Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold245
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: 333457
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 1 of 3
Found at i:2508 original size:52 final size:52
Alignment explanation
Indices: 2451--2568 Score: 236
Period size: 52 Copynumber: 2.3 Consensus size: 52
2441 TACAATTCAT
2451 AATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTTACAAGC
1 AATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTTACAAGC
2503 AATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTTACAAGC
1 AATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTTACAAGC
2555 AATGTATCGATACA
1 AATGTATCGATACA
2569 ATTCATCATG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (52 bp):
AATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTTACAAGC
Found at i:2598 original size:20 final size:20
Alignment explanation
Indices: 2560--2607 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2550 CAAGCAATGT
*
2560 ATCGATACAATTCATCATGA
1 ATCGATACAATTCACCATGA
*
2580 ATCGATACAATGT-ACCATGT
1 ATCGATACAAT-TCACCATGA
2600 ATCGATAC
1 ATCGATAC
2608 GAACAGTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
ATCGATACAATTCACCATGA
Found at i:2683 original size:19 final size:19
Alignment explanation
Indices: 2661--2708 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2651 AATGTCCATA
*
2661 TATCGATACAATA-AATATG
1 TATCGATACAA-AGAAAATG
2680 TATCGATACAAAGAAAATG
1 TATCGATACAAAGAAAATG
*
2699 TATCAATACA
1 TATCGATACA
2709 TTTGGGTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.27
Consensus pattern (19 bp):
TATCGATACAAAGAAAATG
Found at i:3319 original size:13 final size:13
Alignment explanation
Indices: 3301--3328 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3291 CGATGAGTAA
3301 TGTATCGATACAT
1 TGTATCGATACAT
3314 TGTATCGATACAT
1 TGTATCGATACAT
3327 TG
1 TG
3329 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18448 original size:28 final size:28
Alignment explanation
Indices: 18414--18668 Score: 339
Period size: 28 Copynumber: 8.9 Consensus size: 28
18404 CATTCATCTC
*
18414 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
18442 TTCAAAGCCCACAAGTCAGTGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
18470 TTTAAAACCCACGAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
18498 TTCAAAGCCCACGAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
18526 TTCAAAGCCCACGAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
18554 TTCAAAGCCCACGAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
18582 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
18610 TTCAAAGCCCATACAAGTCAGTGGCACTCTT
1 TTCAAAGCCC--ACAAGTCAGTGGCAC-CCT
*
18641 TTCAAAGCCCACACAAGTTAGTGGCACC
1 TTCAAAG-CC-CACAAGTCAGTGGCACC
18669 TTTTTTTTTA
Statistics
Matches: 207, Mismatches: 15, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
28 165 0.80
30 16 0.08
31 23 0.11
32 2 0.01
33 1 0.00
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.21
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:40645 original size:26 final size:26
Alignment explanation
Indices: 40562--40646 Score: 118
Period size: 26 Copynumber: 3.3 Consensus size: 26
40552 TCTATAGAGA
*
40562 TGAGATTGATAAAGTTCAACTTTATC
1 TGAGATTGATAAAGTTTAACTTTATC
* *
40588 TGGGATTGATAAAGTTTAATTTTATC
1 TGAGATTGATAAAGTTTAACTTTATC
*
40614 TAAGATTGATAAAGTTTAACTTTAT-
1 TGAGATTGATAAAGTTTAACTTTATC
40639 TCGAGATT
1 T-GAGATT
40647 CTAGATAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
25 1 0.02
26 50 0.98
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.42
Consensus pattern (26 bp):
TGAGATTGATAAAGTTTAACTTTATC
Found at i:41958 original size:29 final size:29
Alignment explanation
Indices: 41926--41982 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
41916 TTTCCATCAT
* * *
41926 TTTATTTTAAT-ACATTGAGCTATCAAATG
1 TTTATATTAATCAAATTGACCTAT-AAATG
41955 TTTATATTAATCAAATTGACCTATAAAT
1 TTTATATTAATCAAATTGACCTATAAAT
41983 TGAACAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.44
Consensus pattern (29 bp):
TTTATATTAATCAAATTGACCTATAAATG
Found at i:42499 original size:36 final size:36
Alignment explanation
Indices: 42439--42514 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
42429 ACTTATGTTG
* *
42439 TAATATAAGAGCAAGAAAAACTCCAAATAGCATATA
1 TAATATAAGAGAAAAAAAAACTCCAAATAGCATATA
* *
42475 TAATATAAGA-AAAAAAAAAGCTCCAAATCGCATATT
1 TAATATAAGAGAAAAAAAAA-CTCCAAATAGCATATA
42511 TAAT
1 TAAT
42515 CCTATCTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.20
36 28 0.80
ACGTcount: A:0.55, C:0.13, G:0.09, T:0.22
Consensus pattern (36 bp):
TAATATAAGAGAAAAAAAAACTCCAAATAGCATATA
Found at i:48564 original size:21 final size:21
Alignment explanation
Indices: 48518--48566 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
48508 AAAAGGTGTA
48518 TTTGGATGAAATGATGTATTG
1 TTTGGATGAAATGATGTATTG
* *
48539 GTTGGATGAAA-GAATGTATTT
1 TTTGGATGAAATG-ATGTATTG
48560 TTTGGAT
1 TTTGGAT
48567 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (21 bp):
TTTGGATGAAATGATGTATTG
Found at i:51273 original size:20 final size:20
Alignment explanation
Indices: 51248--51290 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
51238 TTTCATTGGA
51248 TTAATAT-ATATATAGATATG
1 TTAATATGA-ATATAGATATG
*
51268 TTAATATGAATATAGATCTG
1 TTAATATGAATATAGATATG
51288 TTA
1 TTA
51291 GGTAATGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (20 bp):
TTAATATGAATATAGATATG
Found at i:51806 original size:17 final size:17
Alignment explanation
Indices: 51784--51845 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
51774 TTATTAGGGT
51784 TAGAAAATCTATGATTA
1 TAGAAAATCTATGATTA
*
51801 TAGAAAATCTCTGATTA
1 TAGAAAATCTATGATTA
* *
51818 TAG-AAATCTGTGATTC
1 TAGAAAATCTATGATTA
51834 T-GAGAAATCTAT
1 TAGA-AAATCTAT
51846 AATTGTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.03
16 12 0.31
17 26 0.67
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (17 bp):
TAGAAAATCTATGATTA
Found at i:54377 original size:16 final size:17
Alignment explanation
Indices: 54358--54391 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54348 AGAAAATCCG
54358 TGATT-ATAAAAATCTA
1 TGATTCATAAAAATCTA
*
54374 TGATTCTTAAAAATCTA
1 TGATTCATAAAAATCTA
54391 T
1 T
54392 AATTGTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (17 bp):
TGATTCATAAAAATCTA
Found at i:56037 original size:22 final size:21
Alignment explanation
Indices: 55996--56037 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55986 TAAAAGATCC
* *
55996 ATCTTTCTTAAAAAAGAATTA
1 ATCTCTCTTAAAAAACAATTA
56017 ATCTCTCTTAAAAAATCAATT
1 ATCTCTCTTAAAAAA-CAATT
56038 TTTCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (21 bp):
ATCTCTCTTAAAAAACAATTA
Found at i:58823 original size:20 final size:20
Alignment explanation
Indices: 58798--58836 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58788 CATGAATATA
* *
58798 AATTTAATAATATTTTAAAG
1 AATTTAAAAATATTATAAAG
58818 AATTTAAAAATATTATAAA
1 AATTTAAAAATATTATAAA
58837 CATTAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AATTTAAAAATATTATAAAG
Found at i:59857 original size:51 final size:51
Alignment explanation
Indices: 59781--59881 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
59771 AGGGAGAAAA
59781 TTCTGATGTTATCCAACAACCTGTCAACATAATTGTTGAGAATGATCAGCT
1 TTCTGATGTTATCCAACAACCTGTCAACATAATTGTTGAGAATGATCAGCT
* *
59832 TTCTGATTTTATCCAACAACTTGTCAACATAATTGTTGAGAATGATCAGC
1 TTCTGATGTTATCCAACAACCTGTCAACATAATTGTTGAGAATGATCAGC
59882 AGTTATCATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (51 bp):
TTCTGATGTTATCCAACAACCTGTCAACATAATTGTTGAGAATGATCAGCT
Found at i:64268 original size:10 final size:9
Alignment explanation
Indices: 64245--64269 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
64235 TATTTAAATA
64245 TAAAAATTT
1 TAAAAATTT
64254 TAAAAATTT
1 TAAAAATTT
64263 TAAAAAT
1 TAAAAAT
64270 AAATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAAATTT
Found at i:65597 original size:18 final size:18
Alignment explanation
Indices: 65574--65608 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65564 TATATAAAAC
*
65574 TATGAGAGGAAATATGAG
1 TATGAGAGCAAATATGAG
65592 TATGAGAGCAAATATGA
1 TATGAGAGCAAATATGA
