Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005817.1 Hibiscus syriacus cultivar Beakdansim tig00013631_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: 46759
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:694 original size:2 final size:2
Alignment explanation
Indices: 687--715 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
677 CCATACATAC
687 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 A
716 ATGTGACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1889 original size:13 final size:13
Alignment explanation
Indices: 1871--1898 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1861 GTAACATTTC
1871 AACCGAAAATGTT
1 AACCGAAAATGTT
1884 AACCGAAAATGTT
1 AACCGAAAATGTT
1897 AA
1 AA
1899 AAGATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (13 bp):
AACCGAAAATGTT
Found at i:5230 original size:20 final size:19
Alignment explanation
Indices: 5205--5249 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5195 AATTTGTAAA
*
5205 TCGCAACACATAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
5225 TCGCAACGCGAAGTCAAAT
1 TCGCAACACGAAGTCAAAT
5244 TCGCAA
1 TCGCAA
5250 TGTGAAACAC
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:0.40, C:0.27, G:0.16, T:0.18
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:5394 original size:22 final size:22
Alignment explanation
Indices: 5369--5419 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5359 CTACGGCGAC
5369 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
5391 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
5413 ATCCGTC
1 ATCCGTC
5420 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:5650 original size:13 final size:13
Alignment explanation
Indices: 5632--5663 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
5622 AGTATTTGTC
5632 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
5645 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
5658 TTTGTT
1 TTTGTT
5664 GAAGAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:5730 original size:19 final size:19
Alignment explanation
Indices: 5692--5732 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
5682 AACACCAAAT
*
5692 TCGCAACGCGAAAATGAAA
1 TCGCAACGCGAAAATAAAA
*
5711 TCGCAACGCGAAACTAAAA
1 TCGCAACGCGAAAATAAAA
5730 TCG
1 TCG
5733 TGTTGCGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAAATAAAA
Found at i:7932 original size:21 final size:22
Alignment explanation
Indices: 7891--7989 Score: 91
Period size: 21 Copynumber: 4.7 Consensus size: 22
7881 GATACACCTA
* * *
7891 TCATCATTCAAGAGACGCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
7913 T-ATCGTTCAAGAGGCCCCT-C
1 TCATCGTTCAAGAGGCCCCTCC
* *
7933 TCATC-ATCGAAGAAGCCCCTCC
1 TCATCGTTC-AAGAGGCCCCTCC
*
7955 -CATCGTTCAAGAGGCCCC-CG
1 TCATCGTTCAAGAGGCCCCTCC
*
7975 TCATCATTCAAGAGG
1 TCATCGTTCAAGAGG
7990 TCCCGTCGCC
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 5 0.08
21 54 0.86
22 4 0.06
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.21
Consensus pattern (22 bp):
TCATCGTTCAAGAGGCCCCTCC
Found at i:7938 original size:42 final size:43
Alignment explanation
Indices: 7891--7988 Score: 132
Period size: 42 Copynumber: 2.3 Consensus size: 43
7881 GATACACCTA
* *
7891 TCATCATTCAAGAGA-CGCCTCCTATCGTTCAAGAGGCCCCTC-
1 TCATCATTCAAGAGAGCCCCTCCCATCGTTCAAGAGGCCCC-CG
7933 TCATCA-TCGAAGA-AGCCCCTCCCATCGTTCAAGAGGCCCCCG
1 TCATCATTC-AAGAGAGCCCCTCCCATCGTTCAAGAGGCCCCCG
7975 TCATCATTCAAGAG
