Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1041
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: 1020100
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 4
Found at i:220106 original size:2 final size:2
Alignment explanation
Indices: 220099--220129 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
220089 TATTTGACTA
*
220099 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
220130 TCAATCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:220391 original size:2 final size:2
Alignment explanation
Indices: 220384--220424 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
220374 TTTTGAACAT
220384 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
220425 TATATATATA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:224466 original size:52 final size:51
Alignment explanation
Indices: 224409--224546 Score: 152
Period size: 51 Copynumber: 2.7 Consensus size: 51
224399 AATACCTTAC
* *
224409 ATGTATCGATACATTAAAGAATGTATCGATACATTT-AGGTCATAAATCCAGA
1 ATGTATCGATACAATAAAGAATGTATCGATACATTTGA-GTCA-AAACCCAGA
* * * *
224461 ATGTATCAATACAATGAAGAATGTATCGATATATTTGAGTTAAAACCCAGA
1 ATGTATCGATACAATAAAGAATGTATCGATACATTTGAGTCAAAACCCAGA
* * * **
224512 ATGTATTGATATAATAAAAAACATATCGATACATT
1 ATGTATCGATACAATAAAGAATGTATCGATACATT
224547 GTAAGCATGC
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
51 35 0.49
52 35 0.49
53 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (51 bp):
ATGTATCGATACAATAAAGAATGTATCGATACATTTGAGTCAAAACCCAGA
Found at i:224697 original size:21 final size:20
Alignment explanation
Indices: 224643--224682 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
224633 ACATTTTAGA
224643 CATGTATCAATACATTCACT
1 CATGTATCAATACATTCACT
224663 CATGTATCAATACATTCACT
1 CATGTATCAATACATTCACT
224683 ATTTGTATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (20 bp):
CATGTATCAATACATTCACT
Found at i:233049 original size:10 final size:11
Alignment explanation
Indices: 233034--233065 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
233024 TCACCATCAT
233034 TATTATAT-TA
1 TATTATATATA
233044 TATTATATATA
1 TATTATATATA
233055 TA-TATATATA
1 TATTATATATA
233065 T
1 T
233066 GTAGCTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTATATATA
Found at i:234883 original size:14 final size:14
Alignment explanation
Indices: 234864--234890 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
234854 TATTAATGTA
234864 TAATTCTTATAATT
1 TAATTCTTATAATT
234878 TAATTCTTATAAT
1 TAATTCTTATAAT
234891 CCATCCAAAT
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:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTCTTATAATT
Found at i:235872 original size:190 final size:191
Alignment explanation
Indices: 235544--235926 Score: 633
Period size: 190 Copynumber: 2.0 Consensus size: 191
235534 TTGAATGTTT
* ** * * * *
235544 AAAGGCTGATTTAGGCATATAAGGAAATGATTTTCAAACCTAAAATCGCGCGATTTGCTTAAGTT
1 AAAGGCTAATTTAGGCATATAAAAAAATGATTTCCAAACCTAAAATCACGCGATTTACTTAAATT
* *
235609 AAAGTCCAGGTCCGTGACACACACAAATACAAATATTAATTCAGATCACTTTTTATTCAAATTCA
66 AAAGTCCAGGTCCATGA-ACACACAAATACAAATATTAATTCAGATCACTTTTTATCCAAATTCA
235674 TTATCTCTCACACATCTCTACCTCTCTGTTTGATACACGAAATCCATTAATTTACAATCACA
130 TTATCTCTCACACATCTCTACCTCTCTGTTTGATACACGAAATCCATTAATTTACAATCACA
* *
235736 AAAGGCTAATTTAGGCATATAAAAAAATTATTTCCAAACCTAAGATCACGCGATTTACTTAAATT
1 AAAGGCTAATTTAGGCATATAAAAAAATGATTTCCAAACCTAAAATCACGCGATTTACTTAAATT
* *
235801 AAAGTCTAGGTCTATG-ACACACAAATACAAATATTAATTCAGATCACTTTTTATCCAAATTCAT
66 AAAGTCCAGGTCCATGAACACACAAATACAAATATTAATTCAGATCACTTTTTATCCAAATTCAT
235865 TATCTCTCACACATCTCTACCTCTCTGTTTGATACACGAAATCCATTAATTTACAATCACA
131 TATCTCTCACACATCTCTACCTCTCTGTTTGATACACGAAATCCATTAATTTACAATCACA
235926 A
1 A
235927 TTGCAGATAT
Statistics
Matches: 178, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
190 109 0.61
192 69 0.39
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (191 bp):
AAAGGCTAATTTAGGCATATAAAAAAATGATTTCCAAACCTAAAATCACGCGATTTACTTAAATT
AAAGTCCAGGTCCATGAACACACAAATACAAATATTAATTCAGATCACTTTTTATCCAAATTCAT
TATCTCTCACACATCTCTACCTCTCTGTTTGATACACGAAATCCATTAATTTACAATCACA
Found at i:237606 original size:3 final size:3
Alignment explanation
Indices: 237600--237630 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
237590 GGAAGAAGCA
237600 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
237631 TCTGAGTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:239654 original size:2 final size:2
Alignment explanation
Indices: 239647--239673 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
239637 TTGATCACCA
239647 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
239674 TTGTTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:239707 original size:3 final size:3
Alignment explanation
Indices: 239699--239737 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
239689 TGCCACAGAG
239699 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT -AT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
239738 TCAAAAGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:240684 original size:42 final size:43
Alignment explanation
Indices: 240625--240710 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 43
240615 ATCGATGTTC
240625 GGAATCATAATTCTCTCTC-GTGTTAAACGTTTCTAGTTTTTT
1 GGAATCATAATTCTCTCTCTGTGTTAAACGTTTCTAGTTTTTT
*
240667 GGAATCATAATTCTCTCTCTTTTGTTAAACGTTTCTAGTTTTTT
1 GGAATCATAATTCTCTCTC-TGTGTTAAACGTTTCTAGTTTTTT
240711 CTCTTCAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 19 0.46
44 22 0.54
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (43 bp):
GGAATCATAATTCTCTCTCTGTGTTAAACGTTTCTAGTTTTTT
Found at i:243366 original size:3 final size:3
Alignment explanation
Indices: 243358--243382 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
243348 TCTTCAACCT
243358 TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC T
243383 TCTTCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:243387 original size:3 final size:3
Alignment explanation
Indices: 243381--243410 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
243371 GCTGCTGCTG
*
243381 CTT CTT CTT CTT CTT CTT CTT CCT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
243411 ATATTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:245968 original size:2 final size:2
Alignment explanation
Indices: 245956--246007 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
245946 GTAATGGATG
*
245956 CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
245998 CT CT CT CT CT
1 CT CT CT CT CT
246008 AATTGCTGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:252894 original size:35 final size:35
Alignment explanation
Indices: 252854--252922 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
252844 AAGTTTTTGA
252854 GTTG-TTAAACTTTAAAAAAAATAAATTTGATATAT
1 GTTGTTTAAA-TTTAAAAAAAATAAATTTGATATAT
* *
252889 GTTGTTTTAATTTAAAAAAATTAAATTTGATATA
1 GTTGTTTAAATTTAAAAAAAATAAATTTGATATA
252923 ATAGCCTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.43
Consensus pattern (35 bp):
GTTGTTTAAATTTAAAAAAAATAAATTTGATATAT
Found at i:253620 original size:16 final size:15
Alignment explanation
Indices: 253601--253644 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
253591 TAATTAATTA
253601 TAAATAAAATTTTATT
1 TAAATAAAATTTTA-T
*
253617 TAAAATTAAATTTTAT
1 T-AAATAAAATTTTAT
253633 TAAATAATAATT
1 TAAATAA-AATT
253645 ATTTATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 5 0.21
16 7 0.29
17 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATAAAATTTTAT
Found at i:255905 original size:43 final size:42
