Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021698.1 Corchorus olitorius cultivar O-4 contig21731, 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: 104331
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:391 original size:36 final size:36
Alignment explanation
Indices: 338--406 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
328 AGATTTTGGA
* *
338 GAAATATAATAATCAAAATTACAAAAAATGTAATAG
1 GAAATATAATAACCAAAATCACAAAAAATGTAATAG
* *
374 GAAATATGATAACCAAAATCACAAAAGATGTAA
1 GAAATATAATAACCAAAATCACAAAAAATGTAA
407 GGTTATTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (36 bp):
GAAATATAATAACCAAAATCACAAAAAATGTAATAG
Found at i:19099 original size:11 final size:12
Alignment explanation
Indices: 19078--19112 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
19068 CCATATTGCA
19078 AAAAGAAATAAT
1 AAAAGAAATAAT
19090 AAAA-AAATAAT
1 AAAAGAAATAAT
19101 AAAAGAGAATAA
1 AAAAGA-AATAA
19113 AACATACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
12 5 0.24
13 5 0.24
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (12 bp):
AAAAGAAATAAT
Found at i:20010 original size:31 final size:30
Alignment explanation
Indices: 19970--20042 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
19960 AAATAGTCAA
*
19970 GGACCCAATTGCTCAATTAACTTCACTTCAG
1 GGACCCAATTGCT-AACTAACTTCACTTCAG
* * *
20001 GGACTCAATTGCTTACTAAGTTCACTTCAG
1 GGACCCAATTGCTAACTAACTTCACTTCAG
*
20031 GGACCCATTTGC
1 GGACCCAATTGC
20043 ACATTTTCCC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 24 0.67
31 12 0.33
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
GGACCCAATTGCTAACTAACTTCACTTCAG
Found at i:20110 original size:12 final size:11
Alignment explanation
Indices: 20089--20120 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
20079 ATAAAAAAAT
20089 TTCATTTTTTC
1 TTCATTTTTTC
20100 TTCATTTTTT-
1 TTCATTTTTTC
20110 TTC-TTTTTTC
1 TTCATTTTTTC
20120 T
1 T
20121 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 6 0.30
10 4 0.20
11 10 0.50
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCATTTTTTC
Found at i:20118 original size:20 final size:19
Alignment explanation
Indices: 20088--20128 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 19
20078 AATAAAAAAA
20088 TTTCATTTTTTCTTCATTTTT
1 TTTCATTTTTTC-T-ATTTTT
20109 TTTC-TTTTTTCTATTTTT
1 TTTCATTTTTTCTATTTTT
20127 TT
1 TT
20129 AAATCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 7 0.35
21 4 0.20
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCATTTTTTCTATTTTT
Found at i:20127 original size:11 final size:10
Alignment explanation
Indices: 20088--20128 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
20078 AATAAAAAAA
20088 TTTCATTTTT
1 TTTCATTTTT
20098 TCTTCATTTTT
1 T-TTCATTTTT
20109 TTTC-TTTTT
1 TTTCATTTTT
*
20118 TCT-ATTTTT
1 TTTCATTTTT
20127 TT
1 TT
20129 AAATCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 13 0.48
10 4 0.15
11 10 0.37
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:23989 original size:12 final size:13
Alignment explanation
Indices: 23972--24000 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