65609 ATATTAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.29, T:0.23
Consensus pattern (18 bp):
TATGAGAGCAAATATGAG
Found at i:66452 original size:22 final size:22
Alignment explanation
Indices: 66427--66515 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 22
66417 TTTTATAAAA
**
66427 TAAATTAATTTAAATTATTATT
1 TAAATTAATTTAAAAAATTATT
66449 TAAA-TAA--TAAAAAATTATT
1 TAAATTAATTTAAAAAATTATT
66468 TAAATATAA-TTATAAAAA-TATTT
1 TAAAT-TAATTTA-AAAAATTA-TT
*
66491 TAATATTAATATAAAAATATTATT
1 TAA-ATTAATTTAAAAA-ATTATT
66515 T
1 T
66516 TACTTTTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
19 14 0.25
21 6 0.11
22 8 0.15
23 17 0.31
24 8 0.15
25 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATTAATTTAAAAAATTATT
Found at i:66830 original size:39 final size:38
Alignment explanation
Indices: 66771--66852 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 38
66761 GATAATGGGA
*
66771 CACCTTAAGAGGTGAGGTAATAAATTTAATGAATTCCTT
1 CACCTTAAGAGGTGACGTAATAAATTTAATGAATT-CTT
66810 CACCTTAAGAGGTGACGTAATAAATTTAATGAATTCTT
1 CACCTTAAGAGGTGACGTAATAAATTTAATGAATTCTT
66848 CACCT
1 CACCT
66853 CAAAAGTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 8 0.19
39 34 0.81
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (38 bp):
CACCTTAAGAGGTGACGTAATAAATTTAATGAATTCTT
Found at i:66868 original size:38 final size:39
Alignment explanation
Indices: 66771--66874 Score: 138
Period size: 39 Copynumber: 2.7 Consensus size: 39
66761 GATAATGGGA
* *
66771 CACCTTAAGAGGTGAGGTAATAAATTTAATGAATTCCTT
1 CACCTCAAAAGGTGAGGTAATAAATTTAATGAATTCCTT
* * *
66810 CACCTTAAGAGGTGACGTAATAAATTTAATGAATT-CTT
1 CACCTCAAAAGGTGAGGTAATAAATTTAATGAATTCCTT
* *
66848 CACCTCAAAAGTTGAGGTAATACATTT
1 CACCTCAAAAGGTGAGGTAATAAATTT
66875 TTCACCAGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 25 0.42
39 34 0.58
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (39 bp):
CACCTCAAAAGGTGAGGTAATAAATTTAATGAATTCCTT
Found at i:67096 original size:21 final size:20
Alignment explanation
Indices: 67038--67079 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
67028 ATCGGAGTAA
* *
67038 TTTAAAAATATTAAAATATT
1 TTTATAAATATTTAAATATT
67058 TTTATAAATATTTAAATATT
1 TTTATAAATATTTAAATATT
67078 TT
1 TT
67080 ATTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTATAAATATTTAAATATT
Found at i:68612 original size:56 final size:54
Alignment explanation
Indices: 68552--68680 Score: 129
Period size: 56 Copynumber: 2.4 Consensus size: 54
68542 TGTACTCTTT
68552 CATATGAAATTTTCAATTAAAC-CTTT-CATAAACAGAATTTTAAATTAAACCTTTTA
1 CATATGAAATTTTCAATTAAACTCTTTGCATAAA-A-AATTTTAAATT-AA-CTTTTA
* * * * * *
68608 CATATAAAATTTTCATTTAGACTCTTTGTATATAAAATTTTTAATTAACTTTTA
1 CATATGAAATTTTCAATTAAACTCTTTGCATAAAAAATTTTAAATTAACTTTTA
*
68662 CTTATAGAAATTTT-AATTA
1 CATAT-GAAATTTTCAATTA
68681 GATTTTCACA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
54 14 0.23
55 9 0.15
56 29 0.48
57 5 0.08
58 4 0.07
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (54 bp):
CATATGAAATTTTCAATTAAACTCTTTGCATAAAAAATTTTAAATTAACTTTTA
Found at i:68618 original size:28 final size:28
Alignment explanation
Indices: 68460--68677 Score: 105
Period size: 28 Copynumber: 7.9 Consensus size: 28
68450 AAATTTGATC
*
68460 AACCTTTTACATATAAAATTGTT-AATTT
1 AACCTTTTACATATAAAATT-TTAAATTA
* ** * * *
68488 AA-TTTTTATGTATGAAATTTTTAGTTA
1 AACCTTTTACATATAAAATTTTAAATTA
* * * * *
68515 AACATTTCACTTATAAAATTTTTAATTTG
1 AACCTTTTACATATAAAA-TTTTAAATTA
* * *
68544 TA-CTCTTT-CATATGAAATTTTCAATTA
1 AACCT-TTTACATATAAAATTTTAAATTA
*
68571 AACC-TTT-CATAAACAGAATTTTAAATTA
1 AACCTTTTACATATA-A-AATTTTAAATTA
* *
68599 AACCTTTTACATATAAAATTTTCATTTA
1 AACCTTTTACATATAAAATTTTAAATTA
* *
68627 GACTCTTTGT--ATATAAAATTTTTAATT-
1 AAC-CTTT-TACATATAAAATTTTAAATTA
*
68654 AA-CTTTTACTTATAGAAATTTTAA
1 AACCTTTTACATATA-AAATTTTAA
68678 TTAGATTTTC
Statistics
Matches: 141, Mismatches: 35, Indels: 29
0.69 0.17 0.14
Matches are distributed among these distances:
24 1 0.01
25 4 0.03
26 13 0.09
27 36 0.26
28 63 0.45
29 18 0.13
30 6 0.04
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (28 bp):
AACCTTTTACATATAAAATTTTAAATTA
Found at i:68686 original size:26 final size:27
Alignment explanation
Indices: 68638--68735 Score: 73
Period size: 26 Copynumber: 3.7 Consensus size: 27
68628 ACTCTTTGTA
68638 TATA-AAATTTTTAATTA-ACTTTTACT
1 TATAGAAATTTTTAATTAGA-TTTTACT
*
68664 TATAGAAA-TTTTAATTAGATTTTCACA
1 TATAGAAATTTTTAATTAGATTTT-ACT
* *
68691 CAT-GAAATTGTTTTATTAGCATTTTA-T
1 TATAGAAATT-TTTAATTAG-ATTTTACT
*
68718 GTATAG-AACTTTTAATTA
1 -TATAGAAATTTTTAATTA
68736 AACTTTAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
26 21 0.37
27 16 0.28
28 14 0.25
29 6 0.11
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (27 bp):
TATAGAAATTTTTAATTAGATTTTACT
Found at i:69192 original size:2 final size:2
Alignment explanation
Indices: 69187--69224 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
69177 ATTTTTACCC
69187 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69225 AAATAACTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:70947 original size:81 final size:82
Alignment explanation
Indices: 70679--70948 Score: 245
Period size: 81 Copynumber: 3.4 Consensus size: 82
70669 TTAGGGGTAA
* * * *
70679 TTTAGTATTTTCATATCAATTTTTGAACC-TTTAAGA-T---CTTAGCACTTTTATGTTAAAAAT
1 TTTAGTATTATCATGTCAA-TCTTGAACCTTTTAAGATTGAGCTTAGCACTTTTATGTCAAAAAT
70739 TGAGCTTTTAGGATTATT
65 TGAGCTTTTAGGATTATT
* * * * * *
70757 TTTAGTATTATCATCTCAATCTTGAACC-TTTAGGGTTGTGTTTAGCACTTTTATG-CCAAAATT
1 TTTAGTATTATCATGTCAATCTTGAACCTTTTAAGATTGAGCTTAGCACTTTTATGTCAAAAATT
* * *
70820 AAACTTTTAGGGA-TA-G
66 GAGCTTTTA-GGATTATT
* * * * *
70836 TTTAGCATTTTCATGTCAATTTTTGAACCTTTTAAGATT-AGCTTAACACTTTCATGTCAAAAAT
1 TTTAGTATTATCATGTCAA-TCTTGAACCTTTTAAGATTGAGCTTAGCACTTTTATGTCAAAAAT
*
70900 CGAGCTTTTAGGATTATT
65 TGAGCTTTTAGGATTATT
* **
70918 TTTAGTATTATCATGTTAATCTCAAACCTTT
1 TTTAGTATTATCATGTCAATCTTGAACCTTT
70949 AGGGTTGTGT
Statistics
Matches: 150, Mismatches: 32, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
77 13 0.09
78 18 0.12
79 16 0.11
80 39 0.26
81 48 0.32
82 16 0.11
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (82 bp):
TTTAGTATTATCATGTCAATCTTGAACCTTTTAAGATTGAGCTTAGCACTTTTATGTCAAAAATT
GAGCTTTTAGGATTATT
Found at i:71017 original size:79 final size:79
Alignment explanation
Indices: 70884--71034 Score: 187
Period size: 79 Copynumber: 1.9 Consensus size: 79
70874 TAGCTTAACA
* * *
70884 CTTTCATGTCAAAAATCGAGCTTTTAGGATTATTTTTAGTATTATCATGTTAATCTCAAACCTTT
1 CTTTCATGTCAAAAATCGAGCTTTTAGGATTATTTGTAGTATTATCATGGTAATC-CAAACCTAT
*
70949 AGGGTTGTGTCAGTG
65 AGGATTGTGTCAGTG
* * * * * * *
70964 CTTTCATGT-TAAAATCTAGCTTTTGGGCTTATTTGTAGTATTTTTATGGTAATCCTAACCTATA
1 CTTTCATGTCAAAAATCGAGCTTTTAGGATTATTTGTAGTATTATCATGGTAATCCAAACCTATA
71028 GGATTGT
66 GGATTGT
71035 ATTAGCACTT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
78 14 0.23
79 37 0.62
80 9 0.15
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (79 bp):
CTTTCATGTCAAAAATCGAGCTTTTAGGATTATTTGTAGTATTATCATGGTAATCCAAACCTATA
GGATTGTGTCAGTG
Found at i:71218 original size:17 final size:18
Alignment explanation
Indices: 71196--71247 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
71186 GTAAGCACTT
71196 TTATATCAAAGCTGAT-A
1 TTATATCAAAGCTGATCA
*
71213 TTATATCAAAGCTGATCT
1 TTATATCAAAGCTGATCA
71231 TTATATCAAAGCTGATC
1 TTATATCAAAGCTGATC
71248 CTTTAGGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 16 0.48
18 17 0.52
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATATCAAAGCTGATCA
Found at i:71236 original size:18 final size:18
Alignment explanation
Indices: 71195--71252 Score: 91
Period size: 17 Copynumber: 3.2 Consensus size: 18
71185 TGTAAGCACT
71195 TTTATATCAAAGCTGAT-
1 TTTATATCAAAGCTGATC
*
71212 ATTATATCAAAGCTGATC
1 TTTATATCAAAGCTGATC
71230 TTTATATCAAAGCTGATCC
1 TTTATATCAAAGCTGAT-C
71249 TTTA
1 TTTA
71253 GGGCTCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 16 0.43
18 16 0.43
19 5 0.14
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (18 bp):
TTTATATCAAAGCTGATC
Found at i:76374 original size:15 final size:17
Alignment explanation
Indices: 76354--76387 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
76344 ATCCATCATT
