Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001318.1 Hibiscus syriacus cultivar Beakdansim tig00002570_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: 123157
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1198 original size:19 final size:19
Alignment explanation
Indices: 1154--1198 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1144 GTTTGGATCA
*
1154 AGGAATATGGGATTCCAAT
1 AGGAATGTGGGATTCCAAT
*
1173 A-GAATGTGGGATTCCCAT
1 AGGAATGTGGGATTCCAAT
1191 AGGAATGT
1 AGGAATGT
1199 AATCTACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (19 bp):
AGGAATGTGGGATTCCAAT
Found at i:1778 original size:18 final size:19
Alignment explanation
Indices: 1755--1797 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1745 CATTCCCAGT
*
1755 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
1773 ATTCCCACTGATAATCTTAC
1 ATT-CCACTGATAATCTTAC
1793 ATTCC
1 ATTCC
1798 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:3464 original size:19 final size:20
Alignment explanation
Indices: 3420--3470 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3410 CCATGTTCGA
*
3420 GTTGCGAATTTGAAAACTGT
1 GTTGCGAATTTGAAAACTGC
*
3440 GTTGCGAATTTGAAATC-GC
1 GTTGCGAATTTGAAAACTGC
*
3459 GTTGCGATTTTG
1 GTTGCGAATTTG
3471 TTGGTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGAAAACTGC
Found at i:3753 original size:12 final size:12
Alignment explanation
Indices: 3736--3766 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3726 GGTGGATGGT
3736 TTGGCACTTGTG
1 TTGGCACTTGTG
3748 TTGGCACTTGTG
1 TTGGCACTTGTG
3760 TTGGCAC
1 TTGGCAC
3767 GTGGTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.19, G:0.32, T:0.39
Consensus pattern (12 bp):
TTGGCACTTGTG
Found at i:7657 original size:36 final size:35
Alignment explanation
Indices: 7609--7694 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 35
7599 AACTTGAAAC
** *
7609 CCTTTAACTACTAAGGTAACTGAGATAACAAACAT
1 CCTTTAACTACTAAGACAACAGAGATAACAAACAT
* * *
7644 CTCTTTAACTACTAAGACAGCAGATATAACAAGCAT
1 C-CTTTAACTACTAAGACAACAGAGATAACAAACAT
7680 CCATTTAACTACTAA
1 CC-TTTAACTACTAA
7695 AGTAGCTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
35 2 0.05
36 41 0.95
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (35 bp):
CCTTTAACTACTAAGACAACAGAGATAACAAACAT
Found at i:7971 original size:29 final size:31
Alignment explanation
Indices: 7935--8001 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
7925 ATTTTGTTTC
*
7935 ATCATTAAAGTT-TCAAAAA-TTATAAAATG
1 ATCATTAAACTTCTCAAAAAGTTATAAAATG
*
7964 ATTATTAAACTTCTCAAAAAGTTATAAAATG
1 ATCATTAAACTTCTCAAAAAGTTATAAAATG
7995 ATCATTA
1 ATCATTA
8002 TAATTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 10 0.30
30 7 0.21
31 16 0.48
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (31 bp):
ATCATTAAACTTCTCAAAAAGTTATAAAATG
Found at i:12307 original size:14 final size:14
Alignment explanation
Indices: 12288--12314 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12278 AACCCCAATC
12288 TTCTTCTTCTTTCT
1 TTCTTCTTCTTTCT
12302 TTCTTCTTCTTTC
1 TTCTTCTTCTTTC
12315 CATGTGTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTCTTCTTTCT
Found at i:20573 original size:21 final size:21
Alignment explanation
Indices: 20548--20598 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
20538 TAAATATGTA
* *
20548 TTTAATAATTTGATTTTTATT
1 TTTAATAATTTGATATCTATT
*
20569 TTTAAT-ATTTTATATCTATT
1 TTTAATAATTTGATATCTATT
*
20589 TTTTATAATT
1 TTTAATAATT
20599 GTATATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTAATAATTTGATATCTATT
Found at i:20621 original size:13 final size:15
Alignment explanation
Indices: 20589--20625 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
20579 TATATCTATT
*
20589 TTTTATAATTGTATA
1 TTTTAAAATTGTATA
20604 TTTTAAAATT-TA-A
1 TTTTAAAATTGTATA
20617 TTTTAAAAT
1 TTTTAAAAT
20626 ATTTTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTAAAATTGTATA
Found at i:36527 original size:21 final size:22
Alignment explanation
Indices: 36503--36543 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
36493 ACATATGATG
36503 TAAAATAA-AACATTTACAACA
