Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001226.1 Hibiscus syriacus cultivar Beakdansim tig00002415_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: 75275
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1343 original size:2 final size:2
Alignment explanation
Indices: 1327--1364 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1317 CGTGGTCTAA
1327 AT AT CAT AT AT -T 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
1365 GTGGCCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2770 original size:14 final size:13
Alignment explanation
Indices: 2728--2770 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
2718 CTATATCGGT
2728 AATTGAGTTGCGA
1 AATTGAGTTGCGA
*
2741 AATTGGATTTGCGA
1 AATT-GAGTTGCGA
*
2755 AATTCGAGTTGTGA
1 AATT-GAGTTGCGA
2769 AA
1 AA
2771 ACGAAATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (13 bp):
AATTGAGTTGCGA
Found at i:2777 original size:20 final size:20
Alignment explanation
Indices: 2752--2789 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2742 ATTGGATTTG
2752 CGAAATTCGA-GTTGTGAAAA
1 CGAAATTC-ACGTTGTGAAAA
2772 CGAAATTCACGTTGTGAA
1 CGAAATTCACGTTGTGAA
2790 TCACTCAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (20 bp):
CGAAATTCACGTTGTGAAAA
Found at i:2970 original size:20 final size:22
Alignment explanation
Indices: 2928--2971 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2918 AAATTTACAC
2928 TTCGCAACACGAATTTGTCAAA
1 TTCGCAACACGAATTTGTCAAA
*
2950 TTCGCAACTC-AATTT-TCAAA
1 TTCGCAACACGAATTTGTCAAA
2970 TT
1 TT
2972 GGTGAATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (22 bp):
TTCGCAACACGAATTTGTCAAA
Found at i:3099 original size:20 final size:20
Alignment explanation
Indices: 3019--3101 Score: 94
Period size: 20 Copynumber: 4.0 Consensus size: 20
3009 GTAATTGAAG
3019 CGAAATTCGCGTTGCTGCAAGAA
1 CGAAATTCGCGTTGC-G-AA-AA
* *
3042 CGAAATTTGCGTTGCGAGAA
1 CGAAATTCGCGTTGCGAAAA
*
3062 CGAAATTCGCGTTACGAAAA
1 CGAAATTCGCGTTGCGAAAA
* *
3082 CAAAATTCGCTTTGCGAAAA
1 CGAAATTCGCGTTGCGAAAA
3102 TTTTCATGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
20 36 0.69
21 1 0.02
22 1 0.02
23 14 0.27
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (20 bp):
CGAAATTCGCGTTGCGAAAA
Found at i:6872 original size:28 final size:28
Alignment explanation
Indices: 6840--6894 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
6830 TTTATTAAGC
6840 GAGGGAAAATAAATTTCAT-CTATAACAA
1 GAGGGAAAATAAATTTCATAC-ATAACAA
*
6868 GAGGGAAAGTAAATTTCATACATAACA
1 GAGGGAAAATAAATTTCATACATAACA
6895 TGATGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (28 bp):
GAGGGAAAATAAATTTCATACATAACAA
Found at i:7147 original size:27 final size:26
Alignment explanation
Indices: 7091--7148 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
7081 TTAAATGGGG
* * *
7091 TTCGGGTTGGGTTTTTTAAGTTTATC
1 TTCGGGTCGGGTTTTTTAAGTTAATA
7117 TTCGGGTCGGGTTTTTTAAGTGTAATA
1 TTCGGGTCGGGTTTTTTAAGT-TAATA
7144 TTCGG
1 TTCGG
7149 TTTGACGACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.14, C:0.09, G:0.29, T:0.48
Consensus pattern (26 bp):
TTCGGGTCGGGTTTTTTAAGTTAATA
Found at i:10617 original size:19 final size:19
Alignment explanation
Indices: 10589--10633 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
10579 ATTTTGCTTA
*
10589 TTAAACAATTTTCAACAAT
1 TTAAACAATTTCCAACAAT
* *
10608 TTAAATAATTTCCACCAAT
1 TTAAACAATTTCCAACAAT
10627 TTAAACA
1 TTAAACA
10634 GGGTATGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAACAATTTCCAACAAT
Found at i:21975 original size:2 final size:2
Alignment explanation
Indices: 21970--21999 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21960 ACAATATACA
21970 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
22000 TCTTCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22527 original size:24 final size:24
Alignment explanation
Indices: 22500--22546 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
22490 CTTTTTAATT
*
22500 TATTTAAAATATAA-ATGTATTATA