76354 CACATA-TCAT-ATCCA
1 CACATATTCATCATCCA
76369 CACATATTCATCATCCA
1 CACATATTCATCATCCA
76386 CA
1 CA
76388 ATTAGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (17 bp):
CACATATTCATCATCCA
Found at i:85417 original size:19 final size:19
Alignment explanation
Indices: 85377--85424 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
85367 ACTGTTAAAA
*
85377 TATATTAAAATATTATTTT
1 TATATTAAAATATTATTAT
*
85396 TATATTAATA-ATTATATAT
1 TATATTAAAATATTAT-TAT
85415 TATAATTAAA
1 TAT-ATTAAA
85425 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.21
19 14 0.58
20 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATATTAAAATATTATTAT
Found at i:86615 original size:2 final size:2
Alignment explanation
Indices: 86610--86658 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
86600 TATGTGTGTG
86610 TA 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 TA
86652 TA TA TA T
1 TA TA TA T
86659 CTTATGTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:89353 original size:21 final size:21
Alignment explanation
Indices: 89329--89395 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
89319 ATTAATTTTG
* *
89329 ATAAGATTAAAAATAATAATT
1 ATAAAATTAAAAATAATAATA
** *
89350 ATAAAATTAATTATTATAATA
1 ATAAAATTAAAAATAATAATA
89371 ATAAAATT-AAAAT-A-AATA
1 ATAAAATTAAAAATAATAATA
89389 ATAAAAT
1 ATAAAAT
89396 ATATTTCAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 11 0.28
19 1 0.03
20 3 0.08
21 24 0.62
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (21 bp):
ATAAAATTAAAAATAATAATA
Found at i:89354 original size:15 final size:15
Alignment explanation
Indices: 89336--89392 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
89326 TTGATAAGAT
89336 TAAAAATAATAATTA
1 TAAAAATAATAATTA
* *
89351 TAAAATTAATTATTA
1 TAAAAATAATAATTA
*
89366 TAATAATAA-AATTA
1 TAAAAATAATAATTA
*
89380 AAATAAATAATAA
1 TAA-AAATAATAA
89393 AATATATTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
14 6 0.18
15 25 0.76
16 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAAATAATAATTA
Found at i:89437 original size:18 final size:17
Alignment explanation
Indices: 89404--89440 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
89394 ATATATTTCA
89404 AATTTAAAAATAATAAT
1 AATTTAAAAATAATAAT
*
89421 AATTTAATAAATTATAAT
1 AATTTAA-AAATAATAAT
89439 AA
1 AA
89441 AAAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTAAAAATAATAAT
Found at i:89521 original size:15 final size:14
Alignment explanation
Indices: 89503--89553 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
89493 ATATTTACAT
89503 TAAAATAAATATTAA
1 TAAAATAAA-ATTAA
*
89518 TAAAATAAAAATAA
1 TAAAATAAAATTAA
*
89532 AAAAATAAAGATTAAA
1 TAAAATAAA-ATT-AA
89548 TAAAAT
1 TAAAAT
89554 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 12 0.40
15 11 0.37
16 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
TAAAATAAAATTAA
Found at i:90089 original size:19 final size:19
Alignment explanation
Indices: 90065--90106 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
90055 AATATTTAAA
*
90065 AAATTTAAATAA-AAATATT
1 AAATTTAAAAAATAAAT-TT
90084 AAATTTAAAAAATAAATTT
1 AAATTTAAAAAATAAATTT
90103 AAAT
1 AAAT
90107 AATATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTTAAAAAATAAATTT
Found at i:90095 original size:29 final size:31
Alignment explanation
Indices: 90049--90127 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 31
90039 GTTCGAAGGT
90049 TAAT-TTAATATTT-AAAAAATTTAAATAA-A
1 TAATATTAA-ATTTAAAAAAATTTAAATAATA
90078 -AATATTAAATTTAAAAAATAAATTTAAATAATA
1 TAATATTAAATTT--AAAA-AAATTTAAATAATA
*
90111 TAATATT-TATTTAAAAA
1 TAATATTAAATTTAAAAA
90128 TGTATAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
28 7 0.17
29 4 0.10
30 1 0.02
31 7 0.17
32 12 0.29
33 5 0.12
34 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TAATATTAAATTTAAAAAAATTTAAATAATA
Found at i:90105 original size:28 final size:29
Alignment explanation
Indices: 90049--90119 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
90039 GTTCGAAGGT
90049 TAAT-TTAATATTTAAAAAATTTAAATAAA
1 TAATATTAATATTTAAAAAA-TTAAATAAA
90078 -AATATTAA-ATTTAAAAAA-TAAATTTAAA
1 TAATATTAATATTTAAAAAATTAAA--TAAA
90106 TAATA-TAATATTTA
1 TAATATTAATATTTA
90120 TTTAAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
26 4 0.11
28 20 0.54
29 13 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATATTAATATTTAAAAAATTAAATAAA
Found at i:90106 original size:32 final size:33
Alignment explanation
Indices: 90065--90127 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
90055 AATATTTAAA
90065 AAATTTAAATAA-A-AATATTAAATTTAAAAAAT
1 AAATTTAAATAATATAATATT-AATTTAAAAAAT
*
90097 AAATTTAAATAATATAATATTTATTTAAAAA
1 AAATTTAAATAATATAATATTAATTTAAAAA
90128 TGTATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.43
33 10 0.36
34 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
AAATTTAAATAATATAATATTAATTTAAAAAAT
Found at i:90953 original size:21 final size:22
Alignment explanation
Indices: 90907--90958 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
90897 GTCTTTTGAG
* *
90907 CAGCATTCTTTTTAAACTTTTAA
1 CAGCATT-TTTATAAAATTTTAA
90930 CAGCATTTTTATAAAATTTT-A
1 CAGCATTTTTATAAAATTTTAA
90951 CAGC-TTTT
1 CAGCATTTT
90959 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 11 0.41
23 7 0.26
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (22 bp):
CAGCATTTTTATAAAATTTTAA
Found at i:93726 original size:3 final size:3
Alignment explanation
Indices: 93709--93750 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
93699 TAATTAATTA
* *
93709 ATT A-T ATT ATT -TT ATT ATT ATT ATT ATT TTT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
93751 GAAAGGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:96298 original size:3 final size:3
Alignment explanation
Indices: 96281--96322 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
96271 TAATTAATTA
* *
96281 ATT A-T ATT ATT -TT ATT ATT ATT ATT ATT TTT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
96323 GAAAGGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:98870 original size:3 final size:3
Alignment explanation
Indices: 98853--98894 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
98843 TAATTAATTA
* *
98853 ATT A-T ATT ATT -TT ATT ATT ATT ATT ATT TTT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
98895 GAAAGGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:106714 original size:3 final size:3
Alignment explanation
Indices: 106697--106738 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
106687 TAATTAATTA
* *
106697 ATT A-T ATT ATT -TT ATT ATT ATT ATT ATT TTT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
106739 GAAAGGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:109286 original size:3 final size:3
Alignment explanation
Indices: 109269--109310 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
109259 TAATTAATTA
* *
109269 ATT A-T ATT ATT -TT ATT ATT ATT ATT ATT TTT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
109311 GAAAGGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:110800 original size:22 final size:21
Alignment explanation
Indices: 110775--110816 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
110765 TTGTTATTAT
110775 TTATCTCAAAGAAAATAAAAAC
1 TTAT-TCAAAGAAAATAAAAAC
* *
110797 TTATTGAAAGAAAATTAAAA
1 TTATTCAAAGAAAATAAAAA
110817 TCTATTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (21 bp):
TTATTCAAAGAAAATAAAAAC
Found at i:111946 original size:16 final size:16
Alignment explanation
Indices: 111927--111970 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
111917 TTATAATATG
*
111927 AAATATTTAAAAATTA
1 AAATAATTAAAAATTA
* * *
111943 AAATAAATCAAATTTA
1 AAATAATTAAAAATTA
111959 AAATAATTAAAA
1 AAATAATTAAAA
111971 GCATGATTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAATTAAAAATTA
Found at i:114198 original size:13 final size:12
Alignment explanation
Indices: 114149--114194 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
114139 ACCTTCACTG
114149 TTTCAAATTGAA
1 TTTCAAATTGAA
*
114161 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
114176 TTTCAAATTGAA
1 TTTCAAATTGAA
114188 TTTCAAA
1 TTTCAAA
114195 ATTGGTGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:114211 original size:12 final size:12