23962 GTTCATTGCC
23972 GTGATTGTGA-TT
1 GTGATTGTGACTT
23984 GTGATTGTGACTT
1 GTGATTGTGACTT
23997 GTGA
1 GTGA
24001 GTGCTTTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.17, C:0.03, G:0.34, T:0.45
Consensus pattern (13 bp):
GTGATTGTGACTT
Found at i:32140 original size:24 final size:24
Alignment explanation
Indices: 32127--32180 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
32117 GCTGCTGAGC
32127 CTGAGATTGAGGCTGCTGTAAAGA
1 CTGAGATTGAGGCTGCTGTAAAGA
* *
32151 CTGAGATTGTGGCTGCTGTAAAGG
1 CTGAGATTGAGGCTGCTGTAAAGA
32175 CTGAGA
1 CTGAGA
32181 AGCTGGCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.35, T:0.26
Consensus pattern (24 bp):
CTGAGATTGAGGCTGCTGTAAAGA
Found at i:46371 original size:43 final size:43
Alignment explanation
Indices: 46322--46407 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
46312 CTTTATGGGG
*
46322 ATATAGTTGCCCTCTTTTGTCCAAATCTTGGATTTTTAAAGCA
1 ATATAGTTGCCCTCATTTGTCCAAATCTTGGATTTTTAAAGCA
46365 ATATAGTTGCCCTCATTTGTCCAAATCTTGGATTTTTAAAGCA
1 ATATAGTTGCCCTCATTTGTCCAAATCTTGGATTTTTAAAGCA
46408 CAGAAGACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (43 bp):
ATATAGTTGCCCTCATTTGTCCAAATCTTGGATTTTTAAAGCA
Found at i:48266 original size:1 final size:1
Alignment explanation
Indices: 48231--48258 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
48221 GGAATGAGGG
48231 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
48259 CACTTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:49575 original size:4 final size:4
Alignment explanation
Indices: 49566--49591 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
49556 TTCTTGAAGA
49566 AATC AATC AATC AATC AATC AATC AA
1 AATC AATC AATC AATC AATC AATC AA
49592 AAACTCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
AATC
Found at i:50159 original size:102 final size:102
Alignment explanation
Indices: 49912--50501 Score: 559
Period size: 102 Copynumber: 5.8 Consensus size: 102
49902 CCAGCGGCAG
** * * * * *
49912 TCTCACTATTTTCTTGAATACCAGGCACTACATTAGTCACTTCTATCTCTTTACTAGAAACCAAA
1 TCTCACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCTTTAGTAGAAACCACA
* *
49977 TCAAGCCCCTCTCTC--TTTTTCAGTTCACCAGCAGCAGCAA
66 TCATGCCCCTCT-TCAATTTTT-AGTTCA-C-G-AGCAGCAT
* * *
50017 TCTCACTATTATCTTGAATACCAGATAATACATT-CATAACTTCAATCTGTTTAGTAGAAACCAC
1 TCTCACTATTTTCTTGAATACCAGATACTACATTAC-TAACTTCAATCTCTTTAGTAGAAACCAC
*
50081 ATCATGCCCCTCTTCAATTTTTAGTTCACGACCAGCAT
65 ATCATGCCCCTCTTCAATTTTTAGTTCACGAGCAGCAT
* * *
50119 TCTCACTATTTTCTTGAATACCAGATACCACATTACTAACTTCAATCTCTTTGGTAGAGACCACA
1 TCTCACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCTTTAGTAGAAACCACA
* * *
50184 GCATGCGCCTCTTC-ATTTGTCT-GTTCACCAGCAGCAT
66 TCATGCCCCTCTTCAATTT-T-TAGTTCACGAGCAGCAT
* * * * *
50221 TCTCACTAGTTTCTTGAATACCAGATACTGCATTATTATCTTCAATCTCTTTACTAGAAACCACA
1 TCTCACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCTTTAGTAGAAACCACA
** * * ** *
50286 AGATGCCTCTCTTCAGTTTCAAGTTCACTAGCAG-AGT
66 TCATGCCCCTCTTCAATTTTTAGTTCACGAGCAGCA-T
** * * * * **
50323 TCTCTGTATTTT-TATAAATACCAGATACTATACTACTAACTTCTATCTCTTTAAAAGAAACCAC
