Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006437.1 Corchorus capsularis cultivar CVL-1 contig06458, 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: 60550
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:6892 original size:102 final size:102
Alignment explanation
Indices: 6646--6946 Score: 369
Period size: 102 Copynumber: 2.9 Consensus size: 102
6636 AAACACAACA
* * * * *
6646 AATTTCACTCATTTTAGCCTCCAAATAAAAAAATTACTAATTTATTTTAAGTGTAAGTCATTAAA
1 AATTTCACTAAGTTTAGTCT-CAAATAAAAAAA-T--TAATTCATTTTAAG-GTAAGTCATCAAA
* * * *
6711 TTGAAAATGTATTCTTATAA-GATATTAGAAATAAAAATTAATG
61 TTTAAAATGTATTATTATAATG-TTTTAGAAA-AAAAATCAATG
6754 AATTTCACTAAGTTTAGTCTCAAATAAAAAAATTAATTCATTTTAAGGTAAGTCATCAAATTTAA
1 AATTTCACTAAGTTTAGTCTCAAATAAAAAAATTAATTCATTTTAAGGTAAGTCATCAAATTTAA
6819 AATGTATTATTATAATGTTTTAGAAAAAAAATCAATG
66 AATGTATTATTATAATGTTTTAGAAAAAAAATCAATG
* * *
6856 AATTTCACTAAGTTTAGTCTCAAATATATAATTTAATTCATTTTAAAGGTAAG-CATCAAA-TT-
1 AATTTCACTAAGTTTAGTCTCAAATAAAAAAATTAATTCATTTT-AAGGTAAGTCATCAAATTTA
*
6918 AAATGTATTGTTAT-ATGGTTTTAGAAAAA
65 AAATGTATTATTATAAT-GTTTTAGAAAAA
6947 TAAGTAGGTG
Statistics
Matches: 177, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
99 2 0.01
100 25 0.14
101 2 0.01
102 58 0.33
103 46 0.26
104 14 0.08
106 1 0.01
107 12 0.07
108 17 0.10
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (102 bp):
AATTTCACTAAGTTTAGTCTCAAATAAAAAAATTAATTCATTTTAAGGTAAGTCATCAAATTTAA
AATGTATTATTATAATGTTTTAGAAAAAAAATCAATG
Found at i:10517 original size:18 final size:18
Alignment explanation
Indices: 10490--10524 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10480 TTTGGTTAGG
*
10490 TATGGATAAAGGAACATT
1 TATGGATAAAGAAACATT
*
10508 TATGGGTAAAGAAACAT
1 TATGGATAAAGAAACAT
10525 CAACCCTCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.26
Consensus pattern (18 bp):
TATGGATAAAGAAACATT
Found at i:14226 original size:15 final size:16
Alignment explanation
Indices: 14206--14242 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
14196 AATCCAATAG
14206 AATTTTTAA-AAAAAA
1 AATTTTTAAGAAAAAA
*
14221 AA-TTTTAAGAAAGAA
1 AATTTTTAAGAAAAAA
14236 AATTTTT
1 AATTTTT
14243 GATCATGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 9 0.47
16 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (16 bp):
AATTTTTAAGAAAAAA
Found at i:20152 original size:11 final size:12
Alignment explanation
Indices: 20120--20323 Score: 61
Period size: 11 Copynumber: 18.1 Consensus size: 12
20110 GAGAATCCGA
*
20120 ATAAATATTTTT
1 ATAAATATATTT
20132 ATATAATATATTT
1 ATA-AATATATTT
20145 A-AAATATA-TT
1 ATAAATATATTT
*
20155 ATATAT-TATATT
1 ATAAATATAT-TT
*
20167 AT--ATATGTTT
1 ATAAATATATTT
* *
20177 -T-TAT-TATAT
1 ATAAATATATTT
*
20186 ATAAATA-AATT
1 ATAAATATATTT
*
20197 A-AAATGTATTT
1 ATAAATATATTT
*
20208 ATATATA-ATTT
1 ATAAATATATTT
20219 ATTAATTATATATATT
1 A-TAA--ATATAT-TT
20235 ATAAATATATTT
1 ATAAATATATTT
20247 A-AAA-ATA-TT
1 ATAAATATATTT
20256 AT--ATATA-TT
