Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006978.1 Hibiscus syriacus cultivar Beakdansim tig00017970_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: 87375
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1476 original size:32 final size:32
Alignment explanation
Indices: 1398--1478 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
1388 AGATTCTTTG
* * *
1398 GATGGCTCCTCTTCGTGGTTTAAGCCAAATGC
1 GATGACTCCTCTTCGCGGTTTAAGCCAAATGA
* * *
1430 GATGAATCCCCTTCGCGGTTTAAGTCAAATGA
1 GATGACTCCTCTTCGCGGTTTAAGCCAAATGA
*
1462 GATGTCTCCTCTTCGCG
1 GATGACTCCTCTTCGCG
1479 AGACTAAGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (32 bp):
GATGACTCCTCTTCGCGGTTTAAGCCAAATGA
Found at i:1853 original size:71 final size:71
Alignment explanation
Indices: 1726--2007 Score: 221
Period size: 71 Copynumber: 4.1 Consensus size: 71
1716 AAGAAAATAA
* * * * * *
1726 GAAATTTTATTTCGAGAGAAACTATCTCGAGTGGGAC-AAAAAATTTCAAGGAAAAATACCACAT
1 GAAATTTTATTTCAAGAGAAACTGTCTCGAGTGAGACGAAAATA-TTCAAGGGAAAATATCACAT
1790 GTGAGAT
65 GTGAGAT
* * * * * * *
1797 AAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGGCGTAAATATTAAAGGGAAAATATTTA-AA
1 GAAATTTTATTTCAAGAGAAACTGTCTCGAGTGAGACGAAAATATTCAAGGGAAAATA-TCACAT
*
1861 GAGAGAT
65 GTGAGAT
* * **
1868 GAAATTTTGTTTC----G--A--GTCTCGAATGAGAAAAAAAGTATTCAA-GGAAAATATCACAT
1 GAAATTTTATTTCAAGAGAAACTGTCTCGAGTGAGACGAAAA-TATTCAAGGGAAAATATCACAT
1924 GTGAGAT
65 GTGAGAT
* * * * * *
1931 GAAATTTTATTTCAAGAGAAATTGTCTCGAGTGACATGTAAATTTTCAAGGGAAAATATCTCA--
1 GAAATTTTATTTCAAGAGAAACTGTCTCGAGTGAGACGAAAATATTCAAGGGAAAATATCACATG
*
1994 AGAGAT
66 TGAGAT
2000 GAAATTTT
1 GAAATTTT
2008 TTTTTGAGGA
Statistics
Matches: 165, Mismatches: 33, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
62 2 0.01
63 41 0.25
64 6 0.04
65 1 0.01
67 2 0.01
69 14 0.08
70 6 0.04
71 88 0.53
72 5 0.03
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (71 bp):
GAAATTTTATTTCAAGAGAAACTGTCTCGAGTGAGACGAAAATATTCAAGGGAAAATATCACATG
TGAGAT
Found at i:1916 original size:134 final size:131
Alignment explanation
Indices: 1763--2007 Score: 348
Period size: 134 Copynumber: 1.8 Consensus size: 131
1753 CGAGTGGGAC
*
1763 AAAAAATTTCAAGGAAAAATACCACATGTGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCGAG
1 AAAAAATTTCAAGGAAAAATACCACATGTGAGATAAAATTTTATTTCAAGAGAAACTGTCTCGAG
** *
1828 TGAGGCGTAAATATTAAAGGGAAAATATTTAAAGAGAGATGAAATTTTGTTTCGAGTCTCGAATG
66 TGACACGTAAATATTAAAGGGAAAATATCT-AA-AGAGATGAAATTTTGTTTCGAGTCTCGAATG
1893 AGA
129 AGA
* * *
1896 AAAAAAGTATTCAAGG-AAAATATCACATGTGAGATGAAATTTTATTTCAAGAGAAATTGTCTCG
1 AAAAAA-T-TTCAAGGAAAAATACCACATGTGAGATAAAATTTTATTTCAAGAGAAACTGTCTCG
* * * *
1960 AGTGACATGTAAATTTTCAAGGGAAAATATCTCAAGAGATGAAATTTT
64 AGTGACACGTAAATATTAAAGGGAAAATATCTAAAGAGATGAAATTTT
2008 TTTTTGAGGA
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
132 14 0.14
133 7 0.07
134 71 0.72
135 7 0.07
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (131 bp):
AAAAAATTTCAAGGAAAAATACCACATGTGAGATAAAATTTTATTTCAAGAGAAACTGTCTCGAG
TGACACGTAAATATTAAAGGGAAAATATCTAAAGAGATGAAATTTTGTTTCGAGTCTCGAATGAG
A
Found at i:7166 original size:22 final size:21
Alignment explanation
Indices: 7115--7192 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
7105 GTGATGTATG
* * *
7115 GGGTATCGATACTTGTATGAA
1 GGGTATCGATACCTATGTGAA
**
7136 CAGTATCGATACCATATG-GAA
1 GGGTATCGATACC-TATGTGAA
*
7157 GAGGTATCGATACCTATGTGGA
1 G-GGTATCGATACCTATGTGAA
*
7179 GGGTATCAATACCT
1 GGGTATCGATACCT
7193 GGTGGAACTT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
21 29 0.64
22 16 0.36
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGTATCGATACCTATGTGAA
Found at i:7197 original size:20 final size:21
Alignment explanation
Indices: 7159--7198 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7149 ATATGGAAGA
* *
7159 GGTATCGATACCTATGTGGAG
