Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007893.1 Hibiscus syriacus cultivar Beakdansim tig00110277_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: 72142
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2634 original size:1 final size:1
Alignment explanation
Indices: 2630--2690 Score: 68
Period size: 1 Copynumber: 61.0 Consensus size: 1
2620 TTTTTGGCTC
*** * * *
2630 TTTTTTTTTTTTTTTTTTTTTTTTTTTTGCCTTTTTTTGTTTTTTGTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2691 GAAAAAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.02, C:0.03, G:0.05, T:0.90
Consensus pattern (1 bp):
T
Found at i:2639 original size:17 final size:16
Alignment explanation
Indices: 2619--2691 Score: 69
Period size: 16 Copynumber: 4.5 Consensus size: 16
2609 AAATTTTGGC
*
2619 TTTTTTGGCTCTTTTTT
1 TTTTTTTGC-CTTTTTT
**
2636 TTTTTTT-TTTTTTTT
1 TTTTTTTGCCTTTTTT
2651 TTTTTTTGCCTTTTTT
1 TTTTTTTGCCTTTTTT
*
2667 TGTTTTTTG-TTTTTTT
1 T-TTTTTTGCCTTTTTT
2683 ATTTTTTTG
1 -TTTTTTTG
2692 AAAAAAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 13 0.28
16 20 0.43
17 14 0.30
ACGTcount: A:0.01, C:0.05, G:0.08, T:0.85
Consensus pattern (16 bp):
TTTTTTTGCCTTTTTT
Found at i:2656 original size:33 final size:34
Alignment explanation
Indices: 2619--2691 Score: 107
Period size: 32 Copynumber: 2.2 Consensus size: 34
2609 AAATTTTGGC
2619 TTTTTTGGCTCTTTTTTT-TTTTTT-TTTTTTT-T
1 TTTTTTGGC-CTTTTTTTGTTTTTTGTTTTTTTAT
*
2651 TTTTTTTGCCTTTTTTTGTTTTTTGTTTTTTTAT
1 TTTTTTGGCCTTTTTTTGTTTTTTGTTTTTTTAT
2685 TTTTTTG
1 TTTTTTG
2692 AAAAAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 8 0.22
32 14 0.39
33 7 0.19
34 7 0.19
ACGTcount: A:0.01, C:0.05, G:0.08, T:0.85
Consensus pattern (34 bp):
TTTTTTGGCCTTTTTTTGTTTTTTGTTTTTTTAT
Found at i:5735 original size:1 final size:1
Alignment explanation
Indices: 5731--5780 Score: 64
Period size: 1 Copynumber: 50.0 Consensus size: 1
5721 AAATTTTGGC
* * * *
5731 TTTTTTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5781 GAAAAAATAG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (1 bp):
T
Found at i:5738 original size:11 final size:11
Alignment explanation
Indices: 5724--5781 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
5714 TTTTTTGAAA
*
5724 TTTTGGCTTTT
1 TTTTGGTTTTT
5735 TTTT-GTTTTT
1 TTTTGGTTTTT
*
5745 TTTTTGTTTTT
1 TTTTGGTTTTT
*
5756 TTTTTG-TTTT
1 TTTTGGTTTTT
*
5766 TTTTGTTTTTT
1 TTTTGGTTTTT
5777 TTTTG
1 TTTTG
5782 AAAAAATAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
10 17 0.40
11 25 0.60
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (11 bp):
TTTTGGTTTTT
Found at i:5747 original size:20 final size:21
Alignment explanation
Indices: 5731--5781 Score: 86
Period size: 20 Copynumber: 2.4 Consensus size: 21
5721 AAATTTTGGC
5731 TTTTTTTTGTTTTTTTTTTGTT
1 TTTTTTTTG-TTTTTTTTTGTT
5753 TTTTTTTTG-TTTTTTTTGTT
1 TTTTTTTTGTTTTTTTTTGTT
5773 TTTTTTTTG
1 TTTTTTTTG
5782 AAAAAATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 20 0.69
22 9 0.31
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (21 bp):
TTTTTTTTGTTTTTTTTTGTT
Found at i:5749 original size:22 final size:22
Alignment explanation
Indices: 5724--5769 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5714 TTTTTTGAAA
5724 TTTTGGCTTTTTTTTGTTTTTT
1 TTTTGGCTTTTTTTTGTTTTTT
**
5746 TTTTGTTTTTTTTTTGTTTTTT
1 TTTTGGCTTTTTTTTGTTTTTT
5768 TT
1 TT
5770 GTTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (22 bp):
TTTTGGCTTTTTTTTGTTTTTT
Found at i:6123 original size:21 final size:21
