Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006424.1 Hibiscus syriacus cultivar Beakdansim tig00015499_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: 98300
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1825 original size:19 final size:19
Alignment explanation
Indices: 1803--1844 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1793 CGGCTAGTAT
1803 AAAAAAAAAAAAATAAATG
1 AAAAAAAAAAAAATAAATG
*
1822 AAAAAAAAAATAATAAATG
1 AAAAAAAAAAAAATAAATG
1841 AAAA
1 AAAA
1845 CAAGTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAAAAAAAAAAATAAATG
Found at i:1844 original size:16 final size:17
Alignment explanation
Indices: 1805--1844 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 17
1795 GCTAGTATAA
1805 AAAAAAAAAAATAAATG
1 AAAAAAAAAAATAAATG
1822 AAAAAAAAAATAATAAATG
1 -AAAAAAAAA-AATAAATG
1841 AAAA
1 AAAA
1845 CAAGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAAAAAAAATAAATG
Found at i:2015 original size:33 final size:33
Alignment explanation
Indices: 1939--2015 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 33
1929 TCGGATTAGG
* *
1939 AAAAGAAAAGAAAATAAAATAAAAAACATGAATT
1 AAAAGAAAA-AAAATAAAAGAAAAAACATAAATT
*
1973 AAATA-AAAAAATAATAAAAGAAAATAC-TAAATT
1 AAA-AGAAAAAA-AATAAAAGAAAAAACATAAATT
2006 AAAAGAAAAA
1 AAAAGAAAAA
2016 TAAAACAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
32 1 0.03
33 15 0.41
34 20 0.54
35 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (33 bp):
AAAAGAAAAAAAATAAAAGAAAAAACATAAATT
Found at i:3686 original size:21 final size:21
Alignment explanation
Indices: 3662--3707 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
3652 AATTAAAATT
3662 AGGAAATTAAAATAGAAAAAA
1 AGGAAATTAAAATAGAAAAAA
3683 AGGAAATTAAAATAGAAAAAA
1 AGGAAATTAAAATAGAAAAAA
3704 AGGA
1 AGGA
3708 CCCTACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (21 bp):
AGGAAATTAAAATAGAAAAAA
Found at i:18947 original size:14 final size:14
Alignment explanation
Indices: 18928--18971 Score: 88
Period size: 14 Copynumber: 3.1 Consensus size: 14
18918 TGCCTAACGA
18928 TCCTACATCCCTTT
1 TCCTACATCCCTTT
18942 TCCTACATCCCTTT
1 TCCTACATCCCTTT
18956 TCCTACATCCCTTT
1 TCCTACATCCCTTT
18970 TC
1 TC
18972 AGCTCCTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (14 bp):
TCCTACATCCCTTT
Found at i:28360 original size:28 final size:28
Alignment explanation
Indices: 28270--28360 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 28
28260 TTTGGTGATG
28270 AAATTGGAATATTCAAAAGTTTAAGGAC
1 AAATTGGAATATTCAAAAGTTTAAGGAC
* * * * * * *
28298 TAATTTAGAATGAGTCATAGGTTT-GGGATG
1 -AAATTGGAAT-ATTCAAAAGTTTAAGGA-C
28328 AAATTGGAATATTCAAAAGTTTAAGGAC
1 AAATTGGAATATTCAAAAGTTTAAGGAC
*
28356 CAATT
1 AAATT
28361 TAAAATAAGA
Statistics
Matches: 44, Mismatches: 15, Indels: 7
0.67 0.23 0.11
Matches are distributed among these distances:
28 13 0.30
29 22 0.50
30 9 0.20
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (28 bp):
AAATTGGAATATTCAAAAGTTTAAGGAC
Found at i:30478 original size:2 final size:2
Alignment explanation
Indices: 30471--30523 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
30461 CAATATAAAT
30471 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30513 TA TA TA TA TA T
1 TA TA TA TA TA T
30524 CCATAATTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35170 original size:21 final size:21
Alignment explanation
Indices: 35146--35187 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35136 ATTGCAATTT
*
35146 TCCAAATTCGCAATGCGATAG
1 TCCAAAATCGCAATGCGATAG
*
35167 TCCAAAATCGCATTGCGATAG
1 TCCAAAATCGCAATGCGATAG
