAATGATCGTGTCTCACAATAACCTGAGTCCG
1 AGAACATTTACGCTCGTCAGCTAATCAGAATCAGAATGATCGTGTCTCATAATAACCTGAGTCCG
* ** ** *
13441685 TAGGACATGTAACAGCTCTGTC
66 CAACACATGTAGGAGCTCGGTC
* * * * * *
13441707 AGAACGTTTATGCTCGTCAGCTAATCAAAATCAAAATGATCGTGTCTCATAATAACTTGAGTTCG
1 AGAACATTTACGCTCGTCAGCTAATCAGAATCAGAATGATCGTGTCTCATAATAACCTGAGTCCG
13441772 CAACACATGCT-GGAGCTCGGTC
66 CAACACATG-TAGGAGCTCGGTC
* * * *
13441794 AGAACATTAACGCTCGTCAGCTAATCAGAATTAGAATGATTGTGTCTCATAATAACCCGAGTCCG
1 AGAACATTTACGCTCGTCAGCTAATCAGAATCAGAATGATCGTGTCTCATAATAACCTGAGTCCG
*
13441859 CAACACATGCAGGAGCTCGGTC
66 CAACACATGTAGGAGCTCGGTC
* * *
13441881 AGAACATTTATGCTCGTCGGCTAATCAGAATCAGAATGATAGTGTC
1 AGAACATTTACGCTCGTCAGCTAATCAGAATCAGAATGATCGTGTC
13441927 AGGTTATCCT
Statistics
Matches: 189, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
87 188 0.99
88 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (87 bp):
AGAACATTTACGCTCGTCAGCTAATCAGAATCAGAATGATCGTGTCTCATAATAACCTGAGTCCG
CAACACATGTAGGAGCTCGGTC
Found at i:13450450 original size:10 final size:10
Alignment explanation
Indices: 13450437--13450485 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
13450427 TTTTTAATAA
13450437 TTTTAAAATT
1 TTTTAAAATT
13450447 TTTTAAAATAT
1 TTTTAAAAT-T
*
13450458 CTTTT--TA-T
1 -TTTTAAAATT
13450466 TTTTAAAATT
1 TTTTAAAATT
13450476 TTTTAAAATT
1 TTTTAAAATT
13450486 AATTAATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
7 4 0.12
8 1 0.03
9 1 0.03
10 21 0.66
11 1 0.03
12 4 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:13453867 original size:55 final size:55
Alignment explanation
Indices: 13453785--13453903 Score: 220
Period size: 55 Copynumber: 2.2 Consensus size: 55
13453775 ACTTGCCTTT
*
13453785 AAAAACTCTCCCTAAATCAAAAAAAATATTTTCAAGTTAAGACTCCACCTGACTA
1 AAAAACTCTCCCTAAATCAAAAAAAATATTTTCAAGTTAAGACTCCACCTCACTA
*
13453840 AAAAACTCTCCCTAAATCAAAAAAAATATTTTCAAGTTAGGACTCCACCTCACTA
1 AAAAACTCTCCCTAAATCAAAAAAAATATTTTCAAGTTAAGACTCCACCTCACTA
13453895 AAAAACTCT
1 AAAAACTCT
13453904 TTGACTACAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.25
Consensus pattern (55 bp):
AAAAACTCTCCCTAAATCAAAAAAAATATTTTCAAGTTAAGACTCCACCTCACTA
Found at i:13457413 original size:23 final size:23
Alignment explanation
Indices: 13457387--13457451 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
13457377 CACATCATCA
*
13457387 TTTAAGCATCAATCACATTAACT
1 TTTAAGCATAAATCACATTAACT
*
13457410 TTTAAGTATAAATCACATTAACT
1 TTTAAGCATAAATCACATTAACT
*
13457433 TTTAAGCATTAATCACATT
1 TTTAAGCATAAATCACATT
13457452 TTGATATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAACT
Found at i:13459304 original size:27 final size:27
Alignment explanation
Indices: 13459266--13459332 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
13459256 AATATATCAG
13459266 GAAAGGAATGCCTTTATGGAAAAATAT
1 GAAAGGAATGCCTTTATGGAAAAATAT
* *
13459293 GAAAGGAATGCCTTTGTGGCAAAATAT
1 GAAAGGAATGCCTTTATGGAAAAATAT
* *
13459320 GAGACGAATGCCT
1 GAAAGGAATGCCT
13459333 CTCTGGCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (27 bp):
GAAAGGAATGCCTTTATGGAAAAATAT
Found at i:13459339 original size:27 final size:27
Alignment explanation
Indices: 13459266--13459343 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
13459256 AATATATCAG
* *
13459266 GAAAGGAATGCCTTTATGGAAAAATAT
1 GAAACGAATGCCTTTATGGCAAAATAT
* *
13459293 GAAAGGAATGCCTTTGTGGCAAAATAT
1 GAAACGAATGCCTTTATGGCAAAATAT
* * *
13459320 GAGACGAATGCCTCTCTGGCAAAA
1 GAAACGAATGCCTTTATGGCAAAA
13459344 GTTTGGATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (27 bp):
GAAACGAATGCCTTTATGGCAAAATAT
Found at i:13470354 original size:23 final size:23
Alignment explanation
Indices: 13470323--13470374 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
13470313 TTAGAAAAGG
13470323 AAAATGAGAAAAAGAAAA-AAAAA
1 AAAATGAG-AAAAGAAAAGAAAAA
13470346 TAAAA-GAGAAAAGAAAAGAAAAA
1 -AAAATGAGAAAAGAAAAGAAAAA
13470369 AAAATG
1 AAAATG
13470375 TTGCTATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 13 0.50
23 9 0.35
24 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (23 bp):
AAAATGAGAAAAGAAAAGAAAAA
Found at i:13470355 original size:17 final size:16
Alignment explanation
Indices: 13470329--13470372 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
13470319 AAGGAAAATG
13470329 AGAAAAAGAAAAAAAA
1 AGAAAAAGAAAAAAAA
* *
13470345 ATAAAAGAGAAAAGAAA
1 AGAAAA-AGAAAAAAAA
13470362 AGAAAAA-AAAA
1 AGAAAAAGAAAA
13470373 TGTTGCTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 6 0.25
17 14 0.58
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (16 bp):
AGAAAAAGAAAAAAAA
Found at i:13472435 original size:22 final size:22
Alignment explanation
Indices: 13472410--13472452 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
13472400 AAAATATCTC
*
13472410 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
13472432 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
13472453 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:13473752 original size:16 final size:17
Alignment explanation
Indices: 13473728--13473760 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13473718 TGCATACTTA
13473728 GGATAATTTGC-TTTAG
1 GGATAATTTGCATTTAG
*
13473744 GGATCATTTGCATTTAG
1 GGATAATTTGCATTTAG
13473761 TTTAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (17 bp):
GGATAATTTGCATTTAG
Found at i:13475238 original size:26 final size:26
Alignment explanation
Indices: 13475202--13475252 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
13475192 CCCTGAATAA
*
13475202 TTGATGTTGAAGATGAGCCTATTGAT
1 TTGATGTTGAAAATGAGCCTATTGAT
* *
13475228 TTGATGTTGAAAATGGGCCTGTTGA
1 TTGATGTTGAAAATGAGCCTATTGA
13475253 GAAGGAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.37
Consensus pattern (26 bp):
TTGATGTTGAAAATGAGCCTATTGAT
Found at i:13491057 original size:26 final size:27
Alignment explanation
Indices: 13491000--13491055 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
13490990 CTAATTGAGT
* *
13491000 TTTAAAATTTTTAAGTTTCTTTTTTTG
1 TTTAAAATTTTTAAGTTTATTTTTATG
*
13491027 TTTAAAA-TTTTAATTTTAATTTTTATG
1 TTTAAAATTTTTAAGTTT-ATTTTTATG
13491054 TT
1 TT
13491056 AATAAAGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (27 bp):
TTTAAAATTTTTAAGTTTATTTTTATG
Found at i:13494671 original size:22 final size:22
Alignment explanation
Indices: 13494646--13494688 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
13494636 AAAATATTTC
*
13494646 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
13494668 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
13494689 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:13496644 original size:147 final size:147
Alignment explanation
