Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006006.1 Hibiscus syriacus cultivar Beakdansim tig00014159_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: 110440
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7520 original size:17 final size:17
Alignment explanation
Indices: 7498--7542 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
7488 TATGCTACAT
7498 GTGTCATAGATA-TAAAA
1 GTGTCAT-GATATTAAAA
7515 GTGTCATGATATTAAAA
1 GTGTCATGATATTAAAA
7532 -TGT-A-GATATTA
1 GTGTCATGATATTA
7543 TAAGAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.26
15 1 0.04
16 7 0.26
17 12 0.44
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (17 bp):
GTGTCATGATATTAAAA
Found at i:8692 original size:12 final size:12
Alignment explanation
Indices: 8671--8747 Score: 75
Period size: 12 Copynumber: 6.4 Consensus size: 12
8661 GTTTGATTCA
*
8671 TTTATGAGCTTG
1 TTTATAAGCTTG
**
8683 TTTATAAGCTAA
1 TTTATAAGCTTG
*
8695 TTTATGAGCTTG
1 TTTATAAGCTTG
**
8707 TTTATAAGCTCA
1 TTTATAAGCTTG
*
8719 TTTATGAGCTTG
1 TTTATAAGCTTG
8731 TTTATAAG-TTCG
1 TTTATAAGCTT-G
8743 TTTAT
1 TTTAT
8748 CGACTCGTTC
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
11 2 0.04
12 49 0.96
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.49
Consensus pattern (12 bp):
TTTATAAGCTTG
Found at i:8746 original size:24 final size:24
Alignment explanation
Indices: 8668--8747 Score: 133
Period size: 24 Copynumber: 3.3 Consensus size: 24
8658 TGTGTTTGAT
8668 TCATTTATGAGCTTGTTTATAAGC
1 TCATTTATGAGCTTGTTTATAAGC
*
8692 TAATTTATGAGCTTGTTTATAAGC
1 TCATTTATGAGCTTGTTTATAAGC
*
8716 TCATTTATGAGCTTGTTTATAAGT
1 TCATTTATGAGCTTGTTTATAAGC
*
8740 TCGTTTAT
1 TCATTTAT
8748 CGACTCGTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (24 bp):
TCATTTATGAGCTTGTTTATAAGC
Found at i:9686 original size:35 final size:35
Alignment explanation
Indices: 9645--9760 Score: 162
Period size: 35 Copynumber: 3.3 Consensus size: 35
9635 TGGTAAGGGA
* *
9645 ATGGTGATGATATAGGCATGAAATGGTGAAAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
9680 ATGGTGATGATATAGGCGT-AAGATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAA-ATGGTGATAGAAG
* * *
9715 ATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAA
1 ATGGTGATGATATAGGCGTG-AAATGGTGATAGAAG
9751 ATGGTGATGA
1 ATGGTGATGA
9761 ACATATAGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
34 2 0.03
35 48 0.67
36 20 0.28
37 2 0.03
ACGTcount: A:0.35, C:0.03, G:0.36, T:0.26
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
Found at i:9752 original size:13 final size:13
Alignment explanation
Indices: 9734--9759 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9724 TTATAGGCGT
9734 GAAAATGGTGATG
1 GAAAATGGTGATG
9747 GAAAATGGTGATG
1 GAAAATGGTGATG
9760 AACATATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GAAAATGGTGATG
Found at i:10142 original size:19 final size:20
Alignment explanation
Indices: 10104--10146 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
10094 GAAACCCCTT
*
10104 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
10124 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
10143 TGAA
1 TGAA
10147 GATAGATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:13587 original size:16 final size:16
Alignment explanation
Indices: 13566--13611 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
13556 TGTAGGAGTC
13566 TTTTCTTCTTTTTGTT
1 TTTTCTTCTTTTTGTT
*
13582 TTTTCTTCTTCTTTCTT
1 TTTTCTTCTT-TTTGTT
13599 TTTTCTT-TTTTTG
1 TTTTCTTCTTTTTG
13612 CAGCAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 3 0.11
16 12 0.44
17 12 0.44
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTCTTCTTTTTGTT
Found at i:14017 original size:13 final size:13
Alignment explanation
Indices: 13999--14056 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
13989 TAGGCGTGCA
13999 ATGGTGATGGAAG
1 ATGGTGATGGAAG
*
14012 ATGGTGAT-G-AT
1 ATGGTGATGGAAG
* *
14023 ATAGGCG-T-GAAA
1 AT-GGTGATGGAAG
14035 ATGGTGATGGAAG
1 ATGGTGATGGAAG
14048 ATGGTGATG
1 ATGGTGATG
14057 AACAGATAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 8 0.22
12 8 0.22
13 20 0.56
ACGTcount: A:0.31, C:0.02, G:0.41, T:0.26
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:14017 original size:35 final size:36
Alignment explanation
Indices: 13977--14057 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
13967 TGGTAAGGGA
*
13977 ATGGTGATGATATAGGCGTG-CAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAAATGGTGATGGAAG
14012 ATGGTGATGATATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAAATGGTGATGGAAG
14048 ATGGTGATGA
1 ATGGTGATGA
14058 ACAGATAGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 20 0.45
36 24 0.55
ACGTcount: A:0.31, C:0.04, G:0.40, T:0.26
Consensus pattern (36 bp):
ATGGTGATGATATAGGCGTGAAAATGGTGATGGAAG
Found at i:14439 original size:19 final size:20
Alignment explanation
Indices: 14401--14443 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
14391 GAAACCCCTT
*
14401 TGAAAAGACATGATTTTTAA
1 TGAAAAGACATGAATTTTAA
*
14421 TGAAAATACAT-AATTTTAA
1 TGAAAAGACATGAATTTTAA
14440 TGAA
1 TGAA
14444 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAAGACATGAATTTTAA
Found at i:17136 original size:33 final size:35
Alignment explanation
Indices: 17094--17158 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
17084 TCTTCTTCAG
*
17094 GTTGCATGT-GGGGG-CTGGACGTGAGCAGAGAAA
1 GTTGCATGTGGGGGGCCTGGACATGAGCAGAGAAA
17127 GTTGCATGTGGGGGGCCTGGACATGAGCAGAG
1 GTTGCATGTGGGGGGCCTGGACATGAGCAGAG
17159 GAAGAAACGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 9 0.31
34 5 0.17
35 15 0.52
ACGTcount: A:0.22, C:0.14, G:0.46, T:0.18
Consensus pattern (35 bp):
GTTGCATGTGGGGGGCCTGGACATGAGCAGAGAAA
Found at i:17222 original size:29 final size:29
Alignment explanation
Indices: 17183--17241 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
17173 GCATGCTGAT
17183 GGGATTTCTCGGCATCTTCTTCAGCATGGG
1 GGGATTTCTCGGCATCTTCTTCA-CATGGG
* *
17213 GGGA-TTCTCGGCGTCTTCTTTACATGGG
1 GGGATTTCTCGGCATCTTCTTCACATGGG
17241 G
1 G
17242 ACCGAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 16 0.59
30 4 0.15
ACGTcount: A:0.12, C:0.22, G:0.32, T:0.34
Consensus pattern (29 bp):
GGGATTTCTCGGCATCTTCTTCACATGGG
Found at i:18415 original size:13 final size:13