35188 CACTGTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
TCCAAAATCGCAATGCGATAG
Found at i:35203 original size:21 final size:21
Alignment explanation
Indices: 35179--35271 Score: 168
Period size: 21 Copynumber: 4.4 Consensus size: 21
35169 CAAAATCGCA
35179 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
35200 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
35221 TTGTGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
35242 TTGCGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
35263 TTGCGATAG
1 TTGCGATAG
35272 TGATCAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:35976 original size:21 final size:21
Alignment explanation
Indices: 35950--35989 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
35940 AATTCGCAAT
35950 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
35971 GTGAACAGTGCTATCGCAA
1 GTGAACAGTGCTATCGCAA
35990 TGCGATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:36005 original size:21 final size:21
Alignment explanation
Indices: 35981--36033 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
35971 GTGAACAGTG
* *
35981 CTATCGCAATGCGATTTTGGA
1 CTATCGCAATGCGAATTCGGA
*
36002 CTATCGCATTGCGAATTCGGA
1 CTATCGCAATGCGAATTCGGA
**
36023 AAATCGCAATG
1 CTATCGCAATG
36034 AGATAGTCAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
CTATCGCAATGCGAATTCGGA
Found at i:41166 original size:25 final size:25
Alignment explanation
Indices: 41119--41171 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
41109 ATAGCACTAG
* *
41119 CTCTTCCTAGATGTTAGGCCACTCC
1 CTCTTCCTAGATGCTACGCCACTCC
*
41144 CTCTTCCTAGATGCTACGTCACTCC
1 CTCTTCCTAGATGCTACGCCACTCC
41169 CTC
1 CTC
41172 GAGCTTCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.15, C:0.40, G:0.13, T:0.32
Consensus pattern (25 bp):
CTCTTCCTAGATGCTACGCCACTCC
Found at i:44577 original size:22 final size:23
Alignment explanation
Indices: 44544--44604 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
44534 TTAATTTATA
44544 AAACATTAAATTATAAAGTA-CT
1 AAACATTAAATTATAAAGTAGCT
*
44566 AAACA-TATAATTATAAATTAGCT
1 AAACATTA-AATTATAAAGTAGCT
*
44589 AAAAATCTAAA-TATAA
1 AAACAT-TAAATTATAA
44605 TTTAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 2 0.06
22 16 0.48
23 11 0.33
24 2 0.06
25 2 0.06
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.31
Consensus pattern (23 bp):
AAACATTAAATTATAAAGTAGCT
Found at i:48021 original size:51 final size:53
Alignment explanation
Indices: 47945--48050 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 53
47935 TTCGGGACCA
*
47945 AAAGTATAAATTGATTGGGTTTGGA-TTTCTAAAAAAAATTC-ATCCGATCCG
1 AAAGTATAAATTGATTGGGTTTGGAGTTTCTAAAAAAAATCCGATCCGATCCG
*
47996 AAAGTATAAATT-TTTGCGGTTTGGATGTTTCTAAAAAAAATCCGATCCGATCCG
1 AAAGTATAAATTGATTG-GGTTTGGA-GTTTCTAAAAAAAATCCGATCCGATCCG
48050 A
1 A
48051 TCCGATCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
50 3 0.06
51 20 0.41
53 15 0.31
54 11 0.22
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (53 bp):
AAAGTATAAATTGATTGGGTTTGGAGTTTCTAAAAAAAATCCGATCCGATCCG
Found at i:49862 original size:2 final size:2
Alignment explanation
Indices: 49855--49894 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
49845 TAATATGATC
49855 AT AT 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 AT AT
49895 TCCATCAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50071 original size:19 final size:20
Alignment explanation
Indices: 50028--50072 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
50018 AACATATCAA
50028 TAAAAATACAATAAAAAATC
1 TAAAAATACAATAAAAAATC
*
