Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018015.1 Corchorus olitorius cultivar O-4 contig18048, 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: 40918
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:922 original size:21 final size:20
Alignment explanation
Indices: 891--955 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
881 AAGTTTTATC
891 AAGGGGCCAAATTAAAAAAA
1 AAGGGGCCAAATTAAAAAAA
* *
911 AACGGGGGCAAATTCAAGAAAA
1 AA-GGGGCCAAATT-AAAAAAA
933 AA-GGGCCAAATTAGAAAATAA
1 AAGGGGCCAAATTA-AAAA-AA
954 AA
1 AA
956 AATGATGGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 14 0.38
21 14 0.38
22 8 0.22
ACGTcount: A:0.57, C:0.11, G:0.22, T:0.11
Consensus pattern (20 bp):
AAGGGGCCAAATTAAAAAAA
Found at i:932 original size:22 final size:21
Alignment explanation
Indices: 893--955 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
883 GTTTTATCAA
893 GGGGCCAAATTAAAAAAAAAC
1 GGGGCCAAATTAAAAAAAAAC
* *
914 GGGGGCAAATTCAAGAAAAAA-
1 GGGGCCAAATT-AAAAAAAAAC
935 -GGGCCAAATTAGAAAATAAAA
1 GGGGCCAAATTA-AAAA-AAAA
956 AATGATGGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.34
21 14 0.40
22 8 0.23
ACGTcount: A:0.56, C:0.11, G:0.22, T:0.11
Consensus pattern (21 bp):
GGGGCCAAATTAAAAAAAAAC
Found at i:2549 original size:44 final size:45
Alignment explanation
Indices: 2499--2600 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
2489 AATCTTAACG
* * * *
2499 AACAT-AATCGAGTTTTAAATGAGTTCTTGAACGAATAATAAACA
1 AACATAAATCGAGTTTTAAACGAATTATTGAACGAACAATAAACA
* *
2543 AACATAAATGGA-TTTTAAACGAATTATTGAACGAACAATAAACG
1 AACATAAATCGAGTTTTAAACGAATTATTGAACGAACAATAAACA
* *
2587 AACATCAACCGAGT
1 AACATAAATCGAGT
2601 ATGTTCACAA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
44 41 0.87
45 6 0.13
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (45 bp):
AACATAAATCGAGTTTTAAACGAATTATTGAACGAACAATAAACA
Found at i:3559 original size:13 final size:14
Alignment explanation
Indices: 3541--3577 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
3531 CTAAATTGAC
3541 ATTATTAAAAATT-
1 ATTATTAAAAATTG
3554 ATTATTTAAAAATTG
1 ATTA-TTAAAAATTG
3569 ATTA-TAAAA
1 ATTATTAAAA
3578 TTTCAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 9 0.41
15 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTATTAAAAATTG
Found at i:3562 original size:14 final size:15
Alignment explanation
Indices: 3541--3573 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3531 CTAAATTGAC
3541 ATTA-TTAAAAATT-
1 ATTATTTAAAAATTG
3554 ATTATTTAAAAATTG
1 ATTATTTAAAAATTG
3569 ATTAT
1 ATTAT
3574 AAAATTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 9 0.50
15 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTATTTAAAAATTG
Found at i:3803 original size:176 final size:165
Alignment explanation
Indices: 3476--3816 Score: 454
Period size: 176 Copynumber: 2.0 Consensus size: 165
3466 TCCATAAAAG
* *
3476 TACGAATAATGGAAAACTTTATGTTTTCCGATTGTATCTTTTTTCAAATATATCTCTAAATTGAC
