Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015914.1 Corchorus olitorius cultivar O-4 contig15947, 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: 11487
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1685 original size:31 final size:32
Alignment explanation
Indices: 1650--2304 Score: 250
Period size: 34 Copynumber: 20.6 Consensus size: 32
1640 GTAAACTAAA
*
1650 AAAGACATGTCTGAGGTCTG-AACTAGAAGAT
1 AAAGACCTGTCTGAGGTCTGAAACTAGAAGAT
*
1681 AAAGA-CTAGTCTGTGGTCGATGTAAACTAG--G--
1 AAAGACCT-GTCTGAGGTC--TG-AAACTAGAAGAT
1712 AAAGACCTGTCTGAGGTCTGAAAC-AGAAGAT
1 AAAGACCTGTCTGAGGTCTGAAACTAGAAGAT
* *
1743 AAAGA-C---CTGAGGTC-G-AATTTGAAAGAT
1 AAAGACCTGTCTGAGGTCTGAAACTAG-AAGAT
* * * *
1770 AAAGACCTATCTGAGGTC-GAAATTAAAAACTGAA
1 AAAGACCTGTCTGAGGTCTGAAACT-AGAA--GAT
1804 AAAGACCTGTCTGAGGTCTGAAACT-GAAAGAT
1 AAAGACCTGTCTGAGGTCTGAAACTAG-AAGAT
* * *
1836 AAAGACCTGTCTGAGGTC-GAAATTTAAAACTGAG
1 AAAGACCTGTCTGAGGTCTGAAA-CTAGAA--GAT
* * * * *
1870 AAAGACCTGTCTGATGTC-G-AATTTGAAAAG
1 AAAGACCTGTCTGAGGTCTGAAACTAGAAGAT
* * * *
1900 AAAGACCTGTTTGAGGTC-GAAATCAAAAACTGAG
1 AAAGACCTGTCTGAGGTCTGAAA-CTAGAA--GAT
* * *
1934 AAAGACCTGTTTGAGGTC-AAAAC-AGAAGGT
1 AAAGACCTGTCTGAGGTCTGAAACTAGAAGAT
* * *
1964 AAAGACCTGTCTGAGGTC-G-AATTTGAAAGAG
1 AAAGACCTGTCTGAGGTCTGAAACTAG-AAGAT
* * * *
1995 AAAGACATGTCTGAGGTC-GATATTA-AAAACT
1 AAAGACCTGTCTGAGGTCTGAAACTAGAAGA-T
* * * *
2026 CAGAAAGACCTGTCTAAGGT-TG-AATTTGAAATAT
1 ---AAAGACCTGTCTGAGGTCTGAAACTAG-AAGAT
* *
2060 AAAGACCTGTTTGAGGTCTGAAAC-AGAAAACTGAG
1 AAAGACCTGTCTGAGGTCTGAAACTAG--AA--GAT
2095 AAAGACCTGTCTGAGGTCTGAAACT-GAAAGAT
1 AAAGACCTGTCTGAGGTCTGAAACTAG-AAGAT
* * *
2127 AAAAGACCTGTCTGAGGTC-GAAATTTAAAACTGAG
1 -AAAGACCTGTCTGAGGTCTGAAA-CTAGAA--GAT
* * * * *
2162 AAAGACTTGTCTGAGGTC-G-AATTTGAAAAG
1 AAAGACCTGTCTGAGGTCTGAAACTAGAAGAT
* * *
2192 AAAGACCTGTCTGAGGT-TGAAATTAAAAATTGAG
1 AAAGACCTGTCTGAGGTCTGAAACT-AGAA--GAT
* *
2226 AAAGACCTGTCTGAGGTC-AAAAC-AGAAGGT
1 AAAGACCTGTCTGAGGTCTGAAACTAGAAGAT
** * * * *
2256 AAAGACCACTCTAAGGTC-G-AATTTGAAAGAG
1 AAAGACCTGTCTGAGGTCTGAAACTAG-AAGAT
2287 AAAGACCTGTCTGAGGTC
1 AAAGACCTGTCTGAGGTC
2305 GATATTAAAA
Statistics
Matches: 484, Mismatches: 81, Indels: 118
0.71 0.12 0.17
Matches are distributed among these distances:
25 2 0.00
26 2 0.00
27 20 0.04
28 5 0.01
29 7 0.01
30 79 0.16
31 106 0.22
32 61 0.13
33 37 0.08
34 124 0.26
35 41 0.08
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (32 bp):
AAAGACCTGTCTGAGGTCTGAAACTAGAAGAT
Found at i:1686 original size:62 final size:62
Alignment explanation
Indices: 1583--1749 Score: 234
Period size: 62 Copynumber: 2.7 Consensus size: 62
1573 TCGACACGAA
* * *
1583 AAACTAAGAAAGACCTGTCTGAGGTCTGAAGTTGAAG---AAGACCAGTCTGTGGTCGGTGT
1 AAACTAAGAAAGACCTGTCTGAGGTCTGAACTAGAAGATAAAGACCAGTCTGTGGTCGATGT
* * *
1642 AAACTAAAAAAGACATGTCTGAGGTCTGAACTAGAAGATAAAGACTAGTCTGTGGTCGATGT
1 AAACTAAGAAAGACCTGTCTGAGGTCTGAACTAGAAGATAAAGACCAGTCTGTGGTCGATGT
*
1704 AAACTAGGAAAGACCTGTCTGAGGTCTGAAAC-AGAAGATAAAGACC
1 AAACTAAGAAAGACCTGTCTGAGGTCTG-AACTAGAAGATAAAGACC
1750 TGAGGTCGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
59 33 0.35
62 58 0.62
63 3 0.03
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (62 bp):
AAACTAAGAAAGACCTGTCTGAGGTCTGAACTAGAAGATAAAGACCAGTCTGTGGTCGATGT
Found at i:1817 original size:34 final size:33
