Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 3 of 27
Found at i:238193 original size:3 final size:3
Alignment explanation
Indices: 238185--238217 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
238175 ACTCTTTGAT
238185 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
238218 ACTTAACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:239167 original size:41 final size:40
Alignment explanation
Indices: 239091--239168 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
239081 AAAAATATAA
*
239091 TAATTAATATTTTAATTTATTAATATAAAATTTTCAAACT
1 TAATTAATATTTTAATTTATTAATATAAAAATTTCAAACT
*
239131 TAATTAATA-TTT-ATTTTTTATATTATTAAAAATTTCAA
1 TAATTAATATTTTAATTTATTA-A-TA-TAAAAATTTCAA
239169 TAAAAAACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
38 7 0.21
39 4 0.12
40 11 0.33
41 11 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (40 bp):
TAATTAATATTTTAATTTATTAATATAAAAATTTCAAACT
Found at i:239593 original size:16 final size:15
Alignment explanation
Indices: 239555--239593 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
239545 TATAAAATTA
*
239555 ATTTAATTTATTTTT
1 ATTTGATTTATTTTT
*
239570 ATTAGATTTATTTTTT
1 ATTTGATTTA-TTTTT
239586 ATTTGATT
1 ATTTGATT
239594 ATATGAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (15 bp):
ATTTGATTTATTTTT
Found at i:239595 original size:15 final size:16
Alignment explanation
Indices: 239560--239593 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
239550 AATTAATTTA
239560 ATTTA-TTTTTATTAG
1 ATTTATTTTTTATTAG
*
239575 ATTTATTTTTTATTTG
1 ATTTATTTTTTATTAG
239591 ATT
1 ATT
239594 ATATGAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
ATTTATTTTTTATTAG
Found at i:240081 original size:70 final size:67
Alignment explanation
Indices: 240006--240139 Score: 189
Period size: 70 Copynumber: 2.0 Consensus size: 67
239996 TTAAATTTTT
* *
240006 TTATTTTTA-TAAAAACATAATAATTAATATTTTAATTTATTAATGTAAATTTTTTAAACTTAAT
1 TTATTTTTAGTAAAAA-ATAATAATTAATATATT-A-TTATTAAT-TAAAATTTTTAAACTTAAT
240070 TAAATA
62 TAAATA
* *
240076 TTATTTTTAGTAAAAAATAATAATTAATATATTATTATTTATTAAAATTTTTAAATTTAATTAA
1 TTATTTTTAGTAAAAAATAATAATTAATATATTATTATTAATTAAAATTTTTAAACTTAATTAA
240140 TTTATAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 20 0.34
68 7 0.12
69 1 0.02
70 25 0.42
71 6 0.10
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (67 bp):
TTATTTTTAGTAAAAAATAATAATTAATATATTATTATTAATTAAAATTTTTAAACTTAATTAAA
TA
Found at i:240104 original size:125 final size:122
Alignment explanation
Indices: 239865--240104 Score: 340
Period size: 125 Copynumber: 1.9 Consensus size: 122
239855 ATTTTTTAGG
*
239865 TTTTTAATTTAAAATTTTTTATTTTAAAAAACATAATTATTAATATTTTAATTTATTAATATAAA
1 TTTTTAATTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTATTAATATAAA
* ** *
239930 TTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATTATAATAAAAACCTT
66 TTTTTAAACTTAATTAAATATTATTTTTTA-TGTAAAAAAAATAATAATAAAAACCTT
* * *
239988 TTTTTATTTTAAATTTTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTATTAATGTA
1 TTTTTAATTTAAAATTTTTTA-TTTTA-AAAAACATAATAATTAATATTTTAATTTATTAATATA
240053 AATTTTTTAAACTTAATTAAATATTA-TTTTTA-GTAAAAAATAATAATTAATA
64 AA-TTTTTAAACTTAATTAAATATTATTTTTTATGTAAAAAA-AATAA-TAATA
240105 TATTATTATT
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
123 24 0.23
124 9 0.09
125 48 0.46
126 23 0.22
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (122 bp):
TTTTTAATTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTATTAATATAAA
TTTTTAAACTTAATTAAATATTATTTTTTATGTAAAAAAAATAATAATAAAAACCTT
Found at i:240467 original size:29 final size:30
Alignment explanation
Indices: 240413--240470 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
240403 TAAATTTAAA
*
240413 AAATTAATTTTATTATTTATAAAATATTAT
1 AAATTAATTTTATTATTAATAAAATATTAT
*
240443 AAATT-ATTTTA-TATTAATATTAATATTA
1 AAATTAATTTTATTATTAATA-AAATATTA
240471 ATATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.28
29 13 0.52
30 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
AAATTAATTTTATTATTAATAAAATATTAT
Found at i:240492 original size:27 final size:28
Alignment explanation
Indices: 240434--240517 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
240424 ATTATTTATA
*
240434 AAATATT--ATAAATTA-TTTTAT-ATT
1 AAATATTAAATAAAATATTTTTATAATT
*
240458 -AATATT-AATATTAATATTTTTATAATT
1 AAATATTAAATA-AAATATTTTTATAATT
240485 AAAT-TTAAATAAAATATTTTTATTAATT
1 AAATATTAAATAAAATATTTTTA-TAATT
240513 AAATA
1 AAATA
240518 ATAATTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
23 6 0.12
24 3 0.06
25 3 0.06
26 6 0.12
27 15 0.31
28 16 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATATTAAATAAAATATTTTTATAATT
Found at i:241080 original size:5 final size:5
Alignment explanation
Indices: 241072--241096 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
241062 ACTTCGACGT
241072 GGATG GGATG GGATG GGATG GGATG
1 GGATG GGATG GGATG GGATG GGATG
241097 AAGGAAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (5 bp):
GGATG
Found at i:241298 original size:16 final size:16
Alignment explanation
Indices: 241251--241307 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
241241 AATGTGAAGA
*
241251 ATTAAAATGTAAAAAAA
1 ATTAAAATGT-AAAAAT
*
241268 ATTAAAAT-AATAAAAT
1 ATTAAAATGTA-AAAAT
*
241284 TTTAAAATGTAAAAAT
1 ATTAAAATGTAAAAAT
*
241300 AATAAAAT
1 ATTAAAAT
241308 TATTTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 1 0.03
16 22 0.69
17 9 0.28
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (16 bp):
ATTAAAATGTAAAAAT
Found at i:241591 original size:19 final size:19
Alignment explanation
Indices: 241567--241642 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 19
241557 AATATTTAAA
*
241567 AAATTTAAATAA-AAATATT
1 AAATTTAAAAAATAAAT-TT
241586 AAATTTAAAAAATAAATTT
1 AAATTTAAAAAATAAATTT
*
241605 AAA--TAAAAAATAAAATT
1 AAATTTAAAAAATAAATTT
* *
241622 -CATTTAAAATATAAA-TT
1 AAATTTAAAAAATAAATTT
241639 AAAT
1 AAAT
241643 ATTGGCTCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.02
17 15 0.31
18 12 0.25
19 16 0.33
20 4 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATTTAAAAAATAAATTT
Found at i:241629 original size:18 final size:18
Alignment explanation
Indices: 241588--241636 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
241578 AAAATATTAA
*
241588 ATTTAAAAAAT-AAATTT
1 ATTTAAAAAATAAAATTC
**
241605 AAATAAAAAATAAAATTC
1 ATTTAAAAAATAAAATTC
*
241623 ATTTAAAATATAAA
1 ATTTAAAAAATAAA
241637 TTAAATATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTTAAAAAATAAAATTC
Found at i:241719 original size:22 final size:20
Alignment explanation
Indices: 241680--241722 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
241670 TGTTTTTAAC
241680 TATATAATATATATTAATTT
1 TATATAATATATATTAATTT
*
241700 TATATTATATATTATGTAATTT
1 TATATAATATA-TAT-TAATTT
241722 T
1 T
241723 CAATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 3 0.15
22 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATATAATATATATTAATTT
Found at i:246517 original size:19 final size:20
Alignment explanation
Indices: 246475--246545 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 20
246465 AATAAATAGG
246475 TAAT-TTATATTATATAAAT
1 TAATATTATATTATATAAAT
*
246494 T--TATTATATT-TATATAT
1 TAATATTATATTATATAAAT
*
246511 TAATATTATA--AGT-GAAAT
1 TAATATTATATTA-TATAAAT
*
246529 TAATATAATATTATATA
1 TAATATTATATTATATA
246546 TTATTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 15
0.66 0.08 0.25
Matches are distributed among these distances:
17 8 0.21
18 19 0.49
19 10 0.26
20 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TAATATTATATTATATAAAT
Found at i:247749 original size:20 final size:20
Alignment explanation
Indices: 247724--247767 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
247714 ATACCTCGAA
247724 ACACTTCCTCCTTGGTCACT
1 ACACTTCCTCCTTGGTCACT
247744 ACACTTCCTCCTTGGTCACT
1 ACACTTCCTCCTTGGTCACT
247764 ACAC
1 ACAC
247768 AACTCCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.41, G:0.09, T:0.32
Consensus pattern (20 bp):
ACACTTCCTCCTTGGTCACT