1 ATAAATATATTT
* *
20265 ATATATATTTTT
1 ATAAATATATTT
** **
20277 AT-TTTATATAA
1 ATAAATATATTT
*
20288 ATAAATAAAATTT
1 ATAAAT-ATATTT
*
20301 A-AAACATATTT
1 ATAAATATATTT
20312 -TAAATATATTT
1 ATAAATATATTT
20323 A
1 A
20324 GAGAACCGAA
Statistics
Matches: 141, Mismatches: 26, Indels: 50
0.65 0.12 0.23
Matches are distributed among these distances:
8 1 0.01
9 14 0.10
10 19 0.13
11 53 0.38
12 24 0.17
13 19 0.13
14 3 0.02
15 5 0.04
16 3 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (12 bp):
ATAAATATATTT
Found at i:20237 original size:9 final size:9
Alignment explanation
Indices: 20206--20286 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 9
20196 TAAAATGTAT
20206 TTATATATAA
1 TTATATAT-A
20216 TT-TAT-TAA
1 TTATATAT-A
20224 TTATATATA
1 TTATATATA
20233 TTATAAATATA
1 TTAT--ATATA
* *
20244 TTTAAAAATA
1 -TTATATATA
20254 TTATATATA
1 TTATATATA
20263 TTATATATA
1 TTATATATA
* *
20272 TT-TTTATT
1 TTATATATA
20280 TTATATA
1 TTATATA
20287 AATAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
8 11 0.19
9 32 0.55
10 7 0.12
11 5 0.09
12 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTATATATA
Found at i:23691 original size:137 final size:139
Alignment explanation
Indices: 23441--23712 Score: 458
Period size: 137 Copynumber: 2.0 Consensus size: 139
23431 TCAATTTTCC
* *
23441 AATAAGCTCTACTAACTTCGATACATGACATTAGAGCGTTGGTTTAAAAAAAAATGAAATCATTC
1 AATAAACTCCACTAACTTCGATACATGACATTAGAGCGTTGGTTT-AAAAAAAA-GAAATCATTC
*
23506 TGATCATTTTCAAATAAATAATATTCCGCGCAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAG
64 TCATCATTTTCAAATAAATAATATTCCGCGCAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAG
*
23571 GTTTTAAAAAA
129 ATTTTAAAAAA
23582 AATAAACTCCACTAACTTCGATACATGACATTAGAGCGTTGGTTT-AAAAAAA-AAATCATTCTC
1 AATAAACTCCACTAACTTCGATACATGACATTAGAGCGTTGGTTTAAAAAAAAGAAATCATTCTC
* *
23645 ATCATTTTCAAATAAATAATGTTCCGCGTAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAGAT
66 ATCATTTTCAAATAAATAATATTCCGCGCAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAGAT
23710 TTT
131 TTT
23713 GAAGAAAACT
Statistics
Matches: 125, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
137 75 0.60
139 7 0.06
141 43 0.34
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (139 bp):
AATAAACTCCACTAACTTCGATACATGACATTAGAGCGTTGGTTTAAAAAAAAGAAATCATTCTC
ATCATTTTCAAATAAATAATATTCCGCGCAAAAACGCACAAAATTGTGAAGTTGAGGTTTTAGAT
TTTAAAAAA
Found at i:24173 original size:22 final size:22
Alignment explanation
Indices: 24140--24264 Score: 101
Period size: 22 Copynumber: 5.7 Consensus size: 22
24130 TTCCAATGTA
*
24140 GAAATATT-GATAACCACATTTT
1 GAAA-ATTCGATAACCACATTAT
*
24162 GAAAATTCGATAACCTCATTAT
1 GAAAATTCGATAACCACATTAT
* * **
24184 GAAATTTCGATAACCTCCCTAT
1 GAAAATTCGATAACCACATTAT
* * * *
24206 GAAAATTTGATAACTACACTGT
1 GAAAATTCGATAACCACATTAT
* *
24228 -AAAATTTTGATAACCACATCAT
1 GAAAA-TTCGATAACCACATTAT
*
24250 GAAATTTCGATAACC
1 GAAAATTCGATAACC
24265 TCAGTGTGAA
Statistics