1 TCTCACTATTTTCT-TGAATACCAGATACTACATTACTAACTTCAATCTCTTTAGTAGAAACCAC
* *
50387 ATCATGCCACTCTTCAATTTTTGGTTCATC-AGCAGCAT
65 ATCATGCCCCTCTTCAATTTTTAGTTCA-CGAGCAGCAT
* * * * * * * *
50425 TATTACTATTTTCTTGAATACCAGATA-TCACGTTACTAGCTTCGATCTCTTTAGCAGAAATCGC
1 TCTCACTATTTTCTTGAATACCAGATACT-ACATTACTAACTTCAATCTCTTTAGTAGAAACCAC
*
50489 ATCATGCCACTCT
65 ATCATGCCCCTCT
50502 AATTCAGATG
Statistics
Matches: 399, Mismatches: 72, Indels: 31
0.79 0.14 0.06
Matches are distributed among these distances:
101 7 0.02
102 304 0.76
103 9 0.02
104 3 0.01
105 71 0.18
106 5 0.01
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (102 bp):
TCTCACTATTTTCTTGAATACCAGATACTACATTACTAACTTCAATCTCTTTAGTAGAAACCACA
TCATGCCCCTCTTCAATTTTTAGTTCACGAGCAGCAT
Found at i:50475 original size:306 final size:308
Alignment explanation
Indices: 49899--50476 Score: 724
Period size: 306 Copynumber: 1.9 Consensus size: 308
49889 CTTTCTTGTG
* * * *
49899 TCACCAGCGGCAGTCTCACTATTTTCTTGAATACCAGGCACTACATTAGTCACTTCTATCTCTTT
1 TCACCAGCAGCAGTCTCACTAGTTTCTTGAATACCAGACACTACATTAGTCACTTCAATCTCTTT
**
49964 ACTAGAAACCAAATCAAGCCCCTCTCTCTTTTTCAGTTCACCAGCAGCAGCAATCTCACTATTAT
66 ACTAGAAACCAAATCAAGCCCCTCTCTCAGTTTCAGTTCACCAGCAGCAG-AATCTCACTATTAT
* * * ** *
50029 CTTGAATACCAGATAATACATTCATAACTTCAATCTGTTTAGTAGAAACCACATCATGCCCCTCT
130 CTTAAATACCAGATAATACATACATAACTTCAATCTCTTTAAAAGAAACCACATCATGCCACTCT
*
50094 TCAATTTTTAGTTCACGACCAGCATTCTCACTATTTTCTTGAATACCAGATACCACATTACTAAC
195 TCAATTTTTAGTTCACGACCAGCATTATCACTATTTTCTTGAATACCAGATACCACATTACTAAC
50159 TTCAATCTCTTTGGTAGAGACCACAGCATGCGCCTCTTCATTTGTCTGT
260 TTCAATCTCTTTGGTAGAGACCACAGCATGCGCCTCTTCATTTGTCTGT
* * * *
50208 TCACCAGCAGCATTCTCACTAGTTTCTTGAATACCAGATACTGCATTA-TTATCTTCAATCTCTT
1 TCACCAGCAGCAGTCTCACTAGTTTCTTGAATACCAGACACTACATTAGTCA-CTTCAATCTCTT
* * * * * **
50272 TACTAGAAACCACAA-GATGCCTCTCT-TCAGTTTCAAGTTCACTAGCAG-AG-TTCTCTGTATT
65 TACTAGAAACCA-AATCAAGCCCCTCTCTCAGTTTC-AGTTCACCAGCAGCAGAATCTCACTATT
* *
50333 -TTTATAAATACCAGATACTATAC-TAC-TAACTTCTATCTCTTTAAAAGAAACCACATCATGCC
128 ATCT-TAAATACCAGATA--ATACATACATAACTTCAATCTCTTTAAAAGAAACCACATCATGCC
* * * * *
50395 ACTCTTCAATTTTTGGTTCATC-AGCAGCATTATTACTATTTTCTTGAATACCAGATATCACGTT
190 ACTCTTCAATTTTTAGTTCA-CGACCAGCATTATCACTATTTTCTTGAATACCAGATACCACATT
* *
50459 ACTAGCTTCGATCTCTTT
254 ACTAACTTCAATCTCTTT
50477 AGCAGAAATC
Statistics
Matches: 229, Mismatches: 33, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
305 2 0.01
306 123 0.54
307 3 0.01
308 14 0.06
309 85 0.37
310 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (308 bp):
TCACCAGCAGCAGTCTCACTAGTTTCTTGAATACCAGACACTACATTAGTCACTTCAATCTCTTT
ACTAGAAACCAAATCAAGCCCCTCTCTCAGTTTCAGTTCACCAGCAGCAGAATCTCACTATTATC
TTAAATACCAGATAATACATACATAACTTCAATCTCTTTAAAAGAAACCACATCATGCCACTCTT
CAATTTTTAGTTCACGACCAGCATTATCACTATTTTCTTGAATACCAGATACCACATTACTAACT
TCAATCTCTTTGGTAGAGACCACAGCATGCGCCTCTTCATTTGTCTGT
Found at i:55825 original size:19 final size:19
Alignment explanation
Indices: 55801--55839 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
55791 GTTCATCATA
*
55801 TATATTCTTGTGTTTCTTT
1 TATATTCTTCTGTTTCTTT
* *
55820 TATATTTTTCTTTTTCTTT
1 TATATTCTTCTGTTTCTTT