Alignment explanation
Indices: 255844--255927 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
255834 ACTTTCCTCA
* **
255844 TTCCATCCTTCTTCCTTTTTTCATCCAATTAAAC-TACCCTTAT
1 TTCCATCCTTCATCC-TTTTT-ATCCAACCAAACATACCCTTAT
255887 TTCCATCCTTCCAT-CTTTTTATCCAACCAAACATACCCTTA
1 TTCCATCCTT-CATCCTTTTTATCCAACCAAACATACCCTTA
255928 ATGCCTAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 10 0.28
42 13 0.36
43 11 0.31
44 2 0.06
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.42
Consensus pattern (42 bp):
TTCCATCCTTCATCCTTTTTATCCAACCAAACATACCCTTAT
Found at i:256054 original size:20 final size:20
Alignment explanation
Indices: 256029--256069 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
256019 TTAAATGATA
*
256029 TAAAGTTTTAAATTAAAAGC
1 TAAAGTTATAAATTAAAAGC
*
256049 TAAAGTTATATATTAAAAGC
1 TAAAGTTATAAATTAAAAGC
256069 T
1 T
256070 TACTTAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (20 bp):
TAAAGTTATAAATTAAAAGC
Found at i:261511 original size:2 final size:2
Alignment explanation
Indices: 261504--261528 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
261494 TGTTTGTCCC
261504 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
261529 TATATATATA
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:261738 original size:2 final size:2
Alignment explanation
Indices: 261731--261757 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
261721 TTCAAATATA
261731 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
261758 TGGTCAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:269309 original size:3 final size:3
Alignment explanation
Indices: 269303--269327 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
269293 GTTGTTGTTG
269303 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
269328 CTAATTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:274499 original size:21 final size:22
Alignment explanation
Indices: 274475--274525 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
274465 AAGTCGGAAA
274475 TATATAAATATTTTTT-TAATT
1 TATATAAATATTTTTTATAATT
* *
274496 TATATTTAATATTTTTTATTATT
1 TATA-TAAATATTTTTTATAATT
274519 TAT-TAAA
1 TATATAAA
274526 AAATATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 7 0.28
22 11 0.44
23 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATATAAATATTTTTTATAATT
Found at i:274583 original size:46 final size:46
Alignment explanation
Indices: 274489--274583 Score: 104
Period size: 46 Copynumber: 2.0 Consensus size: 46
274479 TAAATATTTT
* *
274489 TTTAATTTATATTTAATATTTTTTATTATTTATTAAAAAATATAATA
1 TTTAATTTATATTTAAAATTTTTTA-TATTTATTAAAAAATAAAATA
* **
274536 TTTATATTTA-ATTATAAAATTTTTTA-ATTTATTTAATGATAAAATA
1 TTTA-ATTTATATT-TAAAATTTTTTATATTTATTAAAAAATAAAATA
274582 TT
1 TT
274584 ACGTTATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
46 18 0.44
47 7 0.17
48 16 0.39
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (46 bp):
TTTAATTTATATTTAAAATTTTTTATATTTATTAAAAAATAAAATA
Found at i:274984 original size:3 final size:3
Alignment explanation
Indices: 274963--275011 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
274953 GATTTGCATG
* *
274963 CTT CTT -TT CCTT TTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CTCT
1 CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T
275009 CTT
1 CTT
275012 TTAATCCTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:277008 original size:7 final size:7
Alignment explanation
Indices: 276977--277001 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
276967 GTGTATTGAT
276977 GAAGGAA
1 GAAGGAA
276984 GAAGGAA
1 GAAGGAA
276991 GAAGGAA
1 GAAGGAA
276998 GAAG
1 GAAG
277002 ATGGAAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
GAAGGAA
Found at i:286203 original size:16 final size:16
Alignment explanation
Indices: 286178--286235 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
286168 ATTCGGGTTA
*
286178 TTTTATATTTAAATTT
1 TTTTAGATTTAAATTT
* *
286194 TTTTAGATTTTAATGT
1 TTTTAGATTTAAATTT
*
286210 TTTTAAATTTAAATTT
1 TTTTAGATTTAAATTT
*
286226 ATTTAGATTT
1 TTTTAGATTT
286236 TTGGTTTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTAGATTTAAATTT
Found at i:286245 original size:32 final size:33
Alignment explanation
Indices: 286173--286245 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 33
286163 GGTACATTCG
* *
286173 GGTTATTTTATATTTAAATTTTTTTAGATTTTAAT
1 GGTT-TTTTAAATTTAAATTTATTTAGATTTT-AT
286208 -G-TTTTTAAATTTAAATTTATTTAGATTTT-T
1 GGTTTTTTAAATTTAAATTTATTTAGATTTTAT
286238 GGTTTTTT
1 GGTTTTTT
286246 TGAGTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
30 1 0.03
31 1 0.03
32 30 0.88
33 1 0.03
34 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (33 bp):
GGTTTTTTAAATTTAAATTTATTTAGATTTTAT
Found at i:286277 original size:16 final size:16
Alignment explanation
Indices: 286234--286278 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
286224 TTATTTAGAT
*
286234 TTTTGGTTTTTTTGAG
1 TTTTGATTTTTTTGAG
*
286250 TTTTGATCTTTTTGAG
1 TTTTGATTTTTTTGAG
286266 -TTTGAATTTTTTT
1 TTTTG-ATTTTTTT
286279 AAATTCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.11, C:0.02, G:0.18, T:0.69
Consensus pattern (16 bp):
TTTTGATTTTTTTGAG
Found at i:286454 original size:16 final size:16
Alignment explanation
Indices: 286429--286467 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
286419 TTATACTATA
286429 ATATTT-TTAAAATAT
1 ATATTTATTAAAATAT
*
286444 ATATTTATTAAAATTT
1 ATATTTATTAAAATAT
*
286460 ATGTTTAT
1 ATATTTAT
286468 ATATAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATATTTATTAAAATAT
Found at i:286520 original size:22 final size:20
Alignment explanation
Indices: 286451--286520 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 20
286441 TATATATTTA
*
286451 TTAAAATTTATGT-TTATAT
1 TTAAAATTAATGTATTATAT
* *
286470 ATAAAATTAATTTATTATAT
1 TTAAAATTAATGTATTATAT
286490 ATTACAAATTAATGATATTGATAT
1 -TTA-AAATTAATG-TATT-ATAT
286514 TTAAAAT
1 TTAAAAT
286521 AATTGACATG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
19 10 0.24
20 6 0.15
21 2 0.05
22 12 0.29
23 7 0.17
24 4 0.10
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (20 bp):
TTAAAATTAATGTATTATAT
Found at i:287404 original size:15 final size:16
Alignment explanation
Indices: 287384--287413 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
287374 TTGATAAGAT
287384 ATAATTTATT-TTTTG
1 ATAATTTATTATTTTG
287399 ATAATTTATTATTTT
1 ATAATTTATTATTTT
287414 ATTATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATAATTTATTATTTTG
Found at i:287416 original size:23 final size:22
Alignment explanation
Indices: 287360--287402 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
287350 AAAATTCTTC
287360 ATATAATTTATTTTTTGATAAG
1 ATATAATTTATTTTTTGATAAG
287382 ATATAATTTATTTTTTGATAA
1 ATATAATTTATTTTTTGATAA
287403 TTTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
ATATAATTTATTTTTTGATAAG
Found at i:287459 original size:43 final size:41
Alignment explanation
Indices: 287377--287468 Score: 98
Period size: 43 Copynumber: 2.2 Consensus size: 41
287367 TTATTTTTTG
* * * **
287377 ATAAGATATAATTTATTTTTTGATAATTTATTATTTTATTAT
1 ATAAAATATAATTAATTTTTTAATAATTTATTAAATTATT-T
287419 ATAAAATATAAATTAATTTTTTAAT-ATTTAATTAAATTATTT
1 ATAAAATAT-AATTAATTTTTTAATAATTT-ATTAAATTATTT
287461 A-AAAATAT
1 ATAAAATAT
287469 TAAAATAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 7 0.16
42 14 0.33
43 22 0.51
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (41 bp):
ATAAAATATAATTAATTTTTTAATAATTTATTAAATTATTT
Found at i:287587 original size:16 final size:16
Alignment explanation
