Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006691.1 Hibiscus syriacus cultivar Beakdansim tig00016637_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1195339
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:305026 original size:29 final size:29
Alignment explanation
Indices: 304960--305058 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 29
304950 CTTATCTATA
* *
304960 TTTTCTTTC-TTTAT-TTTTCTTTAT--T
1 TTTTCTTTCTTTTTTCTTTTCTTTTTCCT
*
304985 TTTTCTTTATTTTTTCTTTAT-TTTTTCCT
1 TTTTCTTTCTTTTTTCTTT-TCTTTTTCCT
*
305014 TTTTCTTTC-TTTTTCTTTTCTTTTTCTT
1 TTTTCTTTCTTTTTTCTTTTCTTTTTCCT
*
305042 TCTTTATTTCTTTTTTC
1 T-TTTCTTTCTTTTTTC
305059 AAACGTGGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
25 8 0.13
26 4 0.07
27 8 0.13
28 18 0.30
29 16 0.27
30 6 0.10
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (29 bp):
TTTTCTTTCTTTTTTCTTTTCTTTTTCCT
Found at i:306565 original size:10 final size:10
Alignment explanation
Indices: 306552--306587 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
306542 TAGAAGTGTC
306552 AAGAATGATA
1 AAGAATGATA
306562 AAGAATG-TA
1 AAGAATGATA
*
306571 AAGAATGAAA
1 AAGAATGATA
306581 AAGAATG
1 AAGAATG
306588 TGAAAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (10 bp):
AAGAATGATA
Found at i:306576 original size:19 final size:19
Alignment explanation
Indices: 306538--306601 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
306528 AATACTAATA
*
306538 ATAATAGAAGTGTCAAGAATG
1 ATAA-AGAA-TGTAAAGAATG
306559 ATAAAGAATGTAAAGAATG
1 ATAAAGAATGTAAAGAATG
* *
306578 AAAAAGAATGTGAA-AATG
1 ATAAAGAATGTAAAGAATG
306596 TATAAA
1 -ATAAA
306602 ATTATTACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.11
19 26 0.68
20 4 0.11
21 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (19 bp):
ATAAAGAATGTAAAGAATG
Found at i:318838 original size:16 final size:16
Alignment explanation
Indices: 318805--318838 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
318795 TTGTTTAGCT
*
318805 TGGGGCAGTAATGGTA
1 TGGGGCAGTAATGATA
*
318821 TGGGGCAGTCATGATA
1 TGGGGCAGTAATGATA
318837 TG
1 TG
318839 AGAACATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.41, T:0.26
Consensus pattern (16 bp):
TGGGGCAGTAATGATA
Found at i:325810 original size:80 final size:80
Alignment explanation
Indices: 325660--325966 Score: 440
Period size: 80 Copynumber: 3.8 Consensus size: 80
325650 TTGCCCTCAA
* * * *
325660 CACACAACAAAAAGGGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAGA
1 CACACAAC--AAA-GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGG
*
325724 TCCGTAGGGTTACCTTAAG
62 TCCGTAGGGTTACCTTATG
* * * *
325743 CACACAACTAAGGGTACCAACCTAAGGATATACCTTGGGGA-ATACCCAAGATATCCTTAGGTTC
1 CACACAACAAAGGGAACCAACCTAAGGATATACCTT-GGGACCTACCCAAGATATCCTTAGGTCC
325807 GTAGGGTTACCTTATG
65 GTAGGGTTACCTTATG
325823 CACA-AAGCAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
1 CACACAA-CAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
325887 GTAGGGTTACCTTATG
65 GTAGGGTTACCTTATG
* *
325903 CACACAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCC
1 CACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
325967 TTAAGGACTT
Statistics
Matches: 205, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
79 6 0.03
80 177 0.86
81 11 0.05
82 3 0.01
83 8 0.04
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (80 bp):
CACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCG
TAGGGTTACCTTATG
Found at i:331391 original size:80 final size:80
Alignment explanation
Indices: 331020--331393 Score: 498
Period size: 80 Copynumber: 4.7 Consensus size: 80
331010 TAGCAAAAAG
* * * * *
331020 AGGGAGCCAACCTAAGGATATACCTT-GGATCTACCCATGGACATCCTTAGATCCGTAGGGTTAC
1 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCA-AGATATCCTTAGGTCCGTAGGGTTAC
* * *
331084 CTTAAGAACACAGCTA
65 CTTATGCACACAGCAA
* *
331100 AGGGAACCAACCTAAGGATATACCTTGGGTCCTACCCAAGATATCCTTAGATCCGTAGGGTTACC
1 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACC
**
331165 TTATGCACACAGGTA
66 TTATGCACACAGCAA
* * * *
331180 AGGGACCCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTATGTCTGTAGGGTTACC
1 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACC
*
331245 TTATGCACACAGGAA
66 TTATGCACACAGCAA
* * *
331260 AGGGAACCACCCTAAGGATATACCTTGGGACCTACCCAAGATATCTTTAGGTCCATAGGGTTACC
1 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACC
* *
331325 TTATGTACACAACAA
66 TTATGCACACAGCAA
* * * *
331340 AGGGAACCAACCTAAGGATATTCCTTGGGGCCTACCCAATATATCCCTAGGTCC
1 AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCC
331394 TTAAGGACTT
Statistics
Matches: 263, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
80 254 0.97
81 9 0.03
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (80 bp):
AGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACC
TTATGCACACAGCAA
Found at i:335548 original size:14 final size:14
Alignment explanation
Indices: 335529--335555 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
335519 CAGTACTGAG
335529 AGAAACTCTTTAAT
1 AGAAACTCTTTAAT
335543 AGAAACTCTTTAA
1 AGAAACTCTTTAA
335556 ATACTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (14 bp):
AGAAACTCTTTAAT
Found at i:336293 original size:41 final size:42
Alignment explanation
Indices: 336175--336296 Score: 176
Period size: 42 Copynumber: 2.9 Consensus size: 42
336165 AGCCATGACA
*
336175 AAATAATTATTCTAAGTGA-AAATATAAACACTATTTTGATGC
1 AAATAATTATTCTAAGT-ATAAATATAAACACTGTTTTGATGC
*
336217 AAATAATTATTCTAAGTGTAAATATAAACACTGTTTTGATGC
1 AAATAATTATTCTAAGTATAAATATAAACACTGTTTTGATGC
* * *
336259 AAATAATTATT-TAAGTATAAACATGAACATTGTTTTGA
1 AAATAATTATTCTAAGTATAAATATAAACACTGTTTTGA
336297 ATCTTAACCA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 23 0.32
42 50 0.68
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (42 bp):
AAATAATTATTCTAAGTATAAATATAAACACTGTTTTGATGC
Found at i:339708 original size:3 final size:3
Alignment explanation
Indices: 339700--339752 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
339690 TTCGGGTTAA
*
339700 TAT TAT TAT TAT TAT TAAT TAT TATT TAT TAT TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
339747 T-T TAT T
1 TAT TAT T
339753 TATATTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 37 0.82
4 6 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:339736 original size:26 final size:27
Alignment explanation
Indices: 339700--339759 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 27
339690 TTCGGGTTAA
339700 TATTATTATTATTATTAAT-TATTATT
1 TATTATTATTATTATTAATATATTATT
*
339726 TATTATTATTATTATTAATATTTTATT
1 TATTATTATTATTATTAATATATTATT
339753 TA-TATTA
1 TATTATTA
339760 ATTTTACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 24 0.75
27 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TATTATTATTATTATTAATATATTATT
Found at i:339757 original size:11 final size:12
Alignment explanation
Indices: 339700--339759 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
339690 TTCGGGTTAA
*
339700 TATTATTATTAT
1 TATTAATATTAT
339712 TATTAATTATTATT
1 TATTAA-TATTA-T
*
339726 TATTATTATTAT
1 TATTAATATTAT
339738 TATTAATATT-T
1 TATTAATATTAT
*
339749 TATTTATATTA
1 TATTAATATTA
339760 ATTTTACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 10 0.24
12 15 0.37
13 10 0.24
14 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:345057 original size:20 final size:20
Alignment explanation
Indices: 345019--345057 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
345009 CAAAAAATTA
* *
345019 ATCCCTAACGGCTCCAAAAC
1 ATCCCTAACGACTACAAAAC
*
345039 ATCCCTAACGACTAGAAAA
1 ATCCCTAACGACTACAAAA
345058 GAACCACAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.33, G:0.10, T:0.15
Consensus pattern (20 bp):
ATCCCTAACGACTACAAAAC
Found at i:345550 original size:18 final size:18
Alignment explanation
Indices: 345529--345564 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
345519 AATTCACCCC
345529 CTCTTGGCAAATCACTCG
1 CTCTTGGCAAATCACTCG
345547 CTCTTGGCAAATCACTCG
1 CTCTTGGCAAATCACTCG
345565 GTTGATCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (18 bp):
CTCTTGGCAAATCACTCG
Found at i:346017 original size:2 final size:2
Alignment explanation
Indices: 346012--346059 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
346002 GTGAATTTCG
* * *
346012 AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT TT AT GAT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
346054 AT AT AT