Found at i:255552 original size:102 final size:103
Alignment explanation
Indices: 255441--255707 Score: 310
Period size: 91 Copynumber: 2.7 Consensus size: 103
255431 AATGAGCCAA
*
255441 TGGATAACAAATAATTTTGACAAAAAAGGAGTTCAAATCTTGATAAATTTTGAAGAGCGGGGTTG
1 TGGATAACAAATAATTTTGACAAAAAAGGAGTTCAAATCTAGATAAATTTTGAAGAGCGGGGTTG
* *
255506 GAGTATTCC-CTCCAAAGGTTAAGGTTGGAGTATCCCC-
66 GAGTA-TCCTCTCAAAAGGTCAAGGTTGGAGTATCCCCT
* * *
255543 TGGATAACAAATAATTTT-----AACA--A----AAATCTAGATAAATTTTGAAAAGCGGGGTTA
1 TGGATAACAAATAATTTTGACAAAAAAGGAGTTCAAATCTAGATAAATTTTGAAGAGCGGGGTTG
* *
255597 GAGTATCCTTTCAAAAGGTCGAGGTTGGAGTATCCCCT
66 GAGTATCCTCTCAAAAGGTCAAGGTTGGAGTATCCCCT
* * * *
255635 TTGATAACAAATAATTTTGACAAAAGAGGAGTTCAAATCTAGATAAATTTTGAAGACCGAGGTT-
1 TGGATAACAAATAATTTTGACAAAAAAGGAGTTCAAATCTAGATAAATTTTGAAGAGCGGGGTTG
255699 GAGGTATCC
66 GA-GTATCC
255708 CTTCGAAAGG
Statistics
Matches: 138, Mismatches: 13, Indels: 27
0.78 0.07 0.15
Matches are distributed among these distances:
90 3 0.02
91 57 0.41
92 17 0.12
95 1 0.01
97 6 0.04
99 1 0.01
102 20 0.14
103 33 0.24
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (103 bp):
TGGATAACAAATAATTTTGACAAAAAAGGAGTTCAAATCTAGATAAATTTTGAAGAGCGGGGTTG
GAGTATCCTCTCAAAAGGTCAAGGTTGGAGTATCCCCT
Found at i:260679 original size:11 final size:11
Alignment explanation
Indices: 260663--260690 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
260653 ATTCTTAAAA
260663 AAAAGAGAAAG
1 AAAAGAGAAAG
260674 AAAAGAGAAAG
1 AAAAGAGAAAG
260685 AAAAGA
1 AAAAGA
260691 AAAAATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:263293 original size:21 final size:19
Alignment explanation
Indices: 263249--263294 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
263239 ATCAATTAAC
* *
263249 TATTTATTATATAAGTATT
1 TATTTATTATATAAATAAT
263268 TATTTATTATATTAAATAAAT
1 TATTTATTATA-TAAAT-AAT
263289 TATTTA
1 TATTTA
263295 AATTATTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 4 0.17
21 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTTATTATATAAATAAT
Found at i:263641 original size:14 final size:15
Alignment explanation
Indices: 263624--263662 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
263614 TCTTAAATTT
263624 TATTTTTTTACAA-A
1 TATTTTTTTACAATA
*
263638 TA-TTTTTTAAAATA
1 TATTTTTTTACAATA
263652 TATTTTTTTAC
1 TATTTTTTTAC
263663 GTTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 9 0.43
14 5 0.24
15 7 0.33
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTTTTACAATA
Found at i:263747 original size:43 final size:42
Alignment explanation
Indices: 263699--263789 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 42
263689 AATATTGATG
* * *
263699 AAAAATCATTACTTAAAAT-AGTAATTTATTCATTACTTAATTA
1 AAAAATCATCACTTAAAATGA-TAATTT-TTCAATAATTAATTA
*
263742 AAAAATCATCATTTAAAATGATAATTTTTCAATAATTAATTA
1 AAAAATCATCACTTAAAATGATAATTTTTCAATAATTAATTA
*
263784 AGAAAT
1 AAAAAT
263790 TATCGTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 18 0.43
43 23 0.55
44 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (42 bp):
AAAAATCATCACTTAAAATGATAATTTTTCAATAATTAATTA
Found at i:263782 original size:42 final size:43
Alignment explanation
Indices: 263699--263810 Score: 129
Period size: 42 Copynumber: 2.6 Consensus size: 43
263689 AATATTGATG
* * * *
263699 AAAAATCATTACTTAAAATAGTAATTTATTCATTACTTAATTA
1 AAAAATCATCATTTAAAATAGTAATTTATTCAATAATTAATTA
263742 AAAAATCATCATTTAAAAT-GATAATTT-TTCAATAATTAATTA
1 AAAAATCATCATTTAAAATAG-TAATTTATTCAATAATTAATTA
* * * *
263784 AGAAATTATCGTTTAAAATAGTTATTT
1 AAAAATCATCATTTAAAATAGTAATTT
263811 CTTTATAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 35 0.59
43 24 0.41
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (43 bp):
AAAAATCATCATTTAAAATAGTAATTTATTCAATAATTAATTA
Found at i:263878 original size:10 final size:10
Alignment explanation
Indices: 263865--263899 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
263855 AATTTTTAAA
263865 AAATAAATTT
1 AAATAAATTT
263875 AAATAAATTT
1 AAATAAATTT
*
263885 AAAAAAATATT
1 AAATAAAT-TT
263896 AAAT
1 AAAT
263900 TATCGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATAAATTT
Found at i:264352 original size:72 final size:71
Alignment explanation
Indices: 264261--264480 Score: 266
Period size: 72 Copynumber: 3.1 Consensus size: 71
264251 TTTATAAAAA
* * ** *
264261 TATTTTTAGATATAATTATAAGAGTTTAAATTTTATAAAATATGATTTATTTTTATTTGTAGAAG
1 TATTTTTA-ATTTGATTATAAGAGTTTAAATTTTATAAGGTATGATTTATTTTTATTTGTAGAAA
264326 TTTAAATT
65 TTT-AATT
* * *
264334 TATTTTTAATTTGATTATACGAGTTTACATTTT-TATGGTATGATTTATTTTTATTTGTAGAAAT
1 TATTTTTAATTTGATTATAAGAGTTTAAATTTTATAAGGTATGATTTATTTTTATTTGTAGAAAT
264398 TTAATT
66 TTAATT
* ** * *
264404 TGTTTTTAGGTTGATTATAAGAGTTTAAATTATATTAAGGTATGATTTATTTTTATTTATA-AAA
1 TATTTTTAATTTGATTATAAGAGTTTAAATTTTA-TAAGGTATGATTTATTTTTATTTGTAGAAA
264468 -TTAATT
65 TTTAATT
264474 TGATTTT
1 T-ATTTT
264481 ATGGATATTT
Statistics
Matches: 127, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
70 38 0.30
71 36 0.28
72 45 0.35
73 8 0.06
ACGTcount: A:0.33, C:0.01, G:0.11, T:0.55
Consensus pattern (71 bp):
TATTTTTAATTTGATTATAAGAGTTTAAATTTTATAAGGTATGATTTATTTTTATTTGTAGAAAT
TTAATT
Found at i:264472 original size:70 final size:70
Alignment explanation
Indices: 264275--264481 Score: 249
Period size: 70 Copynumber: 2.9 Consensus size: 70
264265 TTTAGATATA
** * *
264275 ATTATAAGAGTTTAAATTT-TATAAAATATGATTTATTTTTATTTGTAGAAGTTTAAATTTATTT
1 ATTATAAGAGTTTAAATTTAT-TAAGGTATGATTTATTTTTATTTGTAGAA-ATT-AATTTGTTT
*
264339 TTAATTTG
63 TTAAGTTG
* * *
264347 ATTATACGAGTTTACATTT-TTATGGTATGATTTATTTTTATTTGTAGAAATTTAATTTGTTTTT
1 ATTATAAGAGTTTAAATTTATTAAGGTATGATTTATTTTTATTTGTAGAAA-TTAATTTGTTTTT
*
264411 AGGTTG
65 AAGTTG
* *
264417 ATTATAAGAGTTTAAATTATATTAAGGTATGATTTATTTTTATTTATA-AAATTAATTTGATTTT
1 ATTATAAGAGTTTAAATT-TATTAAGGTATGATTTATTTTTATTTGTAGAAATTAATTTGTTTTT
264481 A
65 A
264482 TGGATATTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
70 43 0.36
71 32 0.27
72 43 0.36
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (70 bp):
ATTATAAGAGTTTAAATTTATTAAGGTATGATTTATTTTTATTTGTAGAAATTAATTTGTTTTTA
AGTTG
Found at i:264566 original size:24 final size:23
Alignment explanation
Indices: 264522--264572 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
264512 AGTTTGATTC
* *
264522 TATTAGTGTATTTTTATTG-AAA
1 TATTAGTGTATTTTAAATGAAAA
264544 TATTAGGTAGTATTTTAAATGAAAA
1 TATTA-GT-GTATTTTAAATGAAAA
264569 TATT
1 TATT
264573 TTTTATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 2 0.08
24 10 0.42
25 7 0.29
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (23 bp):
TATTAGTGTATTTTAAATGAAAA
Found at i:265060 original size:24 final size:21
Alignment explanation
Indices: 265016--265059 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
265006 GAAAATAATG
*
265016 ATAATAATATAATTAGTTATT
1 ATAATAATAAAATTAGTTATT
265037 ATAATAATAAAATTAAG-TATT
1 ATAATAATAAAATT-AGTTATT
265058 AT
1 AT
265060 TGTCTCGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
ATAATAATAAAATTAGTTATT
Found at i:265446 original size:16 final size:17
Alignment explanation
Indices: 265427--265460 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
265417 AAAACTTTTT
265427 AAATGA-AAAATTAAAA
1 AAATGACAAAATTAAAA
265443 AAATGACAAAATTAAAA
1 AAATGACAAAATTAAAA
265460 A
1 A
265461 GATAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
AAATGACAAAATTAAAA
Found at i:265475 original size:18 final size:17
Alignment explanation
Indices: 265432--265488 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
265422 TTTTTAAATG
* *
265432 AAAAATTAAAAAAATGA
1 AAAAATTAAAAAGATAA
*
265449 CAAAATTAAAAAGATAA
1 AAAAATTAAAAAGATAA
265466 AAAAATTTAAAAAGATAA
1 AAAAA-TTAAAAAGATAA
265484 AAAAA
1 AAAAA
265489 AAGGTCCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
17 18 0.51
18 17 0.49
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAAATTAAAAAGATAA
Found at i:265730 original size:11 final size:11
Alignment explanation
Indices: 265703--265743 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