Alignment explanation
Indices: 6097--6136 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6087 TTGGTGCTGG
6097 AAACAAGATAA-AATAAGATTA
1 AAACAAGATAAGAA-AAGATTA
6118 AAACAAGATAAGAAAAGAT
1 AAACAAGATAAGAAAAGAT
6137 AAATGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (21 bp):
AAACAAGATAAGAAAAGATTA
Found at i:6137 original size:10 final size:10
Alignment explanation
Indices: 6097--6139 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
6087 TTGGTGCTGG
6097 AAACAAGATA
1 AAACAAGATA
*
6107 AAATAAGATTA
1 AAACAAGA-TA
6118 AAACAAGATA
1 AAACAAGATA
6128 AGAA-AAGATA
1 A-AACAAGATA
6138 AA
1 AA
6140 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 1 0.03
10 17 0.59
11 11 0.38
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (10 bp):
AAACAAGATA
Found at i:6600 original size:45 final size:43
Alignment explanation
Indices: 6527--6631 Score: 108
Period size: 50 Copynumber: 2.3 Consensus size: 43
6517 AATAACTAAA
*
6527 TAAT-AAATAATAAAACTAAACATGTTTTAACTC-A-AATTCC
1 TAATAAAATAATAAAACTAAACATGTTTTAACCCAACAATTCC
*
6567 TAATAAAATAATAATAACTAAAAATATTGTTTTAACCCAACCTTAATTCC
1 TAATAAAATAATAA-AACT--AAACA-TGTTTTAACCCAA-C--AATTCC
6617 TAATAAAATAATAAA
1 TAATAAAATAATAAA
6632 TCTGATTCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
40 4 0.08
41 9 0.17
42 4 0.08
44 4 0.08
45 10 0.19
46 1 0.02
49 1 0.02
50 20 0.38
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.32
Consensus pattern (43 bp):
TAATAAAATAATAAAACTAAACATGTTTTAACCCAACAATTCC
Found at i:10317 original size:10 final size:10
Alignment explanation
Indices: 10304--10332 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
10294 AATTTTGGTA
10304 TTTTTGTTTT
1 TTTTTGTTTT
10314 TTTTTG-TTT
1 TTTTTGTTTT
10323 TTTTTGTTTT
1 TTTTTGTTTT
10333 GCCTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:10318 original size:19 final size:19
Alignment explanation
Indices: 10296--10332 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10286 TTTTTTAAAA
10296 TTTTGGTATTTTTGTTTTT
1 TTTTGGTATTTTTGTTTTT
* *
10315 TTTTGTTTTTTTTGTTTT
1 TTTTGGTATTTTTGTTTT
10333 GCCTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.84
Consensus pattern (19 bp):
TTTTGGTATTTTTGTTTTT
Found at i:10342 original size:10 final size:10
Alignment explanation
Indices: 10329--10373 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
10319 GTTTTTTTTG
10329 TTTTGCCTTT
1 TTTTGCCTTT
10339 TTTTGCCTTTT
1 TTTTGCC-TTT
*
10350 TTTTTCCTTT
1 TTTTGCCTTT
*
10360 TTTTG-TTTT
1 TTTTGCCTTT
10369 TTTTG
1 TTTTG
10374 AAAAAATAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.26
10 14 0.45
11 9 0.29
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (10 bp):
TTTTGCCTTT
Found at i:10353 original size:21 final size:19
Alignment explanation
Indices: 10304--10373 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 19
10294 AATTTTGGTA
*
10304 TTTTTGTTTTTTTT---TG
1 TTTTTGTTTTTTTTGCCTT
*
10320 TTTTT-TTTGTTTTGCCTT
1 TTTTTGTTTTTTTTGCCTT
*
10338 TTTTTGCCTTTTTTTTTCCTT
1 TTTTTG--TTTTTTTTGCCTT
10359 TTTTTGTTTTTTTTG
1 TTTTTGTTTTTTTTG
10374 AAAAAATAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.16
16 5 0.12
18 6 0.14
19 8 0.19
21 17 0.40
ACGTcount: A:0.00, C:0.09, G:0.10, T:0.81
Consensus pattern (19 bp):
TTTTTGTTTTTTTTGCCTT
Found at i:10705 original size:11 final size:11
Alignment explanation
Indices: 10689--10733 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
10679 TTGGTGCTGG
10689 AAATAAGATAA
1 AAATAAGATAA
*
10700 AAATAAGATTA
1 AAATAAGATAA
*
10711 AAACAAGATAA