1 AT AT AT
346060 GAATTAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:350279 original size:27 final size:27
Alignment explanation
Indices: 350213--350279 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
350203 AGTCCTTACT
* **
350213 TTTAAATTCATTACAATGTAGTTTCTTT
1 TTTAAA-TCATTTCAATGTAGTTTCTAC
** * *
350241 TTTATTTTATTTCAATTTAGTTTCTAC
1 TTTAAATCATTTCAATGTAGTTTCTAC
350268 TTTAAATCATTT
1 TTTAAATCATTT
350280 TACTAAATTC
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTAAATCATTTCAATGTAGTTTCTAC
Found at i:350379 original size:13 final size:13
Alignment explanation
Indices: 350363--350387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
350353 TTTCTTAGTC
350363 TTATTTATTTTAT
1 TTATTTATTTTAT
350376 TTATTTATTTTA
1 TTATTTATTTTA
350388 ATTGTTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTATTTTAT
Found at i:352469 original size:29 final size:31
Alignment explanation
Indices: 352432--352489 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
352422 TGACTAATCA
352432 TTTCAACTAAC-TTGATTCT-TTTTGTCTTG
1 TTTCAACTAACATTGATTCTCTTTTGTCTTG
* *
352461 TTTCTACTAACATTGATTTTCTTTTGTCT
1 TTTCAACTAACATTGATTCTCTTTTGTCT
352490 GGTCTTGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 7 0.28
31 8 0.32
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (31 bp):
TTTCAACTAACATTGATTCTCTTTTGTCTTG
Found at i:354451 original size:5 final size:5
Alignment explanation
Indices: 354432--354473 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
354422 AAGAAACCAA
354432 AAAAG AAAA- AGAAAG AAAAG -AAAG AAAAG -AAAG AAAAG AAAA
1 AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
354474 CAAATCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 9 0.27
5 23 0.70
6 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:354452 original size:9 final size:9
Alignment explanation
Indices: 354420--354472 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
354410 GAAGAGAGAT
*
354420 AAAAGAAAC
1 AAAAGAAAG
*
354429 CAAA-AAAG
1 AAAAGAAAG
354437 AAAAAGAAAG
1 -AAAAGAAAG
354447 AAAAGAAAG
1 AAAAGAAAG
354456 AAAAGAAAG
1 AAAAGAAAG
354465 AAAAGAAA
1 AAAAGAAA
354473 ACAAATCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
8 3 0.08
9 32 0.82
10 4 0.10
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:355977 original size:55 final size:55
Alignment explanation
Indices: 355912--356028 Score: 198
Period size: 55 Copynumber: 2.1 Consensus size: 55
355902 TCTTAAAAAA
* * *
355912 AAGATTTGTCTCGCTTGATACAGTTTTTACTCGAAACAAGACATTTCATTTCACTC
1 AAGA-TTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAAACATTTCATTTCACTC
355968 AAGATTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAAACATTTCATTTCACTC
1 AAGATTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAAACATTTCATTTCACTC
356023 AAGATT
1 AAGATT
356029 CTTTTTCTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 54 0.93
56 4 0.07
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (55 bp):
AAGATTGTCTCGCTTGAGACAGTTTTTACTCAAAACAAAACATTTCATTTCACTC
Found at i:356091 original size:39 final size:39
Alignment explanation
Indices: 356047--356371 Score: 438
Period size: 39 Copynumber: 8.4 Consensus size: 39
356037 TAAAACCAGA
* * *
356047 TTTATCTCGCTTAAGATAGTTTCACTCGAAATATAAGAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* *
356086 TTTATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGAC
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* * * *
356125 TTTATCTTGCTTGAGATTGTTTCACTCGAAATAGAAGAC
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
*
356164 TTTATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* *
356203 TTTATCTCACTTGAGATAGTTTCACTCGAAATAGAAGAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* ** * *
356242 TTTATCTTGCTAAAGATAGTTTCACTCGAAATAAAAGAT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
* *
356281 TTTATCTCAG-TTGAGATTGCTTCACTCGAAACAGAAGAT
1 TTTATCTC-GCTTGAGATAGTTTCACTCGAAACAGAAGAT
*
356320 TTTATCTCCCTTGAGATAGTTTCACTCGAAACAGAAGA-
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
*
356358 TTTATCTCACTTGA
1 TTTATCTCGCTTGA
356372 AATTTTTTCT
Statistics
Matches: 255, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
38 13 0.05
39 241 0.95
40 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (39 bp):
TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT
Found at i:356276 original size:21 final size:21
Alignment explanation
Indices: 356216--356276 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 21
356206 ATCTCACTTG
356216 AGATAGTTTCACTCGAAATAGA
1 AGATAGTTTCACTCGAAATA-A
* *
356238 AGAT--TTT-ATCTTG--CTAA
1 AGATAGTTTCA-CTCGAAATAA
356255 AGATAGTTTCACTCGAAATAA
1 AGATAGTTTCACTCGAAATAA
356276 A
1 A
356277 AGATTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 13
0.63 0.09 0.28
Matches are distributed among these distances:
17 5 0.17
18 2 0.07
19 7 0.24
20 7 0.24
21 4 0.14
22 4 0.14
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
AGATAGTTTCACTCGAAATAA
Found at i:358270 original size:13 final size:13
Alignment explanation
Indices: 358254--358285 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
358244 TTTATCAGTC
*
358254 TTATTTATTTTAT
1 TTATTTATTTTAA
358267 TTATTTATTTTAA
1 TTATTTATTTTAA
358280 TTATTT
1 TTATTT
358286 TAATAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTATTTATTTTAA
Found at i:360253 original size:9 final size:9
Alignment explanation
Indices: 360239--360264 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
360229 TAAAAGGGAA
360239 AAATAAAAT
1 AAATAAAAT
360248 AAATAAAAT
1 AAATAAAAT
360257 AAATAAAA
1 AAATAAAA
360265 AAGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:360396 original size:38 final size:40
Alignment explanation
Indices: 360327--360406 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
360317 AATATATATA
*
360327 TATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACACCAAAGTATTAATAAAATAGAA-AAGC
*
360367 TATATATATATACACCAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATACACCAAAGTATTAATAAAATAGAAAAGC
360405 TA
1 TA
360407 CCCTCTCACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (40 bp):
TATATATATATACACCAAAGTATTAATAAAATAGAAAAGC
Found at i:360645 original size:2 final size:2
Alignment explanation
Indices: 360577--360629 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
360567 AAATAATGAA
360577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
360619 AT AT AT AT AT A
1 AT AT AT AT AT A
360630 AAGTTATAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:360905 original size:18 final size:17
Alignment explanation
Indices: 360884--360926 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
360874 ATATATACAT
*
360884 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATAA
*
360902 ATAATAAAAATAAATAA
1 ATAATAATAATAAATAA
360919 ATAA-AATA
1 ATAATAATA
360927 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:360924 original size:62 final size:62
Alignment explanation
Indices: 360804--360927 Score: 148
Period size: 62 Copynumber: 2.0 Consensus size: 62
360794 TATTAAAGAA
* * * *
360804 ATATATATATATATAATAATAATAATAAAATATAGTAAAAGAATGAGAATAATCTAAAATAT
1 ATATATATATATATAATAATAATAATAAAACATAATAAAAAAATGAGAATAATATAAAATAT
360866 ATATATATATATATACAT-ATAATAATAATAACATGAATAATAAAAAT-A-AATAA-ATAAAATA
1 ATATATATATATATA-ATAATAATAATAA-AACAT-AATAA-AAAAATGAGAATAATATAAAATA
360927 T
62 T
360928 CCATATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
62 33 0.61
63 11 0.20
64 5 0.09
65 5 0.09
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.32
Consensus pattern (62 bp):
ATATATATATATATAATAATAATAATAAAACATAATAAAAAAATGAGAATAATATAAAATAT
Found at i:360934 original size:62 final size:64
Alignment explanation
Indices: 360804--360934 Score: 146
Period size: 65 Copynumber: 2.1 Consensus size: 64
360794 TATTAAAGAA
* * * *
360804 ATATATATATATATAATAATAATAATAAAATATAGTAAAAGAATGAGAATAATCTAAAATATAT
1 ATATATATATATACAATAATAATAATAAAATATAGTAAAAAAATGAGAATAATATAAAATATAC
*
360868 ATATATATATATACATATAATAATAATAACATGA-A-TAATAAAAAT-A-AATAA-ATAAAATAT
1 ATATATATATATACA-ATAATAATAATAAAAT-ATAGTAA-AAAAATGAGAATAATATAAAATAT
*
360928 CC
63 AC
360930 ATATA
1 ATATA
360935 ATAAATAAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
62 13 0.22
63 5 0.09
64 18 0.31
65 21 0.36
66 1 0.02
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (64 bp):
ATATATATATATACAATAATAATAATAAAATATAGTAAAAAAATGAGAATAATATAAAATATAC
