Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold265
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: 864291
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 3 of 6
Found at i:331994 original size:13 final size:13
Alignment explanation
Indices: 331976--332000 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331966 ATTACTCAAA
331976 TGTATCGATACAT
1 TGTATCGATACAT
331989 TGTATCGATACA
1 TGTATCGATACA
332001 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:332102 original size:52 final size:52
Alignment explanation
Indices: 332009--332132 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
331999 CACTGATCTT
*
332009 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
332060 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
332112 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
332133 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
51 19 0.28
52 49 0.72
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:337829 original size:11 final size:10
Alignment explanation
Indices: 337809--337878 Score: 68
Period size: 11 Copynumber: 6.4 Consensus size: 10
337799 TCTTCGTACC
337809 AAAAAAACAA
1 AAAAAAACAA
337819 AAAAAAGACAA
1 AAAAAA-ACAA
*
337830 AAAAAACCAA
1 AAAAAAACAA
337840 GGAAAAAAACAA
1 --AAAAAAACAA
*
337852 AAAACAAAAAA
1 AAAA-AAACAA
337863 AAAACAAACGAA
1 AAAA-AAAC-AA
337875 AAAA
1 AAAA
337879 TGGTCCAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
10 13 0.25
11 23 0.45
12 15 0.29
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:337838 original size:29 final size:28
Alignment explanation
Indices: 337806--337864 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
337796 CGTTCTTCGT
* *
337806 ACCAAAAAAACAAAAAAAAGACAAAAAAA
1 ACCAAGAAAA-AAAAAAAAAACAAAAAAA
*
337835 ACCAAGGAAAAAAACAAAAAACAAAAAAA
1 ACCAA-GAAAAAAAAAAAAAACAAAAAAA
337864 A
1 A
337865 AACAAACGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.81, C:0.14, G:0.05, T:0.00
Consensus pattern (28 bp):
ACCAAGAAAAAAAAAAAAAACAAAAAAA
Found at i:337860 original size:15 final size:16
Alignment explanation
Indices: 337809--337878 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
337799 TCTTCGTACC
* *
337809 AAAAAAACAAAAAAAAG
1 AAAAAAA-AAACAAACG
* * *
337826 ACAAAAAAAACCAAGG
1 AAAAAAAAAACAAACG
337842 AAAAAAACAAA-AAAC-
1 AAAAAAA-AAACAAACG
337857 AAAAAAAAAACAAACG
1 AAAAAAAAAACAAACG
337873 AAAAAA
1 AAAAAA
337879 TGGTCCAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
14 3 0.07
15 11 0.26
16 20 0.47
17 9 0.21
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAACG
Found at i:339155 original size:28 final size:28
Alignment explanation
Indices: 339124--339479 Score: 412
Period size: 28 Copynumber: 12.5 Consensus size: 28
339114 TGTTCATCTC
* * *
339124 TTCAAAGCCCACAGGTCAATGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
339152 TTCAAAGCCTACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
339180 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
339208 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
339236 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
339263 CTTCAAAAGACCACAAGTCAGTAGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
*
339293 TTCAAAGCCCACAAGCCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * * * *
339321 TTCAAAACCCACAAGTTAGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
339349 TTCAAAGCCCACAAGTCAATGGCAACCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
339377 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
339407 TTCAAAGCTCACAAGTCGGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * *
339435 TTTAAAGCCCATACAAGTCAGTAGCAACTCTT
1 TTCAAAGCCC--ACAAGTCAGTGGC-A-TCCT
339467 TTCAAAGCCCACA
1 TTCAAAGCCCACA
339480 CAAGTTAGTG
Statistics
Matches: 280, Mismatches: 35, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.02
28 196 0.70
29 25 0.09
30 41 0.15
31 1 0.00
32 10 0.04
33 1 0.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:339386 original size:141 final size:139
Alignment explanation
Indices: 339118--339489 Score: 458
Period size: 141 Copynumber: 2.6 Consensus size: 139
339108 CTAGAATGTT
* * * * *
339118 CATCTCTTCAAAGCCCACAGGTCAATGGCATCTTTTCAAAGCCTACAAGTCAGTGGCACCCTTTC
1 CATCTCTTCAAAG-CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTC
* * * * *
339183 AAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC
65 AAAACCCACAAGTTAGTGGCACCCCTTCAAAGCCCACAAGTCAATGGCAACCTTTCAAAGCCCAC
339248 AAGTCAGTGG
130 AAGTCAGTGG
* *
339258 CATCTCTTCAAAAGACCACAAGTCAGTAGCATCCTTTCAAAGCCCACAAGCCAGTGGCACCTTTT
1 CATCTCTTC-AAAG-CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTT
*
339323 CAAAACCCACAAGTTAGTGGTACCCCTTCAAAGCCCACAAGTCAATGGCAACCTTTCAAAGCCCA
64 CAAAACCCACAAGTTAGTGGCACCCCTTCAAAGCCCACAAGTCAATGGCAACCTTTCAAAGCCCA
339388 CAAGTCAGTGG
129 CAAGTCAGTGG
* * * *
339399 CATACCCTTTCAAAGCTCACAAGTCGGTGGCA-CCTTTTTAAAGCCCATACAAGTCAGTAGCAAC
1 CAT-CTC-TTCAAAGC-CACAAGTCAGTGGCATCC-TTTCAAAGCCC--ACAAGTCAGTGGC-AC
*
339463 TCTTTTCAAAGCCCACACAAGTTAGTG
59 -CTTTTCAAA-ACC-CACAAGTTAGTG
339490 ACACTTTTTT
Statistics
Matches: 200, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
140 9 0.05
141 123 0.62
142 29 0.14
143 3 0.01
144 11 0.05
145 2 0.01
146 9 0.05
147 2 0.01
148 12 0.06
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (139 bp):
CATCTCTTCAAAGCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCA
AAACCCACAAGTTAGTGGCACCCCTTCAAAGCCCACAAGTCAATGGCAACCTTTCAAAGCCCACA
AGTCAGTGG
Found at i:340429 original size:20 final size:20
Alignment explanation
Indices: 340404--340579 Score: 82
Period size: 20 Copynumber: 7.8 Consensus size: 20
340394 TTTTACCCAG
340404 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
340424 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
340444 ATGTATCGATACATTCTATCTTTTTACCTAA
1 ATGTATCGAT--A--C-A--TTTTT--C--A
*
340475 ATGTATCGATAAATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
340495 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
340515 ATGTATCGATACATCTGTCTTTTTACCCA
1 ATGTATCGATACA------TTTTT---CA
*
340544 GATGTATCGATACATTCTTCA
1 -ATGTATCGATACATTTTTCA
340565 ATGTATCGATACATT
1 ATGTATCGATACATT
340580 CTGTCTTTTT
Statistics
Matches: 118, Mismatches: 17, Indels: 42
0.67 0.10 0.24
Matches are distributed among these distances:
20 70 0.59
21 2 0.02
22 2 0.02
24 10 0.08
25 1 0.01
26 4 0.03
27 3 0.03
29 2 0.02
30 13 0.11
31 11 0.09
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:340551 original size:30 final size:30
Alignment explanation
Indices: 340515--340609 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 30
340505 ACATGTATGA
340515 ATGTATCGATACATCTGTCTTTTTACCCAG
1 ATGTATCGATACATCTGTCTTTTTACCCAG
340545 ATGTATCGATACA--T-TC---TT---CA-
1 ATGTATCGATACATCTGTCTTTTTACCCAG
340565 ATGTATCGATACATTCTGTCTTTTTACCCAG
1 ATGTATCGATACA-TCTGTCTTTTTACCCAG
*
340596 ATGTATTGATACAT
1 ATGTATCGATACAT
340610 TTTTCAATGT
Statistics
Matches: 53, Mismatches: 1, Indels: 22
0.70 0.01 0.29
Matches are distributed among these distances:
20 13 0.25
21 2 0.04
23 1 0.02
24 4 0.08
27 4 0.08
28 1 0.02
30 16 0.30
31 12 0.23
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (30 bp):
ATGTATCGATACATCTGTCTTTTTACCCAG
Found at i:340571 original size:70 final size:71
Alignment explanation
Indices: 340393--340578 Score: 311
Period size: 71 Copynumber: 2.6 Consensus size: 71
340383 AAAAGTCACA
*
340393 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATTGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