1 TAAAATAACAACATTTACAACA
*
36524 TAAAATAACAATATTTACAA
1 TAAAATAACAACATTTACAA
36544 TATGTGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATAACAACATTTACAACA
Found at i:36719 original size:30 final size:29
Alignment explanation
Indices: 36685--36760 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
36675 TACAAATAGG
* *
36685 AATTTAAAGGACTAAAATGGCCAAAACATA
1 AATTTAAAGG-CTAAAATAGCAAAAACATA
*
36715 AATTTAAATGGCTAAAATAGTAAAAACATA
1 AATTTAAA-GGCTAAAATAGCAAAAACATA
*
36745 AATTTAAGGGTCTAAA
1 AATTTAAAGG-CTAAA
36761 TAAAAAACAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 2 0.05
30 36 0.90
31 2 0.05
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (29 bp):
AATTTAAAGGCTAAAATAGCAAAAACATA
Found at i:36762 original size:29 final size:28
Alignment explanation
Indices: 36707--36819 Score: 77
Period size: 30 Copynumber: 3.9 Consensus size: 28
36697 TAAAATGGCC
*
36707 AAAACATAAATTTAAATGGCTAAAATAGTA
1 AAAACATAAATTTAAAGGGCTAAAATA--A
36737 AAAACATAAATTT-AAGGGTCT-AAATAA
1 AAAACATAAATTTAAAGGG-CTAAAATAA
* * * * *
36764 AAAACAGAAACTTGAGGGGATAAAATAAA
1 AAAACATAAATTTAAAGGGCTAAAAT-AA
* * **
36793 TAAAACAGAAACTTAAAGAACTAAAAT
1 -AAAACATAAATTTAAAGGGCTAAAAT
36820 GGTATTAACA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
27 13 0.19
28 8 0.12
29 11 0.16
30 36 0.53
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.21
Consensus pattern (28 bp):
AAAACATAAATTTAAAGGGCTAAAATAA
Found at i:36781 original size:27 final size:29
Alignment explanation
Indices: 36727--36808 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 29
36717 TTTAAATGGC
* * * **
36727 TAAAATAGTAAAAACATAAATTTAAGGGTC
1 TAAAATA-AAAAAACAGAAACTTAAGGGGA
*
36757 T-AAAT-AAAAAACAGAAACTTGAGGGGA
1 TAAAATAAAAAAACAGAAACTTAAGGGGA
36784 TAAAATAAATAAAACAGAAACTTAA
1 TAAAATAAA-AAAACAGAAACTTAA
36809 AGAACTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
27 17 0.40
28 4 0.10
29 6 0.14
30 15 0.36
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (29 bp):
TAAAATAAAAAAACAGAAACTTAAGGGGA
Found at i:38486 original size:3 final size:3
Alignment explanation
Indices: 38473--38513 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
38463 TATATGTAAC
38473 ATA ATTA ATA ATA ATA ATA ATA A-A CATA ATA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA A
38514 ATTAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 30 0.86
4 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38503 original size:18 final size:18
Alignment explanation
Indices: 38480--38514 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
38470 AACATAATTA
38480 ATAATAATAATAATAAAC
1 ATAATAATAATAATAAAC
38498 ATAATAATAATAATAAA
1 ATAATAATAATAATAAA
38515 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAATAATAATAATAAAC
Found at i:38930 original size:135 final size:135
Alignment explanation
Indices: 38706--39066 Score: 543
Period size: 135 Copynumber: 2.7 Consensus size: 135
38696 GTTTGGGTCG
* * *
38706 TCTAAGGGTGACACAGA-TCCTACATGATGAGGATATCTGGTCAGGGGATGACACTG-CTCATAC
1 TCTAAGGGTGACACA-ACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACAC-GACTCATAC
**
38769 GTGATGAAGAGTTCTTGGTTATCTTTAGGAAGGGCGATAACTCGATTCCTACGCGATGAGGACGG
64 GTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACTCGATTCCTACGCGATGAGGACGG
38834 CTGGTTA
129 CTGGTTA
*
38841 TCTAAGGGTGACACAACTCCTACGTGATGAGGAGATTTGGTCGGGGGATGACACGACTCATACGT
1 TCTAAGGGTGACACAACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGT
*
38906 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAGGACGGCT
66 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACTCGATTCCTACGCGATGAGGACGGCT
38971 GGTTA
131 GGTTA
* ** * *
38976 TCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGGATGACAC-AGCTCATACG
1 TCTAAGGGTGACACAACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGA-CTCATACG
39040 TGATGAAGAGTTC--GAGCCATCTTTAGG
65 TGATGAAGAGTTCTTG-GCCATCTTTAGG
39067 GATAATGATT
Statistics
Matches: 209, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
133 1 0.00
134 15 0.07
135 193 0.92
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (135 bp):
TCTAAGGGTGACACAACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGT
GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACTCGATTCCTACGCGATGAGGACGGCT
GGTTA
Found at i:39185 original size:29 final size:29
Alignment explanation
Indices: 39079--39175 Score: 149
Period size: 29 Copynumber: 3.3 Consensus size: 29
39069 TAATGATTTC
*
39079 AAAAGAAACCGACTCAAAGATGATGTTTT
1 AAAAGAAACAGACTCAAAGATGATGTTTT
*
39108 AAAAGAAACAGACTCAAAGATGATGTTTC
1 AAAAGAAACAGACTCAAAGATGATGTTTT
*
39137 AAAAGAAACAGACTCAAAGATGATTTTGTT
1 AAAAGAAACAGACTCAAAGATGATGTT-TT
*
39167 AAGAGAAAC
1 AAAAGAAAC
39176 TGTCTCAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 53 0.85
30 9 0.15
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (29 bp):
AAAAGAAACAGACTCAAAGATGATGTTTT
Found at i:39252 original size:32 final size:31
Alignment explanation
Indices: 39213--39285 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
39203 CAAAGGAAAT
* * * *
39213 GACTCAAAGATTGTTTTGTTTTAATAGAAACA
1 GACTCAAAGA-TCTTTTGCTTCAAGAGAAACA
39245 GACTCAAAGA-CTTTTGCTTCAAGAGAAACA
1 GACTCAAAGATCTTTTGCTTCAAGAGAAACA
*
39275 AACTCAAAGAT
1 GACTCAAAGAT
39286 ATTGTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 25 0.71
32 10 0.29
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (31 bp):
GACTCAAAGATCTTTTGCTTCAAGAGAAACA
Found at i:39304 original size:29 final size:30
Alignment explanation
Indices: 39228--39305 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
39218 AAAGATTGTT
* * *
39228 TTGTTTTAATAGAAACAGACTCAAAGACTT
1 TTGTTTTAAGAGAAACAAACTCAAAGACTA
* *
39258 TTGCTTCAAGAGAAACAAACTCAAAGA-TA
1 TTGTTTTAAGAGAAACAAACTCAAAGACTA
*
39287 TTGTTTTAAGAGAGACAAA
1 TTGTTTTAAGAGAAACAAA
39306 ATTTTGTTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (30 bp):
TTGTTTTAAGAGAAACAAACTCAAAGACTA
Found at i:39401 original size:21 final size:19
Alignment explanation
Indices: 39350--39402 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
39340 TTATGTCTCA
39350 AGTGAGACAAAATTTGTTTT
1 AGTGAGACAAAA-TTGTTTT
*
39370 A-AGAGA-AAAATTGTATCTT
1 AGTGAGACAAAATTGT-T-TT
39389 AGTGAGACAAAATT
1 AGTGAGACAAAATT
39403 TTGTTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 7 0.26
20 5 0.19
21 6 0.22
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (19 bp):
AGTGAGACAAAATTGTTTT
Found at i:39600 original size:31 final size:30
Alignment explanation
Indices: 39536--39610 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
39526 ACGAAATCTG
* *
39536 TTTCAAGGGAAACGACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAACTCAAAGAT-GTTTTA
39567 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAAC-AACTCAAAGATGTTT-TA
*
39598 TTTCTAGAGAAAC
1 TTTCAAGAGAAAC
39611 TGCTTCAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.67
32 10 0.26
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATGTTTTA
Found at i:39737 original size:64 final size:66
Alignment explanation
Indices: 39562--39807 Score: 193
Period size: 65 Copynumber: 3.7 Consensus size: 66
39552 TCAAAGATGG
* * * * *
39562 TTTTATTTCAAGAGAAACAAACTCAAAGAT-TTTGTATTTCTAGAGAAACTG-CTTCAAGGGAGA
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATCTTTG--TTTCAAAAGAAATTGTCTTCAA--GAGA
*
39625 TAAAA
62 CAAAA
* * * * * * *
39630 TTTAT-TTT-AATAGAAACGATCTCAAAGGTGGGTAT-TTTCAAAAGAAATTGTC-TCGAGAGAC
1 TTT-TGTTTCAAAAGAAACAAACTCAAAGAT--CTTTGTTTCAAAAGAAATTGTCTTCAAGAGAC
39691 AAAA
63 AAAA
* * * *
39695 TTTTGTTTCAAAGGAAATAAACTCAAAGAT-TTT-TTCTCAAAAGAAATTGTCTTTAAGAGATAA
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATCTTTGTT-TCAAAAGAAATTGTCTTCAAGAGACAA
39758 AA
65 AA
*
39760 TTTTGTTTCAAAAGAAACAGACTCAAAGATCCTTTGTTTCAAAAGAAA
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT-CTTTGTTTCAAAAGAAA
39808 CGACTCAAAG
Statistics
Matches: 143, Mismatches: 23, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
63 4 0.03
64 16 0.11
65 51 0.36
66 15 0.10
67 45 0.31
68 9 0.06
69 1 0.01
70 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (66 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGATCTTTGTTTCAAAAGAAATTGTCTTCAAGAGACAAA
A
Found at i:39815 original size:30 final size:31
