Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004379.1 Hibiscus syriacus cultivar Beakdansim tig00009605_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: 86831
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2812 original size:20 final size:20
Alignment explanation
Indices: 2787--2856 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
2777 TGTTGAATAG
2787 GTATCGATACTGTAAGGGTA
1 GTATCGATACTGTAAGGGTA
*
2807 GTATCGATACTATAAGGGTA
1 GTATCGATACTGTAAGGGTA
* * *
2827 GTATCAATACCTG-AAGGATG
1 GTATCGATA-CTGTAAGGGTA
2847 GTATCGATAC
1 GTATCGATAC
2857 CCTTAAAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
19 1 0.02
20 40 0.93
21 2 0.05
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (20 bp):
GTATCGATACTGTAAGGGTA
Found at i:2971 original size:54 final size:54
Alignment explanation
Indices: 2841--2971 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 54
2831 CAATACCTGA
* * * *
2841 AGGATGGTATCGATACCCTTAAAACATCGAATGTCAGTTTGGTATCGTTACCTTG
1 AGGA-GGTATCGATACCCTTGAAACATCGAATGTCAGTTCGGTATCGGTACCATG
* *
2896 AAGAGGTATCGATACCTTTGAAACATCGAATG-CTA-TATCGGTATCGGTACCATG
1 AGGAGGTATCGATACCCTTGAAACATCGAATGTC-AGT-TCGGTATCGGTACCATG
*
2950 AGGAGGTATAGATACCCTTGAA
1 AGGAGGTATCGATACCCTTGAA
2972 GAGAAGTATC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
53 2 0.03
54 60 0.92
55 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (54 bp):
AGGAGGTATCGATACCCTTGAAACATCGAATGTCAGTTCGGTATCGGTACCATG
Found at i:3559 original size:21 final size:21
Alignment explanation
Indices: 3526--3605 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
3516 TCGAGGGTTT
3526 TATGTGGTC-CTTCGAGACAAA
1 TATGTGGTCACTTCG-GACAAA
*
3547 TATGTGG-CACTTCGGTGCAAA
1 TATGTGGTCACTTCGG-ACAAA
*
3568 CCTATGTGGTCA-TTCGGGACAAT
1 --TATGTGGTCACTTC-GGACAAA
*
3591 TATATGG-CACTTCGG
1 TATGTGGTCACTTCGG
3606 TGCAAATTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
20 6 0.12
21 25 0.52
23 13 0.27
24 4 0.08
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
TATGTGGTCACTTCGGACAAA
Found at i:3589 original size:44 final size:44
Alignment explanation
Indices: 3526--3611 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
3516 TCGAGGGTTT
* *
3526 TATGTGGTCCTTCGAGACAAATATGTGGCACTTCGGTGCAAACC
1 TATGTGGTCATTCGAGACAAATATATGGCACTTCGGTGCAAACC
* *
3570 TATGTGGTCATTCGGGACAATTATATGGCACTTCGGTGCAAA
1 TATGTGGTCATTCGAGACAAATATATGGCACTTCGGTGCAAA
3612 TTACAAGCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (44 bp):
TATGTGGTCATTCGAGACAAATATATGGCACTTCGGTGCAAACC
Found at i:9572 original size:2 final size:2
Alignment explanation
Indices: 9565--9604 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9555 TGATTTAGAC
9565 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
9605 CATTTCCAGT
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:11021 original size:17 final size:17
Alignment explanation
Indices: 10992--11024 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10982 GAGAGAGAAC
10992 AAGAAAAGAAGAAAATA
1 AAGAAAAGAAGAAAATA
11009 AAGAGAAAG-AGAAAAT
1 AAGA-AAAGAAGAAAAT
11025 TTGAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (17 bp):
AAGAAAAGAAGAAAATA
Found at i:12782 original size:2 final size:2
Alignment explanation
Indices: 12775--12804 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12765 AGTAAAGTAA
12775 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
12805 TCATTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12936 original size:2 final size:2
Alignment explanation
Indices: 12929--12953 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12919 AATGAAGTAA
12929 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 A
12954 AATAAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14388 original size:6 final size:6
Alignment explanation
Indices: 14365--14390 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