Indices: 287566--287596 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
287556 TTAATCTCAG
287566 ATTTAAATTCTTTTAA
1 ATTTAAATTCTTTTAA
*
287582 ATTTAAATTTTTTTA
1 ATTTAAATTCTTTTA
287597 TTTCCATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAAATTCTTTTAA
Found at i:294858 original size:2 final size:2
Alignment explanation
Indices: 294839--294874 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
294829 GTAGTTGATG
* *
294839 AT AT AC AT AT AT AC 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
294875 CCACCCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:301842 original size:4 final size:4
Alignment explanation
Indices: 301833--301859 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
301823 CGTTAATCTT
301833 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
301860 TTATGCCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:308283 original size:17 final size:17
Alignment explanation
Indices: 308261--308298 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
308251 TACAAATATA
308261 ATTACAT-ATTTATAAAT
1 ATTACATAATTTAT-AAT
308278 ATTACATAAATTTATAAT
1 ATTACAT-AATTTATAAT
308296 ATT
1 ATT
308299 TTAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTACATAATTTATAAT
Found at i:308441 original size:24 final size:24
Alignment explanation
Indices: 308373--308442 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 24
308363 AAATATACAT
308373 AAAATAAAATAAATTATTAATATGTCA
1 AAAATAAAA-AAA-TA-TAATATGTCA
* *
308400 AAAATATACAAAAATATAATATTTTA
1 AAAATA-A-AAAAATATAATATGTCA
308426 AAAATAAAAAAATATAA
1 AAAATAAAAAAATATAA
308443 ATACAAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 14 0.36
27 8 0.21
28 4 0.10
29 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (24 bp):
AAAATAAAAAAATATAATATGTCA
Found at i:308485 original size:4 final size:4
Alignment explanation
Indices: 308474--308508 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
308464 AATAATTTTT
*
308474 TTTC -TTC TTTC TTTC TTTT TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
308509 CCACTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:308492 original size:16 final size:16
Alignment explanation
Indices: 308473--308507 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
308463 TAATAATTTT
308473 TTTTCTTCTTTCTTTC
1 TTTTCTTCTTTCTTTC
*
308489 TTTTTTTCTTTCTTTC
1 TTTTCTTCTTTCTTTC
308505 TTT
1 TTT
308508 CCCACTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTCTTTCTTTC
Found at i:308636 original size:20 final size:20
Alignment explanation
Indices: 308604--308713 Score: 77
Period size: 20 Copynumber: 5.4 Consensus size: 20
308594 ATATTATCAT
308604 TATAATAAAAAATAATTAAAA
1 TATAAT-AAAAATAATTAAAA
308625 TATAATAAAAAT-A--AAAA
1 TATAATAAAAATAATTAAAA
* *
308642 TATAATATTAAATACTTTAAAA
1 TATAATA-AAAATA-ATTAAAA
* * *
308664 TTTATATAATATTAATTATAAA
1 TATA-ATAAAAATAATTA-AAA
308686 TAT-ATAAAAAT-ATATATAAA
1 TATAATAAAAATAAT-TA-AAA
308706 TATAATAA
1 TATAATAA
308714 TATTTTAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
17 11 0.16
18 4 0.06
19 3 0.04
20 21 0.30
21 13 0.19
22 15 0.21
23 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAATAAAAATAATTAAAA
Found at i:308648 original size:11 final size:11
Alignment explanation
Indices: 308604--308637 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
308594 ATATTATCAT
308604 TATAATAAAAA
1 TATAATAAAAA
*
308615 -ATAATTAAAA
1 TATAATAAAAA
308625 TATAATAAAAA
1 TATAATAAAAA
308636 TA
1 TA
308638 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:308721 original size:60 final size:58
Alignment explanation
Indices: 308616--308745 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 58
308606 TAATAAAAAA
* *
308616 TAATTAAAATATAATAAAAATAAAAATATAATATTAAATACTTTAAAATTTATATAATAT
1 TAATTAAAATATAATAAAAATAAAAATATAATATAAAATACTTT-AAATAT-TATAATAT
* * *
308676 TAATTATAAATAT-ATAAAAATATATATA-AATATAATAATATTTTAAATATTATAATAT
1 TAATTA-AAATATAATAAAAATAAAAATATAATATAA-AATACTTTAAATATTATAATAT
308734 T--TT-AAATATAAT
1 TAATTAAAATATAAT
308746 TATAATTTGG
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
54 6 0.10
55 2 0.03
56 2 0.03
58 9 0.15
59 11 0.18
60 26 0.42
61 6 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.42
Consensus pattern (58 bp):
TAATTAAAATATAATAAAAATAAAAATATAATATAAAATACTTTAAATATTATAATAT
Found at i:308724 original size:17 final size:17
Alignment explanation
Indices: 308687--308745 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
308677 AATTATAAAT
* *
308687 ATATAAAAATATATATAA
1 ATATAATAATAT-TTTAA
308705 ATATAATAATATTTTAA
1 ATATAATAATATTTTAA
*
308722 ATATTATAATATTTTAA
1 ATATAATAATATTTTAA
308739 ATATAAT
1 ATATAAT
308746 TATAATTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 26 0.70
18 11 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATAATATTTTAA
Found at i:308732 original size:8 final size:9
Alignment explanation
Indices: 308678--308742 Score: 62
Period size: 10 Copynumber: 7.2 Consensus size: 9
308668 TATAATATTA
308678 ATTATAAAT
1 ATTATAAAT
*
308687 ATATAAAAAT
1 AT-TATAAAT
308697 ATATATAAAT
1 AT-TATAAAT
*
308707 ATAAT-AAT
1 ATTATAAAT
*
308715 ATTTTAAAT
1 ATTATAAAT
308724 ATTAT-AAT
1 ATTATAAAT
*
308732 ATTTTAAAT
1 ATTATAAAT
308741 AT
1 AT
308743 AATTATAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
8 13 0.28
9 16 0.35
10 17 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATTATAAAT
Found at i:310033 original size:19 final size:20
Alignment explanation
Indices: 310011--310050 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
310001 TAATACACAT
*
310011 TTAACATATAA-ATAAAAAA
1 TTAAAATATAACATAAAAAA
*
310030 TTAAAATATAACATGAAAAA
1 TTAAAATATAACATAAAAAA
310050 T
1 T
310051 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
TTAAAATATAACATAAAAAA
Found at i:310218 original size:21 final size:21
Alignment explanation
Indices: 310191--310238 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
310181 ATATTTAAAA
310191 ATATAATATAAAAATAAATAC
1 ATATAATATAAAAATAAATAC
* * *
310212 GTATAATATAAATATACATAC
1 ATATAATATAAAAATAAATAC
310233 ATATAA
1 ATATAA
310239 AAATATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (21 bp):
ATATAATATAAAAATAAATAC
Found at i:310291 original size:32 final size:30
Alignment explanation
Indices: 310254--310324 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
310244 TATATTAAAT
*
310254 AAAATA-AATTATTAATATATAAAAAATATATA
1 AAAATATAA-TATT-ATAAATAAAAAATA-ATA
*
310286 AAAATATAATATTTTAAATAAAAAATAATA
1 AAAATATAATATTATAAATAAAAAATAATA
*
310316 CAAATATAA
1 AAAATATAA
310325 ACAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.31
31 12 0.34
32 10 0.29
33 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATATAATATTATAAATAAAAAATAATA
Found at i:310322 original size:51 final size:47
Alignment explanation
Indices: 310233--310331 Score: 110
Period size: 51 Copynumber: 2.0 Consensus size: 47
310223 ATATACATAC
* **
310233 ATATAAAAATATATATTAAATAAAATAAATTATTAATATATAAAAAAT
1 ATATAAAAATATATATTAAATAAAATAAAATACAAATATA-AAAAAAT
*
310281 ATATAAAAATATAATATTTTAAATAAAA-AATAATACAAATATAAACAAAT
1 ATATAAAAATAT-ATA--TTAAATAAAATAA-AATACAAATATAAAAAAAT
310331 A
1 A
310332 AATTTTTCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
48 12 0.28
49 3 0.07
50 9 0.21
51 19 0.44
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (47 bp):
ATATAAAAATATATATTAAATAAAATAAAATACAAATATAAAAAAAT
Found at i:310505 original size:15 final size:12
Alignment explanation
Indices: 310492--310603 Score: 63
Period size: 13 Copynumber: 9.1 Consensus size: 12
310482 ATTAGATATT
310492 TAAAAATATAATA
1 TAAAAATA-AATA
310505 TAAAAATAAATA