Found at i:361357 original size:37 final size:36
Alignment explanation
Indices: 361314--361415 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
361304 ATAGTAGAAC
361314 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
361351 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
361385 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
361416 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:362270 original size:105 final size:105
Alignment explanation
Indices: 361963--362728 Score: 1132
Period size: 105 Copynumber: 7.3 Consensus size: 105
361953 CATTGTTCCA
* * ** *
361963 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * *
362027 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
362069 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
362129 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
362169 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
362234 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
362274 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
362339 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
362379 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
362444 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
362484 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
362549 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
362589 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT-GTTGTTGACAAG
* * * * *
362654 CAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
362695 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
362729 CGCGGATGGC
Statistics
Matches: 616, Mismatches: 33, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
99 1 0.00
100 84 0.14
101 1 0.00
102 7 0.01
104 5 0.01
105 409 0.66
106 84 0.14
107 3 0.00
109 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:363491 original size:65 final size:67
Alignment explanation
Indices: 363305--363711 Score: 228
Period size: 65 Copynumber: 5.9 Consensus size: 67
363295 GGAAACGATC
* * * * *
363305 TCAAAGATATATGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAA
363370 TAAAT
63 TAAAT
** * * *
363375 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
363440 AT
66 AT
* * *
363442 TCAAAGA-TTT-TGTTTCAATG-GAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAAC
1 TCAAAGATTTTGTGTTTCAA-GAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTTAAGGGAAA-
*
363503 T--GT
63 TAAAT
** * * * * * * *
363506 CTCAAGAGAGACAAAACTT-AGTTCCAAAAGAAACTCTCTCAAGGGAGACGAAATTTGTTTCAAA
1 -TC-A-A-AG----ATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT-TAA
*
363570 GAGAACAT--AT
57 GGGAA-ATAAAT
* * * * *
363580 TCAAATA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAT-T
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
*
363642 GT
66 AT
**
363644 CTCAAGATAGACGAAATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGG
1 -TC---A-A-A-GATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGG
363708 GAAA
59 GAAA
363712 CTGTCTCAAG
Statistics
Matches: 267, Mismatches: 45, Indels: 48
0.74 0.12 0.13
Matches are distributed among these distances:
63 2 0.01
64 8 0.03
65 76 0.28
66 11 0.04
67 24 0.09
68 35 0.13
69 4 0.01
70 8 0.03
71 2 0.01
72 54 0.20
73 33 0.12
74 9 0.03
75 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:363502 original size:36 final size:35
Alignment explanation
Indices: 363451--363731 Score: 247
Period size: 36 Copynumber: 8.0 Consensus size: 35
363441 TTCAAAGATT
*
363451 TTGTTTCAATG-GAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAA-GAGAAACTGTCTCAAGAGAGAC-AAAA
363487 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
363522 CTTAGTTCCAAAAGAAACTCTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
363560 TTGTTTCAA-AGAGAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAGA-AAC-TGTCTCAAGAGAGACAAAA
*
363589 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
363624 TTTATTTCAAGGGAAATTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
363661 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
363696 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
363732 CTCTTCTAGT
Statistics
Matches: 201, Mismatches: 27, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 2 0.01
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 12 0.06
36 129 0.64
37 32 0.16
38 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:363563 original size:138 final size:135
Alignment explanation
Indices: 363399--363711 Score: 412
Period size: 138 Copynumber: 2.3 Consensus size: 135
363389 TTTCAAGAGT
* *
363399 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAATGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAAT--ATTCAAAGATTTTGTTTCAAGGGA
* *
363464 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
64 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
363528 TCCAAAAGA
127 TCCAAAAGA
* * * * *
363537 AACTCTCTCAAGGGAGACGAAATTTGTTTCAAAGAGAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTT-TAAGGGAA-ATATTCAAAGATTTTGTTTCAAGGGA
* * * * * *
363602 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTGTCTCAAGATAGACGAAATTTGTTT
64 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
363667 CAAGAGA
129 CAAAAGA
*
363674 AACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
363712 CTGTCTCAAG
Statistics
Matches: 151, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
135 1 0.01
136 6 0.04
137 41 0.27
138 96 0.64
139 5 0.03
140 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (135 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATATTCAAAGATTTTGTTTCAAGGGAAA
CTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCA
AAAGA
Found at i:363610 original size:102 final size:100
Alignment explanation
Indices: 363487--363674 Score: 277
Period size: 102 Copynumber: 1.9 Consensus size: 100
363477 TAGACGAAAA
*
363487 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTCTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTCTCTCAAGAGA
363552 GACGAAATTTGTTTCAAAGAGAACATATTCAAATATT
65 GACGAAATTTGTTTC-AAGAGAACATATTCAAATATT
* * * ** * * *
363589 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTCTCTCAAGAGAG
363654 ACGAAATTTGTTTCAAGAGAA
66 ACGAAATTTGTTTCAAGAGAA
363675 ACTGTCTCAA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 7 0.09
101 33 0.43
102 37 0.48
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (100 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTCTCTCAAGAGAG
ACGAAATTTGTTTCAAGAGAACATATTCAAATATT
Found at i:363772 original size:71 final size:72
Alignment explanation
Indices: 363593--363777 Score: 223
Period size: 72 Copynumber: 2.6 Consensus size: 72
363583 AATATTTTGT
* * * * *
363593 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATTGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAGAGACGA
** *
363658 AATTTGT
66 AAACTGC
363665 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAGAGACGA
363729 AAACT-C
66 AAACTGC
* * * *
363735 TTCTAGTGAAAACGGTCTCAAGCGAGAC-AAATCTTGTTTTAAG
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAAT-TTGTTTTAAG
363778 AAAAACAATC
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
70 10 0.10
71 31 0.31
72 58 0.59
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (72 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAGAGACGA
AAACTGC
Found at i:363781 original size:35 final size:35
Alignment explanation
Indices: 363601--363781 Score: 177
Period size: 36 Copynumber: 5.1 Consensus size: 35
363591 GTTTCAAGGG
* * *
363601 AAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGG
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAA-GA
* * * *
363637 AAATTGTCTCAAGATAGACGAAATTTGTTTCAAGA
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
*
363672 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGG
1 -AAACTGTCTCAAGAGAGACAAAATTTGTTTTAA-GA
* * * *
363709 AAACTGTCTCAAGAGAGACAAAA-CTCTTCTAGTGA
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTA-AGA
* *
363744 AAACGGTCTCAAGCGAGAC-AAATCTTGTTTTAAGA
1 AAACTGTCTCAAGAGAGACAAAAT-TTGTTTTAAGA
363779 AAA
1 AAA
363782 ACAATCATGA
Statistics
Matches: 119, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
34 3 0.03
35 29 0.24
36 86 0.72
37 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
Found at i:364238 original size:18 final size:18
Alignment explanation
Indices: 364211--364246 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
364201 TGTTGAATCC
* *