50048 T-AAAATA-TATATAAAAAT-
1 TAAAAATACAATA-AAAAATC
50066 TAAAAAT
1 TAAAAAT
50073 TTTAGGATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 4 0.18
19 17 0.77
20 1 0.05
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAAAATACAATAAAAAATC
Found at i:54910 original size:20 final size:20
Alignment explanation
Indices: 54864--54921 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
54854 GAATGTCCAG
* *
54864 GGGGTACAGATTCCCCACCAT
1 GGGGTACCGATTCCCC-CCAA
54885 GGGGTACCGATTCCCCCCAA
1 GGGGTACCGATTCCCCCCAA
54905 GGGGTACCGATTCCCCC
1 GGGGTACCGATTCCCCC
54922 TGTCTAACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.19, C:0.38, G:0.26, T:0.17
Consensus pattern (20 bp):
GGGGTACCGATTCCCCCCAA
Found at i:56222 original size:19 final size:20
Alignment explanation
Indices: 56198--56245 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
56188 AACGATTTTC
*
56198 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
56217 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
56237 TTTTGAAAA
1 TTTTGAAAA
56246 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:57649 original size:20 final size:21
Alignment explanation
Indices: 57613--57691 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
57603 GAATGTCCAT
57613 GGGGTACAGATTCCCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
*
57634 GGGGTACCGATT-CCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
* *
57654 GGAGAACAGATTCCCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
* *
57675 GGGGTACCGATTTCCCC
1 GGGGTACAGATTCCCCC
57692 ATGTAATGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.35
21 32 0.65
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.15
Consensus pattern (21 bp):
GGGGTACAGATTCCCCCCCAG
Found at i:57669 original size:19 final size:20
Alignment explanation
Indices: 57618--57676 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
57608 TCCATGGGGT
* *
57618 ACAGATTCCCCCCCAGGGGGT
1 ACAGATT-CCCCCCAGGGAGA
*
57639 ACCGATTCCCCCCAGGGAGA
1 ACAGATTCCCCCCAGGGAGA
57659 ACAGATTCCCCCCCAGGG
1 ACAGATT-CCCCCCAGGG
57677 GGTACCGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.22, C:0.41, G:0.25, T:0.12
Consensus pattern (20 bp):
ACAGATTCCCCCCAGGGAGA
Found at i:61810 original size:22 final size:21
Alignment explanation
Indices: 61782--61841 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
61772 ATTACCTATA
*
61782 TCCTTCGGGACATATGGAT-AGG
1 TCCTTCGGGACATA--GATGACG
61804 TCCTTCGGGACATAGATGACG
1 TCCTTCGGGACATAGATGACG
*
61825 TCTTTCGGGACATAGAT
1 TCCTTCGGGACATAGAT
61842 TTCATATGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 3 0.09
21 18 0.51
22 14 0.40
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (21 bp):
TCCTTCGGGACATAGATGACG
Found at i:62687 original size:22 final size:22
Alignment explanation
Indices: 62659--62713 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
62649 TTAGGAGTTA
*
62659 CAGGAGTTATATGATTTAATTT
1 CAGGAGTTATATGATATAATTT
* *
62681 CATGAGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTT
62703 CAGGAGTTATA
1 CAGGAGTTATA
62714 ACAACTGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTT
Found at i:65269 original size:19 final size:19
Alignment explanation
Indices: 65245--65317 Score: 146
Period size: 19 Copynumber: 3.8 Consensus size: 19
65235 ATAAAACCTA
65245 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
65264 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
65283 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
65302 AGTGCATCGATGCATA
1 AGTGCATCGATGCATA