Indices: 13496398--13497024 Score: 748
Period size: 146 Copynumber: 4.3 Consensus size: 147
13496388 TTTTTTCATA
* * *
13496398 ATTTTGAAATAAAAGTTTTGAATTTTAAGAAAAATAGTGATTTTCATAAATAAATAAAAAGAAAG
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTCAT--AT-AATAAAAAGAAA-
* * *
13496463 TTTAGA--TTTAAAA-AAATATATGTTTTTTAGTCATTTTAAAGAAAAAATTTAAATTTTTAAAC
62 TTTAGATTTTTAAAATAAAAATTTGTTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAAC
* *
13496525 AAAATTTTGATTCTTTTAACT
127 AAAATTTTAATTTTTTTAACT
* * *
13496546 ATTTCGAAATAAAAGTTTGGAGTATTAAG-AAAATAGTGATTTTCAT-TAAGAAAAAGAAAGTTT
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTCATATAATAAAAAGAAA-TTT
*
13496609 AGATTTTTAAAAATAAAAATTTGTTTTTTAGTCATTCTAAAGAAAAAGTTTAAATTTTTAAACAA
65 AGATTTTT-AAAATAAAAATTTGTTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAA
* *
13496674 AGTTTT-ATTTTTTTAATT
129 AATTTTAATTTTTTTAACT
* * *
13496692 ATTTTGAAATAAAAGTTTGAATTTTTAAGAAAAATAGTGATTTTTATATAA-AAAAAGAAATTTA
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTCATATAATAAAAAGAAATTTA
** * *
13496756 GATTTTTAAAAATAAAAAACTATTTTTTAGTCATTTTAAAG-AAAAGTTTAAATTTTTAAATAAA
66 GATTTTT-AAAATAAAAATTTGTTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAA
13496820 ATTTTAATTTTTTTAACT
130 ATTTTAATTTTTTTAACT
* * *
13496838 ATTTCGAAATAAAAATTTGGATTTTTAAGTAAAATAGTGATTTT--T-T-TTAAAAA-AAA-TTA
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTCATATAATAAAAAGAAATTTA
* * *
13496897 AATTTTTAAAATAAAAATCTAT-TTTTTTAGGCATTTTAAAAGAGAAAAGTTTAAATTTTTATAC
66 GATTTTTAAAATAAAAAT-T-TGTTTTTTAGTCATTTT-AAAGA-AAAAGTTTAAATTTTTAAAC
13496961 AAAA-TTTAATTTTTTTAACT
127 AAAATTTTAATTTTTTTAACT
* * * *
13496981 ATTTCGGAATAAAAGTTTTGATTTTTTAA-AAAATTAATGATTTT
1 ATTTCGAAATAAAAGTTTGGA-TTTTTAAGAAAAATAGTGATTTT
13497025 ATTTAAAAAA
Statistics
Matches: 424, Mismatches: 41, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
140 10 0.02
141 23 0.05
142 8 0.02
143 70 0.17
144 31 0.07
145 29 0.07
146 131 0.31
147 94 0.22
148 28 0.07
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (147 bp):
ATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTCATATAATAAAAAGAAATTTA
GATTTTTAAAATAAAAATTTGTTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAA
TTTTAATTTTTTTAACT
Found at i:13496832 original size:20 final size:20
Alignment explanation
Indices: 13496789--13496831 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13496779 TTTTTAGTCA
13496789 TTTTAAAGAAAAGTTTAAAT
1 TTTTAAAGAAAAGTTTAAAT
* *
13496809 TTTTAAATAAAA-TTTTAAT
1 TTTTAAAGAAAAGTTTAAAT
13496828 TTTT
1 TTTT
13496832 TTAACTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTTAAAGAAAAGTTTAAAT
Found at i:13496923 original size:21 final size:19
Alignment explanation
Indices: 13496877--13496925 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
13496867 TAAAATAGTG
*
13496877 ATTTTTTTTAAAAAAAATT
1 ATTTTTTTAAAAAAAAATT
**
13496896 AAATTTTTAAAATAAAAATCT
1 ATTTTTTTAAAA-AAAAAT-T
13496917 ATTTTTTTA
1 ATTTTTTTA
13496926 GGCATTTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 9 0.39
20 6 0.26
21 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTTTTAAAAAAAAATT
Found at i:13521611 original size:22 final size:20
Alignment explanation
Indices: 13521563--13521619 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
13521553 TAATCTCCTT
*
13521563 ACAAA-AAAAG-AAGAAGAA
1 ACAAAGAAAAGAAATAAGAA
13521581 ACAAAG-AAAGCAAATAAGAA
1 ACAAAGAAAAG-AAATAAGAA
13521601 ACAAAAAGAAAAGAAATAA
1 AC--AAAGAAAAGAAATAA
13521620 AAGGGGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 9 0.28
20 9 0.28
22 10 0.31
23 4 0.12
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.04
Consensus pattern (20 bp):
ACAAAGAAAAGAAATAAGAA
Found at i:13522689 original size:48 final size:43
Alignment explanation
Indices: 13522567--13522784 Score: 212
Period size: 42 Copynumber: 5.0 Consensus size: 43
13522557 AAGGAAAGCA
* * ** *
13522567 TTCATTGCA-TTTAGAGGCCCAGGTGTAAAGGTTCATTTACTT
1 TTCATCGCATTTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * **
13522609 TTCATTGCA-TTTAGACGTCCAAGTGTAAAGGTCCATTTACTT
1 TTCATCGCATTTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
13522651 TTCATCGCATTTAGAGATAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTT-----TAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
13522699 TTTAGT-GCA-TTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCA-TCGCATTTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
13522741 TTCATCAC-TTTTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
13522783 TT
1 TT
13522785 TTTTTAATTG
Statistics
Matches: 153, Mismatches: 14, Indels: 18
0.83 0.08 0.10
Matches are distributed among these distances:
41 1 0.01
42 114 0.75
43 2 0.01
47 2 0.01
48 33 0.22
49 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TTCATCGCATTTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:13522731 original size:90 final size:84
Alignment explanation
Indices: 13522576--13522785 Score: 249
Period size: 90 Copynumber: 2.4 Consensus size: 84
13522566 ATTCATTGCA
** * * * *
13522576 TTTAGAGGCCCAGGTGTAAAGGTTCATTTACTTTTCATTGCATTTAGACGTCCAAGTGTAAAGGT
1 TTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTTAGTGCATTTAGACGCCCAAGTGTAAAGGT
*
13522641 CCATTTACTTTTCATCGCAT
66 CCATTTACTTTTCATCAC-T
* * * *
13522661 TTAGAGATAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTTAGTGCATTTAGAGGCCCAGGTGTG
1 TT-----TAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTTAGTGCATTTAGACGCCCAAGTGTA
*
13522726 GAGGTCCATTTACTTTTCATCACT
61 AAGGTCCATTTACTTTTCATCACT
*
13522750 TTTAGAGGTCCAGGTGTGGAGGTCCATTTACTTTTT
1 TTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTT
13522786 TTTTAATTGT
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
84 32 0.30
85 2 0.02
89 3 0.03
90 69 0.65
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (84 bp):
TTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTTAGTGCATTTAGACGCCCAAGTGTAAAGGT
CCATTTACTTTTCATCACT
Found at i:13523881 original size:22 final size:21
Alignment explanation
Indices: 13523838--13523883 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
13523828 GTGATTTTCA
* *
13523838 TTAAAAAATAAAGTTTAATTT
1 TTAAAAAATAAAATCTAATTT
*
13523859 TTAAAAAATAAAAATCTATTTT
1 TTAAAAAAT-AAAATCTAATTT
13523881 TTA
1 TTA
13523884 TTCATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAAAAATAAAATCTAATTT
Found at i:13523992 original size:126 final size:123
Alignment explanation
Indices: 13523700--13523952 Score: 386
Period size: 126 Copynumber: 2.0 Consensus size: 123
13523690 GAATTTTAAG
* *
13523700 AAAAATAGTGATTTTCAT-AAAAAGAA-TTAGATTTTT-AAAAATAAAAATCTGTTTTTTAGTCA
1 AAAAATAGTGATTTTCATAAAAAATAAGTTA-ATTTTTAAAAAATAAAAATCTATTTTTTAGTCA