1 TCATCATTCAAGAG
7989 GTCCCGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
41 4 0.08
42 43 0.88
43 2 0.04
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (43 bp):
TCATCATTCAAGAGAGCCCCTCCCATCGTTCAAGAGGCCCCCG
Found at i:7996 original size:20 final size:21
Alignment explanation
Indices: 7891--8008 Score: 77
Period size: 21 Copynumber: 5.7 Consensus size: 21
7881 GATACACCTA
*
7891 TCATCATTCAAGAGACGCCTCC-
1 TCATCATTCAAGAG--GCCCCCG
*
7913 T-ATCGTTCAAGAGGCCCCTC-
1 TCATCATTCAAGAGGCCCC-CG
*
7933 TCATCA-TCGAAGAAGCCCCTC-
1 TCATCATTC-AAGAGGCCCC-CG
* *
7954 CCATCGTTCAAGAGGCCCCCG
1 TCATCATTCAAGAGGCCCCCG
*
7975 TCATCATTCAAGAGG-TCCCG
1 TCATCATTCAAGAGGCCCCCG
**
7995 TCGCCATTCAAGAG
1 TCATCATTCAAGAG
8009 CCTGATTCAT
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
19 4 0.05
20 21 0.27
21 51 0.65
22 3 0.04
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCCG
Found at i:10032 original size:11 final size:11
Alignment explanation
Indices: 10016--10067 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
10006 TTATACATAC
10016 AATGTTCAAAT
1 AATGTTCAAAT
10027 AATGTTCAAAT
1 AATGTTCAAAT
* *
10038 AATGTACCTATAAC
1 AATGT-TC-A-AAT
10052 AATGTTCAAAT
1 AATGTTCAAAT
10063 AATGT
1 AATGT
10068 ACCCACAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 23 0.68
12 2 0.06
13 2 0.06
14 7 0.21
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:10060 original size:25 final size:25
Alignment explanation
Indices: 10027--10082 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
10017 ATGTTCAAAT
* *
10027 AATGTTCAAATAATGTACCTATAAC
1 AATGTTCAAATAATGTACCCACAAC
10052 AATGTTCAAATAATGTACCCACAAC
1 AATGTTCAAATAATGTACCCACAAC
10077 AATGTT
1 AATGTT
10083 TAATTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (25 bp):
AATGTTCAAATAATGTACCCACAAC
Found at i:10212 original size:20 final size:20
Alignment explanation
Indices: 10187--10225 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10177 TTGCGATTTC
*
10187 GCGTTGTGAATTTGACTATT
1 GCGTTGCGAATTTGACTATT
10207 GCGTTGCGAATTTGACTAT
1 GCGTTGCGAATTTGACTAT
10226 CGCAACGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.41
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATT
Found at i:10572 original size:18 final size:18
Alignment explanation
Indices: 10551--10586 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10541 AAGCCGGTTG
*
10551 TGATTGTGATTTTGATTT
1 TGATTGCGATTTTGATTT
10569 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
10587 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.22, T:0.58
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:13000 original size:12 final size:12
Alignment explanation
Indices: 12979--13012 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12969 GGTTATGGGT
*
12979 TTTGAGATTGTG
1 TTTGATATTGTG
12991 TTTGATATTGTG
1 TTTGATATTGTG
*
13003 TTTGGTATTG
1 TTTGATATTG
13013 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:13742 original size:38 final size:38
Alignment explanation
Indices: 13700--13807 Score: 128
Period size: 38 Copynumber: 2.8 Consensus size: 38
13690 AAACATTTGT
*
13700 GTTGCGAAACT-AAATTCGTGTTACGAATTTGAAATTCA
1 GTTGCGAAACTGAAATTC-AGTTACGAATTTGAAATTCA
** *
13738 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAAATTCA
1 GTTGCGAAACTGAAATTCAGTTACGAATTTGAAATTCA
* ** *
13776 GTTGTGAATTTGAAATTCAGTTGCGAATTTGA
1 GTTGCGAAACTGAAATTCAGTTACGAATTTGA
13808 CTTTTGTGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 58 0.91