1 TATTT-AAATATAATATGAATTATA
*
22524 TATTTTAATATAATATGAATTAT
1 TATTTAAATATAATATGAATTAT
22547 GAACTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TATTTAAATATAATATGAATTATA
Found at i:50968 original size:223 final size:223
Alignment explanation
Indices: 50580--51028 Score: 828
Period size: 223 Copynumber: 2.0 Consensus size: 223
50570 CCGATACCCT
50580 CAAAGAGTGAATATGGGTGATCGCCTCCATGCATCTTTCCTTCAAATATAAGTTTCTCTGCTCTA
1 CAAAGAGTGAATATGGGTGATCGCCTCCATGCATCTTTCCTTCAAATATAAGTTTCTCTGCTCTA
*
50645 TCGGACAAGAAGGAAGCAAATGCTTTGGCCCTATATAAGACCTCTGCTTTGCCAGTCAGTCGATA
66 TCGGACAAGAAGGAAGCAAATGCTTTGGCCCTATATAAGAACTCTGCTTTGCCAGTCAGTCGATA
*
50710 GAGTGAAAGGAACACGTATGCGTTTCAGCTTATACCGTGACAGATTCCAACTCGCTTAAGCAGAC
131 GAGTGAAAGGAACACGAATGCGTTTCAGCTTATACCGTGACAGATTCCAACTCGCTTAAGCAGAC
50775 CAAGCTTCCAAACTACCTCTCCGGCATC
196 CAAGCTTCCAAACTACCTCTCCGGCATC
*
50803 CAAAGAGTGAATATGGGTGATCGCCTCCATGCATCTTTCCTTCTAATATAAGTTTCTCTGCTCTA
1 CAAAGAGTGAATATGGGTGATCGCCTCCATGCATCTTTCCTTCAAATATAAGTTTCTCTGCTCTA
*
50868 TCGGACAAGAAGGAAGTAAATGCTTTGGCCCTATATAAGAACTCTGCTTTGCCAGTCAGTCGATA
66 TCGGACAAGAAGGAAGCAAATGCTTTGGCCCTATATAAGAACTCTGCTTTGCCAGTCAGTCGATA
*
50933 GAGTGAAAGGAACACGAATGTGTTTCCA-CTTATACCGTGACAGATTCCAACTCGCTTAAGCAGA
131 GAGTGAAAGGAACACGAATGCGTTT-CAGCTTATACCGTGACAGATTCCAACTCGCTTAAGCAGA
*
50997 CCACGCTTCCAAACTACCTCTCCGGCATC
195 CCAAGCTTCCAAACTACCTCTCCGGCATC
51026 CAA
1 CAA
51029 TGCCGCTTGT
Statistics
Matches: 219, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
223 217 0.99
224 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (223 bp):
CAAAGAGTGAATATGGGTGATCGCCTCCATGCATCTTTCCTTCAAATATAAGTTTCTCTGCTCTA
TCGGACAAGAAGGAAGCAAATGCTTTGGCCCTATATAAGAACTCTGCTTTGCCAGTCAGTCGATA
GAGTGAAAGGAACACGAATGCGTTTCAGCTTATACCGTGACAGATTCCAACTCGCTTAAGCAGAC
CAAGCTTCCAAACTACCTCTCCGGCATC
Found at i:53038 original size:73 final size:73
Alignment explanation
Indices: 52925--53062 Score: 251
Period size: 73 Copynumber: 1.9 Consensus size: 73
52915 TTGTACAATT
52925 TTTCTTACAATTCAATTATAAAATAGGGCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
1 TTTCTTACAATTCAATTATAAAATAGGGCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
52990 CGGTACAA
66 CGGTACAA
*
52998 TTTCTTACAATTCAATTATAAAATA-GGCCCCCTATTTATTTAATAAGTACTATGGCAGACATGA
1 TTTCTTACAATTCAATTATAAAATAGGGCCCCC-ATTTATTTAATAAGCACTATGGCAGACATGA
53062 A
65 A
53063 TGTTATTGTA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
72 7 0.11
73 56 0.89
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (73 bp):
TTTCTTACAATTCAATTATAAAATAGGGCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
CGGTACAA
Found at i:62501 original size:16 final size:16
Alignment explanation
Indices: 62480--62510 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62470 CCTGATCACG
62480 CTCGGCTAATATCTCC
1 CTCGGCTAATATCTCC
*
62496 CTCGGCTCATATCTC
1 CTCGGCTAATATCTC
62511 TCTTTTGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.39, G:0.13, T:0.32
Consensus pattern (16 bp):
CTCGGCTAATATCTCC
Found at i:63038 original size:53 final size:53
Alignment explanation
Indices: 62950--63211 Score: 287
Period size: 53 Copynumber: 4.9 Consensus size: 53
62940 TCTTCAAATG
* * * ****
62950 ACGGG-TCCCTCCCTCTT-ATTCAGGGATTAAGGAACTCGAACAATCTTCTAAAA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCT
* * * * *
63003 ATGGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAATAATATTCTGCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * *
63056 ACGGGTTCGCTCCCTGTTGCTTCAATGG-GTAGAACTCGAACACTCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTC-AGGGAGTAGAACTCGAACAATCTTCTGCCT
* * *
63109 ACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCTGTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * *
63162 ACGGGTTCGCTCCCTCTTGCTTTAGGGAGTAAAACTTGAACAATCTTCTG
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
63212 GTGTGATTCT
Statistics
Matches: 176, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