265693 TATAATAAAA
265703 TATATTTAATTT
1 TATA-TTAATTT
265715 T-TATTAATTT
1 TATATTAATTT
*
265725 TATATTATTTT
1 TATATTAATTT
265736 TATATTAA
1 TATATTAA
265744 AATTGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 8 0.31
11 17 0.65
12 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTAATTT
Found at i:266233 original size:28 final size:31
Alignment explanation
Indices: 266202--266265 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 31
266192 AAACATGTAC
266202 ATATTTTA-TTAAT-TATAAAA-TATATTT-A
1 ATATTTTATTTAATAT-TAAAATTATATTTAA
*
266230 ATA-TTTATTTAATATTAAAATTATTTTTAA
1 ATATTTTATTTAATATTAAAATTATATTTAA
266260 ATATTT
1 ATATTT
266266 AAAAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 4 0.13
28 13 0.43
29 7 0.23
30 4 0.13
31 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
ATATTTTATTTAATATTAAAATTATATTTAA
Found at i:266254 original size:20 final size:20
Alignment explanation
Indices: 266223--266269 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
266213 ATTATAAAAT
* *
266223 ATATTTAATATT-TATTT-A
1 ATATTTAAAATTATTTTTAA
266241 ATA-TTAAAATTATTTTTAA
1 ATATTTAAAATTATTTTTAA
266260 ATATTTAAAA
1 ATATTTAAAA
266270 AATTTATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 4 0.17
20 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTTAAAATTATTTTTAA
Found at i:267412 original size:22 final size:21
Alignment explanation
Indices: 267384--267429 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
267374 TAATTAAATA
267384 ATAAATAAATTTAAAATAAT-TT
1 ATAAATAAA-TTAAAA-AATATT
267406 ATAAATAAATTAAAAAATATT
1 ATAAATAAATTAAAAAATATT
267427 ATA
1 ATA
267430 TTTATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.13
21 11 0.48
22 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAATAAATTAAAAAATATT
Found at i:271396 original size:2 final size:2
Alignment explanation
Indices: 271389--271430 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
271379 TACCAAGATG
271389 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
271431 CTGTTTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273363 original size:28 final size:28
Alignment explanation
Indices: 273332--273388 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
273322 TTATATTAAA
273332 TTAATATCATTTAA-TTCAAAATATCAAT
1 TTAATATCATTTAACTT-AAAATATCAAT
*
273360 TTAATATCATTTAACTTAAAATATTAAT
1 TTAATATCATTTAACTTAAAATATCAAT
273388 T
1 T
273389 CTATTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (28 bp):
TTAATATCATTTAACTTAAAATATCAAT
Found at i:274158 original size:18 final size:18
Alignment explanation
Indices: 274117--274159 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
274107 TTATTTTTTA
* *
274117 AAATTTAATAAAATTAAT
1 AAATTAAATAAAAATAAT
* *
274135 ATATTAAATAAAAATATT
1 AAATTAAATAAAAATAAT
274153 AAATTAA
1 AAATTAA
274160 TAATTATATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTAAATAAAAATAAT
Found at i:275586 original size:2 final size:2
Alignment explanation
Indices: 275579--275606 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
275569 CAAAATTCAT
275579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
275607 CACACACACA
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):
TA
Found at i:276325 original size:3 final size:3
Alignment explanation
Indices: 276319--276373 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
276309 TATTATCATT
276319 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
276367 ATA ATA A
1 ATA ATA A
276374 ATAAAACCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:276491 original size:3 final size:3
Alignment explanation
Indices: 276485--276514 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
276475 TTACTACTAC
276485 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
276515 CAATGTTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:276720 original size:25 final size:23
Alignment explanation
Indices: 276684--276730 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
276674 TTATGTATGA
276684 AATATAATTTTTTTAAAAAAAAT
1 AATATAATTTTTTTAAAAAAAAT
*
276707 AATATATATATTTTTTTAAAAAAA
1 AATATA-AT-TTTTTTAAAAAAAA
276731 GAAAAAGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 2 0.10
25 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATATAATTTTTTTAAAAAAAAT
Found at i:276984 original size:8 final size:8
Alignment explanation
Indices: 276971--277023 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
276961 AGTGAATGTT
276971 TATATTTA
1 TATATTTA
276979 TATATTT-
1 TATATTTA
276986 TATATATTA
1 TATAT-TTA
276995 TTATATTTA
1 -TATATTTA
*
277004 -AAATATTA
1 TATAT-TTA
277012 TATATTTA
1 TATATTTA
277020 TATA
1 TATA
277024 ATTTTTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 8 0.21
8 19 0.50
9 6 0.16
10 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATATTTA
Found at i:276993 original size:17 final size:16
Alignment explanation
Indices: 276969--277023 Score: 69
Period size: 17 Copynumber: 3.5 Consensus size: 16
276959 TCAGTGAATG
276969 TTTATAT-TTATATAT
1 TTTATATATTATATAT
276984 TTTATATATTATTATAT
1 TTTATATATTA-TATAT
* *
277001 TTAAAATATTATATA-
1 TTTATATATTATATAT
277016 TTTATATA
1 TTTATATA
277024 ATTTTTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 13 0.38
16 7 0.21
17 14 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATATATTATATAT
Found at i:277020 original size:25 final size:26
Alignment explanation
Indices: 276970--277038 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 26
276960 CAGTGAATGT
*
276970 TTATATTT-ATATATTTTATATATTA
1 TTATATTTAATATATTATATATATTA
*
276995 TTATATTTAAAATATTATATAT-TTA
1 TTATATTTAATATATTATATATATTA
*
277020 TATAATTTTTAATATATTA
1 T-T-ATATTTAATATATTA
277039 ATAAATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.32
26 12 0.32
27 13 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATATTTAATATATTATATATATTA
Found at i:277050 original size:20 final size:20
Alignment explanation
Indices: 277011--277048 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
277001 TTAAAATATT
*
277011 ATATATTTATATAATTTTTA
1 ATATATTAATATAATTTTTA
277031 ATATATTAATA-AATTTTT
1 ATATATTAATATAATTTTT
277049 TATGTAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATATTAATATAATTTTTA
Found at i:279416 original size:23 final size:21
Alignment explanation
Indices: 279382--279423 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
279372 ATAATGAATC
279382 AAATTAGATCAAAATATCAATT
1 AAATTAGATC-AAATATCAATT
*
279404 AAATTTGACTCAAATATCAA
1 AAATTAGA-TCAAATATCAA
279424 ATATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (21 bp):
AAATTAGATCAAATATCAATT
Found at i:287327 original size:33 final size:33
Alignment explanation
Indices: 287285--287350 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
287275 CTCAAGGTAA
287285 GCAATACTATATCGAAGAGCACATTGTTTTTAT
1 GCAATACTATATCGAAGAGCACATTGTTTTTAT
*
287318 GCAATACTATATCGAAGAGCATATTGTTTTTAT
1 GCAATACTATATCGAAGAGCACATTGTTTTTAT
287351 TTTGGTATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (33 bp):
GCAATACTATATCGAAGAGCACATTGTTTTTAT
Found at i:290699 original size:2 final size:2
Alignment explanation
Indices: 290692--290726 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
290682 CAAAACTCAG
* *
290692 AT AT AT AT AT AT AT AT AT AT GT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
290727 GATAGATAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:292467 original size:20 final size:20
Alignment explanation
Indices: 292429--292467 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
292419 TTATATTTTA
*
292429 TATTATAATTACATTTAAAT
1 TATTATAATTACATATAAAT
* *
292449 TATTATATTTATATATAAA
1 TATTATAATTACATATAAA
292468 ATTTAACTCA
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTACATATAAAT
Found at i:292682 original size:16 final size:18
Alignment explanation
Indices: 292653--292691 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
292643 GAGTAAGCTG
292653 AAAA-AAATTATATTT-T
1 AAAATAAATTATATTTGT
292669 AAAATAAATT-TATTTGT
1 AAAATAAATTATATTTGT
292686 AAAATA