340458 TCTATC
66 TCTATC
* * *
340464 TTTTTACCTAAATGTATCGATAAATTTTTCAATGTATCGATACATGTATGAATGTATCGATACA-
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
*
340528 TCTGTC
66 TCTATC
*
340534 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
340579 TCTGTCTTTT
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
70 46 0.43
71 60 0.57
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
TCTATC
Found at i:340607 original size:51 final size:51
Alignment explanation
Indices: 340495--340630 Score: 213
Period size: 51 Copynumber: 2.7 Consensus size: 51
340485 AAATTTTTCA
* *
340495 ATGTATCGATACATGT-ATGAATGTATCGATACA-TCTGTCTTTTTACCCAG
1 ATGTATCGATACAT-TCTTCAATGTATCGATACATTCTGTCTTTTTACCCAG
340545 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAG
* *
340596 ATGTATTGATACATTTTTCAATGTATCGATACATT
1 ATGTATCGATACATTCTTCAATGTATCGATACATT
340631 GAATAATGTA
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
49 1 0.01
50 29 0.36
51 50 0.62
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (51 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAG
Found at i:345687 original size:45 final size:45
Alignment explanation
Indices: 345616--345705 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
345606 ATCCTCTTGC
*
345616 ATATCATGAATGATGGACCACCATAATCTTAAAAGAAAGTGACAT
1 ATATCATGAATGATGGACCACAATAATCTTAAAAGAAAGTGACAT
*
345661 ATATCAT-ATATGATGGGCCACAATAATCTTAAAAGAAAGTGACAT
1 ATATCATGA-ATGATGGACCACAATAATCTTAAAAGAAAGTGACAT
345706 TTATGGCATG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (45 bp):
ATATCATGAATGATGGACCACAATAATCTTAAAAGAAAGTGACAT
Found at i:348121 original size:17 final size:17
Alignment explanation
Indices: 348099--348144 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
348089 AAAAATTTAA
348099 AATTTTTTATTTAATTT
1 AATTTTTTATTTAATTT
*
348116 AATTTTATA-TT-ATTT
1 AATTTTTTATTTAATTT
*
348131 ATATTTATTATTTA
1 A-ATTTTTTATTTA
348145 TAATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
15 5 0.22
16 8 0.35
17 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTTTATTTAATTT
Found at i:348208 original size:64 final size:63
Alignment explanation
Indices: 348089--348213 Score: 139
Period size: 64 Copynumber: 2.0 Consensus size: 63
348079 TTACCATCTA
* * * *
348089 AAAAATTTAAAATTTTTTATTTAATTTAATTTTATATTATTTATATTTATTATTTATAATAAAT
1 AAAAATTTAAAAATTATTATTTAATTTAATTTTATATTATTTATAATTATAATTTA-AATAAAT
* *
348153 AAAAATTTAAAAAATTATT-TTTAGTTTTATATTTATA-TATTTTATAATTA-AATTTAAATAA
1 AAAAATTT-AAAAATTATTATTTAATTTAAT-TTTATATTA-TTTATAATTATAATTTAAATAA
348214 TTTTTTTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
63 5 0.10
64 24 0.46
65 23 0.44
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (63 bp):
AAAAATTTAAAAATTATTATTTAATTTAATTTTATATTATTTATAATTATAATTTAAATAAAT
Found at i:348572 original size:25 final size:25
Alignment explanation
Indices: 348538--348585 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
348528 ACAAAAGTTA
348538 ATATCTAAATAAGTTTTTATTTTTT
1 ATATCTAAATAAGTTTTTATTTTTT
*
348563 ATATTTAAATAAGTTTTTATTTT
1 ATATCTAAATAAGTTTTTATTTT
348586 AATTAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
ATATCTAAATAAGTTTTTATTTTTT
Found at i:348650 original size:22 final size:23
Alignment explanation
Indices: 348607--348656 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
348597 ATAATTTATG
348607 TTAAAATTTTATTTAAATATAAA
1 TTAAAATTTTATTTAAATATAAA
348630 TTAAAATATTT-TTT-AATATAAA
1 TTAAAAT-TTTATTTAAATATAAA
348652 TTAAA
1 TTAAA
348657 GGTTAGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.50
23 10 0.38
24 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAAATTTTATTTAAATATAAA
Found at i:348939 original size:29 final size:29
Alignment explanation
Indices: 348873--348941 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
348863 TACAGCTAGT
*
348873 AATGAATTTTTTTAATCAAAATTGAATTTTA
1 AATGAA-TTTTTT-ATCAAAATTAAATTTTA
*
348904 ACCTGAATTTTTT-TCAAAATTAAAATTTTA
1 A-ATGAATTTTTTATCAAAATT-AAATTTTA
348934 AATGAATT
1 AATGAATT
348942 AAATTATTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 14 0.42
30 8 0.24
31 7 0.21
32 4 0.12
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (29 bp):
AATGAATTTTTTATCAAAATTAAATTTTA
Found at i:349594 original size:22 final size:22
Alignment explanation
Indices: 349554--349595 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
349544 ATTAAAAAAT
*
349554 TATTTTTATGTTAATATTTATA
1 TATTTTTATATTAATATTTATA
349576 TATTTTTATAATTAA-ATTTA
1 TATTTTTAT-ATTAATATTTA
349596 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTTTTATATTAATATTTATA
Found at i:350162 original size:10 final size:9
Alignment explanation
Indices: 350141--350178 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
350131 TAATTTAATT
350141 TTTTATAT-
1 TTTTATATA
350149 TTTTATAATA
1 TTTTAT-ATA
350159 TTTTATATA
1 TTTTATATA
350168 -TTTATATA
1 TTTTATATA
350176 TTT
1 TTT
350179 AATTCGATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 14 0.52
9 7 0.26
10 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTATATA
Found at i:350162 original size:18 final size:18
Alignment explanation
Indices: 350136--350178 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
350126 GAACATAATT
* *
350136 TAATTTTTTATATTTTTA
1 TAATATTTTATATATTTA
350154 TAATATTTTATATATTTA
1 TAATATTTTATATATTTA
350172 T-ATATTT
1 TAATATTT
350179 AATTCGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATATTTTATATATTTA
Found at i:350167 original size:20 final size:20
Alignment explanation
Indices: 350138--350175 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
350128 ACATAATTTA
* *
350138 ATTTTTTATATTTTTATAAT
1 ATTTTATATATTTATATAAT
350158 ATTTTATATATTTATATA
1 ATTTTATATATTTATATA
350176 TTTAATTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTATATATTTATATAAT
Found at i:352528 original size:10 final size:10
Alignment explanation
Indices: 352513--352547 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
352503 TTTAGTTCCC
352513 ATTAACTTTA
1 ATTAACTTTA
352523 ATTAACTTTA
1 ATTAACTTTA
*
352533 ATTAATTTTA
1 ATTAACTTTA
352543 GATTA
1 -ATTA
352548 TAAGAGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (10 bp):
ATTAACTTTA
Found at i:353092 original size:20 final size:22
Alignment explanation
Indices: 353064--353106 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
353054 AAATATATAT
353064 AAATATATAA-TACTTAAAATA
1 AAATATATAACTACTTAAAATA
*
353085 AAAT-TATAACTAGTTAAAATA
1 AAATATATAACTACTTAAAATA
353106 A
1 A
353107 TATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATATATAACTACTTAAAATA
Found at i:355113 original size:20 final size:18
Alignment explanation
Indices: 355054--355117 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 18
355044 ATATGATATA
* *
355054 AATATAAAATAAAAAATTAA
1 AATATAACATAAAAAA--AT
355074 AATATAACATAAAAAAAT
1 AATATAACATAAAAAAAT
*
355092 AATATGAACGTAAAATAAAT
1 AATAT-AACATAAAA-AAAT
355112 AA-ATAA
1 AATATAA
355118 ATATATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 8 0.21
19 10 0.26
20 21 0.54
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
AATATAACATAAAAAAAT
Found at i:355576 original size:23 final size:23
Alignment explanation
Indices: 355549--355613 Score: 94
Period size: 25 Copynumber: 2.7 Consensus size: 23
355539 TAAAATAATG
355549 TTATTATTCCCATATATAAATTT
1 TTATTATTCCCATATATAAATTT
*
355572 TTATTATTTCCATATATATAAATTT
1 TTATTA-TTCC-CATATATAAATTT