14355 TAATATTAAT
14365 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
14391 ACCAAATGGA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:14861 original size:123 final size:123
Alignment explanation
Indices: 14731--15186 Score: 804
Period size: 123 Copynumber: 3.7 Consensus size: 123
14721 GAATTCAGGC
14731 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
14796 GAACTCTACCTGGCAATGTTGATTCTAATATATCTCCTTCTATGATAGAGTCGAGCAA
66 GAACTCTACCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
*
14854 AAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
14919 GAACTCTACCTGGAAATATTGATGCCGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
66 GAACTCTACCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
*
14977 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGCTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
15042 GAACTCTACCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
66 GAACTCTACCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
* * *
15100 GAGGTTGAAAAAGTTCTTCTCGTTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
15165 GAACTCTACCTGGAAATGTTGA
66 GAACTCTACCTGGAAATGTTGA
15187 GAAAAACAAT
Statistics
Matches: 317, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 317 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTACCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
Found at i:15305 original size:73 final size:73
Alignment explanation
Indices: 15186--15439 Score: 438
Period size: 73 Copynumber: 3.5 Consensus size: 73
15176 GGAAATGTTG
* * *
15186 AGAAAAACAATCTCAAGTGAGATAAATGGCTATTTCGAGTGAAACTTTCTCCAGCGAGAAATAAT
1 AGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAGAAACAAT
15251 TTGTTTTA
66 TTGTTTTA
*
15259 AGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCTAGCGAGAAACAGA
1 AGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAGAAACA-A
15324 -TTGTTTTA
65 TTTGTTTTA
*
15332 AGAAAAACAATCTCAAGTGAAATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAGAAACAAT
1 AGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAGAAACAAT
15397 TTGTTTTA
66 TTGTTTTA
*
15405 AGAAAAACAATCTCAAGTGAGATAAATTGATATTT
1 AGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
15440 GAAAACATCC
Statistics
Matches: 171, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
72 1 0.01
73 169 0.99
74 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (73 bp):
AGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAGAAACAAT
TTGTTTTA
Found at i:16180 original size:22 final size:22
Alignment explanation
Indices: 16152--16204 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
16142 AATAAAGTTT
16152 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
16174 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
16196 TCATCTTTG
1 TCATCTTTG
16205 TAGAATGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:19801 original size:8 final size:8
Alignment explanation
Indices: 19788--19829 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
19778 TTGATTCAAT
19788 TTTTTTCC
1 TTTTTTCC
19796 TTTTTT-C
1 TTTTTTCC
*
19803 TTTTTTTC
1 TTTTTTCC
*
19811 TTTTTTCTT
1 TTTTTTC-C
19820 TTTTTTCC
1 TTTTTTCC
19828 TT
1 TT
19830 ATGATGAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCC
Found at i:19806 original size:6 final size:7
Alignment explanation
Indices: 19788--19823 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
19778 TTGATTCAAT
19788 TTTTTTCC
1 TTTTTT-C
19796 TTTTTTC
1 TTTTTTC
19803 TTTTTTTC
1 -TTTTTTC
19811 TTTTTTC
1 TTTTTTC
19818 TTTTTT
1 TTTTTT
19824 TTCCTTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.52
8 13 0.48
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:19808 original size:15 final size:15
Alignment explanation
Indices: 19788--19823 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
