Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 76 of 199
Found at i:21573357 original size:18 final size:18
Alignment explanation
Indices: 21573329--21573369 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
21573319 TGATGTGAGC
21573329 TTATTGTCTTATGTGTAT
1 TTATTGTCTTATGTGTAT
*
21573347 TGTATTG-CTTATTTGTAT
1 T-TATTGTCTTATGTGTAT
21573365 TTATT
1 TTATT
21573370 AATTATTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (18 bp):
TTATTGTCTTATGTGTAT
Found at i:21576480 original size:18 final size:20
Alignment explanation
Indices: 21576440--21576484 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
21576430 AATATGATAA
21576440 ATTTATAAACGATAAAATAT
1 ATTTATAAACGATAAAATAT
*
21576460 ATTTA-AAATGATAAAAT-T
1 ATTTATAAACGATAAAATAT
21576478 ATTTATA
1 ATTTATA
21576485 TAATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
ATTTATAAACGATAAAATAT
Found at i:21577493 original size:22 final size:24
Alignment explanation
Indices: 21577447--21577496 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
21577437 GAACCAAATA
*
21577447 TAAAAAACATATTAATTTAATAAT
1 TAAAAAACATATTAATTAAATAAT
*
21577471 TAAATAACATA-TAA-TAAATAAT
1 TAAAAAACATATTAATTAAATAAT
21577493 TAAA
1 TAAA
21577497 CATTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 3 0.12
24 10 0.42
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAAAACATATTAATTAAATAAT
Found at i:21588358 original size:25 final size:25
Alignment explanation
Indices: 21588312--21588359 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
21588302 AAATACTATC
*
21588312 AAAAATTTTAAAAATATTTTTTCGT
1 AAAAATTTTAAAAATATCTTTTCGT
*
21588337 AAAACTTTTCAAAAATA-CTTTTC
1 AAAAATTTT-AAAAATATCTTTTC
21588360 AACTTCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAAATTTTAAAAATATCTTTTCGT
Found at i:21590338 original size:24 final size:22
Alignment explanation
Indices: 21590290--21590339 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
21590280 ATACTTATTC
*
21590290 TTTATATATAAATATATTTTCT
1 TTTATATATAAATAAATTTTCT
21590312 TTTATATGAATAAATAAAGTTTT-T
1 TTTATAT--ATAAATAAA-TTTTCT
21590336 TTTA
1 TTTA
21590340 AGATCTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTATATATAAATAAATTTTCT
Found at i:21592172 original size:309 final size:310
Alignment explanation
Indices: 21591555--21592187 Score: 1151
Period size: 309 Copynumber: 2.0 Consensus size: 310
21591545 GATGACATTT
21591555 AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
1 AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
*
21591620 AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCGATTCCATA
66 AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCAATTCCATA
21591685 AAATGAAAAATTATTGAAAGAAAAGAGAAAGAAATGAAGATGGTCATATGCTAAAGAAGGCGAGT
131 AAATGAAAAATTATT----------AGAAAGAAATGAAGATGGTCATATGCTAAAGAAGGCGAGT
21591750 ACTCATGAAGAGACCCAAGGCATAACTTTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAAT
186 ACTCATGAAGAGACCCAAGGCATAACTTTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAAT
21591815 TATAAATATAATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
251 TATAAATATAATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
21591875 AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
1 AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
21591940 AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCAATTCCATA
66 AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCAATTCCATA
*
21592005 AAATGAAAAATTATT-GAAAGAAATGAATATGGTCATATGCTAAAGAAGGCGAGTACTCATGAAG
131 AAATGAAAAATTATTAGAAAGAAATGAAGATGGTCATATGCTAAAGAAGGCGAGTACTCATGAAG
21592069 AGACCCAAGGCATAACTTTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAATTATAAATATA
196 AGACCCAAGGCATAACTTTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAATTATAAATATA
21592134 ATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
261 ATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
21592184 AAAG
1 AAAG
21592188 GAAATTATTG
Statistics
Matches: 311, Mismatches: 2, Indels: 11
0.96 0.01 0.03
Matches are distributed among these distances:
309 167 0.54
320 144 0.46
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (310 bp):
AAAGATTGCATATACTACCTGATACATATACCAACTAAAATGCTCCAAACAATTATATGTCCTAG
AAGGACAACGTGATAAAAATAAGCTTTGGGCATGCTAGAAGCATGACAAACTAGTCAATTCCATA
AAATGAAAAATTATTAGAAAGAAATGAAGATGGTCATATGCTAAAGAAGGCGAGTACTCATGAAG
AGACCCAAGGCATAACTTTTGATAAAACCCTAACAGAGGTTCAGGTACATGAAATTATAAATATA
ATGGAATATCCCAATCAATTATGTCATAATTAAATATGATGGAGCTGACA
Found at i:21593671 original size:3 final size:3
Alignment explanation
Indices: 21593663--21593731 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
21593653 TTCTTTGCAG
* * * * *
21593663 TAT TAT TAT TGT TGT AAT TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21593711 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
21593732 ATAAAACAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:21594066 original size:14 final size:14
Alignment explanation
Indices: 21594047--21594076 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21594037 TACCATTTTA
21594047 TTGCTAATTCTTCT
1 TTGCTAATTCTTCT
21594061 TTGCTAATTCTTCT
1 TTGCTAATTCTTCT
21594075 TT
1 TT
21594077 TACCATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.60
Consensus pattern (14 bp):
TTGCTAATTCTTCT
Found at i:21598345 original size:13 final size:13
Alignment explanation
Indices: 21598327--21598356 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
21598317 AACCCAAACT
21598327 CAATTACCCAACC
1 CAATTACCCAACC
21598340 CAATTACCCAACC
1 CAATTACCCAACC
21598353 CAAT
1 CAAT
21598357 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:21598437 original size:20 final size:20
Alignment explanation
Indices: 21598412--21598451 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21598402 CGTAAAATGA
*
21598412 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
21598432 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
21598452 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:21598441 original size:34 final size:35
Alignment explanation
Indices: 21598397--21598463 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
21598387 CAGTAAAATA
* *
21598397 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
21598431 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
21598464 CTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:21599129 original size:9 final size:9
Alignment explanation
Indices: 21599117--21599202 Score: 84
Period size: 9 Copynumber: 9.4 Consensus size: 9
21599107 AAATAAAAAA
21599117 AATTCGGGT
1 AATTCGGGT
21599126 AATTCGGGT
1 AATTCGGGT
*
21599135 ATTTTTC-GGT
1 A--ATTCGGGT
* *
21599145 AATTCAGTT
1 AATTCGGGT
*
21599154 AATTCGGTT
1 AATTCGGGT
*
21599163 AATTCGGTT
1 AATTCGGGT
*
21599172 AATTCGGTT
1 AATTCGGGT
21599181 AATTCGGGT
1 AATTCGGGT
*
21599190 AATTCGGAT
1 AATTCGGGT
21599199 AATT
1 AATT
21599203 TTTAACCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
8 3 0.04
9 58 0.85
10 4 0.06
11 3 0.04
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:21599167 original size:18 final size:18
Alignment explanation
Indices: 21599139--21599202 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
21599129 TCGGGTATTT
*
21599139 TTCGG-TAATTCAGTTAA
1 TTCGGTTAATTCGGTTAA
21599156 TTCGGTTAATTCGGTTAA
1 TTCGGTTAATTCGGTTAA
*
21599174 TTCGGTTAATTCGGGTAA
1 TTCGGTTAATTCGGTTAA
*
21599192 TTCGGATAATT
1 TTCGGTTAATT
21599203 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 5 0.12
18 38 0.88
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (18 bp):
TTCGGTTAATTCGGTTAA
Found at i:21599181 original size:27 final size:26
Alignment explanation
Indices: 21599125--21599202 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 26