*
355597 TTAGTATTCCCATATAT
1 TTATTATTCCCATATAT
355614 TTATATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 12 0.32
24 8 0.22
25 17 0.46
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTATTCCCATATATAAATTT
Found at i:355683 original size:2 final size:2
Alignment explanation
Indices: 355678--355717 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
355668 TTAAAAAATG
*
355678 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA -A G- GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
355718 TGGGTTTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:357514 original size:19 final size:19
Alignment explanation
Indices: 357477--357514 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
357467 ATAATTAAAT
*
357477 TTAAATAAAAATATTTTTA
1 TTAAATAAAAATATATTTA
357496 TTAAATAAATAATA-ATTTA
1 TTAAATAAA-AATATATTTA
357515 AACTTAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATAAAAATATATTTA
Found at i:358266 original size:26 final size:25
Alignment explanation
Indices: 358228--358278 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
358218 TTGTTTGTAC
*
358228 TATAGTATAAAAAATATTTTAATTTT
1 TATAGTAT-AAAAATAGTTTAATTTT
* *
358254 TATATTATTAAAATAGTTTAATTTT
1 TATAGTATAAAAATAGTTTAATTTT
358279 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TATAGTATAAAAATAGTTTAATTTT
Found at i:358288 original size:24 final size:25
Alignment explanation
Indices: 358238--358291 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
358228 TATAGTATAA
*
358238 AAAATATTTTAATTTTTATATTATT
1 AAAATAGTTTAATTTTTATATTATT
* *
358263 AAAATAGTTTAA-TTTTATTTTTTT
1 AAAATAGTTTAATTTTTATATTATT
358287 AAAAT
1 AAAAT
358292 TATAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
AAAATAGTTTAATTTTTATATTATT
Found at i:358941 original size:22 final size:24
Alignment explanation
Indices: 358916--358975 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 24
358906 AATATAAATT
*
358916 ATTATTAAATAAAAAT-TTTA-AA
1 ATTATTAAATAAAAATATATATAA
358938 ATTAATT-AATAAAAATATATATAA
1 ATT-ATTAAATAAAAATATATATAA
358962 ATT-TTAAAATAAAA
1 ATTATT-AAATAAAA
358976 TAATATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 14 0.44
23 6 0.19
24 12 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTATTAAATAAAAATATATATAA
Found at i:358972 original size:18 final size:19
Alignment explanation
Indices: 358949--359001 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
358939 TTAATTAATA
358949 AAAATATATATAA-ATTTT
1 AAAATATATATAATATTTT
*
358967 AAAATA-AAATAATATTTT
1 AAAATATATATAATATTTT
*
358985 AATAATATATATTATAT
1 AA-AATATATATAATAT
359002 ATAACTAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 5 0.17
18 13 0.45
19 4 0.14
20 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATATATATAATATTTT
Found at i:360459 original size:17 final size:17
Alignment explanation
Indices: 360439--360473 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
360429 TTTAGTATAT
*
360439 TTAATATTTTTTTAAAA
1 TTAAAATTTTTTTAAAA
360456 TTAAAATTTTTTTAAAA
1 TTAAAATTTTTTTAAAA
360473 T
1 T
360474 ATTTAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAAATTTTTTTAAAA
Found at i:366460 original size:15 final size:15
Alignment explanation
Indices: 366427--366460 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
366417 TGTATAAAAT
*
366427 TTTAAAAAAATTTTA
1 TTTAAAAAAATTTAA
366442 -TTAAAAAAATTTAA
1 TTTAAAAAAATTTAA
366456 TTTAA
1 TTTAA
366461 TATAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAAAAAAATTTAA
Found at i:369763 original size:2 final size:2
Alignment explanation
Indices: 369758--369786 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
369748 TATGAAATGA
369758 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
369787 GGAGTTATGG
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:371225 original size:6 final size:6
Alignment explanation
Indices: 371214--371261 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
371204 AACCAACCCT
* * *
371214 TCCCCC TCCCCC TCCCCC TCCTCC TCCCTCC TCCCCT TCCCCT TCCCC
1 TCCCCC TCCCCC TCCCCC TCCCCC TCCC-CC TCCCCC TCCCCC TCCCC
371262 AATGCTTATG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
6 32 0.84
7 6 0.16
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (6 bp):
TCCCCC
Found at i:379112 original size:2 final size:2
Alignment explanation
Indices: 379105--379135 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
379095 TCTGTCCTTG
379105 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
379136 GCATTGTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:379877 original size:12 final size:12
Alignment explanation
Indices: 379862--379891 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
379852 TTCTTTTTTT
379862 AATCATTCAATC
1 AATCATTCAATC
*
379874 AATCAATCAATC
1 AATCATTCAATC
379886 AATCAT
1 AATCAT
379892 CCACCATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (12 bp):
AATCATTCAATC
Found at i:380563 original size:56 final size:57
Alignment explanation
Indices: 380450--380573 Score: 155
Period size: 57 Copynumber: 2.2 Consensus size: 57
380440 CAATAAAAAT
* *
380450 TTAAAATTTCTTATTTATAATCAAATAAATCTATTGAATAAAAATATTTTAATGAAA
1 TTAAATTTTTTTATTTATAATCAAATAAATCTATTGAATAAAAATATTTTAATGAAA
* * *
380507 TTAAATTTTTTTATTTATAAATTAAATAAATTTTATT-AAT-AAACTA-TTTAATGAAA
1 TTAAATTTTTTTATTTAT-AATCAAATAAA-TCTATTGAATAAAAATATTTTAATGAAA
*
380563 TTAAATATTTT
1 TTAAATTTTTT
380574 CGTAAAAAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
56 20 0.34
57 21 0.36
58 13 0.22
59 5 0.08
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (57 bp):
TTAAATTTTTTTATTTATAATCAAATAAATCTATTGAATAAAAATATTTTAATGAAA
Found at i:381435 original size:16 final size:16
Alignment explanation
Indices: 381391--381435 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
381381 TTATTACGTG
*
381391 ATAAATTTAAAAGAATA
1 ATAAA-TTAAAATAATA
381408 ATAAATTAAAATAATA
1 ATAAATTAAAATAATA
381424 ATGAAA-TAAAAT
1 AT-AAATTAAAAT
381436 TATACTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (16 bp):
ATAAATTAAAATAATA
Found at i:381552 original size:15 final size:17
Alignment explanation
Indices: 381522--381555 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
381512 AATCATTGAT
381522 AAAATATAATATATAAA
1 AAAATATAATATATAAA
381539 AAAAT-TAATA-ATAAA
1 AAAATATAATATATAAA
381554 AA
1 AA
381556 TATCATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATAATATATAAA
Found at i:382035 original size:13 final size:12
Alignment explanation
Indices: 382015--382074 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 12
382005 TTTGATATTT
382015 TTAAATATAATA
1 TTAAATATAATA
382027 TTAAAATATAA-A
1 TT-AAATATAATA
*
382039 ATAAATATAATA
1 TTAAATATAATA
* *
382051 TTTTTAATA-AGTA
1 --TTAAATATAATA
382064 TTAAATATAAT
1 TTAAATATAAT
382075 TAGTATAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
11 14 0.38
12 7 0.19
13 11 0.30
14 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TTAAATATAATA
Found at i:383040 original size:21 final size:20
Alignment explanation
Indices: 383016--383094 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 20
383006 TTCATATTAA
*
383016 ATAAAATTATATGAATATAAT
1 ATAAAATAATAT-AATATAAT
*
383037 ATAAAATAATTAAAATATAAT
1 ATAAAATAA-TATAATATAAT
*
383058 AT-AAATAATATAA-ATATT
1 ATAAAATAATATAATATAAT
* *
383076 TTAAAATTTATATAATATA
1 ATAAAA-TAATATAATATA
383095 TATTATTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.10
19 7 0.15
20 13 0.27
21 21 0.44