1 AAATAAGATAA
10722 AGAA-AAGATAA
1 A-AATAAGATAA
10733 A
1 A
10734 TGAATTGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (11 bp):
AAATAAGATAA
Found at i:12066 original size:17 final size:18
Alignment explanation
Indices: 12046--12087 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
12036 AAGAAACAAA
12046 AAGAGAAAAAAT-GAAAG
1 AAGAGAAAAAATAGAAAG
*
12063 AAGAAAAAAAATAGAAAG
1 AAGAGAAAAAATAGAAAG
*
12081 AAAAGAA
1 AAGAGAA
12088 TCCTACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (18 bp):
AAGAGAAAAAATAGAAAG
Found at i:12327 original size:17 final size:17
Alignment explanation
Indices: 12276--12330 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
12266 GTAAGTTATC
* *
12276 TTCACTTTC-TTACTAT
1 TTCATTTTCTTTAGTAT
*
12292 TTCA-TTTCTTTAGTCT
1 TTCATTTTCTTTAGTAT
* *
12308 TTCATTTTTTTTATTAT
1 TTCATTTTCTTTAGTAT
12325 TTCATT
1 TTCATT
12331 ACCATATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 4 0.12
16 13 0.41
17 15 0.47
ACGTcount: A:0.16, C:0.16, G:0.02, T:0.65
Consensus pattern (17 bp):
TTCATTTTCTTTAGTAT
Found at i:21876 original size:13 final size:13
Alignment explanation
Indices: 21858--21926 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
21848 AGATACTAAA
*
21858 CATCACCATCTTC
1 CATCACCATATTC
*
21871 CATCACCAT-TTT
1 CATCACCATATTC
* **
21883 CA-CGCC-TATAA
1 CATCACCATATTC
*
21894 CATCACCATCTTC
1 CATCACCATATTC
*
21907 CATCACCATAGTC
1 CATCACCATATTC
21920 CATCACC
1 CATCACC
21927 TTCACGCCAG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 7 0.16
13 29 0.67
ACGTcount: A:0.28, C:0.42, G:0.03, T:0.28
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:25074 original size:13 final size:13
Alignment explanation
Indices: 25056--25124 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
25046 AGATACTAAA
25056 CATCACCATATTC
1 CATCACCATATTC
*
25069 CATCACCAT-TTT
1 CATCACCATATTC
* **
25081 CAT-GCC-TATAA
1 CATCACCATATTC
*
25092 CATCACCATCTTC
1 CATCACCATATTC
*
25105 CATCACCATAGTC
1 CATCACCATATTC
25118 CATCACC
1 CATCACC
25125 TTCACGCCAG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 7 0.16
13 29 0.67
ACGTcount: A:0.29, C:0.39, G:0.03, T:0.29
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:28407 original size:15 final size:15
Alignment explanation
Indices: 28389--28454 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
28379 CATTTCTATC
*
28389 CATTTCCTTTCTTAT
1 CATTTCCTATCTTAT
*
28404 CATTTCC-ATTCTTTTT
1 CATTTCCTA-TC-TTAT
28420 CCATTTCCTAT-TTAT
1 -CATTTCCTATCTTAT
28435 -ATTTCC-ATCTTAAT
1 CATTTCCTATCTT-AT
28449 CATTTC
1 CATTTC
28455 TCTCTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
12 2 0.05
13 8 0.20
14 2 0.05
15 17 0.41
16 3 0.07
17 8 0.20
18 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (15 bp):
CATTTCCTATCTTAT
Found at i:32029 original size:19 final size:20
Alignment explanation
Indices: 32005--32049 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
31995 CGACCAAGAG
32005 CATGTAACTTCATTAAA-AT
1 CATGTAACTTCATTAAATAT
**
32024 CATGTATTTTCATTAAATAT
1 CATGTAACTTCATTAAATAT
32044 CATGTA
1 CATGTA
32050 TTTTCAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (20 bp):
CATGTAACTTCATTAAATAT
Found at i:32047 original size:20 final size:19
Alignment explanation
Indices: 32013--32055 Score: 77
Period size: 20 Copynumber: 2.2 Consensus size: 19
32003 AGCATGTAAC
32013 TTCATTAAAATCATGTATT
1 TTCATTAAAATCATGTATT
32032 TTCATTAAATATCATGTATT
1 TTCATTAAA-ATCATGTATT
32052 TTCA
1 TTCA
32056 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:32472 original size:33 final size:34