19778 TTGATTCAAT
19788 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTTC
*
19803 TTTTTTTCTTTTTTC
1 TTTTTTCCTTTTTTC
19818 TTTTTT
1 TTTTTT
19824 TTCCTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTCCTTTTTTC
Found at i:19808 original size:16 final size:17
Alignment explanation
Indices: 19787--19829 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
19777 CTTGATTCAA
19787 TTTTTTTCCTTTTTTC-
1 TTTTTTTCCTTTTTTCT
19803 TTTTTTT-CTTTTTTCT
1 TTTTTTTCCTTTTTTCT
19819 TTTTTTTCCTT
1 TTTTTTTCCTT
19830 ATGATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.32
16 14 0.56
17 3 0.12
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTCCTTTTTTCT
Found at i:22447 original size:36 final size:36
Alignment explanation
Indices: 22395--22463 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
22385 TCTTACCGTA
* * *
22395 GAATGCTTTTGGTATCAATCTAACATGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
22431 GAATACTTTTGGTATCAATATAACAGGATCTTT
1 GAATACTTTTGGTATCAATATAACAGGATCTTT
22464 ATGTGCATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:23853 original size:2 final size:2
Alignment explanation
Indices: 23846--23900 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
23836 AAAAGTAAAG
23846 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
23888 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
23901 TTAAGTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24057 original size:2 final size:2
Alignment explanation
Indices: 24050--24110 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
24040 AAAAATGAAG
24050 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
24092 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
24111 CTTTATAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24839 original size:26 final size:26
Alignment explanation
Indices: 24810--24869 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
24800 CTTCCCTCCT
24810 TCTCTCTCTAGACGAGAGATTATAAA
1 TCTCTCTCTAGACGAGAGATTATAAA
24836 TCTCTCTCTAGACGAGAGATTATAAA
1 TCTCTCTCTAGACGAGAGATTATAAA
24862 TCTCTCTC
1 TCTCTCTC
24870 GCTTCTCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (26 bp):
TCTCTCTCTAGACGAGAGATTATAAA
Found at i:25640 original size:22 final size:21
Alignment explanation
Indices: 25613--25655 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
25603 TTGGGCCTGT
25613 AATAATAATGAA-AAAAATAAAT
1 AATAATAAT-AATAAAAA-AAAT
25635 AATAATAATAATAAAAAAAAT
1 AATAATAATAATAAAAAAAAT
25656 CAAATGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (21 bp):
AATAATAATAATAAAAAAAAT
Found at i:25646 original size:25 final size:26
Alignment explanation
Indices: 25612--25660 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
25602 TTTGGGCCTG
*
25612 TAATAATAATGAAAAAAAT-AAATAA
1 TAATAATAATAAAAAAAATCAAATAA
25637 TAATAATAATAAAAAAAATCAAAT
1 TAATAATAATAAAAAAAATCAAAT
25661 GGATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (26 bp):
TAATAATAATAAAAAAAATCAAATAA
Found at i:31651 original size:15 final size:15
Alignment explanation
Indices: 31634--31663 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
31624 ATCTTTCTTT
31634 CCCGTTCTGGATTTTC
1 CCCG-TCTGGATTTTC
31650 CCCGTCTGGATTTT
1 CCCGTCTGGATTTT
31664 GATTTTCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (15 bp):
CCCGTCTGGATTTTC
Found at i:32169 original size:50 final size:50
Alignment explanation
Indices: 32083--32182 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
32073 TAATTGGTTC
* *
32083 GTAAAACATTTGACAACACATGCATCATCTCATGTGGTTTCTGCTCAGAT
1 GTAAAACACTTGACAACACATGCATCATCTCATGTGGCTTCTGCTCAGAT
* * *
32133 GTAAAACACTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGAT
1 GTAAAACACTTGACAACACATGCAT-CATCTCATGTGGCTTCTGCTCAGAT
32183 TTCTCAATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 40 0.91
51 4 0.09
