Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006930.1 Hibiscus syriacus cultivar Beakdansim tig00017786_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: 92764
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2052 original size:19 final size:19
Alignment explanation
Indices: 2014--2053 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2004 CGAATGATTG
* *
2014 AATCGAATATAATATTTTA
1 AATCGAATATAAAATCTTA
2033 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
2052 AA
1 AA
2054 ATTACTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:10825 original size:19 final size:19
Alignment explanation
Indices: 10787--10826 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
10777 CGAATGATTG
* *
10787 AATCAAATATAATATTTTA
1 AATCAAATATAAAATCTTA
*
10806 AATCGAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
10825 AA
1 AA
10827 ATTACTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Found at i:13237 original size:17 final size:17
Alignment explanation
Indices: 13210--13248 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
13200 AATTTACAAT
13210 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
13226 TAATTATAAATAATATC
1 TAATTATAAATAATATC
13243 TAATTA
1 TAATTA
13249 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:14101 original size:17 final size:17
Alignment explanation
Indices: 14072--14120 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
14062 ATTAAGAGTC
*
14072 AGTTTAATAAATGAACT
1 AGTTTAATGAATGAACT
*
14089 AGTTTGATGAATGAACT
1 AGTTTAATGAATGAACT
*
14106 AGTTTAATTAATGAA
1 AGTTTAATGAATGAA
14121 ATAACTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (17 bp):
AGTTTAATGAATGAACT
Found at i:15377 original size:15 final size:15
Alignment explanation
Indices: 15357--15405 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
15347 AAAATTATTC
15357 AAATATTAAAAAATT
1 AAATATTAAAAAATT
* *
15372 AAATATATAAAACACT
1 AAATAT-TAAAAAATT
*
15388 AAATATTAAAATATT
1 AAATATTAAAAAATT
15403 AAA
1 AAA
15406 AAGAATGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTAAAAAATT
Found at i:15399 original size:8 final size:8
Alignment explanation
Indices: 15346--15406 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
15336 ATTTTAGATA
15346 TAAAATTAT
1 TAAAA-TAT
*
15355 TCAAATAT
1 TAAAATAT
*
15363 TAAAAAAT
1 TAAAATAT
15371 T-AAATAT
1 TAAAATAT
* *
15378 ATAAAACAC
1 -TAAAATAT
15387 T-AAATAT
1 TAAAATAT
15394 TAAAATAT
1 TAAAATAT
15402 TAAAA
1 TAAAA
15407 AGAATGAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
7 10 0.24
8 23 0.56
9 8 0.20
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAATAT
Found at i:15407 original size:24 final size:24
Alignment explanation
Indices: 15372--15440 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 24
15362 TTAAAAAATT
15372 AAATA-TATAAAACACTAAATATTA
1 AAATATTA-AAAACACTAAATATTA
* * *
15396 AAATATTAAAAAGAATGAATATT-
1 AAATATTAAAAACACTAAATATTA
* *
15419 -CATATTAAAAATACTAAA-ATTA
1 AAATATTAAAAACACTAAATATTA
15441 TTATAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
21 3 0.08
22 14 0.39
24 17 0.47
25 2 0.06
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (24 bp):
AAATATTAAAAACACTAAATATTA
Found at i:17831 original size:6 final size:5
Alignment explanation
Indices: 17815--17901 Score: 69
Period size: 5 Copynumber: 17.4 Consensus size: 5
17805 CTAATTTTAA
17815 AAAAT AAAAT AACAAT AATAA- AAAAT AAAACAT AAAAT AAAA- AATAA-
1 AAAAT AAAAT AA-AAT AA-AAT AAAAT -AAA-AT AAAAT AAAAT AA-AAT
*