Alignment explanation
Indices: 1749--2323 Score: 416
Period size: 34 Copynumber: 17.8 Consensus size: 33
1739 AGATAAAGAC
** * *
1749 CTGAGGTCG-AATTTGAAA-GATAAAGACCTAT
1 CTGAGGTCGAAATTAAAAATGAGAAAGACCTGT
*
1780 CTGAGGTCGAAATTAAAAACTGAAAAAGACCTGT
1 CTGAGGTCGAAATTAAAAA-TGAGAAAGACCTGT
* * *
1814 CTGAGGTCTGAAACT-GAAA-GATAAAGACCTGT
1 CTGAGGTC-GAAATTAAAAATGAGAAAGACCTGT
*
1846 CTGAGGTCGAAATTTAAAACTGAGAAAGACCTGT
1 CTGAGGTCGAAA-TTAAAAATGAGAAAGACCTGT
* **
1880 CTGATGTCG-AATTTGAAA--AGAAAGACCTGT
1 CTGAGGTCGAAATTAAAAATGAGAAAGACCTGT
* *
1910 TTGAGGTCGAAATCAAAAACTGAGAAAGACCTGT
1 CTGAGGTCGAAATTAAAAA-TGAGAAAGACCTGT
* *
1944 TTGAGGTC-AAA--ACAGAA-G-GTAAAGACCTGT
1 CTGAGGTCGAAATTA-AAAATGAG-AAAGACCTGT
** *
1974 CTGAGGTCG-AATTTGAAA-GAGAAAGACATGT
1 CTGAGGTCGAAATTAAAAATGAGAAAGACCTGT
* *
2005 CTGAGGTCGATATTAAAAACTCAGAAAGACCTGT
1 CTGAGGTCGAAATTAAAAA-TGAGAAAGACCTGT
* * ** *
2039 CTAAGGTTG-AATTTGAAAT-ATAAAGACCTGT
1 CTGAGGTCGAAATTAAAAATGAGAAAGACCTGT
* *
2070 TTGAGGTCTGAAA-CAGAAAACTGAGAAAGACCTGT
1 CTGAGGTC-GAAATTA-AAAA-TGAGAAAGACCTGT
* *
2105 CTGAGGTCTGAAACTGAAAGAT-A-AAAGACCTGT
1 CTGAGGTC-GAAA-TTAAAAATGAGAAAGACCTGT
* *
2138 CTGAGGTCGAAATTTAAAACTGAGAAAGACTTGT
1 CTGAGGTCGAAA-TTAAAAATGAGAAAGACCTGT
**
2172 CTGAGGTCG-AATTTGAAA--AGAAAGACCTGT
1 CTGAGGTCGAAATTAAAAATGAGAAAGACCTGT
*
2202 CTGAGGTTGAAATTAAAAATTGAGAAAGACCTGT
1 CTGAGGTCGAAATTAAAAA-TGAGAAAGACCTGT
* **
2236 CTGAGGTC-AAA--ACAGAA-G-GTAAAGACCACT
1 CTGAGGTCGAAATTA-AAAATGAG-AAAGACCTGT
* **
2266 CTAAGGTCG-AATTTGAAA-GAGAAAGACCTGT
1 CTGAGGTCGAAATTAAAAATGAGAAAGACCTGT
*
2297 CTGAGGTCGATATTAAAAACTGAGAAA
1 CTGAGGTCGAAATTAAAAA-TGAGAAA
2324 AAATGACTTG
Statistics
Matches: 429, Mismatches: 73, Indels: 81
0.74 0.13 0.14
Matches are distributed among these distances:
29 2 0.00
30 76 0.18
31 84 0.20
32 67 0.16
33 42 0.10
34 125 0.29
35 29 0.07
36 3 0.01
37 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (33 bp):
CTGAGGTCGAAATTAAAAATGAGAAAGACCTGT
Found at i:1839 original size:66 final size:65
Alignment explanation
Indices: 1749--2323 Score: 384
Period size: 64 Copynumber: 8.9 Consensus size: 65
1739 AGATAAAGAC
** * *
1749 CTGAGGTCGAATTTGAAAGATAAAGACCTATCTGAGGTCGAAATTAAAAACTGAAAAAGACCTGT
1 CTGAGGTCGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAACTGAGAAAGACCTGT
*
1814 CTGAGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTTAAAACTGAGAAAGACCTG
1 CTGAGGTC-GAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAACTGAGAAAGACCTG
1879 T
65 T
* ** * * *
1880 CTGATGTCGAATTTGAAA-AGAAAGACCTGTTTGAGGTCGAAATCAAAAACTGAGAAAGACCTGT
1 CTGAGGTCGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAACTGAGAAAGACCTGT
* * * * ** *
1944 TTGAGGTCAAAACAG-AAGGTAAAGACCTGTCTGAGGTCG-AATTTGAAA--GAGAAAGACATGT
1 CTGAGGTCGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAACTGAGAAAGACCTGT
* * * * * ** *
2005 CTGAGGTCGATA-TTAAAAACTCAGAAAGACCTGTCTAAGGTTG-AATTTGAAA-T-ATAAAGAC
1 CTGAGGTCGAAACTGAAAGA-T---AAAGACCTGTCTGAGGTCGAAATTAAAAACTGAGAAAGAC
2066 CTGT
62 CTGT
* * * * *
2070 TTGAGGTCTGAAACAGAAAACTGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGA-T-A-AAAG
1 CTGAGGTC-GAAACTG-AAA--GATAAAGACCTGTCTGAGGTC-GAAA-TTAAAAACTGAGAAAG
2132 ACCTGT
60 ACCTGT
* * * * **
2138 CTGAGGTCGAAATTTAAAACTGAGAAAGACTTGTCTGAGGTCG-AATTTGAAA---AGAAAGACC
1 CTGAGGTCGAAA-CTGAAA--GATAAAGACCTGTCTGAGGTCGAAATTAAAAACTGAGAAAGACC
2199 TGT