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (50 bp):
GTAAAACACTTGACAACACATGCATCATCTCATGTGGCTTCTGCTCAGAT
Found at i:42502 original size:14 final size:15
Alignment explanation
Indices: 42470--42502 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42460 TTATTTTTCT
42470 TAAAAGTAATTTATA
1 TAAAAGTAATTTATA
*
42485 TAAAATTAATTT-TA
1 TAAAAGTAATTTATA
42499 TAAA
1 TAAA
42503 TAGGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TAAAAGTAATTTATA
Found at i:44075 original size:3 final size:3
Alignment explanation
Indices: 44067--44135 Score: 102
Period size: 3 Copynumber: 22.7 Consensus size: 3
44057 ATATTTATTA
*
44067 AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
**
44113 TTT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
44136 AACGAAATGA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:53278 original size:96 final size:95
Alignment explanation
Indices: 53152--53376 Score: 265
Period size: 96 Copynumber: 2.4 Consensus size: 95
53142 TACCTAATGA
** *
53152 AGTGGTATCGATACCATGGTGCGGGTATCGATACCGGGTAACATCGAACCTAATTTTGGTATCGA
1 AGTGGTATCGATACCATGGTAAGGGTATCGATACCGGGCAACATCGAACCTAATTTTGGTATCGA
* *
53217 TATCAT-ATA-GGGGTATCGGTACCATAGTAT
66 TA-C-TGATAGGGGGTATCGATACCATAGTAG
* * * * *
53247 AGTGGTATTGATACCTATGGTAAGGGTATCGATACGGGGCCACATCGAATCTAATTTTGGTATTG
1 AGTGGTATCGATACC-ATGGTAAGGGTATCGATACCGGGCAACATCGAACCTAATTTTGGTATCG
* *
53312 ATACTGGTAGGGGGTATCGATACTATAGTAG
65 ATACTGATAGGGGGTATCGATACCATAGTAG
* * **
53343 AGTAGTATCGATACCATAGTTGGGGTATCGATAC
1 AGTGGTATCGATACCATGGTAAGGGTATCGATAC
53377 TGAAGGGCCA
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
94 1 0.01
95 33 0.30
96 76 0.69
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (95 bp):
AGTGGTATCGATACCATGGTAAGGGTATCGATACCGGGCAACATCGAACCTAATTTTGGTATCGA
TACTGATAGGGGGTATCGATACCATAGTAG
Found at i:53280 original size:21 final size:21
Alignment explanation
Indices: 53209--53281 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 21
53199 ACCTAATTTT
* *
53209 GGTATCGATATCATA-TA-GG
1 GGTATCGATACCATAGTATAG
*
53228 GGTATCGGTACCATAGTATAG
1 GGTATCGATACCATAGTATAG
* *
53249 TGGTATTGATACCTATGGTA-AG
1 -GGTATCGATACC-ATAGTATAG
53271 GGTATCGATAC
1 GGTATCGATAC
53282 GGGGCCACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 13 0.30
20 2 0.05
21 11 0.26
22 12 0.28
23 5 0.12
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (21 bp):
GGTATCGATACCATAGTATAG
Found at i:53372 original size:20 final size:20
Alignment explanation
Indices: 53322--53376 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
53312 ATACTGGTAG
*
53322 GGGGTATCGATACTATAGTA
1 GGGGTATCGATACCATAGTA
* *
53342 GAGTAGTATCGATACCATAGTT
1 G-G-GGTATCGATACCATAGTA
53364 GGGGTATCGATAC
1 GGGGTATCGATAC
53377 TGAAGGGCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (20 bp):
GGGGTATCGATACCATAGTA
Found at i:53860 original size:45 final size:45
Alignment explanation
Indices: 53791--54090 Score: 447
Period size: 45 Copynumber: 6.7 Consensus size: 45
53781 TAAAAAAAAT
*
53791 AATGCATATGGGTGCATTATCAACAGAAAAGTATACGATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * * * *
53836 AATGTATATGGGTACATTATCAACATAAAAATATACAATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * *
53881 AATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * *
53926 AATGTATATGGGTACATTATCAACTGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * * *
53971 AATGTATATGGGTACATTATCAACATAAAAGTATACGATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
54016 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAATTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
54061 AATGCATATGGGTGCATTATCAACAGAAAA
1 AATGCATATGGGTGCATTATCAACAGAAAA
54091 ATATTTTATA
Statistics
Matches: 228, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 228 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