17862 AAAAT AAAA- AATA- AAAAT AAAA- AAAAT AAAAT AAACAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
17902 GTACAAGGAC
Statistics
Matches: 70, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
4 16 0.23
5 35 0.50
6 17 0.24
7 2 0.03
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:17841 original size:7 final size:7
Alignment explanation
Indices: 17812--17896 Score: 92
Period size: 7 Copynumber: 12.6 Consensus size: 7
17802 AACCTAATTT
17812 TAAAAAA
1 TAAAAAA
17819 T--AAAA
1 TAAAAAA
17824 TAACAATAA
1 TAA-AA-AA
17833 TAAAAAA
1 TAAAAAA
*
17840 TAAAACA
1 TAAAAAA
17847 T--AAAA
1 TAAAAAA
17852 TAAAAAA
1 TAAAAAA
17859 TAAAAAA
1 TAAAAAA
17866 TAAAAAA
1 TAAAAAA
17873 T-AAAAA
1 TAAAAAA
17879 TAAAAAA
1 TAAAAAA
17886 -AATAAAA
1 TAA-AAAA
17893 TAAA
1 TAAA
17897 CATAAGTACA
Statistics
Matches: 67, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
5 9 0.13
6 8 0.12
7 39 0.58
8 6 0.09
9 5 0.07
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:17852 original size:33 final size:31
Alignment explanation
Indices: 17815--17895 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 31
17805 CTAATTTTAA
17815 AAAATAAAATAACAATAATAAAAAATAAAACAT
1 AAAATAAAATAA-AATAATAAAAAATAAAA-AT
17848 AAAATAAAAAATAAAA-AATAAAAAATAAAAAT
1 AAAAT--AAAATAAAATAATAAAAAATAAAAAT
17880 AAAA-AAAATAAAATAA
1 AAAATAAAATAAAATAA
17896 ACATAAGTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
29 9 0.20
30 2 0.04
32 6 0.13
33 19 0.42
34 2 0.04
35 7 0.16
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (31 bp):
AAAATAAAATAAAATAATAAAAAATAAAAAT
Found at i:17901 original size:20 final size:20
Alignment explanation
Indices: 17815--17901 Score: 88
Period size: 20 Copynumber: 4.1 Consensus size: 20
17805 CTAATTTTAA
17815 AAAATAAAATAACAATAATAAA-
1 AAAA-AAAATAA-AATAA-AAAT
17837 AAATAAAACATAAAATAAAAAAT
1 AAA-AAAA-ATAAAAT-AAAAAT
17860 AAAAAATAA-AAAATAAAAAT
1 AAAAAA-AATAAAATAAAAAT
*
17880 AAAAAAAATAAAATAAACAT
1 AAAAAAAATAAAATAAAAAT
17900 AA
1 AA
17902 GTACAAGGAC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
19 2 0.03
20 24 0.41
21 5 0.09
22 16 0.28
23 11 0.19
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAAAAATAAAATAAAAAT
Found at i:18025 original size:51 final size:51
Alignment explanation
Indices: 17937--18042 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
17927 AAAATAACAT
* * * * *
17937 TGACTAAAATGCAAGAAAATAAAAGTTAGTAGTTAAATAAGAAATAAATAG
1 TGACCAAAATGCAAAAAAATAAAAGTTAGTAGCTAAATAAAAAATAAATAA
*
17988 TGACCAAAATG-AAAAAAATAAAA-TAATAGTAGCTAAATAAAAAATTAATAA
1 TGACCAAAATGCAAAAAAATAAAAGT--TAGTAGCTAAATAAAAAATAAATAA
18039 TGAC
1 TGAC
18043 TAAATTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 1 0.02
50 11 0.23
51 35 0.74
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.23
Consensus pattern (51 bp):
TGACCAAAATGCAAAAAAATAAAAGTTAGTAGCTAAATAAAAAATAAATAA
Found at i:31054 original size:20 final size:20
Alignment explanation
Indices: 31029--31070 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31019 TGATATGCTT
31029 AAAAGAGAACTATGATATAG
1 AAAAGAGAACTATGATATAG
31049 AAAAGAGAACTATGATATAG
1 AAAAGAGAACTATGATATAG
31069 AA
1 AA
31071 GTTATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (20 bp):
AAAAGAGAACTATGATATAG
Found at i:32341 original size:13 final size:13
Alignment explanation
Indices: 32322--32382 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
32312 GACTCGACTC
32322 GACCCGACCCGTT
1 GACCCGACCCGTT
*
32335 TACCCGACCCGTT
1 GACCCGACCCGTT
32348 GACCCGACCCGACTTGTT
1 GACCCGA-CC--C--GTT
32366 GACCCGACCCGTT