22 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
ATAAAATAATATAATATAAT
Found at i:383052 original size:9 final size:10
Alignment explanation
Indices: 383016--383071 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
383006 TTCATATTAA
*
383016 ATAAAATTAT
1 ATAAAATAAT
*
383026 ATGAATATAAT
1 AT-AAAATAAT
383037 ATAAAATAAT
1 ATAAAATAAT
383047 -TAAAAT-AT
1 ATAAAATAAT
383055 AATATAAATAAT
1 -ATA-AAATAAT
383067 ATAAA
1 ATAAA
383072 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
8 2 0.05
9 6 0.16
10 13 0.34
11 15 0.39
12 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
ATAAAATAAT
Found at i:383063 original size:11 final size:11
Alignment explanation
Indices: 383024--383172 Score: 66
Period size: 11 Copynumber: 14.1 Consensus size: 11
383014 AAATAAAATT
*
383024 ATATGAATATA
1 ATATAAATATA
383035 ATATAAA-ATA
1 ATATAAATATA
383045 AT-TAAAATATA
1 ATAT-AAATATA
383056 ATAT-AA-ATA
1 ATATAAATATA
*
383065 ATATAAATATT
1 ATATAAATATA
* *
383076 TTA-AAAT-TT
1 ATATAAATATA
383085 ATATAATATATA
1 ATATAA-ATATA
* *
383097 TTATTAATATA
1 ATATAAATATA
* *
383108 TTA-AAAT-TT
1 ATATAAATATA
383117 ATATAAATATA
1 ATATAAATATA
* * *
383128 AAAT-ATTTTAA
1 ATATAAATAT-A
*
383139 ATATAATTATA
1 ATATAAATATA
* *
383150 GTAT-AATAAAA
1 ATATAAAT-ATA
383161 ATATAAATATA
1 ATATAAATATA
383172 A
1 A
383173 CATATGAATT
Statistics
Matches: 103, Mismatches: 21, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
9 15 0.15
10 30 0.29
11 45 0.44
12 13 0.13
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (11 bp):
ATATAAATATA
Found at i:383090 original size:25 final size:25
Alignment explanation
Indices: 383062--383139 Score: 75
Period size: 32 Copynumber: 2.8 Consensus size: 25
383052 TATAATATAA
383062 ATAATATAAATATTTTAAAATTTAT
1 ATAATATAAATATTTTAAAATTTAT
383087 ATAATATATATTATTAATATATTAAAATTTAT
1 ATAATATA-A--A-T-AT-T-TTAAAATTTAT
383119 ATAAATATAAAATATTTTAAA
1 AT-AATAT-AAATATTTTAAA
383140 TATAATTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
25 8 0.18
26 1 0.02
27 5 0.11
28 2 0.05
29 3 0.07
30 3 0.07
31 2 0.05
32 13 0.30
33 6 0.14
34 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAATATAAATATTTTAAAATTTAT
Found at i:383107 original size:20 final size:17
Alignment explanation
Indices: 383094--383144 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 17
383084 TATATAATAT
383094 ATATTATTAATATATTAAA
1 ATATTATTAA-ATA-TAAA
383113 AT-TTATATAAATATAAA
1 ATATTAT-TAAATATAAA
383130 ATATT-TTAAATATAA
1 ATATTATTAAATATAA
383145 TTATAGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 9 0.30
19 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTATTAAATATAAA
Found at i:383118 original size:18 final size:18
Alignment explanation
Indices: 383077--383131 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
383067 ATAAATATTT
383077 TAAAATTTATATAATATA
1 TAAAATTTATATAATATA
383095 T---A-TTAT-TAATATA
1 TAAAATTTATATAATATA
383108 TTAAAATTTATATAA-ATA
1 -TAAAATTTATATAATATA
383126 TAAAAT
1 TAAAAT
383132 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
13 7 0.23
14 5 0.16
15 1 0.03
17 7 0.23
18 8 0.26
19 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATTTATATAATATA
Found at i:388625 original size:18 final size:19
Alignment explanation
Indices: 388592--388628 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
388582 ATTAGATGAA
*
388592 AATAAATATTTAAAAATTT
1 AATAAATATATAAAAATTT
388611 AATAAATA-ATAAAAATTT
1 AATAAATATATAAAAATTT
388629 TGGATGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAAATATATAAAAATTT
Found at i:390542 original size:22 final size:23
Alignment explanation
Indices: 390524--390573 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
390514 AAGGCATTCA
390524 AATGCTTTTCTTAAA-GCATAAG
1 AATGCTTTTCTTAAAGGCATAAG
*
390546 AATGCTTTTC--AATGGCATAAG
1 AATGCTTTTCTTAAAGGCATAAG
390567 AAT-CTTT
1 AATGCTTT
390574 GTTAATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 10 0.38
22 10 0.38
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (23 bp):
AATGCTTTTCTTAAAGGCATAAG
Found at i:394046 original size:11 final size:11
Alignment explanation
Indices: 394030--394077 Score: 59
Period size: 10 Copynumber: 4.7 Consensus size: 11
394020 AATTTATATA
394030 TTTATATTATT
1 TTTATATTATT
394041 TTTATATTA-T
1 TTTATATTATT
*
394051 ATTATA-T-TT
1 TTTATATTATT
394060 TTTA-ATTATT
1 TTTATATTATT
394070 TTTATATT
1 TTTATATT
394078 TATGAAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 1 0.03
9 6 0.19
10 12 0.39
11 12 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATATTATT
Found at i:394068 original size:18 final size:17
Alignment explanation
Indices: 394021--394060 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 17
394011 ATATTAAATA
394021 ATTTATATATTTATATTAT
1 ATTT-TATA-TTATATTAT
394040 -TTTTATATTATATTAT
1 ATTTTATATTATATTAT
394056 ATTTT
1 ATTTT
394061 TTAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.45
17 8 0.40
18 3 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATATTATATTAT
Found at i:394074 original size:19 final size:19
Alignment explanation
Indices: 394022--394078 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
394012 TATTAAATAA
394022 TTTATA-TAT-TTATATTATT
1 TTTATATTATATTATA-T-TT
394041 TTTATATTATATTATATTT
1 TTTATATTATATTATATTT
*
394060 TTTA-ATTATTTTTATATTT
1 TTTATATTA-TATTATATTT
394079 ATGAAATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 4 0.12
19 21 0.62
20 4 0.12
21 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATATTATATTATATTT
Found at i:394416 original size:2 final size:2
Alignment explanation
Indices: 394409--394443 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
394399 GCTTGTGAAA
394409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
394444 ATTTGAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:394551 original size:21 final size:21
Alignment explanation
Indices: 394527--394566 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
394517 TTTATGTATC
*
394527 TAAATTTATTTTTTAAAATGT
1 TAAATTTATCTTTTAAAATGT
394548 TAAATTTATCTTTTAAAAT
1 TAAATTTATCTTTTAAAAT
394567 ATAATTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
TAAATTTATCTTTTAAAATGT
Found at i:403106 original size:18 final size:17
Alignment explanation
Indices: 403083--403123 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
403073 GTTAATTTAA
403083 TATTAATTAAATTTAAAT
1 TATTAATTAAA-TTAAAT
*
403101 TATTAAATAAATTAAAT
1 TATTAATTAAATTAAAT
403118 T-TTAAT
1 TATTAAT
403124 ATTTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.19
17 7 0.33
18 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTAATTAAATTAAAT
Found at i:403129 original size:23 final size:24
Alignment explanation
Indices: 403077--403130 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
403067 TTTAAAGTTA
*
403077 ATTTAATATTAATTAAATTTAAAT
1 ATTTAATATAAATTAAATTTAAAT
*
403101 -TATTAA-ATAAATTAAATTTTAAT
1 AT-TTAATATAAATTAAATTTAAAT
403124 ATTTAAT
1 ATTTAAT
403131 TTTAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTAATATAAATTAAATTTAAAT
Found at i:403133 original size:13 final size:14
Alignment explanation
Indices: 403075--403142 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 14
403065 AATTTAAAGT
*
403075 TAATTTAATATTAA
1 TAATTTAATTTTAA
403089 TTAAATTTAAATTATTAAA
1 -T-AATTT-AATT-TT-AA
*
403108 TAAATTAAATTTTAA
1 T-AATTTAATTTTAA
403123 T-ATTTAATTTTAA
1 TAATTTAATTTTAA
403136 TAATTTA
1 TAATTTA
403143 TTAATTTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
