Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1987
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: 242289
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:133144 original size:21 final size:21
Alignment explanation
Indices: 133120--133161 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
133110 CAATCTAATG
*
133120 ATTTTTACTTTTA-CTTTATTT
1 ATTTTTA-TTTTATATTTATTT
133141 ATTTTTATTTTATATTTATTT
1 ATTTTTATTTTATATTTATTT
133162 TAATTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (21 bp):
ATTTTTATTTTATATTTATTT
Found at i:136543 original size:21 final size:21
Alignment explanation
Indices: 136517--136563 Score: 87
Period size: 20 Copynumber: 2.3 Consensus size: 21
136507 GCTTATTGAA
136517 TCCCAAAAGCCCTTTTCAATT
1 TCCCAAAAGCCCTTTTCAATT
136538 TCCC-AAAGCCCTTTTCAATT
1 TCCCAAAAGCCCTTTTCAATT
136558 TCCCAA
1 TCCCAA
136564 TACTGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (21 bp):
TCCCAAAAGCCCTTTTCAATT
Found at i:147254 original size:20 final size:21
Alignment explanation
Indices: 147226--147268 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
147216 AATGCTAGTT
147226 TTTCCTC-TTTTTTTGTATTC
1 TTTCCTCTTTTTTTTGTATTC
*
147246 TTTCTTCTTTTTTTTGTATTC
1 TTTCCTCTTTTTTTTGTATTC
147267 TT
1 TT
147269 GAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTCCTCTTTTTTTTGTATTC
Found at i:149653 original size:53 final size:54
Alignment explanation
Indices: 149544--149646 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 54
149534 AAATAACTTG
*
149544 AACCCAATTTAACCTGAATGTTAAACCCAATTGACCTGAATCCAAAATGACCCA
1 AACCCAATTTAACCTGAATGTTAAACCCAATTGACCCGAATCCAAAATGACCCA
* ** *
149598 AACCCAA-TTAA-CTCGAGTGTTAAACCTGATTGACCCGAATCCGAAATGA
1 AACCCAATTTAACCT-GAATGTTAAACCCAATTGACCCGAATCCAAAATGA
149647 TGCAAACTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
52 2 0.05
53 34 0.79
54 7 0.16
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (54 bp):
AACCCAATTTAACCTGAATGTTAAACCCAATTGACCCGAATCCAAAATGACCCA
Found at i:149662 original size:16 final size:16
Alignment explanation
Indices: 149641--149678 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
149631 CCCGAATCCG
*
149641 AAATGATGCAAACTCA
1 AAATGATCCAAACTCA
*
149657 AAATGATCCGAACTCA
1 AAATGATCCAAACTCA
149673 AAATGA
1 AAATGA
149679 CCCGAACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (16 bp):
AAATGATCCAAACTCA
Found at i:149694 original size:17 final size:16
Alignment explanation
Indices: 149651--149696 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
149641 AAATGATGCA
*
149651 AACTCAAAATGATCCG
1 AACTCAAAATGACCCG
149667 AACTCAAAATGACCCG
1 AACTCAAAATGACCCG
*
149683 AACCTGAAAATGAC
1 AA-CTCAAAATGAC
149697 TCAAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (16 bp):
AACTCAAAATGACCCG
Found at i:151270 original size:20 final size:20
Alignment explanation
Indices: 151247--151298 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
151237 TAAAGCAAAC
*
151247 TGTATCGATACATTTAGGAA
1 TGTATCGATACATTTACGAA
* **
151267 TGTATTGATACATTTACTCA
1 TGTATCGATACATTTACGAA
151287 TGTATCGATACA
1 TGTATCGATACA
151299 ATTTTTCAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTACGAA
Found at i:151372 original size:20 final size:20
Alignment explanation
Indices: 151347--151385 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
151337 CATTTGAGAC
151347 ATGTATCGATGCATTCACTT
1 ATGTATCGATGCATTCACTT
*
151367 ATGTATTGATGCATTCACT
1 ATGTATCGATGCATTCACT
151386 AATTGTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (20 bp):
ATGTATCGATGCATTCACTT
Found at i:162679 original size:92 final size:95
Alignment explanation
Indices: 162516--162701 Score: 243
Period size: 92 Copynumber: 2.0 Consensus size: 95
162506 AATTATCCAA
**
162516 TTCTCTTAAAAAATTAAAATACATAATTTCGTTTTTTTAAATACTTTTTCACTCATTATATCTCA
1 TTCTCTTAAAAAATTAAAATACATAATTTC-TTTTTAAAAATACTTTTTCACTCATTATATCTCA
** * **
162581 TGGATATTCTTATTTTAGGTTTGTTTTGCTT
65 CAGATATTCTTATTCTAAATTTGTTTTGCTT
** * *
162612 TTCTCTT-AAAAATTACCATACATAA-TT-TTTTTAAAAATACTTTTTCACTTATTATTTCTCAC
1 TTCTCTTAAAAAATTAAAATACATAATTTCTTTTTAAAAATACTTTTTCACTCATTATATCTCAC