39 6 0.09
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.37
Consensus pattern (38 bp):
GTTGCGAAACTGAAATTCAGTTACGAATTTGAAATTCA
Found at i:13745 original size:19 final size:19
Alignment explanation
Indices: 13723--13807 Score: 161
Period size: 19 Copynumber: 4.5 Consensus size: 19
13713 ATTCGTGTTA
13723 CGAATTTGAAATTCAGTTG
1 CGAATTTGAAATTCAGTTG
13742 CGAATTTGAAATTCAGTTG
1 CGAATTTGAAATTCAGTTG
13761 CGAATTTGAAATTCAGTTG
1 CGAATTTGAAATTCAGTTG
*
13780 TGAATTTGAAATTCAGTTG
1 CGAATTTGAAATTCAGTTG
13799 CGAATTTGA
1 CGAATTTGA
13808 CTTTTGTGTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (19 bp):
CGAATTTGAAATTCAGTTG
Found at i:13828 original size:20 final size:20
Alignment explanation
Indices: 13795--13861 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
13785 TTGAAATTCA
13795 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
13815 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
13835 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
13855 GTTGCGA
1 GTTGCGA
13862 TTTACAGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:13845 original size:40 final size:39
Alignment explanation
Indices: 13795--13882 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 39
13785 TTGAAATTCA
* *
13795 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TATCGC
1 GTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATCGC
13835 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAGAATCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGATTTACA-AATCGC
13875 GTTGCGAA
1 GTTGCGAA
13883 ATTGGAAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 2 0.05
39 4 0.09
40 38 0.86
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (39 bp):
GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATCGC
Found at i:16271 original size:29 final size:29
Alignment explanation
Indices: 16229--16285 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
16219 AGTGTTGGTC
16229 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
16258 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
16286 ACCCTTGCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.35, G:0.32, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:16313 original size:12 final size:12
Alignment explanation
Indices: 16296--16320 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16286 ACCCTTGCGA
16296 GAGAATGAACGT
1 GAGAATGAACGT
16308 GAGAATGAACGT
1 GAGAATGAACGT
16320 G
1 G
16321 TTGCATGGCA
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:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:16382 original size:29 final size:29
Alignment explanation
Indices: 16349--16404 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
16339 TCCCAACACA
*
16349 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGTCATGCACTCCGGGCGACCTTG
16378 TAGGTCGTCATGCACTCCGGGCGACCT
1 TAGGTCGTCATGCACTCCGGGCGACCT
16405 ACCCTCGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.34, G:0.30, T:0.23
Consensus pattern (29 bp):
TAGGTCGTCATGCACTCCGGGCGACCTTG
Found at i:16480 original size:23 final size:23
Alignment explanation
Indices: 16431--16501 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
16421 CCTCGGATTC
* *
16431 CCTCGCATAGCTCGCTT-GGTTGC
1 CCTCGCATAGCTCG-TTCGGATGG
*
16454 CCTCACATAGCTCGTTCGGATGG
1 CCTCGCATAGCTCGTTCGGATGG
*
16477 CCTCGGAT-GCTC--TCGGATGG
1 CCTCGCATAGCTCGTTCGGATGG
16497 CCTCG
1 CCTCG
