Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004369.1 Hibiscus syriacus cultivar Beakdansim tig00009571_pilon, whole genome shotgun sequence
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: 122455
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:1446 original size:23 final size:23
Alignment explanation
Indices: 1420--1471 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1410 CATCGAAGTG
*
1420 CCACGTAGAAATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
* *
1443 CCACATAGATATGTCCCAAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
1466 CCACGT
1 CCACGT
1472 TGAACCCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCAAAGGA
Found at i:1571 original size:14 final size:16
Alignment explanation
Indices: 1552--1590 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1542 TTATACCATT
*
1552 TCACATAG-CTTATA-
1 TCACATAGACATATAG
1566 TCACATAGACATATAG
1 TCACATAGACATATAG
1582 TCACATAGA
1 TCACATAGA
1591 TCATGTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (16 bp):
TCACATAGACATATAG
Found at i:1722 original size:8 final size:8
Alignment explanation
Indices: 1709--1735 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1699 ACACTAGTAT
1709 TCATGAAA
1 TCATGAAA
1717 TCATGAAA
1 TCATGAAA
1725 TCATGAAA
1 TCATGAAA
1733 TCA
1 TCA
1736 AACATTGGAA
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:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (8 bp):
TCATGAAA
Found at i:3366 original size:16 final size:15
Alignment explanation
Indices: 3347--3377 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3337 TAATTTAACA
3347 CTTAATTTTATTAATC
1 CTTAATTTTA-TAATC
3363 CTTAATTTTATAATC
1 CTTAATTTTATAATC
3378 ATGATTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTAATTTTATAATC
Found at i:21200 original size:2 final size:2
Alignment explanation
Indices: 21193--21222 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21183 ATCCTAGCCC
21193 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
21223 GAACACATTT
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:23562 original size:17 final size:16
Alignment explanation
Indices: 23540--23574 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
23530 TAATTAAACA
*
23540 TTATATACATACAAATT
1 TTATATAAATA-AAATT
23557 TTATATAAATAAAATT
1 TTATATAAATAAAATT
23573 TT
1 TT
23575 GACAGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (16 bp):
TTATATAAATAAAATT
Found at i:31392 original size:16 final size:17
Alignment explanation
Indices: 31356--31393 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
31346 ATATTATAAG
31356 TATTTTAAAATATTCAT
1 TATTTTAAAATATTCAT
31373 TATTTTATAAA-ATT-AT
1 TATTTTA-AAATATTCAT
31389 TATTT
1 TATTT
31394 ATTTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 10 0.50
18 3 0.15
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTAAAATATTCAT
Found at i:31410 original size:19 final size:18
Alignment explanation
Indices: 31358--31411 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
31348 ATTATAAGTA
*
31358 TTTTAAAATATTCATTATT
1 TTTTAAAATATAC-TTATT
*
31377 TTATAAAAT-TA-TTATT
1 TTTTAAAATATACTTATT
31393 TATTTAAAATATACTTATT
1 T-TTTAAAATATACTTATT
31412 AATAATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 6 0.21
17 7 0.24
18 3 0.10
19 13 0.45
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAAATATACTTATT
Found at i:34738 original size:21 final size:20
Alignment explanation
Indices: 34713--34767 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
34703 TTAAATTTAC
34713 TTAACTATTTATAATAATCAT
1 TTAACTATTT-TAATAATCAT
* * *
34734 TTAACTCTTTTAATCAAACAG
1 TTAACTATTTTAAT-AATCAT
*
34755 TTAATTATTTTAA
1 TTAACTATTTTAA
34768 ATTATTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAACTATTTTAATAATCAT
Found at i:35437 original size:31 final size:31
Alignment explanation
Indices: 35401--35461 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
35391 AAACTTAAAA
* *
35401 TAGTTTTGCAA-TACTGAGATTTAAATAATTT
1 TAGTTTTACAATTA-TGAAATTTAAATAATTT
35432 TAGTTTTACAATTATGAAATTTAAATAATT
1 TAGTTTTACAATTATGAAATTTAAATAATT
35462 CATACAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (31 bp):
TAGTTTTACAATTATGAAATTTAAATAATTT
Found at i:36022 original size:18 final size:18
Alignment explanation
Indices: 35999--36084 Score: 57
Period size: 23 Copynumber: 4.3 Consensus size: 18
35989 TAAATATCTA
35999 TAATATAATATTAAAAAT
1 TAATATAATATTAAAAAT
36017 TAATATTTAATTTATTTAAAAAT
1 TAATA--TAA--TA-TTAAAAAT