162674 AGATATTCTTATTCTAAATTTGTTTTGC
66 AGATATTCTTATTCTAAATTTGTTTTGC
162702 ATGTTATTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
92 54 0.68
94 2 0.03
95 16 0.20
96 7 0.09
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (95 bp):
TTCTCTTAAAAAATTAAAATACATAATTTCTTTTTAAAAATACTTTTTCACTCATTATATCTCAC
AGATATTCTTATTCTAAATTTGTTTTGCTT
Found at i:174528 original size:21 final size:22
Alignment explanation
Indices: 174502--174549 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
174492 TTTGCATATT
*
174502 TTGCTCGA-TTATGGTTCCCAA
1 TTGCTCAATTTATGGTTCCCAA
*
174523 TTGCTCAATTTATGGTTCCTAA
1 TTGCTCAATTTATGGTTCCCAA
174545 TTGCT
1 TTGCT
174550 TTCACTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.44
Consensus pattern (22 bp):
TTGCTCAATTTATGGTTCCCAA
Found at i:174837 original size:14 final size:14
Alignment explanation
Indices: 174818--174857 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
174808 TATATTAACT
174818 TTAAAATAAATTTA
1 TTAAAATAAATTTA
**
174832 TTAAAATATTTTTA
1 TTAAAATAAATTTA
*
174846 TTTAAATAAATT
1 TTAAAATAAATT
174858 AATTTTCATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAAATAAATTTA
Found at i:175681 original size:6 final size:6
Alignment explanation
Indices: 175670--175715 Score: 65
Period size: 6 Copynumber: 7.2 Consensus size: 6
175660 GAACTCCTGT
175670 AAAATA AAAATA AAAATA AAAATA AATAATA AATAATA AATAATA A
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AA-AATA AA-AATA A
175716 TTATAATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
6 20 0.51
7 19 0.49
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:180494 original size:7 final size:6
Alignment explanation
Indices: 180471--180630 Score: 54
Period size: 6 Copynumber: 27.3 Consensus size: 6
180461 GAAGGGAAGG
* *
180471 AAAGAA AAGGAA AAAGAA AGAAGAA AAA-AA AAATG-- AAAGAA GAAGAA
1 AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA AAA-GAA AAAGAA AAAGAA
** *
180518 AAA-ATA AAAGGG AAAGAAA AAAGTAA AAA-TA AAAGAA AACA-ATA AAA-AA
1 AAAGA-A AAAGAA AAAG-AA AAAG-AA AAAGAA AAAGAA AA-AGA-A AAAGAA
* * ** * * *
180567 AGAGAA GAA-AA AAAGAA AATTAA ATA-AA AAAGCA AAA-AA AAAG-G
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* *
180611 AAGGGA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AA
180631 CAAAAAAATG
Statistics
Matches: 111, Mismatches: 27, Indels: 32
0.65 0.16 0.19
Matches are distributed among these distances:
4 1 0.01
5 31 0.28
6 60 0.54
7 19 0.17
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:180508 original size:25 final size:24
Alignment explanation
Indices: 180466--180556 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 24
180456 AAGGGGAAGG
* * *
180466 GAAGGAAAGAAAAGGAAAAAGAAA
1 GAAGAAAAAAAAAAGAAAAAGAAA
180490 GAAGAAAAAAAAAATG--AAAG-AA
1 GAAGAAAAAAAAAA-GAAAAAGAAA
**
180512 GAAGAAAAAATAAAAGGGAAAGAAA
1 GAAGAAAAAA-AAAAGAAAAAGAAA
* *
180537 AAAGTAAAAATAAAAGAAAA
1 GAAG-AAAAAAAAAAGAAAA
180557 CAATAAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
22 13 0.24
23 8 0.15
24 15 0.28
25 13 0.24
26 5 0.09
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (24 bp):
GAAGAAAAAAAAAAGAAAAAGAAA
Found at i:180534 original size:18 final size:18
Alignment explanation
Indices: 180471--180579 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 18
180461 GAAGGGAAGG
* *
180471 AAAGAAAAGGAAAAAGAA
1 AAAGAAAAGAAAAAATAA
*
180489 AGAAGAAAA-AAAAAAT-G
1 A-AAGAAAAGAAAAAATAA
180506 AAAGAAGAAGAAAAAATAA
1 AAAGAA-AAGAAAAAATAA
* *
180525 AAGGGAAAGAAAAAAGTAA
1 AAAGAAAAGAAAAAA-TAA
*
180544 AAATAAAAGAAAACAATAAAA
1 AAAGAAAAGAAAA-AAT--AA
*
180565 AAAGAGAAGAAAAAA
1 AAAGAAAAGAAAAAA
180580 AGAAAATTAA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
16 5 0.07
17 3 0.04
18 22 0.31
19 25 0.35
20 4 0.06
21 13 0.18
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAGAAAAGAAAAAATAA
Found at i:180547 original size:43 final size:40
Alignment explanation
Indices: 180481--180608 Score: 116
Period size: 42 Copynumber: 3.1 Consensus size: 40
180471 AAAGAAAAGG
* *
180481 AAAA-AGAAAGAAGAAAAAAAAAATGAAAGAAGAAGAAAAAA