Matches: 83, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
21 7 0.08
22 73 0.88
23 3 0.04
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (22 bp):
GAAAATTCGATAACCACATTAT
Found at i:24196 original size:44 final size:44
Alignment explanation
Indices: 24140--24284 Score: 157
Period size: 44 Copynumber: 3.3 Consensus size: 44
24130 TTCCAATGTA
* * * *
24140 GAAATATTGATAACCACATTTTGAAAATTCGATAACCTCATTAT
1 GAAATTTTGATAACCACATTATGAAAATTCGATAACCTCACTGT
* * ** *
24184 GAAATTTCGATAACCTCCCTATGAAAATTTGATAA-CTACACTGT
1 GAAATTTTGATAACCACATTATGAAAATTCGATAACCT-CACTGT
* * * *
24228 AAAATTTTGATAACCACATCATGAAATTTCGATAACCTCAGTGT
1 GAAATTTTGATAACCACATTATGAAAATTCGATAACCTCACTGT
24272 GAAATTTTGATAA
1 GAAATTTTGATAA
24285 TCTGCTTATA
Statistics
Matches: 80, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
43 2 0.03
44 76 0.95
45 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (44 bp):
GAAATTTTGATAACCACATTATGAAAATTCGATAACCTCACTGT
Found at i:24274 original size:22 final size:22
Alignment explanation
Indices: 24161--24284 Score: 110
Period size: 22 Copynumber: 5.6 Consensus size: 22
24151 AACCACATTT
* *
24161 TGAAAATTCGATAACCTCATTA
1 TGAAATTTCGATAACCTCACTA
*
24183 TGAAATTTCGATAACCTCCCTA
1 TGAAATTTCGATAACCTCACTA
*
24205 TGAAAATTT-GATAA-CTACACTG
1 TG-AAATTTCGATAACCT-CACTA
* * *
24227 TAAAATTTTGATAACCACA-TCA
1 TGAAATTTCGATAACCTCACT-A
* *
24249 TGAAATTTCGATAACCTCAGTG
1 TGAAATTTCGATAACCTCACTA
*
24271 TGAAATTTTGATAA
1 TGAAATTTCGATAA
24285 TCTGCTTATA
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
21 9 0.11
22 66 0.80
23 8 0.10
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (22 bp):
TGAAATTTCGATAACCTCACTA
Found at i:24297 original size:66 final size:66
Alignment explanation
Indices: 24170--24357 Score: 175
Period size: 66 Copynumber: 2.8 Consensus size: 66
24160 TTGAAAATTC
* * * *
24170 GATAACCTCATTATGAAATTTCGATAACCTCCCTATGAAAATTTGATAACTACACTGTAAAATTT
1 GATAACCACATCATGAAATTTCGATAACCTCACTATGAAAATTTGATAACTACACTATAAAATTT
24235 T
66 T
* * * * *
24236 GATAACCACATCATGAAATTTCGATAACCTCAGTGTGAAATTTTGATAATCTGC-TTATAAAATT
1 GATAACCACATCATGAAATTTCGATAACCTCACTATGAAAATTTGATAA-CTACACTATAAAATT
24300 TT
65 TT
* * * * * * *
24302 AATAATCACACTAAAT-AAAATTCG-TAACCACACAACGAAAATTTTGATAACTACAC
1 GATAACCACA-T-CATGAAATTTCGATAACCTCACTATGAAAA-TTTGATAACTACAC
24358 CATGCAATTT
Statistics
Matches: 96, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
66 75 0.78
67 19 0.20
68 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (66 bp):
GATAACCACATCATGAAATTTCGATAACCTCACTATGAAAATTTGATAACTACACTATAAAATTT
T
Found at i:26723 original size:257 final size:254
Alignment explanation
Indices: 26266--26750 Score: 801
Period size: 257 Copynumber: 1.9 Consensus size: 254
26256 TAACCTATAA
* *
26266 ATAAATTAAAAATTTTATAATCTAAATATAACTATGAGAAGTAAATTATTAATTACAATTATAGC
1 ATAAATTAAAAATTTTATAATCTAAAAATAACTATGAGAAGTAAATTATTAATTAAAATTATAGC
* *
26331 AGATTATTATCTTTCCATAACTTAAAAAAGTTAAATATATTGGATTTACAATATCTCTCTATAAT