*
13523762 TTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTATTTTTTTAACTATTTCGAAAT
65 TTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTATTTTTTTAACTATTTCAAAAT
*
13523821 AAAAATAGTGATTTTCATTAAAAAATAAAGTTTAATTTTTAAAAAATAAAAATCTATTTTTTATT
1 AAAAATAGTGATTTTCA-TAAAAAAT-AAG-TTAATTTTTAAAAAATAAAAATCTATTTTTTAGT
*
13523886 CATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAAT
63 CATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTT-A-TTTTTTTAACTATTTCAAAAT
13523949 AAAA
1 AAAA
13523953 GTTTTGAATT
Statistics
Matches: 119, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
121 17 0.14
122 1 0.01
123 5 0.04
124 2 0.02
125 6 0.05
126 63 0.53
127 1 0.01
128 24 0.20
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (123 bp):
AAAAATAGTGATTTTCATAAAAAATAAGTTAATTTTTAAAAAATAAAAATCTATTTTTTAGTCAT
TTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTATTTTTTTAACTATTTCAAAAT
Found at i:13524083 original size:149 final size:146
Alignment explanation
Indices: 13523822--13524127 Score: 463
Period size: 149 Copynumber: 2.1 Consensus size: 146
13523812 TTTCGAAATA
* * *
13523822 AAAATAGTGATTTTCATTAAAAAATAAAGTTTAATTTTTAAAAAATAAAAATCTATTTTTTATTC
1 AAAATAGTGATTTTCATAAAAAAAGAAAGTTTAATTTTTAAAAAATAAAAATCTATTTTTTAGTC
*
13523887 ATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATAAA
66 ATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGATTTTTTTTAACTATTTC-AAATAAA
*
13523952 AGTTTTGAATTTTAAG-
130 AGTTTGGAATTTTAAGT
*
13523968 AACAATAGTGATTTTCATAAAAAAAGAAAGTTTAGATTTTT-AAAAATAAAAATCTGGTTTTTTT
1 AA-AATAGTGATTTTCATAAAAAAAGAAAGTTTA-ATTTTTAAAAAATAAAAATCT--ATTTTTT
* * *
13524032 AGTCATTTTAAAGAAGAAGTTTAAGTTTTTAAACAAAATTTTGATTTTTTTTAACTATTTCGAAT
62 AGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGATTTTTTTTAACTATTTCAAAT
*
13524097 AAAAGTTTGGATTTTTAAGT
127 AAAAGTTTGGAATTTTAAGT
13524117 AAAATAGTGAT
1 AAAATAGTGAT
13524128 CTTTTTCTTT
Statistics
Matches: 145, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
146 2 0.01
147 43 0.30
148 35 0.24
149 65 0.45
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (146 bp):
AAAATAGTGATTTTCATAAAAAAAGAAAGTTTAATTTTTAAAAAATAAAAATCTATTTTTTAGTC
ATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAATTTTGATTTTTTTTAACTATTTCAAATAAAA
GTTTGGAATTTTAAGT
Found at i:13524214 original size:50 final size:51
Alignment explanation
Indices: 13523994--13524229 Score: 180
Period size: 50 Copynumber: 4.6 Consensus size: 51
13523984 ATAAAAAAAG
* * * * * *
13523994 AAAGTTTAGATTTTTAAAAATAAAAATCTGGTTTTTTT-AGTCATTT-TAAAGA
1 AAAGTTTAGATTTTTAAACA-AAATAT-TGATTTTTTTAACT-ATTTCGAAATA
*
13524046 AGAAGTTTA-AGTTTTTAAACAAAATTTTGATTTTTTTTAACTATTTCG-AATA
1 A-AAGTTTAGA-TTTTTAAACAAAATATTGA-TTTTTTTAACTATTTCGAAATA
* ** * * * ** *
13524098 AAAGTTTGGATTTTTAAGTAAAATAGTGATCTTTTT--CTTTTTTAAAAAA
1 AAAGTTTAGATTTTTAAACAAAATATTGATTTTTTTAACTATTTCGAAATA
*
13524147 AAAGTTTAAATTTTTAAACAAAAT-TTGATTTTTTTAACTATTTCGAAATA
1 AAAGTTTAGATTTTTAAACAAAATATTGATTTTTTTAACTATTTCGAAATA
* * * *
13524197 AAAGTTTTGATTATTAAAAAAAATAATGATTTT
1 AAAGTTTAGATTTTTAAACAAAATATTGATTTT
13524230 GTTTTAAAAA
Statistics
Matches: 142, Mismatches: 32, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
48 14 0.10
49 23 0.16
50 35 0.25
51 30 0.21
52 22 0.15
53 18 0.13
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (51 bp):
AAAGTTTAGATTTTTAAACAAAATATTGATTTTTTTAACTATTTCGAAATA
Found at i:13524980 original size:16 final size:17
Alignment explanation
Indices: 13524959--13524990 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13524949 CATTATGTCA
13524959 AAGTTTT-TTTTTATTT
1 AAGTTTTCTTTTTATTT
13524975 AAGTTTTCTTTTTATT
1 AAGTTTTCTTTTTATT
13524991 ATTACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (17 bp):
AAGTTTTCTTTTTATTT
Found at i:13525569 original size:3 final size:3
Alignment explanation
Indices: 13525561--13525585 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13525551 AATCTTTTAC
13525561 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
13525586 AAGATCGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13528952 original size:24 final size:24
Alignment explanation
Indices: 13528925--13529093 Score: 137
Period size: 24 Copynumber: 7.0 Consensus size: 24
13528915 AAATACGAAA
* *
13528925 TCATGCTAACGAGCGTAAATGTAT
1 TCATGCTGACGAGCGTAAACGTAT
* *
13528949 TCATGTTGACGAGCGAAAACGTAT
1 TCATGCTGACGAGCGTAAACGTAT
**
13528973 TCATGCTGATAAGCGTAAACG--T
1 TCATGCTGACGAGCGTAAACGTAT
* *
13528995 TCACGCTGACAAGCGTAAACGTAT
1 TCATGCTGACGAGCGTAAACGTAT
* *
13529019 TCATGCTGACGAGCTTATACGTAT
1 TCATGCTGACGAGCGTAAACGTAT
* * *
13529043 ATACATGTTAACTAGCGTAAACGTAGAT
1 -T-CATGCTGACGAGCGTAAACGT--AT
* *
13529071 AT-ATGTTGACGAGCGAAAACGTA
1 -TCATGCTGACGAGCGTAAACGTA
13529094 CAGAATTTTC
Statistics
Matches: 117, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
22 20 0.17
24 59 0.50
25 1 0.01
26 33 0.28
28 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (24 bp):
TCATGCTGACGAGCGTAAACGTAT
Found at i:13529002 original size:22 final size:22
Alignment explanation
Indices: 13528972--13529016 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
13528962 CGAAAACGTA
* *
13528972 TTCATGCTGATAAGCGTAAACG
1 TTCACGCTGACAAGCGTAAACG
13528994 TTCACGCTGACAAGCGTAAACG
1 TTCACGCTGACAAGCGTAAACG
13529016 T
1 T
13529017 ATTCATGCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
TTCACGCTGACAAGCGTAAACG
Found at i:13529720 original size:71 final size:71
Alignment explanation
Indices: 13529602--13529748 Score: 188
Period size: 71 Copynumber: 2.1 Consensus size: 71
13529592 TTGAGTTTAG
* * * * *
13529602 TTGAGTTGTTTCGGAACAACTCTATAAGGTATAGGTAGAAGTGCAAGGGAGAGGATACCTTGGCT
1 TTGAGTTGTTTCGAAACAACTCTACAAAGTATAGGTAGAAGTGCAAGGGAAAGAATACCTTGGCT
13529667 ACTGAC
66 ACTGAC
* * * * *
13529673 TTGAGTTGTTTCTAAACAACTC-ACCAAAGTATCGGTAGATGTTCAAGGGAAAGAATATCTTGGC
1 TTGAGTTGTTTCGAAACAACTCTA-CAAAGTATAGGTAGAAGTGCAAGGGAAAGAATACCTTGGC
13529737 TACTGAC
65 TACTGAC
13529744 TTGAG
1 TTGAG
13529749 AAGTTTCGGT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
70 1 0.02
71 64 0.98
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (71 bp):
TTGAGTTGTTTCGAAACAACTCTACAAAGTATAGGTAGAAGTGCAAGGGAAAGAATACCTTGGCT
ACTGAC
Found at i:13541093 original size:22 final size:22
Alignment explanation
Indices: 13541066--13541118 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
13541056 GCATGTGTAA
**
13541066 TGCTCTCTGATTAGCACATTTG
1 TGCTCTCTGATTAGCACATCGG
* *
13541088 TGCTCTCCGATTAGCACCTCGG
1 TGCTCTCTGATTAGCACATCGG
13541110 TGCTCTCTG
1 TGCTCTCTG
13541119 TTCGTTTGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.13, C:0.30, G:0.21, T:0.36
Consensus pattern (22 bp):