1 AAAAGAGAAAGAA-AAAAAAAAAATAAAAGAA-AACAAAAAA
* * *
180522 TAAAAGGGAAAGAAAAAAGTAAAAATAAAAGAAAACAATAAA
1 -AAAAGAGAAAGAAAAAA-AAAAAATAAAAGAAAACAAAAAA
* *
180564 AAAAGAG-AAGAAAAAAAGAAAATTAAATAAAAAAGCAAAAAA
1 AAAAGAGAAAGAAAAAAA-AAAAATAAA-AGAAAA-CAAAAAA
180606 AAA
1 AAA
180609 GGAAGGGAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
40 17 0.24
41 11 0.15
42 24 0.34
43 19 0.27
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (40 bp):
AAAAGAGAAAGAAAAAAAAAAAATAAAAGAAAACAAAAAA
Found at i:180564 original size:25 final size:25
Alignment explanation
Indices: 180517--180564 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
180507 AAGAAGAAGA
* *
180517 AAAAATAAAAGGGAAAGAAAAAAGT
1 AAAAATAAAAGGAAAACAAAAAAGT
180542 AAAAATAAAA-GAAAACAATAAAA
1 AAAAATAAAAGGAAAACAA-AAAA
180565 AAAGAGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.08
Consensus pattern (25 bp):
AAAAATAAAAGGAAAACAAAAAAGT
Found at i:180577 original size:11 final size:11
Alignment explanation
Indices: 180482--180583 Score: 50
Period size: 11 Copynumber: 8.9 Consensus size: 11
180472 AAGAAAAGGA
180482 AAAAGAAAGAAG
1 AAAA-AAAGAAG
*
180494 AAAAAAAAAATG
1 AAAAAAAGAA-G
*
180506 AAAGAAGAAGAAA
1 AAA-AA-AAGAAG
*
180519 AAATAAAAG-GG
1 AAA-AAAAGAAG
180530 AAAGAAAA-AAG
1 AAA-AAAAGAAG
180541 TAAAAATAA-AAG
1 -AAAAA-AAGAAG
* *
180553 AAAACAATAA-
1 AAAAAAAGAAG
*
180563 AAAAAGAGAAG
1 AAAAAAAGAAG
180574 AAAAAAAGAA
1 AAAAAAAGAA
180584 AATTAAATAA
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
10 9 0.13
11 30 0.43
12 19 0.28
13 7 0.10
14 4 0.06
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:183318 original size:17 final size:17
Alignment explanation
Indices: 183296--183330 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
183286 GTAATTAGGG
183296 TTTAATAAATTAATTAA
1 TTTAATAAATTAATTAA
183313 TTTAATAAATTAATTAA
1 TTTAATAAATTAATTAA
183330 T
1 T
183331 AATGGATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAATAAATTAATTAA
Found at i:183436 original size:36 final size:37
Alignment explanation
Indices: 183346--183438 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 37
183336 ATGATAAAAA
*
183346 ATTAATC-TTTAATTTTTTATAAAATGAAAATTCTATGC
1 ATTAATCTTTTAA-TTTTTATAAAATAAAAATTCTA-GC
* *
183384 TTTAGT-TTTT-ATTTTTATAAAATAAAAATTCTA-C
1 ATTAATCTTTTAATTTTTATAAAATAAAAATTCTAGC
*
183418 ATTAATCTTTTAAATTTTATA
1 ATTAATCTTTTAATTTTTATA
183439 TTTTTTATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
34 5 0.11
35 4 0.09
36 29 0.63
37 1 0.02
38 7 0.15
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (37 bp):
ATTAATCTTTTAATTTTTATAAAATAAAAATTCTAGC
Found at i:183607 original size:23 final size:24
Alignment explanation
Indices: 183572--183616 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
183562 TAATTTCAAG
*
183572 AATATAATGATAAATA-TCAATTAA
1 AATAAAATGAT-AATAGTCAATTAA
183596 AATAAAAT-ATAATAGTCAATT
1 AATAAAATGATAATAGTCAATT
183617 TTAATATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
AATAAAATGATAATAGTCAATTAA
Found at i:184370 original size:1 final size:1
Alignment explanation
Indices: 184366--184393 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
184356 TTTAAAAAGC
184366 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
184394 TCTTGGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:184771 original size:2 final size:2
Alignment explanation
Indices: 184764--184793 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
184754 ATACCTGTAT
184764 TA 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 TA
184794 ACATTTATAA
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):
TA
Found at i:187953 original size:2 final size:2
Alignment explanation
Indices: 187948--187983 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
187938 GATCAGTTTA
*
187948 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
187984 GCTTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:193020 original size:2 final size:2
Alignment explanation
Indices: 193015--193041 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
193005 ATATATGTTT