Alignment explanation
Indices: 114202--114227 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
114192 AAAATTGGTG
114202 GCACAGTTGGCA
1 GCACAGTTGGCA
114214 GCACAGTTGGCA
1 GCACAGTTGGCA
114226 GC
1 GC
114228 CTTTGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.15
Consensus pattern (12 bp):
GCACAGTTGGCA
Found at i:118449 original size:40 final size:41
Alignment explanation
Indices: 118405--118489 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 41
118395 TACGACAAGT
* *
118405 AATAT-TTGGGTGGCT-TGGTCAATCCATGGAAAAATAAATA
1 AATATATTGGGTGGCTAT-GCCAATCCACGGAAAAATAAATA
118445 AATATACAATTGGGTGGCTATGCCAATCCACGGAAAAATAAATA
1 AATAT---ATTGGGTGGCTATGCCAATCCACGGAAAAATAAATA
118489 A
1 A
118490 TAAAAACACA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 5 0.13
44 32 0.84
45 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (41 bp):
AATATATTGGGTGGCTATGCCAATCCACGGAAAAATAAATA
Found at i:119602 original size:28 final size:27
Alignment explanation
Indices: 119571--119646 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 27
119561 AATTTAATTC
119571 AATTAATTTATATAATTATTTTTTAAAA
1 AATTAATTTATATAATTATTTTTT-AAA
*
119599 AATT-ATTTA-ATAAATTTATATTTTAAA
1 AATTAATTTATAT-AA-TTATTTTTTAAA
**
119626 CTTTAATTTATATAATCTATT
1 AATTAATTTATATAAT-TATT
119647 CATGTTTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
26 2 0.05
27 13 0.33
28 22 0.56
29 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (27 bp):
AATTAATTTATATAATTATTTTTTAAA
Found at i:120249 original size:17 final size:18
Alignment explanation
Indices: 120219--120267 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
120209 TGATGTGTTC
**
120219 AATTTATTTTTTAAA-TA
1 AATTTATTAATTAAATTA
120236 AATTTATTAATTAAATTA
1 AATTTATTAATTAAATTA
120254 ATATCTTATTAATT
1 A-AT-TTATTAATT
120268 CGTAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 13 0.48
18 3 0.11
19 2 0.07
20 9 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTTATTAATTAAATTA
Found at i:120691 original size:22 final size:22
Alignment explanation
Indices: 120649--120690 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
120639 AATAATTAAA
*
120649 TATTTATTTTATACTAAAAAAT
1 TATTAATTTTATACTAAAAAAT
120671 TATTAATTTT-TACTAAAAAA
1 TATTAATTTTATACTAAAAAA
120691 ACTGTTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTAATTTTATACTAAAAAAT
Found at i:121370 original size:15 final size:17
Alignment explanation
Indices: 121338--121386 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
121328 CCTATATGCA
* *
121338 TAAAAGAAAAAATCTATT
1 TAAAAG-AAATATATATT
121356 T-AAA-AAATATATATT
1 TAAAAGAAATATATATT
121371 TAAAAGAAATATATAT
1 TAAAAGAAATATATAT
121387 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 13 0.48
18 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
TAAAAGAAATATATATT
Found at i:121384 original size:2 final size:2
Alignment explanation
Indices: 121379--121408 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
121369 TTTAAAAGAA
121379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121409 TAGAAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124327 original size:71 final size:71
Alignment explanation
Indices: 124211--124351 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 71
124201 CTTGCATATA
124211 CCATCCAAGAATCTCTTTCCACGAACGCCATTGTTTGATCCAATTACTTAGCATACCAGTTCTGA
1 CCATCCAAGAATCTCTTTCCACGAACGCCATTGTTTGATCCAATTACTTAGCATACCAGTTCTGA
124276 ACCTGC
66 ACCTGC
** *
124282 CCATCCAAGAATCTCTTTTTACGAAGGCCATTGTTTGATCCAATTACTTAGCATACCAGTTCTGA
1 CCATCCAAGAATCTCTTTCCACGAACGCCATTGTTTGATCCAATTACTTAGCATACCAGTTCTGA
124347 ACCTG
66 ACCTG
124352 TTCCTTCGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.31
Consensus pattern (71 bp):
CCATCCAAGAATCTCTTTCCACGAACGCCATTGTTTGATCCAATTACTTAGCATACCAGTTCTGA
ACCTGC
Found at i:126505 original size:3 final size:3
Alignment explanation
Indices: 126497--126530 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
126487 TTATAATAGC
* *
126497 AAT AAT AAT AAT AAT AAC AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
126531 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:127264 original size:10 final size:10
Alignment explanation
Indices: 127206--127266 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
127196 TAAATTTAGA
127206 TATTTAAATTT
1 TATTTAAA-TT
*
127217 TATTTTAATT
1 TATTTAAATT
*
127227 TATTTATATT
1 TATTTAAATT
*
127237 TATAAATAAA-T
1 TAT--TTAAATT
*
127248 AATTTAAATT
1 TATTTAAATT
127258 TATTTAAAT
1 TATTTAAAT
127267 CGATTTATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
9 4 0.10
10 22 0.56
11 10 0.26
12 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTTAAATT
Found at i:127336 original size:10 final size:10
Alignment explanation
Indices: 127289--127337 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
127279 TATTTTTAAT
*
127289 TTAATTTTTA
1 TTAAATTTTA
*
127299 TAAAATTTT-
1 TTAAATTTTA
*
127308 TTAAATTTAA
1 TTAAATTTTA
*
127318 TTAATTTTTA
1 TTAAATTTTA
127328 TTAAATTTTA
1 TTAAATTTTA
127338 AAATATAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
9 7 0.23
10 24 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTAAATTTTA
Found at i:127341 original size:28 final size:29
Alignment explanation
Indices: 127283--127352 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
127273 ATATTATATT
*
127283 TTTAATTTAATTTTTATAAAATTTTTTAAA
1 TTTAA-TTAATTTTTATAAAATTTTTAAAA
*
127313 TTTAATTAATTTTTATTAAA-TTTTAAAA
1 TTTAATTAATTTTTATAAAATTTTTAAAA
* *
127341 TATAAATAATTT
1 TTTAATTAATTT
127353 AATATATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 17 0.47
29 14 0.39
30 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTAATTAATTTTTATAAAATTTTTAAAA
Found at i:127453 original size:20 final size:23
Alignment explanation
Indices: 127410--127455 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
127400 TTATATAACA
127410 AAAATTATATAATATATTAAATAT
1 AAAATTATATAATATATT-AATAT
127434 AAAATTA-AT-ATATATT-ATAT
1 AAAATTATATAATATATTAATAT
127454 AA
1 AA
127456 TTAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.27
22 7 0.32
23 2 0.09
24 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATTATATAATATATTAATAT
Found at i:129686 original size:21 final size:20
Alignment explanation
Indices: 129635--129687 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
129625 AATAACATAT
*
129635 ATCATTATTAATTTTAATCTT
1 ATCATTA-TAATTTTAATCTC
* *
129656 ATCATCATAACTTTTCATCTC
1 ATCATTATAA-TTTTAATCTC
129677 ATCATTATAAT
1 ATCATTATAAT
129688 AATTAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (20 bp):
ATCATTATAATTTTAATCTC
Found at i:129829 original size:23 final size:25
Alignment explanation
Indices: 129803--129848 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
129793 AATTATTTAA
129803 AATATTATTTTTA-TA-TTAATATT
1 AATATTATTTTTATTATTTAATATT
*
129826 AATATTTTTTTTATTATTTAATA
1 AATATTATTTTTATTATTTAATA
129849 ATTTCAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 2 0.10
25 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
AATATTATTTTTATTATTTAATATT
Found at i:130999 original size:2 final size:2
Alignment explanation
Indices: 130935--130980 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
130925 ATTTAGATCC
*
130935 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
130977 AT AT
1 AT AT
130981 TTAATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:132976 original size:18 final size:18
Alignment explanation
Indices: 132953--132993 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
132943 TTTAATATAA
*
132953 ATATATATATACACACAT
1 ATATATATATACACACAC
*
132971 ATATATATATATACACAC
1 ATATATATATACACACAC
132989 ATATA
1 ATATA
132994 AGATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATATATATACACACAC
Found at i:132978 original size:22 final size:22
Alignment explanation
Indices: 132947--132994 Score: 82
Period size: 20 Copynumber: 2.3 Consensus size: 22
132937 CTGCTCTTTA
132947 ATATAAATATATATATACACAC
1 ATATAAATATATATATACACAC
132969 ATAT--ATATATATATACACAC
1 ATATAAATATATATATACACAC
132989 ATATAA
1 ATATAA
132995 GATTATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 20 0.83
22 4 0.17
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAAATATATATATACACAC
