Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002079.1 Hibiscus syriacus cultivar Beakdansim tig00004249_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: 106825
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:2610 original size:13 final size:13
Alignment explanation
Indices: 2588--2617 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2578 ACTAAACACC
2588 TTTC-ACATACCT
1 TTTCAACATACCT
2600 TTTCAACATACCT
1 TTTCAACATACCT
2613 TTTCA
1 TTTCA
2618 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:4316 original size:36 final size:36
Alignment explanation
Indices: 4269--4373 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
4259 ATAAGATATT
4269 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
4305 GTCCATCACCATTATCACGCCTATATCATCAACATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
4341 TTCCATCACC-TTATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
4374 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:9917 original size:13 final size:11
Alignment explanation
Indices: 9876--9960 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
9866 ACAATCTGTC
9876 CATCACCATTAT
1 CATCACCA-TAT
*
9888 CA-CGCCTATAT
1 CATCACC-ATAT
9899 CATCACCATAGT
1 CATCACCATA-T
9911 CCATCACCATTAT
1 -CATCACCA-TAT
*
9924 CATGC-CTATAT
1 CAT-CACCATAT
9935 CATCACCATATT
1 CATCACCATA-T
9947 CCATCACCATAT
1 -CATCACCATAT
9959 CA
1 CA
9961 CGCCCTATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:9920 original size:36 final size:36
Alignment explanation
Indices: 9873--9978 Score: 169
Period size: 36 Copynumber: 2.9 Consensus size: 36
9863 GATACAATCT
9873 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
9909 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
9945 TTCCATCACCA-TATCACGCCCTATATTATCACCA
1 GTCCATCACCATTATCACG-CCTATATCATCACCA
9979 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 6 0.09
36 59 0.91
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:17477 original size:14 final size:14
Alignment explanation
Indices: 17445--17485 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
17435 ATAGGCATGA
* *
17445 ATGGTGATAGAGA-
1 ATGGTGATGGAAAG
17458 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
17472 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
17486 GTAGTGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:17844 original size:20 final size:21
Alignment explanation
Indices: 17805--17848 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
17795 ATTCGACTAG
**
17805 ATACATGTCTTTTTAATGAAA
1 ATACATGTCTTTAGAATGAAA
17826 ATACATGTC-TTAGAATGAAA
1 ATACATGTCTTTAGAATGAAA
17846 ATA
1 ATA
17849 GATGATGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
ATACATGTCTTTAGAATGAAA
Found at i:27285 original size:3 final size:3
Alignment explanation
Indices: 27277--27393 Score: 168
Period size: 3 Copynumber: 40.0 Consensus size: 3
27267 TTCAGGCCTG
27277 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
27323 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAG TAT TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
27371 -AA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
27394 AAAATAAAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
2 6 0.06
3 97 0.94
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:27307 original size:23 final size:23
Alignment explanation
Indices: 27277--27400 Score: 169
Period size: 23 Copynumber: 5.4 Consensus size: 23
27267 TTCAGGCCTG
27277 TAATAATAATAATAATAATAATA
1 TAATAATAATAATAATAATAATA
27300 TAATAATAATAATAATAATAATA
1 TAATAATAATAATAATAATAATA
27323 TAATAATAATAATAATAATAATAA
1 TAATAATAATAATAATAATAAT-A
* * * *
27347 TAATATTAGTATTAATATTAATA
1 TAATAATAATAATAATAATAATA
* *
27370 AAATAATAATATTAATAATAATA
1 TAATAATAATAATAATAATAATA
*
27393 -AAAAATAA
1 TAATAATAA
27401 AATGGGATAA
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
22 7 0.08
23 65 0.71
24 19 0.21
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (23 bp):
TAATAATAATAATAATAATAATA
Found at i:27612 original size:68 final size:68
Alignment explanation
Indices: 27520--27735 Score: 351
Period size: 68 Copynumber: 3.2 Consensus size: 68
27510 TACCAATTGC
*
27520 ACAGTTAGGCCTCAAATGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
