Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003199.1 Hibiscus syriacus cultivar Beakdansim tig00006733_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: 54971
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1518 original size:20 final size:19
Alignment explanation
Indices: 1463--1509 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1453 TCCGGTATCG
1463 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1482 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1503 TTTTACC
1 TTTTACC
1510 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1687 original size:20 final size:19
Alignment explanation
Indices: 1641--1700 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1631 ATCCGTAACG
1641 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1660 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
*
1681 TTTTACCTGG-TATATCATT
1 TTTTACC-GGTTTTATCATT
1700 T
1 T
1701 GGATCGATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 4 0.11
20 26 0.74
21 5 0.14
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1792 original size:178 final size:180
Alignment explanation
Indices: 1430--1883 Score: 656
Period size: 178 Copynumber: 2.6 Consensus size: 180
1420 CGTACTTACA
*
1430 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
1495 TATCATATTTTTACCTGTTATATC-GTTGGATTGATATATTTTTTTAAAGTATCGACACATTATA
66 TATCATATTTTTACCTGTTATATCATTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
*
1559 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
1609 AAAGTATCGACACTTTCAATATATCC-GTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1673 TATCATATTTTTACCTGGTATATCATTTGGATCGATACATTTTTTAAAAGTATCGACACTTTATA
66 TATCATATTTTTACCTGTTATATCATTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
** *
1738 GGATTTAAAACTGC-T-TCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * *
1787 AAAGTACCGACAC-TT-AATGTATCCGGTAGCGCTTTACCGG--TTATCATTTTAATA-CGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1847 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGAT
66 TATCATATTTTTACCTGTTATATCA-TTTGGATCGAT
1884 TTTTAATTTG
Statistics
Matches: 251, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
174 27 0.11
175 24 0.10
176 8 0.03
177 46 0.18
178 74 0.29
179 72 0.29
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCATTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:3104 original size:36 final size:37
Alignment explanation
Indices: 3064--3141 Score: 90
Period size: 36 Copynumber: 2.1 Consensus size: 37
3054 TATATATATA
*
3064 TATTTATATTTTCT-TCATGTTA-TTTATT-TTATTTTT
1 TATTTATATTTT-TAACATGTTACTTTATTATT-TTTTT
* *
3100 TATTTTTATTTTTAACATTTTACTTTATTATTTTTTT
1 TATTTATATTTTTAACATGTTACTTTATTATTTTTTT
3137 TATTT
1 TATTT
3142 TCTAACCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 1 0.03
36 17 0.47
37 16 0.44
38 2 0.06
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (37 bp):
TATTTATATTTTTAACATGTTACTTTATTATTTTTTT
Found at i:3127 original size:32 final size:31
Alignment explanation
Indices: 3086--3163 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
3076 CTTCATGTTA
3086 TTTATTTTATTTTTTATTTTTATTTT-TAACAT
1 TTTA-TTTATTTTTT-TTTTTATTTTCTAACAT
* *
3118 TTTACTTTATTATTTTTTTTATTTTCTAACCT
1 TTTA-TTTATTTTTTTTTTTATTTTCTAACAT
3150 TTT-TTTATTTTTTT
1 TTTATTTATTTTTTT
3164 GCTTCTCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 10 0.24
31 10 0.24
32 21 0.51
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTATTTATTTTTTTTTTTATTTTCTAACAT
Found at i:3869 original size:17 final size:17
Alignment explanation
Indices: 3847--3903 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
3837 CTTATGTCTT
3847 CGTATGAATTTATTCTC
1 CGTATGAATTTATTCTC
3864 CGTATGAATTTATTCTC
1 CGTATGAATTTATTCTC
3881 CGTATGAATTTATTCTC
1 CGTATGAATTTATTCTC
*
3898 TGTATG
1 CGTATG