1 TACGAATAATGGAAAACTTTATATTTTCCGATTGCATCTTTTTTCAAATATATCTCTAAATTGAC
* *
3541 ATTATTAAAAATTATTATTTAAAAATTGATTATAAAATTTCAATTTAGACCGAATTATAAGTTTG
66 ATTATTAAAAATTATTATTTAAAAATTAATTATAAAATTTCAATTTAGACCGAATTAAAAGTTTG
3606 TAAAATTGGATTTAATTGATGAACATGCAAATTTC
131 TAAAATTGGATTTAATTGATGAACATGCAAATTTC
*
3641 TACGAATAAT-GAGAAACTTTATATTTTCCGATTGCATCCTTTTTTTCAAATATATTTCTAAATT
1 TACGAATAATGGA-AAACTTTATATTTTCCGATTGCAT-C-TTTTTTCAAATATATCTCTAAATT
*
3705 GCCATTATTAAAATTAGTATAATTTTATTATTTAAAAATTAATTA-AAAATTTCAATTTAGACCG
63 GACATTATT---A--A--A-AA--TTATTATTTAAAAATTAATTATAAAATTTCAATTTAGACCG
* **
3769 AATTAAAAGTTTGTCAAATT-GATTTTCGTTGATGAACATGCAAATTTC
118 AATTAAAAGTTTGTAAAATTGGA-TTTAATTGATGAACATGCAAATTTC
3817 CTTTACTATT
Statistics
Matches: 153, Mismatches: 9, Indels: 17
0.85 0.05 0.09
Matches are distributed among these distances:
164 2 0.01
165 32 0.21
166 1 0.01
167 31 0.20
170 1 0.01
172 1 0.01
174 1 0.01
175 4 0.03
176 60 0.39
177 20 0.13
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (165 bp):
TACGAATAATGGAAAACTTTATATTTTCCGATTGCATCTTTTTTCAAATATATCTCTAAATTGAC
ATTATTAAAAATTATTATTTAAAAATTAATTATAAAATTTCAATTTAGACCGAATTAAAAGTTTG
TAAAATTGGATTTAATTGATGAACATGCAAATTTC
Found at i:4091 original size:22 final size:21
Alignment explanation
Indices: 4035--4143 Score: 94
Period size: 22 Copynumber: 5.0 Consensus size: 21
4025 GTCTCTGTGT
*
4035 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * * *
4056 TGATTATTATAATTTTATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
*
4079 GGTTATCAAAA-TTCAATAGTGT
1 GGTTATCAAAATTTC-ATAG-GA
*
4101 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
*
4123 AGTTATCAAAATTTCATAGGA
1 GGTTATCAAAATTTCATAGGA
4144 TCAGGTCATT
Statistics
Matches: 68, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
21 7 0.10
22 54 0.79
23 7 0.10
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.37
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:4604 original size:22 final size:22
Alignment explanation
Indices: 4227--4635 Score: 198
Period size: 22 Copynumber: 18.7 Consensus size: 22
4217 ATCAAAGAGA
* **
4227 TTATCAAAATATCATAGCAAGG
1 TTATCAAAATTTCATAGGGAGG
*
4249 TTAT-AAGAATTTCATA-GTATGG
1 TTATCAA-AATTTCATAGGGA-GG
* *
4271 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
4293 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGGGAGG
*
4315 TTATCAAAA-TT--T--GTA-G
1 TTATCAAAATTTCATAGGGAGG
** *
4331 TTATCAGGATTTCATAAGGAGG
1 TTATCAAAATTTCATAGGGAGG
*
4353 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
4375 TTTATCAAAATATT-ATAGGAAAGT
1 -TTATCAAAAT-TTCATAGG-GAGG
**
4399 TTATCAAAATTTCATAACGAGG
1 TTATCAAAATTTCATAGGGAGG
* * * *
4421 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGGGAGG
* * * *
4443 TTATCAAAATTCCAGT-GTGTGA
1 TTATCAAAATTTCA-TAGGGAGG
* *
4465 TTA-CTAACAA-TTCATATGGACG
1 TTATC-AA-AATTTCATAGGGAGG
* * * ** *
4487 TTTTTAAATTTTCATAACGTGG
1 TTATCAAAATTTCATAGGGAGG
* * **
4509 TTATCAATATATCATATTGAGG