55839 T
1 T
55840 TTTTTTCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.74
Consensus pattern (19 bp):
TATATTCTTCTGTTTCTTT
Found at i:60311 original size:19 final size:19
Alignment explanation
Indices: 60289--60327 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
60279 TCCACATAAA
60289 AATGCAAATTCTTTGGTGG
1 AATGCAAATTCTTTGGTGG
*
60308 AATGCAAATTTTTTGGTGG
1 AATGCAAATTCTTTGGTGG
60327 A
1 A
60328 GTATTTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (19 bp):
AATGCAAATTCTTTGGTGG
Found at i:65757 original size:36 final size:36
Alignment explanation
Indices: 65714--65783 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
65704 TTTGAATCTT
*
65714 TATATATACTACATATTATTTGGAACACTCAATATA
1 TATATATACTACATATTATTTGGAACACCCAATATA
*
65750 TATATATATTACATATTATTTGGAACACCCAATA
1 TATATATACTACATATTATTTGGAACACCCAATA
65784 AAATTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (36 bp):
TATATATACTACATATTATTTGGAACACCCAATATA
Found at i:66403 original size:24 final size:23
Alignment explanation
Indices: 66371--66427 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
66361 GCCTTATACA
**
66371 CAAACTAATGATATGTTTAGGATT
1 CAAACTAATGATATGTACA-GATT
66395 CAAACTAATG---TGTACAGATT
1 CAAACTAATGATATGTACAGATT
66415 CAAACTAATGATA
1 CAAACTAATGATA
66428 AACAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 14 0.50
21 4 0.14
24 10 0.36
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (23 bp):
CAAACTAATGATATGTACAGATT
Found at i:66789 original size:3 final size:3
Alignment explanation
Indices: 66781--66839 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
66771 AAGAAAAATG
66781 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66829 TAA TAA TAA TA
1 TAA TAA TAA TA
66840 TGATAGTAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:67370 original size:23 final size:22
Alignment explanation
Indices: 67336--67398 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
67326 TAACTTCCCA
*
67336 ATGAAATTTTGATAACCAACACT
1 ATGAAATATTGATAACCAACA-T
* **
67359 ATGAAATGTTGATAACCTCCAT
1 ATGAAATATTGATAACCAACAT
*
67381 ATGATATATTGATAACCA
1 ATGAAATATTGATAACCA
67399 CGTTATGGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (22 bp):
ATGAAATATTGATAACCAACAT
Found at i:67371 original size:45 final size:45
Alignment explanation
Indices: 67310--67429 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 45
67300 TTGAAGACCT
* * * *
67310 CACTATGAACTTTTGATAACTTCCCA-ATGAAATTTTGATAACCAA
1 CACTATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAA
*
67355 CACTATGAAATGTTGATAACCTCCATATGATATATTGATAACC-A
1 CACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAA
** * *
67399 CGTTATGGAAAT-TTAAAAACCTCCATATGAA
1 CACTAT-GAAATGTTGATAACCTCCATATGAA
67430 TTGTTAGTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
44 24 0.38
45 39 0.62
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (45 bp):
CACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAA
Found at i:67505 original size:22 final size:22
Alignment explanation
Indices: 67269--67656 Score: 224
Period size: 22 Copynumber: 17.8 Consensus size: 22