Found at i:134212 original size:15 final size:17
Alignment explanation
Indices: 134192--134233 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
134182 TGCTATTAAC
134192 ATAAATTAATTA-A-AA
1 ATAAATTAATTACATAA
134207 ATAAA-TAATTACATAA
1 ATAAATTAATTACATAA
134223 ATAATATTAAT
1 ATAA-ATTAAT
134234 ATAACTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 6 0.26
16 6 0.26
17 1 0.04
18 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAATTAATTACATAA
Found at i:134274 original size:39 final size:39
Alignment explanation
Indices: 134229--134304 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
134219 ATAAATAATA
* * *
134229 TTAATATAACTTTAATTTTATTAAATTTTTAATTATTAT
1 TTAATATAACTATAATCTTAATAAATTTTTAATTATTAT
134268 TTAATATAACTATAATCTTAATAAATTTTTAATTATT
1 TTAATATAACTATAATCTTAATAAATTTTTAATTATT
134305 TATTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (39 bp):
TTAATATAACTATAATCTTAATAAATTTTTAATTATTAT
Found at i:135614 original size:11 final size:11
Alignment explanation
Indices: 135583--135615 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
135573 ATGAAATTAA
135583 AAAAATAAT-T
1 AAAAATAATAT
135593 AAAATATAATAT
1 AAAA-ATAATAT
135605 AAAAATAATAT
1 AAAAATAATAT
135616 TAATATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 12 0.57
12 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:135648 original size:17 final size:17
Alignment explanation
Indices: 135626--135775 Score: 89
Period size: 17 Copynumber: 8.9 Consensus size: 17
135616 TAATATAAAT
135626 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
**
135643 ATATTAATTTTTA-AT-
1 ATATTAAAATTTATATA
135658 ATATTAAAATTTATA-A
1 ATATTAAAATTTATATA
* * *
135674 AAATTAAAAGGTAATATAA
1 ATATTAAAA-TTTATAT-A
*
135693 ATATATTAAATTTATATTA
1 ATAT-TAAAATTTATA-TA
**
135712 ATATTAATTTTTA-AT-
1 ATATTAAAATTTATATA
*
135727 ATATTAATATTTATA-A
1 ATATTAAAATTTATATA
* *
135743 ATTTTAATAATTTAAAT-
1 ATATTAA-AATTTATATA
*
135760 ATAATTAAAATATATA
1 AT-ATTAAAATTTATA
135776 AAACTAATAA
Statistics
Matches: 100, Mismatches: 21, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
15 23 0.23
16 19 0.19
17 30 0.30
18 10 0.10
19 13 0.13
20 5 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:135747 original size:24 final size:21
Alignment explanation
Indices: 135705--135751 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
135695 ATATTAAATT
*
135705 TATATTAATATTAATTTTTAA
1 TATATTAATATTAAATTTTAA
135726 TATATTAATATTTATAAATTTTAA
1 TATATTAATA--T-TAAATTTTAA
135750 TA
1 TA
135752 ATTTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
23 1 0.05
24 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTAATATTAAATTTTAA
Found at i:135801 original size:18 final size:16
Alignment explanation
Indices: 135762--135803 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
135752 ATTTAAATAT
135762 AATTAA-AATATATAA
1 AATTAATAATATATAA
*
135777 AACTAATAATTATATCAA
1 AATTAATAA-TATAT-AA
135795 AATTAATAA
1 AATTAATAA
135804 ATCTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 5 0.23
16 2 0.09
17 5 0.23
18 10 0.45
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAATAATATATAA
Found at i:136012 original size:19 final size:19
Alignment explanation
Indices: 135990--136033 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
135980 ATTTTTAAAA
*
135990 TATTAATTTAATATTTATT
1 TATTAATATAATATTTATT
136009 TATTAATATAATATTTATT
1 TATTAATATAATATTTATT
*
136028 TTTTAA
1 TATTAA
136034 AAAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTAATATAATATTTATT
Found at i:136023 original size:15 final size:15
Alignment explanation
Indices: 135955--136027 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 15
135945 TTAAATTTTA
135955 ATAA-ATTTATTAAT
1 ATAATATTTATTAAT
**
135969 ATAATATTTTTATTTTT
1 ATAATA--TTTATTAAT
* *
135986 AAAATATTAATTTAAT
1 ATAATATTTA-TTAAT
*
136002 AT-TTATTTATTAAT
1 ATAATATTTATTAAT
136016 ATAATATTTATT
1 ATAATATTTATT
136028 TTTTAAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
14 11 0.25
15 17 0.39
16 4 0.09
17 12 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATATTTATTAAT
Found at i:137030 original size:2 final size:2
Alignment explanation
Indices: 137023--137054 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
137013 GATTCCAACA
*
137023 AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
137055 GGGTATTCAA
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:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:140383 original size:34 final size:35
Alignment explanation
Indices: 140327--140394 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
140317 TTGTAATGTA
* * *
140327 AATAAAAAATATGTTAAGTATTAGAATTTAAATTT
1 AATAAAAAATATGTAAAGTATTAAAAATTAAATTT
*
140362 AATAAAAAATA-GTAAATTATTAAAAATTAAATT
1 AATAAAAAATATGTAAAGTATTAAAAATTAAATT
140395 AAAAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (35 bp):
AATAAAAAATATGTAAAGTATTAAAAATTAAATTT
Found at i:140853 original size:25 final size:25
Alignment explanation
Indices: 140803--140853 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
140793 TTTATGTATA
* *
140803 TTTTAATAATATTTAAATTTTTAAT
1 TTTTAATAATATTTAAATTATAAAT
*
140828 TTTTAAT-ATATTTTAATTAATAAAT
1 TTTTAATAATATTTAAATT-ATAAAT
140853 T
1 T
140854 AAAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTAATAATATTTAAATTATAAAT
Found at i:142343 original size:17 final size:17
Alignment explanation
Indices: 142294--142345 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
142284 AACATTCATG
142294 TATTTTATAGTTCATGAA
1 TATTTTA-AGTTCATGAA
**
142312 TA-TTTAAAATCATGAA
1 TATTTTAAGTTCATGAA
*
142328 TATTTTAAGTTTATGAA
1 TATTTTAAGTTCATGAA
142345 T
1 T
142346 GTTCATAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 10 0.36
17 16 0.57
18 2 0.07
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (17 bp):
TATTTTAAGTTCATGAA
Found at i:143494 original size:79 final size:79
Alignment explanation
Indices: 143409--143555 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 79
143399 AGAAAGAATA
* *
143409 GGGTTGGAGTATCCCTGATTAT-AGAAAATCAGTGTTTTGAAAATAAAATCGG-GATTAGAGTAT
1 GGGTTGGAATATCCCTGATTATGAGAAAATCA-TGTTTTGAAAATAAAATAGGAG-TTAGAGTAT
143472 CCCCGTGAAAATAATG
64 CCCCGTGAAAATAATG
* * * * * *
143488 GGGTTGGAATATTCCTGATTGTGAGAAATTGATGTTTTGGAAATAAAATAGGAGTTGGAGTATCC
1 GGGTTGGAATATCCCTGATTATGAGAAAATCATGTTTTGAAAATAAAATAGGAGTTAGAGTATCC
143553 CCG
66 CCG
143556 ATTGTGGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 50 0.86
80 8 0.14
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (79 bp):
GGGTTGGAATATCCCTGATTATGAGAAAATCATGTTTTGAAAATAAAATAGGAGTTAGAGTATCC
CCGTGAAAATAATG
Found at i:143559 original size:51 final size:51
Alignment explanation
Indices: 143490--143604 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
143480 AAATAATGGG
* * * * *
143490 GTTGGAATATTCCTGATTGT-GAGAAATTGATGTTTTGGAAATAAAATAGGA
1 GTTGGAGTATCCCCGATTGTGGA-AAATTGATGTTTTAGAAATAAAACAGGA
* *
143541 GTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAACAGGA
143592 GTTGGAGTATCCC
1 GTTGGAGTATCCC
143605 TTTGGAAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 54 0.96
52 2 0.04
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAACAGGA
Found at i:143576 original size:130 final size:129
Alignment explanation
Indices: 143405--143736 Score: 425
Period size: 130 Copynumber: 2.6 Consensus size: 129
143395 TTTTAGAAAG
* * * * * * *
143405 AATAGGGTTGGAGTATCCCTGATTATAGAAAA-TCAGTGTTTT-GAAAATAAAATCGGGATTAGA
1 AATAGGGTTGGAGTATCCCCGATTGTGGAAAATTGA-TGTTTTAG-AAATAAAACCGGGGTTGGA
* * * * * * * * *
143468 GTATCCCCGTGAAAATAATGGGGTTGGAATATTCCTGATTGTGAGAAATTGATGTTTTGGAAATA
64 GTATCCCCGTGAAAATAACGGGGTTAGAACATCCCCGATGGTGAAAAATCGATGTTTTGAAAATA
143533 A
129 A
143534 AATAGGAGTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAG
1 AATAGG-GTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAG
** * *
143599 TATCCCTTTGGAAATAACGGGGTTAGAGCATCCCCGATGGTGAAAAATCGATGTTTTGAAAATAA
65 TATCCCCGTGAAAATAACGGGGTTAGAACATCCCCGATGGTGAAAAATCGATGTTTTGAAAATAA
*
143664 AACTAGGGTTGGAGTATCTCCGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAG
1 AA-TAGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAG
143729 TATCCCCG