Alignment explanation
Indices: 18394--18426 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
18384 ATTCCATGTT
*
18394 ATTAGTAGTAATC
1 ATTATTAGTAATC
18407 ATTATTAGTAATC
1 ATTATTAGTAATC
18420 ATTATTA
1 ATTATTA
18427 TCAAATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (13 bp):
ATTATTAGTAATC
Found at i:18452 original size:14 final size:14
Alignment explanation
Indices: 18403--18472 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 14
18393 TATTAGTAGT
*
18403 AATCATTATTAGT-
1 AATCATTATTATTA
*
18416 AATCATTATTATCA
1 AATCATTATTATTA
*
18430 AAT-A--CTTATTA
1 AATCATTATTATTA
*
18441 AATCATTATTATCA
1 AATCATTATTATTA
* *
18455 AATCATTAGTAGTA
1 AATCATTATTATTA
18469 AATC
1 AATC
18473 TATAAATCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
11 8 0.18
12 1 0.02
13 12 0.27
14 23 0.52
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (14 bp):
AATCATTATTATTA
Found at i:18479 original size:22 final size:22
Alignment explanation
Indices: 18454--18497 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18444 CATTATTATC
*
18454 AAATCATTAGTAGTAAATCTAT
1 AAATCATTAGTAATAAATCTAT
*
18476 AAATCATTATTAATAAATCTAT
1 AAATCATTAGTAATAAATCTAT
18498 CATTACACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATCATTAGTAATAAATCTAT
Found at i:18622 original size:2 final size:2
Alignment explanation
Indices: 18615--18650 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18605 AAGTAATAAA
18615 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
18651 TCGAATAATT
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:23863 original size:28 final size:30
Alignment explanation
Indices: 23832--23911 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
23822 ATCATAGATT
23832 AAATGAATCTTTATATAAAAA-TTA-AATC
1 AAATGAATCTTTATATAAAAATTTAGAATC
* *
23860 AAATGAGATC-TTATTTAAAAATTTATGTATC
1 AAATGA-ATCTTTATATAAAAATTTA-GAATC
*
23891 AAATGAGTCTTTATATAAAAA
1 AAATGAATCTTTATATAAAAA
23912 AATCACGATC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
28 16 0.37
29 6 0.14
30 2 0.05
31 19 0.44
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (30 bp):
AAATGAATCTTTATATAAAAATTTAGAATC
Found at i:27632 original size:79 final size:79
Alignment explanation
Indices: 27537--27695 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
27527 ACTCTAAAAG
27537 CTACTCCGGCCACACTCAAACAACAATAAAATAAAATAAACTCCAACCAAACTTTCATTTTCTGC
1 CTACTCCGGCCACACTCAAACAACAATAAAATAAAATAAACTCCAACCAAACTTTCATTTTCTGC
27602 CAAAAAAGGAAACT
66 CAAAAAAGGAAACT
*
27616 CTACTCCGGCCACACTCAAACAACAATGAAATAAAATAAACTCCAACCAAACTTTCATTTTCTGC
1 CTACTCCGGCCACACTCAAACAACAATAAAATAAAATAAACTCCAACCAAACTTTCATTTTCTGC
27681 CAAAAAAGGAAACT
66 CAAAAAAGGAAACT
27695 C
1 C
27696 ATAAGTTGTT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.20
Consensus pattern (79 bp):
CTACTCCGGCCACACTCAAACAACAATAAAATAAAATAAACTCCAACCAAACTTTCATTTTCTGC
CAAAAAAGGAAACT
Found at i:32272 original size:24 final size:24
Alignment explanation
Indices: 32240--32288 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
32230 AGTCTTCCTG
32240 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
32264 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
32288 A
1 A
32289 ATGTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:32485 original size:12 final size:13
Alignment explanation
Indices: 32462--32490 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
32452 GTACTAACAT
32462 AAATACATTTCCA
1 AAATACATTTCCA
32475 AAATA-ATTTCCA
1 AAATACATTTCCA
32487 AAAT
1 AAAT
32491 CAGACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATACATTTCCA
Found at i:35767 original size:3 final size:3
Alignment explanation
Indices: 35759--35795 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
35749 TGTTCTATTC
35759 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35796 CAACTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35782 original size:14 final size:14
Alignment explanation
Indices: 35763--35791 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35753 CTATTCAATA
35763 ATAATAATAATAAT
1 ATAATAATAATAAT
35777 ATAATAATAATAAT
1 ATAATAATAATAAT
35791 A
1 A
35792 ATAACAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:35782 original size:17 final size:17
Alignment explanation
Indices: 35760--35794 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
35750 GTTCTATTCA
35760 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
35777 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
35794 A
1 A
35795 ACAACTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:35916 original size:25 final size:26
Alignment explanation
Indices: 35836--35926 Score: 157
Period size: 26 Copynumber: 3.5 Consensus size: 26
35826 AAATTTACGT
*
35836 TTGTCTAACAATATTTTTTGATTAAA
1 TTGTCTAACAATATCTTTTGATTAAA
35862 TTGTCTAACAATATCTTTTGATTAAA
1 TTGTCTAACAATATCTTTTGATTAAA
35888 TTGTCTAACAATATCTTTT-ATTAAA
1 TTGTCTAACAATATCTTTTGATTAAA
*
35913 TTGTCTAATAATAT
1 TTGTCTAACAATAT
35927 TTATATGGGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
25 19 0.30
26 44 0.70
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (26 bp):
TTGTCTAACAATATCTTTTGATTAAA
Found at i:37359 original size:26 final size:26
Alignment explanation
Indices: 37328--37460 Score: 108
Period size: 26 Copynumber: 5.0 Consensus size: 26
37318 TTTTCTTTAA
*
37328 CATTAATCGAACCGAAATTATTTGAT
1 CATTAATCGAACCGAAATTATTTGAC
* *
37354 CGTTAATCGAACCGAAATTTATTTGAA
1 CATTAATCGAACCGAAA-TTATTTGAC
* * * * *
37381 AATT-AT-TAACCGAATTTTTTTCTTTAAC
1 CATTAATCGAACCGAA----ATTATTTGAC
*
37409 CATTAATTGAACCGAAATTATTTGAC
1 CATTAATCGAACCGAAATTATTTGAC
*
37435 CGTTAATCGAACCGAAATTTATTTGA
1 CATTAATCGAACCGAAA-TTATTTGA
37461 AAATTATTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
25 7 0.08
26 40 0.48
27 18 0.22
28 9 0.11
29 2 0.02
30 7 0.08
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (26 bp):
CATTAATCGAACCGAAATTATTTGAC
Found at i:37399 original size:81 final size:82
Alignment explanation
Indices: 37304--37477 Score: 316
Period size: 81 Copynumber: 2.1 Consensus size: 82
37294 ACCGAACCAA
*
37304 ATTAACCGAATTTTTTTTCTTTAA-CATTAATCGAACCGAAATTATTTGATCGTTAATCGAACCG
1 ATTAACCGAATTTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCG
37368 AAATTTATTTGAAAATT