67259 TTAACATTCT
*
67269 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * *
67291 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTCCC
* *
67313 TATGAACTTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCCC
* * *
67335 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCCC
* *
67358 TATGAAATGTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCC
* * * **
67380 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCC
* * *
67402 TATGGAAA-TTTAAAAACCTCCA
1 TAT-GAAATTTTGATAACCTCCC
* * *
67424 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAACCTCCC
* * *
67446 TCTGAAATTTTGATAATCACACC
1 TATGAAATTTTGATAACCTC-CC
* * **
67469 -ATGAAATTGTAATAACCTCGT
1 TATGAAATTTTGATAACCTCCC
*
67490 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTCCC
*
67513 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCC
*
67536 TATAAAATTTTGATAA-----C
1 TATGAAATTTTGATAACCTCCC
* *
67553 TAT-AAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTCCC
** **
67574 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCC
* *
67596 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCC
* * *
67618 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCCC
67640 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
67657 TGTTGCGCAA
Statistics
Matches: 277, Mismatches: 70, Indels: 39
0.72 0.18 0.10
Matches are distributed among these distances:
16 12 0.04
17 4 0.01
20 2 0.01
21 10 0.04
22 179 0.65
23 70 0.25
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:67520 original size:23 final size:23
Alignment explanation
Indices: 67494--67551 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
67484 CCTCGTTATG
*
67494 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
67517 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
67540 AAATTTTGATAA
1 AAATTTTGATAA
67552 CTATAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:67561 original size:16 final size:17
Alignment explanation
Indices: 67535--67567 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
67525 ATAAACCTCC
67535 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
67552 CTAT-AAATTTTGATAA
1 CTATAAAATTTTGATAA
67568 TCTTCCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (17 bp):
CTATAAAATTTTGATAA
Found at i:69681 original size:22 final size:22
Alignment explanation
Indices: 69653--69711 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
69643 ATAACCCTCT
69653 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAAACTAAA
* **
69674 CTATGAAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAAACTAAA
69697 TATGAAATTTTGATA
1 TATGAAATTTTGATA
69712 TCCTCCCTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTAAA
Found at i:69974 original size:22 final size:22
Alignment explanation
Indices: 69898--69980 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 22
69888 GTTGACCCCT
* *
69898 CTATGAAATTCTGATAATAACA
1 CTATGAAATTTTGATAACAACA
* * ** *
69920 TTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACAACA
* *
69942 CTTTGAGATTTTGATAACAACA
1 CTATGAAATTTTGATAACAACA
69964 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