65318 AATTGCATTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (19 bp):
AGTGCATCGATGCATAGAG
Found at i:65756 original size:25 final size:25
Alignment explanation
Indices: 65728--65777 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
65718 CCCCCTTACT
65728 ATAACATTTATCCCCCTTTAAAACA
1 ATAACATTTATCCCCCTTTAAAACA
*
65753 ATAACATTTCTCCCCCTTTAAAACA
1 ATAACATTTATCCCCCTTTAAAACA
65778 TTTTACACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.30, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAACATTTATCCCCCTTTAAAACA
Found at i:65793 original size:25 final size:25
Alignment explanation
Indices: 65728--65797 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
65718 CCCCCTTACT
* *
65728 ATAACATTTATCCCCCTTTAAAACA
1 ATAACACTTCTCCCCCTTTAAAACA
*
65753 ATAACATTTCTCCCCCTTTAAAACA
1 ATAACACTTCTCCCCCTTTAAAACA
* *
65778 TTTTACACTTCTCCCCCTTT
1 -ATAACACTTCTCCCCCTTT
65798 TTGTTAAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 24 0.60
26 16 0.40
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAACACTTCTCCCCCTTTAAAACA
Found at i:66488 original size:21 final size:21
Alignment explanation
Indices: 66464--66507 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
66454 GAGTCGGAGG
* *
66464 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
66485 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
66506 AG
1 AG
66508 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:74044 original size:64 final size:64
Alignment explanation
Indices: 73929--74090 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
73919 CGGTGCACCA
* * *** * *
73929 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCTTGAGTGCATCGGTGCAT-T
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATACATAT
*
73992 -GCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAA-AACCCAAGTGCATCGATACAT
1 AG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-AATAACCCAAGTGCATCGATACAT
74055 AT
63 AT
* *
74057 AGAGTGTATCGATGCATGAAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
74091 CAATTTATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
64 79 0.94
65 3 0.04
66 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATACATAT
Found at i:75721 original size:22 final size:22
Alignment explanation
Indices: 75696--75750 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
75686 TCAGGAGTTA
*
75696 CAGGAGTTATATGATTTAATTT
1 CAGGAGTTATATGATATAATTT
*
75718 CAGGAGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTT
75740 CAGGAGTTATA
1 CAGGAGTTATA
75751 ACAGCTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTT
Found at i:76695 original size:43 final size:43
Alignment explanation
Indices: 76646--77096 Score: 497
Period size: 43 Copynumber: 10.5 Consensus size: 43
76636 AACCAAAAAT
* * *
76646 GCCGCAAAATGTTGAGATCTATAGCGGCATTTTTGGAACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* *
76689 GCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
76732 GCCGCAATAGG-TCACATATATAGCGGCGTTTTTTGGAACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCG-TTTTTGGAACAAAC
* * * **
76775 GCCGCAATATG-TCAAATAGATAGCGGCGTTTTTTGGAACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCG-TTTTTGGAACAAAC
* *
76818 GCCGCAAAAGG-TCAGATCTATAGCGGCATTTTT-TATACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
* *
76860 GCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* **
76903 GCCGCAATAGGTT-AGATAGATAGCGGCGTTTTTTGGAACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCG-TTTTTGGAACAAAC
* *
76946 GCCCCAAAAGG-TCAGATCTATAGCGGCGTTTTT-TATACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
* * *