Alignment explanation
Indices: 32395--32460 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
32385 ACTACCTAAG
*
32395 CATCACCATCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCATCTTCCATCACC--TTTCACGCCAATAA
32431 CATCACCATCTTCCATCACC-TTCACGCCAA
1 CATCACCATCTTCCATCACCTTTCACGCCAA
32461 CTCCATTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 9 0.31
36 20 0.69
ACGTcount: A:0.27, C:0.42, G:0.03, T:0.27
Consensus pattern (34 bp):
CATCACCATCTTCCATCACCTTTCACGCCAATAA
Found at i:32894 original size:22 final size:22
Alignment explanation
Indices: 32869--32914 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
32859 CAAAAGTAAC
*
32869 AAAAAGAGAAA-AAAAAACAAGA
1 AAAAAGAAAAATAAAAAAC-AGA
*
32891 AAAAATAAAAATAAAAAACAGA
1 AAAAAGAAAAATAAAAAACAGA
32913 AA
1 AA
32915 GAAAAGACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.83, C:0.04, G:0.09, T:0.04
Consensus pattern (22 bp):
AAAAAGAAAAATAAAAAACAGA
Found at i:32972 original size:7 final size:6
Alignment explanation
Indices: 32950--32983 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
32940 AGTGCAAAAG
*
32950 AAAGAA AAAGAA AAAGAA TAAAGAA AAACAA AAA
1 AAAGAA AAAGAA AAAGAA -AAAGAA AAAGAA AAA
32984 TTCAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:32974 original size:13 final size:12
Alignment explanation
Indices: 32950--32983 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
32940 AGTGCAAAAG
32950 AAAGAAAAAGAA
1 AAAGAAAAAGAA
32962 AAAGAATAAAGAA
1 AAAGAA-AAAGAA
*
32975 AAACAAAAA
1 AAAGAAAAA
32984 TTCAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAGAAAAAGAA
Found at i:35356 original size:37 final size:37
Alignment explanation
Indices: 35313--35388 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
35303 CATATCATGG
35313 CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
1 CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
35350 CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
1 CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
35387 CA
1 CA
35389 TGCTATGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (37 bp):
CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
Found at i:35905 original size:15 final size:16
Alignment explanation
Indices: 35887--35918 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
35877 TTAGAAGACC
35887 AAAGCTAACTAG-TTG
1 AAAGCTAACTAGCTTG
35902 AAAGCTAACTAGCTTG
1 AAAGCTAACTAGCTTG
35918 A
1 A
35919 GTTCATCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (16 bp):
AAAGCTAACTAGCTTG
Found at i:41632 original size:21 final size:21
Alignment explanation
Indices: 41606--41655 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
41596 TGATAATTAA
41606 GAAAT-GAAAAAAAAGTAAATG
1 GAAATGGAAAAAAAAG-AAATG
* *
41627 GAAATGGAAAGAATAGAAATG
1 GAAATGGAAAAAAAAGAAATG
41648 GAAA-GGAA
1 GAAATGGAA
41656 TGTTATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAATGGAAAAAAAAGAAATG
Found at i:46224 original size:19 final size:20
Alignment explanation
Indices: 46202--46244 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
46192 AGCATGTATC
46202 TTCATT-AAAATCATGAATT
1 TTCATTAAAAATCATGAATT
*
46221 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGAATT
46241 TTCA
1 TTCA
46245 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (20 bp):
TTCATTAAAAATCATGAATT
Found at i:46603 original size:13 final size:13
Alignment explanation
Indices: 46585--46653 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
46575 ACTACCTAAA