21599115 AAAATTCGGG
*
21599125 TAATTCGGGTATTTTTCGGTAATTCAGT
1 TAATTCGGGTA--ATTCGGTAATTCAGT
* *
21599153 TAATTCGGTTAATTCGGTTAATTCGGT
1 TAATTCGGGTAATTCGG-TAATTCAGT
21599180 TAATTCGGGTAATTCGGATAATT
1 TAATTCGGGTAATTCGG-TAATT
21599203 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
26 5 0.11
27 29 0.66
28 10 0.23
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (26 bp):
TAATTCGGGTAATTCGGTAATTCAGT
Found at i:21599876 original size:68 final size:67
Alignment explanation
Indices: 21599804--21599936 Score: 175
Period size: 63 Copynumber: 2.0 Consensus size: 67
21599794 TGGCACTTCT
*
21599804 ATTACTTGCTCTTTGAATTTCTCTTGAGTGTGGTTTTATTGTGGTAGTT-T-TTTTT-TTTTT-T
1 ATTACTTGCTCTTTGAA---CTC--GACTGTGGTTTTATTGTGGTAGTTCTCTTTTTGTTTTTAT
21599865 AGGTTCC
61 AGGTTCC
*
21599872 ATTACTTTCTCTTTGAACTCGACTGTGGTTTTATTGTGGTAGTTCTCTTTTTGTTTTTATAGGTT
1 ATTACTTGCTCTTTGAACTCGACTGTGGTTTTATTGTGGTAGTTCTCTTTTTGTTTTTATAGGTT
21599937 TAGAGAACCA
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
63 23 0.39
64 1 0.02
65 8 0.14
66 5 0.08
67 6 0.10
68 16 0.27
ACGTcount: A:0.13, C:0.11, G:0.19, T:0.57
Consensus pattern (67 bp):
ATTACTTGCTCTTTGAACTCGACTGTGGTTTTATTGTGGTAGTTCTCTTTTTGTTTTTATAGGTT
CC
Found at i:21604719 original size:11 final size:11
Alignment explanation
Indices: 21604683--21604721 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
21604673 TAAATAGTAA
*
21604683 TTTATTAATAT
1 TTTAATAATAT
21604694 TTTAATGAGATAT
1 TTTAAT-A-ATAT
21604707 TTTAATAATAT
1 TTTAATAATAT
21604718 TTTA
1 TTTA
21604722 TTTAAAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 13 0.52
12 2 0.08
13 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:21607941 original size:14 final size:14
Alignment explanation
Indices: 21607918--21607976 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 14
21607908 TATGAATAAT
21607918 AATATAATAAAACAA
1 AATATAATAAAAC-A
21607933 ATATCATAATAAAA-A
1 A-AT-ATAATAAAACA
*
21607948 AATATGATAATAA-A
1 AATATAATAA-AACA
21607962 AATA-AATAAAACA
1 AATATAATAAAACA
21607975 AA
1 AA
21607977 AAAGAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 2 0.05
13 13 0.34
14 9 0.24
15 3 0.08
16 2 0.05
17 9 0.24
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (14 bp):
AATATAATAAAACA
Found at i:21607952 original size:16 final size:16
Alignment explanation
Indices: 21607921--21607963 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
21607911 GAATAATAAT
21607921 ATAATAAAACAAATATC
1 ATAATAAAA-AAATATC
*
21607938 ATAATAAAAAAATATG
1 ATAATAAAAAAATATC
21607954 ATAATAAAAA
1 ATAATAAAAA
21607964 TAAATAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (16 bp):
ATAATAAAAAAATATC
Found at i:21607963 original size:17 final size:17
Alignment explanation
Indices: 21607921--21607969 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
21607911 GAATAATAAT
*
21607921 ATAATAAAACAAATATC
1 ATAATAAAAAAAATATC
*
21607938 ATAAT-AAAAAAATATG
1 ATAATAAAAAAAATATC
21607954 ATAATAAAAATAAATA
1 ATAATAAAAA-AAATA
21607970 AAACAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.50
17 9 0.32
18 5 0.18
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (17 bp):
ATAATAAAAAAAATATC
Found at i:21610092 original size:27 final size:30
Alignment explanation
Indices: 21610058--21610112 Score: 80
Period size: 27 Copynumber: 1.9 Consensus size: 30
21610048 TCTTTATTGA
21610058 TATATTTTTC-TCTTTT-TTT-ATTTTAAT
1 TATATTTTTCATCTTTTCTTTCATTTTAAT
*
21610085 TATATTTTTCATTTTTTCTTTCATTTTA
1 TATATTTTTCATCTTTTCTTTCATTTTA
21610113 TTTTTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 5 0.21
29 3 0.12
30 6 0.25
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (30 bp):
TATATTTTTCATCTTTTCTTTCATTTTAAT
Found at i:21610118 original size:12 final size:12
Alignment explanation
Indices: 21610073--21610118 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
21610063 TTTTCTCTTT
*
21610073 TTTTA-TTTTAA
1 TTTTATTTTTCA
*
21610084 TTATATTTTTCA
1 TTTTATTTTTCA
21610096 TTTT-TTCTTTCA
1 TTTTATT-TTTCA
21610108 TTTTATTTTTC
1 TTTTATTTTTC
21610119 CAATTTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 6 0.21
12 21 0.72
13 2 0.07
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:21620213 original size:2 final size:2
Alignment explanation
Indices: 21620206--21620230 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21620196 TTCCAATAGC
21620206 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21620231 TTAAAATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21621678 original size:30 final size:31
Alignment explanation
Indices: 21621642--21621699 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
21621632 AAAAATCAAG
*
21621642 AAAATTAACATCACAAAC-AAAATCCATTAA
1 AAAATTAACATAACAAACAAAAATCCATTAA
21621672 AAAATTAACATAACAAACAAAAATCCAT
1 AAAATTAACATAACAAACAAAAATCCAT
21621700 CAATCTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (31 bp):
AAAATTAACATAACAAACAAAAATCCATTAA
Found at i:21623517 original size:21 final size:21
Alignment explanation
Indices: 21623488--21623527 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21623478 AATAAAAAAA
21623488 AAAGCCTTTACCAAGAATACT
1 AAAGCCTTTACCAAGAATACT
* *
21623509 AAAGGCTTTTCCAAGAATA
1 AAAGCCTTTACCAAGAATA
21623528 GCAAGAGCAT
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:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (21 bp):
AAAGCCTTTACCAAGAATACT
Found at i:21624176 original size:58 final size:59
Alignment explanation
Indices: 21624065--21624183 Score: 222
Period size: 58 Copynumber: 2.0 Consensus size: 59
21624055 ATAAAACAAA
*
21624065 AGAAAGAATCATCAGCTTCTTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
1 AGAAAGAATCATCAGCTTATTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
21624124 AGAAAGAATCATCAGCTTATTCATTTT-TTTTAACTCCCATCGAAAATCCATTGTTGTT
1 AGAAAGAATCATCAGCTTATTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
21624182 AG
1 AG
21624184 TCTCCAAGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 33 0.56
59 26 0.44
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (59 bp):
AGAAAGAATCATCAGCTTATTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
Found at i:21626151 original size:11 final size:10
Alignment explanation
Indices: 21626112--21626294 Score: 67
Period size: 11 Copynumber: 18.1 Consensus size: 10
21626102 GGCCCATTTT
21626112 TATTTTAAAA
1 TATTTTAAAA
21626122 -ATTTTAAAA
1 TATTTTAAAA
* **
21626131 AATTAAAAAA
1 TATTTTAAAA
21626141 GTATTTTAAAAA
1 -TATTTT-AAAA
21626153 TATTTTAAAAA
1 TATTTT-AAAA
21626164 TATTTT-AAA
1 TATTTTAAAA
**
21626173 -ATTAAAAAA
1 TATTTTAAAA
* **
21626182 AATTAAAAAAA
1 TATT-TTAAAA
21626193 GTATTTTAAAA
1 -TATTTTAAAA
21626204 TTATTTT-AAA
1 -TATTTTAAAA
*
21626214 -A-TTAAAAA
1 TATTTTAAAA
* **
21626222 AATTAAAAAA
1 TATTTTAAAA
21626232 GTATTTTAAAA
1 -TATTTTAAAA
21626243 -ATATTTAAAA
1 TAT-TTTAAAA
*
21626253 -ATTTAAAAA
1 TATTTTAAAA
* *
21626262 AATTTAAAAA
1 TATTTTAAAA
**
21626272 GTATGTAAAAAA
1 -TAT-TTTAAAA
21626284 TATTTTAAAA
1 TATTTTAAAA
21626294 T
1 T
21626295 TAAAAAAATA
Statistics
Matches: 137, Mismatches: 21, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
7 2 0.01
8 7 0.05
9 24 0.18
10 43 0.31
11 48 0.35
12 13 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:21626162 original size:22 final size:21
Alignment explanation
Indices: 21626112--21626173 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
21626102 GGCCCATTTT
21626112 TATTTTAAAA-ATTTTAAAAA
1 TATTTTAAAATATTTTAAAAA
**
21626132 -ATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAA-TATTTTAAAAA
21626153 TATTTTAAAAATATTTTAAAA
1 TATTTT-AAAATATTTTAAAA
21626174 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 7 0.21