1 TAAAAATAAATA
*
310517 CGTATAATATAAATA
1 --TA-AAAATAAATA
*
310532 T--AAATACATA
1 TAAAAATAAATA
*
310542 TAAAAATATATA
1 TAAAAATAAATA
*
310554 T-TAAATAAA-A
1 TAAAAATAAATA
*
310564 TAAATTATTAATATA
1 TAAA--AATAA-ATA
*
310579 TAAAAA-ATATA
1 TAAAAATAAATA
310590 TAAAAATATAATA
1 TAAAAATA-AATA
310603 T
1 T
310604 TTTAAATAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
10 10 0.13
11 16 0.21
12 15 0.20
13 18 0.24
14 3 0.04
15 14 0.18
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (12 bp):
TAAAAATAAATA
Found at i:310522 original size:21 final size:21
Alignment explanation
Indices: 310497--310544 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
310487 ATATTTAAAA
310497 ATATAATATAAAAATAAATAC
1 ATATAATATAAAAATAAATAC
* *
310518 GTATAATATAAATATAAATAC
1 ATATAATATAAAAATAAATAC
310539 ATATAA
1 ATATAA
310545 AAATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
ATATAATATAAAAATAAATAC
Found at i:310527 original size:306 final size:307
Alignment explanation
Indices: 310181--310803 Score: 1140
Period size: 306 Copynumber: 2.0 Consensus size: 307
310171 TTTATAAAAA
*
310181 ATATTTAAAAATATAATATAAAAATAAATACGTATAATATAAATATACATACATATAAAAATATA
1 ATATTTAAAAATATAATATAAAAATAAATACGTATAATATAAATATAAATACATATAAAAATATA
310246 TATTAAATAAAATAAATTATTAATATATAAAAAATATATAAAAATATAATATTTTAAATAAAAAA
66 TATTAAATAAAATAAATTATTAATATATAAAAAATATATAAAAATATAATATTTTAAATAAAAAA
** *
310311 TAATACAAATATAAACAAATAAATTTTTCTCTCTTCTTTCTTTTGTTCCTTTTTCTTCTTTTCTC
131 TAATACAAATATAAACAAATAAATTTTTCTAGCTTCTTACTTTTGTTCCTTTTTCTTCTTTTCTC
*
310376 CTTTCTCTCCTTTCCTTTTTCTTTCTTTCTTTGTCAGCTGAACGAAAAAAAAAAGTAAAAACAGG
196 CTTTCTCTCCTTTCCTTTTTCTTTCTTTCTTTGTCAGCTGAACGAAAAAAAAAAGTAAAAAAAGG
310441 CATGGACAGGTGTCAA-TTCCTCACCTATGTATGTAGTTCAAATTAG
261 CATGGACAGGTGTCAATTTCCTCACCTATGTATGTAGTTCAAATTAG
310487 ATATTTAAAAATATAATATAAAAATAAATACGTATAATATAAATATAAATACATATAAAAATATA
1 ATATTTAAAAATATAATATAAAAATAAATACGTATAATATAAATATAAATACATATAAAAATATA
310552 TATTAAATAAAATAAATTATTAATATATAAAAAATATATAAAAATATAATATTTTAAATAAAAAA
66 TATTAAATAAAATAAATTATTAATATATAAAAAATATATAAAAATATAATATTTTAAATAAAAAA
310617 TAATACAAATATAAACAAATAAATTTTTCTAGCTTCTTACTTTTGTTCCTTTTTCTTCTTTTCTC
131 TAATACAAATATAAACAAATAAATTTTTCTAGCTTCTTACTTTTGTTCCTTTTTCTTCTTTTCTC
310682 CTTTCTCTCCTTTCCTTTTTCTTTCTTTCTTTGTCAGCTGAACGAAAAAAAAAAGTAAAAAAAGG
196 CTTTCTCTCCTTTCCTTTTTCTTTCTTTCTTTGTCAGCTGAACGAAAAAAAAAAGTAAAAAAAGG
310747 CATGGACAGGTGTCAATTCCTCTTTCCTCACCTATGTATGTAGTTCAAATTAG
261 CATGGACAGGTGTCAA------TTTCCTCACCTATGTATGTAGTTCAAATTAG
310800 ATAT
1 ATAT
310804 ATAGTAGATA
Statistics
Matches: 305, Mismatches: 5, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
306 271 0.89
313 34 0.11
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (307 bp):
ATATTTAAAAATATAATATAAAAATAAATACGTATAATATAAATATAAATACATATAAAAATATA
TATTAAATAAAATAAATTATTAATATATAAAAAATATATAAAAATATAATATTTTAAATAAAAAA
TAATACAAATATAAACAAATAAATTTTTCTAGCTTCTTACTTTTGTTCCTTTTTCTTCTTTTCTC
CTTTCTCTCCTTTCCTTTTTCTTTCTTTCTTTGTCAGCTGAACGAAAAAAAAAAGTAAAAAAAGG
CATGGACAGGTGTCAATTTCCTCACCTATGTATGTAGTTCAAATTAG
Found at i:310552 original size:10 final size:10
Alignment explanation
Indices: 310529--310599 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
310519 TATAATATAA
* *
310529 ATATAAATAC
1 ATATAAAAAT
310539 ATATAAAAAT
1 ATATAAAAAT
*
310549 ATATATTAAAT
1 ATATA-AAAAT
310560 A-A-AATAAAT
1 ATATAA-AAAT
* *
310569 -TATTAATAT
1 ATATAAAAAT
310578 ATA-AAAAAT
1 ATATAAAAAT
310587 ATATAAAAAT
1 ATATAAAAAT
310597 ATA
1 ATA
310600 ATATTTTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 16 0.34
10 26 0.55
11 5 0.11
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:310596 original size:32 final size:30
Alignment explanation
Indices: 310560--310630 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
310550 TATATTAAAT
*
310560 AAAATA-AATTATTAATATATAAAAAATATATA
1 AAAATATAA-TATT-ATAAATAAAAAATA-ATA
*
310592 AAAATATAATATTTTAAATAAAAAATAATA
1 AAAATATAATATTATAAATAAAAAATAATA
*
310622 CAAATATAA
1 AAAATATAA
310631 ACAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.31
31 12 0.34
32 10 0.29
33 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATATAATATTATAAATAAAAAATAATA
Found at i:310628 original size:51 final size:47
Alignment explanation
Indices: 310539--310637 Score: 110
Period size: 51 Copynumber: 2.0 Consensus size: 47
310529 ATATAAATAC
* **
310539 ATATAAAAATATATATTAAATAAAATAAATTATTAATATATAAAAAAT
1 ATATAAAAATATATATTAAATAAAATAAAATACAAATATA-AAAAAAT
*
310587 ATATAAAAATATAATATTTTAAATAAAA-AATAATACAAATATAAACAAAT
1 ATATAAAAATAT-ATA--TTAAATAAAATAA-AATACAAATATAAAAAAAT
310637 A
1 A
310638 AATTTTTCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
48 12 0.28
49 3 0.07
50 9 0.21
51 19 0.44
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (47 bp):
ATATAAAAATATATATTAAATAAAATAAAATACAAATATAAAAAAAT
Found at i:311335 original size:5 final size:5
Alignment explanation
Indices: 311325--311350 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
311315 TAGAAGAACC
311325 TCCTT TCCTT TCCTT TCCTT TCCTT T
1 TCCTT TCCTT TCCTT TCCTT TCCTT T
311351 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCCTT
Found at i:311923 original size:14 final size:13
Alignment explanation
Indices: 311884--311929 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
311874 TTCATGGATC
311884 AAATTTTTAAATT
1 AAATTTTTAAATT
*
311897 AAATTTATAAAATT
1 AAATTT-TTAAATT
311911 AAATTTTTCAAATT
1 AAATTTTT-AAATT
*
311925 GAATT
1 AAATT
311930 CATGAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (13 bp):
AAATTTTTAAATT
Found at i:311937 original size:27 final size:26
Alignment explanation
Indices: 311867--311940 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
311857 TAGATTCATG
* *
311867 AATTAAATTCATGGATCAAATTTTTA
1 AATTAAATTCATGAATTAAATTTTTA
* *
311893 AATTAAATTTATAAAATTAAATTTTTCA
1 AATTAAATTCAT-GAATTAAATTTTT-A
*
311921 AATTGAATTCATGAATTAAA
1 AATTAAATTCATGAATTAAA
311941 CCCACCGAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 11 0.28
27 17 0.44
28 11 0.28
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (26 bp):
AATTAAATTCATGAATTAAATTTTTA
Found at i:315808 original size:2 final size:2
Alignment explanation
Indices: 315801--315836 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
315791 GCTGACTAGG
315801 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
315837 ATTTGTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:320245 original size:14 final size:14
Alignment explanation
Indices: 320226--320258 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
320216 GCATATGCTG
*
320226 TTTTTTTCTT-TCT
1 TTTTTTTTTTCTCT
320239 TTTTTTTTTTCTCT
1 TTTTTTTTTTCTCT
320253 TTTTTT
1 TTTTTT
320259 CCTTCTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTCTCT
Found at i:320651 original size:3 final size:3
Alignment explanation
Indices: 320643--320679 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
320633 TATTTTCATA
320643 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
320680 GCTGCTGCTA
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):
TAT
Found at i:323927 original size:129 final size:128
Alignment explanation
Indices: 323672--324053 Score: 630
Period size: 129 Copynumber: 3.0 Consensus size: 128
323662 CAGAGGCCTA
* * * * * *
323672 TGTGGTGAAGTT-GAAGGTTTGAAGCCCTGCATTCATACATCAGTGGAGAAGGAAAACAG-T-GA
1 TGTGGTGAATTTGGAAGGTTTGAAGCCCTGCAGTCATAAATCAATGGAGAAGGAAAGCAGTTAAA
* * *
323734 AAAAAA-A-AAAAACCAAAGTTCTAATAATTATTGGTGCCTCTTTATCATGTCTGGTGCTTTGT
66 AAAAAATAGAAAAAACAAAGTTCT-GTAATTATTGGTGCTTCTTTATCATGTCTGGTGCTTTGT