3904 GGCATAAGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (17 bp):
CGTATGAATTTATTCTC
Found at i:3890 original size:34 final size:35
Alignment explanation
Indices: 3838--3903 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
3828 TTCATATATC
*
3838 TTATGTCTTCGTATGAATTTATTCTCCGTATGAAT
1 TTATGTCTCCGTATGAATTTATTCTCCGTATGAAT
*
3873 TTAT-TCTCCGTATGAATTTATTCTCTGTATG
1 TTATGTCTCCGTATGAATTTATTCTCCGTATG
3904 GGCATAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 25 0.86
35 4 0.14
ACGTcount: A:0.21, C:0.15, G:0.14, T:0.50
Consensus pattern (35 bp):
TTATGTCTCCGTATGAATTTATTCTCCGTATGAAT
Found at i:7211 original size:64 final size:63
Alignment explanation
Indices: 7102--7285 Score: 208
Period size: 64 Copynumber: 2.9 Consensus size: 63
7092 TAATGAAGGT
* * * ** ** * **
7102 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATACATCGATGCACCAATTGCATTCGATGT-TTATTATTAATGGG
* **
7166 ATGCATCGATGCACTCCTTATGTATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATACATCGATGCACCAATTGCATTCGATGTTT-ATTATTAATGGG
**
7230 ATGCATCGATGCACTACTTATACATCGATGCATGAATTGCATTCGATGTTT-TTATT
1 ATGCATCGATGCACTACTTATACATCGATGCACCAATTGCATTCGATGTTTATTATT
7286 TTAAAAGAGT
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
62 5 0.05
63 2 0.02
64 96 0.93
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATACATCGATGCACCAATTGCATTCGATGTTTATTATTAATGGG
Found at i:7320 original size:64 final size:64
Alignment explanation
Indices: 7102--7327 Score: 192
Period size: 64 Copynumber: 3.5 Consensus size: 64
7092 TAATGAAGGT
* ** ** * *** *
7102 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGG
1 ATGCATCGATGCACTACCT-ATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGA
7165 G
64 G
* * *
7166 ATGCATCGATGCACT-CCTTATGTATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACC-TATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
* * ** *
7230 ATGCATCGATGCACTACTTATACATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
* *
7293 AGTGCATCGATGCACTACCAATGCATCGATACACC
1 A-TGCATCGATGCACTACCTATGCATCGATGCACC
7328 TTCAAACAAT
Statistics
Matches: 133, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
63 4 0.03
64 121 0.91
65 8 0.06
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:17002 original size:21 final size:21
Alignment explanation
Indices: 16976--17015 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16966 CAGAACCCCA
*
16976 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
16997 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
17016 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:17050 original size:20 final size:21
Alignment explanation
Indices: 16996--17058 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
16986 GATTCCCCTG
16996 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
17020 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
17040 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
17059 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:20908 original size:22 final size:21
Alignment explanation
Indices: 20866--20905 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20856 GAGTTTGTTT
*
20866 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
20887 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
20906 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:23189 original size:12 final size:12
Alignment explanation
Indices: 23172--23217 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
23162 ATTTTCAACA
**
23172 CATATCACAGGT
1 CATATCACATAT
23184 CATATCACATAT
1 CATATCACATAT
23196 CATATCACATAT
1 CATATCACATAT
23208 CATATCACAT
1 CATATCACAT
23218 GAACATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.30
Consensus pattern (12 bp):
CATATCACATAT
Found at i:23636 original size:64 final size:63