13 12 0.27
14 5 0.11
15 4 0.09
16 7 0.16
17 7 0.16
18 8 0.18
19 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATTTAATTTTAA
Found at i:403174 original size:18 final size:17
Alignment explanation
Indices: 403119--403175 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
403109 AAATTAAATT
* *
403119 TTAATATTTAATTTTAA
1 TTAATTTTTTATTTTAA
* *
403136 -TAATTTATTAATTTAA
1 TTAATTTTTTATTTTAA
403152 TTTAATTTTTTATTTTTAA
1 -TTAATTTTTTA-TTTTAA
403171 TTAAT
1 TTAAT
403176 ATTAAAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 12 0.39
18 14 0.45
19 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTAATTTTTTATTTTAA
Found at i:403419 original size:26 final size:26
Alignment explanation
Indices: 403364--403425 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
403354 ATTCTCAAAT
* **
403364 TTAAAATTAAAATTTGATTTTAATTT
1 TTAAAATTAAAATTTAATTTTAATAA
*
403390 TTAAATTTAAAA-TTAATTTTAATAAA
1 TTAAAATTAAAATTTAATTTTAAT-AA
403416 TTAATAATTA
1 TTAA-AATTA
403426 TTATAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 10 0.34
26 15 0.52
27 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTAAAATTAAAATTTAATTTTAATAA
Found at i:403432 original size:20 final size:21
Alignment explanation
Indices: 403391--403435 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
403381 TTTTAATTTT
*
403391 TAAATTTAAAATTAATTTTAA
1 TAAATTTAAAATTAATTATAA
403412 TAAA-TTAATAATT-ATTATAA
1 TAAATTTAA-AATTAATTATAA
403432 TAAA
1 TAAA
403436 ATTATAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTTAAAATTAATTATAA
Found at i:406690 original size:27 final size:25
Alignment explanation
Indices: 406631--406696 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
406621 ATTTTAATAA
406631 ATTA-ATTATTAAAAAAATAAAATT
1 ATTATATTATTAAAAAAATAAAATT
* *
406655 ATTATTATTATTATAAAATATATATATT
1 ATTA-TATTATTA-AAAAAATA-AAATT
406683 ATTATATTA-TAAAA
1 ATTATATTATTAAAA
406697 TATAAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 4 0.11
25 3 0.08
26 9 0.25
27 12 0.33
28 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTATATTATTAAAAAAATAAAATT
Found at i:406695 original size:24 final size:25
Alignment explanation
Indices: 406654--406700 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
406644 AAAATAAAAT
406654 TATTATTATTATTATAAAATATATA
1 TATTATTATTATTATAAAATATATA
406679 TATTATTA-TATTATAAAATATA
1 TATTATTATTATTATAAAATATA
406701 AATTTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TATTATTATTATTATAAAATATATA
Found at i:406713 original size:22 final size:24
Alignment explanation
Indices: 406644--406718 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
406634 AATTATTAAA
*
406644 AAAATA-AAATTATTATTATTATTAT
1 AAAATATAAA-TATTAGTA-TATTAT
* *
406669 AAAATATATATATTATTATATTAT
1 AAAATATAAATATTAGTATATTAT
406693 AAAATATAAAT-TTAGTA-ATTA-
1 AAAATATAAATATTAGTATATTAT
406714 AAAAT
1 AAAAT
406719 CTTATTCGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.11
22 4 0.09
23 5 0.11
24 16 0.35
25 14 0.30
26 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
AAAATATAAATATTAGTATATTAT
Found at i:406783 original size:13 final size:13
Alignment explanation
Indices: 406765--406794 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
406755 TTTCTTTCAA
406765 ATTTGATTTTTTT
1 ATTTGATTTTTTT
406778 ATTTGATTTTTTT
1 ATTTGATTTTTTT
406791 ATTT
1 ATTT
406795 AAATTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (13 bp):
ATTTGATTTTTTT
Found at i:406807 original size:32 final size:33
Alignment explanation
Indices: 406763--406830 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
406753 TCTTTCTTTC
* * *
406763 AAATTTGATTTTTTTA-TTTGATTTTTTTATTT
1 AAATTTGATTTTTTGAGTTTAATATTTTTATTT
406795 AAATTT-ATTTTTTGAGTTTAATATTTTTATTT
1 AAATTTGATTTTTTGAGTTTAATATTTTTATTT
406827 AAAT
1 AAAT
406831 CTTTTTAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 8 0.25
32 24 0.75
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (33 bp):
AAATTTGATTTTTTGAGTTTAATATTTTTATTT
Found at i:406814 original size:19 final size:20
Alignment explanation
Indices: 406777--406820 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
406767 TTGATTTTTT
*
406777 TATTTGATTTTTTTATTTAA
1 TATTTGATTTTTTGATTTAA
406797 -ATTT-ATTTTTTGAGTTTAA
1 TATTTGATTTTTTGA-TTTAA
406816 TATTT
1 TATTT
406821 TTATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TATTTGATTTTTTGATTTAA
Found at i:410016 original size:11 final size:12
Alignment explanation
Indices: 409994--410020 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
409984 ATTAATCCCT
409994 AAAAATTAAAAA
1 AAAAATTAAAAA
410006 AAAAATTAAAAA
1 AAAAATTAAAAA
410018 AAA
1 AAA
410021 TCTTGACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATTAAAAA
Found at i:411128 original size:2 final size:2
Alignment explanation
Indices: 411121--411160 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
411111 TCACCAACTT
411121 TA TA TA TA TA 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 TA TA TA TA TA
411161 GGCTGGTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:414163 original size:16 final size:16
Alignment explanation
Indices: 414142--414172 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
414132 CTCACCGATA
414142 ATTTTATATATTATAT
1 ATTTTATATATTATAT
414158 ATTTTATATATTATA
1 ATTTTATATATTATA
414173 CTTATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATATATTATAT
Found at i:414180 original size:20 final size:20
Alignment explanation
Indices: 414155--414192 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
414145 TTATATATTA
* *
414155 TATATTTTATATATTATACT
1 TATATTTAAAATATTATACT
414175 TATATTTAAAATATTATA
1 TATATTTAAAATATTATA
414193 ATTTATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATTTAAAATATTATACT
Found at i:414198 original size:27 final size:28
Alignment explanation
Indices: 414168--414222 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
414158 ATTTTATATA
*
414168 TTATAC-TTATATTTA-AAATATTATAAT
1 TTATACATT-TATTTATAAAAATTATAAT
*
414195 TTATTCATTTATTTATAAAAATTATAAT
1 TTATACATTTATTTATAAAAATTATAAT
414223 ATATCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
TTATACATTTATTTATAAAAATTATAAT
Found at i:414233 original size:17 final size:16
Alignment explanation
Indices: 414208--414258 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 16
414198 TTCATTTATT
414208 TATAAAAATTATAATA
1 TATAAAAATTATAATA
*
414224 TATCAAAAATTTATATTA
1 TAT-AAAAA-TTATAATA
414242 TAT-AAAATT-TAATA
1 TATAAAAATTATAATA
414256 TAT
1 TAT
414259 TTATATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 7 0.23
15 2 0.06
16 7 0.23
17 5 0.16
18 10 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAAAAATTATAATA
Found at i:414237 original size:18 final size:17
Alignment explanation
Indices: 414208--414252 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
414198 TTCATTTATT
414208 TATAAAAA-TTATAATA
1 TATAAAAATTTATAATA
*
414224 TATCAAAAATTTATATTA
1 TAT-AAAAATTTATAATA
414242 TAT-AAAATTTA
1 TATAAAAATTTA
414253 ATATATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 11 0.42
17 5 0.19
18 10 0.38
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAAAAATTTATAATA
Found at i:414248 original size:16 final size:16
Alignment explanation
Indices: 414201--414252 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 16
414191 TAATTTATTC
414201 ATTTAT-TTATA-AAA
1 ATTTATATTATATAAA
*
414215 A-TTATAATATATCAAAA
1 ATTTATATTATAT--AAA
414232 ATTTATATTATATAAA
1 ATTTATATTATATAAA
414248 ATTTA
1 ATTTA