1 TTATCAAAATTTCATAGGGAGG
* * **
4531 TTATCAATATCTCATAGTGTTGG
1 TTATCAAAATTTCATAG-GGAGG
* * *
4554 TTATCAAAATTTCATTGGTAAG
1 TTATCAAAATTTCATAGGGAGG
*
4576 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGGGAGG
*
4598 TCT-TCAAAATTTCTTAGGGAGG
1 T-TATCAAAATTTCATAGGGAGG
*
4620 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
4636 AGAAAGTTAA
Statistics
Matches: 293, Mismatches: 69, Indels: 50
0.71 0.17 0.12
Matches are distributed among these distances:
16 8 0.03
17 4 0.01
19 2 0.01
21 12 0.04
22 210 0.72
23 53 0.18
24 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:6101 original size:29 final size:29
Alignment explanation
Indices: 6046--6102 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
6036 ATAAAACAAA
** *
6046 TGGACAATTTGCACCATAAACTTTAATTT
1 TGGACAATTTAAACCATAAACTATAATTT
* *
6075 TGGACAATTTAAACCCTATACTATAATT
1 TGGACAATTTAAACCATAAACTATAATT
6103 CCCGATCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (29 bp):
TGGACAATTTAAACCATAAACTATAATTT
Found at i:7720 original size:21 final size:21
Alignment explanation
Indices: 7691--7730 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
7681 CCTTAGCAAA
*
7691 CCTTTAGTATGTTT-CTAATTT
1 CCTTGAGTA-GTTTACTAATTT
7712 CCTTGAGTAGTTTACTAAT
1 CCTTGAGTAGTTTACTAAT
7731 GAATTGACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (21 bp):
CCTTGAGTAGTTTACTAATTT
Found at i:9408 original size:124 final size:124
Alignment explanation
Indices: 9188--9430 Score: 468
Period size: 124 Copynumber: 2.0 Consensus size: 124
9178 TTTGTTCTCT
9188 AAGCTAAAATTGATAAAGTGTGGTCAGATGAACCACTCCCGGTTGGGAACGTCAAAGAAATTATT
1 AAGCTAAAATTGATAAAGTGTGGTCAGATGAACCACTCCCGGTTGGGAACGTCAAAGAAATTATT
9253 CATGTGCCCCAGAAGGATGATGAAGACTCTCTTCTATTTATTCACTTTTATCAATTTCA
66 CATGTGCCCCAGAAGGATGATGAAGACTCTCTTCTATTTATTCACTTTTATCAATTTCA
*
9312 AAGCTAAAATTGATAAAGTGTGGTCAGATGAAGCACTCCCGGTTGGGAACGTCAAAGAAATTATT
1 AAGCTAAAATTGATAAAGTGTGGTCAGATGAACCACTCCCGGTTGGGAACGTCAAAGAAATTATT
*
9377 CATGTGCCCCAGAAGGATGATGAAGACTCTCTTCTATTTATTCACTTTTCTCAA
66 CATGTGCCCCAGAAGGATGATGAAGACTCTCTTCTATTTATTCACTTTTATCAA
9431 ACAACTAATT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 117 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (124 bp):
AAGCTAAAATTGATAAAGTGTGGTCAGATGAACCACTCCCGGTTGGGAACGTCAAAGAAATTATT
CATGTGCCCCAGAAGGATGATGAAGACTCTCTTCTATTTATTCACTTTTATCAATTTCA
Found at i:17514 original size:13 final size:13
Alignment explanation
Indices: 17496--17520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17486 TTGGAATTCC
17496 AAATAATATTTAT
1 AAATAATATTTAT
17509 AAATAATATTTA
1 AAATAATATTTA
17521 GAATATTGAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:18062 original size:18 final size:18
Alignment explanation
Indices: 18036--18083 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
18026 CTAGTAACTT
* *
18036 CTTAAATTTATTAGTAAC
1 CTTATATTTATTAATAAC
*
18054 CTTATATTTTTTTTAATAAC
1 CTTATA--TTTATTAATAAC
18074 CTTATATTTA
1 CTTATATTTA