69981 TCTTCCTATG
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACAACA
Found at i:70024 original size:25 final size:23
Alignment explanation
Indices: 69855--70063 Score: 74
Period size: 22 Copynumber: 9.5 Consensus size: 23
69845 ATAAACTCTT
*
69855 TATGAAATTTTGATAATCCCT-C
1 TATGAAATTTTGATAATCCTTCC
* * * * * *
69877 GATAAAATTTTGTTGACCCCT-C
1 TATGAAATTTTGATAATCCTTCC
* * *
69899 TATGAAATTCTGATAATAACAT--
1 TATGAAATTTTGATAAT-CCTTCC
*
69921 TATGTAATTTTGATAA-CC-TCGC
1 TATGAAATTTTGATAATCCTTC-C
* * **
69943 TTTGAGATTTTGATAA--CAACAC
1 TATGAAATTTTGATAATCCTTC-C
69965 TATGAAATTTTGATAAT-CTTCC
1 TATGAAATTTTGATAATCCTTCC
*
69987 TATG--ATTTTGATAATCCGATTTC
1 TATGAAATTTTGATAATCC--TTCC
*
70010 TATGAAATTTCGATAATCAC-T-C
1 TATGAAATTTTGATAATC-CTTCC
70032 TAT-AAGA-TTTGATAA-CCTT-C
1 TATGAA-ATTTTGATAATCCTTCC
*
70052 TATCAAATTTTG
1 TATGAAATTTTG
70064 GTACTCCTCA
Statistics
Matches: 143, Mismatches: 28, Indels: 33
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.01
20 19 0.13
21 17 0.12
22 81 0.57
23 12 0.08
25 11 0.08
26 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (23 bp):
TATGAAATTTTGATAATCCTTCC
Found at i:70061 original size:20 final size:22
Alignment explanation
Indices: 70007--70061 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 22
69997 ATAATCCGAT
70007 TTCTATGAAATTTCGATAATCAC
1 TTCTAT-AAATTTCGATAATCAC
70030 -TCTATAAGATTT-GATAA-C-C
1 TTCTATAA-ATTTCGATAATCAC
70049 TTCTATCAAATTT
1 TTCTAT-AAATTT
70062 TGGTACTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 1 0.03
20 10 0.34
21 9 0.31
22 9 0.31
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (22 bp):
TTCTATAAATTTCGATAATCAC
Found at i:70204 original size:22 final size:21
Alignment explanation
Indices: 69921--70247 Score: 105
Period size: 22 Copynumber: 14.8 Consensus size: 21
69911 ATAATAACAT
*
69921 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
* * **
69943 TTTGAGATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTC-C
*
69965 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAA-CCTCC
*
69987 TATG--ATTTTGATAATCCGATTTC
1 TATGAAATTTTGATAA-CC---TCC
*
70010 TATGAAATTTCGATAATCACT-C
1 TATGAAATTTTGATAA-C-CTCC
*
70032 TAT-AAGA-TTTGATAACCTTC
1 TATGAA-ATTTTGATAACCTCC
* *
70052 TATCAAATTTTGGT-A-CTCC
1 TATGAAATTTTGATAACCTCC
* ** *
70071 TCATGAAATTGAGACTTTTATAAGTTTCA
1 T-ATGAAA-T-----TTTGATAA-CCTCC
* *
70100 TATGAAATGTTGATAACCACAC
1 TATGAAATTTTGATAACCTC-C
** *
70122 TAAAAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTC-C
70144 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* ** *
70166 CATGTTATATT-AGTAACCTCC
1 TATGAAATTTTGA-TAACCTCC
* * *
70187 TTATGAAATTTTGTTAACCACAT
1 -TATGAAATTTTGATAACCTC-C
70210 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTC-C
*
70232 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
70248 TCTCTTTGAT
Statistics
Matches: 227, Mismatches: 49, Indels: 58
0.68 0.15 0.17
Matches are distributed among these distances:
19 6 0.03
20 24 0.11
21 23 0.10
22 135 0.59
23 12 0.05
25 11 0.05
26 5 0.02
27 2 0.01
28 6 0.03
29 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:70382 original size:22 final size:21