66 AGATTATTATCTTTCCATAACTTAAAAAAGTTAAATATATTGGATTGACAATATCTCTCCATAAT
* * * *
26396 TAATTAAAAAGTTGAATGACTAAAAAGAATACTTATTTAAATATTATTATACTATAATATTAATG
131 TAATAAAAAAATTGAATGACTAAAAAGAATACTTATTTAAAAATTATTATACTATAATATTAAGG
26461 GTATTTTAGTAATTAACTAATTAAGATTTTTGACACGTCAGTGGATCAAATATTAACCT
196 GTATTTTAGTAATTAACTAATTAAGATTTTTGACACGTCAGTGGATCAAATATTAACCT
*
26520 ATAAATTAAAAATTTTATAATCTAAAAATAATTATGAGAAGTAAATTATTAATTAAAATTATAGC
1 ATAAATTAAAAATTTTATAATCTAAAAATAACTATGAGAAGTAAATTATTAATTAAAATTATAGC
* *
26585 AGATTATTAATATCTTTCCTTAATTTAAAAAAGTTAAATATATTGGATTGACAATATCTCTCCAT
66 AGATTA-T--TATCTTTCCATAACTTAAAAAAGTTAAATATATTGGATTGACAATATCTCTCCAT
*
26650 AATTTATAAAAAAATTGAATGACTAAAAAGAATACTTATTTAAAAATTATTATACTATAGA-ATT
128 AATTAATAAAAAAATTGAATGACTAAAAAGAATACTTATTTAAAAATTATTATACTATA-ATATT
* *
26714 AAGGGTATTTTAGTAATTGATTAATTAAGATTTTTGA
192 AAGGGTATTTTAGTAATTAACTAATTAAGATTTTTGA
26751 ATTCGTACTT
Statistics
Matches: 213, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
254 68 0.32
255 1 0.00
257 143 0.67
258 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (254 bp):
ATAAATTAAAAATTTTATAATCTAAAAATAACTATGAGAAGTAAATTATTAATTAAAATTATAGC
AGATTATTATCTTTCCATAACTTAAAAAAGTTAAATATATTGGATTGACAATATCTCTCCATAAT
TAATAAAAAAATTGAATGACTAAAAAGAATACTTATTTAAAAATTATTATACTATAATATTAAGG
GTATTTTAGTAATTAACTAATTAAGATTTTTGACACGTCAGTGGATCAAATATTAACCT
Found at i:27126 original size:18 final size:18
Alignment explanation
Indices: 27103--27139 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27093 CTAAGGATGT
27103 TTATTTTGGAAAATGGTA
1 TTATTTTGGAAAATGGTA
27121 TTATTTTGGAAAATGGTA
1 TTATTTTGGAAAATGGTA
27139 T
1 T
27140 GTTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (18 bp):
TTATTTTGGAAAATGGTA
Found at i:33194 original size:29 final size:30
Alignment explanation
Indices: 33152--33223 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
33142 ATTTGTAGTG
* *
33152 TTTGGACGTTTTGTCCCATGAACT-TCAAC
1 TTTGGACATTTTGTCCCATGAACTCCCAAC
* * *
33181 TTTGGACATTTTGTCCCTTGTACTCCCAAT
1 TTTGGACATTTTGTCCCATGAACTCCCAAC
33211 TTTGGACATTTTG
1 TTTGGACATTTTG
33224 CCACCCTCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (30 bp):
TTTGGACATTTTGTCCCATGAACTCCCAAC
Found at i:33334 original size:45 final size:45
Alignment explanation
Indices: 33265--33362 Score: 178
Period size: 45 Copynumber: 2.2 Consensus size: 45
33255 TGTCATGCCG
*
33265 CTGACGTGGCATGACCACGTGTCAATGCCACGTCATCAGTTTGGT
1 CTGATGTGGCATGACCACGTGTCAATGCCACGTCATCAGTTTGGT
*
33310 CTGATGTGGCATTACCACGTGTCAATGCCACGTCATCAGTTTGGT
1 CTGATGTGGCATGACCACGTGTCAATGCCACGTCATCAGTTTGGT
33355 CTGATGTG
1 CTGATGTG
33363 TCAATGCCAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (45 bp):
CTGATGTGGCATGACCACGTGTCAATGCCACGTCATCAGTTTGGT
Found at i:33369 original size:32 final size:32
Alignment explanation
Indices: 33328--33408 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
33318 GCATTACCAC
* * *
33328 GTGTCAATGCCACGTCATCAGTTTGGTCTGAT