21 10 0.29
22 13 0.38
23 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TATTTTAAAATATTTTAAAAA
Found at i:21626170 original size:52 final size:52
Alignment explanation
Indices: 21626112--21626214 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
21626102 GGCCCATTTT
**
21626112 TATTTTAAAAATTTTAAAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAAA
1 TATTTT-AAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
*
21626164 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAATTATTTTAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
21626215 TTAAAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 14 0.30
52 33 0.70
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (52 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
Found at i:21626221 original size:39 final size:39
Alignment explanation
Indices: 21626112--21626303 Score: 244
Period size: 40 Copynumber: 4.8 Consensus size: 39
21626102 GGCCCATTTT
* *
21626112 TATTTTAAAAAT-TTTAAAAAATTAAAAAAGTATTTTAAAAA-
1 TATTTTAAAAATATTT-TAAAATTAAAAAA--A-TTAAAAAAG
21626153 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATT-AAAAAAATT-AAAAAAG
*
21626194 TATTTTAAAATTATTTTAAAATTAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
* *
21626233 TATTTTAAAAATATTTAAAAATTTAAAAAAATTTAAAAAG
1 TATTTTAAAAATATTTTAAAA-TTAAAAAAATTAAAAAAG
* *
21626273 TATGTAAAAAATATTTTAAAATTAAAAAAAT
1 TATTTTAAAAATATTTTAAAATTAAAAAAAT
21626304 AAATATATTT
Statistics
Matches: 137, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
39 38 0.28
40 50 0.36
41 40 0.29
42 9 0.07
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (39 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
Found at i:21626229 original size:8 final size:9
Alignment explanation
Indices: 21626211--21626303 Score: 53
Period size: 9 Copynumber: 9.6 Consensus size: 9
21626201 AAATTATTTT
21626211 AAAATTAAA
1 AAAATTAAA
21626220 AAAATTAAA
1 AAAATTAAA
21626229 AAAGTATTTTAAA
1 AAA--A--TTAAA
* *
21626242 AATATTTAA
1 AAAATTAAA
*
21626251 AAATTTAAA
1 AAAATTAAA
21626260 AAAATTTAAA
1 AAAA-TTAAA
*
21626270 AAGTATGTAAA
1 AA-AAT-TAAA
**
21626281 AAATATT-TT
1 AAA-ATTAAA
21626290 AAAATTAAA
1 AAAATTAAA
21626299 AAAAT
1 AAAAT
21626304 AAATATATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
8 3 0.05
9 33 0.52
10 9 0.14
11 11 0.17
13 7 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATTAAA
Found at i:21633673 original size:15 final size:17
Alignment explanation
Indices: 21633638--21633676 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21633628 AAGTTGATTT
*
21633638 TTTTTTTAGATTTGAGC
1 TTTTTTAAGATTTGAGC
21633655 TTTTTTAAG-TTTGAG-
1 TTTTTTAAGATTTGAGC
21633670 TTTTTTA
1 TTTTTTA
21633677 TATTCGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 6 0.29
17 8 0.38
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (17 bp):
TTTTTTAAGATTTGAGC
Found at i:21637348 original size:3 final size:3
Alignment explanation
Indices: 21637340--21637376 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
21637330 TCAGCTTCTT
21637340 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21637377 ATAATATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21642685 original size:4 final size:4
Alignment explanation
Indices: 21642668--21642715 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
21642658 TTATTCTATT
* * * * *
21642668 TTTA TTTA TCTA TTTA TTTA TGTA TTCA TTCA TTTA TTTA TTTC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
21642716 CTCTTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:21642813 original size:12 final size:12
Alignment explanation
Indices: 21642774--21642814 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
21642764 CATTTTATTA
21642774 TTATTGTTGTTG
1 TTATTGTTGTTG
*
21642786 TTGTTGTTG-TG
1 TTATTGTTGTTG
21642797 ATTATTGTTGTTG
1 -TTATTGTTGTTG
21642810 TTATT
1 TTATT
21642815 TATTTTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.10, C:0.00, G:0.24, T:0.66
Consensus pattern (12 bp):
TTATTGTTGTTG
Found at i:21659637 original size:4 final size:4
Alignment explanation
Indices: 21659628--21659673 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
21659618 TATTATTCTA
* * * *
21659628 TATT TATT TATT TATT TATG TATT CATT CATT TATT TATT TCTT TA
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TA
21659674 CTCTTTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:21672020 original size:45 final size:47
Alignment explanation
Indices: 21671971--21672064 Score: 138
Period size: 50 Copynumber: 2.0 Consensus size: 47
21671961 TGCCGAAATT
*
21671971 ATTTAAGCAACT-AAAATT-AAAACAACTTAATTCATTAAACTAATG
1 ATTTAAGCAACTAAAAATTAAAAACAACTTAATTAATTAAACTAATG
21672016 ATTTAAGCAACTAAAGAAAATTAAAAACAACTTAATTAATTAAACTAAT
1 ATTTAAGCAACT--A-AAAATTAAAAACAACTTAATTAATTAAACTAAT
21672065 TTAATTAACC
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 12 0.28
49 6 0.14
50 25 0.58
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (47 bp):
ATTTAAGCAACTAAAAATTAAAAACAACTTAATTAATTAAACTAATG
Found at i:21686858 original size:34 final size:31
Alignment explanation
Indices: 21686806--21686871 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 31
21686796 ATCTCATTAT
21686806 TAAATAAAATAAAAAAAA-TAGTAAATAATTTA
1 TAAATAAAATAAAAAAAATTA-TAAAT-ATTTA
*
21686838 TAAATAATAATTAAATAAAATTATAAATATTTA
1 TAAATAA-AA-TAAAAAAAATTATAAATATTTA
21686871 T
1 T
21686872 TTACAAGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 7 0.23
33 8 0.27
34 13 0.43
35 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
TAAATAAAATAAAAAAAATTATAAATATTTA
Found at i:21697184 original size:25 final size:25
Alignment explanation
Indices: 21697156--21697209 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
21697146 AGCTCCGAAT
*
21697156 AGCCATATATTGGGAAG-TTCAAGCG
1 AGCCATATATTGGGAAGCTTC-AGAG
21697181 AGCC--ATATTGGGAAGCTTCAGAG
1 AGCCATATATTGGGAAGCTTCAGAG
21697204 AGCCAT
1 AGCCAT
21697210 TAATCAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 18 0.72
24 3 0.12
25 4 0.16
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
AGCCATATATTGGGAAGCTTCAGAG
Found at i:21697192 original size:23 final size:23
Alignment explanation
Indices: 21697162--21697209 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
21697152 GAATAGCCAT
*
21697162 ATATTGGGAAG-TTCAAGCGAGCC
1 ATATTGGGAAGCTTC-AGAGAGCC
21697185 ATATTGGGAAGCTTCAGAGAGCC
1 ATATTGGGAAGCTTCAGAGAGCC
21697208 AT
1 AT
21697210 TAATCAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (23 bp):
ATATTGGGAAGCTTCAGAGAGCC
Found at i:21697333 original size:26 final size:26
Alignment explanation
Indices: 21697296--21697368 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
21697286 CGTGATATAT
21697296 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* * ** *
21697322 GGCTCTTTGTGAGATTCTTGATTAAT
1 GGCTCTTCGTGAGCTTCCCGATTAAA
*
21697348 GGCTCTTCG-AAGCTTCCCGAT
1 GGCTCTTCGTGAGCTTCCCGAT
21697369 ATATAGTTAC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
25 8 0.22
26 29 0.78
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:21704377 original size:27 final size:27
Alignment explanation
Indices: 21704340--21704454 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 27
21704330 AGAGGTCAAT
*
21704340 AAATGATCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
21704367 AAATGACCGAATTATCCCCACAGGTTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * * *
21704394 AAATAACCGAATTACCCCTATAGGATA
1 AAATGACCGAATTACCCCCACAGGGTA
** * *
21704421 AAATGACTAAAATACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
21704448 AAATGAC
1 AAATGAC
21704455 TATTATACCC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCACAGGGTA
Found at i:21704812 original size:28 final size:28