76988 GCCGCAAAAGGTTGATATCTATAGTGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* ** *
77031 GCCGCAATAGGTT-AGATAGATAGCGGCGTTTTTTTAGAACAAAC
1 GCCGCAAAAGGTTCAGATCTATAGCGGCG--TTTTTGGAACAAAC
* *
77075 GTCGCAAAAGG-TCAGATATATA
1 GCCGCAAAAGGTTCAGATCTATA
77097 TAGCGACGTT
Statistics
Matches: 352, Mismatches: 44, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.01
42 81 0.23
43 237 0.67
44 32 0.09
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (43 bp):
GCCGCAAAAGGTTCAGATCTATAGCGGCGTTTTTGGAACAAAC
Found at i:76845 original size:171 final size:170
Alignment explanation
Indices: 76646--77110 Score: 614
Period size: 171 Copynumber: 2.7 Consensus size: 170
76636 AACCAAAAAT
*
76646 GCCGCAAAATGTTGAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTAT
1 GCCGCAAAA-GGTGAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTAT
76711 AGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCACATATATAGCGGCGTTTTTTGGAACAAACG
65 AGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCACATATATAGCGGCGTTTTTTGGAACAAACG
* * *
76776 CCGCAATATGTCAAATAGATAGCGGCGTTTTTTGGA-ACAAAC
130 CCCCAAAAGGTCAAATAGATAGCGGCGTTTTTT--ATACAAAC
* *
76818 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTT-TATACAAACGCCGCAAAAGGTTGATATCTAT
1 GCCGCAAAAGGTGAGATCTATAGCGGCATTTTTGGA-ACAAACGCCGCAAAAGGTTGATATCTAT
* * *
76882 AGCGGCGTTTTTGGAACAAACGCCGCAATAGGTTAGATAGATAGCGGCGTTTTTTGGAACAAACG
65 AGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCACATATATAGCGGCGTTTTTTGGAACAAACG
* **
76947 CCCCAAAAGGTCAGATCTATAGCGGCGTTTTTTATACAAAC
130 CCCCAAAAGGTCAAATAGATAGCGGCGTTTTTTATACAAAC
* * * * *
76988 GCCGCAAAAGGTTGATATCTATAGTGGCGTTTTTGGAACAAACGCCGCAATAGGTTAGATA--GA
1 GCCGCAAAAGG-TGAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTT-GATATCTA
* * * * *
77051 TAGCGGCGTTTTTTTAGAACAAACGTCGCAAAAGGTCAGATATATATAGCGACGTTTTTT
64 TAGCGGCG--TTTTTGGAACAAACGCCGCAATAGGTC--ACATATATAGCGGCGTTTTTT
77111 TATACAAACT
Statistics
Matches: 258, Mismatches: 26, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
169 1 0.00
170 27 0.10
171 175 0.68
172 37 0.14
174 18 0.07
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (170 bp):
GCCGCAAAAGGTGAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATA
GCGGCGTTTTTGGAACAAACGCCGCAATAGGTCACATATATAGCGGCGTTTTTTGGAACAAACGC
CCCAAAAGGTCAAATAGATAGCGGCGTTTTTTATACAAAC
Found at i:76898 original size:128 final size:128
Alignment explanation
Indices: 76666--77124 Score: 663
Period size: 128 Copynumber: 3.6 Consensus size: 128
76656 GTTGAGATCT
* * * *
76666 ATAGCGGC-ATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGA-ACA
1 ATAGCGGCGTTTTTTGGAACAAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTT-TATACA
* * * * * * *
76729 AACGCCGCAATAGG-TCACATATATAGCGGCGTTTTTTGGAACAAACGCCGCAATATGTCAAATA
64 AACGCCGCAAAAGGTTGATATCTATAGCGGCG-TTTTTGGAACAAACGCCGCAATAGGTTAGATA
76793 G
128 G
*
76794 ATAGCGGCGTTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTTATACAAA
1 ATAGCGGCGTTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTATACAAA
76859 CGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTTAGATAG
66 CGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTTAGATAG
*
76922 ATAGCGGCGTTTTTTGGAACAAACGCCCCAAAAGGTCAGATCTATAGCGGCGTTTTTTATACAAA
1 ATAGCGGCGTTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTATACAAA
*
76987 CGCCGCAAAAGGTTGATATCTATAGTGGCGTTTTTGGAACAAACGCCGCAATAGGTTAGATAG
66 CGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTTAGATAG
* * * *
77050 ATAGCGGCGTTTTTTTAGAACAAACGTCGCAAAAGGTCAGATATATATAGCGACGTTTTTTTATA