323796 TGTGGTGAATTTGGAAGGTTTGAAGCCCTGCAGTCATAAATCAATGGAGAAGGAAAGCAGTTAAA
1 TGTGGTGAATTTGGAAGGTTTGAAGCCCTGCAGTCATAAATCAATGGAGAAGGAAAGCAGTT-AA
323861 AAAAAAATAGAAAAAACAAAGTTCTGTAATTATTGGTGCTTCTTTATCATGTCTGGTGCTTTGT
65 AAAAAAATAGAAAAAACAAAGTTCTGTAATTATTGGTGCTTCTTTATCATGTCTGGTGCTTTGT
323925 TGTGGTGAATTTGGAAGGTTTGAAGCCCTGCAGTCATAAATCAATGGAGAAGGAAAGCAGTTAAA
1 TGTGGTGAATTTGGAAGGTTTGAAGCCCTGCAGTCATAAATCAATGGAGAAGGAAAGCAGTTAAA
323990 AAAAAATAGAAAAAACAAAGTTCTGTAATTATTGGTGCTTCTTTATCATGTCTGGTGCTTTGT
66 AAAAAATAGAAAAAACAAAGTTCTGTAATTATTGGTGCTTCTTTATCATGTCTGGTGCTTTGT
324053 T
1 T
324054 TAGCCCTGTT
Statistics
Matches: 243, Mismatches: 9, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
124 11 0.05
125 43 0.18
126 1 0.00
128 74 0.30
129 100 0.41
130 14 0.06
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (128 bp):
TGTGGTGAATTTGGAAGGTTTGAAGCCCTGCAGTCATAAATCAATGGAGAAGGAAAGCAGTTAAA
AAAAAATAGAAAAAACAAAGTTCTGTAATTATTGGTGCTTCTTTATCATGTCTGGTGCTTTGT
Found at i:331463 original size:2 final size:2
Alignment explanation
Indices: 331410--331449 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
331400 TGTAACTTGA
*
331410 AT AT -T AT AC AT AT A- 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
331450 GAGATAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:332590 original size:29 final size:29
Alignment explanation
Indices: 332554--332609 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
332544 ATTAATTTAT
*
332554 ATAAATAAAGTCATGAT-AAATATTAATA
1 ATAAATAAAGTAATGATAAAATATTAATA
**
332582 ATAATATAATTTAATGATAAAATATTAA
1 ATAA-ATAAAGTAATGATAAAATATTAA
332610 ATTTCTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 10 0.43
30 9 0.39
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAAATAAAGTAATGATAAAATATTAATA
Found at i:333887 original size:10 final size:10
Alignment explanation
Indices: 333874--333899 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
333864 ATATATATAT
333874 ATATATGCAC
1 ATATATGCAC
333884 ATATATGCAC
1 ATATATGCAC
333894 ATATAT
1 ATATAT
333900 ATAATTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (10 bp):
ATATATGCAC
Found at i:333899 original size:2 final size:2
Alignment explanation
Indices: 333854--333879 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
333844 TGGACCTTTA
333854 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
333880 GCACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:342131 original size:44 final size:44
Alignment explanation
Indices: 342082--342177 Score: 183
Period size: 44 Copynumber: 2.2 Consensus size: 44
342072 AATAATCCCG
342082 GTGACAATATAAATATTCAGGTTCTTTATGAAAAGATTATTGCA
1 GTGACAATATAAATATTCAGGTTCTTTATGAAAAGATTATTGCA
342126 GTGACAATATAAATATTCAGGTTCTTTATGAAAAGATTATTGCA
1 GTGACAATATAAATATTCAGGTTCTTTATGAAAAGATTATTGCA
*
342170 GTGGCAAT
1 GTGACAAT
342178 TGGTTCCTAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (44 bp):
GTGACAATATAAATATTCAGGTTCTTTATGAAAAGATTATTGCA
Found at i:342668 original size:87 final size:87
Alignment explanation
Indices: 342522--342682 Score: 286
Period size: 87 Copynumber: 1.9 Consensus size: 87
342512 ATTAAAAATC
342522 TTTTCATTCTGCTCCAATAACGGGAATACATGAACATTTGGTGGAACTGGGAAAGTTGTGTCCCT
1 TTTTCATTCTGCTCCAATAACGGGAATACATGAACATTTGGTGGAACTGGGAAAGTTGTGTCCCT
342587 GTTGTTTTACTTTATTTGCATA
66 GTTGTTTTACTTTATTTGCATA
* * **
342609 TTTTCATTGTGCTCCGATAACGGGAATACATGAACATTTGGTGGAACTGGGAAAGTTGTGTGTCT
1 TTTTCATTCTGCTCCAATAACGGGAATACATGAACATTTGGTGGAACTGGGAAAGTTGTGTCCCT
342674 GTTGTTTTA
66 GTTGTTTTA
342683 GGTATGGATT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (87 bp):
TTTTCATTCTGCTCCAATAACGGGAATACATGAACATTTGGTGGAACTGGGAAAGTTGTGTCCCT
GTTGTTTTACTTTATTTGCATA
Found at i:343003 original size:15 final size:16
Alignment explanation
Indices: 342974--343003 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
342964 AATGGGTGAG
342974 CTGAATTTAATTGTCT
1 CTGAATTTAATTGTCT
342990 CTGAATTT-ATTGTC
1 CTGAATTTAATTGTC
343004 CTAATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (16 bp):
CTGAATTTAATTGTCT
Found at i:348480 original size:35 final size:35
Alignment explanation
Indices: 348434--348501 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
348424 AAGCATCAGG
348434 GCGAGACTCACGATGAAGGCATAGCCAATTCTGAT
1 GCGAGACTCACGATGAAGGCATAGCCAATTCTGAT
348469 GCGAGACTCACGATGAAGGCATAGCCAATTCTG
1 GCGAGACTCACGATGAAGGCATAGCCAATTCTG
348502 TCCCTACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (35 bp):
GCGAGACTCACGATGAAGGCATAGCCAATTCTGAT
Found at i:349448 original size:21 final size:24
Alignment explanation
Indices: 349414--349456 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
349404 GGCTGGAAAT
349414 TGTCTTTGCAACAGAGG-AAGCTG
1 TGTCTTTGCAACAGAGGTAAGCTG
349437 TGTC-TTGC-ACAGAGGTAAGC
1 TGTCTTTGCAACAGAGGTAAGC
349457 AAGCCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (24 bp):
TGTCTTTGCAACAGAGGTAAGCTG
Found at i:356494 original size:2 final size:2
Alignment explanation
Indices: 356487--356514 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
356477 GAGTTGAGGA
356487 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
356515 TTTACTTTAT
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:357544 original size:2 final size:2
Alignment explanation
Indices: 357537--357563 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
357527 AACGTGGACT
357537 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
357564 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:361580 original size:19 final size:20
Alignment explanation
Indices: 361558--361672 Score: 85
Period size: 19 Copynumber: 5.8 Consensus size: 20
361548 TACTATTATA
*
361558 ATAAAATA-ATAATTATAAT
1 ATAAAATATATAAATATAAT
* *
361577 ATAATATTATATAAATATATT
1 ATAA-AATATATAAATATAAT
* * *
361598 AT-TAATATATCAATATATT
1 ATAAAATATATAAATATAAT
361617 A-AAAATATATAAATATAAT
1 ATAAAATATATAAATATAAT
** *
361636 ATTTTAA-ATATAATTATAAT
1 A-TAAAATATATAAATATAAT
*
361656 AAAAAATTATATAAATA
1 ATAAAA-TATATAAATA
361673 AAAAATTCCA
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
19 36 0.49
20 16 0.22
21 21 0.29
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAATATATAAATATAAT
Found at i:361638 original size:41 final size:41
Alignment explanation
Indices: 361561--361672 Score: 126
Period size: 40 Copynumber: 2.8 Consensus size: 41
361551 TATTATAATA
* * *
361561 AAATAATAATTATAATATAATATTATATAAATAT-AT-TATT
1 AAAT-ATAATTATAATAAAAAATTATATAAATATAATATTTT
*
361601 AATATATCAA-TAT-ATTAAAAA-TATATAAATATAATATTTT
1 AA-ATAT-AATTATAATAAAAAATTATATAAATATAATATTTT
361641 AAATATAATTATAATAAAAAATTATATAAATA
1 AAATATAATTATAATAAAAAATTATATAAATA
361673 AAAAATTCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
38 13 0.22
39 14 0.23
40 19 0.32
41 14 0.23
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (41 bp):
AAATATAATTATAATAAAAAATTATATAAATATAATATTTT
Found at i:366471 original size:39 final size:39
Alignment explanation
Indices: 366410--366526 Score: 98
Period size: 39 Copynumber: 3.0 Consensus size: 39
366400 AGTTCAAACG
366410 AATAGCCCATTCAAACAGATGAAGCC-ATGTCCC-AACTCT
1 AATAGCCCATTCAAACAGATGAA-CCAATG-CCCAAACTCT
* *
366449 AATAGCCCGTTCCAAC-GAATGAACCAATGCCCAAACTCT
1 AATAGCCCATTCAAACAG-ATGAACCAATGCCCAAACTCT
* * * ** *
366488 ACTTGCCCATTCAGATGGATGAGCGC-ATGCCCAAACTCT
1 AATAGCCCATTCAAACAGATGAAC-CAATGCCCAAACTCT
366527 CAGGGCCCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
38 6 0.09
39 56 0.88
40 2 0.03
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (39 bp):
AATAGCCCATTCAAACAGATGAACCAATGCCCAAACTCT
Found at i:371633 original size:437 final size:437