Alignment explanation
Indices: 39761--39819 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
39751 GAGATAAAAT
39761 TTTGTTTCAAAAGAAACAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAACAGACTCAAAGATCC
39792 TTTGTTTCAAAAGAAAC-GACTCAAAGAT
1 TTTGTTTCAAAAGAAACAGACTCAAAGAT
39820 GATGGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGATCC
Found at i:40964 original size:24 final size:24
Alignment explanation
Indices: 40928--40992 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
40918 CTTGTATTTT
*
40928 CAAAAG-TATGAAAATATCAATTAA
1 CAAAAGTTTTGAAAATAT-AATTAA
* *
40952 -AAGAGTTTTGAAAA-ATATTTAA
1 CAAAAGTTTTGAAAATATAATTAA
40974 TCAAAAGTTTTGAAAATAT
1 -CAAAAGTTTTGAAAATAT
40993 TGCCCCTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 5 0.15
23 6 0.18
24 20 0.61
25 2 0.06
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.32
Consensus pattern (24 bp):
CAAAAGTTTTGAAAATATAATTAA
Found at i:41899 original size:16 final size:16
Alignment explanation
Indices: 41850--41904 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
41840 ATTTGTCATC
*
41850 TTTTTGTTCTTTGCTCT
1 TTTTTTTTCTTTGCT-T
41867 TTTCTTTGTT-TTTGCTT
1 TTT-TTT-TTCTTTGCTT
41884 TTTTTTTTCTTTGCTT
1 TTTTTTTTCTTTGCTT
41900 ATTTT
1 -TTTT
41905 CTCTTCGCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 2 0.06
16 10 0.30
17 11 0.33
18 8 0.24
19 2 0.06
ACGTcount: A:0.02, C:0.13, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTTTTTCTTTGCTT
Found at i:41904 original size:18 final size:17
Alignment explanation
Indices: 41850--41904 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
41840 ATTTGTCATC
41850 TTTTTGTTCTTTGCTCTT
1 TTTTTGTTCTTTGCT-TT
41868 TTCTTTGTT-TTTGCTTT
1 TT-TTTGTTCTTTGCTTT
*
41885 TTTTT-TTCTTTGCTTA
1 TTTTTGTTCTTTGCTTT
41901 TTTT
1 TTTT
41905 CTCTTCGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 2 0.06
16 14 0.41
17 4 0.12
18 8 0.24
19 6 0.18
ACGTcount: A:0.02, C:0.13, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTTTGTTCTTTGCTTT
Found at i:42565 original size:28 final size:26
Alignment explanation
Indices: 42534--42588 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
42524 GGAAAAAATG
*
42534 TTTCAAAGTCTCAAGGATAAATGCAATA
1 TTTCAAAGTCTCAAAGA-AAATG-AATA
*
42562 TTTCAAGGTCTCAAAGAAAATGAATA
1 TTTCAAAGTCTCAAAGAAAATGAATA
42588 T
1 T
42589 CACAATTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 5 0.20
28 15 0.60
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (26 bp):
TTTCAAAGTCTCAAAGAAAATGAATA
Found at i:45896 original size:30 final size:30
Alignment explanation
Indices: 45862--45928 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
45852 TACAAATAGG
* *
45862 AATTTAAAGGGCTAAAATGGCCAAAACATA
1 AATTTAAAGGGCTAAAATAGCAAAAACATA
* *
45892 AATTTAAATGGCTAAAATAGTAAAAACATA
1 AATTTAAAGGGCTAAAATAGCAAAAACATA
45922 AATTTAA
1 AATTTAA
45929 GAGTCTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (30 bp):
AATTTAAAGGGCTAAAATAGCAAAAACATA
Found at i:45939 original size:29 final size:28
Alignment explanation
Indices: 45884--45969 Score: 77
Period size: 30 Copynumber: 3.0 Consensus size: 28
45874 TAAAATGGCC
45884 AAAACATAAATTTAAATGGCTAAAATAGTA
1 AAAACATAAATTTAAATGGCTAAAATA--A
*
45914 AAAACATAAATTTAAGA-GTCT-AAATAA
1 AAAACATAAATTTAA-ATGGCTAAAATAA
* * * **
45941 AAAACAGAAACTTGAGGGGCTAAAATAA
1 AAAACATAAATTTAAATGGCTAAAATAA
45969 A
1 A
45970 TAAAACAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
27 16 0.34
28 7 0.15
29 5 0.11
30 18 0.38
31 1 0.02
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.22
Consensus pattern (28 bp):
AAAACATAAATTTAAATGGCTAAAATAA
Found at i:47660 original size:18 final size:18
Alignment explanation
Indices: 47639--47673 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47629 AACATAATTA
47639 ATAATAATAACAATAAAC
1 ATAATAATAACAATAAAC
*
47657 ATAATAATAATAATAAA
1 ATAATAATAACAATAAA
47674 TTAAAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAATAATAACAATAAAC
Found at i:50093 original size:28 final size:28
Alignment explanation
Indices: 50045--50116 Score: 135
Period size: 28 Copynumber: 2.5 Consensus size: 28