*
46585 CATCACCATCTTC
1 CATCACCATATTC
*
46598 CATCACCAT-TTT
1 CATCACCATATTC
* **
46610 CA-CGCC-TATAA
1 CATCACCATATTC
*
46621 CATCACCATCTTC
1 CATCACCATATTC
*
46634 CATCACCATAGTC
1 CATCACCATATTC
46647 CATCACC
1 CATCACC
46654 TTCACTTCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 7 0.16
13 29 0.67
ACGTcount: A:0.28, C:0.42, G:0.03, T:0.28
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:48649 original size:13 final size:13
Alignment explanation
Indices: 48627--48656 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
48617 ACTAAACACC
48627 TTTC-ACATACCT
1 TTTCAACATACCT
48639 TTTCAACATACCT
1 TTTCAACATACCT
48652 TTTCA
1 TTTCA
48657 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:51316 original size:5 final size:5
Alignment explanation
Indices: 51302--51330 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
51292 GTGCTTCCAA
51302 CTTTT C-TTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
51331 TTTCTTGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
CTTTT
Found at i:51342 original size:19 final size:19
Alignment explanation
Indices: 51302--51343 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
51292 GTGCTTCCAA
*
51302 CTTTTCTTTCTTTTCTTTT
1 CTTTTCTTTCTTTTCTTCT
51321 CTTTTCTTT-TTTTCTTGCT
1 CTTTTCTTTCTTTTCTT-CT
51340 CTTT
1 CTTT
51344 GAGTGCTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (19 bp):
CTTTTCTTTCTTTTCTTCT
Found at i:51367 original size:23 final size:21
Alignment explanation
Indices: 51341--51386 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 21
51331 TTTCTTGCTC
51341 TTTGAGTGCTTTCAATTTATTCT
1 TTTGAGTGCTTT-AATTT-TTCT
51364 TTTGAGTGCTTTAATTTTTCT
1 TTTGAGTGCTTTAATTTTTCT
51385 TT
1 TT
51387 GCTGGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.26
22 5 0.22
23 12 0.52
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.61
Consensus pattern (21 bp):
TTTGAGTGCTTTAATTTTTCT
Found at i:52271 original size:65 final size:65
Alignment explanation
Indices: 52172--52295 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 65
52162 GATGCTTGCC
*
52172 CGAATAGGGAGAGAGCTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATGGCTTGGT
1 CGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATGGCTTGGT
* * *
52237 CGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATGG
1 CGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATGG
52296 GGGCTGGTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (65 bp):
CGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATGGCTTGGT
Found at i:52627 original size:21 final size:21
Alignment explanation
Indices: 52601--52650 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
52591 TGATAATTAA
52601 GAAATGAGAAA-AA-AGTAAATG
1 GAAATG-GAAAGAATAG-AAATG
52622 GAAATGGAAAGAATAGAAATG
1 GAAATGGAAAGAATAGAAATG
52643 GAAA-GGAA
1 GAAATGGAA
52651 TGTTATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.30
21 17 0.63
22 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (21 bp):
GAAATGGAAAGAATAGAAATG
Found at i:56297 original size:413 final size:413
Alignment explanation
Indices: 55530--56360 Score: 1644
Period size: 413 Copynumber: 2.0 Consensus size: 413
55520 GATAACTTGG
55530 CATTCATGGACTTGATTTGGGCACATTGGAACCAACACGATCTTTCTCCCTTGGTGTTTGAATGA
1 CATTCATGGACTTGATTTGGGCACATTGGAACCAACACGATCTTTCTCCCTTGGTGTTTGAATGA
55595 ATATTTGTTGGAGAACCCATCATAGAATGCTCGTTTATCGAACTGCCAATGACGTCCAAGGAGTA
66 ATATTTGTTGGAGAACCCATCATAGAATGCTCGTTTATCGAACTGCCAATGACGTCCAAGGAGTA