52 3 0.02
53 150 0.85
54 14 0.08
55 9 0.05
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
Found at i:63359 original size:10 final size:10
Alignment explanation
Indices: 63344--63370 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
63334 TAAAATTTAA
63344 GAGAATCTTT
1 GAGAATCTTT
63354 GAGAATCTTT
1 GAGAATCTTT
63364 GAGAATC
1 GAGAATC
63371 CATTTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (10 bp):
GAGAATCTTT
Found at i:63772 original size:13 final size:13
Alignment explanation
Indices: 63754--63778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63744 TGCTCGAAAG
63754 ACTTACTGATGGC
1 ACTTACTGATGGC
63767 ACTTACTGATGG
1 ACTTACTGATGG
63779 GTTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:63833 original size:93 final size:93
Alignment explanation
Indices: 63674--63859 Score: 293
Period size: 93 Copynumber: 2.0 Consensus size: 93
63664 TGCTCGAAAG
* * *
63674 ACTTACTGATGAATTTGTTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCAGAAAGATTTAAT
63739 CATCATGCTCGAAAGACTTACTGATGGC
66 CATCATGCTCGAAAGACTTACTGATGGC
** *
63767 ACTTACTGATGGGTTTGCTTCACTACTCTTTC-GTGAAGGCTTACAAATTACCATAAAGATTTAA
1 ACTTACTGATGAATTTGCTTCACTACTC-TTCGGTGAAGGCTTACAAATTACCAGAAAGATTTAA
*
63831 TCATCATGCTCTAAAGACTTACTGATGGC
65 TCATCATGCTCGAAAGACTTACTGATGGC
63860 CCTAAGGATT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
93 82 0.96
94 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (93 bp):
ACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCAGAAAGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGC
Found at i:63871 original size:42 final size:42
Alignment explanation
Indices: 63824--63909 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
63814 TTACCATAAA
* * *
63824 GATTTAATCATCATGCTCTAAAGACTTACTGATGGCCCTAAG
1 GATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAG
*
63866 GATTTAAGCATCATGCTCAAAAGACTTATTGATGGCCCGAAG
1 GATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAG
63908 GA
1 GA
63910 CTTACTAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (42 bp):
GATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAG
Found at i:71945 original size:84 final size:84
Alignment explanation
Indices: 71793--71947 Score: 195
Period size: 84 Copynumber: 1.8 Consensus size: 84
71783 AATTTTATTA
* * * * *
71793 ACAGATAGCCCTTCTTGCCTTGAGCTATACTGTAAATGATGTACCTTAGAGCTGAGCATAGTCGA
1 ACAGATAACCCTTCTAGCCTTGAGCTATACTGTAAATGATGTACCCTAGAGCTGAGCATAATCAA
71858 ACTCGAAGGTCTTTTGGTG
66 ACTCGAAGGTCTTTTGGTG
* * * * **
71877 ACAGATAACCCTTCTAGCCTTGAGTTAT-GTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCA
1 ACAGATAACCCTTCTAGCCTTGAGCTATACTGTAAATGATGTACCCTAG-AGCTGAGCATAATCA
71941 AACTCGA
65 AACTCGA
71948 GGGTTTGGTG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
83 16 0.27
84 43 0.73
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (84 bp):
ACAGATAACCCTTCTAGCCTTGAGCTATACTGTAAATGATGTACCCTAGAGCTGAGCATAATCAA
ACTCGAAGGTCTTTTGGTG
Found at i:72071 original size:36 final size:36
Alignment explanation
Indices: 72022--72090 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
72012 AAAGATTGAA
* *
72022 GTTTCAAGGGAAACTGTCTCAAGATAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
72058 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
72091 ACTTCCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:72241 original size:35 final size:35
Alignment explanation
Indices: 72196--72265 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
72186 GCTTCAAGAA
* * **
72196 AAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGG
1 AAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
* *
72231 AAACTATCTCATGAGTGACAAAATTCATTTCAAGG
1 AAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
72266 GAAATGTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (35 bp):
AAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
Found at i:72294 original size:100 final size:101
Alignment explanation