TGCTCTCTGATTAGCACATCGG
Found at i:13544543 original size:29 final size:32
Alignment explanation
Indices: 13544511--13544576 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 32
13544501 AAGTTGGTAG
*
13544511 AAAAATTATT-AAGC-CCTTAAAAATTA-AAA
1 AAAAATTATTGAAACTCCTTAAAAATTAGAAA
*
13544540 AAAAA--ATTGAAACTCCTTAAAAATTAGTAA
1 AAAAATTATTGAAACTCCTTAAAAATTAGAAA
13544570 AAAAATT
1 AAAAATT
13544577 TTAGCTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
27 3 0.10
28 3 0.10
29 17 0.57
30 7 0.23
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (32 bp):
AAAAATTATTGAAACTCCTTAAAAATTAGAAA
Found at i:13547948 original size:6 final size:6
Alignment explanation
Indices: 13547937--13547962 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
13547927 TTTTTAACTA
13547937 ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT AT
13547963 TTTAAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:13571811 original size:68 final size:68
Alignment explanation
Indices: 13571728--13571864 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 68
13571718 TTAGGGCAAC
*
13571728 TAATTTTGTCTATAAATAACAAGGCTTAGGAGGACCTATGAGAGGCTGACAAAAGCTAATTTTTA
1 TAATTTTGTCTATAAATAACAAGGCTTAGGAGGACCTATGAGAGGCTGACAAAAGCCAATTTTTA
13571793 GGG
66 GGG
** * *
13571796 TAATTTTGTCTATAAATAACAAGGCTTAGGCTGACTTATGGGAGGCTGACAAAAGCCAATTTTTA
1 TAATTTTGTCTATAAATAACAAGGCTTAGGAGGACCTATGAGAGGCTGACAAAAGCCAATTTTTA
13571861 GGG
66 GGG
13571864 T
1 T
13571865 TTTTATTCAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (68 bp):
TAATTTTGTCTATAAATAACAAGGCTTAGGAGGACCTATGAGAGGCTGACAAAAGCCAATTTTTA
GGG
Found at i:13572002 original size:39 final size:39
Alignment explanation
Indices: 13571957--13572035 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
13571947 AATTGAGTCC
*
13571957 AAGCGTTCGTTATTTTGTATTATTCAAAAATTTTCTTTT
1 AAGCGTTCATTATTTTGTATTATTCAAAAATTTTCTTTT
* *
13571996 AAGCGTTCATTATTTTGTATTATTCAATATTTTTCTTTT
1 AAGCGTTCATTATTTTGTATTATTCAAAAATTTTCTTTT
13572035 A
1 A
13572036 CTTTTTTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.56
Consensus pattern (39 bp):
AAGCGTTCATTATTTTGTATTATTCAAAAATTTTCTTTT
Found at i:13574254 original size:17 final size:17
Alignment explanation
Indices: 13574232--13574264 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13574222 TTATTCTATT
13574232 TAATTA-ATTTTACTAAA
1 TAATTATATTTT-CTAAA
13574249 TAATTATATTTTCTAA
1 TAATTATATTTTCTAA
13574265 TGCTGCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTATATTTTCTAAA
Found at i:13574356 original size:27 final size:27
Alignment explanation
Indices: 13574322--13574376 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
13574312 TCGATTTAAT
13574322 AAATTTATTTCAAAATCCAATTTTTTG
1 AAATTTATTTCAAAATCCAATTTTTTG
*
13574349 AAATTTATTTTAAAATCCAATTTTTTG
1 AAATTTATTTCAAAATCCAATTTTTTG
13574376 A
1 A
13574377 TATTGACGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (27 bp):
AAATTTATTTCAAAATCCAATTTTTTG
Found at i:13574388 original size:25 final size:26
Alignment explanation
Indices: 13574333--13574390 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
13574323 AATTTATTTC
* **
13574333 AAAATCCAATTTTTTGAAATTTATTTT
1 AAAATCCAATTTTTTGAAATTGA-TCG
*
13574360 AAAATCCAATTTTTTGATATTGA-CG
1 AAAATCCAATTTTTTGAAATTGATCG
13574385 AAAATC
1 AAAATC
13574391 AGGTCGTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 6 0.22
27 21 0.78
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (26 bp):
AAAATCCAATTTTTTGAAATTGATCG
Found at i:13591407 original size:178 final size:179
Alignment explanation
Indices: 13591108--13591461 Score: 638
Period size: 178 Copynumber: 2.0 Consensus size: 179
13591098 TTCATCCCAA
*
13591108 GGAGATTAATTTAATAACATAATATTAACATATGAATTATTGCTTACTTTCGGGCAAAAGAGAAC
1 GGAGATTAATTTAATAACATAATATTAACATATGAATTATTGCATACTTTCGGGCAAAAGAGAAC
* * * *
13591173 AAGATTAACGAGTTTTTTAGCCCTCAAGCTTTATATGAATAAAATCTACGACAAAGTTGAATAAG
66 AAGATTAACAACTTTTTTAGCCCTCAAACTTGATATGAATAAAATCTACGACAAAGTTGAATAAG
13591238 CTTTCTTAAAAGCTATGATGACAAAAATGAGG-TTGAAATGAATTGTCT
131 CTTTCTTAAAAGCTATGATGACAAAAATGAGGTTTGAAATGAATTGTCT
*
13591286 GGAGATTAATTTAATAACATAATATTAACATATGAATTATTGCATACTTTTGGGCAAAAGAGAAC
1 GGAGATTAATTTAATAACATAATATTAACATATGAATTATTGCATACTTTCGGGCAAAAGAGAAC
*
13591351 AAGATTAACAACTTTTTTAGCCCTCAAACTTGATATGAATAAAATCTATGACAAAGTTGAATAAG
66 AAGATTAACAACTTTTTTAGCCCTCAAACTTGATATGAATAAAATCTACGACAAAGTTGAATAAG
13591416 CTTTCTTAAAAGCTATGATGACAAAAATGAGGTTTGAAATGAATTG
131 CTTTCTTAAAAGCTATGATGACAAAAATGAGGTTTGAAATGAATTG
13591462 GGTGGAAATA
Statistics
Matches: 168, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
178 155 0.92
179 13 0.08
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (179 bp):
GGAGATTAATTTAATAACATAATATTAACATATGAATTATTGCATACTTTCGGGCAAAAGAGAAC
AAGATTAACAACTTTTTTAGCCCTCAAACTTGATATGAATAAAATCTACGACAAAGTTGAATAAG
CTTTCTTAAAAGCTATGATGACAAAAATGAGGTTTGAAATGAATTGTCT
Found at i:13598761 original size:10 final size:10
Alignment explanation
Indices: 13598723--13598753 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
13598713 AAAATACTAT
13598723 TATTGTTTTTC
1 TATT-TTTTTC
13598734 TATTTTTTTC
1 TATTTTTTTC
13598744 TATTTTTTTC
1 TATTTTTTTC
13598754 ATTGTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (10 bp):
TATTTTTTTC
Found at i:13601566 original size:18 final size:18
Alignment explanation
Indices: 13601529--13601582 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
13601519 ATTACAAAAT
* *
13601529 AATTTAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
13601548 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTAT-AA
*
13601567 AATTC-GAATATTTATA
1 AATTCAAAATATTTATA
13601583 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 14 0.45
19 16 0.52
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:13612768 original size:17 final size:17
Alignment explanation
Indices: 13612748--13612790 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
13612738 AAATGAACTA
* *
13612748 ACAAGTAAAATGCAACG
1 ACAACTAAAATACAACG
*
13612765 ACAACTAAAATACAATG
1 ACAACTAAAATACAACG
*
13612782 ACAATTAAA
1 ACAACTAAA
13612791 TGAGATGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.16
Consensus pattern (17 bp):
ACAACTAAAATACAACG
Found at i:13625470 original size:18 final size:18
Alignment explanation
Indices: 13625424--13625477 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
13625414 ACTACAATGC
* *
13625424 AAATGTACTAACAATT-A
1 AAATGTAATGACAATTAA
13625441 AAAT-TAAGTGACAATTAA
1 AAATGTAA-TGACAATTAA
*
13625459 AAATGTAATGACAACTAA
1 AAATGTAATGACAATTAA
13625477 A
1 A
13625478 TGCTATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 2 0.06
17 11 0.35
18 15 0.48
19 3 0.10