Alignment explanation
Indices: 370819--371697 Score: 1758
Period size: 437 Copynumber: 2.0 Consensus size: 437
370809 GATTTTAGTT
370819 AAACTTAGACCCCTAAGTTCCTACATCCCTTCAAGGCTTCAACTACTTCCCGGAGATATAGCACG
1 AAACTTAGACCCCTAAGTTCCTACATCCCTTCAAGGCTTCAACTACTTCCCGGAGATATAGCACG
370884 CACTTCACTTCTACTTCTAGGATCTTAAATGGTTCAACTTTAATTAGTTAGACTCTTACCGTCAC
66 CACTTCACTTCTACTTCTAGGATCTTAAATGGTTCAACTTTAATTAGTTAGACTCTTACCGTCAC
370949 TGACTTGCTTAATAGGGTGCTCACTGCCTGGAAAATTATAGCACTAGTAGTTTTATGGAGGATTC
131 TGACTTGCTTAATAGGGTGCTCACTGCCTGGAAAATTATAGCACTAGTAGTTTTATGGAGGATTC
371014 TAAGTTCTAACTCTGAACCTTTTTTTTTTTTTTTCTGAATGGATAAATATGTATGGATGATTTGA
196 TAAGTTCTAACTCTGAACCTTTTTTTTTTTTTTTCTGAATGGATAAATATGTATGGATGATTTGA
371079 TGCATAAACCTGGGTTTTTTCTTCTTCCAGTGACCTGAAGTTCTATTGAAAAAATTAAACCACAA
261 TGCATAAACCTGGGTTTTTTCTTCTTCCAGTGACCTGAAGTTCTATTGAAAAAATTAAACCACAA
371144 ATAAACAAACTTGGGGAAAAGAGCAGAAAGTAATAAATTGAAAGGCCAGGAGCTGCCCATTGTTT
326 ATAAACAAACTTGGGGAAAAGAGCAGAAAGTAATAAATTGAAAGGCCAGGAGCTGCCCATTGTTT
371209 TCGACTGCTTCTTAAGGATTTGAAAATTTTAAAAAAAAATAATACAG
391 TCGACTGCTTCTTAAGGATTTGAAAATTTTAAAAAAAAATAATACAG
371256 AAACTTAGACCCCTAAGTTCCTACATCCCTTCAAGGCTTCAACTACTTCCCGGAGATATAGCACG
1 AAACTTAGACCCCTAAGTTCCTACATCCCTTCAAGGCTTCAACTACTTCCCGGAGATATAGCACG
371321 CACTTCACTTCTACTTCTAGGATCTTAAATGGTTCAACTTTAATTAGTTAGACTCTTACCGTCAC
66 CACTTCACTTCTACTTCTAGGATCTTAAATGGTTCAACTTTAATTAGTTAGACTCTTACCGTCAC
371386 TGACTTGCTTAATAGGGTGCTCACTGCCTGGAAAATTATAGCACTAGTAGTTTTATGGAGGATTC
131 TGACTTGCTTAATAGGGTGCTCACTGCCTGGAAAATTATAGCACTAGTAGTTTTATGGAGGATTC
371451 TAAGTTCTAACTCTGAACCTTTTTTTTTTTTTTTCTGAATGGATAAATATGTATGGATGATTTGA
196 TAAGTTCTAACTCTGAACCTTTTTTTTTTTTTTTCTGAATGGATAAATATGTATGGATGATTTGA
371516 TGCATAAACCTGGGTTTTTTCTTCTTCCAGTGACCTGAAGTTCTATTGAAAAAATTAAACCACAA
261 TGCATAAACCTGGGTTTTTTCTTCTTCCAGTGACCTGAAGTTCTATTGAAAAAATTAAACCACAA
371581 ATAAACAAACTTGGGGAAAAGAGCAGAAAGTAATAAATTGAAAGGCCAGGAGCTGCCCATTGTTT
326 ATAAACAAACTTGGGGAAAAGAGCAGAAAGTAATAAATTGAAAGGCCAGGAGCTGCCCATTGTTT
371646 TCGACTGCTTCTTAAGGATTTGAAAATTTTAAAAAAAAATAATACAG
391 TCGACTGCTTCTTAAGGATTTGAAAATTTTAAAAAAAAATAATACAG
371693 AAACT
1 AAACT
371698 AATGGAATAT
Statistics
Matches: 442, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
437 442 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (437 bp):
AAACTTAGACCCCTAAGTTCCTACATCCCTTCAAGGCTTCAACTACTTCCCGGAGATATAGCACG
CACTTCACTTCTACTTCTAGGATCTTAAATGGTTCAACTTTAATTAGTTAGACTCTTACCGTCAC
TGACTTGCTTAATAGGGTGCTCACTGCCTGGAAAATTATAGCACTAGTAGTTTTATGGAGGATTC
TAAGTTCTAACTCTGAACCTTTTTTTTTTTTTTTCTGAATGGATAAATATGTATGGATGATTTGA
TGCATAAACCTGGGTTTTTTCTTCTTCCAGTGACCTGAAGTTCTATTGAAAAAATTAAACCACAA
ATAAACAAACTTGGGGAAAAGAGCAGAAAGTAATAAATTGAAAGGCCAGGAGCTGCCCATTGTTT
TCGACTGCTTCTTAAGGATTTGAAAATTTTAAAAAAAAATAATACAG
Found at i:372509 original size:5 final size:6
Alignment explanation
Indices: 372487--372524 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
372477 CTTAAAAACC
* *
372487 ATTTCT ATTTTT CTTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT
372525 AATAAATCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:377706 original size:2 final size:2
Alignment explanation
Indices: 377699--377731 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
377689 AAGAAAATGT
377699 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
377732 TTTGAGGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:377759 original size:10 final size:10
Alignment explanation
Indices: 377703--377761 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
377693 AAATGTGAGA
*
377703 GAGAGAGAGA
1 GAGAGAGAGT
*
377713 GAGAGAGAGA
1 GAGAGAGAGT
377723 GAGAGAGAGTTT
1 GAGAGAGAG--T
377735 GAG-GA-AGTT
1 GAGAGAGAG-T
377744 GCAGAGAGAGT
1 G-AGAGAGAGT
377755 GAGAGAG
1 GAGAGAG
377762 CGGAGAGTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
9 3 0.07
10 29 0.67
11 6 0.14
12 5 0.12
ACGTcount: A:0.41, C:0.02, G:0.47, T:0.10
Consensus pattern (10 bp):
GAGAGAGAGT
Found at i:378673 original size:27 final size:29
Alignment explanation
Indices: 378643--378705 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
378633 ATTTTAAATT
*
378643 TTTATATAAATTTT-AATATATTAATA-A
1 TTTATATAAATTTTAAAAATATTAATATA
** *
378670 TTTATATATTTTTTAAAAATATTTATATA
1 TTTATATAAATTTTAAAAATATTAATATA
378699 TTTATAT
1 TTTATAT
378706 TAAGACCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 12 0.40
28 10 0.33
29 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTATATAAATTTTAAAAATATTAATATA
Found at i:378748 original size:2 final size:2
Alignment explanation
Indices: 378743--378781 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
378733 AAAACGTAAC
378743 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
378782 TAATGGTGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:379748 original size:33 final size:31
Alignment explanation
Indices: 379677--379748 Score: 72
Period size: 33 Copynumber: 2.2 Consensus size: 31
379667 GGTTATTAAA
* * *
379677 AATTTATTTTATAATTAAATTTAAATAAAAT
1 AATTTATTATAAAATAAAATTTAAATAAAAT
* *
379708 ATTTTTATTATAAAATAATAATTTAAATTAAATT
1 A-ATTTATTATAAAATAA-AATTTAAA-TAAAAT
379742 AATTTAT
1 AATTTAT
379749 ATCAACTATC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
31 1 0.03
32 12 0.38
33 13 0.41
34 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
AATTTATTATAAAATAAAATTTAAATAAAAT
Found at i:382147 original size:21 final size:22
Alignment explanation
Indices: 382099--382161 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
382089 TTTCAATCAT
*
382099 TAATATTTTAAATTTAATAAAAA
1 TAATA-TTTAAATTAAATAAAAA
* *
382122 TAATATTTATATTAAATATAAA
1 TAATATTTAAATTAAATAAAAA
*
382144 -AATATTTAAATAAAATAA
1 TAATATTTAAATTAAATAA
382162 TTTTTAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 15 0.44
22 14 0.41
23 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATATTTAAATTAAATAAAAA
Found at i:388023 original size:2 final size:2
Alignment explanation
Indices: 388016--388054 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
388006 GTAGGGAGTT
388016 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
388055 GGTTTAGGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:404090 original size:2 final size:2
Alignment explanation
Indices: 404083--404111 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
404073 AATTGACTAT
404083 TA TA 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 TA TA T
404112 TTGCTTGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:404306 original size:21 final size:19
Alignment explanation
Indices: 404264--404311 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
404254 TTATTTTTAA
*
404264 TATAAATTTAATTATTATT
1 TATAAATATAATTATTATT
*
404283 TATAAATATAATTTTTAAATT
1 TATAAATATAATTATT--ATT
404304 TATAAATA
1 TATAAATA
404312 AATCTTCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.56
21 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATAAATATAATTATTATT
Found at i:404335 original size:10 final size:10
Alignment explanation
Indices: 404320--404364 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
404310 TAAATCTTCC
404320 ATAATAAATA
1 ATAATAAATA
*
404330 ATAATAATTA
1 ATAATAAATA
*
404340 ATATATTAAAAA
1 ATA-A-TAAATA
404352 ATAATAAATA
1 ATAATAAATA
404362 ATA
1 ATA
404365 TCTCAATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 20 0.69
11 2 0.07
12 7 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAATAAATA
Found at i:404349 original size:22 final size:22
Alignment explanation
Indices: 404324--404365 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
404314 TCTTCCATAA