Alignment explanation
Indices: 23528--23711 Score: 244
Period size: 64 Copynumber: 2.9 Consensus size: 63
23518 TAATGAAGGT
* * ** * **
23528 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
23592 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
*
23656 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATT
23712 TTAAAAGAGT
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
62 5 0.05
63 2 0.02
64 99 0.93
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:23725 original size:64 final size:64
Alignment explanation
Indices: 23528--23736 Score: 217
Period size: 64 Copynumber: 3.3 Consensus size: 64
23518 TAATGAAGGT
* * ** ** * *** *
23528 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * *
23592 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
23656 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
23719 AGTGCATCGATGCACTAC
1 A-TGCATCGATGCACTAC
23737 CAATGCATGT
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
63 4 0.03
64 116 0.92
65 6 0.05
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:26028 original size:100 final size:100
Alignment explanation
Indices: 25786--26127 Score: 358
Period size: 94 Copynumber: 3.4 Consensus size: 100
25776 GCTTCCCAAT
* * * *
25786 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAAACAACACAAACTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
*
25851 CAGCGAAGGGGCGGCTGACTGTCAACAAACA--AC-
66 CAGCGAAGGGGCGGCTGACTGTCAACAAA-ATTTCA
* *
25884 TTC----CCAATTTCAACTTCACAGCGAAGGATATTGGAC-CAAAGACAACACAAGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTC-AAGACAACACAAGCTCAACTTC
** * * * *
25944 ACAATGAATGAGCGGCTGATTATCAACAAAATTTCA
65 ACAGCGAAGGGGCGGCTGACTGTCAACAAAATTTCA
* * * * * *
25980 TTCAGAGTCAATTTCAACTTCACAACGAATGATATTAGACTCGAGACAACAAAAGATCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
26045 CAGCGAAGGGGCGGCTGACTGTCAACAAATAATTTCCCA
66 CAGCGAAGGGGCGGCTGACTGTCAAC-AA-AATTT--CA
* * *
26084 GTTCCAGAACCAATTTCAACTTCACGACGGAGGATATTAGACTC
1 -TT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTC
26128 GGAACAATAC
Statistics
Matches: 201, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
93 2 0.01
94 77 0.38
95 1 0.00
96 3 0.01
98 3 0.01
100 68 0.34
101 3 0.01
102 5 0.02
104 2 0.01
105 2 0.01
106 35 0.17
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (100 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CAGCGAAGGGGCGGCTGACTGTCAACAAAATTTCA
Found at i:26513 original size:111 final size:111
Alignment explanation
Indices: 26385--26605 Score: 336
Period size: 111 Copynumber: 2.0 Consensus size: 111
26375 GCAACTTACA
* * *
26385 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTTAC-AATGAATGGGCCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACGAAT-AAGGGGCCA
*
26449 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGTTCACCAGCAAC
65 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAAC
* * * *
26496 TTGGATTTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACGACTTAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACGAATAAGGGGCCAT
* *
26561 CCACGGTTTCAATTTCACGACGAAGGGAATTGTGCTCACCAGCAA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAA
26606 TATTCATCTT
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
111 97 0.98
112 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (111 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACGAATAAGGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAAC
Found at i:26720 original size:29 final size:30
Alignment explanation
Indices: 26675--26733 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
26665 AAGGGGTCAT
26675 ATCTCTTGAGATAGTTTCCCT-TGAAACAAA
1 ATCTCTTGAGATAGTTTCCCTAT-AAACAAA
*
26705 ATCT-TTGA-ATATGTTTTCCTATAAACAAA
1 ATCTCTTGAGATA-GTTTCCCTATAAACAAA
26734 TTTCGTCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (30 bp):