50035 AAGTAATATC
50045 TAATAATCAAAAAATTATTTTATAATTTT
1 TAATAAT-AAAAAATTATTTTATAATTTT
50074 TAATAATAAAAAATTATTTTATAATTTT
1 TAATAATAAAAAATTATTTTATAATTTT
50102 TAATAATAAAAAATT
1 TAATAATAAAAAATT
50117 TAAGAAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 36 0.84
29 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATAATAAAAAATTATTTTATAATTTT
Found at i:54778 original size:11 final size:11
Alignment explanation
Indices: 54759--54792 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
54749 TTTCAGGTTC
*
54759 TTTTTATTTAA
1 TTTTAATTTAA
54770 TTTTAATTTTAA
1 TTTTAA-TTTAA
54782 TTTTAATTTAA
1 TTTTAATTTAA
54793 ATCTTTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:54791 original size:5 final size:6
Alignment explanation
Indices: 54765--54790 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54755 GTTCTTTTTA
54765 TTTAAT TTTAAT TTTAAT TTTAAT TT
1 TTTAAT TTTAAT TTTAAT TTTAAT TT
54791 AAATCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:54836 original size:10 final size:10
Alignment explanation
Indices: 54823--54877 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
54813 ATTTTTTTTT
54823 AAAAAAACAC
1 AAAAAAACAC
*
54833 AAAAAAAAAAC
1 -AAAAAAACAC
**
54844 AAAAAAAGGC
1 AAAAAAACAC
54854 AAAAAAACA-
1 AAAAAAACAC
*
54863 AAAAAAGC-C
1 AAAAAAACAC
54872 AAAAAA
1 AAAAAA
54878 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
9 13 0.35
10 15 0.41
11 9 0.24
ACGTcount: A:0.82, C:0.13, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAACAC
Found at i:54875 original size:9 final size:9
Alignment explanation
Indices: 54845--54884 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
54835 AAAAAAAACA
*
54845 AAAAAAGGC
1 AAAAAAGCC
* *
54854 AAAAAAACA
1 AAAAAAGCC
54863 AAAAAAGCC
1 AAAAAAGCC
54872 AAAAAAGCC
1 AAAAAAGCC
54881 AAAA
1 AAAA
54885 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.75, C:0.15, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAGCC
Found at i:54884 original size:18 final size:18
Alignment explanation
Indices: 54836--54877 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
54826 AAAACACAAA
*
54836 AAAAAAACAAAAAAAGGC
1 AAAAAAACAAAAAAAGCC
54854 AAAAAAACAAAAAAAGCC
1 AAAAAAACAAAAAAAGCC
54872 AAAAAA
1 AAAAAA
54878 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAGCC
Found at i:59745 original size:21 final size:20
Alignment explanation
Indices: 59721--59762 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
59711 GTCATGCAAC
*
59721 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
59742 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
59762 T
1 T
59763 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:68998 original size:21 final size:21
Alignment explanation
Indices: 68974--69017 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
68964 TTTTGTTCGT
* *
68974 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
68995 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
69016 TT
1 TT
69018 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:72304 original size:20 final size:20
Alignment explanation
Indices: 72279--72317 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
72269 CAAGTGGAAG
72279 ATTATTAGTTGTCATGCAAA
1 ATTATTAGTTGTCATGCAAA
72299 ATTATTAGTTGTCATGCAA
1 ATTATTAGTTGTCATGCAA
72318 CTAATAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTATTAGTTGTCATGCAAA
Found at i:72343 original size:21 final size:20
Alignment explanation
Indices: 72319--72360 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
72309 GTCATGCAAC
*
72319 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
72340 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
72360 T
1 T
72361 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:80384 original size:31 final size:32
Alignment explanation
Indices: 80321--80384 Score: 76
Period size: 36 Copynumber: 1.9 Consensus size: 32
80311 TTTGACTATT
80321 TTATAAAATATTATTTTGTTGAGTTTTCTCTTTAAA
1 TTATAAAATATTATTTTGTTGAG---T-TCTTTAAA
*
80357 TTATAAAGTATTATTTTGTTGAG-TCTTT
1 TTATAAAATATTATTTTGTTGAGTTCTTT