Alignment explanation
Indices: 21704770--21704849 Score: 142
Period size: 28 Copynumber: 2.9 Consensus size: 28
21704760 ACTGTACCGA
*
21704770 TACTGTATTAGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
21704798 TGCTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
21704826 TACTGTATTGGGCTAAGGCCCACA
1 TACTGTATTGGGCTAAGGCCCACA
21704850 CTATACTGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:21715850 original size:15 final size:16
Alignment explanation
Indices: 21715826--21715862 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21715816 TTGAATTAAC
*
21715826 TTTA-TTTATTT-ATT
1 TTTATTTTATTTGACT
21715840 TTTATTTTATTTGACT
1 TTTATTTTATTTGACT
21715856 TTTATTT
1 TTTATTT
21715863 AGTGAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 9 0.45
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTTGACT
Found at i:21717113 original size:6 final size:6
Alignment explanation
Indices: 21717102--21717133 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
21717092 GAAGACTGAT
21717102 TTTGCA TTTGCA TTTGCA TTTCGCA TTTGCA T
1 TTTGCA TTTGCA TTTGCA TTT-GCA TTTGCA T
21717134 GAAAATTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (6 bp):
TTTGCA
Found at i:21717127 original size:13 final size:12
Alignment explanation
Indices: 21717102--21717133 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
21717092 GAAGACTGAT
21717102 TTTGCATTTGCA
1 TTTGCATTTGCA
21717114 TTTGCATTTCGCA
1 TTTGCATTT-GCA
21717127 TTTGCAT
1 TTTGCAT
21717134 GAAAATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:21719973 original size:25 final size:25
Alignment explanation
Indices: 21719943--21719990 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
21719933 AGGTTTGTTT
21719943 GTGAAATTATTAAGGACTTTAATCA
1 GTGAAATTATTAAGGACTTTAATCA
**
21719968 GTGAAATTATTCGGGACTTTAAT
1 GTGAAATTATTAAGGACTTTAAT
21719991 GAGGACTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (25 bp):
GTGAAATTATTAAGGACTTTAATCA
Found at i:21727079 original size:9 final size:9
Alignment explanation
Indices: 21727065--21727106 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
21727055 AACTTTGAAA
21727065 AAAATATTT
1 AAAATATTT
21727074 AAAATA-TT
1 AAAATATTT
*
21727082 AAAATTTTT
1 AAAATATTT
21727091 AAATATATATT
1 AAA-ATAT-TT
21727102 AAAAT
1 AAAAT
21727107 GAGGTAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.25
9 11 0.39
10 5 0.18
11 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAAATATTT
Found at i:21727091 original size:17 final size:18
Alignment explanation
Indices: 21727065--21727098 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21727055 AACTTTGAAA
21727065 AAAATATTTAAA-ATATT
1 AAAATATTTAAATATATT
*
21727082 AAAATTTTTAAATATAT
1 AAAATATTTAAATATAT
21727099 ATTAAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATATTTAAATATATT
Found at i:21737673 original size:25 final size:24
Alignment explanation
Indices: 21737617--21737714 Score: 74
Period size: 25 Copynumber: 4.0 Consensus size: 24
21737607 ACCACAGGTT
*
21737617 GTATGAGCTTACCGATTTCAGCTC
1 GTATGAGCTTACCGATTACAGCTC
* *
21737641 ATGA-GAGCTTACTGATTCACAGCTC
1 GT-ATGAGCTTACCGATT-ACAGCTC
*
21737666 GTATGAGCTTACC-ATTTTTCAGCTC
1 GTATGAGCTTACCGA--TTACAGCTC
* * * *
21737691 GAAAGAGCTTACCGTTTACCGCTC
1 GTATGAGCTTACCGATTACAGCTC
21737715 TTATAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
24 22 0.39
25 33 0.58
26 2 0.04
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (24 bp):
GTATGAGCTTACCGATTACAGCTC
Found at i:21740567 original size:18 final size:17
Alignment explanation
Indices: 21740540--21740581 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
21740530 ACATAAATTC
*
21740540 AAATAACAAAACACCTAA
1 AAATAGCAAAACA-CTAA
*
21740558 AAATAGC-AAACACTGA
1 AAATAGCAAAACACTAA
21740574 AAATAGCA
1 AAATAGCA
21740582 GTCCTAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 6 0.29
ACGTcount: A:0.62, C:0.19, G:0.07, T:0.12
Consensus pattern (17 bp):
AAATAGCAAAACACTAA
Found at i:21749166 original size:20 final size:19
Alignment explanation
Indices: 21749126--21749176 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
21749116 TAATTTCGCC
*
21749126 ATTTTTTAGTTTAATATTT
1 ATTTTTTAATTTAATATTT
21749145 ATGTTTTTAATTTAAT-TATT
1 AT-TTTTTAATTTAATAT-TT
*
21749165 ATATTTTAATTT
1 ATTTTTTAATTT
21749177 TTTTTGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTTAATTTAATATTT
Found at i:21757028 original size:3 final size:3
Alignment explanation
Indices: 21757022--21757071 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
21757012 AAACTAATAA
* * * * *
21757022 ATT ATT ATT ATT AGT AGT ATT AAT ATT ATT ATT AAT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21757070 AT
1 AT
21757072 CATCATATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:21757235 original size:18 final size:18
Alignment explanation
Indices: 21757204--21757238 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21757194 ATATATACGC
* *
21757204 TTATATTTTTTATATATT
1 TTATAATTTATATATATT
21757222 TTATAATTTATATATAT
1 TTATAATTTATATATAT
21757239 GTATGTATTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATAATTTATATATATT
Found at i:21758175 original size:10 final size:11
Alignment explanation
Indices: 21758150--21758174 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21758140 ATTTGGGAGC
21758150 AAAATGAATGA
1 AAAATGAATGA
21758161 AAAATGAATGA
1 AAAATGAATGA
21758172 AAA
1 AAA
21758175 TCGGAGCTTC
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (11 bp):
AAAATGAATGA
Found at i:21758779 original size:22 final size:22
Alignment explanation
Indices: 21758754--21758812 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
21758744 GAAACATAAG
* *
21758754 ATATCAGATATAGTTACAGAAC
1 ATATTAGATATAGATACAGAAC
21758776 ATATTAGATATAGATACAGAAC
1 ATATTAGATATAGATACAGAAC
* *
21758798 AGATTAGATACAGAT
1 ATATTAGATATAGAT
21758813 GTAGATTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.27
Consensus pattern (22 bp):
ATATTAGATATAGATACAGAAC
Found at i:21765941 original size:50 final size:50
Alignment explanation
Indices: 21765825--21766115 Score: 429
Period size: 50 Copynumber: 5.8 Consensus size: 50
21765815 GATCATAATC
* * ** *
21765825 TGCCAAAGCCATGTCCCAGACGTGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* **
21765876 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
21765926 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
21765976 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
21766026 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
21766076 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT
21766116 TTTTACCCAA
Statistics
Matches: 217, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
50 184 0.85
51 33 0.15
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:21789474 original size:16 final size:16
Alignment explanation
Indices: 21789453--21789502 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 16
21789443 ATATCTAATC
21789453 ATATAATAAATTATTA
1 ATATAATAAATTATTA
21789469 ATATAAT--A-TATTA
1 ATATAATAAATTATTA
*
21789482 ATTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
21789499 ATAT
1 ATAT
21789503 TTCAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 1 0.04
16 9 0.32
17 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:21790466 original size:29 final size:29
Alignment explanation
Indices: 21790433--21790490 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
21790423 AAAATATTAT
* *
21790433 AAAATAAAATA-CTATTTGAAACTTTAAAC
1 AAAATAAAATATC-ACTGGAAACTTTAAAC
21790462 AAAATAAAATATCACTGGAAACTTTAAAC
1 AAAATAAAATATCACTGGAAACTTTAAAC
21790491 GAGAGGGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAATAAAATATCACTGGAAACTTTAAAC