63 TGT
* * * * *
2202 CTGAGGTTGAAATTAAAAATTGAGAAAGACCTGTCTGAGGTC-AAA--ACAGAA--G-GTAAAGA
1 CTGAGGTCGAAACT-GAAA--GATAAAGACCTGTCTGAGGTCGAAATTA-AAAACTGAG-AAAGA
**
2261 CCACT
61 CCTGT
* ** * *
2266 CTAAGGTCGAATTTGAAAGAGAAAGACCTGTCTGAGGTCGATATTAAAAACTGAGAAA
1 CTGAGGTCGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAACTGAGAAA
2324 AAATGACTTG
Statistics
Matches: 410, Mismatches: 71, Indels: 58
0.76 0.13 0.11
Matches are distributed among these distances:
61 44 0.11
62 3 0.01
63 20 0.05
64 140 0.34
65 65 0.16
66 80 0.20
67 30 0.07
68 22 0.05
69 5 0.01
70 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (65 bp):
CTGAGGTCGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAAACTGAGAAAGACCTGT
Found at i:2195 original size:292 final size:290
Alignment explanation
Indices: 1752--2323 Score: 948
Period size: 292 Copynumber: 2.0 Consensus size: 290
1742 TAAAGACCTG
*
1752 AGGTCGAATTTGAAAGATAAAGACCTATCTGAGGTCGAAATTAAAAACTGAAAAAGACCTGTCTG
1 AGGTCGAATTTGAAAGATAAAGACCTATCTGAGGTCGAAATCAAAAACTGAAAAAGACCTGTCTG
1817 AGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTTAAAACTGAGAAAGACCTGTCT
66 AGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTTAAAACTGAGAAAGACCTGTCT
* * *
1882 GATGTCGAATTTGAAAAGAAAGACCTGTTTGAGGTCGAAATCAAAAACTGAGAAAGACCTGTTTG
131 GAGGTCGAATTTGAAAAGAAAGACCTGTCTGAGGTCGAAATCAAAAACTGAGAAAGACCTGTCTG
** *
1947 AGGTCAAAACAGAAGGTAAAGACCTGTCTGAGGTCGAATTTGAAAGAGAAAGACATGTCTGAGGT
196 AGGTCAAAACAGAAGGTAAAGACCACTCTAAGGTCGAATTTGAAAGAGAAAGACATGTCTGAGGT
2012 CGATATTAAAAACTCAGAAAGACCTGTCTA
261 CGATATTAAAAACTCAGAAAGACCTGTCTA
* * * * *
2042 AGGTTGAATTTGAAATATAAAGACCTGTTTGAGGTCTGAAA-CAGAAAACTGAGAAAGACCTGTC
1 AGGTCGAATTTGAAAGATAAAGACCTATCTGAGGTC-GAAATCA-AAAACTGAAAAAGACCTGTC
*
2106 TGAGGTCTGAAACTGAAAGATAAAAGACCTGTCTGAGGTCGAAATTTAAAACTGAGAAAGACTTG
64 TGAGGTCTGAAACTGAAAGAT-AAAGACCTGTCTGAGGTCGAAATTTAAAACTGAGAAAGACCTG
* * *
2171 TCTGAGGTCGAATTTGAAAAGAAAGACCTGTCTGAGGTTGAAATTAAAAATTGAGAAAGACCTGT
128 TCTGAGGTCGAATTTGAAAAGAAAGACCTGTCTGAGGTCGAAATCAAAAACTGAGAAAGACCTGT
*
2236 CTGAGGTCAAAACAGAAGGTAAAGACCACTCTAAGGTCGAATTTGAAAGAGAAAGACCTGTCTGA
193 CTGAGGTCAAAACAGAAGGTAAAGACCACTCTAAGGTCGAATTTGAAAGAGAAAGACATGTCTGA
*
2301 GGTCGATATTAAAAACTGAGAAA
258 GGTCGATATTAAAAACTCAGAAA
2324 AAATGACTTG
Statistics
Matches: 261, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
290 33 0.13
291 44 0.17
292 184 0.70
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (290 bp):
AGGTCGAATTTGAAAGATAAAGACCTATCTGAGGTCGAAATCAAAAACTGAAAAAGACCTGTCTG
AGGTCTGAAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTTAAAACTGAGAAAGACCTGTCT
GAGGTCGAATTTGAAAAGAAAGACCTGTCTGAGGTCGAAATCAAAAACTGAGAAAGACCTGTCTG
AGGTCAAAACAGAAGGTAAAGACCACTCTAAGGTCGAATTTGAAAGAGAAAGACATGTCTGAGGT
CGATATTAAAAACTCAGAAAGACCTGTCTA
Found at i:2406 original size:39 final size:39
Alignment explanation
Indices: 2320--2531 Score: 345
Period size: 39 Copynumber: 5.5 Consensus size: 39
2310 TAAAAACTGA
* * *
2320 GAAAAAATGACTTGTTTCTAGTCAACTTTGAT-AATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* *
2358 GAAAAGATGACATGCTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
2397 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* * *
2436 GAAAAGATAACCTGTTTGCAGTCAACTTTTATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
2475 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