414253 ATATATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 4 0.13
14 5 0.16
16 8 0.26
17 4 0.13
18 10 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTATATTATATAAA
Found at i:414263 original size:18 final size:18
Alignment explanation
Indices: 414204--414263 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 18
414194 TTTATTCATT
414204 TATTTATAAAAATTATAATA
1 TATTTAT-AAAATT-TAATA
*
414224 TA-TCA-AAAATTT-ATA
1 TATTTATAAAATTTAATA
*
414239 T-TATATAAAATTTAATA
1 TATTTATAAAATTTAATA
414256 TATTTATA
1 TATTTATA
414264 TATTAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 5 0.16
16 8 0.25
17 10 0.31
18 5 0.16
19 2 0.06
20 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTATAAAATTTAATA
Found at i:414273 original size:33 final size:33
Alignment explanation
Indices: 414154--414277 Score: 100
Period size: 33 Copynumber: 3.8 Consensus size: 33
414144 TTTATATATT
414154 ATATATTT-TATATATTATACTTATATTTAAAATATT-
1 ATATATTTATATAT-TTATA-TTATA--TAAAAT-TTA
414190 ATA-ATTTAT-TCATTTAT-TTATA-AAAATTATA
1 ATATATTTATAT-ATTTATATTATATAAAATT-TA
* * *
414221 ATATA-TCAAAAATTTATATTATATAAAATTTA
1 ATATATTTATATATTTATATTATATAAAATTTA
*
414253 ATATATTTATATATTAATATTATAT
1 ATATATTTATATATTTATATTATAT
414278 TTTATATTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
29 1 0.01
30 6 0.08
31 11 0.15
32 13 0.18
33 26 0.36
35 9 0.12
36 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
ATATATTTATATATTTATATTATATAAAATTTA
Found at i:414294 original size:12 final size:12
Alignment explanation
Indices: 414254--414310 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
414244 TAAAATTTAA
414254 TATATTTATATAT
1 TATATTT-TATAT
* *
414267 TAATATTATATTT
1 T-ATATTTTATAT
*
414280 TATATTTTAT-C
1 TATATTTTATAT
414291 T-TATTTTATAT
1 TATATTTTATAT
414302 TATATTTTA
1 TATATTTTA
414311 ATTTTTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.22
11 2 0.06
12 15 0.42
13 6 0.17
14 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:414302 original size:29 final size:26
Alignment explanation
Indices: 414269--414322 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 26
414259 TTATATATTA
414269 ATATTATATTTTATATTTTATCTTATTTT
1 ATATTATATTTTA-ATTTT-T-TTATTTT
414298 ATATTATATTTTAATTTTTTTATTT
1 ATATTATATTTTAATTTTTTTATTT
414323 CGTATAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.24
27 1 0.04
28 5 0.20
29 13 0.52
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (26 bp):
ATATTATATTTTAATTTTTTTATTTT
Found at i:414663 original size:2 final size:2
Alignment explanation
Indices: 414656--414692 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
414646 ATACCTCAAG
414656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
414693 ATAATTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:415652 original size:14 final size:13
Alignment explanation
Indices: 415635--415691 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
415625 ATATATATTT
415635 TATTATATTTTAAA
1 TATTATA-TTTAAA
*
415649 TATT-T-TATAAA
1 TATTATATTTAAA
*
415660 TATTATATTTATA
1 TATTATATTTAAA
415673 TAATTATATTT-AA
1 T-ATTATATTTAAA
415686 TATTAT
1 TATTAT
415692 TAAGTTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 9 0.25
12 6 0.17
13 8 0.22
14 13 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATTTAAA
Found at i:419571 original size:20 final size:19
Alignment explanation
Indices: 419543--419590 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
419533 TTTAATTTCG
*
419543 ATTTATTTAGGTAATATTAT
1 ATTTATTTAGATAAT-TTAT
* *
419563 ATTTTTTTATATAATTTAT
1 ATTTATTTAGATAATTTAT
419582 ATTTATTTA
1 ATTTATTTA
419591 ATTTAATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTTATTTAGATAATTTAT
Found at i:419589 original size:10 final size:10
Alignment explanation
Indices: 419559--419617 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
419549 TTAGGTAATA
*
419559 TTATATTTTT
1 TTATATTTAT
*
419569 TTATA-TAAT
1 TTATATTTAT
419578 TTATATTTAT
1 TTATATTTAT
*
419588 TTA-ATTTAA
1 TTATATTTAT
*
419597 TTATCATAT-T
1 TTAT-ATTTAT
419607 TTATATTTAT
1 TTATATTTAT
419617 T
1 T
419618 ATGATAAACA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 18 0.47
10 17 0.45
11 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATATTTAT
Found at i:419600 original size:19 final size:18
Alignment explanation
Indices: 419558--419600 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
419548 TTTAGGTAAT
*
419558 ATTATATTTTTTTATATA
1 ATTATATTTTTTAATATA
*
419576 ATTTATATTTATTTAATTTA
1 A-TTATATTT-TTTAATATA
419596 ATTAT
1 ATTAT
419601 CATATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 12 0.57
20 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATATTTTTTAATATA
Found at i:419653 original size:21 final size:23
Alignment explanation
Indices: 419627--419673 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
419617 TATGATAAAC
419627 ATAATT-ATATTATT-AAAT-TTA
1 ATAATTAAT-TTATTAAAATATTA
419648 ATAATTAATTTATTAAAATATTA
1 ATAATTAATTTATTAAAATATTA
419671 ATA
1 ATA
419674 GTATAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.48
22 6 0.26
23 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATTAATTTATTAAAATATTA
Found at i:419926 original size:3 final size:3
Alignment explanation
Indices: 419918--419947 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
419908 GGAATATGTA
419918 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
419948 GGATAGGGAG
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:420404 original size:15 final size:14
Alignment explanation
Indices: 420364--420412 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
420354 TTATTTTATG
420364 ATAAATTTTTTAAA
1 ATAAATTTTTTAAA
* *
420378 ATAAATTATTTAACT
1 ATAAATTTTTTAA-A
*
420393 ATTAATTTTTTAAA
1 ATAAATTTTTTAAA
420407 ATAAAT
1 ATAAAT
420413 CATAATTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAAATTTTTTAAA
Found at i:420429 original size:24 final size:25
Alignment explanation
Indices: 420402--420465 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
420392 TATTAATTTT
420402 TTAAAATAAATCAT-AAT-TTAAAAA
1 TTAAAATAAAT-ATAAATATTAAAAA
*
420426 TTAAAA-AAATATAAATATTAAAAT
1 TTAAAATAAATATAAATATTAAAAA
420450 TTAAAATTTAAATATA
1 TTAAAA--TAAATATA
420466 TTTAATGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
22 2 0.06
23 7 0.21
24 18 0.53
27 7 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TTAAAATAAATATAAATATTAAAAA
Found at i:420429 original size:32 final size:29
Alignment explanation
Indices: 420367--420429 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
420357 TTTTATGATA
**
420367 AATTTTTTAAAATAAATTATTTAACTATT
1 AATTTTTTAAAATAAATTATTTAAAAATT
420396 AATTTTTTAAAATAAATCATAATTTAAAAATT
1 AATTTTTTAAAATAAAT--T-ATTTAAAAATT
420428 AA
1 AA
420430 AAAAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 17 0.59
31 1 0.03
32 11 0.38
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTTTTAAAATAAATTATTTAAAAATT
Found at i:420540 original size:7 final size:8
Alignment explanation
Indices: 420513--420539 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
420503 TTAAATTAAA
420513 TTTTAATT
1 TTTTAATT
420521 TTTTAATT
1 TTTTAATT
420529 TTTTAATT
1 TTTTAATT
420537 TTT
1 TTT
420540 ATTATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTAATT
Found at i:421199 original size:2 final size:2
Alignment explanation
Indices: 421194--421224 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
421184 TATATATATA
421194 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