1 GGTATCAATACCTAGGTGGAG
7180 GGTATCAATACCT-GGTGGA
1 GGTATCAATACCTAGGTGGA
7199 ACTTCGAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (21 bp):
GGTATCAATACCTAGGTGGAG
Found at i:8176 original size:30 final size:31
Alignment explanation
Indices: 8109--8179 Score: 99
Period size: 32 Copynumber: 2.3 Consensus size: 31
8099 GAGTCGAGGG
* *
8109 TTACCTATGTCCTTCGGGACATATGGACAGGA
1 TTACCTATGGCCTTCGGGACATATAGACA-GA
*
8141 TTACCTATGGCCTTTGGGACATATAGACA-A
1 TTACCTATGGCCTTCGGGACATATAGACAGA
8171 TTACCTATG
1 TTACCTATG
8180 TTCTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 10 0.28
32 26 0.72
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (31 bp):
TTACCTATGGCCTTCGGGACATATAGACAGA
Found at i:15756 original size:21 final size:22
Alignment explanation
Indices: 15712--15764 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
15702 GTATTAATAA
15712 TATCGATACCATATGGAAGAGG
1 TATCGATACCATATGGAAGAGG
*
15734 TATCGATACC-TATGTGGAG-GG
1 TATCGATACCATATG-GAAGAGG
*
15755 TATTGATACC
1 TATCGATACC
15765 CGGTGGAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (22 bp):
TATCGATACCATATGGAAGAGG
Found at i:16575 original size:30 final size:31
Alignment explanation
Indices: 16509--16579 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
16499 TTGGTTCTGG
** *
16509 ACATATGGACAGGATTACCTATGTCCTTTGGG
1 ACATATGGACA-GATTACCTATGTCCTTCAGA
*
16541 ACATATGGACA-ATTACCTATGTTCTTCAGA
1 ACATATGGACAGATTACCTATGTCCTTCAGA
16571 ACATATGGA
1 ACATATGGA
16580 TAGGTCCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 24 0.69
32 11 0.31
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGATTACCTATGTCCTTCAGA
Found at i:27413 original size:47 final size:45
Alignment explanation
Indices: 27345--27486 Score: 181
Period size: 47 Copynumber: 3.3 Consensus size: 45
27335 ATAAAATCTT
*
27345 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
27390 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
*
27437 TTGCCA-TTATT-CATAAGCTCGTAAGCTTA-TTTA-C---ATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
27475 TTACCATTTATT
1 TTACCATTTATT
27487 AACCAATAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
38 9 0.10
39 5 0.06
41 1 0.01
42 4 0.04
43 18 0.20
44 3 0.03
45 9 0.10
46 2 0.02
47 38 0.43
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:30221 original size:119 final size:119
Alignment explanation
Indices: 30086--30348 Score: 393
Period size: 119 Copynumber: 2.2 Consensus size: 119
30076 GGGTATCGGC
* * *
30086 ACTACTATATTCAGTAGTATCGATAC-GATATATAGTATCGATACCATTTTAGTATACTCGAATT
1 ACTACTATACTAAGTAGTATCGATACTG-TATATAGTATCGATACCATTTTAGAATACTCGAATT
*
30150 TTGACGGATTCAAAGCCAAAAAGGTAGTATCGGTACCACCACTTAGAGAATCGAT
65 TTGACGGATTCAAAACCAAAAAGGTAGTATCGGTACCACCACTTAGAGAATCGAT
* * ** *
30205 ACTACTATACTAAGTAGTATCGATACTGTGTATAGTATCGGTACCATTTTAGAATTTTGGAATTT
1 ACTACTATACTAAGTAGTATCGATACTGTATATAGTATCGATACCATTTTAGAATACTCGAATTT
* * * *
30270 TTACGGATTCAAAACCAAAAAGGTAGTATCTGTACCACCACTTAGAGTATCGGT
66 TGACGGATTCAAAACCAAAAAGGTAGTATCGGTACCACCACTTAGAGAATCGAT
30324 ACTACTATACTAAGTAGTATCGATA
1 ACTACTATACTAAGTAGTATCGATA
30349 TCATTTTAGT
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
119 129 0.99
120 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (119 bp):
ACTACTATACTAAGTAGTATCGATACTGTATATAGTATCGATACCATTTTAGAATACTCGAATTT
TGACGGATTCAAAACCAAAAAGGTAGTATCGGTACCACCACTTAGAGAATCGAT
Found at i:32029 original size:28 final size:27
Alignment explanation
Indices: 31989--32069 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 27
31979 GAAGGACCAC
*
31989 TATGTCACGAAGGACCACATAGAACACA
1 TATGTC-CGAAGGACCACGTAGAACACA
32017 TATGTCCTGAAGGACCACGTAGAACACA
1 TATGTCC-GAAGGACCACGTAGAACACA
*
32045 TATATCCCGAAGGACCACGTAGAAC
1 TATGT-CCGAAGGACCACGTAGAAC
32070 CCTATAGTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.02