**
36040 TAATATTTAA-ATTAATATCT
1 TAATA--TAATATTAA-AAAT
*
36060 ATAATATAATATTAAAAAA
1 -TAATATAATATTAAAAAT
36079 TAATAT
1 TAATAT
36085 TTAATTTATT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
18 11 0.20
19 8 0.15
20 11 0.20
21 5 0.09
22 2 0.04
23 18 0.33
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATATAATATTAAAAAT
Found at i:36070 original size:62 final size:63
Alignment explanation
Indices: 35983--36133 Score: 236
Period size: 62 Copynumber: 2.4 Consensus size: 63
35973 TTATATGATA
*
35983 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAATAATATTTAATTTATTTAAAAAATTAATAT
*
36046 TTAAATTAATATCTATAATATAATATTAAAAAATAATATTTAATTTATTTAAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATAATATTTAATTTATTT-AAAAAATTAATAT
*
36110 TAAAATTAAAATC-A-AATATAATAT
1 TAAAATTAATATCTATAATATAATAT
36134 AATATAAAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
62 52 0.63
63 7 0.09
64 23 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATAATATTTAATTTATTTAAAAAATTAATAT
Found at i:36083 original size:39 final size:35
Alignment explanation
Indices: 36003--36088 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 35
35993 TATCTATAAT
* *
36003 ATAATATTAAAAATTAATATTTAATTTATTTAAAAA
1 ATAATATT-TAAATTAATATTTAATTAATTTAAAAA
*
36039 TTAATATTTAAATTAATATCTATAATATAATATTAAAAA
1 ATAATATTTAAATTAATAT-T-TAAT-TAAT-TTAAAAA
36078 ATAATATTTAA
1 ATAATATTTAA
36089 TTTATTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 10 0.24
36 8 0.19
37 4 0.10
38 3 0.07
39 17 0.40
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (35 bp):
ATAATATTTAAATTAATATTTAATTAATTTAAAAA
Found at i:36089 original size:25 final size:26
Alignment explanation
Indices: 36048--36118 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 26
36038 ATTAATATTT
36048 AAATTAATATCTATAATATAATATT-AAA
1 AAATTAATAT-TATAAT-TAAT-TTAAAA
*
36076 AAA-TAATATT-TAATTTATTTAAAA
1 AAATTAATATTATAATTAATTTAAAA
*
36100 AAATTAATATTAAAATTAA
1 AAATTAATATTATAATTAA
36119 AATCAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.05
24 9 0.24
25 11 0.30
26 6 0.16
27 6 0.16
28 3 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATTAATATTATAATTAATTTAAAA
Found at i:36143 original size:22 final size:22
Alignment explanation
Indices: 36116--36157 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
36106 ATATTAAAAT
36116 TAAAATCAAA-TATAATATAATA
1 TAAAATCAAATTA-AATATAATA
*
36138 TAAAATTAAATTAAATATAA
1 TAAAATCAAATTAAATATAA
36158 AACCTCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATCAAATTAAATATAATA
Found at i:36194 original size:20 final size:20
Alignment explanation
Indices: 36169--36209 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
36159 ACCTCTTTGA
* *
36169 AGATATTAGAAGACGTCTGC
1 AGATATAAGAACACGTCTGC
*
36189 AGATATAAGATCACGTCTGC
1 AGATATAAGAACACGTCTGC
36209 A
1 A
36210 CCGTACAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (20 bp):
AGATATAAGAACACGTCTGC
Found at i:48089 original size:18 final size:18
Alignment explanation
Indices: 48066--48102 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
48056 ATTAAACATA
48066 AAGTCAAACTAAAATAAC
1 AAGTCAAACTAAAATAAC
48084 AAGTCAAACTAAAATAAC
1 AAGTCAAACTAAAATAAC
48102 A
1 A
48103 GAACAATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AAGTCAAACTAAAATAAC
Found at i:50245 original size:21 final size:22
Alignment explanation
Indices: 50221--50262 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
50211 TGAACCCTCA
*
50221 AATTTAGAAATTAAAT-GATTG
1 AATTGAGAAATTAAATCGATTG
*
50242 AATTGAGAAATTGAATCGATT
1 AATTGAGAAATTAAATCGATT
50263 AAATATTTTG
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:0.02, G:0.17, T:0.36
Consensus pattern (22 bp):
AATTGAGAAATTAAATCGATTG
Found at i:50957 original size:31 final size:31
Alignment explanation
Indices: 50906--50972 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
50896 TAAGGGTACA
* * * **
50906 TAGTCGCTAACGTTATCGATTCGTTCGGTTT
1 TAGTCCCTAACGTTACCGATTCATTCAATTT
*
50937 TAGTCCCTAATGTTACCGATTCATTCAATTT
1 TAGTCCCTAACGTTACCGATTCATTCAATTT
50968 TAGTC
1 TAGTC
50973 TCTCAGTCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (31 bp):
TAGTCCCTAACGTTACCGATTCATTCAATTT
Found at i:53299 original size:23 final size:23
Alignment explanation
Indices: 53273--53318 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53263 CACCACAACT
*
53273 CATATAAATGCACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
* *
53296 CATAGAATTGCACCGTAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