364211 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
364229 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
364247 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:364740 original size:22 final size:22
Alignment explanation
Indices: 364663--364733 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
364653 TTGTGTTTGG
*
364663 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
364685 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
364707 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
364729 TCAAA
1 TCAAA
364734 AGATTGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:365403 original size:16 final size:15
Alignment explanation
Indices: 365384--365467 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 15
365374 TCTTTTTGAT
365384 TTTTGCTCTTTTTTTC
1 TTTTGCT-TTTTTTTC
365400 TTTTG-TTCTTGTTTCTC
1 TTTTGCTT-TT-TTT-TC
* *
365417 TTTTTCTTTGTTTTTTT
1 TTTTGC-TT-TTTTTTC
365434 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTT--TTC
365451 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTT-TTC
365466 TT
1 TT
365468 GATTGGATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
14 1 0.02
15 12 0.22
16 17 0.31
17 18 0.33
18 3 0.05
19 4 0.07
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.77
Consensus pattern (15 bp):
TTTTGCTTTTTTTTC
Found at i:365414 original size:15 final size:14
Alignment explanation
Indices: 365400--365468 Score: 54
Period size: 16 Copynumber: 4.8 Consensus size: 14
365390 TCTTTTTTTC
365400 TTTTGTTCTTGTTT
1 TTTTGTTCTTGTTT
365414 CTCTTT-TTCTTTGTTT
1 -T-TTTGTTC-TTGTTT
*
365430 TTTT-TT-TTGCTT
1 TTTTGTTCTTGTTT
*
365442 TTTTGCTTCTTTTCTT
1 TTTTG-TTCTTGT-TT
365458 TTTTGTTCTTG
1 TTTTGTTCTTG
365469 ATTGGATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 9 0.20
14 7 0.16
15 12 0.27
16 16 0.36
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTTGTTCTTGTTT
Found at i:368513 original size:4 final size:4
Alignment explanation
Indices: 368499--368542 Score: 52
Period size: 4 Copynumber: 10.2 Consensus size: 4
368489 TAAAAGGGAA
*
368499 AAAT AAAAT AAAT AAAAT AAAT AAAAT AAAT AAAT AAAA AAAT A
1 AAAT -AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT A
368543 GTAAAGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
4 23 0.66
5 12 0.34
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:368513 original size:9 final size:9
Alignment explanation
Indices: 368499--368542 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
368489 TAAAAGGGAA
368499 AAATAAAAT
1 AAATAAAAT
368508 AAATAAAAT
1 AAATAAAAT
368517 AAATAAAAT
1 AAATAAAAT
368526 AAAT-AAAT
1 AAATAAAAT
368534 AAA-AAAAT
1 AAATAAAAT
368542 A
1 A
368543 GTAAAGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
8 12 0.35
9 22 0.65
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:368520 original size:13 final size:12
Alignment explanation
Indices: 368497--368542 Score: 65
Period size: 13 Copynumber: 3.6 Consensus size: 12
368487 GATAAAAGGG
368497 AAAAATAAAATAA
1 AAAAAT-AAATAA
368510 ATAAAATAAATAA
1 A-AAAATAAATAA
368523 AATAAATAAATAA
1 AA-AAATAAATAA
368536 AAAAATA
1 AAAAATA
368543 GTAAAGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.19
13 20 0.65
14 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:368661 original size:38 final size:40
Alignment explanation
Indices: 368592--368671 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
368582 AAAAAATATA
*
368592 TATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACACCAAAGTATTAATAAAATAGAA-AAGC
*
368632 TATATATATATACACCAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATACACCAAAGTATTAATAAAATAGAAAAGC
368670 TA
1 TA
368672 CCCTCTCACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (40 bp):
TATATATATATACACCAAAGTATTAATAAAATAGAAAAGC
Found at i:368897 original size:2 final size:2
Alignment explanation
Indices: 368841--368881 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
368831 AAATAATGAA
368841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
368882 AAGTTATAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:369157 original size:18 final size:17
Alignment explanation
Indices: 369136--369178 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
369126 ATATATACAT
*
369136 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATAA
*
369154 ATAATAAAAATAAATAA
1 ATAATAATAATAAATAA
369171 ATAA-AATA
1 ATAATAATA
369179 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:369176 original size:60 final size:60
Alignment explanation
Indices: 369060--369179 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 60
369050 TATTAAAGAA
* * * *
369060 ATATATATATATAATAATAATAATAAAATATAGTAAAAGAATGAGAATAATCTAAAATAT
1 ATATATATATATAATAATAATAATAAAACATAATAAAAAAATGAGAATAATATAAAATAT
369120 ATATATATATATACAT-ATAATAATAATAACATGAATAATAAAAAT-A-AATAA-ATAAAATAT
1 ATATATATATATA-ATAATAATAATAA-AACAT-AATAA-AAAAATGAGAATAATATAAAATAT
369180 CCATATAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
60 31 0.60
61 11 0.21
62 5 0.10
63 5 0.10
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (60 bp):
ATATATATATATAATAATAATAATAAAACATAATAAAAAAATGAGAATAATATAAAATAT
Found at i:369186 original size:60 final size:62
Alignment explanation
Indices: 369060--369186 Score: 138
Period size: 63 Copynumber: 2.1 Consensus size: 62
369050 TATTAAAGAA
* * * *
369060 ATATATATATATAATAATAATAATAAAATATAGTAAAAGAATGAGAATAATCTAAAATATAT
1 ATATATATATACAATAATAATAATAAAATATAGTAAAAAAATGAGAATAATATAAAATATAC
* *
369122 ATATATATATACATATAATAATAATAACATGA-A-TAATAAAAAT-A-AATAA-ATAAAATATCC
1 ATATATATATACA-ATAATAATAATAAAAT-ATAGTAA-AAAAATGAGAATAATATAAAATATAC
369182 ATATA
1 ATATA
369187 ATAAATAAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
60 13 0.23
61 5 0.09
62 16 0.29
63 21 0.38
64 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (62 bp):
ATATATATATACAATAATAATAATAAAATATAGTAAAAAAATGAGAATAATATAAAATATAC
Found at i:369609 original size:37 final size:36
Alignment explanation
Indices: 369566--369667 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
369556 ATAGTAGAAC
369566 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
369603 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
369637 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
369668 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:370841 original size:27 final size:27
Alignment explanation
Indices: 370785--370841 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
370775 CATATGAGTC
* *
370785 TTTTGATCATTTATAAACTTAAGGATA
1 TTTTGATCATTTATAAACTTAACGAAA
*
370812 TTTTGATCCTTT-TAACACTTAACGAAA
1 TTTTGATCATTTATAA-ACTTAACGAAA
370839 TTT
1 TTT
370842 GAATAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (27 bp):
TTTTGATCATTTATAAACTTAACGAAA
Found at i:371596 original size:17 final size:17
Alignment explanation
Indices: 371554--371588 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
371544 AAAAAATACC
*
371554 TAAAAAGATTTAAAATT
1 TAAAAAAATTTAAAATT
371571 TAAAAAAATTTAAAATT
1 TAAAAAAATTTAAAATT
371588 T
1 T
371589 TCAAAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAAAAAATTTAAAATT
Found at i:372771 original size:18 final size:18
Alignment explanation
Indices: 372750--372790 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
372740 CGACCCGTTT
372750 ACCCGACCCATTGACCCA
1 ACCCGACCCATTGACCCA
**
372768 ACCCGACCTGTTGACCCA
1 ACCCGACCCATTGACCCA
372786 ACCCG
1 ACCCG
372791 TTGACCGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.49, G:0.15, T:0.12
Consensus pattern (18 bp):
ACCCGACCCATTGACCCA
Found at i:372771 original size:31 final size:31
Alignment explanation
Indices: 372736--372796 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
372726 GACCGATCAT
* *
372736 AACCCGACCCGTTTACCCGACCCATTGACCC
1 AACCCGACCCGTTGACCCAACCCATTGACCC
* *
372767 AACCCGACCTGTTGACCCAACCCGTTGACC
1 AACCCGACCCGTTGACCCAACCCATTGACC
372797 GGCGTTGACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.46, G:0.15, T:0.16
Consensus pattern (31 bp):
AACCCGACCCGTTGACCCAACCCATTGACCC
Found at i:375333 original size:24 final size:24
Alignment explanation
Indices: 375280--375352 Score: 112
Period size: 24 Copynumber: 3.1 Consensus size: 24
375270 ATGGTACCTA
375280 ACCTGGATTCTGATCTGATA-TTG
1 ACCTGGATTCTGATCTGATACTTG
* *
375303 ACATGGATTCTGATCTGATACATG
1 ACCTGGATTCTGATCTGATACTTG
*
375327 ACCTGGATTCTGATATGATACTTG
1 ACCTGGATTCTGATCTGATACTTG
375351 AC
1 AC