28 46 0.94
29 2 0.04
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (27 bp):
TATGTCCGAAGGACCACGTAGAACACA
Found at i:33502 original size:13 final size:13
Alignment explanation
Indices: 33474--33520 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
33464 TAGTTGACCC
*
33474 GACCCGA-CCATT
1 GACCCGACCCGTT
33486 GACCCGACCCGTT
1 GACCCGACCCGTT
33499 GACCCGACCCGTT
1 GACCCGACCCGTT
33512 GACCCGACC
1 GACCCGACC
33521 TGACCGTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 7 0.21
13 26 0.79
ACGTcount: A:0.19, C:0.47, G:0.21, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:33529 original size:17 final size:16
Alignment explanation
Indices: 33452--33532 Score: 66
Period size: 17 Copynumber: 5.2 Consensus size: 16
33442 GACTGGTCAC
**
33452 GACCCGACCCGATAGTT
1 GACCCGA-CCGACCGTT
*
33469 GACCCGACCCGACCATT
1 GACCCGA-CCGACCGTT
33486 GACCCGA-C--CCGTT
1 GACCCGACCGACCGTT
33499 GACCCGA-C--CCGTT
1 GACCCGACCGACCGTT
33512 GACCCGACCTGACCGTT
1 GACCCGACC-GACCGTT
33529 GACC
1 GACC
33533 TTTGACCGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
13 24 0.43
14 1 0.02
15 1 0.02
17 30 0.54
ACGTcount: A:0.20, C:0.43, G:0.22, T:0.15
Consensus pattern (16 bp):
GACCCGACCGACCGTT
Found at i:33537 original size:7 final size:7
Alignment explanation
Indices: 33521--33561 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
33511 TGACCCGACC
33521 TGACCGT
1 TGACCGT
*
33528 TGACCTT
1 TGACCGT
33535 TGACCGT
1 TGACCGT
33542 TGACCGT
1 TGACCGT
33549 TGACCGT
1 TGACCGT
33556 TGACCG
1 TGACCG
33562 GTGCTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.29
Consensus pattern (7 bp):
TGACCGT
Found at i:40745 original size:17 final size:17
Alignment explanation
Indices: 40723--40803 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 17
40713 GACCGGTCAC
*
40723 GACCCGACCCGATAGTT
1 GACCCGACCCGACAGTT
*
40740 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
40757 GACCCGA-CC--C-GTT
1 GACCCGACCCGACAGTT
40770 GACCCGA-CC--C-GTT
1 GACCCGACCCGACAGTT
*
40783 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
40800 GACC
1 GACC
40804 GTTGACCGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
13 23 0.40
14 3 0.05
16 3 0.05
17 29 0.50
ACGTcount: A:0.19, C:0.44, G:0.23, T:0.14
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:40770 original size:13 final size:13
Alignment explanation
Indices: 40745--40793 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
40735 TAGTTGACCC
40745 GACCCGA-CCGTT
1 GACCCGACCCGTT
40757 GACCCGACCCGTT
1 GACCCGACCCGTT
40770 GACCCGACCCGTT
1 GACCCGACCCGTT
40783 GACCCGACCCG
1 GACCCGACCCG
40794 ACCGTTGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 7 0.19
13 29 0.81
ACGTcount: A:0.16, C:0.47, G:0.24, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:40805 original size:7 final size:7
Alignment explanation
Indices: 40793--40832 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
40783 GACCCGACCC
40793 GACCGTT
1 GACCGTT
40800 GACCGTT
1 GACCGTT
40807 GACCGTT
1 GACCGTT
40814 GACCGTT
1 GACCGTT
*
40821 GAACGTT
1 GACCGTT
40828 GACCG
1 GACCG
40833 GTGCTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:62787 original size:72 final size:73
Alignment explanation
Indices: 62609--62798 Score: 233
Period size: 75 Copynumber: 2.6 Consensus size: 73
62599 TTTTATCTTT
* * * **
62609 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTATC
1 GTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTTAGAATATTATTTAAATATTTA-C
* *
62674 TTTGTTTTAG
64 TGTGTTTTAC
*
62684 GTATTTTACTTTAAATAGATTTTAGTATTTTAATTAGGATTTAGAATATTATTATAAATA-TTA-
1 GTATTTTAGTTTAAATAG-TTTTAGTATTTTAATTAGGATTTAGAATATTATT-TAAATATTTAC
62747 TGT-TTTTAC
64 TGTGTTTTAC
*
62756 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
62799 AGATGTTTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
71 4 0.04