Found at i:21790716 original size:24 final size:25
Alignment explanation
Indices: 21790647--21790723 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 25
21790637 ATTTAAATTT
* *
21790647 ATTTTTATAATATAAAATACATATTCA
1 ATTTTTAT-ATATAAAATA-ATTTTAA
21790674 ATTATTTAATATAATAAAATAATTTTAA
1 ATT-TTT-ATAT-ATAAAATAATTTTAA
*
21790702 ATTTTTATATA-AAAATATTTTT
1 ATTTTTATATATAAAATAATTTT
21790724 CAAAAATACA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
24 10 0.23
25 1 0.02
26 4 0.09
27 6 0.14
28 13 0.30
29 10 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTTTATATATAAAATAATTTTAA
Found at i:21792651 original size:40 final size:40
Alignment explanation
Indices: 21792586--21792718 Score: 189
Period size: 41 Copynumber: 3.3 Consensus size: 40
21792576 AATTTATTTT
*
21792586 AAAAATTAAAAAAAGTATTTT-AAAATATTTTTAAATTAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAATTAA
*
21792625 AAAAATTTTAAAAAGTATTTTAAAAATATTTTTAAAATT-A
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTT-AAATTAA
* * *
21792665 AAAAATAATAAAAAATTATTTTAAAAATATTTTAAAATTAA
1 AAAAAT-TTAAAAAAGTATTTTAAAAATATTTTTAAATTAA
21792706 AAAAATTTAAAAA
1 AAAAATTTAAAAA
21792719 TAAATATATT
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
39 19 0.23
40 29 0.35
41 35 0.42
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (40 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAATTAA
Found at i:21792662 original size:11 final size:11
Alignment explanation
Indices: 21792621--21792701 Score: 71
Period size: 11 Copynumber: 7.5 Consensus size: 11
21792611 TATTTTTAAA
*
21792621 TTAAAAAAATT
1 TTAAAAATATT
21792632 TTAAAAAGTATT
1 TTAAAAA-TATT
21792644 TTAAAAATATT
1 TTAAAAATATT
*
21792655 TT-TAAA-A-T
1 TTAAAAATATT
* *
21792663 TAAAAAATA-A
1 TTAAAAATATT
*
21792673 TAAAAAATTATT
1 TTAAAAA-TATT
21792685 TTAAAAATATT
1 TTAAAAATATT
21792696 TTAAAA
1 TTAAAA
21792702 TTAAAAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
8 2 0.03
9 4 0.07
10 11 0.19
11 25 0.43
12 16 0.28
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:21792663 original size:41 final size:41
Alignment explanation
Indices: 21792586--21792718 Score: 193
Period size: 40 Copynumber: 3.3 Consensus size: 41
21792576 AATTTATTTT
*
21792586 AAAAATTAAAAAAAGTATTTT-AAAATATTTTT-AAATTAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATTAA
*
21792625 AAAAATTTTAAAAAGTATTTTAAAAATATTTTTAAAATT-A
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATTAA
* *
21792665 AAAAATAATAAAAAATTATTTTAAAAATA-TTTTAAAATTAA
1 AAAAAT-TTAAAAAAGTATTTTAAAAATATTTTTAAAATTAA
21792706 AAAAATTTAAAAA
1 AAAAATTTAAAAA
21792719 TAAATATATT
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
39 19 0.23
40 34 0.40
41 31 0.37
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTTAAAATTAA
Found at i:21792707 original size:17 final size:17
Alignment explanation
Indices: 21792685--21792729 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
21792675 AAAAATTATT
21792685 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
21792702 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
21792718 ATAAATATATTT
1 TTAAAAATATTT
21792730 ATTATATCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:21798552 original size:3 final size:3
Alignment explanation
Indices: 21798544--21798573 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21798534 CACGAACGAG
21798544 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
21798574 AATCTGGGGA
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:21800762 original size:31 final size:29
Alignment explanation
Indices: 21800727--21800786 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
21800717 TTTAACAGCC
*
21800727 TTTTATAACTTTTTGAATAGTTCAATGACCA
1 TTTTATAACCTTTTGAA-A-TTCAATGACCA
*
21800758 TTTTATAACCTTTTGAAATTGAATGACCA
1 TTTTATAACCTTTTGAAATTCAATGACCA
21800787 AAATGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (29 bp):
TTTTATAACCTTTTGAAATTCAATGACCA
Found at i:21801033 original size:16 final size:16
Alignment explanation
Indices: 21801012--21801050 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
21801002 TAAAATTGTT
21801012 TATTTGAGAA-TTAAAA
1 TATTTGA-AATTTAAAA
21801028 TATTTGAAATTTAAAA
1 TATTTGAAATTTAAAA
21801044 T-TTTGAA
1 TATTTGAA
21801051 TTAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (16 bp):
TATTTGAAATTTAAAA
Found at i:21802252 original size:15 final size:16
Alignment explanation
Indices: 21802226--21802256 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
21802216 CAATTCTATC
21802226 TATTTTTAAATAATTT
1 TATTTTTAAATAATTT
21802242 TATTTTT-AATAATTT
1 TATTTTTAAATAATTT
21802257 ATTCAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAAATAATTT
Found at i:21815657 original size:23 final size:22
Alignment explanation
Indices: 21815616--21815665 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
21815606 GCTTTATTTG
*
21815616 TTAATATGTTTTGATATAACAAA
1 TTAAAATGTTTTGATATAA-AAA
*
21815639 TTAAAATGTTTTTGA-ATAAAAG
1 TTAAAATG-TTTTGATATAAAAA
21815661 TTAAA
1 TTAAA
21815666 GTTGAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 11 0.46
24 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (22 bp):
TTAAAATGTTTTGATATAAAAA
Found at i:21815903 original size:22 final size:21
Alignment explanation
Indices: 21815859--21815900 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21815849 TTCAATTTAC
*
21815859 ACAAAAAGTGTCGACACCTTT
1 ACAAAAAGTATCGACACCTTT
*
21815880 ACAAAAAGTATCGATACCTTT
1 ACAAAAAGTATCGACACCTTT
21815901 TACTAGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (21 bp):
ACAAAAAGTATCGACACCTTT
Found at i:21818888 original size:19 final size:19
Alignment explanation
Indices: 21818841--21818898 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
21818831 AAAATGATAA
21818841 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
**
21818861 AATTGAGTTAAACAT-TTTC
1 AATCAAGTTAAA-ATGTTTC
21818880 AATCAAGTTAAAACTGTTT
1 AATCAAGTTAAAA-TGTTT
21818899 TAAAACAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 13 0.42
21 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:21821937 original size:3 final size:3
Alignment explanation
Indices: 21821929--21822013 Score: 75
Period size: 3 Copynumber: 27.3 Consensus size: 3
21821919 ATATATAAGT
* * *
21821929 ATA ATA ATA TTA ATA TGTA AT- ATA ATA ATAA ATA ATA CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
*
21821975 ATA CAGTA ATA ATA ACA ATA ATA ATA ATTA AT- ATA ATA A
1 ATA -A-TA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
21822014 AATTAATGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 4 0.06
3 51 0.76
4 10 0.15
5 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:21822019 original size:14 final size:15
Alignment explanation
Indices: 21821992--21822029 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
21821982 AATAATAACA
21821992 ATAATAATAATTAAT-
1 ATAATAA-AATTAATG
21822007 ATAATAAAATTAATG
1 ATAATAAAATTAATG
21822022 AT-ATAAAA
1 ATAATAAAA
21822030 GAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATAATAAAATTAATG
Found at i:21824185 original size:25 final size:23
Alignment explanation
Indices: 21824134--21824178 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
21824124 GTAATTATAA
21824134 ATACATGTGTAATAAATATATGC
1 ATACATGTGTAATAAATATATGC
* *
21824157 ATACATTTGTAATTAATATATG
1 ATACATGTGTAATAAATATATG
21824179 TACATACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGC
Found at i:21824199 original size:25 final size:24
Alignment explanation
Indices: 21824134--21824199 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
21824124 GTAATTATAA
*
21824134 ATACATGTGTAA-TAAATATATGC
1 ATACATTTGTAATTAAATATATGC