66 AAATTTATTTGAAAATT
*
37385 ATTAACCGAA-TTTTTTTCTTTAACCATTAATTGAACCGAAATTATTTGACCGTTAATCGAACCG
1 ATTAACCGAATTTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCG
37449 AAATTTATTTGAAAATT
66 AAATTTATTTGAAAATT
37466 ATTAACCGAATT
1 ATTAACCGAATT
37478 AACCGAATAA
Statistics
Matches: 89, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
80 13 0.15
81 75 0.84
82 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (82 bp):
ATTAACCGAATTTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCG
AAATTTATTTGAAAATT
Found at i:38214 original size:2 final size:2
Alignment explanation
Indices: 38209--38239 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38199 ATACTCAATA
38209 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 A
38240 AATGGACGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38364 original size:10 final size:10
Alignment explanation
Indices: 38337--38390 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 10
38327 CCTATTTAAT
*
38337 TAATAATA-G
1 TAATAATATA
38346 TAA-AATATA
1 TAATAATATA
38355 TAATAATATA
1 TAATAATATA
38365 T-ATAAT-TA
1 TAATAATATA
38373 TAACTAATAT-
1 TAA-TAATATA
38383 TAATAATA
1 TAATAATA
38391 ACTAATAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 7 0.18
9 17 0.44
10 14 0.36
11 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
TAATAATATA
Found at i:38391 original size:16 final size:16
Alignment explanation
Indices: 38354--38402 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
38344 AGTAAAATAT
38354 ATAATAA-T-ATATATA
1 ATAATAACTAATAT-TA
*
38369 ATTATAACTAATATTA
1 ATAATAACTAATATTA
38385 ATAATAACTAATAGTTA
1 ATAATAACTAATA-TTA
38402 A
1 A
38403 CCCATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 8 0.28
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (16 bp):
ATAATAACTAATATTA
Found at i:38413 original size:2 final size:2
Alignment explanation
Indices: 38406--38436 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38396 TAGTTAACCC
38406 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 A
38437 ACAAGCACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40771 original size:23 final size:23
Alignment explanation
Indices: 40741--40826 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
40731 TCGAGGGTTC
*
40741 TATGTGGTCATTCGGGACAAAAT
1 TATGTGGTCATTCGGGACAAACT
* *
40764 TATGTGGTCATTCAGGACAAACC
1 TATGTGGTCATTCGGGACAAACT
* *
40787 TATGTGGTCCTTCGAGACAAACT
1 TATGTGGTCATTCGGGACAAACT
*
40810 TATGTGGTCCTTCGGGA
1 TATGTGGTCATTCGGGA
40827 TAATTATGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (23 bp):
TATGTGGTCATTCGGGACAAACT
Found at i:44075 original size:19 final size:19
Alignment explanation
Indices: 44051--44092 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
44041 TTTATTTATT
44051 CTAAGATTACATTTTTGGA
1 CTAAGATTACATTTTTGGA
44070 CTAAGATTACATTTTTGGA
1 CTAAGATTACATTTTTGGA
44089 CTAA
1 CTAA
44093 TCATTTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (19 bp):
CTAAGATTACATTTTTGGA
Found at i:44775 original size:14 final size:15
Alignment explanation
Indices: 44756--44792 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
44746 CCTTGTTCCA
*
44756 TTTGCATCTCGCA-T
1 TTTGCATCTCCCATT
44770 TTTGCA-CTCCCATT
1 TTTGCATCTCCCATT
44784 TTTGCATCT
1 TTTGCATCT
44793 TTGCATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.14, C:0.30, G:0.11, T:0.46
Consensus pattern (15 bp):
TTTGCATCTCCCATT
Found at i:46836 original size:39 final size:39
Alignment explanation
Indices: 46776--46920 Score: 186
Period size: 39 Copynumber: 3.7 Consensus size: 39
46766 TTGTTTTTAA
* ** * *
46776 AGAATATTTTATCTCTATTGAGATAGTTTCCCTTGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
46815 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
46854 AGAAGATTTTATCTCGCTTGAGATTGTTTCCCTCAAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
46893 AGAAGATTTGT-T-TCGCTTGAGACAGTTT
1 AGAAGATTT-TATCTCGCTTGAGATAGTTT
46921 TTACTTGAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
38 14 0.15
39 79 0.84
40 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:46931 original size:78 final size:78
Alignment explanation
Indices: 46775--47065 Score: 222
Period size: 76 Copynumber: 3.8 Consensus size: 78
46765 ATTGTTTTTA
* * * *
46775 AAGAATATTTTATCTCTA-TTGAGATAGTTTCCCTTGAAATATAAGATTT-TATCTCGCTTGAGA
1 AAGAAGATTTTATCTC-ACTTGAGATTGTTTCCCTTAAAACA-AAGATTTGT-T-TCGCTTGAGA
**
46838 TAG-TTTCCCTCGAAAC
62 TAGTTTTTACTCGAAAC
* * *
46854 -AGAAGATTTTATCTCGCTTGAGATTGTTTCCCTCAAAACAGAAGATTTGTTTCGCTTGAGACAG
1 AAGAAGATTTTATCTCACTTGAGATTGTTTCCCTTAAAACA-AAGATTTGTTTCGCTTGAGATAG
*
46918 TTTTTACTTGAAAC
65 TTTTTACTCGAAAC
* * ** ** * ** *
46932 AAAAAGA-TTTATTTCACTCAAGATTGTTTTTCTTAAAAC-AAGATTTGTCTCTTTTGAGATGGT
1 AAGAAGATTTTATCTCACTTGAGATTGTTTCCCTTAAAACAAAGATTTGTTTCGCTTGAGATAGT
46995 TTTTACTCGAAAC
66 TTTTACTCGAAAC
* * * ** **
47008 AAGAAGA-TTTAT-TTAATTCAAGATTGTTTTTCTTAAAAC-AAGATTTGTCCCGCTTGAG
1 AAGAAGATTTTATCTCACTT-GAGATTGTTTCCCTTAAAACAAAGATTTGTTTCGCTTGAG
47066 TCGGTTTTTA
Statistics
Matches: 175, Mismatches: 32, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
75 3 0.02
76 78 0.45
77 12 0.07
78 76 0.43
79 6 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (78 bp):
AAGAAGATTTTATCTCACTTGAGATTGTTTCCCTTAAAACAAAGATTTGTTTCGCTTGAGATAGT
TTTTACTCGAAAC
Found at i:46932 original size:39 final size:40
Alignment explanation
Indices: 46889--47017 Score: 106
Period size: 40 Copynumber: 3.4 Consensus size: 40
46879 GTTTCCCTCA
* *
46889 AAAC-AGAAGATTTGTTTCGCTTGAGACAGTTTTTACTTG
1 AAACAAGAAGATTTGTTTCACTTGAGATAGTTTTTACTTG
* * ** *
46928 AAACAAAAAGATTTATTTCACTCAAGATTGTTTTT-CTT-
1 AAACAAGAAGATTTGTTTCACTTGAGATAGTTTTTACTTG
* * ** * *
46966 -AA-AACAAGATTTGTCTCTTTTGAGATGGTTTTTACTCG
1 AAACAAGAAGATTTGTTTCACTTGAGATAGTTTTTACTTG
47004 AAACAAGAAGATTT
1 AAACAAGAAGATTT
47018 ATTTAATTCA
Statistics
Matches: 68, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
36 23 0.34
37 4 0.06
39 9 0.13
40 32 0.47
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (40 bp):
AAACAAGAAGATTTGTTTCACTTGAGATAGTTTTTACTTG
Found at i:46961 original size:40 final size:39
Alignment explanation
Indices: 46917--47048 Score: 117
Period size: 40 Copynumber: 3.4 Consensus size: 39
46907 GCTTGAGACA
*
46917 GTTTTTACTTGAAACAAAAAGATTTATTTCACTCAAGATT