1 AAAATA
292692 TAAGATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AAAATAAATTATATTTGT
Found at i:292948 original size:23 final size:23
Alignment explanation
Indices: 292918--292998 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 23
292908 AATTTATATA
292918 ATATTTATATATTTTATATTTTT
1 ATATTTATATATTTTATATTTTT
*
292941 ATATTTATATCATATTTATTTTGTGTTGT
1 ATATTTATAT-AT-TTTA-TAT-T-TT-T
* *
292970 ATATTAATTTATTTT-TA-TTTT
1 ATATTTATATATTTTATATTTTT
292991 ATATTTAT
1 ATATTTAT
292999 GTTATTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
21 8 0.17
22 2 0.04
23 11 0.23
24 2 0.04
25 5 0.11
26 2 0.04
27 4 0.09
28 4 0.09
29 9 0.19
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (23 bp):
ATATTTATATATTTTATATTTTT
Found at i:292979 original size:22 final size:21
Alignment explanation
Indices: 292934--293007 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
292924 ATATATTTTA
* *
292934 TATTTTTATATTTATATCATATT
1 TATTTTTAT-TGTATATTA-ATT
*
292957 TATTTTGTGTTGTATATTAATT
1 TATTTT-TATTGTATATTAATT
* *
292979 TATTTTTATTTTATATTTATGT
1 TATTTTTATTGTATATTAAT-T
293001 TATTTTT
1 TATTTTT
293008 TATATATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 11 0.26
22 17 0.40
23 13 0.30
24 2 0.05
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.69
Consensus pattern (21 bp):
TATTTTTATTGTATATTAATT
Found at i:293007 original size:23 final size:22
Alignment explanation
Indices: 292953--293010 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
292943 ATTTATATCA
* * *
292953 TATTTATTTTGTGTTGTATATT
1 TATTTATTTTTTATTTTATATT
*
292975 AATTTA-TTTTTATTTTATATT
1 TATTTATTTTTTATTTTATATT
292996 TATGTTATTTTTTAT
1 TAT-TTATTTTTTAT
293011 ATATTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.48
22 8 0.28
23 7 0.24
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (22 bp):
TATTTATTTTTTATTTTATATT
Found at i:293017 original size:37 final size:37
Alignment explanation
Indices: 292909--293017 Score: 89
Period size: 39 Copynumber: 3.0 Consensus size: 37
292899 AGTATTATGA
* * *
292909 ATTTATATAATATTTA---TATATTTTATATTTTTAT
1 ATTTATATCATATTTATGTTATGTTTTATATATTTAT
* * *
292943 ATTTATATCATATTTATTTTGTGTTGTATATTAATTTAT
1 ATTTATATCATATTTATGTTATGTTTTATA-T-ATTTAT
* * * *
292982 TTTTATTTTATATTTATGTTATTTTTTATATATTTA
1 ATTTATATCATATTTATGTTATGTTTTATATATTTA
293018 AAATATTAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
34 15 0.26
37 13 0.22
38 2 0.03
39 28 0.48
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (37 bp):
ATTTATATCATATTTATGTTATGTTTTATATATTTAT
Found at i:293544 original size:20 final size:20
Alignment explanation
Indices: 293493--293552 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
293483 GGCGTTGAAT
*
293493 TGAGAGAGAAATAAAGAAAGGA
1 TGAGAGAGAAAGAAAGAAA--A
*
293515 TGA-A-AAAAAGAAAGAAAA
1 TGAGAGAGAAAGAAAGAAAA
293533 TGAGAGAGAAAGAAAGAAAA
1 TGAGAGAGAAAGAAAGAAAA
293553 AATTTTTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 24 0.73
21 1 0.03
22 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (20 bp):
TGAGAGAGAAAGAAAGAAAA
Found at i:294798 original size:35 final size:33
Alignment explanation
Indices: 294751--294820 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
294741 AAAATTTATT
*
294751 TTTAATTTTAAATATATAATTATTATTTAATAA-AA
1 TTTAATTATAAAT-TA-AATTATTA-TTAATAATAA
*
294786 TTTAATTATAAATTAAATTTTTATTAATAATAA
1 TTTAATTATAAATTAAATTATTATTAATAATAA
294819 TT
1 TT
294821 AAAATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 7 0.22
33 11 0.34
34 2 0.06
35 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTTAATTATAAATTAAATTATTATTAATAATAA
Found at i:294830 original size:35 final size:34
Alignment explanation
Indices: 294754--294837 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 34
294744 ATTTATTTTT
*
294754 AATTT-TAAATATATAATTATTATTTAATAAAATTT
1 AATTTATAAAT-TA-AATTATTATTTAATAAAATTA
*
294789 AA-TTATAAATTAAATTTTTA-TTAATAATAATTAA
1 AATTTATAAATTAAATTATTATTTAATAA-AATT-A
*
294823 AATTTATAAAATAAA
1 AATTTATAAATTAAA
294838 AATAAAAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
32 7 0.17
33 11 0.26
34 6 0.14
35 18 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
AATTTATAAATTAAATTATTATTTAATAAAATTA
Found at i:295380 original size:18 final size:16
Alignment explanation
Indices: 295344--295374 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
295334 GTTAATTTTT
295344 TTTAAAAAAAATTATA
1 TTTAAAAAAAATTATA
*
295360 TTTAAATAAAATTAT
1 TTTAAAAAAAATTAT
295375 GTATTTTTTA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAAAAAATTATA
Found at i:295557 original size:23 final size:24
Alignment explanation
Indices: 295527--295574 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
295517 ATTTTATGTT
*
295527 TAATTTTT-TAATAATATATT-AAA
1 TAATTTTTATAA-AATAAATTCAAA
295550 TAATTTTTATAAAATAAATTCAAA
1 TAATTTTTATAAAATAAATTCAAA
295574 T
1 T
295575 CTTATAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTTTTATAAAATAAATTCAAA
Found at i:295902 original size:106 final size:106
Alignment explanation
Indices: 295717--295929 Score: 417
Period size: 106 Copynumber: 2.0 Consensus size: 106
295707 CAGAAAAGAT
295717 TTTCATGTTGTCTTCCCCTGCTTCGTACGCATACTGTCTTTCCCATTGGCCTTCTCTCTCTGTCT
1 TTTCATGTTGTCTTCCCCTGCTTCGTACGCATACTGTCTTTCCCATTGGCCTTCTCTCTCTGTCT
295782 GCTTTCTCTGTAAGCTCACAGATCTCTCTCTTAAGCTCGAA
66 GCTTTCTCTGTAAGCTCACAGATCTCTCTCTTAAGCTCGAA
*
295823 TTTCATGTTGTCTTCCCCTGCTTCGTACGCATACTGTCTTTCCCTTTGGCCTTCTCTCTCTGTCT
1 TTTCATGTTGTCTTCCCCTGCTTCGTACGCATACTGTCTTTCCCATTGGCCTTCTCTCTCTGTCT
295888 GCTTTCTCTGTAAGCTCACAGATCTCTCTCTTAAGCTCGAA
66 GCTTTCTCTGTAAGCTCACAGATCTCTCTCTTAAGCTCGAA
295929 T
1 T
295930 CACTCACGAA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.13, C:0.32, G:0.14, T:0.41
Consensus pattern (106 bp):
TTTCATGTTGTCTTCCCCTGCTTCGTACGCATACTGTCTTTCCCATTGGCCTTCTCTCTCTGTCT
GCTTTCTCTGTAAGCTCACAGATCTCTCTCTTAAGCTCGAA
Found at i:299434 original size:25 final size:25
Alignment explanation
Indices: 299405--299456 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
299395 TTAGATCCAT
299405 ATCTTTCCTATTTTAATCAATAAAG
1 ATCTTTCCTATTTTAATCAATAAAG
*
299430 ATCTTTTCTATTTTAATCAATAAAG
1 ATCTTTCCTATTTTAATCAATAAAG
299455 AT
1 AT
299457 AATGATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (25 bp):
ATCTTTCCTATTTTAATCAATAAAG
Found at i:301503 original size:13 final size:14
Alignment explanation
Indices: 301487--301534 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 14
301477 TAATCTTTTA
301487 ATATTTAAAAATA-
1 ATATTTAAAAATAT
301500 ATA-TTAAAAATTAT
1 ATATTTAAAAA-TAT
*
301514 ATCATTTAATAATAT
1 AT-ATTTAAAAATAT
301529 ATATTT
1 ATATTT
301535 TTATTAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.23
13 5 0.17
14 6 0.20
15 6 0.20
16 6 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATTTAAAAATAT
Found at i:301555 original size:16 final size:16
Alignment explanation
Indices: 301536--301566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
301526 TATATATTTT
301536 TATTAAATATTTATTA
1 TATTAAATATTTATTA
*
301552 TATTTAATATTTATT
1 TATTAAATATTTATT
301567 CAATACTTAA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTAAATATTTATTA
Found at i:306509 original size:18 final size:18
Alignment explanation
Indices: 306486--306523 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
306476 AAAAACTATC
*
306486 AAGAAACATTAAGAGATT
1 AAGAAACATTAAAAGATT
306504 AAGAAACATTAAAAGATT
1 AAGAAACATTAAAAGATT
306522 AA
1 AA
306524 AGCATTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (18 bp):
AAGAAACATTAAAAGATT
Found at i:306569 original size:21 final size:18
Alignment explanation
Indices: 306531--306566 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
306521 TAAAGCATTC
306531 AAAGTTTCATTATTTTTT
1 AAAGTTTCATTATTTTTT
306549 AAAGTTTCATTATTTTTT
1 AAAGTTTCATTATTTTTT
306567 TTTTCAAGAG
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:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (18 bp):
AAAGTTTCATTATTTTTT
Found at i:314381 original size:13 final size:13
Alignment explanation