27585 AGA
66 AGA
* * *
27588 ATAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAATTGGCTTATATGACACCTTTCTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
*
27653 AGC
66 AGA
* *
27656 ACAGTTAGACCTCAAAGACACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
*
27721 AAA
66 AGA
*
27724 ACATTTAGGCCT
1 ACAGTTAGGCCT
27736 ATTAATCCTT
Statistics
Matches: 134, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 134 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (68 bp):
ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATA
AGA
Found at i:29758 original size:63 final size:64
Alignment explanation
Indices: 29635--29773 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 64
29625 AATGAATAAA
** *
29635 TCTT-CATGAATGTATCTTCATGGCTGAATCCTTTCTCCCATGTGTGAACATGTTTGATTTGTCT
1 TCTTGCATGAATGTATCTT-ATGGCTGAATCCTTTCTCCCATGTGTGAACATGACTGATTTGGCT
* * *
29699 TCTATGGATGAATGTATC-T-TGGCTGAAATTC-TTCTCCCCTTGTGTGAACATGACT-ATTTGG
1 TCT-TGCATGAATGTATCTTATGGCTG-AATCCTTTCT-CCCATGTGTGAACATGACTGATTTGG
29760 CT
63 CT
29762 TCTTGCATGAAT
1 TCTTGCATGAAT
29774 ATGCATGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
62 8 0.12
63 20 0.31
64 23 0.36
65 2 0.03
66 11 0.17
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (64 bp):
TCTTGCATGAATGTATCTTATGGCTGAATCCTTTCTCCCATGTGTGAACATGACTGATTTGGCT
Found at i:30910 original size:91 final size:91
Alignment explanation
Indices: 30755--30935 Score: 281
Period size: 91 Copynumber: 2.0 Consensus size: 91
30745 CCTAGAACAC
*
30755 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGAATATGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGAATATGGATCATTTAGGCACCAAGATG
30820 AAGAGTTCTCTCCCTATTCGGCCAAA
66 AAGAGTTCTCTCCCTATTCGGCCAAA
** * * * * * *
30846 CCATGTGTTTTGCATGTGATCAGCCCCCATGTTCCTTGCATGTGGTTCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGAATATGGATCATTTAGGCACCAAGATG
30911 AAGAGTTCTCTCCCTATTCGGCCAA
66 AAGAGTTCTCTCCCTATTCGGCCAA
30936 GCATCAACTA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 81 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGAATATGGATCATTTAGGCACCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAA
Found at i:38088 original size:24 final size:21
Alignment explanation
Indices: 38054--38099 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
38044 TCCACAAGAC
*
38054 ATGTCCTTTGACATTTCAAAAG
1 ATGTCCTTTGA-AATTCAAAAG
38076 ATGTACCTCTTGAAATTCAAAAG
1 ATGT-CCT-TTGAAATTCAAAAG
38099 A
1 A
38100 ATGTGCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAAG
Found at i:38112 original size:24 final size:23
Alignment explanation
Indices: 38068--38113 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
38058 CCTTTGACAT
**
38068 TTCAAAAGATGTACCTCTTGAAA
1 TTCAAAAGATGTACCAATTGAAA
*
38091 TTCAAAAGAATGTGCCAATTGAA
1 TTCAAAAG-ATGTACCAATTGAA
38114 GTACCAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (23 bp):
TTCAAAAGATGTACCAATTGAAA
Found at i:41016 original size:35 final size:37
Alignment explanation
Indices: 40947--41026 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
40937 ATACTATTTC
*
40947 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
40984 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
41019 CATCACCA
1 CATCACCA
41027 AATTCTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:41490 original size:14 final size:15
Alignment explanation
Indices: 41456--41502 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
41446 AATTTGGAGT
41456 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
41471 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
41485 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
41502 G
1 G
41503 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:45481 original size:35 final size:36
Alignment explanation
Indices: 45413--45491 Score: 115
Period size: 35 Copynumber: 2.2 Consensus size: 36
45403 ATACTATTTC
**
45413 CATCACCATAATCCATCTTCATTATCACGCCTATAT
1 CATCACCATAATCCATCACCATTATCACGCCTATAT
* *
45449 CATCACCATAGTCCATCACCA-TATCATGCCTATAT
1 CATCACCATAATCCATCACCATTATCACGCCTATAT
45484 CATCACCA
1 CATCACCA
45492 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 21 0.54
36 18 0.46