Found at i:54103 original size:135 final size:135
Alignment explanation
Indices: 53791--54090 Score: 510
Period size: 135 Copynumber: 2.2 Consensus size: 135
53781 TAAAAAAAAT
*
53791 AATGCATATGGGTGCATTATCAACAGAAAAGTATACGATAGTTGAAATGTATATGGGTACATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
* *
53856 CAACATAAAAATATACAATAGTTGAAATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTAGA
66 CAACATAAAAATATACAATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGA
*
53921 GTTGA
131 ATTGA
* * *
53926 AATGTATATGGGTACATTATCAACTGAAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
* * *
53991 CAACATAAAAGTATACGATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATA
66 CAACATAAAAATATACAATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGA
54056 ATTGA
131 ATTGA
54061 AATGCATATGGGTGCATTATCAACAGAAAA
1 AATGCATATGGGTGCATTATCAACAGAAAA
54091 ATATTTTATA
Statistics
Matches: 152, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 152 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (135 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGAAATGTATATGGGTACATTAT
CAACATAAAAATATACAATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGA
ATTGA
Found at i:58588 original size:40 final size:40
Alignment explanation
Indices: 58544--58619 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
58534 CCCTTACCTA
* *
58544 AGGTATCGATACCATATGAACAATATCGGTATTTCTCATG
1 AGGTATCGATACCATAAGAACAATATCGGTACTTCTCATG
** *
58584 AGGTATCGATACTGTAAGAACAATATTGGTACTTCT
1 AGGTATCGATACCATAAGAACAATATCGGTACTTCT
58620 TGTCGAGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (40 bp):
AGGTATCGATACCATAAGAACAATATCGGTACTTCTCATG
Found at i:60396 original size:21 final size:21
Alignment explanation
Indices: 60348--60408 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
60338 TACGTGCTCA
* **
60348 TTTGGGACATATATGT-AATC
1 TTTGGAACATATATGTGGTTC
60368 TTTGGGAACATATATGTGGTTC
1 TTT-GGAACATATATGTGGTTC
* *
60390 TTTGGAACACATATTTGGT
1 TTTGGAACATATATGTGGT
60409 CATTTAGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 3 0.09
21 26 0.76
22 5 0.15
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (21 bp):
TTTGGAACATATATGTGGTTC
Found at i:69469 original size:13 final size:13
Alignment explanation
Indices: 69451--69477 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
69441 TTACAGACGC
69451 GCATATGAAGACT
1 GCATATGAAGACT
69464 GCATATGAAGACT
1 GCATATGAAGACT
69477 G
1 G
69478 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:74359 original size:30 final size:30
Alignment explanation
Indices: 74276--74359 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
74266 CCCGAAAGAC
*
74276 CTATCCATAGGTCACAAAGAACCCCGACAA
1 CTATCCATAGGTCACAAAGAACCTCGACAA
* *
74306 CTATCCAGAGGTCATAAAGAACCTCGACAA
1 CTATCCATAGGTCACAAAGAACCTCGACAA
* * *
74336 CTGTCCATAGGTCCCGAAGAACCT
1 CTATCCATAGGTCACAAAGAACCT
74360 AGGTAAACTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.36, C:0.31, G:0.17, T:0.17
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCTCGACAA
Found at i:77679 original size:13 final size:12
Alignment explanation
Indices: 77651--77693 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
77641 CCATTTCAAT
77651 ATCAACACCATC
1 ATCAACACCATC
*
77663 ATCAACATCCTTC
1 ATCAACA-CCATC
*
77676 ATCAAGACCATC
1 ATCAACACCATC
*
77688 ACCAAC
1 ATCAAC
77694 TTCATACTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.40, C:0.40, G:0.02, T:0.19
Consensus pattern (12 bp):
ATCAACACCATC
Found at i:77743 original size:21 final size:22
Alignment explanation
Indices: 77712--77757 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
77702 TCTGCAACCA
*
77712 TTTCTTTTCTATCTT-TATTTCT
1 TTTCTTTTCTAT-TTCTATTACT
77734 TTTC-TTTCTATTTCTATTACT
1 TTTCTTTTCTATTTCTATTACT
77755 TTT
1 TTT
77758 ATTATTATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 16 0.73