53319 TATAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:53505 original size:103 final size:103
Alignment explanation
Indices: 53334--53548 Score: 430
Period size: 103 Copynumber: 2.1 Consensus size: 103
53324 TAATGTCCAT
53334 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
53399 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
53437 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
53502 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
53540 AAGGACCAC
1 AAGGACCAC
53549 GTAGACCCTC
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:54719 original size:31 final size:31
Alignment explanation
Indices: 54681--54836 Score: 215
Period size: 31 Copynumber: 5.0 Consensus size: 31
54671 CCCGAAGGAC
* *
54681 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
54712 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* * *
54743 CAGTTCGTATGTTCCGAAGAACATATGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
54774 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
54805 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
54836 C
1 C
54837 CCTCGACCCT
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 110 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:55330 original size:16 final size:18
Alignment explanation
Indices: 55309--55349 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
55299 GCATGTTAAC
55309 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
55325 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
55343 TCATATA
1 ACATATA
55350 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:55732 original size:21 final size:21
Alignment explanation
Indices: 55702--55746 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55692 ATTCTATCGT
* *
55702 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
55723 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
55744 TTG
1 TTG
55747 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:58698 original size:31 final size:31
Alignment explanation
Indices: 58660--58815 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
58650 CCCGAAGGAC
* *
58660 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
58691 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
58722 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
58753 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
58784 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
58815 C
1 C
58816 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:59310 original size:16 final size:18
Alignment explanation
Indices: 59289--59329 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
59279 GCATGTTAAC
59289 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
59305 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
59323 TCATATA
1 ACATATA
59330 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:59711 original size:21 final size:21
Alignment explanation
Indices: 59681--59725 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59671 ATTCTATCGT
* *
59681 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
59702 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
59723 TTG
1 TTG
59726 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:62681 original size:31 final size:31
Alignment explanation
Indices: 62643--62798 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
62633 CCCGAAGGAC
* *
62643 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
62674 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
62705 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
62736 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
62767 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
62798 C
1 C
62799 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:63296 original size:16 final size:18
Alignment explanation
Indices: 63275--63315 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
63265 GCATGTTAAC
63275 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
63291 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
63309 TCATATA
1 ACATATA
63316 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:63698 original size:21 final size:21
Alignment explanation
Indices: 63668--63712 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
63658 ATTCTATCGT
* *
63668 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
63689 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
63710 TTG
1 TTG