Indices: 72165--72519 Score: 423
Period size: 102 Copynumber: 3.5 Consensus size: 101
72155 TGTTTCAAAT
* * *
72165 GAAACTGTTTTCAAAGTTTATGCTTCAAGAAAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAA
1 GAAA-TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTTGTTTCAA
* *
72229 GGAAACTATCTCATGAGTGACAAAATTCATTTCAAGG
65 GGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
* * *
72266 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAG
1 GAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTTGTTTCAA-
* *
72331 GGAACCTATCTCAAGAGAGACAAAATTCATCTCAAGG
65 GGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
* * *
72368 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAA--GAGACAAAACTTAGTTCCAAA
1 GAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTTGTTTC-AA
* * * **
72431 AGAAA-TATCTCAAGGGAGACGAAATTTGTTTCAAGG
65 GGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
**** **
72467 GAAACAAATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAAAGAGACAAAA
1 GAAATGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA
72520 TTCATTTCAA
Statistics
Matches: 225, Mismatches: 23, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
99 59 0.26
100 67 0.30
101 25 0.11
102 74 0.33
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (101 bp):
GAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTTGTTTCAAG
GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
Found at i:72343 original size:37 final size:37
Alignment explanation
Indices: 72285--72357 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
72275 TCAATGTTTA
* *
72285 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
72322 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
72358 CATCTCAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:72521 original size:65 final size:65
Alignment explanation
Indices: 72431--72584 Score: 186
Period size: 65 Copynumber: 2.4 Consensus size: 65
72421 TAGTTCCAAA
* * **
72431 AGAAA-TATCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATTCAAAGATTT-TGTTTCAA
1 AGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAAATTCAAAG-TTTATGTTTCAA
72494 G
65 G
* * **** *
72495 AGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGTGAAATGTTTTCAATGTTTATGTTTCAAG
1 AGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAAATTCAAAGTTTATGTTTCAAG
72560 AGAAACTATCTCAAGAGAGACAAAA
1 AGAAACTATCTCAAGAGAGACAAAA
72585 CTTAGTTCCA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 8 0.11
65 68 0.89
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (65 bp):
AGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAAATTCAAAGTTTATGTTTCAAG
Found at i:72701 original size:65 final size:65
Alignment explanation
Indices: 72626--72753 Score: 170
Period size: 65 Copynumber: 2.0 Consensus size: 65
72616 ACGAAATTTG
72626 TTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATT
1 TTTCAAGGGAAA-AGTATTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATT
72689 CA
64 CA
* * * * **
72691 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATT
72754 TAGTTCCAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
64 4 0.07
65 51 0.93
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (65 bp):
TTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCA
Found at i:72822 original size:167 final size:166
Alignment explanation
Indices: 72314--72835 Score: 845
Period size: 167 Copynumber: 3.2 Consensus size: 166
72304 TCAAGGGAGA
* * * *
72314 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAATGTTTT
*
72378 CAATGTTTATGTTTCAAGAGAAACTATCTCAA-GAGACAAAACTTAGTTCCAAAA-GAAATATCT
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGGAGACAAAACTTAGTTCCAAAAGGAAATGTCT
*
72441 CAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
131 CAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
*
72477 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGTGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAATGTTTT
*