1 ATAGCGGCG-TTTTTTGGAACAAACGCCGCAAAAGGTCAG--ATCTATAGCGGCG-TTTTTTATA
*
77115 CAAACTCCGC
62 CAAACGCCGC
77125 TAATTTCCGT
Statistics
Matches: 303, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
127 1 0.00
128 207 0.68
129 66 0.22
131 11 0.04
132 18 0.06
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (128 bp):
ATAGCGGCGTTTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTATACAAA
CGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTTAGATAG
Found at i:77648 original size:18 final size:19
Alignment explanation
Indices: 77613--77649 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
77603 CACGGAATGT
77613 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
77633 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
77650 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:81771 original size:42 final size:39
Alignment explanation
Indices: 81659--81794 Score: 114
Period size: 42 Copynumber: 3.3 Consensus size: 39
81649 ACGTTTACTG
* *
81659 AAAAACGCCACTATA-TATAATTTTATTGCGGCGTTTTTAT
1 AAAAACGCCACTAAAGTATAA-TTT-TTGCGGCGTTTTTAC
**
81699 AAAAACGCCACTAAAGTACGATTCATTTGCGGCGTTTGTTAC
1 AAAAACGCCACTAAAGTATAATT--TTTGCGGCGTTT-TTAC
* * *
81741 AAAAACGCCGCTAAAGTTATAATTTGTTGCGACTTTTATTA-
1 AAAAACGCCACTAAAG-TATAATTT-TTGCGGCGTTT-TTAC
*
81782 AAAAATGCCACTA
1 AAAAACGCCACTA
81795 TAGGTGAACC
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
40 16 0.21
41 26 0.33
42 31 0.40
43 5 0.06
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (39 bp):
AAAAACGCCACTAAAGTATAATTTTTGCGGCGTTTTTAC
Found at i:81851 original size:82 final size:83
Alignment explanation
Indices: 81728--81900 Score: 237
Period size: 82 Copynumber: 2.1 Consensus size: 83
81718 GATTCATTTG
* *
81728 CGGCGTTTGTTACAAAAACGCCGCTAAAGTTATAATTTGTTGCGACTTTTATT-AAAAAATGCCA
1 CGGCGTTTGTTACAAAAACGCCGCTAAAGTTATAATATGTTGCGACTTTTATTGAAAAAACGCCA
* *
81792 CTATAGGT-GAACCCTATTA
66 CAATAGATAG-A-CCTATTA
* *
81811 CGGCGTTTG-TATAAAAACGCCGCTAAAG-TACTAATATGTTGCGGCTTTTATTGAAAAAACGCC
1 CGGCGTTTGTTACAAAAACGCCGCTAAAGTTA-TAATATGTTGCGACTTTTATTGAAAAAACGCC
81874 ACAATAGATAGACCTATTA
65 ACAATAGATAGACCTATTA
81893 CGGCGTTT
1 CGGCGTTT
81901 ATTGAAAAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
81 2 0.02
82 52 0.64
83 26 0.32
84 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (83 bp):
CGGCGTTTGTTACAAAAACGCCGCTAAAGTTATAATATGTTGCGACTTTTATTGAAAAAACGCCA
CAATAGATAGACCTATTA
Found at i:81902 original size:41 final size:42
Alignment explanation
Indices: 81851--81955 Score: 126
Period size: 41 Copynumber: 2.5 Consensus size: 42
81841 CTAATATGTT
* * *
81851 GCGGCTTTTATTGAAAAAACGCCACAATAGATAGA-CCTATTA
1 GCGGCGTTTATTGAAAAAACGCCACAATAGATAAACCCTA-AA
* *
81893 -CGGCGTTTATTGAAAAAATGCCACTATAGATAAACCCTAAA
1 GCGGCGTTTATTGAAAAAACGCCACAATAGATAAACCCTAAA
*
81934 GTGGCGTTTA-TGAAAAAACGCC
1 GCGGCGTTTATTGAAAAAACGCC
81956 GCTAAAGTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
41 42 0.78
42 12 0.22
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (42 bp):
GCGGCGTTTATTGAAAAAACGCCACAATAGATAAACCCTAAA
Found at i:84990 original size:38 final size:38
Alignment explanation
Indices: 84939--85031 Score: 159
Period size: 38 Copynumber: 2.4 Consensus size: 38
84929 CATGCAAAAT
*
84939 ATACTTGCAAATTAATTTAAATATTAATATGCTCAGTC
1 ATACTTACAAATTAATTTAAATATTAATATGCTCAGTC
*
84977 ATACTTACAAATTAATTTAAATATTAATATGCTTAGTC
1 ATACTTACAAATTAATTTAAATATTAATATGCTCAGTC
*
85015 ATGCTTACAAATTAATT
1 ATACTTACAAATTAATT
85032 ACATGTTTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (38 bp):
ATACTTACAAATTAATTTAAATATTAATATGCTCAGTC
Done.