2514 GAAAAGATGACCTGTTTC
1 GAAAAGATGACCTGTTTC
2532 ATTGAAGTAA
Statistics
Matches: 161, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
38 28 0.17
39 133 0.83
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (39 bp):
GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
Found at i:2630 original size:56 final size:56
Alignment explanation
Indices: 2565--2921 Score: 493
Period size: 56 Copynumber: 6.4 Consensus size: 56
2555 AGAACTAAAG
* * * *
2565 AATTGAAGCATTGAATATTTGAAATTGAAGAAAGACCACCCTGGATCATTGAGGTA
1 AATTGAAGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTA
* *
2621 AATTGAAGCATTGAATATTTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTA
1 AATTGAAGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTA
* *
2677 AATTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGCAGTA
1 AATTGAAGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTA
* * *
2733 AATTGATGCATTGAAGAATCGAAATTGAAGAAAGACCACCTTGGATCGTTGAAGTA
1 AATTGAAGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTA
* * * * * *
2789 AATTGATGCATTAAAAAATCGAAATTGAAAAAAGACCACACTGGATCGTTGAAGTA
1 AATTGAAGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTA
** * *
2845 AATTGAATAATTGAA-AATTGAAGTTGAAGAAAGACCACACTGGATCGTTGAAGTA
1 AATTGAAGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTA
**
2900 AATTGAATAATTGAA-AATTGAA
1 AATTGAAGCATTGAAGAATTGAA
2922 GAACTGAAGT
Statistics
Matches: 280, Mismatches: 21, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
55 59 0.21
56 221 0.79
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (56 bp):
AATTGAAGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTA
Found at i:2971 original size:93 final size:93
Alignment explanation
Indices: 2844--3054 Score: 345
Period size: 93 Copynumber: 2.3 Consensus size: 93
2834 TCGTTGAAGT
* * * *
2844 AAATTGAATA-ATTGAA-AATTGAAGTTGAAGAAAGACCACACTGGATCGTTGAAGTAAATTGAA
1 AAATTGAA-ACATTGAAGGATTGAATTTCAAGAAAGACCACACTGGATCATTGAAGTAAATTGAA
2907 TAATTGAAAATTGAAGAACTGAAGTACTG
65 TAATTGAAAATTGAAGAACTGAAGTACTG
2936 AAATTGAAACATTGAAGGATTGAATTTCAAGAAAGACCACACTGGATCATTGAAGTAAATTGAAT
1 AAATTGAAACATTGAAGGATTGAATTTCAAGAAAGACCACACTGGATCATTGAAGTAAATTGAAT
*
3001 AATTGAAAATTGAAGAACTGAAGTATTG
66 AATTGAAAATTGAAGAACTGAAGTACTG
*
3029 AAATTGAAACATTGAGGGATTGAATT
1 AAATTGAAACATTGAAGGATTGAATT
3055 GAAATTGAAC
Statistics
Matches: 111, Mismatches: 6, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
91 1 0.01
92 14 0.13
93 96 0.86
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (93 bp):
AAATTGAAACATTGAAGGATTGAATTTCAAGAAAGACCACACTGGATCATTGAAGTAAATTGAAT
AATTGAAAATTGAAGAACTGAAGTACTG
Found at i:3006 original size:8 final size:7
Alignment explanation
Indices: 2992--3206 Score: 78
Period size: 8 Copynumber: 30.1 Consensus size: 7
2982 TCATTGAAGT
2992 AAATTGA
1 AAATTGA
2999 ATAATTGA
1 A-AATTGA
3007 AAATTGA
1 AAATTGA
*
3014 AGAACTGA
1 A-AATTGA
*
3022 AGTATTG-
1 A-AATTGA
3029 AAATTGA
1 AAATTGA
3036 AACATTGA
1 AA-ATTGA
**
3044 GGGATTG-
1 -AAATTGA
3051 -AATTG-
1 AAATTGA
3056 AAATTGA
1 AAATTGA
*
3063 ACCATTGA
1 A-AATTGA
*
3071 AGGATTG-
1 A-AATTGA
*
3078 AATTTGAA
1 AAATTG-A
3086 AAATTGA
1 AAATTGA
*
3093 AGAATCG-
1 A-AATTGA
3100 -AATTG-
1 AAATTGA
3105 AAATTGA
1 AAATTGA
*
3112 AGCATTGA
1 A-AATTGA
3120 AATATTG-
1 AA-ATTGA
3127 AAATTGA
1 AAATTGA
3134 AGAATTG-