193015 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 T
193042 TAGATTCTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:197943 original size:18 final size:18
Alignment explanation
Indices: 197920--197957 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
197910 TTATTATTTT
197920 TTTTTGTAGACAATTTAA
1 TTTTTGTAGACAATTTAA
*
197938 TTTTTGTAGACAGTTTAA
1 TTTTTGTAGACAATTTAA
197956 TT
1 TT
197958 GCTTCCTTAT
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:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (18 bp):
TTTTTGTAGACAATTTAA
Found at i:200633 original size:18 final size:18
Alignment explanation
Indices: 200602--200652 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
200592 TATTTGACAT
*
200602 TAAAAAATAATAAAA-AA
1 TAAAAAAGAATAAAAGAA
200619 TATAATAAA-AATAAAAGAA
1 TA-AA-AAAGAATAAAAGAA
200638 TAAAAAAGAATAAAA
1 TAAAAAAGAATAAAA
200653 TTAAATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.17
18 18 0.60
19 7 0.23
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (18 bp):
TAAAAAAGAATAAAAGAA
Found at i:200651 original size:10 final size:9
Alignment explanation
Indices: 200602--200652 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
200592 TATTTGACAT
200602 TAAAAAATAA
1 TAAAAAA-AA
*
200612 TAAAAAATA
1 TAAAAAAAA
*
200621 TAATAAAAA
1 TAAAAAAAA
*
200630 T-AAAAGAA
1 TAAAAAAAA
200638 TAAAAAAGAA
1 TAAAAAA-AA
200648 TAAAA
1 TAAAA
200653 TTAAATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 6 0.18
9 13 0.39
10 14 0.42
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:200870 original size:57 final size:57
Alignment explanation
Indices: 200733--200908 Score: 246
Period size: 57 Copynumber: 3.0 Consensus size: 57
200723 CCAAATTTGG
* * *
200733 TGGATTTCATATTTACTTTGCTGCCACCTAAGCTGTCT-AGATGCCACTGCATTGCATTGCAT
1 TGGATTTCATATTTAATTTGCTGCCACCTAAGCTTTTTAAG-TG----T-CATTGCATTGCAT
*
200795 TGGATTTGATATTTAATTTGCTGCCACCTAAGCTTTTTAAGTGTCATTGCATTGCAT
1 TGGATTTCATATTTAATTTGCTGCCACCTAAGCTTTTTAAGTGTCATTGCATTGCAT
*
200852 TGGATTTCATATTTAATTTGCTGCCACCTAAGCTTTTTAGGTGTCATTGCATTGCAT
1 TGGATTTCATATTTAATTTGCTGCCACCTAAGCTTTTTAAGTGTCATTGCATTGCAT
200909 GCTTTCATTT
Statistics
Matches: 107, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
57 68 0.64
58 1 0.01
62 36 0.34
63 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (57 bp):
TGGATTTCATATTTAATTTGCTGCCACCTAAGCTTTTTAAGTGTCATTGCATTGCAT
Found at i:201248 original size:20 final size:20
Alignment explanation
Indices: 201203--201242 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
201193 AAGAATTGAA
201203 GAGGGATATAAGAGAAGGAT
1 GAGGGATATAAGAGAAGGAT
* *
201223 GAGGGATGTAAGAGATGGAT
1 GAGGGATATAAGAGAAGGAT
201243 TTGGGAGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.42, T:0.17
Consensus pattern (20 bp):
GAGGGATATAAGAGAAGGAT
Found at i:201357 original size:25 final size:25
Alignment explanation
Indices: 201295--201364 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
201285 AATAAAAATT
*
201295 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
201319 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
201344 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
201365 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:201388 original size:28 final size:27
Alignment explanation
Indices: 201297--201419 Score: 96
Period size: 25 Copynumber: 4.7 Consensus size: 27
201287 TAAAAATTAG
* * *
201297 CCACCAATTTTGAC-AA-ACAACA-AG
1 CCACCATTTTTGACAAATACAAAATAA
* * *
201321 CCACCAATTTTGACAAATA-AACA-AG
1 CCACCATTTTTGACAAATACAAAATAA
* *
201346 CCTCCATATTTGACAAATACAAAGGA-AA
1 CCACCATTTTTGACAAATACAAA--ATAA
*
201374 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGACAAATACAAAATAA
*
201401 CCACCATTTTTTACAAATA
1 CCACCATTTTTGACAAATA
201420 AATGGGTGGC
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
24 14 0.17
25 24 0.29
26 4 0.05
27 19 0.23
28 22 0.27
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.23
Consensus pattern (27 bp):
CCACCATTTTTGACAAATACAAAATAA
Found at i:201410 original size:27 final size:27
Alignment explanation