375353 TTGAATTATG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 19 0.43
24 25 0.57
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (24 bp):
ACCTGGATTCTGATCTGATACTTG
Found at i:376168 original size:24 final size:24
Alignment explanation
Indices: 376132--376204 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
376122 GTAAATGGAG
* *
376132 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGATATCAGAACAGAATTC
376156 ATATCAGATATCAGAACAGAATTC
1 ATATCAGATATCAGAACAGAATTC
* *
376180 AGATAACG-TATCAGAACAGAATTC
1 ATATCA-GATATCAGAACAGAATTC
376204 A
1 A
376205 ATTCGGAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.22
Consensus pattern (24 bp):
ATATCAGATATCAGAACAGAATTC
Found at i:376216 original size:24 final size:24
Alignment explanation
Indices: 376132--376218 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 24
376122 GTAAATGGAG
*
376132 ATATCAGAAATCAAAACAGAATTC-
1 ATATC-GAAATCAGAACAGAATTCA
*
376156 ATATCAGATATCAGAACAGAATTCA
1 ATATC-GAAATCAGAACAGAATTCA
* *
376181 GATAACG-TATCAGAACAGAATTCA
1 -ATATCGAAATCAGAACAGAATTCA
376205 AT-TCGGAAATCAGA
1 ATATC-GAAATCAGA
376219 TAAAATATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.02
23 3 0.06
24 45 0.83
25 1 0.02
26 4 0.07
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATATCGAAATCAGAACAGAATTCA
Found at i:382070 original size:18 final size:18
Alignment explanation
Indices: 382043--382083 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
382033 GTCATAACCC
* *
382043 GACCCGACCCGACCCGTT
1 GACCCAACCCAACCCGTT
*
382061 GACCCAACCCAACCTGTT
1 GACCCAACCCAACCCGTT
382079 GACCC
1 GACCC
382084 GACTCGTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.49, G:0.17, T:0.12
Consensus pattern (18 bp):
GACCCAACCCAACCCGTT
Found at i:382083 original size:13 final size:13
Alignment explanation
Indices: 382067--382108 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
382057 CGTTGACCCA
382067 ACCCAAC-CTGTTG
1 ACCCAACTC-GTTG
*
382080 ACCCGACTCGTTG
1 ACCCAACTCGTTG
*
382093 ACCCGACTCGTTG
1 ACCCAACTCGTTG
382106 ACC
1 ACC
382109 TGTTGACCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 26 0.96
14 1 0.04
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.21
Consensus pattern (13 bp):
ACCCAACTCGTTG
Found at i:384665 original size:23 final size:24
Alignment explanation
Indices: 384614--384704 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
384604 TCAAATTTGA
* * * *
384614 ATTCTGTTATGATACCTGACGTGG
1 ATTCTGATCTGATACTTGACATGG
*
384638 ATTCTGATCTGATA-TTGATATGG
1 ATTCTGATCTGATACTTGACATGG
* *
384661 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACATGG
*
384685 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
384705 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:386877 original size:18 final size:18
Alignment explanation
Indices: 386838--386880 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
386828 ACCGGTCATA
* *
386838 ACCCGACCTGACTCGTTT
1 ACCCGACCCGACTCGTTG
386856 ACCCGACCCGAC-CTGTTG
1 ACCCGACCCGACTC-GTTG
386874 ACCCGAC
1 ACCCGAC
386881 TCGTTGACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.19
Consensus pattern (18 bp):
ACCCGACCCGACTCGTTG
Found at i:389450 original size:24 final size:24
Alignment explanation
Indices: 389388--389469 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
389378 AATTTTGTTA
* *
389388 TGATACATAACCTGGATTCTGATC
1 TGATACATGACATGGATTCTGATC
*
389412 TGATA-TTGACATGGATTCTGATC
1 TGATACATGACATGGATTCTGATC
*
389435 TGATACATGACATGGATTCTGATA
1 TGATACATGACATGGATTCTGATC
*
389459 TGATACTTGAC
1 TGATACATGAC
389470 TTGAATTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 20 0.39
24 31 0.61
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (24 bp):
TGATACATGACATGGATTCTGATC
Found at i:389689 original size:2 final size:2
Alignment explanation
Indices: 389682--389728 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
389672 CGGATGGGGG
*
389682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
389724 TA TA T
1 TA TA T
389729 GTTTTAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:394141 original size:24 final size:24
Alignment explanation
Indices: 394114--394199 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
394104 TCAAATTTGA
* *
394114 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACATGACCTGG
* * * *
394138 ATTCTGATCTGATA-TTGACATGA
1 ATTCTGATATGATACATGACCTGG
*
394161 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
394185 ATTCTGATATGATAC
1 ATTCTGATATGATAC
394200 TTTACTTGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:395697 original size:31 final size:31
Alignment explanation
Indices: 395662--395721 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
395652 ACCGGTCATA
*
395662 ACCCGACCCGTTTACCCGACCCGTTTACCTG
1 ACCCGACCCGTTGACCCGACCCGTTTACCTG
* *
395693 ACCCGACCTGTTGACCCGACTCGTTTACC
1 ACCCGACCCGTTGACCCGACCCGTTTACC
395722 CGTTGACCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.17, C:0.43, G:0.17, T:0.23
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGTTTACCTG
Found at i:395723 original size:13 final size:13
Alignment explanation
Indices: 395662--395697 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
395652 ACCGGTCATA
395662 ACCCGACCCGTTT
1 ACCCGACCCGTTT
395675 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
395688 ACCTGACCCG
1 ACCCGACCCG
395698 ACCTGTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.47, G:0.17, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:398263 original size:24 final size:24
Alignment explanation
Indices: 398236--398317 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
398226 AATTCTATTA
* *
398236 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACATGGATTCTGATC
*
398260 TGATA-TTGACATTGATTCTGATC
1 TGATACTTGACATGGATTCTGATC
* * *
398283 TGATACATGATATGGATTCTGATA
1 TGATACTTGACATGGATTCTGATC
398307 TGATACTTGAC
1 TGATACTTGAC
398318 TTGAATTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
23 20 0.42
24 28 0.58
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
TGATACTTGACATGGATTCTGATC
Found at i:400462 original size:13 final size:13
Alignment explanation
Indices: 400444--400479 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
400434 ACCGGTCATA
400444 ACCCGACCCGTTT
1 ACCCGACCCGTTT
400457 ACCCGACCCGTTT
1 ACCCGACCCGTTT
400470 ACCCGACCCG
1 ACCCGACCCG
400480 ACCTGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:400478 original size:18 final size:18
Alignment explanation
Indices: 400457--400494 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
400447 CGACCCGTTT
*
400457 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCG
*
400475 ACCCGACCTGTTGACCCG
1 ACCCGACCCGTTGACCCG
400493 AC
1 AC
400495 TCGTTTACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:400479 original size:31 final size:31
Alignment explanation
Indices: 400444--400505 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
400434 ACCGGTCATA
*
400444 ACCCGACCCGTTTACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCGACCCGTTTACCCG
* *
400475 ACCCGACCTGTTGACCCGACTCGTTTACCCG
1 ACCCGACCCGTTGACCCGACCCGTTTACCCG
400506 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.45, G:0.18, T:0.21
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGTTTACCCG
Found at i:403045 original size:24 final size:24
Alignment explanation
Indices: 403018--403099 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
403008 AATTCTATTA
* *
403018 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACATGGATTCTGATC
*
403042 TGATA-TTGACATTGATTCTGATC
1 TGATACTTGACATGGATTCTGATC
* * *
403065 TGATACATGATATGGATTCTGATA
1 TGATACTTGACATGGATTCTGATC
403089 TGATACTTGAC
1 TGATACTTGAC
403100 TTGAATTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
23 20 0.42
24 28 0.58
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
TGATACTTGACATGGATTCTGATC
Found at i:405246 original size:18 final size:18
Alignment explanation
Indices: 405221--405268 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
405211 TGACCGGTCA
405221 TAACCCGACTCGACCCGT
1 TAACCCGACTCGACCCGT
* * *
405239 TTACCCGACCCGACCTGT
1 TAACCCGACTCGACCCGT
405257 TAACCCGACTCG
1 TAACCCGACTCG
405269 TTGACCCGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.44, G:0.17, T:0.19
Consensus pattern (18 bp):
TAACCCGACTCGACCCGT
Found at i:406653 original size:18 final size:18
Alignment explanation