* *
404324 TAAATAATAATAATTAATATAT
1 TAAAAAATAATAAATAATATAT
404346 TAAAAAATAATAAATAATAT
1 TAAAAAATAATAAATAATAT
404366 CTCAATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAAAATAATAAATAATATAT
Found at i:406018 original size:2 final size:2
Alignment explanation
Indices: 406011--406043 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
406001 ACAGTATTTC
*
406011 CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
406044 CAAACTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
CT
Found at i:410038 original size:21 final size:23
Alignment explanation
Indices: 410002--410074 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
409992 TATAATTTTA
*
410002 AATATAATATAATAA-TAAAATAT
1 AATATAA-AAAATAATTAAAATAT
*
410025 AA-ATAAAAAATAATTAAAATGT
1 AATATAAAAAATAATTAAAATAT
*
410047 AATAT-AAAAA-AATTATGAATAT
1 AATATAAAAAATAATTA-AAATAT
410069 AATATA
1 AATATA
410075 TCAAAGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 11 0.26
22 27 0.64
23 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
AATATAAAAAATAATTAAAATAT
Found at i:410071 original size:22 final size:22
Alignment explanation
Indices: 410002--410176 Score: 71
Period size: 22 Copynumber: 7.8 Consensus size: 22
409992 TATAATTTTA
410002 AATATAATATAATAA-TAAAATAT
1 AATATAA-A-AATAATTAAAATAT
*
410025 AA-ATAAAAAATAATTAAAATGT
1 AATAT-AAAAATAATTAAAATAT
*
410047 AATATAAAAA-AATTATGAATAT
1 AATATAAAAATAATTA-AAATAT
* *
410069 AATATATCAAAGT-TTATAAAATAT
1 AATATA--AAAATAAT-TAAAATAT
**
410093 AA-ATTATCAATATATTAAAATAT
1 AATA-TAAAAATA-ATTAAAATAT
* *
410116 TATAT-AAAAT-A-TAATATTAT
1 AATATAAAAATAATTAA-AATAT
* * *
410136 AACAATAAAATTAAATAAAAT-T
1 AA-TATAAAAATAATTAAAATAT
*
410158 GAATACAAAAATAATTAAA
1 -AATATAAAAATAATTAAA
410177 TTTAAAAGTA
Statistics
Matches: 112, Mismatches: 22, Indels: 37
0.65 0.13 0.22
Matches are distributed among these distances:
19 3 0.03
20 6 0.05
21 12 0.11
22 49 0.44
23 22 0.20
24 18 0.16
25 2 0.02
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AATATAAAAATAATTAAAATAT
Found at i:411470 original size:30 final size:31
Alignment explanation
Indices: 411435--411587 Score: 114
Period size: 30 Copynumber: 5.1 Consensus size: 31
411425 TGATGATATT
*
411435 AATTATTATTATATAA-ATAAAAT-TTTTAA
1 AATTATTATAATATAATATAAAATATTTTAA
411464 ATATTA-TATAATATAATATAAAATATTTTAA
1 A-ATTATTATAATATAATATAAAATATTTTAA
* *
411495 AATT-TTATAATATTACAT-TATTAAT-TTAATAA
1 AATTATTATAATA-TA-ATATA-AAATATT-TTAA
411527 AA-T-TTAT-ATA-AATATAAAATATTTTAA
1 AATTATTATAATATAATATAAAATATTTTAA
* *
411554 ATATAATTATAATAT-AT-TAAAATATATTATA
1 A-ATTATTATAATATAATATAAAATATTTTA-A
411585 AAT
1 AAT
411588 ATATAAATTT
Statistics
Matches: 101, Mismatches: 7, Indels: 31
0.73 0.05 0.22
Matches are distributed among these distances:
27 9 0.09
28 6 0.06
29 10 0.10
30 41 0.41
31 25 0.25
32 10 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
AATTATTATAATATAATATAAAATATTTTAA
Found at i:411557 original size:22 final size:21
Alignment explanation
Indices: 411532--411579 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
411522 AATAAAATTT
*
411532 ATATAAATATAAAATATTTTAA
1 ATATAAATATAAAATA-TTAAA
* *
411554 ATATAATTATAATATATTAAA
1 ATATAAATATAAAATATTAAA
411575 ATATA
1 ATATA
411580 TTATAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAAATATAAAATATTAAA
Found at i:411594 original size:20 final size:21
Alignment explanation
Indices: 411532--411591 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
411522 AATAAAATTT
* * *
411532 ATATAAATATAAAATATTTTAA
1 ATATAATTATAATATA-TTAAA
411554 ATATAATTATAATATATTAAA
1 ATATAATTATAATATATTAAA
411575 ATAT-ATTATAAATATAT
1 ATATAATTAT-AATATAT
411592 AAATTTTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.15
21 15 0.44
22 14 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAATTATAATATATTAAA
Found at i:412003 original size:18 final size:19
Alignment explanation
Indices: 411980--412017 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
411970 GCCCTGCCGG
411980 CCTTAACCCTAAT-CCAAC
1 CCTTAACCCTAATCCCAAC
411998 CCTTAACCCTAATCCCAAC
1 CCTTAACCCTAATCCCAAC
412017 C
1 C
412018 TCTGACTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (19 bp):
CCTTAACCCTAATCCCAAC
Found at i:417280 original size:18 final size:17
Alignment explanation
Indices: 417229--417268 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
417219 AATGGTTAAA
*
417229 AAATAATATAATTATCAAT
1 AAATATTATAATTAT--AT
417248 AAATATTATAATTATAT
1 AAATATTATAATTATAT
417265 AAAT
1 AAAT
417269 TATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
19 14 0.70
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTATAATTATAT
Found at i:417346 original size:38 final size:35
Alignment explanation
Indices: 417289--417358 Score: 88
Period size: 38 Copynumber: 1.9 Consensus size: 35
417279 ATTGTATAAA
417289 TTATTATAATTGATAATATAAATTAATATTACATATTT
1 TTATTATAATTGATAATAT--ATT-ATATTACATATTT
*
417327 TTATTATAATT-ATGCATATATTATATTACATA
1 TTATTATAATTGAT-AATATATTATATTACATA
417359 AATAGTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 10 0.33
36 3 0.10
37 2 0.07
38 15 0.50
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (35 bp):
TTATTATAATTGATAATATATTATATTACATATTT
Found at i:417931 original size:21 final size:19
Alignment explanation
Indices: 417889--417931 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
417879 ACTAGATTAC
* *
417889 ATATAAATATTATATAGTT
1 ATATAAATATCATATAGCT
417908 ATATAAAATATCATCATAGCT
1 ATAT-AAATATCAT-ATAGCT
417929 ATA
1 ATA
417932 ATGAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 8 0.40
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (19 bp):
ATATAAATATCATATAGCT
Found at i:418513 original size:35 final size:37
Alignment explanation
Indices: 418473--418552 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 37
418463 TTCATAGTTA
* *
418473 ATTATTTTATTTAAA-AT-AATAAAAAATATT-TTTAT
1 ATTATTATAATTAAATATAAAT-AAAAATATTATTTAT
*
418508 ATTATTATAATTAAATTTAAATAAAAATATTATTTAT
1 ATTATTATAATTAAATATAAATAAAAATATTATTTAT
*
418545 -TAATTATA
1 ATTATTATA
418553 TAATAGTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
35 13 0.34
36 17 0.45
37 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
ATTATTATAATTAAATATAAATAAAAATATTATTTAT
Found at i:418577 original size:22 final size:21
Alignment explanation
Indices: 418533--418579 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
418523 TTTAAATAAA
*
418533 AATATTATTTATTAATTATAT
1 AATATTATTTATTAATTACAT
418554 AATAGTTATTTA-TAATTAACAT
1 AATA-TTATTTATTAATT-ACAT
418576 AATA
1 AATA
418580 AAAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATTATTTATTAATTACAT
Found at i:420585 original size:2 final size:2
Alignment explanation
Indices: 420578--420605 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
420568 GGTGGTAGTA
420578 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
420606 AAACCCTTCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:429630 original size:3 final size:3
Alignment explanation
Indices: 429622--429652 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
429612 GCAAGCATTG
429622 TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
429653 GAAGCAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:439972 original size:20 final size:20
Alignment explanation
Indices: 439924--439964 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
439914 ACAACAAAGA
*
439924 AAGGATTTTCTAATTGGGTT
1 AAGGATTTTCTAATTGGCTT
439944 AAGGATTTTCTAATTGGCTT
1 AAGGATTTTCTAATTGGCTT
439964 A
1 A
439965 CCGGTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (20 bp):