63713 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:66670 original size:31 final size:31
Alignment explanation
Indices: 66632--66786 Score: 231
Period size: 31 Copynumber: 5.0 Consensus size: 31
66622 CCCGAAGGAC
* *
66632 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
66663 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
66694 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
66725 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
66756 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
66787 ACCTCGACCC
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:67280 original size:14 final size:15
Alignment explanation
Indices: 67261--67289 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
67251 AGCATGTTAA
67261 CACATATAA-TCATG
1 CACATATAATTCATG
67275 CACATATAATTCATG
1 CACATATAATTCATG
67290 TCATTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (15 bp):
CACATATAATTCATG
Found at i:67683 original size:21 final size:21
Alignment explanation
Indices: 67653--67697 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
67643 ATTCTATCGT
* *
67653 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
67674 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
67695 TTG
1 TTG
67698 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:68945 original size:2 final size:2
Alignment explanation
Indices: 68938--68973 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
68928 GTAATATTTC
68938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68974 CAAAGATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75020 original size:84 final size:84
Alignment explanation
Indices: 74896--75086 Score: 256
Period size: 84 Copynumber: 2.3 Consensus size: 84
74886 CTGGGACGGA
* ** * * * * *
74896 GATGATTCAGACAAAAAACCAAATACCAAGGATTCTCCCGACAGCAAAGGAATCAATGATCCTGA
1 GATGATTCATACGCAAAACCCAACACTAAGGATTCACCCGACAACAAAGGAATCAATGATCCTGA
** *
74961 ATTTGGTGCTTATGGGTAC
66 ATTTGGTAATTATGCGTAC
* * *
74980 GATGATTCATACGCAAAATCCAACACTAAGGATTCACCCGACAATAAAGGAATCCATGATCCTGA
1 GATGATTCATACGCAAAACCCAACACTAAGGATTCACCCGACAACAAAGGAATCAATGATCCTGA
75045 ATTTGGTAATTATGCGTAC
66 ATTTGGTAATTATGCGTAC
75064 GATGATTCATACGCAAAACCCAA
1 GATGATTCATACGCAAAACCCAA
75087 AACTGAAGAT
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (84 bp):
GATGATTCATACGCAAAACCCAACACTAAGGATTCACCCGACAACAAAGGAATCAATGATCCTGA
ATTTGGTAATTATGCGTAC
Found at i:88219 original size:35 final size:35
Alignment explanation
Indices: 88173--88243 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
88163 TACGTGTTGT
88173 AGTCTCACTAATGGCCAGAGATGAAAAAACTCATG
1 AGTCTCACTAATGGCCAGAGATGAAAAAACTCATG
**
88208 AGTCTCACTAATGGCCAGAGATGAAAGTACTCATG
1 AGTCTCACTAATGGCCAGAGATGAAAAAACTCATG
88243 A
1 A
88244 AGCATCCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (35 bp):
AGTCTCACTAATGGCCAGAGATGAAAAAACTCATG
Found at i:88483 original size:21 final size:21
Alignment explanation
Indices: 88457--88504 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
88447 GTTTCCAGAT
88457 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
88478 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
88499 TCGCAA
1 TCGCAA
88505 TACGATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:88547 original size:21 final size:21
Alignment explanation
Indices: 88521--88702 Score: 187
Period size: 21 Copynumber: 8.8 Consensus size: 21
88511 TTTCCAAATT
*
88521 CGTTGCGATAGTCCAAGTCCG
1 CGTTGCGATAGTCCAAGTTCG
88542 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
88561 CGTTGTGATAGTCAAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * * *
88582 CGTTGAGATTTATTCTAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
88603 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
88624 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
88645 CGTTGTGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
88666 TGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
88687 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
88703 AATCGCAACG
Statistics
Matches: 134, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
19 32 0.24
21 84 0.63
23 18 0.13
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:88613 original size:42 final size:40
Alignment explanation
Indices: 88513--88702 Score: 218
Period size: 42 Copynumber: 4.6 Consensus size: 40
88503 AATACGATTT
* *
88513 TCCAAATTCGTTGCGATAGTCCAAGTCCGCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
* * * *
88553 TCCAAGTTCGTTGTGATAGTCAAAGTTCGCGTTGAGATTTAT