21824157 ATACATTTGTAATT-AATATATGTAC
1 ATACATTTGTAATTAAATATATG--C
21824182 ATAC-TTAT-TAATTAAATA
1 ATACATT-TGTAATTAAATA
21824200 AAAGATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 19 0.51
24 8 0.22
25 10 0.27
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (24 bp):
ATACATTTGTAATTAAATATATGC
Found at i:21824330 original size:26 final size:27
Alignment explanation
Indices: 21824279--21824335 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
21824269 ATAGAATAGC
* *
21824279 AAAACGAAAACAGGGGAGAAAGGAAAG
1 AAAAAGAAAACAGGGAAGAAAGGAAAG
21824306 AAAAAGAAAA-AGGGAAGGAAA-GAAAG
1 AAAAAGAAAACAGGGAA-GAAAGGAAAG
21824332 AAAA
1 AAAA
21824336 TTTGAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.67, C:0.04, G:0.30, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAACAGGGAAGAAAGGAAAG
Found at i:21825231 original size:11 final size:11
Alignment explanation
Indices: 21825215--21825240 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21825205 TTGCTGGATG
21825215 ATATTTTGGTT
1 ATATTTTGGTT
21825226 ATATTTTGGTT
1 ATATTTTGGTT
21825237 ATAT
1 ATAT
21825241 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:21827927 original size:22 final size:20
Alignment explanation
Indices: 21827884--21827922 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21827874 TAATTTAAAA
21827884 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
21827904 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
21827923 ATGTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:21828027 original size:14 final size:15
Alignment explanation
Indices: 21828005--21828081 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
21827995 CAATCAAACA
21828005 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
21828019 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
21828034 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
21828054 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
21828068 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
21828082 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:21828046 original size:20 final size:20
Alignment explanation
Indices: 21828021--21828060 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21828011 AATATTTTCC
*
21828021 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
21828041 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
21828061 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:21828066 original size:34 final size:35
Alignment explanation
Indices: 21828009--21828075 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
21827999 CAAACACCAG
*
21828009 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
21828044 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
21828076 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:21828082 original size:14 final size:14
Alignment explanation
Indices: 21828044--21828083 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
21828034 ACAGAAAAGT
*
21828044 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
21828058 AAATCATTTTACGG
1 AAAACATTTTACAG
21828072 AAAACATTTTAC
1 AAAACATTTTAC
21828084 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:21828631 original size:25 final size:25
Alignment explanation
Indices: 21828602--21828685 Score: 132
Period size: 25 Copynumber: 3.4 Consensus size: 25
21828592 GAACTTTAGT
*
21828602 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACGTCA
*
21828627 ATGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACGTCA
* *
21828652 GTGCTCTCTGAGTACTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACGTCA
21828677 GTGCTCTCT
1 GTGCTCTCT
21828686 ATTTAGCACT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACGTCA
Found at i:21834796 original size:20 final size:20
Alignment explanation
Indices: 21834771--21834808 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21834761 AAAGGTTAAC
21834771 TTAGTAAAATAATAATAATG
1 TTAGTAAAATAATAATAATG
* *
21834791 TTAGTATAATGATAATAA
1 TTAGTAAAATAATAATAA
21834809 AATAAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGTAAAATAATAATAATG
Found at i:21835748 original size:41 final size:42
Alignment explanation
Indices: 21835670--21835769 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 42
21835660 CTATATGATT
* * *
21835670 AGCACTAAGTGTGCG-AATTAAATGATGAGGTTGAATAA-CG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAATCG
* *
21835710 AGCACTAAGTGTGCGAAACTAAATAATGATGTTAAATAATTG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAATCG
21835752 -GCACTAAGTGTGCGAAAC
1 AGCACTAAGTGTGCGAAAC
21835770 CGAGATCAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
40 15 0.28
41 37 0.70
42 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (42 bp):
AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATAATCG
Found at i:21852950 original size:21 final size:20
Alignment explanation
Indices: 21852919--21852958 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
21852909 TATTTAAAAA
*
21852919 ATATTTTTAATTATTTTTAT
1 ATATTTTTAATAATTTTTAT
21852939 ATATTTTCTAATAATTTTTA
1 ATATTTT-TAATAATTTTTA
21852959 GTCTAATATT
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):
ATATTTTTAATAATTTTTAT
Found at i:21853429 original size:17 final size:18
Alignment explanation
Indices: 21853407--21853451 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
21853397 TTATGAATTA
21853407 AAAAATAATTATA-AAAG
1 AAAAATAATTATACAAAG
*
21853424 AAAAATAGTTATACTAAAG
1 AAAAATAATTATAC-AAAG
*
21853443 ATAAATAAT
1 AAAAATAAT
21853452 ATGAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
AAAAATAATTATACAAAG
Found at i:21855307 original size:6 final size:6
Alignment explanation
Indices: 21855283--21855320 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
21855273 ACAAAATTAG
21855283 AAAG-A AAAGAAA GAAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAG-AA -AAAGAA AAAGAA AAAGAA AAAGAA A
21855321 GAAAACCCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.13
6 19 0.63
7 3 0.10
8 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:21855320 original size:35 final size:34
Alignment explanation
Indices: 21855243--21855325 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 34
21855233 GCAAAAAAGT
**
21855243 AATA-AAAGAAAGAGAAAGAAAGAAAGCCAAACAA
1 AATAGAAAGAAA-AGAAAGAAAGAAAGAAAAACAA
*
21855277 AATTAGAAAGAAAAGAAAGAAAGAAAAAGAAAAAGAA
1 AA-TAGAAAGAAAAGAAAGAAAG--AAAGAAAAACAA
21855314 AA-AGAAAGAAAA
1 AATAGAAAGAAAA
21855326 CCCACGGCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 2 0.05
35 22 0.52
36 7 0.17
37 11 0.26
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (34 bp):
AATAGAAAGAAAAGAAAGAAAGAAAGAAAAACAA
Found at i:21860396 original size:15 final size:14
Alignment explanation
Indices: 21860375--21860410 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
21860365 ATAATCATTA
*
21860375 ATAATTATCTTAAT
1 ATAATTATCCTAAT
21860389 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
21860404 ATAATTA
1 ATAATTA
21860411 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:21862357 original size:5 final size:5
Alignment explanation
Indices: 21862347--21862419 Score: 55
Period size: 5 Copynumber: 14.6 Consensus size: 5
21862337 AGTAATAAAT
* *
21862347 AATAA AATAA AATAA AGTAATA AATAA AGT-A AATAA AATAA AATAATA
1 AATAA AATAA AATAA AAT-A-A AATAA AATAA AATAA AATAA AAT-A-A
*
21862395 AATAA AA-AA CA-AA AATAA AA-AA AAT
1 AATAA AATAA AATAA AATAA AATAA AAT
21862420 TTGGGTTGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 13 0.24
5 31 0.56
6 4 0.07
7 7 0.13
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:21862361 original size:13 final size:12
Alignment explanation
Indices: 21862339--21862401 Score: 65