1 A-AATTGA
3141 AAATTGA
1 AAATTGA
*
3148 AACGTTGA
1 AA-ATTGA
*
3156 AGGATT-A
1 A-AATTGA
*
3163 AATTTGA
1 AAATTGA
3170 AGAATTG-
1 A-AATTGA
3177 AAATTGA
1 AAATTGA
3184 AACATTGA
1 AA-ATTGA
3192 AATATTG-
1 AA-ATTGA
3199 AAATTGA
1 AAATTGA
3206 A
1 A
3207 GAAAGACCAC
Statistics
Matches: 159, Mismatches: 24, Indels: 50
0.68 0.10 0.21
Matches are distributed among these distances:
5 8 0.05
6 37 0.23
7 32 0.20
8 82 0.52
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.30
Consensus pattern (7 bp):
AAATTGA
Found at i:3059 original size:27 final size:27
Alignment explanation
Indices: 3025--3143 Score: 104
Period size: 27 Copynumber: 4.5 Consensus size: 27
3015 GAACTGAAGT
*
3025 ATTGAAATTGAAACATTGAGGGATTGA
1 ATTGAAATTGAAACATTGAAGGATTGA
*
3052 ATTGAAATTGAACCATTGAAGGATTGA
1 ATTGAAATTGAAACATTGAAGGATTGA
* * *
3079 A-T----TTGAAAAATTGAAGAATCGA
1 ATTGAAATTGAAACATTGAAGGATTGA
* **
3101 ATTGAAATTGAAGCATTGAAATATTGAA
1 ATTGAAATTGAAACATTGAAGGATTG-A
3129 ATTGAAGAATTGAAA
1 ATTG-A-AATTGAAA
3144 TTGAAACGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
22 17 0.24
23 1 0.01
26 1 0.01
27 40 0.56
28 5 0.07
29 1 0.01
30 7 0.10
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.29
Consensus pattern (27 bp):
ATTGAAATTGAAACATTGAAGGATTGA
Found at i:3061 original size:49 final size:49
Alignment explanation
Indices: 3001--3142 Score: 176
Period size: 49 Copynumber: 2.9 Consensus size: 49
2991 TAAATTGAAT
* * * * * *
3001 AATTGAAAATTGAAGAACTGAAGTATTGAAATTGAAACATTGAGGGATTG
1 AATTG-AAATTGAAGCATTGAAGTATTGAAATTGAAAAATTGAAGAATCG
* * *
3051 AATTGAAATTGAACCATTGAAGGATTGAATTTGAAAAATTGAAGAATCG
1 AATTGAAATTGAAGCATTGAAGTATTGAAATTGAAAAATTGAAGAATCG
* *
3100 AATTGAAATTGAAGCATTGAAATATTGAAATTGAAGAATTGAA
1 AATTGAAATTGAAGCATTGAAGTATTGAAATTGAAAAATTGAA
3143 ATTGAAACGT
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 73 0.94
50 5 0.06
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (49 bp):
AATTGAAATTGAAGCATTGAAGTATTGAAATTGAAAAATTGAAGAATCG
Found at i:3084 original size:22 final size:20
Alignment explanation
Indices: 3050--3170 Score: 100
Period size: 22 Copynumber: 5.7 Consensus size: 20
3040 TTGAGGGATT
*
3050 GAATTGAAATTGAACCATTGAA
1 GAATTGAATTTGAA--ATTGAA
*
3072 GGATTGAATTTGAAAAATTGAA
1 GAATTGAATTTG--AAATTGAA
*
3094 GAATCGAA-TTGAAATTGAA
1 GAATTGAATTTGAAATTGAA
*
3113 GCATTGAAATATTGAAATTGAA
1 GAATTG-AAT-TTGAAATTGAA
*
3135 GAATTGAAATTGAAACGTTGAA
1 GAATTGAATTTGAAA--TTGAA
* *
3157 GGATTAAATTTGAA
1 GAATTGAATTTGAA
3171 GAATTGAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
19 12 0.15
20 8 0.10
21 5 0.06
22 54 0.67
24 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (20 bp):
GAATTGAATTTGAAATTGAA
Found at i:3120 original size:14 final size:13
Alignment explanation
Indices: 2992--3194 Score: 62
Period size: 14 Copynumber: 14.3 Consensus size: 13
2982 TCATTGAAGT
*
2992 AAATTGAATAATTG
1 AAATTGAA-GATTG
*
3006 AAAATTGAAGAACTG
1 -AAATTGAAG-ATTG
3021 AAGTATTGAA-ATTG
1 AA--ATTGAAGATTG
*
3035 AAACATTGAGGGATTG
1 -AA-ATTGA-AGATTG
3051 -AATTGAA-ATTG
1 AAATTGAAGATTG
3062 AACCATTGAAGGATTG
1 AA--ATTGAA-GATTG
* *
3078 AATTTGAAAAATTG
1 AAATTG-AAGATTG
*
3092 AAGAATCG-A-ATTG
1 -A-AATTGAAGATTG
3105 AAATTGAAGCATTG
1 AAATTGAAG-ATTG
3119 AAATATTGAA-ATTG
1 -AA-ATTGAAGATTG
3133 AAGAATTGAA-ATTG
1 -A-AATTGAAGATTG
3147 AAACGTTGAAGGATT-