80385 TAACTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 5 0.19
36 22 0.81
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (32 bp):
TTATAAAATATTATTTTGTTGAGTTCTTTAAA
Found at i:80635 original size:93 final size:93
Alignment explanation
Indices: 80528--80709 Score: 310
Period size: 93 Copynumber: 2.0 Consensus size: 93
80518 TCAAAGCTCA
* * *
80528 ATAAATACTCTACTTAAAAGGACTCGACTCGAGTTTTTAATGAGTCAAAACGAGTTACTTGATAA
1 ATAAATACTCTACTTAAAAAGACTCGACTCGAGTTTTTAATGAGCCAAAACGAGTTACTTAATAA
*
80593 TCTACTTGAAAAGCTAACGAGCAATAAT
66 TCTACTCGAAAAGCTAACGAGCAATAAT
*
80621 ATAAATACTCTACTTAAAAAGACTCGACTCGAGTTTTTAATGAGCCAAAACGAGTTACTTAATAC
1 ATAAATACTCTACTTAAAAAGACTCGACTCGAGTTTTTAATGAGCCAAAACGAGTTACTTAATAA
*
80686 TCTACTCGAAAAGCTCACGAGCAA
66 TCTACTCGAAAAGCTAACGAGCAA
80710 CTTAAAAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (93 bp):
ATAAATACTCTACTTAAAAAGACTCGACTCGAGTTTTTAATGAGCCAAAACGAGTTACTTAATAA
TCTACTCGAAAAGCTAACGAGCAATAAT
Found at i:84084 original size:14 final size:14
Alignment explanation
Indices: 84065--84100 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
84055 AAATTAATGG
84065 GATTTGATGATTTA
1 GATTTGATGATTTA
84079 GATTTGATGATTTA
1 GATTTGATGATTTA
84093 GATTTGAT
1 GATTTGAT
84101 AAAGGCTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (14 bp):
GATTTGATGATTTA
Found at i:86588 original size:12 final size:12
Alignment explanation
Indices: 86571--86597 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
86561 TAAGAGATAA
86571 CCTTTACAACTC
1 CCTTTACAACTC
86583 CCTTTACAACTC
1 CCTTTACAACTC
86595 CCT
1 CCT
86598 AGCTTTTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.44, G:0.00, T:0.33
Consensus pattern (12 bp):
CCTTTACAACTC
Found at i:87754 original size:29 final size:30
Alignment explanation
Indices: 87712--87774 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
87702 TATACAATAC
* *
87712 AAAAATTATATTAACATAACAAT-AATCGT
1 AAAAATAATATTAACATAACAATCAATAGT
*
87741 AAAAATAATATTAACATAATAATCAATAGT
1 AAAAATAATATTAACATAACAATCAATAGT
87771 AAAA
1 AAAA
87775 TATCTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAAATAATATTAACATAACAATCAATAGT
Found at i:91382 original size:19 final size:19
Alignment explanation
Indices: 91348--91392 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
91338 ATTTAGACAT
91348 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
91366 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
91385 TTTGCATT
1 TTTGCATT
91393 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:94838 original size:81 final size:82
Alignment explanation
Indices: 94639--95182 Score: 587
Period size: 81 Copynumber: 6.6 Consensus size: 82
94629 TAAACAAACT
* ** *
94639 ATTTACAGCATAACTCAAGGCTAGAAGGGATATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTG--ACCAAAAGACCCCCGAGTTCGACTACA
94704 CTCAGCTCCAAGGCACATC
64 CTCAGCTCCAAGGCACATC
* * * * * * *
94723 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CC-GAAGACCCCCGAGTTCGATTACACT
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGACCAAAAGACCCCCGAGTTCGACTACACT
* *
94786 CAGCTTCGAGGGCACATC
66 CAGC-TCCAAGGCACATC
* * ** *
94804 ATTTACAGCATAACTCAAGGCTAGGAGGGTTATCTGTGACCAAAAGACCGTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATC--TGACCAAAAGACCCCCGAGTTCGACTACA
94869 CTCAGCTCCAAGGCACATC
64 CTCAGCTCCAAGGCACATC
* * * * * * *
94888 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CC-AAGGACCCCCGAGTTCGATTACACT
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGACCAAAAGACCCCCGAGTTCGACTACACT
* *
94951 CAGCTTCGAGGGCACATC
66 CAGC-TCCAAGGCACATC
* ** *
94969 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTG--ACCAAAAGACCCCCGAGTTCGACTACA
95034 CTCAGCTCCAAGGCACATC
64 CTCAGCTCCAAGGCACATC
* * * * * *
95053 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CC-AAAGACCCCCGAGTTCGATTACACT
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGACCAAAAGACCCCCGAGTTCGACTACACT
* *
95116 CAGCTTCGAGGGCACATC
66 CAGC-TCCAAGGCACATC
*
95134 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGCTATC--TGACCAAAAGACC
95183 TTCGAGTGAA
Statistics
Matches: 373, Mismatches: 72, Indels: 29