16502 GTCGGATGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
20 13 0.31
22 6 0.14
23 23 0.55
ACGTcount: A:0.11, C:0.34, G:0.28, T:0.27
Consensus pattern (23 bp):
CCTCGCATAGCTCGTTCGGATGG
Found at i:16508 original size:14 final size:14
Alignment explanation
Indices: 16489--16516 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16479 TCGGATGCTC
16489 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
16503 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
16517 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:16519 original size:10 final size:10
Alignment explanation
Indices: 16469--16502 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
16459 CATAGCTCGT
16469 TCGGATGGCC
1 TCGGATGGCC
16479 TCGGAT-GCTC
1 TCGGATGGC-C
16489 TCGGATGGCC
1 TCGGATGGCC
16499 TCGG
1 TCGG
16503 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:20359 original size:13 final size:13
Alignment explanation
Indices: 20341--20365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20331 GTCCTTTTCA
20341 TTTCACGTCAAAC
1 TTTCACGTCAAAC
20354 TTTCACGTCAAA
1 TTTCACGTCAAA
20366 TTAGTTGTTG
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:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTCACGTCAAAC
Found at i:22213 original size:66 final size:67
Alignment explanation
Indices: 22095--22242 Score: 183
Period size: 66 Copynumber: 2.2 Consensus size: 67
22085 GCTCGAATCT
* * * *
22095 ACTCATTGCTCGTTAAGCTCGTTAAAATTTTAGTTGAATCATGCTCGTTAAGAAAATTTGTTGTT
1 ACTCATTGCTCGTTAAGCTCGTTAAAATTTTAGTCGAATCATGCTCATTAAGAAAATTTATTGGT
22160 CG
66 CG
* * * * *
22162 ACTCGTTGCTC-TTAAGCTCGTT-AAATTTTTGCTCGAATCGTGTTCATTAAGAGAATTTATTGG
1 ACTCATTGCTCGTTAAGCTCGTTAAAATTTTAG-TCGAATCATGCTCATTAAGAAAATTTATTGG
22225 TCG
65 TCG
*
22228 AATCATTGCTCGTTA
1 ACTCATTGCTCGTTA
22243 CTCCTTAAGC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
65 8 0.12
66 47 0.69
67 13 0.19
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (67 bp):
ACTCATTGCTCGTTAAGCTCGTTAAAATTTTAGTCGAATCATGCTCATTAAGAAAATTTATTGGT
CG
Found at i:31106 original size:28 final size:28
Alignment explanation
Indices: 31066--31121 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
31056 AGCTGAAGAG
31066 GTATTTCAATTTTCATTGATTTTCCCAC
1 GTATTTCAATTTTCATTGATTTTCCCAC
31094 GTATTTCAATTTTCATTGATTTTCCCAC
1 GTATTTCAATTTTCATTGATTTTCCCAC
31122 TTTCTCCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (28 bp):
GTATTTCAATTTTCATTGATTTTCCCAC
Found at i:31741 original size:32 final size:33
Alignment explanation
Indices: 31691--31756 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
31681 TTCATTAGTC
*
31691 AGTTAAATTTGCTCTATCATACTGGATCTGTAT
1 AGTTAAATTTGCTCTATCACACTGGATCTGTAT
*
31724 AGTTAAA-TTGCTTTATCACACTGGATCTGTAT
1 AGTTAAATTTGCTCTATCACACTGGATCTGTAT
31756 A
1 A
31757 CTTTATCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (33 bp):
AGTTAAATTTGCTCTATCACACTGGATCTGTAT
Found at i:39587 original size:57 final size:56
Alignment explanation
Indices: 39512--39683 Score: 197
Period size: 57 Copynumber: 3.0 Consensus size: 56
39502 AATAGAGACC
* *
39512 CCGAAATCGAGTATATCTATCAATTTTTACTATTAATAAGTCCTAAAAAATAAGGGT
1 CCGAAATCGAGTATATCTATCAGTTTTTACTATTAAGAAG-CCTAAAAAATAAGGGT
* *
39569 CCGAAATCGAGTATATCTATCAGTTGTTGAC-ATTAAGAAG-CTCAAAAAAT-AGAGAT
1 CCGAAATCGAGTATATCTATCAGTT-TTTACTATTAAGAAGCCT-AAAAAATAAG-GGT
* * * * *
39625 CCCGAAATCGAGTATATCTATTAGTTGTTGCTATTAAGAAACCCAAAAAATAAGGGT