72 41 0.40
73 2 0.02
74 1 0.01
75 50 0.49
76 4 0.04
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.55
Consensus pattern (73 bp):
GTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTAAATATTTACTG
TGTTTTAC
Found at i:63467 original size:18 final size:18
Alignment explanation
Indices: 63444--63485 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
63434 AAAACCCTTT
63444 TTTATTTTACTACTATTA
1 TTTATTTTACTACTATTA
* * *
63462 TTTATTATATTATTATTA
1 TTTATTTTACTACTATTA
63480 -TTATTT
1 TTTATTT
63486 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTTACTACTATTA
Found at i:69041 original size:27 final size:27
Alignment explanation
Indices: 69003--69055 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
68993 GGGAGGTAAC
*
69003 CCATTTCA-TTTTATTTTTTTATTTTTT
1 CCATTTCATTTTTATTTTATT-TTTTTT
*
69030 CCATTTTATTTTTATTTTATTTTTTT
1 CCATTTCATTTTTATTTTATTTTTTT
69056 AGCAAACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.75
Consensus pattern (27 bp):
CCATTTCATTTTTATTTTATTTTTTTT
Found at i:69088 original size:5 final size:5
Alignment explanation
Indices: 69063--69110 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
69053 TTTAGCAAAC
* * *
69063 TTTAT TTTCAT TCTA- TTTAT TTTAT TTTAA TTAAT TTTAT TTTAT TTT
1 TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
69111 TCTCTGAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 3 0.09
5 28 0.80
6 4 0.11
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:71059 original size:71 final size:74
Alignment explanation
Indices: 70878--71067 Score: 257
Period size: 76 Copynumber: 2.6 Consensus size: 74
70868 TTTTATCTTT
* * *
70878 GTATTTTAGTTTAAATAGGTTTTAGTATTTAAATTAAGTTTTAGGATATTATTTTTATAATTTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGATATTATTTTTATAATTTA-
70943 CTTTGTTTTAG
65 -TTTGTTTTAG
70954 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA-GAGTATTA-TTTTA-AATATT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGA-TATTATTTTTATAAT-TT
71016 A-TT-TTTTAG
64 ATTTGTTTTAG
*
71025 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
71068 AGATGTTTTA
Statistics
Matches: 107, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
70 5 0.05
71 42 0.39
72 2 0.02
74 3 0.03
75 10 0.09
76 45 0.42
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (74 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGATATTATTTTTATAATTTAT
TTGTTTTAG
Found at i:71735 original size:18 final size:17
Alignment explanation
Indices: 71712--71756 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
71702 AAAACCCCTT
71712 TTTATTTTACTACTATTA
1 TTTATTTTA-TACTATTA
*
71730 TTTATTATTATATTATTA
1 TTTATT-TTATACTATTA
71748 TTTATTTTA
1 TTTATTTTA
71757 AAATCTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTTTATACTATTA
Found at i:72885 original size:8 final size:9
Alignment explanation
Indices: 72866--72896 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
72856 AAACAAAGAT
72866 AAAAATGAA
1 AAAAATGAA
72875 AAAAATGAAA
1 AAAAATG-AA
72885 AAAAATGAA
1 AAAAATGAA
72894 AAA
1 AAA
72897 GTAGAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAATGAA
Found at i:72886 original size:10 final size:10
Alignment explanation
Indices: 72866--72896 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
72856 AAACAAAGAT
72866 AAAAATG-AA
1 AAAAATGAAA
72875 AAAAATGAAA
1 AAAAATGAAA
72885 AAAAATGAAA
1 AAAAATGAAA
72895 AA
1 AA
72897 GTAGAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:74278 original size:22 final size:21
Alignment explanation
Indices: 74234--74279 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
74224 GTGTTTCATG
* *
74234 TTTTAAAAGATTTATACACAT
1 TTTTAAAACATTTATAAACAT
*
74255 TTTTAAAACACTTTATAAATAT
1 TTTTAAAACA-TTTATAAACAT
74277 TTT
1 TTT
74280 AATCAACTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTAAAACATTTATAAACAT
Done.