Indices: 314363--314389 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
314353 ACTTTATGCT
314363 TTGTATCGATACA
1 TTGTATCGATACA
314376 TTGTATCGATACA
1 TTGTATCGATACA
314389 T
1 T
314390 GCTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:314399 original size:19 final size:19
Alignment explanation
Indices: 314374--314428 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
314364 TGTATCGATA
314374 CATTGTATCGATACATGCT
1 CATTGTATCGATACATGCT
* * *
314393 TATTGTATCGATATATACT
1 CATTGTATCGATACATGCT
* *
314412 CAATATATCGATACATG
1 CATTGTATCGATACATG
314429 AAACTGCAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:314490 original size:13 final size:13
Alignment explanation
Indices: 314472--314501 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
314462 GATACATGGG
314472 ACATTATATCGAC
1 ACATTATATCGAC
*
314485 ACATTATATCGAT
1 ACATTATATCGAC
314498 ACAT
1 ACAT
314502 GGTAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (13 bp):
ACATTATATCGAC
Found at i:314522 original size:33 final size:33
Alignment explanation
Indices: 314458--314522 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
314448 AAGTGAATTG
* **
314458 TATCGATACATGGGACATTATATCGACACATTA
1 TATCGATACATGGGAAAAAATATCGACACATTA
* * *
314491 TATCGATACATGGTAAAAAATATTGATACATT
1 TATCGATACATGGGAAAAAATATCGACACATT
314523 GTGACTAACG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (33 bp):
TATCGATACATGGGAAAAAATATCGACACATTA
Found at i:320322 original size:2 final size:2
Alignment explanation
Indices: 320315--320343 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
320305 TCAAAAACCA
320315 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
320344 AAGTTTTAAT
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:320929 original size:14 final size:14
Alignment explanation
Indices: 320912--320960 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
320902 ATAGGCTTTT
320912 TTTTTTAGTAAATA
1 TTTTTTAGTAAATA
320926 TTTTTTA--AAATA
1 TTTTTTAGTAAATA
*
320938 TATCTTTTAGTAAACA
1 T-T-TTTTAGTAAATA
320954 TTTTTTA
1 TTTTTTA
320961 AGTTTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
12 6 0.20
13 1 0.03
14 17 0.57
15 1 0.03
16 5 0.17
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (14 bp):
TTTTTTAGTAAATA
Found at i:321278 original size:39 final size:38
Alignment explanation
Indices: 321217--321343 Score: 123
Period size: 39 Copynumber: 3.3 Consensus size: 38
321207 GGATTAATTG
*
321217 AAATTT-AAA-ATATGTAATTAATGCATAAATTTTTTATT
1 AAATTTAAAAGATAT-TAA-TAATGTATAAATTTTTTATT
* * *
321255 AGAATCTAAAAGATATTAATAATGTATAGATTATTTATT
1 A-AATTTAAAAGATATTAATAATGTATAAATTTTTTATT
* * * *
321294 CAAATTTAAAAGATGTGATTAATATATAAATTTTTTATT
1 -AAATTTAAAAGATATTAATAATGTATAAATTTTTTATT
321333 ATAATTTAAAA
1 A-AATTTAAAA
321344 AATAAGGCTA
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
38 2 0.03
39 60 0.82
40 7 0.10
41 4 0.05
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (38 bp):
AAATTTAAAAGATATTAATAATGTATAAATTTTTTATT
Found at i:321872 original size:12 final size:12
Alignment explanation
Indices: 321851--321889 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
321841 CTCATGCATC
*
321851 ATTATTATTTTT
1 ATTATCATTTTT
321863 ATTATCATTTTT
1 ATTATCATTTTT
* *
321875 GTTCTCATTTTT
1 ATTATCATTTTT
321887 ATT
1 ATT
321890 TTTTGTTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (12 bp):
ATTATCATTTTT
Found at i:322186 original size:73 final size:72
Alignment explanation
Indices: 322119--322283 Score: 194
Period size: 73 Copynumber: 2.3 Consensus size: 72
322109 AAAAAACAAG
* *
322119 TTTAAATTTCTATAAATAAAAATAAATTATACCTTTAAAATTTTAAA-TCATATAATCATATCTA
1 TTTAAATTTCTATAAATAAAAATAAATTATACC-CTAAAAATTTAAACTCATATAATCATATCTA
322183 AAAATTACA
65 AAAA-TACA
* * * * *
322192 TTTAAATTTTTATAAATCAAAATAAATTTTACCCTAAAAATTTAAACTCGTATAATCA-AAC-AA
1 TTTAAATTTCTATAAATAAAAATAAATTATACCCTAAAAATTTAAACTCATATAATCATATCTAA
*
322255 AAATAAA
66 AAATACA
*
322262 TTTAAACTTT-TACAAATAAAAA
1 TTTAAA-TTTCTATAAATAAAAA
322284 AATAAATTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
70 19 0.24
71 8 0.10
72 13 0.16
73 40 0.50
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (72 bp):
TTTAAATTTCTATAAATAAAAATAAATTATACCCTAAAAATTTAAACTCATATAATCATATCTAA
AAATACA
Found at i:322283 original size:27 final size:28
Alignment explanation
Indices: 322253--322318 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
322243 ATAATCAAAC
322253 AAAAATAAATTTAAACTTTTACAAATAA
1 AAAAATAAATTTAAACTTTTACAAATAA
322281 AAAAATAAATTTAAACTTTTACAAAT-A
1 AAAAATAAATTTAAACTTTTACAAATAA
322308 AAAAATAAATT
1 AAAAATAAATT
322319 ATATCTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 12 0.32
28 26 0.68
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAAATAAATTTAAACTTTTACAAATAA
Found at i:322294 original size:98 final size:101
Alignment explanation
Indices: 322182--322383 Score: 232
Period size: 98 Copynumber: 2.0 Consensus size: 101
322172 AATCATATCT
* * * * * *
322182 AAAAATTACATTTAAATTTTTATAAAT-CAAAATAAATTTTACCCTAAAAATTTAAACTCGTATA
1 AAAAAATAAATTTAAACTTTTACAAATAAAAAATAAATTATA-CCTAAAAATTTAAACTCGTATA
*
322246 ATCA-A-AC-AAAAATAAATTTAAACTTTTACAAATA
65 ATCATATACTAAAAACAAATTTAAACTTTTACAAATA
* ** *
322280 AAAAAATAAATTTAAACTTTTACAAATAAAAAATAAATTATATCTTCAAATTTAAACTTGTATAA
1 AAAAAATAAATTTAAACTTTTACAAATAAAAAATAAATTATACCTAAAAATTTAAACTCGTATAA
* * * *
322345 TTATATTCTACAAACAAATTTAAATTTTTACAAATA
66 TCATATACTAAAAACAAATTTAAACTTTTACAAATA
322381 AAA
1 AAA
322384 TACCTTCAAT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
98 44 0.52
99 13 0.15
100 1 0.01
101 27 0.32
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.36
Consensus pattern (101 bp):
AAAAAATAAATTTAAACTTTTACAAATAAAAAATAAATTATACCTAAAAATTTAAACTCGTATAA
TCATATACTAAAAACAAATTTAAACTTTTACAAATA
Found at i:322893 original size:74 final size:76
Alignment explanation
Indices: 322757--322919 Score: 217
Period size: 74 Copynumber: 2.2 Consensus size: 76
322747 TAATGTAAAA
* * **
322757 TTTTT-ATTTTATTAAATATCAATAGTTAATATTTTAATTTTTAATATAATTTTTTTAAATTTAG
1 TTTTTAATTTTATTAAAAATCAATAATTAATACATTAATTTTTAATATAATTTTTTTAAATTTAG
322821 TCAAATTTTAT
66 TCAAATTTTAT
*
322832 TTTTTAATTTTATTAAAAAATTAATAATTAATACATTAA-TTTT-A-ATAATTTTTTTAAATTTA
1 TTTTTAATTTTATT-AAAAATCAATAATTAATACATTAATTTTTAATATAATTTTTTTAAATTTA
* *
322894 TTTAAATTTTAT
65 GTCAAATTTTAT
322906 TTTTTAAGTTTTAT
1 TTTTTAA-TTTTAT
322920 CTCAGGTAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
74 35 0.45
75 12 0.15
76 12 0.15
77 19 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (76 bp):
TTTTTAATTTTATTAAAAATCAATAATTAATACATTAATTTTTAATATAATTTTTTTAAATTTAG
TCAAATTTTAT
Found at i:323482 original size:92 final size:94
Alignment explanation
Indices: 323319--323497 Score: 281
Period size: 92 Copynumber: 1.9 Consensus size: 94
323309 AAATTTATTC
*
323319 AAATCTCGAATTACTATTTAAAAATAATAAAAAATTAAAATAATATTTTATATTAAATGTTGAAT
1 AAATCTCAAATTACTATTTAAAAATAATAAAAAATTAAAATAATATTTTATATTAAATGTTGAAT
*
323384 TACTATTTAAAAAATTAAAAATATTTTTT
66 TACTATTTAAAAAATAAAAAATATTTTTT
* * * * *
323413 AAATCTCAAATTATTATTT-AAAGTAATAAAAAATTTAAA-AATCTTTTATATTAAATTTTGAAT
1 AAATCTCAAATTACTATTTAAAAATAATAAAAAATTAAAATAATATTTTATATTAAATGTTGAAT
323476 TACTATTTAAAAAATAAAAAAT
66 TACTATTTAAAAAATAAAAAAT
323498 TTAAAAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 43 0.55
93 18 0.23
94 17 0.22
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (94 bp):
AAATCTCAAATTACTATTTAAAAATAATAAAAAATTAAAATAATATTTTATATTAAATGTTGAAT
TACTATTTAAAAAATAAAAAATATTTTTT
Found at i:323645 original size:108 final size:100
Alignment explanation
Indices: 323391--323645 Score: 237
Period size: 108 Copynumber: 2.5 Consensus size: 100
323381 AATTACTATT
* *
323391 TAAAAAATTAAAAATATTTT-TTAAATCTCAAATTATTATTTAAAGTAATAAAAAATTTAAAAAT
1 TAAAAAATTTAAAATATTTTATTAAATCTTAAATTATTATTTAAAGTAATAAAAAATTTAAAAAT
* * **
323455 CTTTTATATTAAATTTTGAATTACTATTTAAAAAA
66 CTTTTACATTAAATCTCAAATTACTATTTAAAAAA
* *
323490 TAAAAAATTTAAAA-ATTTTATTAATAT-TTATATATTTTTATAATTAAATTTAAATAAAAATAA