1 GTTTTT-CTTGAAACAAAAAGATTTATTTCATTCAAGATT
* * * * ** *
46957 GTTTTTCTT--AA-AACAAGATTTGTCTCTTTTGAGATG
1 GTTTTTCTTGAAACAAAAAGATTTATTTCATTCAAGATT
* * *
46993 GTTTTTACTCGAAACAAGAAGATTTATTTAATTCAAGATT
1 GTTTTT-CTTGAAACAAAAAGATTTATTTCATTCAAGATT
*
47033 GTTTTTCTTAAAACAA
1 GTTTTTCTTGAAACAA
47049 GATTTGTCCC
Statistics
Matches: 69, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
36 23 0.33
37 4 0.06
39 13 0.19
40 29 0.42
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (39 bp):
GTTTTTCTTGAAACAAAAAGATTTATTTCATTCAAGATT
Found at i:47007 original size:76 final size:75
Alignment explanation
Indices: 46895--47114 Score: 266
Period size: 76 Copynumber: 2.9 Consensus size: 75
46885 CTCAAAACAG
** * *
46895 AAGATTTGTTTCGCTTGAGACAGTTTTTACTTGAAACAAAAAGATTTATTTCACTCAAGATTGTT
1 AAGATTTGTCCCGCTTGAGTCGGTTTTTAC-TGAAACAAAAAGATTTATTTCACTCAAGATTGTT
46960 TTTCTTAAAAC
65 TTTCTTAAAAC
* ** * * *
46971 AAGATTTGTCTCTTTTGAGAT-GGTTTTTACTCGAAACAAGAAGATTTATTTAATTCAAGATTGT
1 AAGATTTGTCCCGCTTGAG-TCGGTTTTTACT-GAAACAAAAAGATTTATTTCACTCAAGATTGT
47035 TTTTCTTAAAAC
64 TTTTCTTAAAAC
*
47047 AAGATTTGTCCCGCTTGAGTCGGTTTTTACT-AAA-AAAAAGACATTCCATTTCACTCAAGATTG
1 AAGATTTGTCCCGCTTGAGTCGGTTTTTACTGAAACAAAAAG--ATT-TATTTCACTCAAGATTG
47110 TTTTT
63 TTTTT
47115 AAAGAAGATT
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
73 5 0.04
74 3 0.02
75 5 0.04
76 110 0.89
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (75 bp):
AAGATTTGTCCCGCTTGAGTCGGTTTTTACTGAAACAAAAAGATTTATTTCACTCAAGATTGTTT
TTCTTAAAAC
Found at i:47452 original size:36 final size:36
Alignment explanation
Indices: 47122--47450 Score: 374
Period size: 36 Copynumber: 9.1 Consensus size: 36
47112 TTTAAAGAAG
*
47122 ATTTTATCTCTCTTGAGATC-GTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGA-CAGTTTCCCTTGAAACAA
* *
47158 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAA-AT
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* * * *
47193 GTTTTGGTCTCTCTTGAGACAATTACCTTTGAAACAA
1 ATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAA
*
47230 ATTTTGTCTCTTTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* * * * *
47266 ATTTCGTCTCCCTTGAGACAATTTCTCTTGAAGCAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* * * *
47302 ATTTTGTCTCTCTTGAGACAATTTCTCTTGTAGCAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* * *
47338 ATTCTGTCTCTCTTGACACAATTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* * *
47374 GTTTTGTCTCTCTAGAGACAGTTTCCCTCGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* * * * *
47410 ATTTTATCTCACTTGAGATAGTTTCTCTCGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
47446 ATTTT
1 ATTTT
47451 ATTTCACTTA
Statistics
Matches: 250, Mismatches: 40, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
35 6 0.02
36 239 0.96
37 5 0.02
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.40
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
Found at i:47458 original size:36 final size:36
Alignment explanation
Indices: 47388--47490 Score: 136
Period size: 36 Copynumber: 2.9 Consensus size: 36
47378 TGTCTCTCTA
* * *
47388 GAGACAGTTTCCCTCGAAACAAATTTTATCTCACTT
1 GAGATAGTTTCTCTCGAAACAAATTTTATTTCACTT
47424 GAGATAGTTTCTCTCGAAACAAATTTTATTTCACTT
1 GAGATAGTTTCTCTCGAAACAAATTTTATTTCACTT
* * *
47460 AAGATAGTTTCTCTTC-AGACAAATTTCATTT
1 GAGATAGTTTCTC-TCGAAACAAATTTTATTT
47491 GATTCATTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 58 0.97
37 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
GAGATAGTTTCTCTCGAAACAAATTTTATTTCACTT
Found at i:47946 original size:118 final size:117
Alignment explanation
Indices: 47749--48112 Score: 500
Period size: 118 Copynumber: 3.1 Consensus size: 117
47739 AAGATAAACC
* * * *
47749 GATCAACATTT-CCAATGGAGAATTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GATCAACATTTCCCAATGGATAGTTCATAATGAGAAGAACTCATCTGA-TGAGGGAGAAGAAGTT
*
47813 CATAATGAGAAGAACTTGTTCAACCTTGGTACGGTTCCATCACAGAAGGAGGTG
65 CATAATGAGAAGAACTTGTTCAACCTTGGTTC-GTTCCATCACAGAAGGAGGTG
* * *
47867 GATCAATATTTCCCAATGGATAGTTCATAATGAGAAGAACTAATCTGATGAGGGAGAAGAAGTTA
1 GATCAACATTTCCCAATGGATAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTC
**
47932 ATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGGAGGCA
66 ATAATGAGAAGAACTTGTTCAACCTTGGTTCG-TTCCATCACAGAAGGAGGTG
* * * * * *
47985 GATCAACATTTTCCAGTGGATGGTTCATAATGAGAAGAACTCAT-TCGATTAGAGAGAAGAAATT
1 GATCAACATTTCCCAATGGATAGTTCATAATGAGAAGAACTCATCT-GATGAGGGAGAAGAAGTT
* * *
48049 CATAATGAGAAGAACTTGTTCAATCTTAGTTC-ATCCATCACAGAAGGAGGTG
65 CATAATGAGAAGAACTTGTTCAACCTTGGTTCGTTCCATCACAGAAGGAGGTG
48101 GATCAACATTTC
1 GATCAACATTTC
48113 TAGTAGAGAA
Statistics
Matches: 218, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
116 28 0.13
117 2 0.01
118 156 0.72
119 32 0.15
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (117 bp):
GATCAACATTTCCCAATGGATAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTGGTTCGTTCCATCACAGAAGGAGGTG
Found at i:48497 original size:132 final size:132
Alignment explanation
Indices: 48142--48878 Score: 837
Period size: 132 Copynumber: 5.7 Consensus size: 132
48132 AAGAGATTGT
** * * * *
48142 TCAAC-TTTTGCTTAATTCTATCACATAAGGAGATAGATCAGCACCGACATCTCATTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
*
48206 TCACAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
48271 CA
131 CA
* * * *
48273 TCAACGTTTTTGATCGATTCTATCACAGAAGGAGGTAGATCAACACTGACATCTCATTCAATTCC
1 TCAAC-TTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCC
* ** *
48338 ATCATAGAAGGAGGTGGATTAACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTTGATCA
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
48403 ACA
130 GCA
* * * * *
48406 TCAACTTTTTGCTCGATTCTATCATAGAAGGAGGTAGATTAACATCAACATCTCGTTCGATTCTA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
* * * *
48471 TCGCAGAAGGAGGTGGATCGATATTTTTATTTTGCTCAAATCCATCGCAGAAGAAGTTGGATCAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
48536 CA
131 CA
* * * * *
48538 TCAA-TATTTTGCTCGATTTTATCACAGAAGGAGGTAGTTCAGCATCGACATCACGTTCGATTCC
1 TCAACT-TTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCC
* * * * * *
48602 ATCACATAAAGAGATGGATCGACA--TTT-TTTCACTCAAATTCATCACAGAAGGAGTTGGATCA
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