65 TATCCCCG
143737 ATTATGAAAA
Statistics
Matches: 176, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
129 6 0.03
130 163 0.93
131 7 0.04
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (129 bp):
AATAGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
ATCCCCGTGAAAATAACGGGGTTAGAACATCCCCGATGGTGAAAAATCGATGTTTTGAAAATAA
Found at i:143687 original size:51 final size:51
Alignment explanation
Indices: 143618--143786 Score: 232
Period size: 51 Copynumber: 3.3 Consensus size: 51
143608 GGAAATAACG
* * * *
143618 GGGTTAGAGCATCCCCGATGGTGAAAAATCGATGTTTTGAAAATAAAACTA
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACTA
* * **
143669 GGGTTGGAGTATCTCCGATTGTGGAAAATTGATGTTTT-AGAAATAAAACCG
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGA-AAATAAAACTA
* *
143720 GGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACTA
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACTA
143771 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
143787 TCGAAAATAA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.01
51 100 0.98
52 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACTA
Found at i:143700 original size:181 final size:182
Alignment explanation
Indices: 143488--143847 Score: 485
Period size: 181 Copynumber: 2.0 Consensus size: 182
143478 GAAAATAATG
* *
143488 GGGTTGGAATATTCCTGATTGTGAGAAATTGATGTTTTGGAAATAAAATAGGAGTTGGAGTATCC
1 GGGTTGGAATATTCCTGATTGTGAGAAATTGATGTTTTAGAAATAAAACAGGAGTTGGAGTATCC
* * * * * *
143553 CCGATTGTGGAAAATTGATGTTTT-AGAAATAAAACCGGGGTTGGAGTATCCCTTTGGAAATAAC
66 CCGATTATGAAAAATTGATGTTTTGA-AAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAAC
*
143617 GGGGTTAGAGCATCCCCGATGGT-GAAAAATCGATGTTTTGAAAATAAAACTA
130 GGGGTTAGAGCATCCCCGATGGTAAAAAAATCGATGTTTTGAAAATAAAACTA
* * *
143669 GGGTTGGAGTATCTCC-GATTGTG-GAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 GGGTTGGAATAT-TCCTGATTGTGAG-AAATTGATGTTTTAGAAATAAAACAGGAGTTGGAGTAT
* *
143732 CCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACTAGGGTTGGAGTATCCCCTCGAAAATAA
64 CCCCGATTATGAAAAATTGATGTTTTGAAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAA
* * * * * *
143797 CGGGGTTGGAGTATCCCCGATTGTAAAAAAATTGGTGTTTTGGAAATAAAA
129 CGGGGTTAGAGCATCCCCGATGGTAAAAAAATCGATGTTTTGAAAATAAAA
143848 ACATGAATGA
Statistics
Matches: 155, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
180 1 0.01
181 128 0.83
182 26 0.17
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (182 bp):
GGGTTGGAATATTCCTGATTGTGAGAAATTGATGTTTTAGAAATAAAACAGGAGTTGGAGTATCC
CCGATTATGAAAAATTGATGTTTTGAAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAACG
GGGTTAGAGCATCCCCGATGGTAAAAAAATCGATGTTTTGAAAATAAAACTA
Found at i:146531 original size:61 final size:61
Alignment explanation
Indices: 146405--147167 Score: 869
Period size: 61 Copynumber: 12.5 Consensus size: 61
146395 GAAGGAAATG
* * * *
146405 AAGTGCCACCAACTTGTGTTGGCTTTAAAA-AAAAAGGCATCCTGCTCTTTAAGGACT-AGA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-A
* * *
146465 AAGTGCCACCAACTTGTGTGAGCTTTAAAAGGAAAAGGCGTCCTGCTCCTTGGGGACTGAA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* ** * * *
146526 AAGTGCCACCAATTTGAATGGGCTTTAAAAGCAAAAGGCGTCCTGCTCTTTGAAGACTAAA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * * * * * *
146587 AAGTGCCACCAACTTGTGTTGGTTTTAAAAGAAAAAGGTGTCTTGCTCCTTAAGGACTAAA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * *
146648 AAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCCTTGAGGACTAAA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * * *
146709 AAGTGCCACCATCTTATGTGGGCTTTAAAAGGAAAAAGGTGTCCTGTTCTTTGAGGGCT-AGA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAGGCGTCCTGCTCTTTGAGGACTGA-A
* * *
146771 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAATGCGTCCTGCTCTTTGGGGACTG-A
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * * * * *
146831 AGGTGCCACCAGCTTGTGTGGGCTTTGAAAGGAAAATGTGTCCTGCTTTTTGAGGA-TTAGA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-A
* * *
146892 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGGCTG-A
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * * * * *
146952 AGGTGCCACCAGCTCGTGTGGGCTTTGAAAGGAAAAAGCATCCTGTTCTTTGAGGACT-AGA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-A
*
147013 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGCGTCCTGCTCTTTGAGGACTAGAA
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAGGCGTCCTGCTCTTTGAGGACT-GAA
* * * * **
147076 AGGTGCCACCAACTTGTGTGAGCTTCGAAAA--AAAAAGTATCCTGCTCTTTGAGGACTGAA
1 AAGTGCCACCAACTTGTGTGGGCTT-TAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
*
147136 AAATGCCACCAACTTGTGTGGGCTTTAAAAGG
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
147168 CATCTTGCTC
Statistics
Matches: 601, Mismatches: 86, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
59 5 0.01
60 156 0.26
61 334 0.56
62 76 0.13
63 25 0.04
64 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (61 bp):
AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
Found at i:148253 original size:1 final size:1
Alignment explanation
Indices: 148247--148344 Score: 61
Period size: 1 Copynumber: 98.0 Consensus size: 1
148237 AAGCAGGTTC
* * ** * * * ** * *
148247 TTTTTTTTTTCTCTTTTTTCCTTTTTTGTTTTTTTTTATTTTTTTGTTTTTTGATTCTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * *
148312 TTTTTGGTTTTTTTTTTGTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
148345 AAAAAGAATG
Statistics
Matches: 72, Mismatches: 25, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:148328 original size:21 final size:19
Alignment explanation
Indices: 148268--148344 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 19
148258 TCTTTTTTCC
*
148268 TTTTTTGTTTTTTT-TTAT
1 TTTTTTGTTTTTTTGTTTT
*
148286 TTTTTTG-TTTTTTGATTCT
1 TTTTTTGTTTTTTTG-TTTT
* *
148305 TTTGTT-TTTTTTGGTTTT
1 TTTTTTGTTTTTTTGTTTT
148323 TTTTTTGTTTTTTTGTTTT
1 TTTTTTGTTTTTTTGTTTT
148342 TTT
1 TTT
148345 AAAAAGAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
17 6 0.12
18 15 0.31
19 28 0.57
ACGTcount: A:0.03, C:0.01, G:0.10, T:0.86
Consensus pattern (19 bp):
TTTTTTGTTTTTTTGTTTT
Found at i:160911 original size:51 final size:52
Alignment explanation
Indices: 160832--160931 Score: 168
Period size: 51 Copynumber: 1.9 Consensus size: 52
160822 AAATAATGGG
*
160832 GTTGGAGTATCCCCCGATTGTGAGAAATTGATGTTTTGGAAATAAAATCAAA
1 GTTGGAGTATCCCCCGATTGTGAGAAATTGATGTTTTAGAAATAAAATCAAA
160884 GTTGGAGTAT-CCCCGATTGT-AGAAAATTGATGTTTTAGAAATAAAATC
1 GTTGGAGTATCCCCCGATTGTGAG-AAATTGATGTTTTAGAAATAAAATC
160932 GGCGTTAGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 2 0.04
51 34 0.74
52 10 0.22
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (52 bp):
GTTGGAGTATCCCCCGATTGTGAGAAATTGATGTTTTAGAAATAAAATCAAA
Found at i:160943 original size:51 final size:51
Alignment explanation
Indices: 160836--160948 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
160826 AATGGGGTTG
* *
160836 GAGTATCCCCCGATTGTGAGAAATTGATGTTTTGGAAATAAAATCAAAGTTG
1 GAGTAT-CCCCGATTGTGAGAAATTGATGTTTTAGAAATAAAATCAAAGTTA
***
160888 GAGTATCCCCGATTGT-AGAAAATTGATGTTTTAGAAATAAAATCGGCGTTA
1 GAGTATCCCCGATTGTGAG-AAATTGATGTTTTAGAAATAAAATCAAAGTTA
160939 GAGTATCCCC
1 GAGTATCCCC
160949 TTGAAAATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 2 0.04
51 47 0.85
52 6 0.11
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATTGATGTTTTAGAAATAAAATCAAAGTTA
Found at i:161022 original size:51 final size:51
Alignment explanation
Indices: 160959--161077 Score: 136
Period size: 51 Copynumber: 2.3 Consensus size: 51
160949 TTGAAAATAA
160959 TAGGGTTAGAGTATCCCCGA-TGATGGAAAA-TCAATGTTTT-GAAAATAAAAC
1 TAGGGTTAGAGTATCCCCGATTG-T-GAAAAGTCAATGTTTTAG-AAATAAAAC
* **
161010 TAGGGTTAGAGTATCCCTGATTGTGAAAAGTTGATGTTTTAGAAATAAAAC
1 TAGGGTTAGAGTATCCCCGATTGTGAAAAGTCAATGTTTTAGAAATAAAAC
** *
161061 CGGGGTTGGAGTATCCC
1 TAGGGTTAGAGTATCCC
161078 TTTGGAGATA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
50 5 0.08
51 51 0.86
52 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (51 bp):
TAGGGTTAGAGTATCCCCGATTGTGAAAAGTCAATGTTTTAGAAATAAAAC
Found at i:161050 original size:130 final size:127
Alignment explanation
Indices: 160750--161154 Score: 397
Period size: 130 Copynumber: 3.1 Consensus size: 127