1 GACCCGACCCGTT
32379 GACC
1 GACC
32383 GTTGACCGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 25 0.61
14 2 0.05
15 1 0.02
16 1 0.02
17 2 0.05
18 10 0.24
ACGTcount: A:0.16, C:0.44, G:0.21, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:32356 original size:31 final size:31
Alignment explanation
Indices: 32321--32382 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
32311 CGACTCGACT
*
32321 CGACCCGACCCGTTTACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACCCGACCCGTTGACC
**
32352 CGACCCGACTTGTTGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACCCGACCCGTTGACC
32383 GTTGACCGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.45, G:0.21, T:0.18
Consensus pattern (31 bp):
CGACCCGACCCGTTGACCCGACCCGTTGACC
Found at i:32357 original size:18 final size:18
Alignment explanation
Indices: 32336--32376 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
32326 CGACCCGTTT
32336 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
**
32354 ACCCGACTTGTTGACCCG
1 ACCCGACCCGTTGACCCG
32372 ACCCG
1 ACCCG
32377 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:34977 original size:24 final size:24
Alignment explanation
Indices: 34883--34982 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
34873 ATATTTTATC
* *
34883 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
34907 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
34931 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
34955 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
34979 TGAT
1 TGAT
34983 TTTTGATATC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:37096 original size:18 final size:18
Alignment explanation
Indices: 37052--37098 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
37042 GTCACGACTC
37052 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
* **
37070 TACCCGACCCGACTTGTT
1 GACCCGACCCGACCCGTT
*
37088 GACCTGACCCG
1 GACCCGACCCG
37099 TTGACCCGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:37104 original size:26 final size:27
Alignment explanation
Indices: 37075--37129 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
37065 CCGTTTACCC
**
37075 GACCCGACTTGTTGACC-TGACCCGTT
1 GACCCGACCCGTTGACCGTGACCCGTT
37101 GACCCGACCCGTTGACCGTTGACCCGTT
1 GACCCGACCCGTTGACCG-TGACCCGTT
37129 G
1 G
37130 GCCGACGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.60
28 10 0.40
ACGTcount: A:0.15, C:0.36, G:0.25, T:0.24
Consensus pattern (27 bp):
GACCCGACCCGTTGACCGTGACCCGTT
Found at i:37114 original size:13 final size:13
Alignment explanation
Indices: 37075--37117 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
37065 CCGTTTACCC
**
37075 GACCCGACTTGTT
1 GACCCGACCCGTT
*
37088 GACCTGACCCGTT
1 GACCCGACCCGTT
37101 GACCCGACCCGTT
1 GACCCGACCCGTT
37114 GACC
1 GACC
37118 GTTGACCCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.16, C:0.40, G:0.23, T:0.21
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:40831 original size:23 final size:23
Alignment explanation
Indices: 40805--40888 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
40795 TATGGCACTA
*
40805 CGGTGCATTTCTACACGGTACTT
1 CGGTGCATTTCTACGCGGTACTT
* * * *
40828 CGGTGCAATTCTACGTGGCACTA
1 CGGTGCATTTCTACGCGGTACTT
40851 CGGTGCATTTCTACGCGGTACTT
1 CGGTGCATTTCTACGCGGTACTT
*
40874 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
40889 AGCTGTGGTG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGGTACTT
Found at i:48604 original size:6 final size:6
Alignment explanation
Indices: 48595--48662 Score: 70