48664 GTA
130 GCA
* * * *
48667 TCAA-TATTTTGCTCGATTCTATCACAGAAAGAGGTAAATCAACACCAATATCTCGTTCGATTCC
1 TCAACT-TTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCC
* * * * *
48731 ATCACAGAAGGGGGTGGATCG--A----TATTT---T--TATCCAGCGCATAAGGAATTGGATCA
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
48785 ACA
130 GCA
* * * * *
48788 TCAA-TTCTTTGCTTGATTCTATCACAGAAGGAGGTAGATCAACACCCATATCTTGTT-AATTCC
1 TCAACTT-TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCC
48851 ATCACAGAAGGAGGTGGATCGACATTTT
65 ATCACAGAAGGAGGTGGATCGACATTTT
48879 CATTCATCAC
Statistics
Matches: 516, Mismatches: 79, Indels: 27
0.83 0.13 0.04
Matches are distributed among these distances:
120 26 0.05
121 71 0.14
122 1 0.00
123 1 0.00
125 1 0.00
126 3 0.01
127 1 0.00
129 104 0.20
130 3 0.01
131 6 0.01
132 182 0.35
133 117 0.23
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (132 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
CA
Found at i:48540 original size:88 final size:88
Alignment explanation
Indices: 48147--48572 Score: 269
Period size: 88 Copynumber: 4.8 Consensus size: 88
48137 ATTGTTCAAC
* * * * * * * * * ** *
48147 TTTTGCTTAATTCTATCACATAAGGAGATAGATCAGCACCGACATCTCATTCGATTCCATCACAG
1 TTTTGCTCAAATCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGCTCGATTCTATCACAG
*
48212 AAGGAGGTGGATCGACATTTTTA
66 AAGGAGGTGGATCAACATTTTTA
* * * * *
48235 TTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCATCAACGTTTTTGATCGATTCTATCACA
1 TTTTGCTCAAATCCATCACAGAAGGAGGTGGATCAGCATCAAC-ATTTCGCTCGATTCTATCACA
* * ***
48300 GAAGGAGGTAGATCAACACTGACA
65 GAAGGAGGTGGATCAACATTTTTA
* *** * * * * **** * * * *
48324 TCTCATTCAATTCCATCATAGAAGGAGGTGGATTAACATTTTTATTTCGCTCAAATCCATCGCAG
1 TTTTGCTCAAATCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGCTCGATTCTATCACAG
* * ***
48389 AAGGAGTTTGATCAACATCAACT-
66 AAGGAGGTGGATCAACAT-TTTTA
* * * * * * * * * *
48412 TTTTGCTCGATTCTATCATAGAAGGAGGTAGATTAACATCAACATCTCGTTCGATTCTATCGCAG
1 TTTTGCTCAAATCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGCTCGATTCTATCACAG
* *
48477 AAGGAGGTGGATCGATATTTTTA
66 AAGGAGGTGGATCAACATTTTTA
* * * * * *
48500 TTTTGCTCAAATCCATCGCAGAAGAAGTTGGATCAGCATCAATATTTTGCTCGATTTTATCACAG
1 TTTTGCTCAAATCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGCTCGATTCTATCACAG
48565 AAGGAGGT
66 AAGGAGGT
48573 AGTTCAGCAT
Statistics
Matches: 247, Mismatches: 88, Indels: 6
0.72 0.26 0.02
Matches are distributed among these distances:
87 1 0.00
88 184 0.74
89 62 0.25
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (88 bp):
TTTTGCTCAAATCCATCACAGAAGGAGGTGGATCAGCATCAACATTTCGCTCGATTCTATCACAG
AAGGAGGTGGATCAACATTTTTA
Found at i:48692 original size:44 final size:44
Alignment explanation
Indices: 48197--48750 Score: 239
Period size: 44 Copynumber: 12.6 Consensus size: 44
48187 GACATCTCAT
* ***
48197 TCGATTCCATCACAGAAGGAGGTGGATC-GACATTTTTATTTTGC
1 TCGATTCTATCACAGAAGGAGGTGGATCAG-CATCAATATTTTGC
* * * * * *
48241 TCAAATCCATCGCAGAAGGAGTTGGATCAGCATCAACGT-TTTTGA
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAA--TATTTTGC
* * * * **
48286 TCGATTCTATCACAGAAGGAGGTAGATCAACACTGACATCTCAT--
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCA-TCA-ATATTTTGC
* * * * * *** *
48330 TCAATTCCATCATAGAAGGAGGTGGATTAACATTTTTATTTCGC
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAATATTTTGC
* * * * * * *
48374 TCAAATCCATCGCAGAAGGAGTTTGATCAACATCAACT-TTTTGC
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAA-TATTTTGC
* * * * * * * *
48418 TCGATTCTATCATAGAAGGAGGTAGATTAACATCAACATCTCGT
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAATATTTTGC
* * ***
48462 TCGATTCTATCGCAGAAGGAGGTGGATC-GATATTTTTATTTTGC
1 TCGATTCTATCACAGAAGGAGGTGGATCAG-CATCAATATTTTGC
* * * * * *
48506 TCAAATCCATCGCAGAAGAAGTTGGATCAGCATCAATATTTTGC
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAATATTTTGC
* * * * * *** *
48550 TCGATTTTATCACAGAAGGAGGTAGTTCAGCATCGACATCACGT
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAATATTTTGC
* * * * * *
48594 TCGATTCCATCACATAAAGAGATGGATC-G-A-C-ATTTTTTCAC
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAATATTTT-GC
* * *
48635 TCAAATTC-ATCACAGAAGGAGTTGGATCAGTATCAATATTTTGC
1 TC-GATTCTATCACAGAAGGAGGTGGATCAGCATCAATATTTTGC
* ** * * * * *
48679 TCGATTCTATCACAGAAAGAGGTAAATCAACACCAATATCTCGT
1 TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAATATTTTGC
* *
48723 TCGATTCCATCACAGAAGGGGGTGGATC
1 TCGATTCTATCACAGAAGGAGGTGGATC
48751 GATATTTTTA
Statistics
Matches: 366, Mismatches: 125, Indels: 38
0.69 0.24 0.07
Matches are distributed among these distances:
40 2 0.01
41 20 0.05
42 8 0.02
43 7 0.02
44 283 0.77
45 40 0.11
46 5 0.01
47 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
TCGATTCTATCACAGAAGGAGGTGGATCAGCATCAATATTTTGC
Found at i:50195 original size:25 final size:25
Alignment explanation
Indices: 50162--50213 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
50152 TAGATCTTTA
50162 TTTTATGTTTATT-TTA-TTTTATTT
1 TTTTATGTTT-TTATTACTTTTATTT
50186 TTTTAATGTTTTTATTATCTTTTATTT
1 TTTT-ATGTTTTTATTA-CTTTTATTT
50213 T
1 T
50214 AATTATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 6 0.25
25 9 0.38
27 9 0.38
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTATGTTTTTATTACTTTTATTT
Found at i:53875 original size:23 final size:23
Alignment explanation
Indices: 53845--53904 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
53835 TATTTTATAT
53845 GGCACTTCAGTGCAATTCTACGC
1 GGCACTTCAGTGCAATTCTACGC
* * *
53868 GGCACTTCGGTGCAATTCTATGT
1 GGCACTTCAGTGCAATTCTACGC
*
53891 GGCACTTCAATGCA
1 GGCACTTCAGTGCA
53905 TTTATACGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTCTACGC
Found at i:58797 original size:23 final size:23
Alignment explanation
Indices: 58729--58789 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
58719 ACATTTTATA
58729 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
58752 CGGCACTTCGGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
58775 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
58790 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:69531 original size:19 final size:19
Alignment explanation
Indices: 69507--69544 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
69497 TACCTAAGCG
*
69507 TTGACTTTGATTTTGACCA