1 GTGTCAATGCCACATCATCAGTTTGATCCGAT
*
33360 GTGTCAATGCCACATCATCGGTTTGATCCGAT
1 GTGTCAATGCCACATCATCAGTTTGATCCGAT
* *
33392 GTGGCAATGCTACATCA
1 GTGTCAATGCCACATCA
33409 GTGGCATGAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (32 bp):
GTGTCAATGCCACATCATCAGTTTGATCCGAT
Found at i:33544 original size:31 final size:28
Alignment explanation
Indices: 33482--33544 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 28
33472 TCAGGGGAAA
* *
33482 AAAATGTCCAAAATTAAAATTCAGGGAC
1 AAAACGTCCAAAACTAAAATTCAGGGAC
*
33510 AAAACGTCCAAACACTACAAATTTAGGAGAC
1 AAAACGTCCAAA-ACTA-AAATTCAGG-GAC
33541 AAAA
1 AAAA
33545 AGGTATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.38
29 3 0.10
30 8 0.28
31 7 0.24
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.17
Consensus pattern (28 bp):
AAAACGTCCAAAACTAAAATTCAGGGAC
Found at i:35793 original size:30 final size:30
Alignment explanation
Indices: 35757--35815 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
35747 AAGAAATTGT
*
35757 TCATGCTCCCAGCTTGAAAGTGATAATTTA
1 TCATGCTCCCAGCTTGAAAGAGATAATTTA
* *
35787 TCATGCTCCCGGCTTGAAAGAGATTATTT
1 TCATGCTCCCAGCTTGAAAGAGATAATTT
35816 CTAAGCTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (30 bp):
TCATGCTCCCAGCTTGAAAGAGATAATTTA
Found at i:39503 original size:14 final size:15
Alignment explanation
Indices: 39476--39504 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39466 ATGGTTGTAC
39476 TTTTTCCTTGCTTTT
1 TTTTTCCTTGCTTTT
39491 TTTTTCCTT-CTTTT
1 TTTTTCCTTGCTTTT
39505 AATTTCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTCCTTGCTTTT
Found at i:42469 original size:14 final size:15
Alignment explanation
Indices: 42450--42478 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42440 AGACTTGTAT
42450 GAAAAGG-GCAAACA
1 GAAAAGGAGCAAACA
42464 GAAAAGGAGCAAACA
1 GAAAAGGAGCAAACA
42479 ACTACAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.14, G:0.28, T:0.00
Consensus pattern (15 bp):
GAAAAGGAGCAAACA
Found at i:45989 original size:21 final size:22
Alignment explanation
Indices: 45948--45990 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
45938 ATATTTTATT
45948 TTATTTTACCTACTCAAAAAAA
1 TTATTTTACCTACTCAAAAAAA
*
45970 TTATTTTA-CTACT-AATAAAA
1 TTATTTTACCTACTCAAAAAAA
45990 T
1 T
45991 GAAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (22 bp):
TTATTTTACCTACTCAAAAAAA
Found at i:48947 original size:162 final size:161
Alignment explanation
Indices: 48673--49003 Score: 574
Period size: 162 Copynumber: 2.0 Consensus size: 161
48663 TTATATACCT
*
48673 TAGAGATTAGGGTTTTGCTAGTGGGCTTGGGCCCAAAATAAAGTATGACCAACAATTGCCCCCCA
1 TAGAG-TTAGGGTTTTGCTAGTGGGCTTGGGCCCAAAAAAAAGTATGACCAACAATTGCCCCCCA
*
48738 GTCGTAAGAGCGACCATAAAGTGGTTGGACGAGCGACTTAACTTTTTCGGTGTTTTGAGTTCGTC
65 GTCGTAAGAGCGACCATAAAGTGGTCGGACGAGCGACTTAACTTTTTCGGTGTTTTGAGTTCGTC
48803 ATGTTAGTTTATACTCAATCGCGGAGTCCATG
130 ATGTTAGTTTATACTCAATCGCGGAGTCCATG
*
48835 TAGAGTT-GGGTTTTGCTAGTGGGCTTGGGCCCAAAAAAAAAAGTATGATCAACAATTGCCCCCC