0.79 0.15 0.06
Matches are distributed among these distances:
80 73 0.20
81 124 0.33
82 2 0.01
83 4 0.01
84 115 0.31
85 55 0.15
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (82 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGACCAAAAGACCCCCGAGTTCGACTACACT
CAGCTCCAAGGCACATC
Found at i:94911 original size:165 final size:164
Alignment explanation
Indices: 94639--95189 Score: 1030
Period size: 165 Copynumber: 3.3 Consensus size: 164
94629 TAAACAAACT
*
94639 ATTTACAGCATAACTCAAGGCTAGAAGGGATATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
94704 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCGAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAGACCC
94769 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * *
94804 ATTTACAGCATAACTCAAGGCTAGGAGGGTTATCTGTGACCAAAAGACCGTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
94869 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA-GACCC
94934 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
94969 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
95034 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAGACCC
95099 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
*
95134 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGT
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGT
95190 GAAGGGTTAT
Statistics
Matches: 376, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
164 2 0.01
165 372 0.99
166 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (164 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGACCCC
CGAGTTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:95199 original size:33 final size:33
Alignment explanation
Indices: 95157--95222 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
95147 CTCAAGGCTA
95157 GAAGGGTTATCTGTGACCAAAAGACCTTCGAGT
1 GAAGGGTTATCTGTGACCAAAAGACCTTCGAGT
95190 GAAGGGTTATCTGTGACCAAAAGACCTTCGAGT
1 GAAGGGTTATCTGTGACCAAAAGACCTTCGAGT
95223 TCGACTCCGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (33 bp):
GAAGGGTTATCTGTGACCAAAAGACCTTCGAGT
Found at i:101822 original size:128 final size:128
Alignment explanation
Indices: 101590--102201 Score: 1064
Period size: 128 Copynumber: 4.8 Consensus size: 128
101580 GTCTTCTCTG
* * * *
101590 GCGTTCCCAGGGGCGCGACTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTC
1 GCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTC
* ***
101655 ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-TTCACATGAAGGC
66 ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACATGAAGGC
** *
101718 GCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTC
1 GCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTC
* *
101783 ACTCATGTCCCTCGGCGACACTAGATATATCAGTGCCTATTATTTCTCAGGGGACATGAAGGC
66 ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACATGAAGGC
*
101846 GCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTC
1 GCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTC
101911 ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACATGAAGGC
66 ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACATGAAGGC
*
101974 GCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCTTATTATGTC
1 GCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTC
102039 ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACATGAAGGC
66 ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACATGAAGGC
*
102102 GCGTTCCCGGGGGCGCGCCTTCCATTATTTTTTCATAGAATATGTTATCATTGCCCTATTATGTC
1 GCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTC
102167 ACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 ACTCATGTCCCTCGGGGACACTAGATATATCAGTA
102202 AATCAGGTAA
Statistics
Matches: 464, Mismatches: 19, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
127 1 0.00
128 463 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (128 bp):
GCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTC
ACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACATGAAGGC
Found at i:102663 original size:33 final size:34
Alignment explanation
Indices: 102602--102701 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