Alignment explanation
Indices: 70265--70483 Score: 150
Period size: 22 Copynumber: 9.9 Consensus size: 21
70255 GATATCCTTT
* * *
70265 CTATAAAATTGTGATAACCAC
1 CTATGAAATTTTGATAACCTC
**
70286 ACTATGAAATTTCAATAACCTTC
1 -CTATGAAATTTTGATAACC-TC
* * *
70309 CTAAGAAATTTTAAAAACCTGATC
1 CTATGAAATTTTGATAACC---TC
* * * *
70333 CTATGAAATTTAGGTAAGCAC
1 CTATGAAATTTTGATAACCTC
*
70354 ACTATGAATTTTTGATAACCTTC
1 -CTATGAAATTTTGATAACC-TC
* **
70377 CCATGAAATTTTGATAAGTTC
1 CTATGAAATTTTGATAACCTC
* *
70398 CATATGAAATTTTGGTAACCAC
1 C-TATGAAATTTTGATAACCTC
*
70420 ATTATGAAATTTTGATAACCTC
1 -CTATGAAATTTTGATAACCTC
*
70442 CTCATGAAATTATGATAACCATC
1 CT-ATGAAATTTTGATAACC-TC
*
70465 TTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAACC
70484 ACACAAAGAC
Statistics
Matches: 151, Mismatches: 37, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
21 5 0.03
22 126 0.83
23 5 0.03
24 15 0.10
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:70433 original size:66 final size:66
Alignment explanation
Indices: 70265--70487 Score: 234
Period size: 66 Copynumber: 3.3 Consensus size: 66
70255 GATATCCTTT
* * ** * * * *
70265 CTATAAAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATTTTAAAAACCTG
1 CTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAA-C-G
70330 ATC
64 ATC
* * * * *
70333 CTATGAAATTTAGGTAAGCACACTATGAATTTTTGATAACCTTCCCATGAAATTTTGATAA-GTT
1 CTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACGAT
70397 C
66 C
* * * *
70398 CATATGAAATTTTGGTAACCACATTATGAAATTTTGATAACC-TCCTCATGAAATTATGATAACC
1 C-TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATTTTGATAACG
70462 ATC
64 ATC
*
70465 TTATGAAATTTTGATAACCACAC
1 CTATGAAATTTTGATAACCACAC
70488 AAAGACAAGG
Statistics
Matches: 129, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
65 7 0.05
66 71 0.55
67 2 0.02
68 49 0.38
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACGAT
C
Found at i:79916 original size:12 final size:11
Alignment explanation
Indices: 79894--79919 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
79884 CTTTGTGTTG
79894 TTTTGTTTTTT
1 TTTTGTTTTTT
79905 TTTTGTTTTTT
1 TTTTGTTTTTT
79916 TTTT
1 TTTT
79920 CTTTAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:80269 original size:2 final size:2
Alignment explanation
Indices: 80264--80288 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
80254 TTTCTCCTTT
80264 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
80289 TTGTATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:88496 original size:2 final size:2
Alignment explanation
Indices: 88489--88519 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
88479 GTTTTAAATA
*
88489 CT CT CT CT CT CT CT CT CT CA CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
88520 CTGCAGAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.52, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:89651 original size:23 final size:23
Alignment explanation
Indices: 89608--89652 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
89598 CATTTGTGAA
*
89608 AAACTGCTTAAGTCATCTGGCAC
1 AAACTGCTTAAGTCAACTGGCAC