Period size: 6 Copynumber: 11.3 Consensus size: 6
48585 GGCTAAAGCT
* *
48595 CTCTCT CTCTCCC CCCTCC CTCCCTCC CTCT-- CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCT-CC CTCTCC CT--CTCC CTCTCC CTCTCC CTCTCC CTCTCC
48644 CTCTCC CTCTCC C-CTCC CT
1 CTCTCC CTCTCC CTCTCC CT
48663 GTCTCTCCCC
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
4 4 0.08
5 5 0.09
6 34 0.64
7 4 0.08
8 6 0.11
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTCC
Found at i:48648 original size:51 final size:52
Alignment explanation
Indices: 48593--48707 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 52
48583 ATGGCTAAAG
*
48593 CTCTCTCTCTCTCCC-CCCTCCCTC-CCTCCCTCTCTCTCCCTCTCCCTCTCC
1 CTCTCTCTCTCTCCCTCCCTCCCTCTCC-CCCTCTCTCTCCCCCTCCCTCTCC
* ** * **
48644 CTCTCCCTCTC-CCCTCCCTGTCTCTCCCCCTGTCTCTCCCCCTGTCTCTCC
1 CTCTCTCTCTCTCCCTCCCTCCCTCTCCCCCTCTCTCTCCCCCTCCCTCTCC
*
48695 CCCTCTCTCTCTC
1 CTCTCTCTCTCTC
48708 TATATGAAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
50 3 0.06
51 46 0.88
52 3 0.06
ACGTcount: A:0.00, C:0.63, G:0.03, T:0.34
Consensus pattern (52 bp):
CTCTCTCTCTCTCCCTCCCTCCCTCTCCCCCTCTCTCTCCCCCTCCCTCTCC
Found at i:48674 original size:12 final size:12
Alignment explanation
Indices: 48659--48705 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
48649 CCTCTCCCCT
48659 CCCTGTCTCTCC
1 CCCTGTCTCTCC
48671 CCCTGTCTCTCC
1 CCCTGTCTCTCC
48683 CCCTGTCTCTCC
1 CCCTGTCTCTCC
*
48695 CCCTCTCTCTC
1 CCCTGTCTCTC
48706 TCTATATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.00, C:0.60, G:0.06, T:0.34
Consensus pattern (12 bp):
CCCTGTCTCTCC
Found at i:50293 original size:2 final size:2
Alignment explanation
Indices: 50286--50406 Score: 242
Period size: 2 Copynumber: 60.5 Consensus size: 2
50276 TGATCTTGTC
50286 AT 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 AT
50328 AT 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 AT
50370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50407 CATGTAGTGT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 119 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50832 original size:29 final size:29
Alignment explanation
Indices: 50741--50827 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 29
50731 AAAATAATTT
*
50741 TTTGAAAGTTAGAGTGATTAAATTAGAAGTGA
1 TTTGAAAGTTA-AGT-ATTAAATTA-AAGTAA
*
50773 TTTGAAAGTGAA-TATTAAATTAAGAGTAA
1 TTTGAAAGTTAAGTATTAAATTAA-AGTAA
50802 TTTGAAAGTTAAGTAATTAAATTAAA
1 TTTGAAAGTTAAGT-ATTAAATTAAA
50828 AAATTAAACT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.02
29 24 0.49
30 3 0.06
31 11 0.22
32 10 0.20
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (29 bp):
TTTGAAAGTTAAGTATTAAATTAAAGTAA
Found at i:51168 original size:23 final size:23
Alignment explanation
Indices: 51141--51185 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
51131 TAATTAAAAA
51141 TAATTTT-TTATAATTTAATCTTT
1 TAATTTTATT-TAATTTAATCTTT
51164 TAATTTTATTTAATTTAATCTT
1 TAATTTTATTTAATTTAATCTT
51186 ATAACTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
TAATTTTATTTAATTTAATCTTT
Found at i:51260 original size:11 final size:11
Alignment explanation
Indices: 51244--51271 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
51234 ATAAGATTAA
51244 ATAAAAAAATT
1 ATAAAAAAATT
51255 ATAAAAAAATT
1 ATAAAAAAATT
51266 ATAAAA
1 ATAAAA
51272 TGTTTGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
ATAAAAAAATT
Found at i:54408 original size:29 final size:26
Alignment explanation
Indices: 54354--54417 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 26