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (18 bp):
AAATGTAATGACAATTAA
Found at i:13633646 original size:18 final size:17
Alignment explanation
Indices: 13633623--13633672 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
13633613 GCGTAGTCTA
13633623 TTGTGACTGCATTCTAGC
1 TTGTGACTGCATT-TAGC
*
13633641 TTGTGATTGCATTTAGC
1 TTGTGACTGCATTTAGC
13633658 TATGT-ACCTGCATTT
1 T-TGTGA-CTGCATTT
13633673 GATCAGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (17 bp):
TTGTGACTGCATTTAGC
Found at i:13639279 original size:11 final size:11
Alignment explanation
Indices: 13639263--13639287 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13639253 GTTTAATAGA
13639263 TTTGATTTAAT
1 TTTGATTTAAT
13639274 TTTGATTTAAT
1 TTTGATTTAAT
13639285 TTT
1 TTT
13639288 CAAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTGATTTAAT
Found at i:13643618 original size:94 final size:95
Alignment explanation
Indices: 13643511--13643705 Score: 365
Period size: 94 Copynumber: 2.1 Consensus size: 95
13643501 TTCTTTTGTT
*
13643511 TCTACTCATCTCTATTTATCTCTTTTTGACTAAACTAAAGTTCATACATTATATTGAGTTTTCTA
1 TCTACTCATCTCTATTTATCTCTTTTTGACTAAACTAAAGTTCATACATTATATTGAGTTTCCTA
13643576 -TTTTATTTTGTAACCTCCACCTTAATGTG
66 TTTTTATTTTGTAACCTCCACCTTAATGTG
*
13643605 TCTACTCATCTCTATTTATCTCTTTTTGGCTAAACTAAAGTTCATACATTATATTGAGTTTCCTA
1 TCTACTCATCTCTATTTATCTCTTTTTGACTAAACTAAAGTTCATACATTATATTGAGTTTCCTA
13643670 TTTTTATTTTGTAACCTCCACCTTAATGTG
66 TTTTTATTTTGTAACCTCCACCTTAATGTG
13643700 TCTACT
1 TCTACT
13643706 TACCCTCGAT
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 63 0.64
95 35 0.36
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.48
Consensus pattern (95 bp):
TCTACTCATCTCTATTTATCTCTTTTTGACTAAACTAAAGTTCATACATTATATTGAGTTTCCTA
TTTTTATTTTGTAACCTCCACCTTAATGTG
Found at i:13647716 original size:3 final size:3
Alignment explanation
Indices: 13647708--13647737 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13647698 CTATAGCCTA
13647708 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13647738 GAAAATAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13650568 original size:16 final size:16
Alignment explanation
Indices: 13650539--13650581 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
13650529 GACAATATAT
13650539 CAATTAATATTGTTT-C
1 CAATTAA-ATTGTTTAC
13650555 CAAATTAAATTGTTTAC
1 C-AATTAAATTGTTTAC
13650572 CAATTAAATT
1 CAATTAAATT
13650582 TGATTCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (16 bp):
CAATTAAATTGTTTAC
Found at i:13657693 original size:7 final size:7
Alignment explanation
Indices: 13657681--13657707 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13657671 TCTTTATGAT
13657681 TTCTTCA
1 TTCTTCA
13657688 TTCTTCA
1 TTCTTCA
13657695 TTCTTCA
1 TTCTTCA
13657702 TTCTTC
1 TTCTTC
13657708 TATTTATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCTTCA
Found at i:13659172 original size:18 final size:19
Alignment explanation
Indices: 13659151--13659193 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
13659141 TAACAAAAGG
* *
13659151 AATGCAGTGACAA-AATAA
1 AATGCAGGGACAATAAAAA
13659169 AATGCAGGGACAATAAAAA
1 AATGCAGGGACAATAAAAA
13659188 AATGCA
1 AATGCA
13659194 TGAAAATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.14
Consensus pattern (19 bp):
AATGCAGGGACAATAAAAA
Found at i:13659267 original size:3 final size:3
Alignment explanation
Indices: 13659259--13659284 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13659249 TGTCTTTGTT
13659259 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
13659285 TGGGCGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:13694079 original size:209 final size:208
Alignment explanation
Indices: 13693720--13694345 Score: 898
Period size: 209 Copynumber: 3.0 Consensus size: 208
13693710 TCTGCATACT
* * * * * ** *
13693720 TGATCTGTCGATTTCATACCTAGCAGCTTGAACTATTTTTCACATTTGAAGAGCTTGGAATCAAC
1 TGATCTGTCGGTTTTATACCTAGCAGATTGAACTATTTTTCACACTTGAAAAGCTTTAAATCAAG
* * * *
13693785 TTTTTTTTTATGTTTTC-ATAGGATTTAGTTTAGATTTCTTATTTGAATAAATTGTGTAACCTAA
66 TATTTTATTATG-TTTCAATAAGATTTAGTTTAGATTTCTTATTTAAATAAATTGTGTAACCTAA
* ** *
13693849 GTGTTGAAATGTTGTTTTATTTGTCTTTAACGCCAAATCAGGACTAAAGGTTAGCTAATATATTT
130 GTGTTAAAATGTCATTTTATTTGTCTTTAAGGCCAAATCAGGACTAAAGGTTAGCTAATATATTT
13693914 GGTGAGTGTGCAGG
195 GGTGAGTGTGCAGG
*
13693928 TGATCTGTCGGTTTTATACCTAGCAGATTGAACTATTTTTCACACTTGAAAAGCTTTAAATTAAG
1 TGATCTGTCGGTTTTATACCTAGCAGATTGAACTATTTTTCACACTTGAAAAGCTTTAAATCAAG
13693993 TATTTTCATTATGTTTCAATAAGATTTAGTTTAGATTTCTTATTTAAATAAATTGTGTAACCTAA
66 TATTTT-ATTATGTTTCAATAAGATTTAGTTTAGATTTCTTATTTAAATAAATTGTGTAACCTAA
* *
13694058 GTGTTAAAATGTCATTTTATTTGTCTTTAAGGCCAAATCAGGACTAAAGGTTACCTAATGTATTT
130 GTGTTAAAATGTCATTTTATTTGTCTTTAAGGCCAAATCAGGACTAAAGGTTAGCTAATATATTT
*
13694123 GGTAAGTGTGCAGG
195 GGTGAGTGTGCAGG
*
13694137 TGATCTGTCGGTTTTATACCTAGCAGATTGAACTTTTTTTCACACTT-AAAGAGCTTTAAATCAA
1 TGATCTGTCGGTTTTATACCTAGCAGATTGAACTATTTTTCACACTTGAAA-AGCTTTAAATCAA
* * *
13694201 GTATTTTAGTTATGTTTTAATAAGATTTAGTTTCGATTTCTTATTTAAATAAATTGTCTAACCTA
65 GTATTTTA-TTATGTTTCAATAAGATTTAGTTTAGATTTCTTATTTAAATAAATTGTGTAACCTA
* * * * * * * *
13694266 AGTGTTAAAATGATGA-CTTAGTTATCTTTAAGGCCAAATAAGGCCTAAAGGTTAGCTAACATAC
129 AGTGTTAAAATG-TCATTTTATTTGTCTTTAAGGCCAAATCAGGACTAAAGGTTAGCTAATATAT
13694330 TTGGTGAGTGTGCAGG
193 TTGGTGAGTGTGCAGG
13694346 AGACCACAAG
Statistics
Matches: 377, Mismatches: 36, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
208 69 0.18
209 306 0.81
210 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (208 bp):
TGATCTGTCGGTTTTATACCTAGCAGATTGAACTATTTTTCACACTTGAAAAGCTTTAAATCAAG
TATTTTATTATGTTTCAATAAGATTTAGTTTAGATTTCTTATTTAAATAAATTGTGTAACCTAAG
TGTTAAAATGTCATTTTATTTGTCTTTAAGGCCAAATCAGGACTAAAGGTTAGCTAATATATTTG
GTGAGTGTGCAGG
Found at i:13708334 original size:28 final size:27
Alignment explanation
Indices: 13708303--13708363 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
13708293 TTTTATTCAC
13708303 TATTTGAGACAATTTTTATTTTTATTTT
1 TATTTGA-ACAATTTTTATTTTTATTTT
* ***
13708331 TATTTTTATTTATTTTTATTTTTATTTT
1 TA-TTTGAACAATTTTTATTTTTATTTT
13708359 TATTT
1 TATTT
13708364 TATTTTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 3 0.11
28 21 0.75
29 4 0.14
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (27 bp):
TATTTGAACAATTTTTATTTTTATTTT
Found at i:13708342 original size:16 final size:16
Alignment explanation
Indices: 13708323--13708370 Score: 78
Period size: 16 Copynumber: 2.9 Consensus size: 16
13708313 AATTTTTATT
13708323 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
13708339 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
*
13708355 TTTTTATTTTATTTTT