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAG
* *
88595 TCTAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
* * * *
88635 TCGAAGTTCGCGTTGTGATAGTCCAAGTTCGTGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAG
88679 TCCAAGTTCGTTGCGATAGTCCAA
1 TCCAAGTTCGTTGCGATAGTCCAA
88703 AATCGCAACG
Statistics
Matches: 125, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
40 40 0.32
42 76 0.61
44 9 0.07
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (40 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
Found at i:88700 original size:84 final size:82
Alignment explanation
Indices: 88512--88702 Score: 301
Period size: 84 Copynumber: 2.3 Consensus size: 82
88502 CAATACGATT
88512 TTCCAAATTCGTTGCGATAGTCCAAGTCCGCGTTGCGATAGTCCAAGTTCGTTGTGATAGTCAAA
1 TTCCAAATTCGTTGCGATAGTCCAAGTCCGCGTTGCGATAGTCCAAGTTCGTTGTGATAGTCAAA
88577 GTTCGCGTTGAGATTTA
66 GTTCGCGTTGAGATTTA
* * * *
88594 TTCTAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGTGATAGTCC
1 TTCCAAATTCGTTGCGATAGTCCAAGTCCGCGTTGCGATAGTCCAAGTT--CGTTGTGATAGTCA
* *
88659 AAGTTCGTGTTGCGATTTA
64 AAGTTCGCGTTGAGATTTA
*
88678 TTCCAAGTTCGTTGCGATAGTCCAA
1 TTCCAAATTCGTTGCGATAGTCCAA
88703 AATCGCAACG
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 46 0.46
84 53 0.54
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (82 bp):
TTCCAAATTCGTTGCGATAGTCCAAGTCCGCGTTGCGATAGTCCAAGTTCGTTGTGATAGTCAAA
GTTCGCGTTGAGATTTA
Found at i:88803 original size:6 final size:6
Alignment explanation
Indices: 88792--88816 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
88782 GACACGTATT
88792 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
88817 GACGAGACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:89521 original size:20 final size:21
Alignment explanation
Indices: 89472--89523 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
89462 TGCAATTTTG
*
89472 GACTATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTCC
*
89493 GACTATCGCAACGCGATCTCC
1 GACTATCGCAACGCGAACTCC
*
89514 G-GTATCGCAA
1 GACTATCGCAA
89524 ATCGGTTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.27, C:0.33, G:0.21, T:0.19
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTCC
Found at i:90814 original size:19 final size:20
Alignment explanation
Indices: 90790--90829 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
90780 AAATCTATTA
*
90790 TCATAT-TATTATGCATTTT
1 TCATATATACTATGCATTTT
90809 TCATATATACTATGCATTTT
1 TCATATATACTATGCATTTT
90829 T
1 T
90830 TTTCTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (20 bp):
TCATATATACTATGCATTTT
Found at i:91646 original size:198 final size:198
Alignment explanation
Indices: 91239--92540 Score: 1795
Period size: 198 Copynumber: 6.6 Consensus size: 198
91229 GATAAATTTA
* *
91239 CGGTAAATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATGTT
1 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
91304 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCATGCACCTCGTTGGACATTCATT
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACC-CATTGGACATTCATT
*
91369 CTGGACAAAAAGTATCGACACAAGTTACCCAAGTGTCGGTACATTATGTAGACATGTTTTCTCAT
130 CTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCAT
91434 AAAC
195 AAAC
* **
91438 CGGTAAATTTCTACTTGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
1 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
* * **
91503 TTTGGGATCGATACTTTTTAGAAATGTATCGACACTTTATCCGTGCACCCAAAGGACATTCATTC
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCATTGGACATTCATTC
*
91568 TGGACAAAAAGTATCGACACAAGTTACATAAGTGTCGGTACATTATGTAGACATGTTTTCTCATA
131 TGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCATA
91633 AAC
196 AAC
* * * *
91636 CGGTAAATTTCTACCGGTTACATTGTAAATTTACTTATTACATTATCATTATGGGTTTCGATATT
1 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
** *
91701 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCAAAGGGA-TTTCATT
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCC-ATTGGACATTCATT
**
91765 CTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGATTTGTTTTCTCAT
130 CTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCAT
91830 AAAC
195 AAAC
* * *
91834 CGGTAAATTTCTACCGGTTACATTGTAAATTTACCTACTACATTATAATTATGGGTTTCGACGTT
1 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
91899 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTCTGGGCATTCATT
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCAT-TGGACATTCATT
* * *
91964 CTAGACAAAAAGTATCGACACAAGTTACACAAGTGTCGATACATTATGTAGATC-TATTTTCTCA