55660 GATGGCTTGAATTCATAGAAACAACATCACACAAAACTTCATCTTTATATCCCCCAATTGAAAAT
131 GATGGCTTGAATTCATAGAAACAACATCACACAAAACTTCATCTTTATATCCCCCAATTGAAAAT
55725 GACACACGTACTTGCTCCATGACTTCTAACTCTTCATCTTCATTTAATCCTTGCAAAACATATGG
196 GACACACGTACTTGCTCCATGACTTCTAACTCTTCATCTTCATTTAATCCTTGCAAAACATATGG
55790 ACTGGGATGTTTGAATGTTATAAGCCCCAACTTCTCAACCATGTATGTGCTTGCAAGATTTGCAC
261 ACTGGGATGTTTGAATGTTATAAGCCCCAACTTCTCAACCATGTATGTGCTTGCAAGATTTGCAC
*
55855 AACTACCATCATCAATGGCTACAAGGCATACTTTATCATTCACATGAAAACGAGTATGAAATGGA
326 AACTACCACCATCAATGGCTACAAGGCATACTTTATCATTCACATGAAAACGAGTATGAAATGGA
55920 TTCCTCCTTTGCTGTCCGTAATC
391 TTCCTCCTTTGCTGTCCGTAATC
55943 CATTCATGGACTTGATTTGGGCACATTGGAACCAACACGATCTTTCTCCCTTGGTGTTTGAATGA
1 CATTCATGGACTTGATTTGGGCACATTGGAACCAACACGATCTTTCTCCCTTGGTGTTTGAATGA
*
56008 ATATTTGTTGGAGAACCCATCATAGAATGCTTGTTTATCGAACTGCCAATGACGTCCAAGGAGTA
66 ATATTTGTTGGAGAACCCATCATAGAATGCTCGTTTATCGAACTGCCAATGACGTCCAAGGAGTA
56073 GATGGCTTGAATTCATAGAAACAACATCACACAAAACTTCATCTTTATATCCCCCAATTGAAAAT
131 GATGGCTTGAATTCATAGAAACAACATCACACAAAACTTCATCTTTATATCCCCCAATTGAAAAT
56138 GACACACGTACTTGCTCCATGACTTCTAACTCTTCATCTTCATTTAATCCTTGCAAAACATATGG
196 GACACACGTACTTGCTCCATGACTTCTAACTCTTCATCTTCATTTAATCCTTGCAAAACATATGG
56203 ACTGGGATGTTTGAATGTTATAAGCCCCAACTTCTCAACCATGTATGTGCTTGCAAGATTTGCAC
261 ACTGGGATGTTTGAATGTTATAAGCCCCAACTTCTCAACCATGTATGTGCTTGCAAGATTTGCAC
56268 AACTACCACCATCAATGGCTACAAGGCATACTTTATCATTCACATGAAAACGAGTATGAAATGGA
326 AACTACCACCATCAATGGCTACAAGGCATACTTTATCATTCACATGAAAACGAGTATGAAATGGA
56333 TTCCTCCTTTGCTGTCCGTAATC
391 TTCCTCCTTTGCTGTCCGTAATC
56356 CATTC
1 CATTC
56361 GAAAGATGGG
Statistics
Matches: 416, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
413 416 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (413 bp):
CATTCATGGACTTGATTTGGGCACATTGGAACCAACACGATCTTTCTCCCTTGGTGTTTGAATGA
ATATTTGTTGGAGAACCCATCATAGAATGCTCGTTTATCGAACTGCCAATGACGTCCAAGGAGTA
GATGGCTTGAATTCATAGAAACAACATCACACAAAACTTCATCTTTATATCCCCCAATTGAAAAT
GACACACGTACTTGCTCCATGACTTCTAACTCTTCATCTTCATTTAATCCTTGCAAAACATATGG
ACTGGGATGTTTGAATGTTATAAGCCCCAACTTCTCAACCATGTATGTGCTTGCAAGATTTGCAC
AACTACCACCATCAATGGCTACAAGGCATACTTTATCATTCACATGAAAACGAGTATGAAATGGA
TTCCTCCTTTGCTGTCCGTAATC
Found at i:58301 original size:21 final size:21
Alignment explanation
Indices: 58275--58324 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
58265 TGATAATTAA
58275 GAAAT-GAAAAAAAAGTAAATG
1 GAAATGGAAAAAAAAG-AAATG
* *
58296 GAAATGGAAAGAATAGAAATG
1 GAAATGGAAAAAAAAGAAATG
58317 GAAA-GGAA
1 GAAATGGAA
58325 TGTTATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAATGGAAAAAAAAGAAATG
Found at i:65833 original size:28 final size:27
Alignment explanation
Indices: 65776--65839 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
65766 TTTCTTTTCT
* * *
65776 TTTCTTTTCTTCTTTTTGAATGCTGAA
1 TTTCTTTTTTTCTTTTGGAATGCTCAA
*
65803 TTTCTTTTTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTTTTTCTTTTGGAATGC-TCAA
65831 TTTCTTTTT
1 TTTCTTTTT
65840 GATTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.64
Consensus pattern (27 bp):
TTTCTTTTTTTCTTTTGGAATGCTCAA
Found at i:65973 original size:24 final size:26
Alignment explanation
Indices: 65946--65994 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
65936 CTTATTACCG
65946 CTTGATGTAA-G-TCTTCTGATGCCA
1 CTTGATGTAAGGCTCTTCTGATGCCA
65970 CTTGATGTAAGGCTCTTCTGATGCC
1 CTTGATGTAAGGCTCTTCTGATGCC
65995 TTAACAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
26 12 0.52
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
CTTGATGTAAGGCTCTTCTGATGCCA
Done.