1 TTGACTTTGACTTTGACCA
69526 TTGACTTTGACTTTGACCA
1 TTGACTTTGACTTTGACCA
69545 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (19 bp):
TTGACTTTGACTTTGACCA
Found at i:69898 original size:4 final size:4
Alignment explanation
Indices: 69889--71939 Score: 4029
Period size: 4 Copynumber: 513.8 Consensus size: 4
69879 GAATTAGAAC
69889 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
69937 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
69985 TACA TACA TACA TACA TACA TACA TACA TACG TACG TACG TACG TACG
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70033 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70081 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70129 TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70175 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70223 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70271 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70319 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70367 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70415 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70463 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70511 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70559 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70607 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70655 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70703 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70751 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70799 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70847 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70895 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70943 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
70991 TACA TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71037 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71085 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71133 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71181 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71229 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71277 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71325 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71373 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71421 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71469 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71517 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71565 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71613 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71661 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71709 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71757 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71805 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71853 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
71901 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
71940 CGCTGATGTT
Statistics
Matches: 2041, Mismatches: 2, Indels: 8
1.00 0.00 0.00
Matches are distributed among these distances:
2 4 0.00
4 2037 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:74138 original size:20 final size:21
Alignment explanation
Indices: 74113--74153 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
74103 CTTGAAGTTA
74113 TAGGTTTTAATTTTCA-TTTT
1 TAGGTTTTAATTTTCAGTTTT
74133 TAGGTTTTAATTTTCAGTTTT
1 TAGGTTTTAATTTTCAGTTTT
74154 GATATTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.20, C:0.05, G:0.12, T:0.63
Consensus pattern (21 bp):
TAGGTTTTAATTTTCAGTTTT
Found at i:74389 original size:3 final size:3
Alignment explanation
Indices: 74335--74379 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
74325 GGGTGAATTG
74335 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
74380 TCGATTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:82963 original size:2 final size:2
Alignment explanation
Indices: 82956--83008 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
82946 CTATGTTGTT
* *
82956 TA TA TA TA T- TA TA TCA TA T- TA TT TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
82997 TA TA TA TA TA TA
1 TA TA TA TA TA TA
83009 AATTAATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:83089 original size:18 final size:19
Alignment explanation
Indices: 83053--83090 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
83043 TAACGTCTAT
*
83053 TTTATTTTATTTGACTTTA
1 TTTATTTTATTTCACTTTA
*
83072 TTTA-TTTATTTCATTTTA
1 TTTATTTTATTTCACTTTA
83090 T
1 T
83091 AAGATGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTATTTTATTTCACTTTA
Found at i:94563 original size:9 final size:9
Alignment explanation
Indices: 94539--94615 Score: 73
Period size: 9 Copynumber: 9.4 Consensus size: 9
94529 AAAAGGGAAC
94539 AAAT-AAAA
1 AAATGAAAA
*
94547 AGAT-AAAA
1 AAATGAAAA
94555 AAATGAAAA
1 AAATGAAAA
94564 AGAA--AAAA
1 A-AATGAAAA
94572 AAATGAAAA
1 AAATGAAAA
94581 AAATG---A
1 AAATGAAAA
94587 AAATGAAAA
1 AAATGAAAA
94596 AAATG--AA
1 AAATGAAAA
94603 AAATGAAAA
1 AAATGAAAA
94612 AAAT
1 AAAT
94616 AAATGAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
6 6 0.10
7 9 0.16
8 15 0.26
9 26 0.45
10 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (9 bp):
AAATGAAAA
Found at i:94571 original size:15 final size:15
Alignment explanation
Indices: 94551--94640 Score: 86
Period size: 15 Copynumber: 6.3 Consensus size: 15
94541 ATAAAAAGAT
94551 AAAAAAATGAAAAAG
1 AAAAAAATGAAAAAG
*
94566 --AAAAA--AAAATG
1 AAAAAAATGAAAAAG
*
94577 AAAAAAATGAAAATG
1 AAAAAAATGAAAAAG
94592 AAAAAAATGAAAAATG
1 AAAAAAATGAAAAA-G
*
94608 AAAAAAAT--AAATG
1 AAAAAAATGAAAAAG
94621 -AAAAAATGAAAAGAG
1 AAAAAAATGAAAA-AG
94636 AAAAA
1 AAAAA
94641 GGAGGGTTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
11 5 0.08
12 7 0.11
13 11 0.18
14 6 0.10
15 20 0.32
16 13 0.21
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (15 bp):
AAAAAAATGAAAAAG
Found at i:94572 original size:26 final size:26
Alignment explanation
Indices: 94568--94640 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 26
94558 TGAAAAAGAA
**
94568 AAAAAAATG-AAAA-AAATGAAAATG
1 AAAAAAATGAAAAAGAAAAAAAAATG
94592 AAAAAAATGAAAAATGAAAAAAATAAATG