Indices: 201349--201417 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
201339 AAACAAGCCT
* *
201349 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
201377 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
*
201404 CCATTTTTTACAAA
1 CCATTTTTGACAAA
201418 TAAATGGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.49
28 18 0.49
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:205951 original size:25 final size:25
Alignment explanation
Indices: 205889--205958 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
205879 AATAAAAATT
*
205889 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
205913 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
205938 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
205959 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:206004 original size:27 final size:27
Alignment explanation
Indices: 205943--206013 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
205933 AAACAAGCCT
* *
205943 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
205971 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
205998 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
206014 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:206016 original size:24 final size:24
Alignment explanation
Indices: 205891--206016 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
205881 TAAAAATTAG
* *
205891 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
205915 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
205939 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
205968 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
205995 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
206017 GGGTGGCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 13 0.15
26 4 0.05
27 20 0.24
28 17 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:206226 original size:73 final size:74
Alignment explanation
Indices: 206136--206287 Score: 261
Period size: 73 Copynumber: 2.1 Consensus size: 74
206126 GAAAACAATT
* *
206136 AAACAGCTACTGTAGCTGCTAAACAAGAAGAAGAAACGCAAGAACAAAAGCAAGTAACAGCAGCA
1 AAACAGCTACTGCAGCTGCTAAACAAGAAGAAGAAACGCAAGAACAAAAGCAAGTAACAACAGCA
206201 ACAAGAAAG
66 ACAAGAAAG
* *
206210 AAAC-GCTACTGCAGCTGCTGAACAAGAAGAAGAAATGCAAGAACAAAAGCAAGTAACAACAGCA
1 AAACAGCTACTGCAGCTGCTAAACAAGAAGAAGAAACGCAAGAACAAAAGCAAGTAACAACAGCA
206274 ACAAGAAAG
66 ACAAGAAAG
206283 AAACA
1 AAACA
206288 AAGGAATTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 69 0.95
74 4 0.05
ACGTcount: A:0.53, C:0.19, G:0.20, T:0.08
Consensus pattern (74 bp):
AAACAGCTACTGCAGCTGCTAAACAAGAAGAAGAAACGCAAGAACAAAAGCAAGTAACAACAGCA
ACAAGAAAG
Found at i:207108 original size:19 final size:19
Alignment explanation
Indices: 207084--207135 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
207074 AGCACAATCT
*
207084 AGCAGCAAAGCAACATTCC
1 AGCAGCAAAGCAACACTCC
207103 AGCAGCAAAGCAACACTCC
1 AGCAGCAAAGCAACACTCC
* *
207122 AACAACAAA-CAACA
1 AGCAGCAAAGCAACA
207136 ACAACAAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 5 0.17
19 25 0.83
ACGTcount: A:0.50, C:0.33, G:0.12, T:0.06
Consensus pattern (19 bp):
AGCAGCAAAGCAACACTCC
Found at i:210059 original size:22 final size:20
Alignment explanation
Indices: 209988--210066 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 20
209978 TGTTGGGCTG
*
209988 ATTGTATCGATACAATTCTAG
1 ATTGTATCGATAC-ATTCTAA
*
210009 A-TGTATTGATACATTCTGAA
1 ATTGTATCGATACATTCT-AA
*
210029 ATTGTATCGATACATTCCTAT
1 ATTGTATCGATACATT-CTAA
210050 ATGTGTATCGATACATT
1 AT-TGTATCGATACATT
210067 TGAAGAGTAG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.10
20 12 0.24
21 17 0.34
22 16 0.32
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
ATTGTATCGATACATTCTAA
Found at i:212890 original size:10 final size:10
Alignment explanation
Indices: 212877--212912 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
212867 GGGTTTTTCC
212877 TTTTT-TTTT
1 TTTTTGTTTT
*
212886 GTTTTGTTTT
1 TTTTTGTTTT
212896 TTTTTGTTTT
1 TTTTTGTTTT
212906 TTTTTGT
1 TTTTTGT
212913 GAAGAGTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:212897 original size:15 final size:14