1 AAA--TTGAA-GATTG
3162 AAATTTGAAGAATTG
1 AAA-TTGAAG-ATTG
*
3177 AAATTGAAACATTG
1 AAATTG-AAGATTG
3191 AAAT
1 AAAT
3195 ATTGAAATTG
Statistics
Matches: 148, Mismatches: 13, Indels: 55
0.69 0.06 0.25
Matches are distributed among these distances:
11 8 0.05
12 5 0.03
13 11 0.07
14 69 0.47
15 27 0.18
16 28 0.19
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (13 bp):
AAATTGAAGATTG
Found at i:3146 original size:36 final size:36
Alignment explanation
Indices: 3099--3209 Score: 170
Period size: 36 Copynumber: 3.1 Consensus size: 36
3089 TTGAAGAATC
*
3099 GAATTGAAATTGAAGCATTGAAATATTGAAATTGAA
1 GAATTGAAATTGAAACATTGAAATATTGAAATTGAA
* **
3135 GAATTGAAATTGAAACGTTGAAGGATT-AAATTTGAA
1 GAATTGAAATTGAAACATTGAAATATTGAAA-TTGAA
3171 GAATTGAAATTGAAACATTGAAATATTGAAATTGAA
1 GAATTGAAATTGAAACATTGAAATATTGAAATTGAA
3207 GAA
1 GAA
3210 AGACCACCCC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 3 0.05
36 60 0.91
37 3 0.05
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.30
Consensus pattern (36 bp):
GAATTGAAATTGAAACATTGAAATATTGAAATTGAA
Found at i:3204 original size:14 final size:14
Alignment explanation
Indices: 3115--3206 Score: 68
Period size: 14 Copynumber: 6.4 Consensus size: 14
3105 AAATTGAAGC
3115 ATTGAAATATTGAA
1 ATTGAAATATTGAA
3129 ATTGAAGA-ATTGAA
1 ATTGAA-ATATTGAA
**
3143 ATTGAAACGTTGAA
1 ATTGAAATATTGAA
3157 GGATT-AAAT-TTGAAGA
1 --ATTGAAATATTG-A-A
3173 ATTG-AA-ATTGAAA
1 ATTGAAATATTG-AA
3186 CATTGAAATATTGAA
1 -ATTGAAATATTGAA
3201 ATTGAA
1 ATTGAA
3207 GAAAGACCAC
Statistics
Matches: 65, Mismatches: 2, Indels: 22
0.73 0.02 0.25
Matches are distributed among these distances:
13 2 0.03
14 46 0.71
15 9 0.14
16 8 0.12
ACGTcount: A:0.48, C:0.02, G:0.18, T:0.32
Consensus pattern (14 bp):
ATTGAAATATTGAA
Found at i:4392 original size:8 final size:7
Alignment explanation
Indices: 4374--4420 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
4364 CTAGACTGCC
4374 CTTTTTT
1 CTTTTTT
4381 CTTTTGTT
1 CTTTT-TT
4389 C-TTTTT
1 CTTTTTT
4395 C-TTTTT
1 CTTTTTT
*
4401 CTTTTCT
1 CTTTTTT
4408 C-TTTTT
1 CTTTTTT
4414 CTTTTTT
1 CTTTTTT
4421 TCTCTCTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 14 0.40
7 18 0.51
8 3 0.09
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (7 bp):
CTTTTTT
Found at i:4395 original size:14 final size:13
Alignment explanation
Indices: 4374--4420 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
4364 CTAGACTGCC
4374 CTTTTTTCTTTTGT
1 CTTTTTTCTTTT-T
4388 -TCTTTTTCTTTTT
1 CT-TTTTTCTTTTT
*
4401 CTTTTCTCTTTTT
1 CTTTTTTCTTTTT
4414 CTTTTTT
1 CTTTTTT
4421 TCTCTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:4396 original size:6 final size:6
Alignment explanation
Indices: 4376--4419 Score: 61
Period size: 6 Copynumber: 6.8 Consensus size: 6
4366 AGACTGCCCT
4376 TTTTTC TTTTGTTC TTTTTC TTTTTC TTTTCTC TTTTTC TTTTT
1 TTTTTC -TTT-TTC TTTTTC TTTTTC TTTT-TC TTTTTC TTTTT
4420 TTCTCTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 20 0.57
7 12 0.34
8 3 0.09
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:4410 original size:13 final size:13
Alignment explanation
Indices: 4377--4418 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
4367 GACTGCCCTT
4377 TTTTCT-TTTGTTC
1 TTTTCTCTTT-TTC
4390 TTTT-TCTTTTTC
1 TTTTCTCTTTTTC
4402 TTTTCTCTTTTTC
1 TTTTCTCTTTTTC
4415 TTTT
1 TTTT