22 4 0.18
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTCTTTTCTATTTCTATTACT
Found at i:78401 original size:24 final size:22
Alignment explanation
Indices: 78349--78403 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
78339 AGATTTAATT
* *
78349 AAAATTTATAACTCATAAATAC
1 AAAATTTTTAACTCATAAAAAC
*
78371 ATAATTTTTAACTCATAATAAAC
1 AAAATTTTTAACTCATAA-AAAC
78394 AAATATTTTT
1 AAA-ATTTTT
78404 TAGGGTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 16 0.59
23 5 0.19
24 6 0.22
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTTTTAACTCATAAAAAC
Found at i:81384 original size:2 final size:2
Alignment explanation
Indices: 81379--81434 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
81369 TCTCTATCTA
* * * *
81379 AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AC AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81421 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
81435 TAAATAAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:82054 original size:32 final size:31
Alignment explanation
Indices: 82018--82082 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
82008 CAGATCGAAT
* *
82018 TCGGATGGAGGATATATATATTTCGAGTCAAA
1 TCGGATGAAGGATATA-AAATTTCGAGTCAAA
* * *
82050 TCGGATGAATGATATAAAATTTTGAGTTAAA
1 TCGGATGAAGGATATAAAATTTCGAGTCAAA
82081 TC
1 TC
82083 AAGTTCGGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.34
Consensus pattern (31 bp):
TCGGATGAAGGATATAAAATTTCGAGTCAAA
Found at i:83814 original size:28 final size:29
Alignment explanation
Indices: 83760--83815 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
83750 TTTCATTCAC
* *
83760 TTAGACCCTATAAGGGTAATTTGGTAATT
1 TTAGACCCTATAAGGGCAATTTAGTAATT
* *
83789 TTAG-CCCTCTAAGGGCATTTTAGTAAT
1 TTAGACCCTATAAGGGCAATTTAGTAAT
83816 CTTTCACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (29 bp):
TTAGACCCTATAAGGGCAATTTAGTAATT
Found at i:83948 original size:20 final size:19
Alignment explanation
Indices: 83925--83963 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
83915 GATACTAAGC
83925 CTTCGGTATGGATACACAAT
1 CTTCGGTATGGATAC-CAAT
83945 CTTCGGTATGGATACCAAT
1 CTTCGGTATGGATACCAAT
83964 TCATCTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (19 bp):
CTTCGGTATGGATACCAAT
Found at i:83974 original size:41 final size:41
Alignment explanation
Indices: 83928--84021 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 41
83918 ACTAAGCCTT
*
83928 CGGTATGGATACACAATCTTCGGTATGGATACCAATTCATC
1 CGGTATGGATACACAACCTTCGGTATGGATACCAATTCATC
* * **** * *
83969 TGGTATGTATACTTGCCCTTCGGTATGGATACCAGTTTATC
1 CGGTATGGATACACAACCTTCGGTATGGATACCAATTCATC
*
84010 CAGTATGGATAC
1 CGGTATGGATAC
84022 TAGCCCATCG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (41 bp):
CGGTATGGATACACAACCTTCGGTATGGATACCAATTCATC
Found at i:83975 original size:21 final size:20
Alignment explanation
Indices: 83927--83980 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
83917 TACTAAGCCT
*
83927 TCGGTATGGATACACAATCT
1 TCGGTATGGATACACAATCA
83947 TCGGTATGGATAC-CAATTCA
1 TCGGTATGGATACACAA-TCA
*
83967 TCTGGTATGTATAC
1 TC-GGTATGGATAC
83981 TTGCCCTTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 17 0.57
21 10 0.33
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (20 bp):
TCGGTATGGATACACAATCA
Found at i:84022 original size:41 final size:41
Alignment explanation
Indices: 83945--84044 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
83935 GATACACAAT
** * *
83945 CTTCGGTATGGATACCAATTCATCTGGTATGTATACTTGCC
1 CTTCGGTATGGATACCAATTCATCCAGTATGGATACTAGCC
* *
83986 CTTCGGTATGGATACCAGTTTATCCAGTATGGATACTAGCC
1 CTTCGGTATGGATACCAATTCATCCAGTATGGATACTAGCC
* *
84027 CATCGGTATCGATACCAA
1 CTTCGGTATGGATACCAA
84045 GCATATGGTA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
CTTCGGTATGGATACCAATTCATCCAGTATGGATACTAGCC
Done.