AAGGATTTTCTAATTGGCTT
Found at i:440391 original size:32 final size:32
Alignment explanation
Indices: 440345--440441 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 32
440335 TTCTTATGGA
*
440345 AAAGCAGTGATTTTGCTGTCAGTTTTCTGTTT
1 AAAGAAGTGATTTTGCTGTCAGTTTTCTGTTT
*
440377 AAAGAAGTGATTTTGCTG-CGTGTTTTCTGTTT
1 AAAGAAGTGATTTTGCTGTC-AGTTTTCTGTTT
* * * *
440409 AAAGAAGTGACTTTCCTGTGAGGTTTCTGTTT
1 AAAGAAGTGATTTTGCTGTCAGTTTTCTGTTT
440441 A
1 A
440442 TAGCAGGAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 1 0.02
32 55 0.98
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.44
Consensus pattern (32 bp):
AAAGAAGTGATTTTGCTGTCAGTTTTCTGTTT
Found at i:443075 original size:37 final size:37
Alignment explanation
Indices: 443031--443105 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
443021 AATTGCAAAG
443031 CTATCCAATGAAGTAAGTATTTCCTTTTCAAATTGCA
1 CTATCCAATGAAGTAAGTATTTCCTTTTCAAATTGCA
443068 CTATCCAATGAAGTAAGTATTTCCTTTTCAAATTGCA
1 CTATCCAATGAAGTAAGTATTTCCTTTTCAAATTGCA
443105 C
1 C
443106 ATTCTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (37 bp):
CTATCCAATGAAGTAAGTATTTCCTTTTCAAATTGCA
Found at i:452531 original size:26 final size:29
Alignment explanation
Indices: 452502--452555 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
452492 TTTAAAAAGT
452502 TAAATT-AATATTA-A-TCATAAATTTGA
1 TAAATTAAATATTATACTCATAAATTTGA
452528 TAAATTAAATATTATTACTCATAAATTT
1 TAAATTAAATATTA-TACTCATAAATTT
452556 AATTACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.25
27 7 0.29
29 1 0.04
30 10 0.42
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (29 bp):
TAAATTAAATATTATACTCATAAATTTGA
Found at i:456556 original size:3 final size:3
Alignment explanation
Indices: 456548--456585 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
456538 ACTTATTACT
456548 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
456586 TTGGCTACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:458022 original size:27 final size:26
Alignment explanation
Indices: 457969--458022 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
457959 ATTATTATTT
* * *
457969 ATTTAATAAAAAATATTTATATTTAA
1 ATTTAATAAAAAATATATACATATAA
*
457995 ATTTAATTAAAAAGTATATACATATAA
1 ATTTAA-TAAAAAATATATACATATAA
458022 A
1 A
458023 AATATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
ATTTAATAAAAAATATATACATATAA
Found at i:458343 original size:71 final size:71
Alignment explanation
Indices: 458233--458372 Score: 219
Period size: 71 Copynumber: 2.0 Consensus size: 71
458223 ATAGAATTAT
* *
458233 TATTATTATTATAGGTCCTATAAGAAATGAGAAGTATGAGGTTTCAATGTAACTATAATTCCATC
1 TATTATTATTATA-GTCCTAAAAGAAATGAGAAGCATGAGGTTTCAATGTAACTATAATTCCATC
458298 CTCCTTA
65 CTCCTTA
* *
458305 TATTATTATTATCA-TCCTAAAATAAATGAGAAGCATGAGGTTTCAGTGTAACTATAATTCCATC
1 TATTATTATTAT-AGTCCTAAAAGAAATGAGAAGCATGAGGTTTCAATGTAACTATAATTCCATC
458369 CTCC
65 CTCC
458373 CTATCATCTA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
71 50 0.79
72 12 0.19
73 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (71 bp):
TATTATTATTATAGTCCTAAAAGAAATGAGAAGCATGAGGTTTCAATGTAACTATAATTCCATCC
TCCTTA
Found at i:458636 original size:2 final size:2
Alignment explanation
Indices: 458629--458658 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
458619 ATGATTCTGC
458629 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
458659 GTTAAATAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:469366 original size:16 final size:16
Alignment explanation
Indices: 469340--469427 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
469330 TTTGAATCAT
*
469340 TTTTAAATTTAAATTA
1 TTTTAATTTTAAATTA
*
469356 TTTTGATTTTAAGTATT-
1 TTTTAATTTTAA--ATTA
469373 TTTT-A-TTTAAATTA
1 TTTTAATTTTAAATTA
* *
469387 TTTTAATTTTGAATCA
1 TTTTAATTTTAAATTA
469403 TTTTAAATTTT-AATTA
1 TTTT-AATTTTAAATTA
*
469419 TTTAAATTT
1 TTTTAATTT
469428 AATATTTGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
13 3 0.05
14 4 0.07
15 11 0.18
16 29 0.48
17 10 0.17
18 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTAATTTTAAATTA
Found at i:469423 original size:31 final size:32
Alignment explanation
Indices: 469329--469427 Score: 121
Period size: 32 Copynumber: 3.1 Consensus size: 32
469319 GTATTTAAGT
*
469329 TTTTGAATCATTTTTAAATTTAAATTATTTTGA
1 TTTTGAATCA-TTTTAAATTTAAATTATTTTAA
**
469362 TTTT-AAGT-ATTTTTTATTTAAATTATTTTAA
1 TTTTGAA-TCATTTTAAATTTAAATTATTTTAA
* *
469393 TTTTGAATCATTTTAAATTTTAATTATTTAAA
1 TTTTGAATCATTTTAAATTTAAATTATTTTAA
469425 TTT
1 TTT
469428 AATATTTGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
31 24 0.43
32 27 0.48
33 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (32 bp):
TTTTGAATCATTTTAAATTTAAATTATTTTAA
Found at i:469994 original size:11 final size:11
Alignment explanation
Indices: 469960--470001 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 11
469950 AAATCTCGAT
469960 TTTAATTTGAAA
1 TTTAATTT-AAA
469972 TTTATGATTTAAA
1 TTTA--ATTTAAA
469985 TTTAATTTAAA
1 TTTAATTTAAA
469996 TTTAAT
1 TTTAAT
470002 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 13 0.46
12 4 0.14
13 7 0.25
14 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:470004 original size:20 final size:22
Alignment explanation
Indices: 469981--470031 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
469971 ATTTATGATT
469981 TAAATTTAATTT-AAATTT-AA
1 TAAATTTAATTTAAAATTTAAA
*
470001 TAAATTT-TTTTAAAATTTAAA
1 TAAATTTAATTTAAAATTTAAA
470022 TATAATTTAA
1 TA-AATTTAA
470032 AATAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 13 0.52
21 4 0.16
22 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAATTTAATTTAAAATTTAAA
Found at i:471054 original size:12 final size:13
Alignment explanation
Indices: 471011--471070 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 13
471001 ATTCAATTCA
471011 TTATTTAATATATAT
1 TTATTT-ATAT-TAT
*
471026 ATATATTATTATTAT
1 TTAT-TTA-TATTAT
471041 TTATTTAT-TTAT
1 TTATTTATATTAT
471053 TTATTTATATATAT
1 TTATTTATAT-TAT
471067 TTAT
1 TTAT
471071 AATTCAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 12 0.31
13 2 0.05
14 10 0.26
15 10 0.26
16 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTTATATTAT
Found at i:473359 original size:2 final size:2
Alignment explanation
Indices: 473352--473380 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
473342 GCTTTGAAAC
473352 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 A
473381 ACGTCTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:475273 original size:20 final size:20
Alignment explanation
Indices: 475233--475273 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
475223 TCTATATCAC
*
475233 TTTTTATTGTATTTTAATTA
1 TTTTTATTGTATTATAATTA
* *
475253 TTTTTTTTGTATTATATTTA
1 TTTTTATTGTATTATAATTA
475273 T
1 T
475274 AATGTCTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTTATTGTATTATAATTA
Found at i:483507 original size:26 final size:26
Alignment explanation
Indices: 483471--483523 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
483461 ACCAAGCAAT
*
483471 CAACCACCTTCGATATGTGAGTCTAG
1 CAACCACCTTCAATATGTGAGTCTAG
483497 CAACCACCTTCAATATGTGAGTCTAG
1 CAACCACCTTCAATATGTGAGTCTAG
483523 C
1 C
483524 TCCAACAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (26 bp):
CAACCACCTTCAATATGTGAGTCTAG
Found at i:489763 original size:2 final size:2
Alignment explanation
Indices: 489756--489780 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
489746 ATGTAACCAA
489756 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
489781 GTAATTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.