1 TTTAT-TTTTATTTTT
13708371 TTGAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 20 0.67
17 10 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:13708342 original size:22 final size:23
Alignment explanation
Indices: 13708316--13708370 Score: 103
Period size: 22 Copynumber: 2.4 Consensus size: 23
13708306 TTGAGACAAT
13708316 TTTTATTTTTATTTTTATTTTTA
1 TTTTATTTTTATTTTTATTTTTA
13708339 -TTTATTTTTATTTTTATTTTTA
1 TTTTATTTTTATTTTTATTTTTA
13708361 TTTTATTTTT
1 TTTTATTTTT
13708371 TTGAATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTATTTTTATTTTTATTTTTA
Found at i:13708396 original size:5 final size:6
Alignment explanation
Indices: 13708314--13708370 Score: 93
Period size: 6 Copynumber: 10.0 Consensus size: 6
13708304 ATTTGAGACA
13708314 ATTTTT ATTTTT ATTTTT ATTTTT A--TTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
13708360 A-TTTT ATTTTT
1 ATTTTT ATTTTT
13708371 TTGAATAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.08
5 5 0.10
6 39 0.81
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:13709267 original size:20 final size:22
Alignment explanation
Indices: 13709245--13709288 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
13709235 CCAGAATAAG
13709245 AAAAATAGAGAA-AAA-AAAAGA
1 AAAAAT-GAGAAGAAACAAAAGA
13709266 AAAAATGAGAAGAAACAAAAGA
1 AAAAATGAGAAGAAACAAAAGA
13709288 A
1 A
13709289 GTGTGAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (22 bp):
AAAAATGAGAAGAAACAAAAGA
Found at i:13721481 original size:23 final size:25
Alignment explanation
Indices: 13721442--13721488 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
13721432 AGGGAAAAGA
*
13721442 ACAAAATGAAAATGAGTAA-AAAAT
1 ACAAAAAGAAAATGAGTAAGAAAAT
13721466 ACAAAAAGAAAA-GAGTAAGAAAA
1 ACAAAAAGAAAATGAGTAAGAAAA
13721489 AGTGTGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (25 bp):
ACAAAAAGAAAATGAGTAAGAAAAT
Found at i:13724399 original size:17 final size:17
Alignment explanation
Indices: 13724370--13724402 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13724360 AAACTTCGCT
13724370 TTTATTTTCTATTTTAG
1 TTTATTTTCTATTTTAG
13724387 TTTATCTTT-TATTTTA
1 TTTAT-TTTCTATTTTA
13724403 TGCTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTATTTTCTATTTTAG
Found at i:13729678 original size:40 final size:40
Alignment explanation
Indices: 13729619--13729776 Score: 156
Period size: 40 Copynumber: 4.0 Consensus size: 40
13729609 ATTTTACCAC
* *
13729619 TTCACCGACTCATAGCCTGCTAAGCCATAGCTTGAATCAT
1 TTCACCGACTAAAAGCCTGCTAAGCCATAGCTTGAATCAT
* * *
13729659 TTCACCTACTTGAAA-CCTGCTAAGCCGTAGCTTGAATCAT
1 TTCACCGAC-TAAAAGCCTGCTAAGCCATAGCTTGAATCAT
* * * * *
13729699 TTCATCGGCTAAAAGCCTACTAAACCATAACTTGAATCAT
1 TTCACCGACTAAAAGCCTGCTAAGCCATAGCTTGAATCAT
* * * * * *
13729739 TTCACTGGCTTAAAGCTTGCTAAGTCGTAGCTTGAATC
1 TTCACCGACTAAAAGCCTGCTAAGCCATAGCTTGAATC
13729777 GTATCGCATT
Statistics
Matches: 95, Mismatches: 21, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
39 4 0.04
40 88 0.93
41 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (40 bp):
TTCACCGACTAAAAGCCTGCTAAGCCATAGCTTGAATCAT
Found at i:13734367 original size:8 final size:8
Alignment explanation
Indices: 13734345--13734373 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
13734335 TATATTATGT
13734345 TAATTTAA
1 TAATTTAA
13734353 T-ATTTAA
1 TAATTTAA
13734360 TAATTTAA
1 TAATTTAA
13734368 TAATTT
1 TAATTT
13734374 TTTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TAATTTAA
Found at i:13734959 original size:11 final size:11
Alignment explanation
Indices: 13734926--13734965 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
13734916 ATGAAAATAT
13734926 TTATAAAATTA
1 TTATAAAATTA
*
13734937 TAATATAAATTA
1 TTATA-AAATTA
13734949 TTATAAAATTA
1 TTATAAAATTA
*
13734960 ATATAA
1 TTATAA
13734966 GAATATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TTATAAAATTA
Found at i:13735106 original size:31 final size:30
Alignment explanation
Indices: 13735035--13735117 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 30
13735025 TACAATTTGA
*
13735035 TCACTGAACTATTCAAAGTTTTTAATTAAG
1 TCACTGAATTATTCAAAGTTTTTAATTAAG
** * *
13735065 TCGTTAAATTATTCAAAAGTTTTTATTTAAG
1 TCACTGAATTATTC-AAAGTTTTTAATTAAG
*
13735096 TCACTGAATTATT-AAATTTTTT
1 TCACTGAATTATTCAAAGTTTTT
13735118 TAAAGGTTCC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
29 8 0.19
30 10 0.23
31 25 0.58
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (30 bp):
TCACTGAATTATTCAAAGTTTTTAATTAAG
Found at i:13738563 original size:15 final size:14
Alignment explanation
Indices: 13738542--13738576 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13738532 AAAAAATAAT
*
13738542 TCATTTTTCAAAAA
1 TCATTTTTTAAAAA
*
13738556 TTATTTTTTAAAAA
1 TCATTTTTTAAAAA
13738570 TCATTTT
1 TCATTTT
13738577 CAATCAAACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (14 bp):
TCATTTTTTAAAAA
Found at i:13740148 original size:52 final size:51
Alignment explanation
Indices: 13740070--13740172 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
13740060 TAAGTAGTCA
*
13740070 TATCTTGAGCATCTATTGTTTCCTTGTTATGTTTCTATTATAATTGTCTTAG
1 TATCTTGAGCATCTATGGTTTCCTTG-TATGTTTCTATTATAATTGTCTTAG
13740122 TATCTTGAGCATCTATGGTTTCCTTGTATGTTTCTATTATAATTGTCTTAG
1 TATCTTGAGCATCTATGGTTTCCTTGTATGTTTCTATTATAATTGTCTTAG
13740173 CTTTTACATC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 25 0.50
52 25 0.50
ACGTcount: A:0.19, C:0.14, G:0.15, T:0.52
Consensus pattern (51 bp):
TATCTTGAGCATCTATGGTTTCCTTGTATGTTTCTATTATAATTGTCTTAG
Found at i:13751423 original size:88 final size:85
Alignment explanation
Indices: 13751172--13751428 Score: 248
Period size: 88 Copynumber: 2.9 Consensus size: 85
13751162 AATGCGATAT
* *
13751172 AAATGTTCAAGTATTTAATTGAGTGCACAAAAAAAAT-GAGGTCTTAATTGTTTTTTTTTTAAAG
1 AAAT-TTCAAGTATTCAATTGAGTGCA-AAAAAAAATAGAGGT-TTAATTG-TTTTTTTTTAAAA
*
13751236 TTGAGGGTTTTTTTATGTATTTTA
62 TTGAGGGTTTTTTTATATATTTTA
* * * * * *
13751260 AAAGTTTTAAGTATTCAATTGAGTGTAAAATAAAAGTAGGGGTTTAATTATTTTTATTTTAAATT
1 AAA-TTTCAAGTATTCAATTGAGTGCAAAA-AAAAATAGAGGTTTAATTGTTTTT-TTTTAAAAT
* * *
13751325 TGAAGATTTTTTTGATATATTTTG
63 TGAGGGTTTTTTT-ATATATTTTA
* * ** **
13751349 AAATTTCAAGGATTCAAATGAGTGCAAAAAAAAATAGAAATTTAATTGCTTATTTTTAAAAAATT
1 AAATTTCAAGTATTCAATTGAGTGCAAAAAAAAATAGAGGTTTAATTG-TT-TTTTTTTAAAATT
13751414 GAGGG-TTTTTTATAT
64 GAGGGTTTTTTTATAT
13751429 CATTAAATCT
Statistics
Matches: 137, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
86 4 0.03
87 28 0.20
88 86 0.63
89 19 0.14
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.44
Consensus pattern (85 bp):
AAATTTCAAGTATTCAATTGAGTGCAAAAAAAAATAGAGGTTTAATTGTTTTTTTTTAAAATTGA
GGGTTTTTTTATATATTTTA