1 AAAAAAATGAAAAA-G-AAAAAA-AAATG
94621 -AAAAAATGAAAAGAGAAAAA
1 AAAAAAATGAAAA-AGAAAAA
94641 GGAGGGTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
24 9 0.22
25 4 0.10
27 5 0.12
28 17 0.41
29 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (26 bp):
AAAAAAATGAAAAAGAAAAAAAAATG
Found at i:94598 original size:43 final size:40
Alignment explanation
Indices: 94521--94640 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 40
94511 ACTATGCTTG
* * *
94521 AAGAAAAAAAAAGGGAACAAATAAAAAGATAAAAAAATGAAA
1 AAGAAAAAAAAA-TGAAAAAATGAAAAGA-AAAAAAATGAAA
94563 AAGAAAAAAAAATGAAAAAAATGAAAATG-AAAAAAATGAAA
1 AAGAAAAAAAAATG-AAAAAATGAAAA-GAAAAAAAATGAAA
*
94604 AATGAAAAAAATAAATGAAAAAATGAAAAGAGAAAAA
1 AA-G-AAAAAA-AAATGAAAAAATGAAAAGAAAAAAA
94641 GGAGGGTTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
41 15 0.22
42 24 0.35
43 24 0.35
44 5 0.07
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.09
Consensus pattern (40 bp):
AAGAAAAAAAAATGAAAAAATGAAAAGAAAAAAAATGAAA
Found at i:94627 original size:8 final size:8
Alignment explanation
Indices: 94539--94632 Score: 67
Period size: 9 Copynumber: 12.1 Consensus size: 8
94529 AAAAGGGAAC
94539 AAAT-AAA
1 AAATGAAA
*
94546 AAGATAAAA
1 AA-ATGAAA
94555 AAATGAAA
1 AAATGAAA
**
94563 AAGAAAAAA
1 AA-ATGAAA
94572 AAATGAAAA
1 AAATG-AAA
94581 AAATG--A
1 AAATGAAA
94587 AAATGAAAA
1 AAATG-AAA
94596 AAATG-AA
1 AAATGAAA
94603 AAATG-AA
1 AAATGAAA
*
94610 AAA--AAT
1 AAATGAAA
94616 AAATGAAA
1 AAATGAAA
94624 AAATGAAA
1 AAATGAAA
94632 A
1 A
94633 GAGAAAAAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
6 10 0.14
7 14 0.20
8 21 0.30
9 25 0.36
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:95770 original size:134 final size:136
Alignment explanation
Indices: 95513--95817 Score: 515
Period size: 134 Copynumber: 2.3 Consensus size: 136
95503 AGGTGAACCA
*
95513 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* *
95578 GAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTTGAATCAGTGACACCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAG
95643 GGATCG
131 GGATCG
*
95649 ACATTTTC-A-GGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* * **
95712 GAGAAGAGCTTGTTTGACCTATCACTTGATTCACGACATTTCGAATCAGTGATGCCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAG
95777 GGATCG
131 GGATCG
*
95783 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACT
95818 TGTTCCTTTC
Statistics
Matches: 157, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
134 125 0.80
135 2 0.01
136 30 0.19
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (136 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAG
GGATCG
Found at i:98415 original size:2 final size:2
Alignment explanation
Indices: 98408--98462 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
98398 CTATGTTGTT
* *
98408 TA TA TA TA T- TA TA TCA TA T- TA TT TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
98449 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
98463 AATTAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:98543 original size:18 final size:19
Alignment explanation
Indices: 98507--98544 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
98497 TAACGTCTAT
*
98507 TTTATTTTATTTGACTTTA
1 TTTATTTTATTTCACTTTA
*
98526 TTTA-TTTATTTCATTTTA
1 TTTATTTTATTTCACTTTA
98544 T
1 T
98545 AAGATGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTATTTTATTTCACTTTA
Found at i:101910 original size:46 final size:46
Alignment explanation
Indices: 101851--102106 Score: 381
Period size: 46 Copynumber: 5.6 Consensus size: 46
101841 TTTATGTCGT
* *
101851 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* *
101897 TAATGCACTGTTATGCATTTTCATTTATGGCATCCTTTCATGCTGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
101943 TAATGCACCGTTATGCATTTTCA-TTATGGCATCCTTTCATGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
* * * * **
101988 TAATACATCATTATGCATTTTCATTTATGACATCCTTTCATGATGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
102034 TAATGCACCGTTATGCA-TTTCATTTATGGCATCCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
*
102079 TAATGCACCATTATGCATTTTCATTTAT
1 TAATGCACCGTTATGCATTTTCATTTAT
102107 TCATTCATTT
Statistics
Matches: 187, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 80 0.43
46 107 0.57
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGA
Found at i:101916 original size:40 final size:41
Alignment explanation
Indices: 101871--102098 Score: 145
Period size: 45 Copynumber: 5.1 Consensus size: 41
101861 TTATGCATTT
* *
101871 TCATTTGTGGCATCCTTTCATGCCAATAATGCACTGTTATG
1 TCATTTATGGCATCCTTTCATGCCAATAATGCACCGTTATG
**
101912 CATTTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATG
1 -----TCATTTATGGCATCCTTTCATGCCAATAATGCACCGTTATG
* * * * *
101958 -CATTTTCATTATGGCATCCTTTCATGTCGATAATACATCATTATG
1 TCA---T--TTATGGCATCCTTTCATGCCAATAATGCACCGTTATG
* ***
102003 CATTTTCATTTATGACATCCTTTCATGATGATAATGCACCGTTATG
1 -----TCATTTATGGCATCCTTTCATGCCAATAATGCACCGTTATG
*
102049 CATTTCATTTATGGCATCCTTTCATGCCAATAATGCACCATTATG
1 ----TCATTTATGGCATCCTTTCATGCCAATAATGCACCGTTATG
102094 -CATTT
1 TCATTT
102099 TCATTTATTC
Statistics
Matches: 149, Mismatches: 22, Indels: 28
0.75 0.11 0.14
Matches are distributed among these distances:
40 7 0.05
43 1 0.01
45 70 0.47
46 68 0.46
48 1 0.01
51 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (41 bp):
TCATTTATGGCATCCTTTCATGCCAATAATGCACCGTTATG
Found at i:102007 original size:91 final size:91
Alignment explanation
Indices: 101851--102106 Score: 408
Period size: 91 Copynumber: 2.8 Consensus size: 91
101841 TTTATGTCGT
* *
101851 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCAATAATGCACTGTTATGCATT
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCAC-ATTATGCATT
* *
101916 TTCATTTATGGCATCCTTTCATGCTGA
65 TTCATTTATGACATCCTTTCATGATGA
* * *
101943 TAATGCACCGTTATGCATTTTCA-TTATGGCATCCTTTCATGTCGATAATACATCATTATGCATT
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCA-CATTATGCATT
102007 TTCATTTATGACATCCTTTCATGATGA
65 TTCATTTATGACATCCTTTCATGATGA
102034 TAATGCACCGTTATGCA-TTTCATTTATGGCATCCTTTCATGCCAATAATGCACCATTATGCATT
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCA-CATTATGCATT
102098 TTCATTTAT
65 TTCATTTAT
102107 TCATTCATTT
Statistics