1 TAGAGTTAGGGTTTTGCTAGTGGGCTTGGGCCC--AAAAAAAAGTATGACCAACAATTGCCCCCC
* * *
48899 AGTCGTGAGAGCGATCATAAAGTGGTCGGACGAGCGACTTACCTTTTTCGGTGTTTTGAGTTCGT
64 AGTCGTAAGAGCGACCATAAAGTGGTCGGACGAGCGACTTAACTTTTTCGGTGTTTTGAGTTCGT
48964 CATGTTAGTTTATACTCAATCGCGGAGTCCATG
129 CATGTTAGTTTATACTCAATCGCGGAGTCCATG
48997 TAGAGTT
1 TAGAGTT
49004 CATTTAGTTT
Statistics
Matches: 161, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
160 25 0.16
161 2 0.01
162 134 0.83
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (161 bp):
TAGAGTTAGGGTTTTGCTAGTGGGCTTGGGCCCAAAAAAAAGTATGACCAACAATTGCCCCCCAG
TCGTAAGAGCGACCATAAAGTGGTCGGACGAGCGACTTAACTTTTTCGGTGTTTTGAGTTCGTCA
TGTTAGTTTATACTCAATCGCGGAGTCCATG
Found at i:52244 original size:16 final size:17
Alignment explanation
Indices: 52217--52258 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
52207 GATAATCCAA
* *
52217 AATTTAGAAGTTTAGA-
1 AATTTTGAAGTTGAGAG
*
52233 AGTTTTGAAGTTGAGAG
1 AATTTTGAAGTTGAGAG
52250 AATTTTGAA
1 AATTTTGAA
52259 AAAAAGAGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (17 bp):
AATTTTGAAGTTGAGAG
Found at i:54020 original size:21 final size:20
Alignment explanation
Indices: 53980--54020 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
53970 TCGCTCGGTC
* *
53980 TCTACAAACCAATCATCACA
1 TCTACAAACCAAACACCACA
54000 TCTACCAAACCAAACACCACA
1 TCTA-CAAACCAAACACCACA
54021 ATAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (20 bp):
TCTACAAACCAAACACCACA
Found at i:54955 original size:61 final size:61
Alignment explanation
Indices: 54885--55094 Score: 145
Period size: 61 Copynumber: 3.2 Consensus size: 61
54875 CTATTTCAAT
54885 TAAAAGGTTTAAAGTTGAATTAAGCAATTCGTCAAAAGTTTAAACTTAATTTGTTTTCATA
1 TAAAAGGTTTAAAGTTGAATTAAGCAATTCGTCAAAAGTTTAAACTTAATTTGTTTTCATA
* ** ** ** * * * *
54946 TAAATGGTTTAATCTCAAAGTCGAGCATTTC-ACAAAATTAGTCTTAAATTTGTCATTTGGTCAT
1 TAAAAGGTTTAAAGTTGAA-TTAAGCAATTCGTC-AAA--AGT-TTAAA-CT-TAATTT-G---T
55010 ATTTTTTTCA-A
55 -----TTTCATA
55021 TTAAAAGGTTTAAAGTTGAATTAAGCAATTCGTCAAAAGTTTAAACTTAATTTGTTTTCATA
1 -TAAAAGGTTTAAAGTTGAATTAAGCAATTCGTCAAAAGTTTAAACTTAATTTGTTTTCATA
*
55083 TAAATGGTTTAA
1 TAAAAGGTTTAA
55095 TCTCAAAGTC
Statistics
Matches: 107, Mismatches: 23, Indels: 38
0.64 0.14 0.23
Matches are distributed among these distances:
61 31 0.29
62 12 0.11
64 3 0.03
65 5 0.05
66 2 0.02
67 5 0.05
68 1 0.01
69 1 0.01
70 5 0.05
71 2 0.02
72 5 0.05
73 3 0.03
75 12 0.11
76 20 0.19
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (61 bp):
TAAAAGGTTTAAAGTTGAATTAAGCAATTCGTCAAAAGTTTAAACTTAATTTGTTTTCATA
Found at i:56192 original size:13 final size:13
Alignment explanation
Indices: 56176--56200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56166 TAACAAAATT
56176 TTAGATCTACAAC
1 TTAGATCTACAAC
56189 TTAGATCTACAA
1 TTAGATCTACAA
56201 AATAACAACA
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:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TTAGATCTACAAC
Done.