130 CTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGA-CATGTTTTCTCA
92028 TAAAC
194 TAAAC
* * * * * *
92033 TGGTAAATTTATACCGGTTACATTGAAAAATTATCTATTACATTATAATTATGAGTTTTGATGTT
1 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
* * * ** *
92098 TTTGGGATCGATA-TCTTTTATAAATGTATCGACACTTTTTTCCTGCA-CTTTTGGGCATTCATT
66 TTTGGGATCGATACT-TTTTATAAATGTATCGACACTTTATGCGTGCACCCATTGGACATTCATT
* * * * * * *
92161 CTGGACAAAAAGTATCGACACAAATTTA-AAAATTGTTGATACATTATGTAGACCTATTTTCTCA
130 CTGGACAAAAAGTATCGACAC-AAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCA
92225 TAAAAC
194 T-AAAC
* * * * * * *
92231 CGGTATATTTATATCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAGTTTTGATATT
1 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
* * * * ** *
92296 TTTGGGATCGATATTTTTTATAAATGTATCGACACTTTTTTCCTGCAGTCATTTTGGGCATTCAT
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCA--TTGGACATTCAT
* * * *
92361 TATGGACAAAAAGTATTGACACAAGTTACACAAGTGTAGGTACATTATGTAGACTTGTTTTCTCA
129 TCTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCA
92426 TAAAC
194 TAAAC
* * ** * * * * *
92431 CGATAAAATTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATAGTTTTCGGTATT
1 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
*
92496 TTTGGGATCGATATTTTTTATAAATGTATCGACACTTTATGCGTG
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTG
92541 TCTATTCTCT
Statistics
Matches: 1003, Mismatches: 87, Indels: 25
0.90 0.08 0.02
Matches are distributed among these distances:
196 1 0.00
197 64 0.06
198 489 0.49
199 280 0.28
200 106 0.11
201 63 0.06
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (198 bp):
CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCATTGGACATTCATTC
TGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCATA
AAC
Found at i:92000 original size:397 final size:394
Alignment explanation
Indices: 91239--92540 Score: 1813
Period size: 397 Copynumber: 3.3 Consensus size: 394
91229 GATAAATTTA
* * * *
91239 CGGTAAATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATGTT
1 CGGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAGTTTCGATATT
* * *
91304 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCATGCACCTCGTTGGACATTCATT
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACC-C-ATGG-GATTCATT
*
91369 CTGGACAAAAAGTATCGACACAAGTTACCCAAGTGTCGGTACATTATGTAGACATGTTTTCTCAT
128 CTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCAT
**
91434 AAACCGGTAAATTTCTACTTGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGA
193 AAACCGGTAAATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * *
91499 TGTTTTTGGGATCGATACTTTTTAGAAATGTATCGACACTTTATCCGTGCACCC-AAAGGACATT
258 TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATCCGTGCACCCTTATGGGCATT
*
91563 CATTCTGGACAAAAAGTATCGACACAAGTTACATAAGTGTCGGTACATTATGTAGACATGTTTTC
323 CATTCTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGAC-TGTTTTC
91628 TCATAAAC
387 TCATAAAC
* * * * * *
91636 CGGTAAATTTCTACCGGTTACATTGTAAATTTACTTATTACATTATCATTATGGGTTTCGATATT
1 CGGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAGTTTCGATATT
*
91701 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCAAAGGGATTTCATTC
66 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCC-ATGGGA-TTCATTC
**
91766 TGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGATTTGTTTTCTCATA
129 TGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCATA
* *
91831 AACCGGTAAATTTCTACCGGTTACATTGTAAATTTACCTACTACATTATAATTATGGGTTTCGAC
194 AACCGGTAAATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGAT
* *
91896 GTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTCTGGGCATTC
259 GTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATCCGTGCACCCTTATGGGCATTC
* * *
91961 ATTCTAGACAAAAAGTATCGACACAAGTTACACAAGTGTCGATACATTATGTAGATCTATTTTCT
324 ATTCTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGA-CTGTTTTCT
92026 CATAAAC
388 CATAAAC
* * * *
92033 TGGTAAATTTATACCGGTTACATTGAAAAATTATCTATTACATTATAATTATGAGTTTTGATGTT
1 CGGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAGTTTCGATATT
* * * ***
92098 TTTGGGATCGATA-TCTTTTATAAATGTATCGACACTTTTTTCCTGCACTTTTGGGCATTCATTC
66 TTTGGGATCGATACT-TTTTATAAATGTATCGACACTTTATGCGTGCACCCATGGG-ATTCATTC
* * * * * * *
92162 TGGACAAAAAGTATCGACACAAATTTA-AAAATTGTTGATACATTATGTAGACCTATTTTCTCAT
129 TGGACAAAAAGTATCGACAC-AAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCAT
* * * * * * *
92226 AAAACCGGTATATTTATATCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAGTTTTG
193 -AAACCGGTAAATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCG
* * * * * *
92291 ATATTTTTGGGATCGATATTTTTTATAAATGTATCGACACTTTTTTCC-TGCAGTCATTTTGGGC
257 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACAC-TTTATCCGTGCA-CCCTTATGGGC
* * *
92355 ATTCATTATGGACAAAAAGTATTGACACAAGTTACACAAGTGTAGGTACATTATGTAGACTTGTT
320 ATTCATTCTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGAC-TGTT
92420 TTCTCATAAAC
384 TTCTCATAAAC
* * * *
92431 CGATAAAATTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTAT-AGTTTTCGGTAT
1 CGGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAG-TTTCGATAT
*
92495 TTTTGGGATCGATATTTTTTATAAATGTATCGACACTTTATGCGTG
65 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTG
92541 TCTATTCTCT
Statistics
Matches: 807, Mismatches: 86, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
395 1 0.00
396 245 0.30
397 384 0.48
398 176 0.22
399 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (394 bp):
CGGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGAGTTTCGATATT
TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCATGGGATTCATTCTG
GACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACATGTTTTCTCATAAA
CCGGTAAATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGT
TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATCCGTGCACCCTTATGGGCATTCAT
TCTGGACAAAAAGTATCGACACAAGTTACACAAGTGTCGGTACATTATGTAGACTGTTTTCTCAT
AAAC
Found at i:92920 original size:19 final size:19
Alignment explanation
Indices: 92896--92944 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
92886 TTACATTCAC
92896 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
92915 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
*
92934 ATAAAAAATTA
1 ATACAAAATTA
92945 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:93183 original size:22 final size:21
Alignment explanation
Indices: 93152--93205 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
93142 CGGCTCAACC
*
93152 TAAATTTTTTTGATTTTTTTAT
1 TAAA-TTTTTTGATATTTTTAT
*
93174 TAAATGTTTTTGGTATTTTTAT
1 TAAAT-TTTTTGATATTTTTAT
*
93196 TTAATTTTTT
1 TAAATTTTTT
93206 AAATAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
TAAATTTTTTGATATTTTTAT
Found at i:95644 original size:31 final size:31
Alignment explanation
Indices: 95555--95681 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
95545 AGAGTCGAGG
95555 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
95586 GAATTACCTATG-TCTTTC-GAGATATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
95618 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
95649 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
95680 GT
1 GT
95682 TGCCAAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:95723 original size:30 final size:30
Alignment explanation
Indices: 95669--95740 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
95659 GTTCTTCGGA
* * *
95669 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
95699 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
95729 ACCTCTGGATAG
1 ACCTCTGGATAG
95741 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:97244 original size:182 final size:183
Alignment explanation
Indices: 96661--97378 Score: 844
Period size: 182 Copynumber: 3.9 Consensus size: 183
96651 CTATGATTAC
* *
96661 TTGTCTTTTAAATTCTAAAAGTGTTGATACTTATAATAAAGTATCGACACGTTT-AACATATCCG
1 TTGTCTTTTAAATTCTAAAAGTGTCGACACTTATAATAAAGTATCGACACGTTTCAACATATCCG
* * * * *
96725 GTGGCGCTGTACCAGTTTTGTCATTTTGAGATCGATTTTACCATATTTTTACCTGTTATATTGTT
66 GTGGCGCTTTACCGGTTTTGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTT
*
96790 AAGTGTCGATACA-TTTTTTTAGAGTATCGACACTTTATAGGCGTTATTACTGT
131 AAGTGTCGATACATTTTTTTTA-AGTATCGACACTTTATAGGCGTTATAACTGT
*
96843 TTGTCTTTTAAATTCTAAAAGTGTCGATACTTGTCAATACTTATAATAAAGTATCGACAC-TTTT
1 TTGTCTTTTAAATTCTAAAAGTGTCG--A-----C---ACTTATAATAAAGTATCGACACGTTTC
* * * * * *
96907 AACATATCTGGTGGCACTTTATCGGTTTTGTCATTTTCAGACTGGTTTTATCACATTTTTTACCT
56 AACATATCCGGTGGCGCTTTACCGGTTTTGTCATTTTGAGACCGGTTTTATCATA-TTTTTACCT
* * * * * *
96972 TTTATATTGTTAAGTGTCGATACATTTTTTTAAAGTATCGACACCTTATAGGCTTTATGACTGC
120 GTTATATTGTTAAGTGTCGATACATTTTTTTTAAGTATCGACACTTTATAGGCGTTATAACTGT
*
97036 TTGTCTTTTAAATT-TCAAAAGTGTCGACACTTATAATAAAGTATCGACAC-TTTCAACATATCT
1 TTGTCTTTTAAATTCT-AAAAGTGTCGACACTTATAATAAAGTATCGACACGTTTCAACATATCC
* * * *
97099 GGTGGCTCTTTATCGGTTTTGTCATTTTGAGACCGGTTGTATCATATTTTTACCTATTATATTGT
65 GGTGGCGCTTTACCGGTTTTGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGT
** * *
97164 TAAGTGTCGATACATTTTTTTTAAGTATTAACACTTTATAGGCGCTATAATTGT
130 TAAGTGTCGATACATTTTTTTTAAGTATCGACACTTTATAGGCGTTATAACTGT
* * * * *
97218 TTTTCTTTTAAATTGC-AAAAGTGTCGATACTTTTAATAAAGTATCGACACTTTTGC-A-ATTTC
1 TTGTCTTTTAAATT-CTAAAAGTGTCGACACTTATAATAAAGTATCGACACGTTT-CAACATATC
* * *
97280 CGGTAGCGCTTTACCGGTTTGGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTAAATTG
64 CGGTGGCGCTTTACCGGTTTTGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTG
* * *
97345 ATATG-GATCGATACATTTTTTATT-TGTATCGACA
129 TTAAGTG-TCGATACATTTTTT-TTAAGTATCGACA
97379 TAAACCGACA
Statistics
Matches: 464, Mismatches: 52, Indels: 40
0.83 0.09 0.07
Matches are distributed among these distances:
181 1 0.00
182 218 0.47
183 81 0.17
184 2 0.00
186 1 0.00
191 4 0.01
192 67 0.14
193 83 0.18
194 7 0.02
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (183 bp):
TTGTCTTTTAAATTCTAAAAGTGTCGACACTTATAATAAAGTATCGACACGTTTCAACATATCCG
GTGGCGCTTTACCGGTTTTGTCATTTTGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTT
AAGTGTCGATACATTTTTTTTAAGTATCGACACTTTATAGGCGTTATAACTGT
Found at i:99920 original size:16 final size:16
Alignment explanation
Indices: 99888--99931 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
99878 AAAATAATCG
99888 AAAACCGAT--CC-AA
1 AAAACCGATAACCGAA
99901 AAAACCGATAACCGAA
1 AAAACCGATAACCGAA
99917 AAAACCCGA-AACCGA
1 AAAA-CCGATAACCGA
99932 TTTAGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
15 2 0.07
16 12 0.44
17 4 0.15
ACGTcount: A:0.55, C:0.30, G:0.11, T:0.05
Consensus pattern (16 bp):
AAAACCGATAACCGAA
Found at i:105677 original size:2 final size:2
Alignment explanation
Indices: 105670--105706 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
105660 TTAGATTTTC
105670 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
105707 GATTTTTAAA
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:112718 original size:39 final size:40
Alignment explanation
Indices: 112652--112730 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
112642 AGTAGGAGCT
112652 TTACCAAAATGCATATGCTAAAGTAGGATAAATGTTAAATA
1 TTACCAAAATGCA-ATGCTAAAGTAGGATAAATGTTAAATA
* *
112693 TTACCAATATGC-ATGCTAATGTAGGATAAATGTTAAAT
1 TTACCAAAATGCAATGCTAAAGTAGGATAAATGTTAAAT
112731 TTGTAAGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 25 0.69
41 11 0.31
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (40 bp):
TTACCAAAATGCAATGCTAAAGTAGGATAAATGTTAAATA
Found at i:115960 original size:31 final size:31
Alignment explanation
Indices: 115902--115961 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
115892 AAATAATTTA
*
115902 AAATTCATATTATATATTAAATAAATATTGT
1 AAATTCATATTATATAATAAATAAATATTGT
* * * *
115933 AAATTTATATTTTATAATAATTTAATATT
1 AAATTCATATTATATAATAAATAAATATT
115962 ATTTTTATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (31 bp):
AAATTCATATTATATAATAAATAAATATTGT
Found at i:115975 original size:21 final size:23
Alignment explanation
Indices: 115932--115980 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
115922 ATAAATATTG
*
115932 TAAAT-TTATATTTTATAATAAT
1 TAAATATTATATTTTATAACAAT
*
115954 TTAATATTAT-TTTTAT-ACAAT
1 TAAATATTATATTTTATAACAAT
115975 TAAATA
1 TAAATA
115981 AATAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.39
22 10 0.43
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATATTATATTTTATAACAAT
Found at i:118272 original size:103 final size:103
Alignment explanation
Indices: 118047--118264 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
118037 GTCGAGGGTT
* *
118047 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
118112 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
118150 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
118215 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
118253 TATGTGGTCCTT
1 TATGTGGTCCTT
118265 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:118330 original size:23 final size:23
Alignment explanation
Indices: 118271--118347 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
118261 CCTTATGGAC
118271 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATATGGCACTACGGTGCA
* *** *
118295 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATATGGCACTACGGTGCA
* *
118318 ATTATATATGGCACTTCGATGCA
1 ATTATATATGGCACTACGGTGCA
118341 ATTATAT
1 ATTATAT
118348 GAGCTGTGGT
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 0.93
24 3 0.07
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (23 bp):
ATTATATATGGCACTACGGTGCA
Done.