Indices: 406627--406661 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
406617 GGACTGAAGG
* *
406627 AAATGATAAGATTGGATT
1 AAATAATAAGATCGGATT
406645 AAATAATAAGATCGGAT
1 AAATAATAAGATCGGAT
406662 GGAGGAAAAA
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:0.49, C:0.03, G:0.20, T:0.29
Consensus pattern (18 bp):
AAATAATAAGATCGGATT
Found at i:407844 original size:47 final size:48
Alignment explanation
Indices: 407793--407883 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
407783 TCAAATTTGA
* * * *
407793 ATTCTGTTATGATACCTGACCTGGATTTTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
407840 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
407884 TTGAATTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:407864 original size:24 final size:24
Alignment explanation
Indices: 407793--407883 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
407783 TCAAATTTGA
* *
407793 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* * *
407817 ATTTTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
407840 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
407864 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
407884 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:408701 original size:3 final size:3
Alignment explanation
Indices: 408693--408718 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
408683 CTAGATTAAT
408693 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
408719 TATGGATTTT
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:409346 original size:28 final size:28
Alignment explanation
Indices: 409283--409348 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
409273 TTATTATTTT
*
409283 ACTCCAAACCCTATAAATTACATCATAA
1 ACTCCAATCCCTATAAATTACATCATAA
* *
409311 ACTTCAATCCCTATAAATTATATCATAA
1 ACTCCAATCCCTATAAATTACATCATAA
409339 TA-TCCAATCC
1 -ACTCCAATCC
409349 TATGAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (28 bp):
ACTCCAATCCCTATAAATTACATCATAA
Found at i:409600 original size:6 final size:6
Alignment explanation
Indices: 409589--411676 Score: 3882
Period size: 6 Copynumber: 352.8 Consensus size: 6
409579 AATATAAGGC
409589 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
409637 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
409685 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
409733 --TATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
409779 TATATG TATATG TATATG TATATG TATATG TATATG TATA-G --TATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
409824 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
409872 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
409920 --TATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
409966 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410014 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410062 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410110 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410158 TATATG TATATG TATATG TATATG TATATG TATATG TATATG --TATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410204 TATATG TATATG TATATG TATA-- TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410250 TATATG TATATG --TATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410296 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
410344 TATATG TATATG TATGTATG TATATG TATATG TATATA TATATG TATATG
1 TATATG TATATG TA--TATG TATATG TATATG TATATG TATATG TATATG
410394 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410442 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410490 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410538 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410586 TATATG TATATG TATATG TATATG TATATG TATATG --TATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410632 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410680 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* *
410728 TATATG TATATG TATATG TATATG TATATA TGTATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410776 TATATG TATATG --TATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410822 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410870 --TATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410916 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
410964 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411012 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411060 TATATG TATATG TATATG TATATG TATATG TATA-- TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411106 TATATG TATATG TATATG TATATG --TATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411152 TATATG TATATG TATATG TATATG TATGTATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TA--TATG TATATG TATATG TATATG
411202 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411250 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411298 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411346 TATATG TATATG TATATG TATATG --TATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411392 TATATG TATATG TATATG TATATG TATATG --TATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411438 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411486 TATATG --TATG TATATG TATATG --TATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411530 TATATG TATATG TATATG --TATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411576 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411624 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
411672 TATAT
1 TATAT
411677 ACAATACAAT
Statistics
Matches: 2039, Mismatches: 6, Indels: 74
0.96 0.00 0.03
Matches are distributed among these distances:
3 2 0.00
4 61 0.03
5 1 0.00
6 1963 0.96
8 12 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:414765 original size:29 final size:29
Alignment explanation
Indices: 414728--414906 Score: 243
Period size: 29 Copynumber: 6.2 Consensus size: 29
414718 ACACAATTAT
414728 CACCCTTTTAAGAAATATTTACGAAACTAA
1 CACCCTTTTAA-AAATATTTACGAAACTAA
* * * **
414758 CATCTTTTTAAAAATATTTATGAAACTGC
1 CACCCTTTTAAAAATATTTACGAAACTAA
*
414787 CA-CCTTTTAAAAATATTTACGAAAATAA
1 CACCCTTTTAAAAATATTTACGAAACTAA
* * *
414815 CAGCCTTTTAAAAATATTTACAAAAATAA
1 CACCCTTTTAAAAATATTTACGAAACTAA
*
414844 CACCCTTTTAAAAATATTTACGAAAGTAA
1 CACCCTTTTAAAAATATTTACGAAACTAA
*
414873 CACCCTTTTAAAAATATTTACAAAACTAA
1 CACCCTTTTAAAAATATTTACGAAACTAA
414902 CACCC
1 CACCC
414907 GGTCAACGGT
Statistics
Matches: 132, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
28 23 0.17
29 100 0.76
30 9 0.07
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.32
Consensus pattern (29 bp):
CACCCTTTTAAAAATATTTACGAAACTAA
Found at i:422026 original size:20 final size:21
Alignment explanation
Indices: 421984--422027 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
421974 ATTTTACATA
*
421984 ATTATCACCCTTTTAAGAAAT
1 ATTAACACCCTTTTAAGAAAT
422005 ATTAACACCCTTTTAA-AAAT
1 ATTAACACCCTTTTAAGAAAT
422025 ATT
1 ATT
422028 TACGAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTAACACCCTTTTAAGAAAT
Found at i:426554 original size:2 final size:2
Alignment explanation
Indices: 426547--426574 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
426537 CTTACAAACA
426547 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
426575 GAATAAGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:429686 original size:14 final size:15
Alignment explanation
Indices: 429660--429688 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
429650 ATGCATAACA
429660 TCACCATATATAATG
1 TCACCATATATAATG
429675 TCACCA-ATATAATG
1 TCACCATATATAATG
429689 GCAAAACCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (15 bp):
TCACCATATATAATG
Found at i:432876 original size:21 final size:21
Alignment explanation
Indices: 432852--432891 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
432842 GATGGGCACG
432852 GACCCGAACTCGAT-GGGTTTC
1 GACCCGAAC-CGATCGGGTTTC
432873 GACCCGAACCGATCGGGTT
1 GACCCGAACCGATCGGGTT
432892 GGGTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (21 bp):
GACCCGAACCGATCGGGTTTC
Found at i:433479 original size:15 final size:16
Alignment explanation
Indices: 433442--433472 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
433432 TTTTTCTTTA
433442 ATAATTACTAAAACTT
1 ATAATTACTAAAACTT
433458 ATAATTAC-AAAACTT
1 ATAATTACTAAAACTT
433473 GTCATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATTACTAAAACTT
Found at i:433679 original size:17 final size:16
Alignment explanation
Indices: 433659--433700 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
433649 ACTTATCTAT
433659 TTTGTGACAAAAGTAA
1 TTTGTGACAAAAGTAA
*
433675 TTT-TGACAAAATTAAA
1 TTTGTGACAAAAGT-AA
*
433691 TTTGTCACAA
1 TTTGTGACAA
433701 TAATAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 8 0.36
17 5 0.23
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (16 bp):
TTTGTGACAAAAGTAA
Found at i:449017 original size:27 final size:27
Alignment explanation
Indices: 448979--449035 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
448969 TTTCTTGTCA
448979 TTAAGGCCATATACCAATATTTTCCCT
1 TTAAGGCCATATACCAATATTTTCCCT
* *
449006 TTAAGGTCATATACTAATATTTTCCCT
1 TTAAGGCCATATACCAATATTTTCCCT
449033 TTA
1 TTA
449036 TGTCTAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (27 bp):
TTAAGGCCATATACCAATATTTTCCCT
Found at i:449286 original size:6 final size:6
Alignment explanation
Indices: 449275--449338 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
449265 TCTTTATCCT
449275 TCAATA TCAATA TCAATA TCAATA TCAATA TCAATA TCAATA TCAATA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAATA TCAATA TCAATA
449323 TCAATA TCAATA TCAA
1 TCAATA TCAATA TCAA
449339 GGGGTTGGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TCAATA
Found at i:450799 original size:30 final size:31
Alignment explanation
Indices: 450765--450827 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
450755 TAAGAGCATG
450765 AACTTTATATA-AATTATC-ATTTGACCCTTA
1 AACTTTATATATAA-TATCAATTTGACCCTTA
*
450795 AACTTTATATATAATATCAATTTGATCCTTA
1 AACTTTATATATAATATCAATTTGACCCTTA
450826 AA
1 AA
450828 TTTGACAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (31 bp):
AACTTTATATATAATATCAATTTGACCCTTA
Found at i:452435 original size:25 final size:23
Alignment explanation
Indices: 452380--452436 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
452370 TTCGTTTTTA
452380 AAATTATAAATTTTTTAAAATTAT
1 AAATTATAAATTTTTT-AAATTAT
452404 AATATTATGAAATTTTTT-AATTCAT
1 AA-ATTAT-AAATTTTTTAAATT-AT
452429 CAAATTAT
1 -AAATTAT
452437 TTTATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 6 0.21
25 12 0.41
26 11 0.38
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATTATAAATTTTTTAAATTAT
Found at i:457015 original size:21 final size:21
Alignment explanation
Indices: 456991--457036 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
456981 CTTCACAAGC
456991 AGTATCAATATTACTGTTATA
1 AGTATCAATATTACTGTTATA
*
457012 AGTATCCATATTACTGTTATA
1 AGTATCAATATTACTGTTATA
457033 AGTA
1 AGTA
457037 GTATCGATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (21 bp):
AGTATCAATATTACTGTTATA
Found at i:488939 original size:24 final size:24
Alignment explanation
Indices: 488912--489018 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
488902 AAACGAAGAT
*
488912 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
488936 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
488960 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
488984 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
489008 ATCAGAAATCA
1 ATCAGAAATCA
489019 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:489018 original size:48 final size:48
Alignment explanation
Indices: 488912--489020 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
488902 AAACGAAGAT
* * * *
488912 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
488960 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
489008 ATCAGAAATCAGA
1 ATCAGAAATCAGA
489021 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:490123 original size:18 final size:18
Alignment explanation
Indices: 490102--490137 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
490092 CTTCCATCTG
*
490102 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
490120 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
490138 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:491496 original size:18 final size:18
Alignment explanation
Indices: 491473--491548 Score: 90
Period size: 18 Copynumber: 4.5 Consensus size: 18
491463 CAACGGTCAA
491473 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
491491 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
491504 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
*
491522 TGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
491540 CGGGCCGGG
1 CGGGTCGGG
491549 CCGGGTTGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
13 12 0.25
18 36 0.75
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:491505 original size:31 final size:31
Alignment explanation
Indices: 491467--491543 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
491457 ACGGGTCAAC
*
491467 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
*
491498 GGTCAACGGGTCGGGTAAACGGGTTGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
491529 GGTCAACGGGTCGGG
1 GGTCAACGGGTCGGG
491544 CCGGGCCGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:491509 original size:8 final size:8
Alignment explanation
Indices: 491452--491491 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
491442 GGTCAACTCC
491452 GGTCAACG
1 GGTCAACG
491460 GGTCAAC-
1 GGTCAACG
491467 GGTCAACG
1 GGTCAACG
491475 GGT---CG
1 GGTCAACG
491480 GGTCAACG
1 GGTCAACG
491488 GGTC
1 GGTC
491492 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:491518 original size:13 final size:13
Alignment explanation
Indices: 491491--491526 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
491481 GTCAACGGGT
*
491491 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
491504 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
*
491517 CGGGTTGGGT
1 CGGGTCGGGT
491527 CGGGTCAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.17, G:0.50, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:491543 original size:13 final size:13
Alignment explanation
Indices: 491452--491496 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
491442 GGTCAACTCC
*
491452 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
491467 GGTCAACGGGTCG
1 GGTCAACGGGTCG
491480 GGTCAACGGGTCG
1 GGTCAACGGGTCG
491493 GGTC
1 GGTC
491497 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:505646 original size:16 final size:17
Alignment explanation
Indices: 505616--505648 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
505606 CTTCCTACCT
505616 TTAAAATTAATAAAAAA
1 TTAAAATTAATAAAAAA
505633 TTAAAATT-ATAAAAAA
1 TTAAAATTAATAAAAAA
505649 CATAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAAATTAATAAAAAA
Found at i:505658 original size:17 final size:16
Alignment explanation
Indices: 505617--505659 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
505607 TTCCTACCTT
*
505617 TAAAATTAATAAAAAAT
1 TAAAATT-ATAAAAAAA
505634 TAAAATTATAAAAAACA
1 TAAAATTATAAAAAA-A
*
505651 TAATATTAT
1 TAAAATTAT
505660 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATTATAAAAAAA
Found at i:506536 original size:16 final size:16
Alignment explanation
Indices: 506515--506547 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
506505 TAATAAATAA
506515 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
506531 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
506547 A
1 A
506548 AAAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:506628 original size:10 final size:10
Alignment explanation
Indices: 506613--506687 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
506603 CATTTAATAA
506613 ATAAACGAAC
1 ATAAACGAAC
506623 ATAAACGAAC
1 ATAAACGAAC
506633 ----ACGAAC
1 ATAAACGAAC
506639 ATAAACGAAC
1 ATAAACGAAC
** *
506649 ACGAAC-ATAA
1 ATAAACGA-AC
506659 ATGAACACGAAC
1 AT-AA-ACGAAC
506671 ATAAACGAAC
1 ATAAACGAAC
506681 ATAAACG
1 ATAAACG
506688 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:506638 original size:16 final size:16
Alignment explanation
Indices: 506617--506681 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
506607 TAATAAATAA
506617 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
506633 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
506649 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
506665 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
506681 A
1 A
506682 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:508698 original size:22 final size:22
Alignment explanation
Indices: 508673--508714 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