4419 TTTCTCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTCTCTTTTTC
Found at i:4420 original size:20 final size:21
Alignment explanation
Indices: 4374--4420 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
4364 CTAGACTGCC
*
4374 CTTTTTTCTTTTGTTCTTTTT
1 CTTTTTTCTTTTGCTCTTTTT
4395 C-TTTTTCTTTT-CTCTTTTT
1 CTTTTTTCTTTTGCTCTTTTT
4414 CTTTTTT
1 CTTTTTT
4421 TCTCTCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (21 bp):
CTTTTTTCTTTTGCTCTTTTT
Found at i:4421 original size:8 final size:8
Alignment explanation
Indices: 4375--4423 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
4365 TAGACTGCCC
4375 TTTTTTCT
1 TTTTTTCT
*
4383 TTTGTTCT
1 TTTTTTCT
4391 TTTTCTT-T
1 TTTT-TTCT
4399 TTCTTTTCT
1 TT-TTTTCT
*
4408 CTTTTTCT
1 TTTTTTCT
4416 TTTTTTCT
1 TTTTTTCT
4424 CTCTTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 28 0.82
9 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Found at i:4428 original size:25 final size:25
Alignment explanation
Indices: 4377--4429 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
4367 GACTGCCCTT
*
4377 TTTTCTTTTGTTCTTTTTCTTTTTC
1 TTTTCTTTTGTTCTTTTTCTTTCTC
4402 TTTTCTCTTT-TTCTTTTT-TTCTCTC
1 TTTTCT-TTTGTTCTTTTTCTT-TCTC
4427 TTT
1 TTT
4430 ATTTTACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 20 0.80
26 3 0.12
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTCTTTTGTTCTTTTTCTTTCTC
Found at i:4523 original size:20 final size:21
Alignment explanation
Indices: 4498--4537 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4488 ACCTTTTTGA
* *
4498 GAAAAA-CATTTTTTTCTTTC
1 GAAAAATCAATTTCTTCTTTC
4518 GAAAAATCAATTTCTTCTTT
1 GAAAAATCAATTTCTTCTTT
4538 TTAAACAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (21 bp):
GAAAAATCAATTTCTTCTTTC
Found at i:6135 original size:14 final size:13
Alignment explanation
Indices: 6092--6142 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
6082 TAAAAACTCA
6092 AAAACCTTTTT-G
1 AAAACCTTTTTCG
6104 AAAACTCATTTTTC-
1 AAAAC-C-TTTTTCG
6118 AAAACCTTTTCTCG
1 AAAACCTTTT-TCG
*
6132 AAAACATTTTT
1 AAAACCTTTTT
6143 TTTGAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
12 9 0.27
13 5 0.15
14 19 0.58
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (13 bp):
AAAACCTTTTTCG
Found at i:6139 original size:26 final size:25
Alignment explanation
Indices: 6092--6142 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
6082 TAAAAACTCA
6092 AAAACCTTTTTGAAAACTCATTTTTC
1 AAAACCTTTTTGAAAAC-CATTTTTC
6118 AAAACCTTTTCTCGAAAA-CATTTTT
1 AAAACCTTTT-T-GAAAACCATTTTT
6143 TTTGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 17 0.74
27 1 0.04
28 5 0.22
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (25 bp):
AAAACCTTTTTGAAAACCATTTTTC
Found at i:9027 original size:52 final size:52
Alignment explanation
Indices: 8881--9297 Score: 554
Period size: 52 Copynumber: 8.0 Consensus size: 52
8871 ATTTGGAAAC
* * * **
8881 TGAAACCTGATGGGAACTTTCCCAATTCGAAACGGAGCTAAATTGAATACTT
1 TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
*
8933 TGAAAACTGGTGGGAA----CCCAATTTGAAAAAGAGCTAGATTGAATACTT
1 TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
* * *
8981 TGAAAAGTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACAT
1 TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
* * * *
9033 TGAAGACTGGCGAGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTT
1 TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
* * * *
9085 TGAAAACTGGTGGGGACTTTCACAATTTGAAAAAAAAAGGGCTAGATTGAATACTT
1 TGAAAACTGGTGGGAACTTTCCCAATTTG----AAAAAGAGCTAAATTGAATACTT
* * * * *
9141 TGAAGACTGGTGGGAACTTTCGCAACTTGAAAAAGAGTTAAATTGAATAATT
1 TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
9193 TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
1 TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
* *
9245 TGAAAATTGGTGGGAACTTTCCCAATTTGAAAAAGTGCTAAATTGAATACTT
1 TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
9297 T
1 T
9298 CTTTTTGATT
Statistics
Matches: 323, Mismatches: 34, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
48 43 0.13
52 233 0.72
56 47 0.15
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (52 bp):
TGAAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT
Found at i:9177 original size:160 final size:159
Alignment explanation
Indices: 8894--9278 Score: 543
Period size: 160 Copynumber: 2.5 Consensus size: 159
8884 AACCTGATGG
* **
8894 GAACTTTCCCAATTCGAAACGGAGCTAAATTGAATACTTTGAAAACTGGTGGGAAC---CCAATT
1 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGGAACTTTCCAATT
* *
8956 TG----AAAAAGAGCTAGATTGAATACTTTGAAAAGTGGTGGGAACTTTCCCAATTTGAAAAAGA
66 TGAAAAAAAAAGAGCTAGATTGAATACTTTGAAAACTGGTGGGAACTTTCCCAACTTGAAAAAGA
* *
9017 GCTAGATTGAATACA-TTGAAGACTGGCGA
131 GCTAAATTGAATA-ATTTGAAAACTGGCGA
* *
9046 GAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAAACTGGTGGGGACTTTCACAAT
1 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGGAACTTTC-CAAT
* * *
9111 TTGAAAAAAAAAGGGCTAGATTGAATACTTTGAAGACTGGTGGGAACTTTCGCAACTTGAAAAAG
65 TTGAAAAAAAAAGAGCTAGATTGAATACTTTGAAAACTGGTGGGAACTTTCCCAACTTGAAAAAG
* * *
9176 AGTTAAATTGAATAATTTGAAAACTGGTGG
130 AGCTAAATTGAATAATTTGAAAACTGGCGA
*
9206 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAATTGGTGGGAACTTTCCCAAT
1 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGGAACTTT-CCAAT
9271 TTGAAAAA
65 TTGAAAAA
9279 GTGCTAAATT
Statistics
Matches: 205, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
152 51 0.25
155 1 0.00
156 7 0.03
159 1 0.00
160 144 0.70
161 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (159 bp):
GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGGAACTTTCCAATT
TGAAAAAAAAAGAGCTAGATTGAATACTTTGAAAACTGGTGGGAACTTTCCCAACTTGAAAAAGA
GCTAAATTGAATAATTTGAAAACTGGCGA
Found at i:9328 original size:18 final size:18
Alignment explanation
Indices: 9305--9339 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9295 TTTCTTTTTG
9305 ATTTTTGAGT-TTTTGAAT
1 ATTTTTG-GTGTTTTGAAT
9323 ATTTTTGGTGTTTTGAA
1 ATTTTTGGTGTTTTGAA
9340 AACCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (18 bp):
ATTTTTGGTGTTTTGAAT
Found at i:10423 original size:42 final size:43
Alignment explanation
Indices: 10372--10465 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 43
10362 AATCAATTAC
*
10372 CTAA-ATTCTA-CTCCATCTCTAGGTGA-TTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGAT-ATTTCATCAAAATAAAG
10413 CTAATATTCTACTCCTCCATCTCTAGATATTTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATATTTCATCAAAATAAAG
*
10458 TTAATATT
1 CTAATATT
10466 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 35 0.76
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATATTTCATCAAAATAAAG
Done.