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
CATCACCATAATCCATCACCATTATCACGCCTATAT
Found at i:49746 original size:27 final size:28
Alignment explanation
Indices: 49716--49777 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
49706 CTTTTCTTTA
* *
49716 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
*
49743 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAATTT
49771 CTTTTCT
1 CTTTTCT
49778 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:52695 original size:11 final size:13
Alignment explanation
Indices: 52663--52692 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52653 TGGCCAAAGA
52663 TGAAAAGGTATGT
1 TGAAAAGGTATGT
52676 TGAAAAGGTATG-
1 TGAAAAGGTATGT
52688 TGAAA
1 TGAAA
52693 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:60012 original size:24 final size:24
Alignment explanation
Indices: 59963--60013 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
59953 TTTCTTTGTT
* *
59963 TTTTCTTCTTTTTGAGTACTGGAA
1 TTTTCTTCTTTTGGAGTACTGCAA
* *
59987 TTTTCTTCTTTTGGAGTGCTTCAA
1 TTTTCTTCTTTTGGAGTACTGCAA
60011 TTT
1 TTT
60014 GTTTGCTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.57
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTACTGCAA
Found at i:61031 original size:90 final size:91
Alignment explanation
Indices: 60885--61056 Score: 265
Period size: 90 Copynumber: 1.9 Consensus size: 91
60875 CCCATGTGCC
* * **
60885 TTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGATTTCT
1 TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
60950 CTCCCTATTCGGCCAAGTCATGTGTT
66 CTCCCTATTCGGCCAAGTCATGTGTT
* * * *
60976 TTGCATCTGAACAG-CCCCATATGCCTTGCATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTCT
1 TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
61040 CTCCCTATTCGGCCAAG
66 CTCCCTATTCGGCCAAG
61057 CATCATTCCC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 61 0.84
91 12 0.16
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (91 bp):
TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
CTCCCTATTCGGCCAAGTCATGTGTT
Found at i:61779 original size:2 final size:2
Alignment explanation
Indices: 61772--61814 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
61762 CAACAACAAA
61772 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
61814 A
1 A
61815 CAAAAAGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61897 original size:23 final size:24
Alignment explanation
Indices: 61869--61928 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
61859 AAAATCAGCA
*
61869 AAGAAAAAAAAAGCACTC-AAAAG
1 AAGAAAAAGAAAGCACTCGAAAAG
*
61892 AAGAAATAGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTCGAAAAG
61916 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
61929 AAAGAAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.67, C:0.10, G:0.18, T:0.05
Consensus pattern (24 bp):
AAGAAAAAGAAAGCACTCGAAAAG
Found at i:70931 original size:1 final size:1
Alignment explanation
Indices: 70927--70974 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
70917 TCTTTTTGGC
* * * *
70927 TTTTTTTTTGTTTTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
70975 GAAAAAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (1 bp):
T
Found at i:70937 original size:20 final size:19
Alignment explanation
Indices: 70912--70963 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
70902 TTTTTTGAAA
70912 TTTTGTCTTTTTGGCTTTTT
1 TTTTGT-TTTTTGGCTTTTT
* *
70932 TTTTGTTTTTTTTTGTTTTTT
1 TTTTG--TTTTTTGGCTTTTT
70953 TTTTGTTTTTT
1 TTTTGTTTTTT
70964 TTTGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 6 0.21
20 5 0.18
21 16 0.57
22 1 0.04
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.85
Consensus pattern (19 bp):
TTTTGTTTTTTGGCTTTTT
Found at i:70941 original size:11 final size:10
Alignment explanation
Indices: 70927--70974 Score: 87
Period size: 10 Copynumber: 4.7 Consensus size: 10
70917 TCTTTTTGGC
70927 TTTTTTTTTG
1 TTTTTTTTTG
70937 TTTTTTTTTG
1 TTTTTTTTTG
70947 TTTTTTTTTTG
1 -TTTTTTTTTG
70958 TTTTTTTTTG
1 TTTTTTTTTG
70968 TTTTTTT
1 TTTTTTT
70975 GAAAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
10 27 0.73
11 10 0.27
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:70964 original size:20 final size:21