1 TAAAAAATTTAAAATATTTTATTAA-ATCTTA-A-ATTATTAT--TTAAA-GT-AAT-AAAA-AA
** ** * *
323553 TTTTTATTTGCTTTTACATTAAATCTCAAATTATTATTTAAAGTAA
57 TTTAAAAAT-CTTTTACATTAAATCTCAAATTACTATTTAAA-AAA
*
323599 TAAAAAATTTAAAATATTTTATATTAAATCTTGAATTATTATTTAAA
1 TAAAAAATTTAAAATA-TTT-TATTAAATCTTAAATTATTATTTAAA
323646 AAATTATATT
Statistics
Matches: 124, Mismatches: 16, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
98 5 0.04
99 19 0.15
100 3 0.02
101 7 0.06
103 5 0.04
104 1 0.01
105 3 0.02
106 4 0.03
107 7 0.06
108 32 0.26
109 16 0.13
110 8 0.06
111 6 0.05
112 8 0.06
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (100 bp):
TAAAAAATTTAAAATATTTTATTAAATCTTAAATTATTATTTAAAGTAATAAAAAATTTAAAAAT
CTTTTACATTAAATCTCAAATTACTATTTAAAAAA
Found at i:324523 original size:15 final size:15
Alignment explanation
Indices: 324503--324537 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
324493 AAAAAAATAA
324503 AAATTATTTTTATTT
1 AAATTATTTTTATTT
324518 AAATTATTTTTATTT
1 AAATTATTTTTATTT
324533 AAATT
1 AAATT
324538 TAATTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AAATTATTTTTATTT
Found at i:324567 original size:22 final size:23
Alignment explanation
Indices: 324533--324591 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
324523 ATTTTTATTT
324533 AAATTTAATTATAAAA-ATTTAC
1 AAATTTAATTATAAAATATTTAC
*
324555 AAATATTAA-TATAAAATATTTTAA
1 AAAT-TTAATTATAAAATA-TTTAC
324579 AAATTTTAATTAT
1 AAA-TTTAATTAT
324592 TTTTAAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 11 0.35
23 5 0.16
24 11 0.35
25 4 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTTAATTATAAAATATTTAC
Found at i:324587 original size:24 final size:22
Alignment explanation
Indices: 324536--324588 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
324526 TTTATTTAAA
*
324536 TTTAATTATAAAAATTTACAAAT
1 TTTAA-TATAAAAATTTAAAAAT
*
324559 ATTAATATAAAATATTTTAAAAAT
1 TTTAATATAAAA-A-TTTAAAAAT
324583 TTTAAT
1 TTTAAT
324589 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 7 0.28
23 5 0.20
24 13 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAATATAAAAATTTAAAAAT
Found at i:324645 original size:54 final size:54
Alignment explanation
Indices: 324548--324687 Score: 183
Period size: 54 Copynumber: 2.6 Consensus size: 54
324538 TAATTATAAA
*
324548 AATTTACAAATATTAATATAAAA-TATTTTAAAAATTTTAATTATTTTTAAATAGT
1 AATTTA-AAAT-TTAATATAAAATTTTTTTAAAAATTTTAATTATTTTTAAATAGT
* * ** * *
324603 AATTTGAGATTTAATATAAAATTTTTTTTTAAATTTTTATTATTTTTAAGTAGT
1 AATTTAAAATTTAATATAAAATTTTTTTAAAAATTTTAATTATTTTTAAATAGT
*
324657 AATTTAAAATTTAATATAAAATATTTTTAAA
1 AATTTAAAATTTAATATAAAATTTTTTTAAA
324688 TACTAATTCA
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 11 0.15
54 56 0.78
55 5 0.07
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (54 bp):
AATTTAAAATTTAATATAAAATTTTTTTAAAAATTTTAATTATTTTTAAATAGT
Found at i:325899 original size:15 final size:15
Alignment explanation
Indices: 325879--325917 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
325869 CATTAAAAAA
325879 ATAATATATAATATT
1 ATAATATATAATATT
325894 ATAATATA-AATATT
1 ATAATATATAATATT
*
325908 A-AAAATATAA
1 ATAATATATAA
325918 ACTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 9 0.41
15 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATATATAATATT
Found at i:326326 original size:10 final size:10
Alignment explanation
Indices: 326311--326464 Score: 59
Period size: 10 Copynumber: 15.4 Consensus size: 10
326301 GAACACTTTG
326311 GAATGTTCTA
1 GAATGTTCTA
*
326321 GAATGTTCTG
1 GAATGTTCTA
*
326331 GAATATTCTA
1 GAATGTTCTA
* *
326341 GAAT-ATCGTG
1 GAATGTTC-TA
* * *
326351 GAAGGCTCTG
1 GAATGTTCTA
326361 GAA-GATTCTA
1 GAATG-TTCTA
326371 GAATGTTCTA
1 GAATGTTCTA
* *
326381 GAAT-ATCGTG
1 GAATGTTC-TA
* * *
326391 GAAGGCTCTG
1 GAATGTTCTA
326401 GAA-GATTCTA
1 GAATG-TTCTA
326411 GAATGTTCTA
1 GAATGTTCTA
* *
326421 GAATATTAT-
1 GAATGTTCTA
* * *
326430 GAAAGGCTCTG
1 G-AATGTTCTA
326441 GAA-GATTCTA
1 GAATG-TTCTA
326451 GAATGTTCTA
1 GAATGTTCTA
326461 GAAT
1 GAAT
326465 ATTGTGGAAG
Statistics
Matches: 109, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
9 8 0.07
10 93 0.85
11 8 0.07
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (10 bp):
GAATGTTCTA
Found at i:326353 original size:40 final size:40
Alignment explanation
Indices: 326326--326479 Score: 254
Period size: 40 Copynumber: 3.9 Consensus size: 40
326316 TTCTAGAATG
* *
326326 TTCTGGAATATTCTAGAATATCGTGGAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
326366 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
** *
326406 TTCTAGAATGTTCTAGAATATTATGAAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
*
326446 TTCTAGAATGTTCTAGAATATTGTGGAAGGCTCT
1 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCT
326480 AGAACTTTAT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (40 bp):
TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
Found at i:330738 original size:10 final size:10
Alignment explanation
Indices: 330723--330756 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
330713 GAACACTTTG
330723 GAATGTTCTA
1 GAATGTTCTA
*
330733 GAATGTTCTG
1 GAATGTTCTA
*
330743 GAATATTCTA
1 GAATGTTCTA
330753 GAAT
1 GAAT
330757 ATCGTGGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (10 bp):
GAATGTTCTA
Found at i:330764 original size:20 final size:20
Alignment explanation
Indices: 330721--330765 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
330711 TAGAACACTT
* *
330721 TGGAATGTTCTAGAATGTTC
1 TGGAATATTCTAGAATGATC
330741 TGGAATATTCTAGAAT-ATC
1 TGGAATATTCTAGAATGATC
330760 GTGGAA
1 -TGGAA
330766 GGCTATGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (20 bp):
TGGAATATTCTAGAATGATC
Found at i:330765 original size:40 final size:40
Alignment explanation
Indices: 330738--330891 Score: 245
Period size: 40 Copynumber: 3.9 Consensus size: 40
330728 TTCTAGAATG
* * *
330738 TTCTGGAATATTCTAGAATATCGTGGAAGGCTATGGAAGA
1 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
330778 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
**
330818 TTCTAGAATGTTCTAGAATATTATGGAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
* *
330858 TTCTAGAATGTTTTAGAATATTGTGGAAGGCTCT
1 TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCT
330892 AGAACTTTAT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (40 bp):
TTCTAGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
Found at i:330845 original size:30 final size:29
Alignment explanation
Indices: 330811--330934 Score: 88
Period size: 30 Copynumber: 4.1 Consensus size: 29
330801 TGGAAGGCTC
*
330811 TGGAAGATTCTAGAATGTTCTAGAATATTA
1 TGGAAGATTCTGGAATGTTCTAGAAT-TTA
** *
330841 TGGAAGGCTCTGGAA-GATTCTAGAATGTTT
1 TGGAAGATTCTGGAATG-TTCTAGAAT-TTA
* * * * *
330871 TAGAATATTGTGGAAGGCTCTAGAACTTTA
1 TGGAAGATTCTGGAATGTTCTAGAA-TTTA
* * *
330901 TGGAGGATTATGGAATGTTCTAGAAGCTTA
1 TGGAAGATTCTGGAATGTTCTAGAA-TTTA
330931 TGGA
1 TGGA
330935 GAATTCTCCA
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
29 1 0.01
30 68 0.96
31 2 0.03
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (29 bp):
TGGAAGATTCTGGAATGTTCTAGAATTTA
Found at i:332112 original size:24 final size:23
Alignment explanation
Indices: 332081--332154 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 23
332071 TTATATATTT
* *
332081 AATAAATATAAAATTTATATAAA
1 AATAAATATAAAATATATTTAAA
*
332104 AATATA-ATAAAATATATTTAAA
1 AATAAATATAAAATATATTTAAA
*
332126 AATAATTATTAAAATATATTTAATA
1 AATAAATA-TAAAATATATTTAA-A
332151 AATA
1 AATA
332155 TTTTATTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
22 18 0.42
23 6 0.14
24 14 0.33
25 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATAAATATAAAATATATTTAAA
Found at i:332120 original size:12 final size:11
Alignment explanation
Indices: 332081--332144 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
332071 TTATATATTT
*
332081 AATAAATATAA
1 AATATATATAA
*
332092 AATTTATATAA
1 AATATATATAA
332103 AA-ATATAATAA
1 AATATAT-ATAA
*
332114 AATATATTTAA
1 AATATATATAA
332125 AA-ATAATTATTAA
1 AATAT-A-TA-TAA
332138 AATATAT