ATCTCTTGAGATAGTTTCCCTATAAACAAA
Found at i:26818 original size:21 final size:20
Alignment explanation
Indices: 26793--26857 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
26783 TGAGACGGTT
26793 TCTCTTGAAACAAATTTTATC
1 TCTCTTGAAACAAATTTT-TC
* *
26814 TCTCTTGAGAC--A-GTTTC
1 TCTCTTGAAACAAATTTTTC
26831 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTT-TC
26850 TCTCTTGA
1 TCTCTTGA
26858 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 15 0.44
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.42
Consensus pattern (20 bp):
TCTCTTGAAACAAATTTTTC
Found at i:26823 original size:36 final size:36
Alignment explanation
Indices: 26727--26876 Score: 201
Period size: 36 Copynumber: 4.1 Consensus size: 36
26717 GTTTTCCTAT
* * * **
26727 AAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
26763 GAACTAAGTTTTGTCTCTCTTGAGACGGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
26800 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
26836 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
26872 AAACA
1 AAACA
26877 CCAATCTTTG
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 71 0.71
37 29 0.29
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:27784 original size:20 final size:20
Alignment explanation
Indices: 27761--27816 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
27751 AGTTTCCAAA
*
27761 TTCGCAACGCGATTTTATTT
1 TTCGCAACGCGAATTTATTT
27781 TTCGCAACGCGAATTTATTT
1 TTCGCAACGCGAATTTATTT
27801 TTCGCAACGCGAATTT
1 TTCGCAACGCGAATTT
27817 CCAAATTCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (20 bp):
TTCGCAACGCGAATTTATTT
Found at i:28881 original size:21 final size:21
Alignment explanation
Indices: 28855--28900 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
28845 TTTGGTTTGT
28855 GAAACTTTAAGTTCGCATTGC
1 GAAACTTTAAGTTCGCATTGC
28876 GAAACTTTAAGTTCGCATTGC
1 GAAACTTTAAGTTCGCATTGC
28897 GAAA
1 GAAA
28901 ATAAACATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (21 bp):
GAAACTTTAAGTTCGCATTGC
Found at i:29082 original size:20 final size:21
Alignment explanation
Indices: 28968--29091 Score: 87
Period size: 20 Copynumber: 6.0 Consensus size: 21
28958 TTTATCAGAT
* *
28968 AAAATCGCGTTGCGAATTTGG
1 AAAATCGTGTTGCGAAATTGG
* * * *
28989 AAATTCGCGTTGCAAAAAAT--
1 AAAATCGTGTTGC-GAAATTGG
* *
29009 AAAATCGCGTTGCGAATTTGG
1 AAAATCGTGTTGCGAAATTGG
*
29030 AAAATCGTGTTGCGAAAAAT--
1 AAAATCGTGTTGCG-AAATTGG
** *
29050 AAAATCGCATTGCGAATTTGG
1 AAAATCGTGTTGCGAAATTGG
29071 AAAAT-GTGTTGCGAAATTGG
1 AAAATCGTGTTGCGAAATTGG
29091 A
1 A
29092 GTTCGCGTTG
Statistics
Matches: 79, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
19 6 0.08
20 37 0.47
21 30 0.38
22 6 0.08
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (21 bp):
AAAATCGTGTTGCGAAATTGG
Found at i:29109 original size:40 final size:41
Alignment explanation
Indices: 28966--29086 Score: 199
Period size: 41 Copynumber: 3.0 Consensus size: 41
28956 AGTTTATCAG
* * *
28966 ATAAAATCGCGTTGCGAATTTGGAAATTCGCGTTGCAAAAA
1 ATAAAATCGCGTTGCGAATTTGGAAAATCGTGTTGCGAAAA
29007 ATAAAATCGCGTTGCGAATTTGGAAAATCGTGTTGCGAAAA
1 ATAAAATCGCGTTGCGAATTTGGAAAATCGTGTTGCGAAAA
*
29048 ATAAAATCGCATTGCGAATTTGGAAAAT-GTGTTGCGAAA
1 ATAAAATCGCGTTGCGAATTTGGAAAATCGTGTTGCGAAA
29087 TTGGAGTTCG
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
40 11 0.14
41 65 0.86
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.27
Consensus pattern (41 bp):
ATAAAATCGCGTTGCGAATTTGGAAAATCGTGTTGCGAAAA
Found at i:30109 original size:19 final size:19
Alignment explanation
Indices: 30085--30121 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30075 TATATATATA
*
30085 TATTTTCTTCATGTTATTT
1 TATTTTATTCATGTTATTT
*
30104 TATTTTATTTATGTTATT
1 TATTTTATTCATGTTATT
30122 ATTTTTAACA