1 -CCGAAATCGAGTATATCTATCAGTTTTTACTATTAAGAAGCCTAAAAAATAAGGGT
39682 CC
1 CC
39684 AAAAATAAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
55 4 0.04
56 13 0.13
57 73 0.75
58 7 0.07
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (56 bp):
CCGAAATCGAGTATATCTATCAGTTTTTACTATTAAGAAGCCTAAAAAATAAGGGT
Found at i:40845 original size:29 final size:29
Alignment explanation
Indices: 40807--40883 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
40797 TAAAATTATC
40807 TTTTTGTTTTTGTTTTAACTTATTAAATA
1 TTTTTGTTTTTGTTTTAACTTATTAAATA
* * *
40836 TTTTTATTTTTGTCTTAATTTATTAAATA
1 TTTTTGTTTTTGTTTTAACTTATTAAATA
*
40865 TATTTTGTTTTTATTTTAA
1 T-TTTTGTTTTTGTTTTAA
40884 TGTAAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 27 0.66
30 14 0.34
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (29 bp):
TTTTTGTTTTTGTTTTAACTTATTAAATA
Found at i:41038 original size:28 final size:27
Alignment explanation
Indices: 41001--41067 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
40991 TATATTACTC
*
41001 TTACTTTTAATTAAAAATATTCAATATT
1 TTACTATTAATT-AAAATATTCAATATT
** * *
41029 TTACTATTAATTAATTTTTTTAATATT
1 TTACTATTAATTAAAATATTCAATATT
41056 TTACTATTAATT
1 TTACTATTAATT
41068 TATTTGGCGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (27 bp):
TTACTATTAATTAAAATATTCAATATT
Found at i:41204 original size:33 final size:34
Alignment explanation
Indices: 41126--41223 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 34
41116 AAATATTTTT
41126 AATTAATAGTAAAATATTAAATATTTTTAAATAA
1 AATTAATAGTAAAATATTAAATATTTTTAAATAA
* * * * *
41160 AAATAAGAGTAAAATA-TATATATTTTTATATTA
1 AATTAATAGTAAAATATTAAATATTTTTAAATAA
41193 AATTAATAGT-AAATATTTAAATATATTTTAA
1 AATTAATAGTAAAATA-TTAAATAT-TTTTAA
41224 GTTAAGATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
32 5 0.10
33 22 0.42
34 20 0.38
35 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (34 bp):
AATTAATAGTAAAATATTAAATATTTTTAAATAA
Found at i:41313 original size:29 final size:29
Alignment explanation
Indices: 41281--41357 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
41271 ATAATTTTAC
**
41281 ATTAAAATGAAAAC-AAAATATATTAATAA
1 ATTAAAACAAAAACAAAAATAT-TTAATAA
* *
41310 ATTAAGACAAAAATAAAAATATTTAATAA
1 ATTAAAACAAAAACAAAAATATTTAATAA
* *
41339 GTTAAAACAAAAATAAAAA
1 ATTAAAACAAAAACAAAAA
41358 AATAATTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 34 0.83
30 7 0.17
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (29 bp):
ATTAAAACAAAAACAAAAATATTTAATAA
Found at i:41358 original size:30 final size:30
Alignment explanation
Indices: 41295--41357 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
41285 AAATGAAAAC
*
41295 AAAATATATTAATAAATTAAGACAAAAATA
1 AAAATATATTAATAAATTAAAACAAAAATA
*
41325 AAAATAT-TTAATAAGTTAAAACAAAAATA
1 AAAATATATTAATAAATTAAAACAAAAATA
41354 AAAA
1 AAAA
41358 AATAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (30 bp):
AAAATATATTAATAAATTAAAACAAAAATA
Found at i:43666 original size:25 final size:26
Alignment explanation
Indices: 43633--43699 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
43623 ACTTAAATTA
*
43633 ATAATAAAATA-TATTAGTAAGTTAAT
1 ATAATAAAATATTATTA-AAAGTTAAT
*
43659 ATAA-AAAATATTTTTAAAAGTTAAT
1 ATAATAAAATATTATTAAAAGTTAAT
*
43684 ATATATAAAAAATTAT
1 ATA-ATAAAATATTAT
43700 AAATTTAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 17 0.50
26 9 0.26
27 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
ATAATAAAATATTATTAAAAGTTAAT
Done.