508663 GTCAAAGAAA
508673 GTCAACGGTCCGGTCGGGTCGG
1 GTCAACGGTCCGGTCGGGTCGG
*
508695 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCCGGTCGGGTC
508715 AACGGTCGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.45, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCCGGTCGGGTCGG
Found at i:508705 original size:17 final size:17
Alignment explanation
Indices: 508683--508732 Score: 100
Period size: 17 Copynumber: 2.9 Consensus size: 17
508673 GTCAACGGTC
508683 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
508700 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
508717 CGGTCGGGTCGGGTCA
1 CGGTCGGGTCGGGTCA
508733 GACTGGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.18
Consensus pattern (17 bp):
CGGTCGGGTCGGGTCAA
Found at i:508752 original size:19 final size:19
Alignment explanation
Indices: 508730--508807 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
508720 TCGGGTCGGG
*
508730 TCAGACTGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
508749 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
508768 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
508787 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
508807 T
1 T
508808 GAAAACTGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
18 3 0.06
19 38 0.76
20 9 0.18
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:508758 original size:10 final size:9
Alignment explanation
Indices: 508737--508806 Score: 77
Period size: 10 Copynumber: 7.3 Consensus size: 9
508727 GGGTCAGACT
508737 GGTCAAACC
1 GGTCAAACC
*
508746 GGTTCAGACC
1 GG-TCAAACC
508756 GGTCAAACC
1 GGTCAAACC
*
508765 GGTTCGAACC
1 GG-TCAAACC
*
508775 GGTTGAAACC
1 GG-TCAAACC
508785 GGTCAAACC
1 GGTCAAACC
508794 GGTCAGAACC
1 GGTCA-AACC
508804 GGT
1 GGT
508807 TGAAAACTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
9 21 0.40
10 31 0.60
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:508811 original size:29 final size:27
Alignment explanation
Indices: 508742--508806 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
508732 AGACTGGTCA
* *
508742 AACCGGTTCAGACCGGTCAAACCGGTTCG
1 AACCGG-TCAAACCGGTCAAACCGG-TAG
*
508771 AACCGGTTGAAACCGGTCAAACCGGTCAG
1 AACCGG-TCAAACCGGTCAAACCGGT-AG
508800 AACCGGT
1 AACCGGT
508807 TGAAAACTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.28, C:0.29, G:0.28, T:0.15
Consensus pattern (27 bp):
AACCGGTCAAACCGGTCAAACCGGTAG
Found at i:516026 original size:17 final size:17
Alignment explanation
Indices: 516017--516066 Score: 100
Period size: 17 Copynumber: 2.9 Consensus size: 17
516007 GTCAACGGTC
516017 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
516034 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
516051 CGGTCGGGTCGGGTCA
1 CGGTCGGGTCGGGTCA
516067 GACCGGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.18
Consensus pattern (17 bp):
CGGTCGGGTCGGGTCAA
Found at i:516061 original size:22 final size:22
Alignment explanation
Indices: 516006--516048 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
515996 GAAAGTCAAC
516006 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCG
*
516028 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCCGGTCGGGTC
516049 AACGGTCGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.26, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCCGGTCGGGTCG
Found at i:516086 original size:19 final size:19
Alignment explanation
Indices: 516064--516141 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
516054 TCGGGTCGGG
516064 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
516083 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
516102 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
* *
516121 TCAAATCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
516141 T
1 T
516142 GAAAACTGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
18 3 0.06
19 38 0.76
20 9 0.18
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:516092 original size:10 final size:10
Alignment explanation
Indices: 516064--516112 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
516054 TCGGGTCGGG
516064 TCAGACCGG-
1 TCAGACCGGT
*
516073 TCAAACCGGT
1 TCAGACCGGT
516083 TCAGACCGG-
1 TCAGACCGGT
*
516092 TCAAACCGGT
1 TCAGACCGGT
516102 TC-GAACCGGT
1 TCAG-ACCGGT
516112 T
1 T
516113 GAAACCGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:516118 original size:10 final size:10
Alignment explanation
Indices: 516068--516161 Score: 81
Period size: 9 Copynumber: 9.7 Consensus size: 10
516058 GTCGGGTCAG
516068 ACCGG-TCAA
1 ACCGGTTCAA
*
516077 ACCGGTTCAG
1 ACCGGTTCAA
516087 ACCGG-TCAA
1 ACCGGTTCAA
*
516096 ACCGGTTCGA
1 ACCGGTTCAA
*
516106 ACCGGTTGAA
1 ACCGGTTCAA
516116 ACCGG-TCAA
1 ACCGGTTCAA
*
516125 ATCGG-TCAGA
1 ACCGGTTCA-A
*
516135 ACCGGTTGAAA
1 ACCGGTT-CAA
*
516146 ACTGGTT-AA
1 ACCGGTTCAA
516155 ACCGGTT
1 ACCGGTT
516162 TCCAACAGCC
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
9 31 0.45
10 29 0.42
11 8 0.12
12 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.19
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:516119 original size:29 final size:28
Alignment explanation
Indices: 516063--516160 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 28
516053 GTCGGGTCGG
* *
516063 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTAAGACCG
*
516091 GTCAAACCGGTTCGAACCGGTTGAA-ACCG
1 GTCAAACCGG-TCAAACCGGTT-AAGACCG
* * *
516120 GTCAAATCGGTCAGAACCGGTTGAAAACTG
1 GTCAAACCGGTCA-AACCGGTT-AAGACCG
*
516150 GTTAAACCGGT
1 GTCAAACCGGT
516161 TTCCAACAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 11 0.19
29 34 0.59
30 13 0.22
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.18
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTAAGACCG
Found at i:517186 original size:14 final size:14
Alignment explanation
Indices: 517169--517199 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
517159 AATGAACATA
*
517169 AACGAACATAATCG
1 AACGAACATAAACG
517183 AACGAACATAAACG
1 AACGAACATAAACG
517197 AAC
1 AAC
517200 ATAACCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:517189 original size:24 final size:24
Alignment explanation
Indices: 517149--517225 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
517139 GATTGTGTTA
*
517149 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
517173 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * * *
517197 AACATAACCAAACAAACATAACCG
1 AACATAATCGAACGAACATAAACG
517221 AACAT
1 AACAT
517226 TCACGAACGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.57, C:0.21, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:519738 original size:17 final size:18
Alignment explanation
Indices: 519707--519740 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
519697 TTTCCTACAT
519707 TTAAAATTAATAAAAAAA
1 TTAAAATTAATAAAAAAA
519725 TTAAAATT-ATAAAAAA
1 TTAAAATTAATAAAAAA
519741 CATAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAATTAATAAAAAAA
Found at i:521055 original size:2 final size:2
Alignment explanation
Indices: 521048--521087 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
521038 CTAATTTATC
521048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
521088 GCCTCATGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523192 original size:24 final size:23
Alignment explanation
Indices: 523164--523251 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 23
523154 AGATATCAAA
* *
523164 AATCAAAACATAATTCATATCAG
1 AATCAGAACAGAATTCATATCAG
* *
523187 ATATCAGAACAGAATCCAGATCAG
1 A-ATCAGAACAGAATTCATATCAG
*
523211 AATCAGAACAGAATTCAGGTAAC-G
1 AATCAGAACAGAATTCA--TATCAG
*
523235 TATCAGAACAGAATTCA
1 AATCAGAACAGAATTCA
523252 ATTCGGAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
23 16 0.30
24 36 0.67
25 2 0.04
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (23 bp):
AATCAGAACAGAATTCATATCAG
Found at i:523206 original size:12 final size:11
Alignment explanation
Indices: 523184--523248 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
523174 TAATTCATAT
523184 CAGATATCAGAA
1 CAGA-ATCAGAA
*
523196 CAGAATCCAGAT
1 CAGAAT-CAGAA
523208 CAGAATCAGAA
1 CAGAATCAGAA
523219 CAGAATTCAGGTAA
1 CAGAA-TCA-G-AA
*
523233 C-GTATCAGAA
1 CAGAATCAGAA
523243 CAGAAT
1 CAGAAT
523249 TCAATTCGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 15 0.34
12 20 0.45
13 3 0.07
14 3 0.07
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (11 bp):
CAGAATCAGAA
Done.