Found at i:13752264 original size:9 final size:9
Alignment explanation
Indices: 13752250--13752285 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
13752240 ATTTTCGAAT
*
13752250 TCGAATAAC
1 TCGAATAAA
*
13752259 TCGAATAAT
1 TCGAATAAA
13752268 TCGAATAAA
1 TCGAATAAA
13752277 TCGAATAAA
1 TCGAATAAA
13752286 ACTATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (9 bp):
TCGAATAAA
Found at i:13752268 original size:18 final size:18
Alignment explanation
Indices: 13752247--13752284 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
13752237 TGAATTTTCG
*
13752247 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCGAAT
13752265 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCGAAT
13752283 AA
1 AA
13752285 AACTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:13753336 original size:15 final size:16
Alignment explanation
Indices: 13753312--13753350 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
13753302 AATTTTTATT
13753312 TTTTTCTTTAATGTA-A
1 TTTTT-TTTAATGTATA
*
13753328 TTTTTTTTAATTTATA
1 TTTTTTTTAATGTATA
13753344 TTTTTTT
1 TTTTTTT
13753351 ATCTATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTTTAATGTATA
Found at i:13755212 original size:22 final size:22
Alignment explanation
Indices: 13755176--13755218 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13755166 TTATTAATGG
* *
13755176 CAGTTTATTTGCAAATCAGTGA
1 CAGTTTATCTACAAATCAGTGA
*
13755198 CAGTTTATCTACAAATTAGTG
1 CAGTTTATCTACAAATCAGTG
13755219 GTGGCATGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (22 bp):
CAGTTTATCTACAAATCAGTGA
Found at i:13755327 original size:17 final size:17
Alignment explanation
Indices: 13755305--13755337 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13755295 GGAATTTTTA
*
13755305 TAAAATGTGCATCGATT
1 TAAAATATGCATCGATT
13755322 TAAAATATGCATCGAT
1 TAAAATATGCATCGAT
13755338 ATGTCCATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (17 bp):
TAAAATATGCATCGATT
Found at i:13755811 original size:21 final size:20
Alignment explanation
Indices: 13755773--13755811 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13755763 CGAACATGAA
*
13755773 TTTTTAAAATAATTATAATG
1 TTTTTAAAATAATAATAATG
*
13755793 TTTTTCAAATAATCAATAA
1 TTTTTAAAATAAT-AATAA
13755812 GATTATTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
TTTTTAAAATAATAATAATG
Found at i:13756298 original size:26 final size:26
Alignment explanation
Indices: 13756269--13756343 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
13756259 ATATAAAGTT
**
13756269 TGATAGATATTCACTGACACAATGCC
1 TGATAGATATTCACTGACACAAAACC
*
13756295 TGATAGATATTCA-TCGGCACAAAACC
1 TGATAGATATTCACT-GACACAAAACC
*
13756321 TGATAGATATTCACAGACACAAA
1 TGATAGATATTCACTGACACAAA
13756344 GCTTGCTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 1 0.02
26 41 0.98
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (26 bp):
TGATAGATATTCACTGACACAAAACC
Found at i:13756844 original size:16 final size:16
Alignment explanation
Indices: 13756816--13756850 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13756806 AGTCCTTGCA
13756816 ATTTTGTCACTTTAAC
1 ATTTTGTCACTTTAAC
13756832 ATTTTAGTC-CTTTAAC
1 ATTTT-GTCACTTTAAC
13756848 ATT
1 ATT
13756851 AAAATTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (16 bp):
ATTTTGTCACTTTAAC
Found at i:13760073 original size:17 final size:19
Alignment explanation
Indices: 13760002--13760080 Score: 108
Period size: 19 Copynumber: 4.3 Consensus size: 19
13759992 AACACATTTG
*
13760002 ATATTCACATCAATTTAAC
1 ATATTCACATCAATTTCAC
* * *
13760021 ATACTCACATCAATGTCAT
1 ATATTCACATCAATTTCAC
13760040 ATATTCACATCAATTTCAC
1 ATATTCACATCAATTTCAC
13760059 ATATTC-CAT-AATTTCAC
1 ATATTCACATCAATTTCAC
13760076 ATATT
1 ATATT
13760081 TTCATATCTC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
17 13 0.25
18 3 0.06
19 37 0.70
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (19 bp):
ATATTCACATCAATTTCAC
Found at i:13760370 original size:45 final size:45
Alignment explanation
Indices: 13760297--13760425 Score: 132
Period size: 45 Copynumber: 2.9 Consensus size: 45
13760287 ATGACTCGCC
* ** * * *
13760297 ACCCCGGGTTGCCTAACAACGATGGCTCACTTATATTGAATTGCT
1 ACCCCAGGTTGCCCGACAAAGATAGCTCACTTATATCGAATTGCT
* **
13760342 ACCCCAGGTTGCCCGGCAAAGATAGCTCACTTACGTCGAATTGCT
1 ACCCCAGGTTGCCCGACAAAGATAGCTCACTTATATCGAATTGCT
* * * * *
13760387 GCCCCGGGTTGCCCGATAACGATAGCTCACTTATGTCGA
1 ACCCCAGGTTGCCCGACAAAGATAGCTCACTTATATCGA
13760426 TATGCAGTTA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.25
Consensus pattern (45 bp):
ACCCCAGGTTGCCCGACAAAGATAGCTCACTTATATCGAATTGCT
Found at i:13761330 original size:14 final size:14
Alignment explanation
Indices: 13761311--13761340 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13761301 GCATTTACTC
13761311 AAACCTTAAACCCT
1 AAACCTTAAACCCT
*
13761325 AAACCTTAAACTCT
1 AAACCTTAAACCCT
13761339 AA
1 AA
13761341 CATTTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:13761740 original size:5 final size:5
Alignment explanation
Indices: 13761730--13761757 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
13761720 TCTTTCAAAG
13761730 AATAC AATAC AATAC AATAC AATAC AAT
1 AATAC AATAC AATAC AATAC AATAC AAT
13761758 GAATGGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAC
Found at i:13761960 original size:32 final size:32
Alignment explanation
Indices: 13761913--13761977 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
13761903 GACAGGCTTC
* * * *
13761913 TCCAACAATTTGTTGAATCGGGTTAATTCATG
1 TCCAACAATTCGTTGAATCAGATCAATTCATG
*
13761945 TCCATCAATTCGTTGAATCAGATCAATTCATG
1 TCCAACAATTCGTTGAATCAGATCAATTCATG
13761977 T
1 T
13761978 GGATTAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (32 bp):
TCCAACAATTCGTTGAATCAGATCAATTCATG
Found at i:13762269 original size:2 final size:2
Alignment explanation
Indices: 13762264--13762293 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13762254 ATATATATAA
13762264 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13762294 TTGGTAGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13766501 original size:37 final size:37
Alignment explanation
Indices: 13766407--13766505 Score: 94
Period size: 37 Copynumber: 2.6 Consensus size: 37
13766397 CACCCAATGC
* * *
13766407 CTCATCGGAATGTATAAAGTAATTAGTTTGTGCCTAACA
1 CTCATCGGAA-GT-TGAAGTAAATAGTTTGTGCCCAACA
*
13766446 CTCATCGGTATAGTTGAAGTAAAT-G-TTGTGCCCAGCA
1 CTCATCGG-A-AGTTGAAGTAAATAGTTTGTGCCCAACA
13766483 CTCATCGGAACGTCTGAAGTAAA
1 CTCATCGGAA-GT-TGAAGTAAA
13766506 ATGCTTCCAG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
35 1 0.02
36 3 0.06
37 27 0.52
38 1 0.02
39 16 0.31
40 3 0.06
41 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (37 bp):