Alignment explanation
Indices: 212877--212910 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
212867 GGGTTTTTCC
212877 TTTTTTTTTGTTTT
1 TTTTTTTTTGTTTT
212891 GTTTTTTTTTGTTTT
1 -TTTTTTTTTGTTTT
212906 TTTTT
1 TTTTT
212911 GTGAAGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (14 bp):
TTTTTTTTTGTTTT
Found at i:220226 original size:20 final size:18
Alignment explanation
Indices: 220184--220234 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 18
220174 ATTTGCCTGC
220184 ATGTATCGATAC-ATTTA
1 ATGTATCGATACAATTTA
*
220201 ATGTATCGATACATATTTTT
1 ATGTATCGATACA-A-TTTA
220221 ATGTATCGATACAA
1 ATGTATCGATACAA
220235 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 12 0.40
19 2 0.07
20 16 0.53
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (18 bp):
ATGTATCGATACAATTTA
Found at i:222588 original size:32 final size:29
Alignment explanation
Indices: 222518--222573 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
222508 GGACATGGGT
*
222518 GGCTGGCAAGGGTACTAGGCAGAAAGGGG
1 GGCTGGCAGGGGTACTAGGCAGAAAGGGG
*
222547 GGCTGGCAGGGGTGCTAGGCA-AAAGGG
1 GGCTGGCAGGGGTACTAGGCAGAAAGGG
222574 AAAGAGGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.25, C:0.14, G:0.50, T:0.11
Consensus pattern (29 bp):
GGCTGGCAGGGGTACTAGGCAGAAAGGGG
Found at i:226050 original size:20 final size:20
Alignment explanation
Indices: 226021--226096 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
226011 TTTTTACCCA
226021 GATGTATCGATACATTTTTC
1 GATGTATCGATACATTTTTC
* * *
226041 GATATATCGATACATGTAT-
1 GATGTATCGATACATTTTTC
* *
226060 GAATGTATCGATATATTCTTC
1 G-ATGTATCGATACATTTTTC
*
226081 AATGTATCGATACATT
1 GATGTATCGATACATT
226097 ATATCTTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (20 bp):
GATGTATCGATACATTTTTC
Found at i:227032 original size:23 final size:23
Alignment explanation
Indices: 227005--227061 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
226995 AGCCTTTGAC
227005 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
227028 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
227051 CATGCATTTTT
1 CATGCATTTTT
227062 AACATGTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:227068 original size:20 final size:21
Alignment explanation
Indices: 227013--227068 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 21
227003 ACCATGCATT
**
227013 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
227034 TTTTTTTTATTATGTTTCATGCA
1 --TTTTTTAACATGTTTCATGCA
227057 -TTTTTAACATGT
1 TTTTTTAACATGT
227069 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 10 0.32
23 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:240136 original size:12 final size:12
Alignment explanation
Indices: 240119--240172 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
240109 CTTTACACCC
240119 AAAAAAAAAAC-
1 AAAAAAAAAACA
*
240130 AAAAAAAAAGCA
1 AAAAAAAAAACA
240142 AAAAAAAAAACA
1 AAAAAAAAAACA
*
240154 AAACAAAAAACA
1 AAAAAAAAAACA
240166 AAAAAAA
1 AAAAAAA
240173 GAAAAAATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
11 10 0.26
12 28 0.74
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:240145 original size:23 final size:24
Alignment explanation
Indices: 240119--240172 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
240109 CTTTACACCC
*
240119 AAAAAAAAAACAAAA-AAAAAGCA
1 AAAAAAAAAACAAAACAAAAAACA
240142 AAAAAAAAAACAAAACAAAAAACA
1 AAAAAAAAAACAAAACAAAAAACA
240166 AAAAAAA
1 AAAAAAA
240173 GAAAAAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAACAAAACAAAAAACA
Found at i:240190 original size:1 final size:1
Alignment explanation
Indices: 240119--240179 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
240109 CTTTACACCC
* ** * * * *
240119 AAAAAAAAAACAAAAAAAAAGCAAAAAAAAAAACAAAACAAAAAACAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
240180 TAGGAAAAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:241507 original size:28 final size:28
Alignment explanation
Indices: 241374--242289 Score: 1094
Period size: 28 Copynumber: 32.2 Consensus size: 28
241364 GAATGTTCAT