1 AATATAT
332145 TTAATAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
10 5 0.12
11 23 0.55
12 6 0.14
13 6 0.14
14 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATATATAA
Found at i:332414 original size:11 final size:11
Alignment explanation
Indices: 332377--332435 Score: 64
Period size: 11 Copynumber: 5.0 Consensus size: 11
332367 ACAAGTGATA
332377 AAAAATAATAGTT
1 AAAAATAATA--T
*
332390 AAAATATAAAAT
1 AAAA-ATAATAT
332402 AAAAATAATAT
1 AAAAATAATAT
332413 AAAAATTAATAT
1 AAAAA-TAATAT
*
332425 AAATATAATAT
1 AAAAATAATAT
332436 TAATATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 17 0.41
12 15 0.37
13 4 0.10
14 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:332417 original size:12 final size:12
Alignment explanation
Indices: 332374--332427 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
332364 ATTACAAGTG
332374 ATAAAAAATAAT
1 ATAAAAAATAAT
* *
332386 AGTTAAAATATAAA
1 A--TAAAAAATAAT
332400 AT-AAAAATAAT
1 ATAAAAAATAAT
*
332411 ATAAAAATTAAT
1 ATAAAAAATAAT
332423 ATAAA
1 ATAAA
332428 TATAATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 9 0.26
12 15 0.44
14 10 0.29
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:332432 original size:23 final size:24
Alignment explanation
Indices: 332377--332435 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
332367 ACAAGTGATA
*
332377 AAAAATAATAGTTAAAATATAAAAT
1 AAAAATAATA-TAAAAATATAAAAT
*
332402 AAAAATAATATAAAAAT-TAATAT
1 AAAAATAATATAAAAATATAAAAT
*
332425 AAATATAATAT
1 AAAAATAATAT
332436 TAATATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 15 0.48
24 6 0.19
25 10 0.32
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAATAATATAAAAATATAAAAT
Found at i:332440 original size:11 final size:11
Alignment explanation
Indices: 332391--332441 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
332381 ATAATAGTTA
*
332391 AAATATAAAAT
1 AAATATAATAT
*
332402 AAAAATAATAT
1 AAATATAATAT
*
332413 AAAAATTAATAT
1 AAATA-TAATAT
332425 AAATATAATAT
1 AAATATAATAT
*
332436 TAATAT
1 AAATAT
332442 TTAAATGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATAATAT
Found at i:332464 original size:33 final size:33
Alignment explanation
Indices: 332427--332557 Score: 100
Period size: 32 Copynumber: 4.0 Consensus size: 33
332417 ATTAATATAA
*
332427 ATATAATATTAATATTTAAATGTATTAAATTTT
1 ATATAATATTAATATTTAAATATATTAAATTTT
* *
332460 ATATAAT-TTAA-ATTATTAACATATTCAAA-TTT
1 ATATAATATTAATATT-TAAATATATT-AAATTTT
*
332492 ATATAAATATATAATATTTTAAATATAATTATAA-TAT
1 ATAT-AATAT-TAATA-TTTAAATAT-ATTA-AATTTT
332529 ATA-AATA-TAATA--TAAATATA-TAAATTTT
1 ATATAATATTAATATTTAAATATATTAAATTTT
332557 A
1 A
332558 AATTTTAAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
27 2 0.02
28 5 0.06
29 1 0.01
30 7 0.09
31 3 0.04
32 18 0.22
33 18 0.22
34 1 0.01
35 7 0.09
36 7 0.09
37 12 0.15
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.47
Consensus pattern (33 bp):
ATATAATATTAATATTTAAATATATTAAATTTT
Found at i:332473 original size:54 final size:51
Alignment explanation
Indices: 332415--332564 Score: 134
Period size: 54 Copynumber: 2.9 Consensus size: 51
332405 AATAATATAA
*
332415 AAATTAATATAAATATAATATTAATATTTAAATGTATTAAATTTTATATAATTT
1 AAATT-ATATAAATATAATATTAATATATAAAT-TATTAAATTTTATATAA-TT
332469 AAATTAT-TAACATATTCAA-ATT--TATATAAA-TATATAATATTTTAAATATAATT
1 AAATTATATAA-ATA-T-AATATTAATATATAAATTAT-TAA-ATTTT--ATATAATT
*
332522 ATAA-TATATAAATATAATATAAATATATAAATT-TTAAATTTTA
1 A-AATTATATAAATATAATATTAATATATAAATTATTAAATTTTA
332565 AATGTGTTTA
Statistics
Matches: 81, Mismatches: 2, Indels: 30
0.72 0.02 0.27
Matches are distributed among these distances:
50 4 0.05
51 5 0.06
52 23 0.28
53 17 0.21
54 29 0.36
55 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (51 bp):
AAATTATATAAATATAATATTAATATATAAATTATTAAATTTTATATAATT
Found at i:332501 original size:18 final size:17
Alignment explanation
Indices: 332449--332501 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
332439 TATTTAAATG
332449 TATTAAATTT-TATATAA
1 TATTAAATTTATATA-AA
332466 T-TTAAA-TTAT-TAACA
1 TATTAAATTTATATAA-A
332481 TATTCAAATTTATATAAA
1 TATT-AAATTTATATAAA
332499 TAT
1 TAT
332502 ATAATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
14 1 0.03
15 6 0.20
16 8 0.27
17 4 0.13
18 8 0.27
19 3 0.10
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTAAATTTATATAAA
Found at i:332526 original size:6 final size:6
Alignment explanation
Indices: 332492--332548 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 6
332482 ATTCAAATTT
*
332492 ATATAA ATATATA ATATTTTAA ATATAA TTATAA TATATAA ATAT-A ATATAA
1 ATATAA ATATA-A ATA---TAA ATATAA ATATAA -ATATAA ATATAA ATATAA
332544 ATATA
1 ATATA
332549 TAAATTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 5 0.12
6 23 0.53
7 9 0.21
9 4 0.09
10 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATATAA
Found at i:332532 original size:13 final size:13
Alignment explanation
Indices: 332514--332551 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
332504 AATATTTTAA
332514 ATATAATTATAAT
1 ATATAATTATAAT
*
332527 ATATAAATATAAT
1 ATATAATTATAAT
332540 ATA-AATATATAA
1 ATATAAT-TATAA
332552 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 2 0.09
13 20 0.91
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATTATAAT
Found at i:332535 original size:19 final size:18
Alignment explanation
Indices: 332500--332553 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
332490 TTATATAAAT
*
332500 ATATAATATTTTAAATATA
1 ATATAATA-TATAAATATA
332519 ATTATAATATATAAATATA
1 A-TATAATATATAAATATA
332538 ATATAAATATATAAAT
1 ATAT-AATATATAAAT
332554 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 3 0.09
19 22 0.69
20 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATATATAAATATA
Found at i:332741 original size:20 final size:19
Alignment explanation
Indices: 332718--332772 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 19
332708 TAAAATTATT
332718 ATTATTAAATAATAATTTAA
1 ATTATTAAAT-ATAATTTAA
332738 ATTAAATTAAAT-TAATTTAA
1 ATT--ATTAAATATAATTTAA
332758 ATATATATAAATATA
1 AT-TAT-TAAATATA
332773 TACCAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
19 2 0.07
20 18 0.60
21 3 0.10
22 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTATTAAATATAATTTAA
Found at i:336788 original size:20 final size:20
Alignment explanation
Indices: 336763--336816 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
336753 TTTTAACTAG
* *
336763 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTCAAAA
* *
336783 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTCAAAA
336803 ATGTATCGATACAT
1 ATGTATCGATACAT
336817 CAAGGTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCAAAA
Found at i:340575 original size:15 final size:15
Alignment explanation
Indices: 340533--340578 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
340523 CCAAAACCAA
*
340533 AATAAATTACATAAT
1 AATAAATTACAAAAT
*
340548 AAT-AATAACAAAAT
1 AATAAATTACAAAAT
*
340562 TATAAATTACAAAAT
1 AATAAATTACAAAAT
340577 AA
1 AA
340579 AACATACTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAAATTACAAAAT
Found at i:341679 original size:24 final size:24
Alignment explanation
Indices: 341652--341776 Score: 160
Period size: 24 Copynumber: 5.2 Consensus size: 24
341642 TGATGGAGTA
* *
341652 GTTGTTGTGACGGGAGTTGTTGGT
1 GTTGTAGTAACGGGAGTTGTTGGT
*
341676 GTTGTAGTAACGGGGGTTGTTGGT
1 GTTGTAGTAACGGGAGTTGTTGGT
341700 GTTGTAGTAACGGGAGTTGTTGGT
1 GTTGTAGTAACGGGAGTTGTTGGT
* *
341724 GTTGTAGTAACGGGAGTTGTCGGC
1 GTTGTAGTAACGGGAGTTGTTGGT
* * * * *
341748 GTTGTTGTGACCGGAGTTGCTGGA
1 GTTGTAGTAACGGGAGTTGTTGGT
341772 GTTGT
1 GTTGT
341777 GGTGGTGCCT
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 89 1.00
ACGTcount: A:0.13, C:0.07, G:0.43, T:0.37
Consensus pattern (24 bp):
GTTGTAGTAACGGGAGTTGTTGGT
Found at i:341716 original size:48 final size:48
Alignment explanation
Indices: 341652--341776 Score: 178
Period size: 48 Copynumber: 2.6 Consensus size: 48
341642 TGATGGAGTA
* * *
341652 GTTGTTGTGACGGGAGTTGTTGGTGTTGTAGTAACGGGGGTTGTTGGT