CTCATCGGAAGTTGAAGTAAATAGTTTGTGCCCAACA
Found at i:13773277 original size:18 final size:18
Alignment explanation
Indices: 13773251--13773287 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13773241 AGGTAGACAA
* *
13773251 AAACGTGCCATAAGGTAG
1 AAACATGCCACAAGGTAG
13773269 AAACATGCCACAAGGTAG
1 AAACATGCCACAAGGTAG
13773287 A
1 A
13773288 GAAAAAGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (18 bp):
AAACATGCCACAAGGTAG
Found at i:13774360 original size:13 final size:13
Alignment explanation
Indices: 13774344--13774371 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13774334 ACCAAAATGA
13774344 TATTACAAAAAGT
1 TATTACAAAAAGT
13774357 TATTACAAAAAGT
1 TATTACAAAAAGT
13774370 TA
1 TA
13774372 AAATAATAAA
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:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (13 bp):
TATTACAAAAAGT
Found at i:13780929 original size:12 final size:12
Alignment explanation
Indices: 13780914--13780939 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13780904 AATTAAAGAA
13780914 ATAATAGCATTC
1 ATAATAGCATTC
13780926 ATAATAGCATTC
1 ATAATAGCATTC
13780938 AT
1 AT
13780940 CATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:13783113 original size:18 final size:18
Alignment explanation
Indices: 13783079--13783113 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13783069 TCCTCATTAC
*
13783079 TAAAAATAATAGAGAATG
1 TAAAAATAAAAGAGAATG
*
13783097 TAAAAATAAAAGTGAAT
1 TAAAAATAAAAGAGAAT
13783114 AAATACTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (18 bp):
TAAAAATAAAAGAGAATG
Found at i:13785456 original size:19 final size:21
Alignment explanation
Indices: 13785422--13785462 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
13785412 TAGTAAATAA
*
13785422 TTTTAAAATTACTAAAATTAT
1 TTTTAAAATTACTAAAAGTAT
13785443 TTTTAAAA-TA-TAAAAGTAT
1 TTTTAAAATTACTAAAAGTAT
13785462 T
1 T
13785463 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTAAAATTACTAAAAGTAT
Found at i:13785495 original size:32 final size:28
Alignment explanation
Indices: 13785425--13785497 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
13785415 TAAATAATTT
*
13785425 TAAAATTACTAAAATTATTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTAAAATA
* *
13785453 TAAAAGTATTAAAATTATTTTTTTTGAAATAA
1 TAAAATTATTAAAATTA---TTTTTAAAAT-A
13785485 TAAAATTATTAAA
1 TAAAATTATTAAA
13785498 TAATTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.41
31 9 0.24
32 13 0.35
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTAAAATA
Found at i:13801937 original size:157 final size:156
Alignment explanation
Indices: 13801636--13801924 Score: 407
Period size: 157 Copynumber: 1.8 Consensus size: 156
13801626 ATTTTTGGAT
* *
13801636 TTACAGGTTATATGGTTGCTGGTATTAGATGTCCTACTAATGGATGAGATCCGACATATGTTGCG
1 TTACAGGTTATATGGGTGCTGGTATTAGATGTCCTACTAATGGATGAGATCCGACATATGTTACG
* * *
13801701 GATTCTCACAGCTCGTGTGAGCAGCATCGTGTAGCCTTACATCTTGACCCACAGCTCATGTGAGC
66 GATTCTCAAAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCATGACCCACAGCTCATGTGAGC
*
13801766 AAGCCTACTTTACAGCTCATGTGAGCA
131 AA-CCTACTATACAGCTCATGTGAGCA
* * * * * * *
13801793 TTACATGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGATCTGATATATGTTATG
1 TTACAGGTTATATGGGTGCTGGTATTAGATGTCCTACTAATGGATGAGATCCGACATATGTTACG
* * * *
13801858 GATTCTCCAAAGCTCGTGTTAGCAGTATCGTGTAGTCTAACATCATGACCCACAGCTCGTGTGAG
66 GATTCT-CAAAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCATGACCCACAGCTCATGTGAG
13801923 CA
130 CA
13801925 CTACATGATA
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
157 62 0.54
158 53 0.46
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (156 bp):
TTACAGGTTATATGGGTGCTGGTATTAGATGTCCTACTAATGGATGAGATCCGACATATGTTACG
GATTCTCAAAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCATGACCCACAGCTCATGTGAGC
AACCTACTATACAGCTCATGTGAGCA
Found at i:13803108 original size:15 final size:16
Alignment explanation
Indices: 13803090--13803133 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
13803080 CCTAAAGTAT
*
13803090 TCTAAACTAAATTA-A
1 TCTAAATTAAATTAGA
*
13803105 TCTAAGTTAAATTAGA
1 TCTAAATTAAATTAGA
*
13803121 ACTAAATTAAATT
1 TCTAAATTAAATT
13803134 CCTATGCACG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (16 bp):
TCTAAATTAAATTAGA
Found at i:13821620 original size:12 final size:12
Alignment explanation
Indices: 13821590--13821625 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
13821580 ATGACTAGCT
13821590 GAAGGAA-AAG-
1 GAAGGAAGAAGA
13821600 GAA-GAAGAAGA
1 GAAGGAAGAAGA
13821611 GAAGGAAGAAGA
1 GAAGGAAGAAGA
13821623 GAA
1 GAA
13821626 TAAAGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 6 0.26
11 3 0.13
12 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
GAAGGAAGAAGA
Found at i:13822727 original size:16 final size:16
Alignment explanation
Indices: 13822708--13822738 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13822698 AAAATGAATG
*
13822708 AGAAAAAGGAAGAAAA
1 AGAAAAAGAAAGAAAA
13822724 AGAAAAAGAAAGAAA
1 AGAAAAAGAAAGAAA
13822739 TTTTTGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAGAAAA
Found at i:13826127 original size:12 final size:12
Alignment explanation
Indices: 13826112--13826136 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13826102 ATTAAAGAAT
13826112 TAATAGCATTCA
1 TAATAGCATTCA
13826124 TAATAGCATTCA
1 TAATAGCATTCA
13826136 T
1 T
13826137 CATGATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:13827622 original size:6 final size:7
Alignment explanation
Indices: 13827604--13827637 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
13827594 AGTACATATG
13827604 CTTTTTT
1 CTTTTTT
13827611 CTTTTTT
1 CTTTTTT
13827618 CTTTTTT
1 CTTTTTT
13827625 -TCTTTTT
1 CT-TTTTT
13827632 CTTTTT
1 CTTTTT
13827638 GAACATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 23 0.92
8 1 0.04
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:13853759 original size:21 final size:20
Alignment explanation
Indices: 13853719--13853760 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
13853709 AATTCAGTAC
*
13853719 AAATTAATTATTTTATAATT
1 AAATTAATTATTTTACAATT
13853739 AAATTAAATT-TTTTAACAATT
1 AAATT-AATTATTTT-ACAATT
13853760 A
1 A
13853761 TTACTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTAATTATTTTACAATT
Found at i:13855140 original size:15 final size:14
Alignment explanation
Indices: 13855120--13855151 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
13855110 TTCCTCACAT
13855120 CAAGGGAGTTATAGA
1 CAAGGGAGTTATA-A
13855135 CAAGGGAGTTATAA
1 CAAGGGAGTTATAA
13855149 CAA
1 CAA
13855152 CAATCAGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (14 bp):
CAAGGGAGTTATAA
Done.