Period size: 12 Copynumber: 5.0 Consensus size: 12
21862329 TCCAAATAAG
21862339 TAATAAATAATAA
1 TAATAAATAA-AA
*
21862352 -AATAAAATAAAG
1 TAAT-AAATAAAA
*
21862364 TAATAAATAAAG
1 TAATAAATAAAA
21862376 TAAATAAAATAAAA
1 T-AAT-AAATAAAA
21862390 TAATAAATAAAA
1 TAATAAATAAAA
21862402 AACAAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
12 21 0.48
13 15 0.34
14 8 0.18
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
TAATAAATAAAA
Found at i:21862362 original size:17 final size:16
Alignment explanation
Indices: 21862340--21862418 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 16
21862330 CCAAATAAGT
21862340 AATAAATAATAAAATAA
1 AATAAATAA-AAAATAA
*
21862357 AATAAAGTAATAAATAA
1 AATAAA-TAAAAAATAA
*
21862374 AGTAAATAAAATAA-AA
1 AATAAATAAAA-AATAA
*
21862390 TAATAAATAAAAAACAAA
1 -AATAAATAAAAAA-TAA
21862408 AATAAA-AAAAA
1 AATAAATAAAAA
21862419 TTTGGGTTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 13 0.25
17 35 0.66
18 5 0.09
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (16 bp):
AATAAATAAAAAATAA
Found at i:21862387 original size:26 final size:26
Alignment explanation
Indices: 21862332--21862413 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
21862322 ATTAATATCC
21862332 AAAT-AAGTAATAAAT-AATAAAATA
1 AAATAAAGTAATAAATAAATAAAATA
21862356 AAATAAAGTAATAAATAAAGT-AAATA
1 AAATAAAGTAATAAATAAA-TAAAATA
*
21862382 AAATAAAATAATAAATAAA-AAACA-A
1 AAATAAAGTAATAAATAAATAAA-ATA
21862407 AAATAAA
1 AAATAAA
21862414 AAAAATTTGG
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
24 4 0.08
25 21 0.40
26 26 0.50
27 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (26 bp):
AAATAAAGTAATAAATAAATAAAATA
Found at i:21862416 original size:13 final size:12
Alignment explanation
Indices: 21862343--21862418 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
21862333 AATAAGTAAT
*
21862343 AAATAATAAAATA
1 AAATAA-AAAAAA
** *
21862356 AAATAAAGTAAT
1 AAATAAAAAAAA
*
21862368 AAATAAAGTAAATA
1 AAATAAA--AAAAA
* *
21862382 AAATAAAATAAT
1 AAATAAAAAAAA
21862394 AAATAAAAAACAA
1 AAATAAAAAA-AA
21862407 AAATAAAAAAAA
1 AAATAAAAAAAA
21862419 TTTGGGTTGC
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
12 22 0.47
13 17 0.36
14 8 0.17
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (12 bp):
AAATAAAAAAAA
Found at i:21868763 original size:15 final size:14
Alignment explanation
Indices: 21868742--21868777 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
21868732 ATAATCCTTA
*
21868742 ATAATTATCTTAAT
1 ATAATTATCCTAAT
21868756 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
21868771 ATAATTA
1 ATAATTA
21868778 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:21870155 original size:15 final size:15
Alignment explanation
Indices: 21870135--21870176 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
21870125 TGGAGATTGG
21870135 GAAAGGAGAGGAAAA
1 GAAAGGAGAGGAAAA
*
21870150 GAAAGGAGAGGAGAA
1 GAAAGGAGAGGAAAA
*
21870165 GAGAGGAGAGGA
1 GAAAGGAGAGGA
21870177 GGAGAGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (15 bp):
GAAAGGAGAGGAAAA
Found at i:21870177 original size:15 final size:15
Alignment explanation
Indices: 21870138--21870183 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
21870128 AGATTGGGAA
* *
21870138 AGGAGAGGAAAAGAA
1 AGGAGAGGAGAAGAG
21870153 AGGAGAGGAGAAGAG
1 AGGAGAGGAGAAGAG
*
21870168 AGGAGAGGAGGAGAG
1 AGGAGAGGAGAAGAG
21870183 A
1 A
21870184 TTGGAGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
AGGAGAGGAGAAGAG
Found at i:21886769 original size:17 final size:19
Alignment explanation
Indices: 21886736--21886770 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
21886726 TAATAGAATA
21886736 GAAAATAGTGTAAATTGAT
1 GAAAATAGTGTAAATTGAT
21886755 GAAAATA-TG-AAATTGA
1 GAAAATAGTGTAAATTGA
21886771 CTTTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (19 bp):
GAAAATAGTGTAAATTGAT
Found at i:21886924 original size:27 final size:28
Alignment explanation
Indices: 21886862--21886925 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
21886852 GATGAAAATA
21886862 GTGTAAATT-GAAATATGCATACTTAAT
1 GTGTAAATTGGAAATATGCATACTTAAT
*
21886889 GTTGT-AATTGGATATATGCATACTT-AT
1 G-TGTAAATTGGAAATATGCATACTTAAT
21886916 GTGTAAATTG
1 GTGTAAATTG
21886926 ATGAAAATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 13 0.39
28 17 0.52
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (28 bp):
GTGTAAATTGGAAATATGCATACTTAAT
Found at i:21887611 original size:35 final size:35
Alignment explanation
Indices: 21887564--21887654 Score: 121
Period size: 35 Copynumber: 2.6 Consensus size: 35
21887554 TCAAAGGTGA
* * *
21887564 CTTTAAAAAGGTTGGGATAGACCCGTCTAAGGCAAC
1 CTTT-AAAAGGTTGGGATAGACACATCTAAGCCAAC
21887600 CTTTAAAAGGTTGGGATAGACACATCTAAGCCAAC
1 CTTTAAAAGGTTGGGATAGACACATCTAAGCCAAC
*
21887635 C-TTAAATATGTTGGGATAGA
1 CTTTAAA-AGGTTGGGATAGA
21887655 TAAGTCTAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 5 0.10
35 41 0.82
36 4 0.08
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (35 bp):
CTTTAAAAGGTTGGGATAGACACATCTAAGCCAAC
Found at i:21887777 original size:6 final size:6
Alignment explanation
Indices: 21887760--21887789 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
21887750 ATACAACTAA
21887760 AAAATAT AAAATT AAAATT AAAATT AAAAT
1 AAAAT-T AAAATT AAAATT AAAATT AAAAT
21887790 AAAGGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:21890504 original size:37 final size:37
Alignment explanation
Indices: 21890463--21890558 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 37
21890453 TAATGAAAAA
** *
21890463 AGTGTAAGATAATATTTTTTGTATTAAACAAATAGAT
1 AGTGTAAGATAATATTTTGGGTATTAAACAAATAGAG
21890500 AGTGTAA-ATTTAATGAAATTTTGGGTATTAAACAAATAGAG
1 AGTGTAAGA--TAAT---ATTTTGGGTATTAAACAAATAGAG
21890541 AGTGTAAGATAATATTTT
1 AGTGTAAGATAATATTTT
21890559 ATTTAATTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
36 1 0.02
37 12 0.24
38 4 0.08
40 4 0.08
41 28 0.56
42 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.39
Consensus pattern (37 bp):
AGTGTAAGATAATATTTTGGGTATTAAACAAATAGAG
Found at i:21891134 original size:136 final size:136
Alignment explanation
Indices: 21890931--21891182 Score: 414
Period size: 136 Copynumber: 1.9 Consensus size: 136
21890921 AAAAACTGAC
*
21890931 TCTTATTTAAGCGTTGCCTTAGGCATACATAACCCAACCCTTATACAAAGAGTTGGCCAAAGAGT
1 TCTTATTTAAACGTTGCCTTAGGCATACATAACCCAACCCTTATACAAAGAGTTGGCCAAAGAGT
* * * *
21890996 ATGTCGGTAAGTCTATCCTAACACTTAGGAAAGTTTCGGCCCAAAAGTGTCGGCATTGTGACAAA
66 ATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCACAAAAGTGTCGGCATTGTGACAAA
21891061 TCCGAA
131 TCCGAA
* * * *
21891067 TCTTATTTAAACGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCTAAAGCGT
1 TCTTATTTAAACGTTGCCTTAGGCATACATAACCCAACCCTTATACAAAGAGTTGGCCAAAGAGT
*
21891132 ATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCACAAAAGTGTC
66 ATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCACAAAAGTGTC
21891183 ATCTTAAGAC
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
136 106 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (136 bp):
TCTTATTTAAACGTTGCCTTAGGCATACATAACCCAACCCTTATACAAAGAGTTGGCCAAAGAGT
ATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCACAAAAGTGTCGGCATTGTGACAAA
TCCGAA
Found at i:21891992 original size:20 final size:20
Alignment explanation
Indices: 21891963--21892020 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
21891953 GAACAAAGGG
21891963 TAAT-TAAATAATAATATTT
1 TAATATAAATAATAATATTT
21891982 TAATATAAATAATAATATTT
1 TAATATAAATAATAATATTT
21892002 TAATATAAA-AATAA-ATTT
1 TAATATAAATAATAATATTT
21892020 T
1 T
21892021 CCTATTTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 5 0.13
19 9 0.24
20 24 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATAAATAATAATATTT
Found at i:21903881 original size:14 final size:14
Alignment explanation
Indices: 21903862--21903889 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21903852 TTGTTGTCTT
21903862 CTGAGCAAGCAAAG
1 CTGAGCAAGCAAAG
21903876 CTGAGCAAGCAAAG
1 CTGAGCAAGCAAAG
21903890 TATAGATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.29, T:0.07
Consensus pattern (14 bp):
CTGAGCAAGCAAAG
Found at i:21915225 original size:12 final size:12
Alignment explanation
Indices: 21915208--21915232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21915198 TTGCAGGAGA
21915208 TGTTTTCTTATT
1 TGTTTTCTTATT
21915220 TGTTTTCTTATT
1 TGTTTTCTTATT
21915232 T
1 T
21915233 TATCAGGTCT
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:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTTTCTTATT
Found at i:21916355 original size:17 final size:18
Alignment explanation
Indices: 21916307--21916355 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
21916297 TTTTAATTTA
*
21916307 TTAAATAAAA-AATAATT
1 TTAAATAAAATAATTATT
**
21916324 TTAGTTAAAAT-ATTA-T
1 TTAAATAAAATAATTATT
21916340 TTAAATAAAATAATTA
1 TTAAATAAAATAATTA
21916356 AATTCCAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAAATAAAATAATTATT
Found at i:21917585 original size:20 final size:21
Alignment explanation
Indices: 21917529--21917585 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
21917519 TTTGTATTTT
*
21917529 GTAGATATAGGATAAAAGTGTCA
1 GTAGATATAGGATAAAA--GTAA
21917552 -TAGATAT-GGAATAAAA-TAA
1 GTAGATATAGG-ATAAAAGTAA
21917571 GTAGATATAGGATAA
1 GTAGATATAGGATAA
21917586 TTGTAACAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 2 0.07
20 11 0.37
21 4 0.13
22 13 0.43
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.26
Consensus pattern (21 bp):
GTAGATATAGGATAAAAGTAA
Found at i:21924897 original size:14 final size:14
Alignment explanation
Indices: 21924878--21924912 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21924868 ATTTAAAAGT
21924878 TAACTAAATTTTAA
1 TAACTAAATTTTAA
21924892 TAACTAAATTTTAA
1 TAACTAAATTTTAA
21924906 TAA-TAAA
1 TAACTAAA
21924913 CTAACTACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
TAACTAAATTTTAA
Found at i:21933372 original size:7 final size:7
Alignment explanation
Indices: 21933362--21933403 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
21933352 ATTAACAATT
21933362 AATAAAA
1 AATAAAA
21933369 AATAAAA
1 AATAAAA
21933376 AATAAAA
1 AATAAAA
21933383 AATAAAA
1 AATAAAA
21933390 TAA-AATAA
1 -AATAA-AA
21933398 AATAAA
1 AATAAA
21933404 GTTGATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AATAAAA
Found at i:21933382 original size:5 final size:5
Alignment explanation
Indices: 21933367--21933403 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
21933357 CAATTAATAA
21933367 AAAAT AAAA- AATAA- AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAA
21933404 GTTGATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:21938297 original size:32 final size:31
Alignment explanation
Indices: 21938223--21938318 Score: 92
Period size: 32 Copynumber: 3.2 Consensus size: 31
21938213 ATTATTTCTA
* *
21938223 TTTTTATAAT-T-TATACATCTA-AT-TATT
1 TTTTTATAATATATATATATATATATCTATT
*
21938250 TTTTTATAATATATATATGTATATATCTATT
1 TTTTTATAATATATATATATATATATCTATT
* * *
21938281 TTTTTATATATGTATATGTATATATATTTATAT
1 TTTTTATA-ATATATATATATATATATCTAT-T
21938314 TTTTT
1 TTTTT
21938319 TTCTAACGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
27 10 0.18
28 1 0.02
29 7 0.12
30 2 0.04
31 12 0.21
32 18 0.32
33 6 0.11
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTTTATAATATATATATATATATATCTATT
Found at i:21938310 original size:24 final size:24
Alignment explanation
Indices: 21938261--21938313 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
21938251 TTTTATAATA
* * *
21938261 TATATATGTATATATCTATTTTTT
1 TATATATGTATATATATATATATT
*
21938285 TATATATGTATATGTATATATATT
1 TATATATGTATATATATATATATT
21938309 TATAT
1 TATAT
21938314 TTTTTTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TATATATGTATATATATATATATT
Found at i:21945811 original size:30 final size:30
Alignment explanation
Indices: 21945776--21945840 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
21945766 ATTTAAAACC
*
21945776 TTTTTT-AGAAATTAAATATATATTTTGAAT
1 TTTTTTGAAAAATTAAATATA-ATTTTGAAT
** *
21945806 TTTTTTGAAAAATTATTTTTAATTTTGAAT
1 TTTTTTGAAAAATTAAATATAATTTTGAAT
21945836 TTTTT
1 TTTTT
21945841 CTATAACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (30 bp):
TTTTTTGAAAAATTAAATATAATTTTGAAT
Found at i:21948047 original size:13 final size:13
Alignment explanation
Indices: 21948031--21948093 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
21948021 TTTAAACCAA
*
21948031 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
*
21948044 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
21948057 ACTTTTCTATAGC
1 ACTTTTCAAAAGC
*
21948070 AGTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
21948083 ACTTCTCAAAA
1 ACTTTTCAAAA
21948094 ACAATGAAGA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:21964598 original size:5 final size:5
Alignment explanation
Indices: 21964588--21964655 Score: 84
Period size: 5 Copynumber: 13.0 Consensus size: 5
21964578 TATTAACATA
*
21964588 AAAAT AAAAT AAAAT AAAAT AAAAT AGAAAAT AAAAT -ATAT ATAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT A-AAAT
21964635 AAAAT AAAAT AAAAAT AAAAT
1 AAAAT AAAAT -AAAAT AAAAT
21964656 TAGGTTGCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
4 3 0.05
5 39 0.70
6 9 0.16
7 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:21970566 original size:19 final size:19
Alignment explanation
Indices: 21970542--21970585 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
21970532 TAAAAGCAAT
21970542 ACAACATCAA-CCCAAATAA
1 ACAACAT-AAGCCCAAATAA
*
21970561 ACAACATAAGTCCAAATAA
1 ACAACATAAGCCCAAATAA
21970580 ACAACA
1 ACAACA
21970586 AAAACAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.59, C:0.27, G:0.02, T:0.11
Consensus pattern (19 bp):
ACAACATAAGCCCAAATAA
Found at i:21977701 original size:51 final size:49
Alignment explanation
Indices: 21977645--21977771 Score: 132
Period size: 51 Copynumber: 2.5 Consensus size: 49
21977635 ACTTTAAATG
* *
21977645 TAAAAATTAAGAATTAAAATATTTTTATTTATATTAATTAT-TTAAAATATA
1 TAAAAATTAA-AATTAAATTATTTTT-TGTATA-TAATTATATTAAAATATA
* * *
21977696 TAAAAATT-AAATTAAATTATATTTTGTATATAATTATATTAAATTATT
1 TAAAAATTAAAATTAAATTATTTTTTGTATATAATTATATTAAAATATA
* *
21977744 TAAATATTATATAATTTAATTATTTTTT
1 TAAAAATTA-A-AATTAAATTATTTTTT
21977772 TATTTTCTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
47 7 0.11
48 20 0.31
49 13 0.20
50 2 0.03
51 22 0.34
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (49 bp):
TAAAAATTAAAATTAAATTATTTTTTGTATATAATTATATTAAAATATA
Found at i:21980001 original size:4 final size:4
Alignment explanation
Indices: 21979992--21980042 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
21979982 ATGTATGCAA
21979992 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
21980040 ATA
1 ATA
21980043 GAATCGTTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:21980109 original size:25 final size:26
Alignment explanation
Indices: 21980081--21980143 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
21980071 ATACGTGACT
21980081 GCATGCATAGATCCTA-AATAGTGCG
1 GCATGCATAGATCCTATAATAGTGCG
* *
21980106 GCATGCATAGATCCTATAATGGTGCT
1 GCATGCATAGATCCTATAATAGTGCG
*
21980132 ACATGCATAGAT
1 GCATGCATAGAT
21980144 AGTGTTACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 16 0.47
26 18 0.53
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (26 bp):
GCATGCATAGATCCTATAATAGTGCG
Done.