160740 CGAAAATAAC
* ** *
160750 AGGGTTGGAGTATCCTTGATTAAAGAAAATCGATGTTTT-GAAAATAAAATCGGGATTGGAGTAT
1 AGGGTTGGAGTATCCCTGATT-GTGAAAATTGATGTTTTAG-AAATAAAATCGGG-TTGGAGTAT
** * * * *
160814 TTCCGTAAAAATAATGGGGTTGGAGTATCCCCCGAT-TGTGAGAAATTGATGTTTTGGAAATAAA
63 CCCCTTGAAAATAATAGGGTTGGAGTAT-CCCCGATATG-GA-AAATTGATGTTTTGAAAATAAA
160878 A-T
125 ACT
** * *
160880 CAAAGTTGGAGTATCCCCGATTGTAGAAAATTGATGTTTTAGAAATAAAATCGGCGTTAGAGTAT
1 -AGGGTTGGAGTATCCCTGATTGT-GAAAATTGATGTTTTAGAAATAAAATCGG-GTTGGAGTAT
* **
160945 CCCCTTGAAAATAATAGGGTTAGAGTATCCCCGATGATGGAAAATCAATGTTTTGAAAATAAAAC
63 CCCCTTGAAAATAATAGGGTTGGAGTATCCCCGAT-ATGGAAAATTGATGTTTTGAAAATAAAAC
161010 T
127 T
* *
161011 AGGGTTAGAGTATCCCTGATTGTGAAAAGTTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
1 AGGGTTGGAGTATCCCTGATTGTGAAAA-TTGATGTTTTAGAAATAAAATC-GGGTTGGAGTATC
* * * ** * *
161076 CCTTTGGAGAT-ACCGGGTTGGAGTATCCTCGATTAT-AAAAATTTGATGTTTTGAAAATAAAAC
64 CCCTTGAAAATAATAGGGTTGGAGTATCCCCGA-TATGGAAAA-TTGATGTTTTGAAAATAAAAC
*
161139 C
127 T
*
161140 AGGGTTTGAGTATCC
1 AGGGTTGGAGTATCC
161155 TCTCAGAAAT
Statistics
Matches: 229, Mismatches: 35, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
128 4 0.02
129 57 0.25
130 86 0.38
131 78 0.34
132 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (127 bp):
AGGGTTGGAGTATCCCTGATTGTGAAAATTGATGTTTTAGAAATAAAATCGGGTTGGAGTATCCC
CTTGAAAATAATAGGGTTGGAGTATCCCCGATATGGAAAATTGATGTTTTGAAAATAAAACT
Found at i:161103 original size:78 final size:77
Alignment explanation
Indices: 161012--161217 Score: 218
Period size: 78 Copynumber: 2.6 Consensus size: 77
161002 AATAAAACTA
* * * *
161012 GGGTTAGAGTATCCCTGATTGTGAAAAGTTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCTGATTGTAAAAAATTGATGTTTT-GAAATAAAACCAGGGTTGGAGTATCC
** *
161077 -CTTTGGAGATACC
65 TC-TCAGAAATACC
* * *
161090 GGGTTGGAGTAT-CCTCGATTATAAAAATTTGATGTTTTGAAAATAAAACCAGGGTTTGAGTATC
1 GGGTTGGAGTATCCCT-GATTGTAAAAAATTGATGTTTTG-AAATAAAACCAGGGTTGGAGTATC
*
161154 CTCTCAGAAATAGC
64 CTCTCAGAAATACC
* *
161168 GGGATTGGAGTATCCCCGATTGTAAAAAAATTGGTGTTTTGGAAATAAAA
1 GGG-TTGGAGTATCCCTGATTGT-AAAAAATTGATGTTTT-GAAATAAAA
161218 ACATGAATGA
Statistics
Matches: 107, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
77 4 0.04
78 63 0.59
79 15 0.14
80 24 0.22
81 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (77 bp):
GGGTTGGAGTATCCCTGATTGTAAAAAATTGATGTTTTGAAATAAAACCAGGGTTGGAGTATCCT
CTCAGAAATACC
Found at i:163048 original size:33 final size:33
Alignment explanation
Indices: 163001--163067 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
162991 GTGAAAGTGT
*
163001 GAGGAATATGGAGTTTTTAGAGGTTCTTTGGTG
1 GAGGAATATAGAGTTTTTAGAGGTTCTTTGGTG
163034 GAGGAATATAGAGTTTTTAGAGGTTCTTTGGTG
1 GAGGAATATAGAGTTTTTAGAGGTTCTTTGGTG
163067 G
1 G
163068 TGGTTTGTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.03, G:0.36, T:0.39
Consensus pattern (33 bp):
GAGGAATATAGAGTTTTTAGAGGTTCTTTGGTG
Found at i:166111 original size:31 final size:32
Alignment explanation
Indices: 166073--166133 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
166063 AAAATCAAAA
* *
166073 CCCAAACTC-AAAAAACTCGAATTTGAAATAG
1 CCCAAACTCAAAAAAACCCGAACTTGAAATAG
166104 CCCAAACTCGAAAAAAACCCGAACTTGAAA
1 CCCAAACTC-AAAAAAACCCGAACTTGAAA
166134 GAAACCGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 9 0.35
33 17 0.65
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (32 bp):
CCCAAACTCAAAAAAACCCGAACTTGAAATAG
Found at i:166133 original size:17 final size:16
Alignment explanation
Indices: 166108--166168 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
166098 AAATAGCCCA
166108 AACTCGAAAAAAACCCG
1 AACTCGAAAAAAA-CCG
* *
166125 AACTTGAAAGAAACCG
1 AACTCGAAAAAAACCG
* * * *
166141 AACCCGAAAGAATCTG
1 AACTCGAAAAAAACCG
166157 AACTCGAAAAAA
1 AACTCGAAAAAA
166169 TCTAAATTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 25 0.69
17 11 0.31
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.10
Consensus pattern (16 bp):
AACTCGAAAAAAACCG
Found at i:166143 original size:16 final size:17
Alignment explanation
Indices: 166108--166168 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 17
166098 AAATAGCCCA
166108 AACTCGAAAAAAACCCG
1 AACTCGAAAAAAACCCG
* *
166125 AACTTGAAAGAAA-CCG
1 AACTCGAAAAAAACCCG
* * * *
166141 AACCCG-AAAGAATCTG
1 AACTCGAAAAAAACCCG
166157 AACTCGAAAAAA
1 AACTCGAAAAAA
166169 TCTAAATTTG
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
15 4 0.12
16 14 0.42
17 15 0.45
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.10
Consensus pattern (17 bp):
AACTCGAAAAAAACCCG
Found at i:166400 original size:22 final size:22
Alignment explanation
Indices: 166372--166415 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
166362 AACTAATAAT
166372 TTATCAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
*
166394 TTATCAAAAAGTAACTTATATC
1 TTATCAAAAAGTAAATTATATC
166416 ATGAGCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (22 bp):
TTATCAAAAAGTAAATTATATC
Found at i:167386 original size:19 final size:18
Alignment explanation
Indices: 167337--167398 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
167327 AATAAATATT
167337 TAAAA-ATTAATTTTATA
1 TAAAATATTAATTTTATA
*
167354 TAACATATTAATTTTATA
1 TAAAATATTAATTTTATA
167372 TATAAATA-TAGATTTTA-A
1 TA-AAATATTA-ATTTTATA
167390 TAAATATAT
1 TAAA-ATAT
167399 ATTAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 6 0.16
18 22 0.58
19 10 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TAAAATATTAATTTTATA
Found at i:167423 original size:19 final size:17
Alignment explanation
Indices: 167388--167426 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
167378 TATAGATTTT
*
167388 AATAAATATATATTAAA
1 AATAAATATATAATAAA
167405 AATAATATATTATAATAAA
1 AATAA-ATA-TATAATAAA
167424 AAT
1 AAT
167427 TCACTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 3 0.16
19 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAAATATATAATAAA
Found at i:167643 original size:16 final size:16
Alignment explanation
Indices: 167624--167668 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
167614 AAAAAGACTA
*
167624 AACCTGAATAAGTCAT
1 AACCTAAATAAGTCAT
*
167640 AACCTAAATAAGTCCT
1 AACCTAAATAAGTCAT
*
167656 AACCCAAATAAGT
1 AACCTAAATAAGT
167669 TCGAACCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (16 bp):
AACCTAAATAAGTCAT
Found at i:167675 original size:16 final size:16
Alignment explanation
Indices: 167630--167679 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
167620 ACTAAACCTG
** *
167630 AATAAGTCATAACCTA
1 AATAAGTCCGAACCCA
*
167646 AATAAGTCCTAACCCA
1 AATAAGTCCGAACCCA
*
167662 AATAAGTTCGAACCCA
1 AATAAGTCCGAACCCA
167678 AA
1 AA
167680 AAAATCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (16 bp):
AATAAGTCCGAACCCA
Found at i:167844 original size:22 final size:22
Alignment explanation
Indices: 167819--167862 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
167809 AATTAATTTA
167819 ATTTTAATTTTA-AATTTATATT
1 ATTTTAATTTTATAA-TTATATT
*
167841 ATTTTTATTTTATAATTATATT
1 ATTTTAATTTTATAATTATATT
167863 CAATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTAATTTTATAATTATATT
Found at i:168281 original size:3 final size:3
Alignment explanation
Indices: 168273--168309 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
168263 TTTTAGTTGT
168273 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
168310 ATATAAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:171247 original size:31 final size:33
Alignment explanation
Indices: 171209--171290 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 33
171199 GTTCAATTTC
171209 GAATTCTCTAGCC-A-CCGGCCAATTCCAAATT
1 GAATTCTCTAGCCAACCCGGCCAATTCCAAATT
*
171240 GAATTCTCTAGTCGTCAACCGCCGGCCAATTTCAAATT
1 GAATTCTCTAG-C--CAA-C-CCGGCCAATTCCAAATT
171278 GAATTCTCTAGCC
1 GAATTCTCTAGCC
171291 GTCAGCCTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
31 11 0.26
32 1 0.02
34 1 0.02
35 2 0.05
37 1 0.02
38 27 0.63
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (33 bp):
GAATTCTCTAGCCAACCCGGCCAATTCCAAATT
Found at i:175947 original size:38 final size:38
Alignment explanation
Indices: 175907--176051 Score: 209
Period size: 38 Copynumber: 3.8 Consensus size: 38
175897 CCAGTCACCG