421225 TTAACTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:421454 original size:7 final size:7
Alignment explanation
Indices: 421442--421482 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
421432 TATATTGTTA
421442 TATATTC
1 TATATTC
421449 TATATTC
1 TATATTC
* *
421456 TTTATTT
1 TATATTC
421463 TATATTC
1 TATATTC
421470 TATATTC
1 TATATTC
*
421477 TTTATT
1 TATATT
421483 TCCATCATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (7 bp):
TATATTC
Found at i:421466 original size:21 final size:21
Alignment explanation
Indices: 421442--421483 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
421432 TATATTGTTA
421442 TATATTCTATATTCTTTATTT
1 TATATTCTATATTCTTTATTT
421463 TATATTCTATATTCTTTATTT
1 TATATTCTATATTCTTTATTT
421484 CCATCATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (21 bp):
TATATTCTATATTCTTTATTT
Found at i:422166 original size:236 final size:241
Alignment explanation
Indices: 421609--422166 Score: 630
Period size: 236 Copynumber: 2.3 Consensus size: 241
421599 GTGCATGTAC
* * * * *
421609 ATACCAAAATCTCCCAATAAATTTCATCTTTACATTAAATAGGTAAAACAAT-AAGAATTCTTTC
1 ATACCAAAATCTCTCAATAAGTTTCATCTTTACATAAAATAAGTAAAAGAATAAAG-ATTCTTTC
* * * * *
421673 AATCTCCTCTAGG-GATAGATCCAAAGAGACCGGTTGGAGCTTTGGTCGATCCTTAATCCTCTCT
65 AATCTCCTCTAGGAG-TGGGTCCAAA-AG---GATCGGA-TTTTGGTCGATCCTTAATCCTCTCT
*
421737 CTTGACTCTTTTAAACTCTTTAAATTTTTAACAATTATTTAATTCAAAAAAAAAAAAAAAGATAA
124 CTTGACTCTTTTAAACTCTTTAAATTCTTAACAATTATTTAATT---AAAAAAAAAAAAAGATAA
* * * *
421802 AAACTTATATTTTGATCTCAAAAATTTATAATTTGATAATTTTTGACAAATTATAT
186 AAACTTATATTTTGATCTAAAAAATTTATAATTTAATAACTTTTAACAAATTATAT
* * * * * * * *
421858 GTGCCATAATCTCTCATTGAGTTTCATCTTTACATTAAATAGGTAAAAGAATAAGGATTCTTTCA
1 ATACCAAAATCTCTCAATAAGTTTCATCTTTACATAAAATAAGTAAAAGAATAAAGATTCTTTCA
*
421923 ATCTCCTCTAGGAGTGGGTCCAAAAGGATCGGATTTTGGTCGATCTTTAAT-CT-TCT-TTCGAC
66 ATCTCCTCTAGGAGTGGGTCCAAAAGGATCGGATTTTGGTCGATCCTTAATCCTCTCTCTT-GAC
* *** * * *
421985 TCTTTTAAATTCTTTGTGTTCTTAACAATTATTTAATT-AAAAAAACAATA-A-AAAAACTTATC
130 TCTTTTAAACTCTTTAAATTCTTAACAATTATTTAATTAAAAAAAAAAAAAGATAAAAACTTATA
422047 TTTTGATCTAAAAAATTTATAATTTAATAACTTTTAACAAATTATAT
195 TTTTGATCTAAAAAATTTATAATTTAATAACTTTTAACAAATTATAT
* * *
422094 ATACTAAAATCTCTCAATAAGTTTCATCTTTACATAAAATAAGT-AAAGAATTAAAGATTGTTTT
1 ATACCAAAATCTCTCAATAAGTTTCATCTTTACATAAAATAAGTAAAAGAA-TAAAGATTCTTTC
*
422158 AGTCTCCTC
65 AATCTCCTC
422167 CATGGGCAAG
Statistics
Matches: 266, Mismatches: 39, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
235 6 0.02
236 107 0.40
237 1 0.00
238 10 0.04
241 2 0.01
242 39 0.15
243 2 0.01
244 16 0.06
245 5 0.02
248 2 0.01
249 73 0.27
250 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (241 bp):
ATACCAAAATCTCTCAATAAGTTTCATCTTTACATAAAATAAGTAAAAGAATAAAGATTCTTTCA
ATCTCCTCTAGGAGTGGGTCCAAAAGGATCGGATTTTGGTCGATCCTTAATCCTCTCTCTTGACT
CTTTTAAACTCTTTAAATTCTTAACAATTATTTAATTAAAAAAAAAAAAAGATAAAAACTTATAT
TTTGATCTAAAAAATTTATAATTTAATAACTTTTAACAAATTATAT
Found at i:423893 original size:3 final size:3
Alignment explanation
Indices: 423885--423920 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
423875 TTAAAATAAG
423885 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
423921 TTCTTTTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:426366 original size:11 final size:10
Alignment explanation
Indices: 426341--426369 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
426331 AAATTAAATT
426341 ATTTTTTAAA
1 ATTTTTTAAA
426351 ATTTTTTAAA
1 ATTTTTTAAA
426361 ATTTTTTAA
1 ATTTTTTAA
426370 TTATGTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:432073 original size:18 final size:17
Alignment explanation
Indices: 432050--432105 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
432040 TATTTAAAAT
432050 ATTTTATATTTATTATAA
1 ATTTTATATTTA-TATAA
*
432068 ATTTTA-ATATAT-TAA
1 ATTTTATATTTATATAA
*
432083 TTATTTATA-TTATATAA
1 AT-TTTATATTTATATAA
432100 ATTTTA
1 ATTTTA
432106 AAATAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 4 0.13
16 12 0.39
17 9 0.29
18 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:432096 original size:30 final size:31
Alignment explanation
Indices: 432062--432152 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 31
432052 TTTATATTTA
432062 TTATAAATTTTAATATATTAATTATTTATAT
1 TTATAAATTTTAATATATTAATTATTTATAT
*
432093 TATATAAATTTTAA-A-A-TAAATATTTATATT
1 T-TATAAATTTTAATATATTAATTATTTATA-T
*
432123 TTATTATATTTTAAT-TATT--TTATTTATAT
1 TTA-TAAATTTTAATATATTAATTATTTATAT
432152 T
1 T
432153 AAATTTATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
29 15 0.29
30 20 0.39
31 3 0.06
32 13 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTATAAATTTTAATATATTAATTATTTATAT
Found at i:432157 original size:19 final size:19
Alignment explanation
Indices: 432119--432157 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
432109 TAAATATTTA
*
432119 TATTTTATTATATTTTAAT
1 TATTTTATTATATTTAAAT
432138 TATTTTATT-TATATTAAAT
1 TATTTTATTATAT-TTAAAT
432157 T
1 T
432158 TATATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTATTATATTTAAAT
Found at i:433536 original size:20 final size:20
Alignment explanation
Indices: 433513--433576 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 20
433503 AATTAATATA
*
433513 ATAAAATTATAACTATTATT
1 ATAAAATTATAAATATTATT
* *
433533 AT-AAA-TATATATTTATATT
1 ATAAAATTATAAATAT-TATT
*
433552 ATAAAA-TATAAATATTATA
1 ATAAAATTATAAATATTATT
433571 ATAAAA
1 ATAAAA
433577 AAGTATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
18 6 0.17
19 18 0.50
20 12 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAATTATAAATATTATT
Found at i:433577 original size:20 final size:20
Alignment explanation
Indices: 433509--433577 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
433499 CAATAATTAA
* *
433509 TATAATAAAATTATAACTAT
1 TATAATAAAAATATAAATAT
* *
433529 TAT--TATAAATATATAT-T
1 TATAATAAAAATATAAATAT
*
433546 TATATTATAAAATATAAATAT
1 TATAATA-AAAATATAAATAT
433567 TATAATAAAAA
1 TATAATAAAAA
433578 AGTATTTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 4 0.11
18 9 0.24
19 2 0.05
20 16 0.42
21 7 0.18
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAATAAAAATATAAATAT
Found at i:433584 original size:38 final size:39
Alignment explanation
Indices: 433508--433585 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 39
433498 TCAATAATTA
* * *
433508 ATATAATAAAATTATAACTATTATTATAAATATATATTT
1 ATATAATAAAATTATAAATATTATAATAAATAAATATTT
*
433547 ATATTATAAAA-TATAAATATTATAATAAA-AAAGTATTT
1 ATATAATAAAATTATAAATATTATAATAAATAAA-TATTT
433585 A
1 A
433586 AACATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.06
38 22 0.65
39 10 0.29
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (39 bp):
ATATAATAAAATTATAAATATTATAATAAATAAATATTT
Found at i:433640 original size:15 final size:17
Alignment explanation
Indices: 433620--433651 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
433610 TCGATTATTT
433620 TTTAAAT-T-TTTTTTG
1 TTTAAATCTATTTTTTG
433635 TTTAAATCTATTTTTTG
1 TTTAAATCTATTTTTTG
433652 AATCAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTAAATCTATTTTTTG
Found at i:433750 original size:4 final size:4
Alignment explanation
Indices: 433741--433765 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
433731 TAAGCTAAAA
433741 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
433766 TAGTTTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:434162 original size:16 final size:17