54344 AATAATTAAT
*
54354 AATTTAAAATTATTTTTTATTAATAA
1 AATTTAAAATTATTTTTCATTAATAA
54380 AATTTAAGAATTATTTCTTCCATTAATAA
1 AATTTAA-AATTATTT-TT-CATTAATAA
*
54409 AAATTAAAA
1 AATTTAAAA
54418 ACAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 7 0.21
27 8 0.24
28 4 0.12
29 14 0.42
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (26 bp):
AATTTAAAATTATTTTTCATTAATAA
Found at i:62735 original size:31 final size:31
Alignment explanation
Indices: 62699--62763 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
62689 TTTGGTAGCT
62699 AAAGTAGAAATTTGAGAAAAAATTAAGGATC
1 AAAGTAGAAATTTGAGAAAAAATTAAGGATC
*
62730 AAAGTAGAAATTTGAGAAAAAATTAAGGTTC
1 AAAGTAGAAATTTGAGAAAAAATTAAGGATC
62761 AAA
1 AAA
62764 ATAAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.23
Consensus pattern (31 bp):
AAAGTAGAAATTTGAGAAAAAATTAAGGATC
Found at i:62782 original size:32 final size:31
Alignment explanation
Indices: 62706--62785 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
62696 GCTAAAGTAG
* * *
62706 AAATTTGAGAAAAAATTAAGGATCAAAGTAG
1 AAATTTCAGAAAAAATTAAGGATCAAAATAA
* *
62737 AAATTTGAGAAAAAATTAAGGTTCAAAATAAA
1 AAATTTCAGAAAAAATTAAGGATCAAAAT-AA
*
62769 AAATTTC-CAAAAAATTA
1 AAATTTCAGAAAAAATTA
62786 TTCTATAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 36 0.84
32 7 0.16
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (31 bp):
AAATTTCAGAAAAAATTAAGGATCAAAATAA
Found at i:72441 original size:23 final size:25
Alignment explanation
Indices: 72411--72461 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
72401 TTTGAGTTTA
72411 AATCCCA-C-CATTAGGGAACATAT
1 AATCCCACCTCATTAGGGAACATAT
72434 AATCCCACCTTCATTAGGGAACATAT
1 AATCCCACC-TCATTAGGGAACATAT
72460 AA
1 AA
72462 ACTGAAGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.28
24 1 0.04
26 17 0.68
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (25 bp):
AATCCCACCTCATTAGGGAACATAT
Found at i:83192 original size:21 final size:21
Alignment explanation
Indices: 83166--83209 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
83156 AATATTGTAA
83166 ATTAGTATTTTCTATGTTTTT
1 ATTAGTATTTTCTATGTTTTT
*
83187 ATTAGTATTTTTTATGTTTTT
1 ATTAGTATTTTCTATGTTTTT
83208 AT
1 AT
83210 GTTTGTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.68
Consensus pattern (21 bp):
ATTAGTATTTTCTATGTTTTT
Found at i:83333 original size:11 final size:10
Alignment explanation
Indices: 83309--83344 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
83299 TGAATTTAAA
* *
83309 AAAAAATCAT
1 AAAAAAGCAG
83319 AAAAAAGCAG
1 AAAAAAGCAG
83329 AAAAAAGCAG
1 AAAAAAGCAG
83339 AAAAAA
1 AAAAAA
83345 TCAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.75, C:0.08, G:0.11, T:0.06
Consensus pattern (10 bp):
AAAAAAGCAG
Found at i:83734 original size:16 final size:17
Alignment explanation
Indices: 83713--83753 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
83703 TGTTCTTAAC
83713 TAATTTTAT-AATATTT
1 TAATTTTATGAATATTT
*
83729 TAATTTT-TGAATGTTT
1 TAATTTTATGAATATTT
83745 TAATATTTA
1 TAAT-TTTA
83754 ATTACAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 17 0.81
17 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
TAATTTTATGAATATTT
Found at i:89798 original size:12 final size:12
Alignment explanation
Indices: 89781--89805 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89771 ATTTTTTGCG
89781 AGGTTACTATTC
1 AGGTTACTATTC
89793 AGGTTACTATTC
1 AGGTTACTATTC
89805 A
1 A
89806 TGTGAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Done.