* * * *
175907 GCCAATTTCAAATTGAATTCTCTAATCGTCAGCTGTCG
1 GCCAATTTCAAATTGAATTCTCTAACCGTCAGCCGCCA
* *
175945 GCCAATTTCAAATTGACTTCTCTAGCCGTCAGCCGCCA
1 GCCAATTTCAAATTGAATTCTCTAACCGTCAGCCGCCA
* *
175983 GCAAATTTTAAATTGAATTCTCTAACCGTCAGCCGCCA
1 GCCAATTTCAAATTGAATTCTCTAACCGTCAGCCGCCA
*
176021 ACCAATTTCAAATTGAATTCTCTAACCGTCA
1 GCCAATTTCAAATTGAATTCTCTAACCGTCA
176052 ACTAATTCAA
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 94 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (38 bp):
GCCAATTTCAAATTGAATTCTCTAACCGTCAGCCGCCA
Found at i:177834 original size:26 final size:24
Alignment explanation
Indices: 177790--177864 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 24
177780 TTTATATTTA
177790 TATATTATATAAATATAAAAATAT
1 TATATTATATAAATATAAAAATAT
177814 TATATTA-ATAAATACGTTAAAAATAT
1 TATATTATATAAATA---TAAAAATAT
* *
177840 T-TA-AATATAAATATAATATATAT
1 TATATTATATAAATATAA-AAATAT
177863 TA
1 TA
177865 AATATGTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
22 3 0.07
23 13 0.30
24 8 0.19
25 9 0.21
26 10 0.23
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (24 bp):
TATATTATATAAATATAAAAATAT
Found at i:177889 original size:24 final size:23
Alignment explanation
Indices: 177836--177912 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
177826 TACGTTAAAA
*
177836 ATATTTAAATATAAATA-TAA-T
1 ATATTTAAATATTAATATTAATT
177857 ATATATTAAATATGTAATATTAATT
1 ATAT-TTAAATAT-TAATATTAATT
* *
177882 ATATTTAAATATATCATATTATTT
1 ATATTTAAATAT-TAATATTAATT
177906 ATATTTA
1 ATATTTA
177913 TTATATTGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 4 0.08
22 8 0.17
23 4 0.08
24 27 0.56
25 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
ATATTTAAATATTAATATTAATT
Found at i:181416 original size:29 final size:28
Alignment explanation
Indices: 181359--181417 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
181349 TTTTTTTTAA
**
181359 TAAAAAATAAATATAAATATATTTTTAT
1 TAAAAAATAAATATAAATATATTAATAT
*
181387 TAAAATAATATAATAT-AATTTATTAATAT
1 TAAAA-AATA-AATATAAATATATTAATAT
181416 TA
1 TA
181418 CGTTATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 16 0.62
30 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAAAAAATAAATATAAATATATTAATAT
Found at i:181559 original size:12 final size:12
Alignment explanation
Indices: 181544--181591 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
181534 TTTTAGACAT
181544 AATAATATAAAA
1 AATAATATAAAA
*
181556 AATAATTAAAATATA
1 AATAA-TATAA-A-A
181571 ATATAATATAAAA
1 A-ATAATATAAAA
181584 AATAATAT
1 AATAATAT
181592 TAACATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 2 0.07
15 6 0.20
16 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAATATAAAA
Found at i:181588 original size:17 final size:17
Alignment explanation
Indices: 181557--181610 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
181547 AATATAAAAA
*
181557 ATAAT-TAAAATATAAT
1 ATAATATAAAAAATAAT
181573 ATAATATAAAAAATAAT
1 ATAATATAAAAAATAAT
*
181590 ATTAACATAAAAAAT-AT
1 A-TAATATAAAAAATAAT
181607 ATAA
1 ATAA
181611 ATTTTAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 8 0.24
17 14 0.41
18 12 0.35
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAATATAAAAAATAAT
Found at i:181636 original size:25 final size:25
Alignment explanation
Indices: 181606--181662 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
181596 ATAAAAAATA
*
181606 TATAAATT-TTAATCAATTTAAATTTT
1 TATAAATTATTAAT--ATATAAATTTT
181632 T-TAAATTATTAATATATAAATTTT
1 TATAAATTATTAATATATAAATTTT
181656 TATAAAT
1 TATAAAT
181663 ATAATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 11 0.39
25 11 0.39
26 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TATAAATTATTAATATATAAATTTT
Found at i:181651 original size:15 final size:15
Alignment explanation
Indices: 181633--181730 Score: 66
Period size: 15 Copynumber: 6.7 Consensus size: 15
181623 TTAAATTTTT
*
181633 TAAATTATTAATATA
1 TAAATTATTAATAAA
*
181648 TAAATT-TTTATAAA
1 TAAATTATTAATAAA
181662 TATAATTATT-ATAAA
1 TA-AATTATTAATAAA
181677 TATAATTA-TAATATAA
1 TA-AATTATTAATA-AA
*
181693 -AAA-TAAT-ATAAA
1 TAAATTATTAATAAA
* *
181705 TAAAATA-CAATTAAA
1 TAAATTATTAA-TAAA
181720 TAAATTATTAA
1 TAAATTATTAA
181731 ATTTAATAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.03
13 8 0.12
14 15 0.22
15 37 0.54
16 6 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATTATTAATAAA
Found at i:181677 original size:40 final size:40
Alignment explanation
Indices: 181602--181677 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
181592 TAACATAAAA
* * *
181602 AATATATAAATTTTAATCAATTTAAATTTTTTAAATTATT
1 AATATATAAATTTTAATAAATATAAATTTTATAAATTATT
*
181642 AATATATAAATTTTTATAAATAT-AATTATTATAAAT
1 AATATATAAATTTTAATAAATATAAATT-TTATAAAT
181678 ATAATTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (40 bp):
AATATATAAATTTTAATAAATATAAATTTTATAAATTATT
Found at i:181691 original size:11 final size:11
Alignment explanation
Indices: 181656--181727 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 11
181646 TATAAATTTT
*
181656 TATAAATATAA
1 TATAATTATAA
181667 T-T-ATTATAAA
1 TATAATTAT-AA
181677 TATAATTATAA
1 TATAATTATAA
**
181688 TATAAAAATAA
1 TATAATTATAA
* *
181699 TATAAATAAAA
1 TATAATTATAA
*
181710 TACAATTA-AA
1 TATAATTATAA
181720 TA-AATTAT
1 TATAATTAT
181728 TAAATTTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
9 9 0.18
10 8 0.16
11 28 0.56
12 5 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAATTATAA
Found at i:187564 original size:24 final size:23
Alignment explanation
Indices: 187535--187607 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 23
187525 TGGAGAGACA
187535 TATTTATAATTTAATTTAAATTAT
1 TATTTA-AATTTAATTTAAATTAT
* *
187559 TATTTAAA--TAA-TAAAATAAAT
1 TATTTAAATTTAATTTAAAT-TAT
*
187580 TATTTAAATTTAATTATAAATTAA
1 TATTTAAATTTAATT-TAAATTAT
187604 TATT
1 TATT
187608 ATTTTAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 5 0.13
21 13 0.33
23 5 0.13
24 12 0.31
25 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTAAATTTAATTTAAATTAT
Found at i:187600 original size:45 final size:48
Alignment explanation
Indices: 187535--187629 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 48
187525 TGGAGAGACA
187535 TATTTATAATTTAATTTAAA-T-TATTA-TTTAAATAATAAAATAAAT
1 TATTTATAATTTAATTTAAATTATATTATTTTAAATAATAAAATAAAT
*
187580 TATTTA-AATTTAATTATAAATTAATATTATTTTAAATAATGAAATAAAT
1 TATTTATAATTTAATT-TAAATT-ATATTATTTTAAATAATAAAATAAAT
187629 T
1 T
187630 GTTAAGTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
44 9 0.20
45 10 0.23
46 1 0.02
48 5 0.11
49 19 0.43
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (48 bp):
TATTTATAATTTAATTTAAATTATATTATTTTAAATAATAAAATAAAT
Found at i:187608 original size:27 final size:28
Alignment explanation
Indices: 187560--187616 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
187550 TTAAATTATT
187560 ATTTAAATAATAAAATAAATTA-TTTAA
1 ATTTAAATAATAAAATAAATTATTTTAA
* *
187587 ATTT-AATTATAAATTAATATTATTTTAA
1 ATTTAAATAATAAAATAA-ATTATTTTAA
187615 AT
1 AT
187617 AATGAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 11 0.42
27 8 0.31
28 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTAAATAATAAAATAAATTATTTTAA
Found at i:187710 original size:15 final size:16
Alignment explanation
Indices: 187690--187726 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
187680 TCAAGATTAC
187690 TTTTAAT-TATAATTT
1 TTTTAATATATAATTT
187705 TTTTAATATATAATTT
1 TTTTAATATATAATTT
187721 TTTTAA
1 TTTTAA
187727 AAAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATATATAATTT
Found at i:187733 original size:16 final size:16
Alignment explanation
Indices: 187698--187733 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
187688 ACTTTTAATT
* *
187698 ATAATTTTTTTAATAT
1 ATAATTTTTTTAAAAA
187714 ATAATTTTTTTAAAAA
1 ATAATTTTTTTAAAAA
187730 ATAA
1 ATAA
187734 ATATATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATTTTTTTAAAAA
Found at i:189658 original size:2 final size:2
Alignment explanation
Indices: 189651--189676 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
189641 ATCCCATTTC
189651 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
189677 GAGTACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.