1 GTTGTTGTGACGGGAGTTGTTGGTGTTGTAGTAACGGGAGTTGTCGGC
* *
341700 GTTGTAGTAACGGGAGTTGTTGGTGTTGTAGTAACGGGAGTTGTCGGC
1 GTTGTTGTGACGGGAGTTGTTGGTGTTGTAGTAACGGGAGTTGTCGGC
* * *
341748 GTTGTTGTGACCGGAGTTGCTGGAGTTGT
1 GTTGTTGTGACGGGAGTTGTTGGTGTTGT
341777 GGTGGTGCCT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.13, C:0.07, G:0.43, T:0.37
Consensus pattern (48 bp):
GTTGTTGTGACGGGAGTTGTTGGTGTTGTAGTAACGGGAGTTGTCGGC
Found at i:342704 original size:13 final size:13
Alignment explanation
Indices: 342686--342768 Score: 75
Period size: 13 Copynumber: 6.5 Consensus size: 13
342676 AATATTTTTG
342686 AAAATATAATATA
1 AAAATATAATATA
*
342699 AAAATATTATATA
1 AAAATATAATATA
* *
342712 AACATAAAATAT-
1 AAAATATAATATA
*
342724 ATAATA-AATATA
1 AAAATATAATATA
342736 AAAATA-ATATAATA
1 AAAATATA-AT-ATA
*
342750 AAAA-ATAATTTA
1 AAAATATAATATA
342762 AAAATAT
1 AAAATAT
342769 TAACAAAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
11 5 0.09
12 16 0.28
13 28 0.49
14 8 0.14
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATAATATA
Found at i:342712 original size:18 final size:17
Alignment explanation
Indices: 342689--342756 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
342679 ATTTTTGAAA
342689 ATATAATATAAAAATATT
1 ATATAATATAAAAATA-T
*
342707 ATATAA-ACATAAAATAT
1 ATATAATATA-AAAATAT
342724 ATAATAAATATAAAAATA-
1 AT-AT-AATATAAAAATAT
342742 ATATAATA-AAAAATA
1 ATATAATATAAAAATA
342757 ATTTAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
15 7 0.16
16 4 0.09
17 7 0.16
18 16 0.36
19 8 0.18
20 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (17 bp):
ATATAATATAAAAATAT
Found at i:342717 original size:45 final size:45
Alignment explanation
Indices: 342633--342718 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
342623 ATTTTATTTT
* * **
342633 TATTTTTATAAATATAATCTAATTAATATTATTTGACATAATTAA
1 TATTTTTATAAATATAATATAATAAATATTATTAAACATAATTAA
342678 TATTTTTGA-AAATATAATATAA-AAATATTATATAAACATAA
1 TATTTTT-ATAAATATAATATAATAAATATTAT-TAAACATAA
342719 AATATATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 8 0.23
45 26 0.74
46 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (45 bp):
TATTTTTATAAATATAATATAATAAATATTATTAAACATAATTAA
Found at i:342734 original size:11 final size:11
Alignment explanation
Indices: 342717--342781 Score: 55
Period size: 11 Copynumber: 5.8 Consensus size: 11
342707 ATATAAACAT
342717 AAAATATATAA
1 AAAATATATAA
*
342728 TAAATATA-AA
1 AAAATATATAA
342738 AATAATATAATAA
1 AA-AATAT-ATAA
*
342751 AAAATA-ATTTA
1 AAAATATA-TAA
342762 AAAATAT-TAA
1 AAAATATATAA
342772 CAAAATATAT
1 -AAAATATAT
342782 TTAATATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
10 6 0.14
11 27 0.63
12 6 0.14
13 4 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATATATAA
Found at i:342734 original size:24 final size:23
Alignment explanation
Indices: 342707--342756 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
342697 TAAAAATATT
* *
342707 ATATAAACATAAAATATATAATAA
1 ATATAAAAATAAAATA-ATAAAAA
*
342731 ATATAAAAATAATATAATAAAAA
1 ATATAAAAATAAAATAATAAAAA
342754 ATA
1 ATA
342757 ATTTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
ATATAAAAATAAAATAATAAAAA
Found at i:343637 original size:30 final size:29
Alignment explanation
Indices: 343602--343672 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
343592 AACATCATAA
* *
343602 TTTAAAGATAAATTTTTTTAAATATTAATT
1 TTTAAAGATAAA-TTTATAAAATATTAATT
* *
343632 TTTAAAGTTTAAATTTATAAAATATTATTT
1 TTTAAAG-ATAAATTTATAAAATATTAATT
*
343662 TTTAAAAATAA
1 TTTAAAGATAA
343673 TTACGTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 3 0.09
30 27 0.79
31 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTAAAGATAAATTTATAAAATATTAATT
Found at i:343646 original size:15 final size:14
Alignment explanation
Indices: 343616--343667 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
343606 AAGATAAATT
343616 TTTTTAAATATTAA
1 TTTTTAAATATTAA
343630 TTTTTAAAGT-TTAAA
1 TTTTTAAA-TATT-AA
* *
343645 TTTATAAAATATTAT
1 TTT-TTAAATATTAA
343660 TTTTTAAA
1 TTTTTAAA
343668 AATAATTACG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 14 0.45
15 11 0.35
16 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TTTTTAAATATTAA
Found at i:343668 original size:15 final size:15
Alignment explanation
Indices: 343615--343668 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
343605 AAAGATAAAT
*
343615 TTTTTTAAATATTAA
1 TTTTTAAAATATTAA
*
343630 TTTTTAAAGT-TTAAA
1 TTTTTAAAATATT-AA
* *
343645 TTTATAAAATATTAT
1 TTTTTAAAATATTAA
343660 TTTTTAAAA
1 TTTTTAAAA
343669 ATAATTACGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTTTAAAATATTAA
Found at i:343675 original size:17 final size:18
Alignment explanation
Indices: 343645--343695 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
343635 AAAGTTTAAA
343645 TTTATAAAAT-ATTA-TTT
1 TTTA-AAAATAATTACTTT
343662 TTTAAAAATAATTACGTTT
1 TTTAAAAATAATTAC-TTT
*
343681 TTTAAATATAATTAC
1 TTTAAAAATAATTAC
343696 GTAAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 5 0.17
17 8 0.27
19 17 0.57
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTAAAAATAATTACTTT
Found at i:343683 original size:19 final size:19
Alignment explanation
Indices: 343659--343697 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
343649 TAAAATATTA
343659 TTTTTTAAAAATAATTACG
1 TTTTTTAAAAATAATTACG
*
343678 TTTTTTAAATATAATTACG
1 TTTTTTAAAAATAATTACG
343697 T
1 T
343698 AAATAATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTTTTAAAAATAATTACG
Found at i:346316 original size:11 final size:11
Alignment explanation
Indices: 346302--346328 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
346292 TATATAAGAT
346302 ATATATTTTAA
1 ATATATTTTAA
346313 ATATATTTTAA
1 ATATATTTTAA
346324 ATATA
1 ATATA
346329 ATTAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATTTTAA
Found at i:346610 original size:2 final size:2
Alignment explanation
Indices: 346603--346627 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
346593 TTAGAATAGA
346603 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
346628 GCTTCGTTCA
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
Found at i:346788 original size:6 final size:6
Alignment explanation
Indices: 346772--346820 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
346762 TTTGTTGGTC
*
346772 ATATAA TTATAA ATAT-A ATATAA ATAATTAA ATATAA ATATAA TATATA
1 ATATAA ATATAA ATATAA ATATAA AT-A-TAA ATATAA ATATAA -ATATA
346821 TTAAATGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
5 5 0.14
6 20 0.54
7 7 0.19
8 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:346859 original size:37 final size:38
Alignment explanation
Indices: 346808--346895 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 38
346798 ATTAAATATA
346808 AATATAATATATATTAAATGTATTATT-TTAATTATATTT
1 AATA-AAT-TATATTAAATGTATTATTATTAATTATATTT
* * **
346847 AATAAATTATATTATATTTATTATTATTTTTTATATTT
1 AATAAATTATATTAAATGTATTATTATTAATTATATTT
*
346885 -ATTAATTATAT
1 AATAAATTATAT
346896 GATAATAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
37 26 0.60
38 13 0.30
39 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (38 bp):
AATAAATTATATTAAATGTATTATTATTAATTATATTT
Found at i:346873 original size:6 final size:5
Alignment explanation
Indices: 346828--346956 Score: 64
Period size: 5 Copynumber: 27.4 Consensus size: 5
346818 ATATTAAATG
* * *
346828 TATTA TTTTA -ATTA TATT- TAATA AATTA TATTA TATT- TATTA TTATT-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA
* * * * *
346875 TTTTA TATT- TATTA -ATTA TATGA TAATAA CATT- TAAATA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA T-ATTA TATTA T-ATTA TATTA TATTA
* *
346924 TATT- T-TTA TAATA TTTTA TATTA T-TTA T-TTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
346957 AATCACGTCA
Statistics
Matches: 92, Mismatches: 19, Indels: 26
0.67 0.14 0.19
Matches are distributed among these distances:
3 2 0.02
4 31 0.34
5 51 0.55
6 8 0.09
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (5 bp):
TATTA
Done.