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:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (19 bp):
TATTTTATTCATGTTATTT
Found at i:30137 original size:23 final size:21
Alignment explanation
Indices: 30111--30171 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 21
30101 TTTTATTTTA
30111 TTTATGTTATTATTTTTAACATT
1 TTTAT-TTATT-TTTTTAACATT
*
30134 TTTACTTTATTTTTTCTAACCTT
1 TTTA-TTTATTTTTT-TAACATT
30157 TTT-TTTATTCTTTTT
1 TTTATTTATT-TTTTT
30172 GCTTCTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 7 0.21
22 8 0.24
23 18 0.53
24 1 0.03
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTATTTATTTTTTTAACATT
Found at i:36524 original size:81 final size:81
Alignment explanation
Indices: 36389--36551 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
36379 ACCTATATAT
36389 AATTTTTCATAACCAGTGCCCCATCACTGTTCATTCGATTTTTCCATCTCGTTTTCAAATCTTTC
1 AATTTTTCATAACCAGTGCCCCATCACTGTTCATTCGATTTTTCCATCTCGTTTTCAAATCTTTC
36454 TTCGTTAATTTTCTCG
66 TTCGTTAATTTTCTCG
36470 AATTTTTCATAACCAGTGCCCCATCACTGTTCATTCGATTTTTCCATCTCGTTTTCAAATCTTTC
1 AATTTTTCATAACCAGTGCCCCATCACTGTTCATTCGATTTTTCCATCTCGTTTTCAAATCTTTC
36535 TTCGTTAATTTTCTCG
66 TTCGTTAATTTTCTCG
36551 A
1 A
36552 GAAAAAAATG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.20, C:0.26, G:0.09, T:0.45
Consensus pattern (81 bp):
AATTTTTCATAACCAGTGCCCCATCACTGTTCATTCGATTTTTCCATCTCGTTTTCAAATCTTTC
TTCGTTAATTTTCTCG
Found at i:44211 original size:85 final size:85
Alignment explanation
Indices: 44080--44337 Score: 277
Period size: 85 Copynumber: 3.0 Consensus size: 85
44070 GACACGCAAT
* * * * *
44080 TGTGTCATAAATCTATGACACACATTTATAAAGTT-CATTGAGCGTCATTGAAGCCCCCGTCATA
1 TGTGTCATAAATTTATGACACGCATGTAT-AACTTACATTGAACGTCATTGAAGCCCCCGTCATA
44144 AATAAAGATGACACACATTTG
65 AATAAAGATGACACACATTTG
* * *
44165 TGTGTCATAAATTTATGACTCGCATGTATAACTTACATTGAACGTCATTGAATCCCCCATCATAA
1 TGTGTCATAAATTTATGACACGCATGTATAACTTACATTGAACGTCATTGAAGCCCCCGTCATAA
** ** * * *
44230 ATCTACTTGACATAAATTTA
66 ATAAAGATGACACACATTTG
* ** * * * *
44250 TGTGTCATAAATTTATGAAACGCATGTATGGCTTACATTGCATGTCATTGAAGCACACGTCATTA
1 TGTGTCATAAATTTATGACACGCATGTATAACTTACATTGAACGTCATTGAAGCCCCCGTCA-TA
*
44315 AA-AAAGATGACACACATTCG
65 AATAAAGATGACACACATTTG
44335 TGT
1 TGT
44338 ATCGTGATTG
Statistics
Matches: 138, Mismatches: 33, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
84 4 0.03
85 130 0.94
86 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (85 bp):
TGTGTCATAAATTTATGACACGCATGTATAACTTACATTGAACGTCATTGAAGCCCCCGTCATAA
ATAAAGATGACACACATTTG
Found at i:44623 original size:11 final size:11
Alignment explanation
Indices: 44607--44631 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44597 TTCCTTCCCC
44607 AATAGAGCTCT
1 AATAGAGCTCT
44618 AATAGAGCTCT
1 AATAGAGCTCT
44629 AAT
1 AAT
44632 TTCTTAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (11 bp):
AATAGAGCTCT
Found at i:48135 original size:3 final size:3
Alignment explanation
Indices: 48127--48155 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
48117 AGTTTCAAAA
48127 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
48156 TTTCATGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:49868 original size:65 final size:63
Alignment explanation
Indices: 49749--49958 Score: 203
Period size: 65 Copynumber: 3.3 Consensus size: 63
49739 TTTATCAAAG
* * *
49749 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
49811 ATT
61 ATT
* *
49814 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
49878 T
63 T
* * * * * * *
49879 TGTTGTATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
49943 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
49959 TCTTAGTAAG
Statistics
Matches: 121, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 45 0.37
65 67 0.55
66 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Done.