Matches: 151, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
90 5 0.03
91 122 0.81
92 24 0.16
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (91 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATGCACATTATGCATTT
TCATTTATGACATCCTTTCATGATGA
Found at i:103751 original size:68 final size:68
Alignment explanation
Indices: 103670--103798 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 68
103660 GCATACTACA
* * *
103670 AAATTAGTGTCCTCCTCCTAATAACCCATCTCAAGCATAATACAATATGTCATACAATAAATGGA
1 AAATCAGTGTCCTCCTCCTAACAACCCATCTCAAGCATAATACAATATGACATACAATAAATGGA
103735 TAT
66 TAT
* * * *
103738 AAATCAGTGTCCTCTTCCTAACAACCCATCTCATGCTTGATACAATATGACATACAATAAA
1 AAATCAGTGTCCTCCTCCTAACAACCCATCTCAAGCATAATACAATATGACATACAATAAA
103799 CGAGTATATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.29
Consensus pattern (68 bp):
AAATCAGTGTCCTCCTCCTAACAACCCATCTCAAGCATAATACAATATGACATACAATAAATGGA
TAT
Found at i:104094 original size:28 final size:29
Alignment explanation
Indices: 104062--104132 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 29
104052 AACAATACAT
104062 ACAAATGTTTAG-CACAAATGAAGCACAC
1 ACAAATGTTTAGACACAAATGAAGCACAC
*
104090 ACAAATGTTTGTAGATTACAAATGAAGCACAC
1 ACAAATG-TT-TAGA-CACAAATGAAGCACAC
104122 ACAAATGTTTA
1 ACAAATGTTTA
104133 TAGATTAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 7 0.18
29 2 0.05
30 5 0.13
31 2 0.05
32 22 0.58
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (29 bp):
ACAAATGTTTAGACACAAATGAAGCACAC
Found at i:104116 original size:32 final size:32
Alignment explanation
Indices: 104075--104139 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
104065 AATGTTTAGC
*
104075 ACAAATGAAGCACACACAAATGTTTGTAGATT
1 ACAAATGAAGCACACACAAATGTTTATAGATT
104107 ACAAATGAAGCACACACAAATGTTTATAGATT
1 ACAAATGAAGCACACACAAATGTTTATAGATT
104139 A
1 A
104140 ACACCCACAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (32 bp):
ACAAATGAAGCACACACAAATGTTTATAGATT
Found at i:104347 original size:41 final size:41
Alignment explanation
Indices: 104276--104353 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
104266 TGTTTGTAGT
* *
104276 AAAAACGCTGCAATAGAGTTGATATATAGCGGCGTTTTCCA
1 AAAAACGCTGCAATAGAGTAGAAATATAGCGGCGTTTTCCA
*
104317 AAAAACGCTGCAATAGGGTAGTAAAT-TAGCGGCGTTT
1 AAAAACGCTGCAATAGAGTAG-AAATATAGCGGCGTTT
104354 ATACCACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 30 0.91
42 3 0.09
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (41 bp):
AAAAACGCTGCAATAGAGTAGAAATATAGCGGCGTTTTCCA
Found at i:104383 original size:41 final size:41
Alignment explanation
Indices: 104276--104384 Score: 107
Period size: 41 Copynumber: 2.7 Consensus size: 41
104266 TGTTTGTAGT
* * *
104276 AAAAACGCTGCAATAGAGTTG-ATATATAGCGGCGTTTTCCA
1 AAAAACGCCGCAATAGAGTAGTAAAT-TAGCGGCGTTTTCCA
* *
104317 AAAAACGCTGCAATAGGGTAGTAAATTAGCGGCGTTTATACC-
1 AAAAACGCCGCAATAGAGTAGTAAATTAGCGGCGTTT-T-CCA
* *
104359 ACAAACGCCGTAATAGAGTA-TAAATT
1 AAAAACGCCGCAATAGAGTAGTAAATT
104385 TTGAGGCGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 36 0.62
42 20 0.34
43 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (41 bp):
AAAAACGCCGCAATAGAGTAGTAAATTAGCGGCGTTTTCCA
Found at i:104475 original size:71 final size:71
Alignment explanation
Indices: 104359--104497 Score: 233
Period size: 71 Copynumber: 2.0 Consensus size: 71
104349 CGTTTATACC
* * * *
104359 ACAAACGCCGTAATAGAGTATAAATTTTGAGGCGATTTAGCCAAAACACCGCATTAGAGTGGTAA
1 ACAAACGCCGCAATAGAGTATAAATTTTGAGGCAATTGAGCCAAAACACCGCAATAGAGTGGTAA
104424 ATTGGT
66 ATTGGT
*
104430 ACAAACGCCGCAATAGAGTATAAATTTTGTGGCAATTGAGCCAAAACACCGCAATAGAGTGGTAA
1 ACAAACGCCGCAATAGAGTATAAATTTTGAGGCAATTGAGCCAAAACACCGCAATAGAGTGGTAA
104495 ATT
66 ATT
104498 AGCGGCGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (71 bp):
ACAAACGCCGCAATAGAGTATAAATTTTGAGGCAATTGAGCCAAAACACCGCAATAGAGTGGTAA
ATTGGT
Found at i:104611 original size:41 final size:40
Alignment explanation
Indices: 104556--104770 Score: 254
Period size: 41 Copynumber: 5.3 Consensus size: 40
104546 GTTTATTCCT
104556 CAAACGCCGCAATAGTGATAATCAATAGTGGCATTTTTAGA
1 CAAACGCCGCAATAGTG-TAATCAATAGTGGCATTTTTAGA
* *
104597 CAAACGCCGCAATAGTGTTAATCAATAATGGCGTTTTTAGA
1 CAAACGCCGCAATAGTG-TAATCAATAGTGGCATTTTTAGA
* * * **
104638 AAAATGCCGCAATAATGTTAATCAATAGTGGCGCTTTTAGA
1 CAAACGCCGCAATAGTG-TAATCAATAGTGGCATTTTTAGA
*
104679 CAAACGCCGCAATAGT-TAATCAATAGTGGCGTTTTTTA-A
1 CAAACGCCGCAATAGTGTAATCAATAGTGGC-ATTTTTAGA
* ** *
104718 CAAACGTCATAATAGTGTAATCAATAGTGGCATTTTTTGTA
1 CAAACGCCGCAATAGTGTAATCAATAGTGGCATTTTTAG-A
*
104759 TAAACGCCGCAA
1 CAAACGCCGCAA
104771 AATGTTAAAT
Statistics
Matches: 148, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
39 33 0.22
40 19 0.13
41 96 0.65
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (40 bp):
CAAACGCCGCAATAGTGTAATCAATAGTGGCATTTTTAGA
Found at i:104714 original size:121 final size:121
Alignment explanation
Indices: 104556--104778 Score: 308
Period size: 121 Copynumber: 1.8 Consensus size: 121
104546 GTTTATTCCT
*
104556 CAAACGCCGCAATAGTGATAATCAATAGTGGCA-TTTTTAGACAAACGCCGCAATAGTGTTAATC
1 CAAACGCCGCAATAGT-ATAATCAATAGTGGCATTTTTTA-ACAAACGCCACAATAGTG-TAATC
* *
104620 AATAATGGCGTTTTTAG-AAAAATGCCGCAATAATGTTAATCAATAGTGGCGCTTTTAGA
63 AATAATGGCATTTTTAGTAAAAACGCCGCAA-AATGTTAATCAATAGTGGCGCTTTTAGA
* * *
104679 CAAACGCCGCAATAGT-TAATCAATAGTGGCGTTTTTTAACAAACGTCATAATAGTGTAATCAAT
1 CAAACGCCGCAATAGTATAATCAATAGTGGCATTTTTTAACAAACGCCACAATAGTGTAATCAAT
* * *
104743 AGTGGCATTTTTTGTATAAACGCCGCAAAATGTTAA
66 AATGGCATTTTTAGTAAAAACGCCGCAAAATGTTAA
104779 ATATATAGTC
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
120 27 0.30
121 40 0.45
122 6 0.07
123 16 0.18
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (121 bp):
CAAACGCCGCAATAGTATAATCAATAGTGGCATTTTTTAACAAACGCCACAATAGTGTAATCAAT
AATGGCATTTTTAGTAAAAACGCCGCAAAATGTTAATCAATAGTGGCGCTTTTAGA
Found at i:105769 original size:18 final size:18
Alignment explanation
Indices: 105740--105792 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
105730 GTTCCTAACA
*
105740 TTCTCTACCAGCGCAACC
1 TTCTCCACCAGCGCAACC
* *
105758 TTCTCCAGCAGCGCAATC
1 TTCTCCACCAGCGCAACC
105776 TTCTCCACCAGCGCAAC
1 TTCTCCACCAGCGCAAC
105793 GACCACCAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (18 bp):
TTCTCCACCAGCGCAACC
Done.