Alignment explanation
Indices: 434129--434170 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
434119 TTAAATTTTA
*
434129 ATAAAT-AATTTGATTT
1 ATAAATAAATTTGAATT
434145 ATAAATAAATTT-AATT
1 ATAAATAAATTTGAATT
*
434161 ATAGATAAAT
1 ATAAATAAAT
434171 AACGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
ATAAATAAATTTGAATT
Found at i:435840 original size:2 final size:2
Alignment explanation
Indices: 435835--435862 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
435825 GTGTGTGTGT
435835 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
435863 AAGACTTAAC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:436599 original size:2 final size:2
Alignment explanation
Indices: 436586--436617 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
436576 GAGGATTATC
*
436586 AT AT AG 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
436618 TAATAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:443992 original size:15 final size:16
Alignment explanation
Indices: 443964--443996 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
443954 CTCAAACTCG
443964 AAAATAAATAAAATCT
1 AAAATAAATAAAATCT
*
443980 AAAA-AAATCAAATCT
1 AAAATAAATAAAATCT
443995 AA
1 AA
443997 TAAATCCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAATAAAATCT
Found at i:445820 original size:2 final size:2
Alignment explanation
Indices: 445813--445847 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
445803 CAGCAACGGC
*
445813 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
445848 AGGTCATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:449095 original size:2 final size:2
Alignment explanation
Indices: 449090--449120 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
449080 GAAGACACAC
449090 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
449121 CTTACTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:457676 original size:16 final size:16
Alignment explanation
Indices: 457657--457691 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
457647 ACTTTTCAAT
*
457657 TTTTTATAGTTTTTTA
1 TTTTTATAGTTTTATA
*
457673 TTTTTATTGTTTTATA
1 TTTTTATAGTTTTATA
457689 TTT
1 TTT
457692 GATTTGAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTTATAGTTTTATA
Found at i:460811 original size:21 final size:22
Alignment explanation
Indices: 460786--460827 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
460776 TGGCTCATTT
460786 AAGGATAT-AAAAAAAGCTCAA
1 AAGGATATAAAAAAAAGCTCAA
460807 AAGGATATAAAAAAAAGCTCA
1 AAGGATATAAAAAAAAGCTCA
460828 TGGATACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (22 bp):
AAGGATATAAAAAAAAGCTCAA
Found at i:460957 original size:21 final size:20
Alignment explanation
Indices: 460927--460967 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
460917 ATTAAAAAAT
460927 TATATTTAT-ATTAATATTTA
1 TATATTTATAATTAA-ATTTA
460947 TATATTTTATAATTAAATTTA
1 TATA-TTTATAATTAAATTTA
460968 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTTATAATTAAATTTA
Found at i:461264 original size:23 final size:20
Alignment explanation
Indices: 461237--461302 Score: 53
Period size: 23 Copynumber: 3.0 Consensus size: 20
461227 ATGTTAATAA
461237 ATTATCCTAATTTTATTTTTT
1 ATTAT-CTAATTTTATTTTTT
*
461258 ACTTTATTCTTATCTTATATTTTTT
1 A--TTA-TCTAAT-TT-TATTTTTT
*
461283 ATTAT-TATTTTTATTTTTT
1 ATTATCTAATTTTATTTTTT
461302 A
1 A
461303 AATAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
19 9 0.24
20 2 0.05
21 3 0.08
22 1 0.03
23 10 0.27
24 3 0.08
25 9 0.24
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTATCTAATTTTATTTTTT
Found at i:461285 original size:20 final size:19
Alignment explanation
Indices: 461260--461302 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
461250 TATTTTTTAC
*
461260 TTTATTCTTATCTTATATTT
1 TTTATTATTAT-TTATATTT
*
461280 TTTATTATTATTTTTATTT
1 TTTATTATTATTTATATTT
461299 TTTA
1 TTTA
461303 AATAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTATTATTTATATTT
Found at i:461896 original size:22 final size:22
Alignment explanation
Indices: 461849--461907 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
461839 GTAACATGTG
* * *
461849 ATATTTTTAAAATAATGACGTG
1 ATATTTTTAAAATAATAACATA
*
461871 ATATTTTTAAAATAATAATATA
1 ATATTTTTAAAATAATAACATA
* *
461893 ATATTTATAACATAA
1 ATATTTTTAAAATAA
461908 CATTTTACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (22 bp):
ATATTTTTAAAATAATAACATA
Found at i:462190 original size:17 final size:17
Alignment explanation
Indices: 462170--462209 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
462160 ATTCGTGTGA
462170 ATGTTAAATATGAATAT
1 ATGTTAAATATGAATAT
* *
462187 ATGTTTAATATTAATAT
1 ATGTTAAATATGAATAT
462204 AT-TTAA
1 ATGTTAA
462210 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
ATGTTAAATATGAATAT
Found at i:462631 original size:2 final size:2
Alignment explanation
Indices: 462624--462672 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
462614 GTCAGATAAG
*
462624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
462666 TA TA TA T
1 TA TA TA T
462673 CCTCTGCTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:463535 original size:211 final size:212
Alignment explanation
Indices: 463204--463625 Score: 542
Period size: 211 Copynumber: 2.0 Consensus size: 212
463194 TGAGGGTAAT
** *
463204 ATGACTACTGCATGTTTACCTGTTACCAAGACACGAAAAACAAGTGTTAGATACAGTTATGTATT
1 ATGACTACTGCATGTTTACCTGTTACCAAGACACGAAAAACAAGCATTAGATACAGATATGTATT
** * * * * *
463269 TAACACGGATATGTTCAATTTGTTTTGAAGTTTTCTTACGTATTTAAATGATCATACTTCGATAT
66 TAACAAAGATATGTTCAATTTCTTTTGAAGTTTTCTCACATATTTAAAGGATCATACTCCGATAT
* * *
463334 TCATATCGATATATGTGTAAAATATAGATATGTAAAGAAAAATGAAAAATCAAGATGATATAAGA
131 TCATATCGAAATATGTGTAAAATACAAATATGTAAAGAAAAATGAAAAATCAAGATGATATAAGA
*
463399 TACAAGATCACAAGCAC
196 TACAAGAACACAAGCAC
* * * * *
463416 ATGACTACTGCATGTTTATCTGTTACCAAGACAC-AAAAATGAA-CATTGGATGCAGATATGTGT
1 ATGACTACTGCATGTTTACCTGTTACCAAGACACGAAAAA-CAAGCATTAGATACAGATATGTAT
* * * *
463479 TTGACAAAGATATGTTCAATTTCTTTTTATGTTTTCTCATATATTTAAAGGATCATACTCCGATA
65 TTAACAAAGATATGTTCAATTTCTTTTGAAGTTTTCTCACATATTTAAAGGATCATACTCCGATA
* * * *** * *
463544 TTCATATCGAAATATGTGTCAAATACAAATATTTTAAGAAAAATGAAGTGTCTATATGATATAAG
130 TTCATATCGAAATATGTGTAAAATACAAATATGTAAAGAAAAATGAAAAATCAAGATGATATAAG
463609 ATACAAGAACACAAGCA
195 ATACAAGAACACAAGCA
463626 TAATATGGCT
Statistics
Matches: 178, Mismatches: 31, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
211 143 0.80
212 35 0.20
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (212 bp):
ATGACTACTGCATGTTTACCTGTTACCAAGACACGAAAAACAAGCATTAGATACAGATATGTATT
TAACAAAGATATGTTCAATTTCTTTTGAAGTTTTCTCACATATTTAAAGGATCATACTCCGATAT
TCATATCGAAATATGTGTAAAATACAAATATGTAAAGAAAAATGAAAAATCAAGATGATATAAGA
TACAAGAACACAAGCAC
Found at i:469579 original size:19 final size:19
Alignment explanation
Indices: 469555--469591 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
469545 TAAAAAATAT
*
469555 ATATTATTTTAATTTAAAA
1 ATATTATTTTAAATTAAAA
469574 ATATTATTTTAAATTAAA
1 ATATTATTTTAAATTAAA
469592 TTAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTATTTTAAATTAAAA
Found at i:470085 original size:14 final size:12
Alignment explanation
Indices: 470054--470078 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
470044 TTTTATGCTG
470054 AAATTAAAAAAT
1 AAATTAAAAAAT
470066 AAATTAAAAAAT
1 AAATTAAAAAAT
470078 A
1 A
470079 TATATTAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATTAAAAAAT
Done.