89631 AAACTGCTTAAGT-AACATGGCA
1 AAACTGCTTAAGTCAAC-TGGCA
89653 GTTTTCAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (23 bp):
AAACTGCTTAAGTCAACTGGCAC
Found at i:91310 original size:184 final size:187
Alignment explanation
Indices: 90994--91364 Score: 606
Period size: 184 Copynumber: 2.0 Consensus size: 187
90984 CATTTTTTTT
*
90994 AGTCTAAGGAGATCTTACAGATGTTCTGTTATTTATCCTCTTATCTTTACTCATTTTCTTCTCTA
1 AGTCTAAGGAGATCTTACAGATGTTCTGTTATTTATCCTCTTATCTATACTCATTTTCTTCTC--
*
91059 AAGTCTAAACTGGCTATAGACCTTTTGGTCAATTCTCGTTCAGTCAACTGAGATGTGTTAGTTTT
64 -A-TCTAAACTGGCTATAGACCTTTTGGTCAATTCTCGTCCAGTCAACTGAGATGTGTTAGTTTT
*
91124 CTTCTTATGGGGAGGCAACTTTTAATTTGATTCAGTTAATCTAGAAGGTTTTAAAGCGGTC
127 CTTCTTATGGGGAGGCAACTTTTAATTTAATTCAGTTAATCTAGAAGGTTTTAAAGCGGTC
* *
91185 AGTCTAAGTG-GATCTTACAGATGTTCTGTTATTTATCCTCTTATCTATATTCGTTTTC-T-TC-
1 AGTCTAAG-GAGATCTTACAGATGTTCTGTTATTTATCCTCTTATCTATACTCATTTTCTTCTCA
*
91246 TCTAAACTGGCTATAGACCTTTTGGTCAATTCTCGTCCAGTCAACTGAGATGTGTTATTTTTCTT
65 TCTAAACTGGCTATAGACCTTTTGGTCAATTCTCGTCCAGTCAACTGAGATGTGTTAGTTTTCTT
*
91311 CTTATGGGGAGGCAACTTTTAATTTAATTCAGTTAATCTAGAAGGTTTTTAAGC
130 CTTATGGGGAGGCAACTTTTAATTTAATTCAGTTAATCTAGAAGGTTTTAAAGC
91365 ATTTAGTCAT
Statistics
Matches: 172, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
184 115 0.67
189 2 0.01
190 1 0.01
191 53 0.31
192 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (187 bp):
AGTCTAAGGAGATCTTACAGATGTTCTGTTATTTATCCTCTTATCTATACTCATTTTCTTCTCAT
CTAAACTGGCTATAGACCTTTTGGTCAATTCTCGTCCAGTCAACTGAGATGTGTTAGTTTTCTTC
TTATGGGGAGGCAACTTTTAATTTAATTCAGTTAATCTAGAAGGTTTTAAAGCGGTC
Found at i:96318 original size:16 final size:17
Alignment explanation
Indices: 96284--96324 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
96274 TAGGAAAAAT
96284 ATTTTTTATTAACTTAA
1 ATTTTTTATTAACTTAA
96301 ATGTTTTT-TTAA-TTAA
1 AT-TTTTTATTAACTTAA
96317 ATTTTTTA
1 ATTTTTTA
96325 GGAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.23
16 6 0.27
17 6 0.27
18 5 0.23
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTTTATTAACTTAA
Found at i:96954 original size:13 final size:13
Alignment explanation
Indices: 96938--96962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
96928 TCTTATTATC
96938 AAGTTTAATTAAA
1 AAGTTTAATTAAA
96951 AAGTTTAATTAA
1 AAGTTTAATTAA
96963 TATCCTTATA
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGTTTAATTAAA
Found at i:99119 original size:84 final size:84
Alignment explanation
Indices: 99031--99188 Score: 217
Period size: 84 Copynumber: 1.9 Consensus size: 84
99021 TTATCCCGCT
* * * ** *
99031 TTAGCTTTCTCACACTCGAGATAGAGATTCCTTGTCACCAATTCTTCATTTTGTTTTCTTAATAC
1 TTAGCTTTCTCACACTCGAGAAAGAGATTCCTCGCCACCAATTCTTCAAATTGTTTTCTTAACAC
99096 TGCAGAATCTCGATCAGCC
66 TGCAGAATCTCGATCAGCC
* * * * *
99115 TTAGCTTTCTCATATTCGAGAAAGAGATTCCTCGCCACCATTTTTTCAAATTGTTTTCTTAACAT
1 TTAGCTTTCTCACACTCGAGAAAGAGATTCCTCGCCACCAATTCTTCAAATTGTTTTCTTAACAC
99180 TGCAGAATC
66 TGCAGAATC
99189 ATCAGCTTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (84 bp):
TTAGCTTTCTCACACTCGAGAAAGAGATTCCTCGCCACCAATTCTTCAAATTGTTTTCTTAACAC
TGCAGAATCTCGATCAGCC
Done.