241374 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
241402 CTCCTTTCAAAGCCCATAAGACAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
241431 CTCTTTTCAAAGCCCACAAATCAATGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
241460 CTCTTTTTAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
241489 CCATTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
241517 -CC-TTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
241543 CCCTTGCAGAAGCCCGCAATTCAGT-GCA
1 CCCTTTCA-AAGCCCACAAGTCAGTGGCA
*
241571 CTCTTTCAAAAGCCCACAAGTCAGTGGCA
1 CCCTTTC-AAAGCCCACAAGTCAGTGGCA
*
241600 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
241628 -CCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
241655 CCCTTGCGAAGCCCACAA-TCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
241682 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
241710 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
241738 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* *
241768 CCCTTTTAGAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
241796 -CCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
241823 CCCTTGCGAAGCCCACAATTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
241851 CTCTTTTAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
241879 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* *
241909 CTCCTTTTAAAAGCCCACGCAAGTTAGTGGCA
1 C-CC-TTTCAAAGCCCA--CAAGTCAGTGGCA
* *
241941 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
241969 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
241997 CTCTTTCAAAAGCCCACAAGTCAGTGGCA
1 CCCTTTC-AAAGCCCACAAGTCAGTGGCA
* * * *
242026 CCCTTGCGAAGCCCATAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
242054 CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
242082 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
242110 CCCTTGCGAAAGCCC-CTAATTCAGTGGCA
1 CCCTTTC-AAAGCCCAC-AAGTCAGTGGCA
* * *
242139 CGCTTTGAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
242167 CCC-TTCGAAGCCCACAAGTCAGTGGGCAA
1 CCCTTTCAAAGCCCACAAGTCAGT-GGC-A
* * *
242196 CCCTTGCGAAGCCCACAAATTCAGTGGCAA
1 CCCTTTCAAAGCCCAC-AAGTCAGTGGC-A
*
242226 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
242254 CCCTTTCAAAGCCGACAACAAGT-AGTGGCA
1 CCCTTTCAAAGCC--C-ACAAGTCAGTGGCA
242284 CTCCTT
1 C-CCTT
Statistics
Matches: 770, Mismatches: 89, Indels: 55
0.84 0.10 0.06
Matches are distributed among these distances:
26 23 0.03
27 93 0.12
28 354 0.46
29 167 0.22
30 91 0.12
31 22 0.03
32 20 0.03
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:241818 original size:113 final size:112
Alignment explanation
Indices: 241374--242289 Score: 1103
Period size: 113 Copynumber: 8.0 Consensus size: 112
241364 GAATGTTCAT
* * *
241374 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCATAAGACAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
* * *
241439 AAAGCCCACAAATCAATGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCA
64 AAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCA
* * *
241489 CCATTTCAAAGCCCACAAGTCAGTGGCA-CC-TTCGAAGCCCACAAGTCAGTGGCACCCTTGCAG
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA-
* *
241552 AAGCCCGCAATTCAGT-GCACTCTTTCAAAAGCCCACAAGTCAGTGGCA
65 AAGCCCACAAGTCAGTGGCACTCTTTC-AAAGCCCACAAGTCAGTGGCA
* * * *
241600 CCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTCGAAGCCCACAAGTCAGTGGCACCCTTGCGA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
241664 AGCCCACAA-TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
66 AGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
*
241710 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACCCTTTT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCACCCTTTC
* *
241775 AGAGCCCACAAGTCAGTGGCAC-CTTTCGAAGCCCACAAGTCAGTGGCA
64 AAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * *
241823 CCCTTGCGAAGCCCACAATTTAGTGGCACTCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
* *
241888 AGCCCACACAAGTCAGTGGCACTCCTTTTAAAAGCCCACGCAAGTTAGTGGCA
66 AG-CC-CACAAGTCAGTGGCACT-C-TTTCAAAGCCCA--CAAGTCAGTGGCA
* * * * *
241941 CCTTTTCAAAGCCCACGAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC-A
* * * * *
242006 AAGCCCACAAGTCAGTGGCACCCTTGCGAAGCCCATAATTCAGTGGCA
65 AAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
242054 CTCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCACCCTTGCGA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC-A
* * * *
242119 AAGCCC-CTAATTCAGTGGCACGCTTTGAAAGCCCACAAGTTAGTGGCA
65 AAGCCCAC-AAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
242167 CCC-TTCGAAGCCCACAAGTCAGTGGGCAACCCTTGCGAAGCCCACAAATTCAGTGGCAACTCTT
1 CCCTTTCAAAGCCCACAAGTCAGT-GGC-ACCCTTTCAAAGCCCAC-AAGTCAGTGGC-ACCCTT
*
242231 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCGACAACAAGT-AGTGGCA
62 TCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCC--C-ACAAGTCAGTGGCA
242284 CTCCTT
1 C-CCTT
Statistics
Matches: 696, Mismatches: 78, Indels: 50
0.84 0.09 0.06
Matches are distributed among these distances:
110 56 0.08
111 112 0.16
112 91 0.13
113 213 0.31
114 26 0.04
115 76 0.11
116 18 0.03
117 25 0.04
118 74 0.11
119 5 0.01
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (112 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
AGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:241838 original size:141 final size:139
Alignment explanation
Indices: 241375--242289 Score: 1079
Period size: 141 Copynumber: 6.4 Consensus size: 139
241365 AATGTTCATC
* * * *
241375 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCATAAGACAGTGGCACTCTTTTCA
1 CCTTTCGAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
* * * * * *
241440 AAGCCCACAAATCAATGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCACCATTTCAAAGCCCAC
64 AAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCAC
241505 AAGTCAGTGGCA
128 AAGTCAGTGGCA
* * * *
241517 CC-TTCGAAGCCCACAAGTCAGTGGCACCCTTGCAGAAGCCCGCAATTCAGT-GCACTCTTTCAA
1 CCTTTCGAAGCCCACAAGTCAGTGGCACCCTTTCA-AAGCCCACAAGTCAGTGGCACCCTTTC-A
* **
241580 AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTCGAAGCCCACA
64 AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACA
241644 AGTCAGTGGCA
129 AGTCAGTGGCA
* *
241655 CCCTTGCGAAGCCCACAA-TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 -CCTTTCGAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
*
241719 AGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACCCTTTTAGAGCCCAC
65 AGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCACCCTTTTAAAGCCCAC
241784 AAGTCAGTGGCA
128 AAGTCAGTGGCA
* * * * * *
241796 CCTTTCGAAGCCCACAAGTCAGTGGCACCCTTGCGAAGCCCACAATTTAGTGGCACTCTTTTAAA
1 CCTTTCGAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
241861 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAAGCCCA
66 GCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTTTT-AAAGCCCA
*
241926 CGCAAGTTAGTGGCA
127 --CAAGTCAGTGGCA
* * * * *
241941 CCTTTTCAAAGCCCACGAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAA
1 CC-TTTCGAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC-A
* * * * * *
242006 AAGCCCACAAGTCAGTGGCACCCTTGCGAAGCCCATAATTCAGTGGCACTCTTTCAAAGCCCACA
64 AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACA
*
242071 AGTTAGTGGCA
129 AGTCAGTGGCA
* * * *
242082 CCCTTTCGAAGCCCACAAGTCAGTGGCACCCTTGCGAAAGCCC-CTAATTCAGTGGCACGCTTTG
1 -CCTTTCGAAGCCCACAAGTCAGTGGCACCCTTTC-AAAGCCCAC-AAGTCAGTGGCACCCTTTC
* * ***
242146 AAAGCCCACAAGTTAGTGGCACCC-TTCGAAGCCCACAAGTCAGTGGGCAACCCTTGCGAAGCCC
63 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGT-GGC-ACCCTTTTAAAGCCC
*
242210 ACAAATTCAGTGGCAA
126 AC-AAGTCAGTGGC-A
*
242226 CTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCGACAACAAGT-AGTGGCACTCCTT
1 C-CTTTCGAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC--C-ACAAGTCAGTGGCAC-CCTT
Statistics
Matches: 674, Mismatches: 71, Indels: 52
0.85 0.09 0.07
Matches are distributed among these distances:
138 71 0.11
139 56 0.08
140 90 0.13
141 217 0.32
142 46 0.07
143 31 0.05
144 36 0.05
145 37 0.05
146 59 0.09
147 31 0.05
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.20
Consensus pattern (139 bp):
CCTTTCGAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAG
TCAGTGGCA
Done.