72542 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAG-GAGACAAAACTTAGTTCCAAAAGGAAATGTC
72607 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
130 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
72644 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* *
72709 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGGAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAA-GGAGACAAAACTTAGTTCCAAAAGGAAATGTC
* * * *
72774 TCAAGGGAGACGAAATTAGTTTCAATGAAAATAGATT
130 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
* *
72811 TAAATATTTTGTTTCAA-ATGAAACT
1 CAAAGATTTTGTTTCAAGA-GAAACT
72836 TGGAAATTGT
Statistics
Matches: 335, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
163 4 0.01
164 87 0.26
166 23 0.07
167 220 0.66
168 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (166 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGGAGACAAAACTTAGTTCCAAAAGGAAATGTCT
CAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
Found at i:73176 original size:106 final size:106
Alignment explanation
Indices: 72971--73304 Score: 411
Period size: 106 Copynumber: 3.2 Consensus size: 106
72961 TCCAAGAAAG
* * * * **
72971 TTGTATTGT-TCCGAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAA
1 TTGTATTGTCT-CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
* * * * * * *
73034 TTGTTTGTTGACAGCCAGCCGCCCCTTTGCTATGAAGTTGAGC
64 TTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
* * *
73077 TTATACTGTCTCGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
1 TTGTATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
*
73142 GTTTGTTGACAACCAGTCGTCCATTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
* * *
73183 TTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATT
1 TTGTATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* * * *
73248 ATTTGTTGAAAACTAGTCGTCCCTTCGTTGTGGAGTTGAAC
66 GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
*
73289 TTGTTTTGTCTCGAGT
1 TTGTATTGTCTCGAGT
73305 GGCACGATAT
Statistics
Matches: 197, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
106 195 0.99
107 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (106 bp):
TTGTATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
Found at i:73916 original size:30 final size:32
Alignment explanation
Indices: 73880--73966 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
73870 TTTGCATCAG
*
73880 GATGTTGAAT-TCCAAAGATGCCC-AATATTC
1 GATGTTGAATCTCCAAAGATGCCCTAACATTC
*
73910 GATGTTGAATCTCACAAA-ATGCCCTAACATTT
1 GATGTTGAATCTC-CAAAGATGCCCTAACATTC
*
73942 GATGTTGAATCTTCAAAGATGCCCT
1 GATGTTGAATCTCCAAAGATGCCCT
73967 CATTGTTCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 10 0.20
31 12 0.24
32 28 0.56
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCTAACATTC
Found at i:74986 original size:68 final size:68
Alignment explanation
Indices: 74876--75011 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 68
74866 TGTCTCTCTC
*
74876 TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATTAATC
1 TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCG-AAATGATTGTGCTTGATCAATC
74941 TCAT
65 TCAT
*
74945 TTGATGCTCTA-GATCTTCGAGTGAAGTGATTCAGTGATTCGAAATGATTGTGCTTGATCAATCT
1 TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCGAAATGATTGTGCTTGATCAATCT
75009 CAT
66 CAT
75012 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 25 0.38
68 29 0.45
69 11 0.17
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (68 bp):
TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCGAAATGATTGTGCTTGATCAATCT
CAT
Found at i:75104 original size:29 final size:29
Alignment explanation
Indices: 75072--75128 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
75062 TTGTCTTCTT
75072 TTTTCTT-CAATTTTC-CTTTGTTTTTTTTA
1 TTTTCTTGC-ATTTTCTCTTT-TTTTTTTTA
*
75101 TTTTCTTGCTTTTTCTCTTTTTTTTTTT
1 TTTTCTTGCATTTTCTCTTTTTTTTTTT
75129 GTTCTGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (29 bp):
TTTTCTTGCATTTTCTCTTTTTTTTTTTA
Done.