Alignment explanation
Indices: 70927--70974 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
70917 TCTTTTTGGC
70927 TTTTTTTTTGTTTTTTTTTGT
1 TTTTTTTTTGTTTTTTTTTGT
70948 TTTTTTTTTGTTTTTTTTTGT
1 TTTTTTTTTGTTTTTTTTTGT
70969 TTTTTT
1 TTTTTT
70975 GAAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (21 bp):
TTTTTTTTTGTTTTTTTTTGT
Found at i:77879 original size:68 final size:68
Alignment explanation
Indices: 77664--77875 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
77654 AAGGATTAAT
* *
77664 AGGCCTAAATGTTCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTACCT
1 AGGCCTAAATGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCCT
77729 TTG
66 TTG
*
77732 AGGTCTAAATGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAAATGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCCT
*
77797 TTA
66 TTG
* *
77800 AGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCAT
1 AGGCCTAAATGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCCT
77865 TTG
66 TTG
77868 AGGCCTAA
1 AGGCCTAA
77876 CTGTACAATT
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 136 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (68 bp):
AGGCCTAAATGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:78014 original size:3 final size:3
Alignment explanation
Indices: 78006--78064 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
77996 ATTTTATTTT
* * * * *
78006 TTA TTA TTA TTA ATA TTA TT- TTA TTA ATA TCA ATA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
78053 TTA TTA TTA TTA
1 TTA TTA TTA TTA
78065 CATGCCCGAA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:79260 original size:22 final size:21
Alignment explanation
Indices: 79205--79265 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
79195 AATTAAGGCC
79205 TTTAATCTTGATATTTTATAT
1 TTTAATCTTGATATTTTATAT
*
79226 TTTATTCTTGATATTTTATAT
1 TTTAATCTTGATATTTTATAT
79247 TTTAATCCTTGATATTTTA
1 TTTAAT-CTTGATATTTTA
79266 ATTATTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTAATCTTGATATTTTATAT
Found at i:84311 original size:27 final size:25
Alignment explanation
Indices: 84281--84351 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
84271 AAAGTGCTAC
84281 AACAAAAAGCAATAAGAAAGAAGAAAA
1 AACAAAAAGCAA-AAGAAA-AAGAAAA
*
84308 AACAAAAAG-AAAAGAAAAAGAAGA
1 AACAAAAAGCAAAAGAAAAAGAAAA
* *
84332 ATCGAAAAGC-AAAGAAAAAG
1 AACAAAAAGCAAAAGAAAAAG
84352 TGAAGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
24 23 0.57
25 6 0.15
26 2 0.05
27 9 0.22
ACGTcount: A:0.73, C:0.07, G:0.17, T:0.03
Consensus pattern (25 bp):
AACAAAAAGCAAAAGAAAAAGAAAA
Found at i:92135 original size:13 final size:13
Alignment explanation
Indices: 92117--92141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92107 TAGGAGTCTT
92117 TTTCTTTTCTTTA
1 TTTCTTTTCTTTA
92130 TTTCTTTTCTTT
1 TTTCTTTTCTTT
92142 CTTTTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTTCTTTA
Found at i:92144 original size:17 final size:18
Alignment explanation
Indices: 92116--92164 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
92106 GTAGGAGTCT
92116 TTTTCTTTTCTTTATT-TC
1 TTTTCTTTTCTTT-TTCTC
92134 TTTTC-TTTCTTTTTCTC
1 TTTTCTTTTCTTTTTCTC
92151 TTTT-TGTTTCTTTT
1 TTTTCT-TTTCTTTT
92165 GTTGCAGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.07
17 13 0.46
18 13 0.46
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTCTC
Found at i:96468 original size:90 final size:92
Alignment explanation
Indices: 96310--96475 Score: 257
Period size: 90 Copynumber: 1.8 Consensus size: 92
96300 TATACTCATA
* * *
96310 TATATTATTATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAATCACCCCGGC
1 TATATTATTATATAGACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAATAACCCCGAC
96375 TTTATGGATAATATTCAGCTAGTCTAT
66 TTTATGGATAATATTCAGCTAGTCTAT
* *
96402 TATATTATTATAT-GA-AATAAAGCTTGA-TCTGTCCCTCTAGAGCAATTGGTTAATAACCCCTA
1 TATATTATTATATAGACAATAAAGCTTGAGT-TGTCCCTCTAAAGCAATTGGTTAATAACCCCGA
96464 CTTTATGGATAA
65 CTTTATGGATAA
96476 GTTTCAAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
89 1 0.01
90 53 0.78
91 1 0.01
92 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (92 bp):
TATATTATTATATAGACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAATAACCCCGAC
TTTATGGATAATATTCAGCTAGTCTAT
Found at i:98633 original size:42 final size:42
Alignment explanation
Indices: 98586--98667 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
98576 GAGATGAAAG
** * *
98586 TAAATCCTTTGGGTCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCAGGTCATCAGTAAGCCTTTCGAGCAAGATGCT
*
98628 TAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAGATG
1 TAAATCCTTCAGGTCATCAGTAAGCCTTTCGAGCAAGATG
98668 ATAAGACCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAATCCTTCAGGTCATCAGTAAGCCTTTCGAGCAAGATGCT
Found at i:98646 original size:216 final size:220
Alignment explanation
Indices: 98161--98715 Score: 775
Period size: 216 Copynumber: 2.5 Consensus size: 220
98151 ACCTTCAGGC
* *
98161 CATCAGTAAGTCTTTCGAGCATTATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTTGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAG
** * *
98226 ATGATAAGACCTTTGATCCATCCATAAGACCTTCAGTGCTGGATGTTTTGAACATTTTCGTTACT
66 ATGATAAGACCTTTGGGCCATCCATAAGACCTTCAGTGCTGGATGTTTTCAACATTTTCGTTACA
* * *
98291 TGATTCATGACATTTCGAACACAATGTCTTGCTTGAGAAAGTTTCACTTGAATAGTAATTGTCTC
131 TGATTCACGACATTTCGAACACAACGTCTTGCTTGAGAAAGCTTCACTTGAATAGTAA-TG--TC
* *
98356 ACTCGAGATTAAAGTAAATCCTTCGAAT
193 AATCGAGATGAAAGTAAATCCTTCGAAT
* *
98384 CATCAGTAAGTATTTCGAACATGATGCTTAAATCCTTC-GAGTCATCTGTAAGCCTTTCGAGCAA
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAG-GTCATCTGTAAGCCTTTCGAGCAA
* *
98448 GATGATAAGACCTTTGGGCCATCCATAAGA-CTTCAGTGCTGGATGTTTTCAACATTTTTGTTGC
65 GATGATAAGACCTTTGGGCCATCCATAAGACCTTCAGTGCTGGATGTTTTCAACATTTTCGTTAC
* *
98512 ATGATTCACGACATTTGGAATCAACAACGTCTTGCTTTAGAAAGCTTCACTTGAA-A-T-A-G-C
130 ATGATTCACGACATTTCGAA-C-ACAACGTCTTGCTTGAGAAAGCTTCACTTGAATAGTAATGTC
* **
98572 AATCGAGATGAAAGTAAATCCTTTGGGT
193 AATCGAGATGAAAGTAAATCCTTCGAAT
98600 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAG
* ** * *
98665 ATGATAAGACCATCAGGCCATCCATAAGACCTTC-GGGCAGGATGTTTTCAA
66 ATGATAAGACCTTTGGGCCATCCATAAGACCTTCAGTGCTGGATGTTTTCAA
98716 ATGAGATTTA
Statistics
Matches: 300, Mismatches: 27, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
216 126 0.42
217 5 0.02
219 1 0.00
221 1 0.00
222 50 0.17
223 88 0.29
224 29 0.10
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (220 bp):
CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAG
ATGATAAGACCTTTGGGCCATCCATAAGACCTTCAGTGCTGGATGTTTTCAACATTTTCGTTACA
TGATTCACGACATTTCGAACACAACGTCTTGCTTGAGAAAGCTTCACTTGAATAGTAATGTCAAT
CGAGATGAAAGTAAATCCTTCGAAT
Found at i:99379 original size:3 final size:3
Alignment explanation
Indices: 99364--99426 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
99354 TTTAATATAA
* * * *
99364 TAT TAT TAA TAT TAT TAT TAT T-G TAT TCT TA- TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
99410 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
99427 CAAGCCCGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 3 0.06
3 47 0.94
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:99385 original size:31 final size:31
Alignment explanation
Indices: 99350--99416 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
99340 TTATCCCATT
* *
99350 TTATTTTAATATAATATTATTAATATTATTA
1 TTATTGTAATATAATATTATTAATATTAATA
* * * *
99381 TTATTGTATTCTTATATTATTATTATTAATA
1 TTATTGTAATATAATATTATTAATATTAATA
99412 TTATT
1 TTATT
99417 ATTATTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (31 bp):
TTATTGTAATATAATATTATTAATATTAATA
Found at i:99865 original size:12 final size:12
Alignment explanation
Indices: 99836--99873 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
99826 GAACCCATAT
*
99836 TTATATGATTATC
1 TTATATTATTA-C
99849 TTATATTATTAC
1 TTATATTATTAC
99861 TTATATTA-TAC
1 TTATATTATTAC
99872 TT
1 TT
99874 TCTTTTGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 5 0.21
12 9 0.38
13 10 0.42
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (12 bp):
TTATATTATTAC
Found at i:103980 original size:5 final size:5
Alignment explanation
Indices: 103970--104001 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
103960 TTCAGCATTC
*
103970 AAAAG AAAAG AAAAG CAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
104002 GAAAGTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Done.