102592 AAATTTAATG
* *
102602 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTTTATTTTAAAT
* * *
102636 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTTTATTTTAAAT
102669 TTAAATTTCGAATAATATAATTTTTATTTTAAA
1 TTAAATTTCGAATAATATAATTTTTATTTTAAA
102702 AACATTTATC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 28 0.49
34 29 0.51
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTTTATTTTAAAT
Found at i:103251 original size:21 final size:21
Alignment explanation
Indices: 103221--103314 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
103211 TATGGTATAA
*
103221 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
103242 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
**
103263 AACCCTGCGGGCTCCGAATGT
1 AACCCTGCGGGCTAGGAATGT
* *
103284 AACCCTGCGGGCTCGAAATGT
1 AACCCTGCGGGCTAGGAATGT
*
103305 AACCTTGCGG
1 AACCCTGCGG
103315 AGATGGCATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.05
21 59 0.91
22 3 0.05
ACGTcount: A:0.21, C:0.28, G:0.32, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:103344 original size:21 final size:21
Alignment explanation
Indices: 103318--103365 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
103308 CTTGCGGAGA
*
103318 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
103339 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
103360 GGGCAT
1 TGGCAT
103366 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:105141 original size:18 final size:16
Alignment explanation
Indices: 105094--105151 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
105084 TTCTAAATAA
*
105094 ATAATAATTATATAAAT
1 ATAATATTTA-ATAAAT
*
105111 ATTAT-TTTAATAAAAT
1 ATAATATTTAAT-AAAT
105127 ATAATATTTACATAAAT
1 ATAATATTTA-ATAAAT
105144 ATTAATAT
1 A-TAATAT
105152 AAAAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 2 0.06
16 11 0.32
17 13 0.38
18 8 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATATTTAATAAAT
Found at i:106800 original size:42 final size:42
Alignment explanation
Indices: 106752--106846 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
106742 CATATTCACA
**
106752 TTGCGATAGTAC-AAGTTCGCGTTACGATTTATTCCAAGTTCG
1 TTGCGATAGT-CGAAGTTCGCGTTACGATTTATAACAAGTTCG
** *
106794 TTGCGATAGTCGAAGTTCGCGTTGTGATTTATAATAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTACGATTTATAACAAGTTCG
106836 TTGCGATAGTC
1 TTGCGATAGTC
106847 CAAAATCGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTACGATTTATAACAAGTTCG
Found at i:106816 original size:21 final size:20
Alignment explanation
Indices: 106752--106817 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 20
106742 CATATTCACA
106752 TTGCGATAGTACAAGTTCGCG
1 TTGCGATAGT-CAAGTTCGCG
* *
106773 TTACGATTTATTCCAAGTT--CG
1 TTGCGA--TAGT-CAAGTTCGCG
106794 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTC-AAGTTCGCG
106815 TTG
1 TTG
106818 TGATTTATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
18 1 0.03
19 8 0.23
21 17 0.49
23 9 0.26
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAGTTCGCG
Found at i:107292 original size:61 final size:61
Alignment explanation
Indices: 107226--107347 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
107216 ATTAAATGTC
107226 AATCTACAATCAATCGCGATTATTGCAATTTTAAGCAAAACATTCAAAAATAATATCACTA
1 AATCTACAATCAATCGCGATTATTGCAATTTTAAGCAAAACATTCAAAAATAATATCACTA
107287 AATCTACAATCAATCGCGATTATTGCAATTTTAAGCAAAACATTCAAAAATAATATCACTA
1 AATCTACAATCAATCGCGATTATTGCAATTTTAAGCAAAACATTCAAAAATAATATCACTA
107348 TTTAAGGCTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.30
Consensus pattern (61 bp):
AATCTACAATCAATCGCGATTATTGCAATTTTAAGCAAAACATTCAAAAATAATATCACTA
Found at i:120344 original size:31 final size:31
Alignment explanation
Indices: 120316--120377 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
120306 GATTTTAAAG
120316 ATTAAAAATAAAGAAATAGCAAGGTTTAATA
1 ATTAAAAATAAAGAAATAGCAAGGTTTAATA
120347 ATTAAAAATAAAGAAATAGCAAGGTTTAATA
1 ATTAAAAATAAAGAAATAGCAAGGTTTAATA
120378 CATAATTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (31 bp):
ATTAAAAATAAAGAAATAGCAAGGTTTAATA
Done.