18084 GTAACCGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.54
Consensus pattern (18 bp):
CTTATATTTATTAATAAC
Found at i:18249 original size:21 final size:21
Alignment explanation
Indices: 18225--18282 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
18215 TTTACTTTAA
* *
18225 CTTATTAAGATTTTTAGTAAG
1 CTTATTAAGATTTTTAGAAAC
* * *
18246 CTTATCATGAATTTTAGAAAC
1 CTTATTAAGATTTTTAGAAAC
*
18267 CTTATTAAGCTTTTTA
1 CTTATTAAGATTTTTA
18283 AATAATTTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (21 bp):
CTTATTAAGATTTTTAGAAAC
Found at i:18565 original size:58 final size:58
Alignment explanation
Indices: 18477--18626 Score: 237
Period size: 58 Copynumber: 2.6 Consensus size: 58
18467 GTTGCAATAT
* *
18477 AATTTGTAGAAGAAATATTACTAAATCTTTATTTTGCTCATACTATGTAAAACTTTTAC
1 AATTTGTAGAA-AAATATTACTAAATCTTTATTTTACTCATACTATGTAAAACCTTTAC
* *
18536 AATTTGTAGAAAAATATTACTAAACCTTTATTTTACTCATACTGTGTAAAACCTTTAC
1 AATTTGTAGAAAAATATTACTAAATCTTTATTTTACTCATACTATGTAAAACCTTTAC
* *
18594 AATTTGTAGAAAAATATTAGTAAATCTTCATTT
1 AATTTGTAGAAAAATATTACTAAATCTTTATTT
18627 GACTAAATCT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
58 73 0.87
59 11 0.13
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (58 bp):
AATTTGTAGAAAAATATTACTAAATCTTTATTTTACTCATACTATGTAAAACCTTTAC
Found at i:29678 original size:74 final size:77
Alignment explanation
Indices: 29510--29665 Score: 221
Period size: 78 Copynumber: 2.1 Consensus size: 77
29500 GTATCTTTAA
* * *
29510 AATAAAATTAAAAATTTCATTTGGAGCTAAATTTAGTGATATTAGTTTTATATTTTATTGCTCCT
1 AATAAAATTAAAATTTTAATTTGGAGCTAAATTTAGTGATATTAATTTTATATTTTATT-CTCCT
*
29575 AAAACCCTATAAC
65 AAAACCCGATAAC
29588 AATAAAATTAAAATTTTAATTTAGGA-CTAAATTTAGTGA-ATTAATTTTATATTTTATT-T-CT
1 AATAAAATTAAAATTTTAATTT-GGAGCTAAATTTAGTGATATTAATTTTATATTTTATTCTCCT
*
29649 AAAACTCGATAAC
65 AAAACCCGATAAC
29662 AATA
1 AATA
29666 TGTTATTAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
74 17 0.24
75 1 0.01
77 18 0.25
78 33 0.46
79 3 0.04
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (77 bp):
AATAAAATTAAAATTTTAATTTGGAGCTAAATTTAGTGATATTAATTTTATATTTTATTCTCCTA
AAACCCGATAAC
Found at i:29781 original size:103 final size:102
Alignment explanation
Indices: 29590--29864 Score: 288
Period size: 103 Copynumber: 2.6 Consensus size: 102
29580 CCTATAACAA
* *
29590 TAAAATTAAAA-TTTTAATTTAGGACTAAATTTAGTG-AATTAATTTTATATTTTATTTCTAAAA
1 TAAAA-TAAAATTTTTAATTTGGGACTAAATTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
** * * *
29653 CTCGATAACAATATGTTATTAATTTTGGAATTTATCCT
65 CTCGATAACAATAAATAATTAATTTTAGAATTTACCCT
*
29691 TAAAATAAAATTTATTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
1 TAAAATAAAATTT-TTAATTTGGGACTAAATTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
* *
29756 -TCCTATACCAATAAATAATTAATTTTAGAATTTACCCT
65 CT-CGATAACAATAAATAATTAATTTTAGAATTTACCCT
* * * * * *
29794 TAAAATAAGATTAAAATTTTAA-TTGGGCCTAAACTTAGTGACATCAGTTTTATATATCTAATTT
1 TAAAAT---A--AAATTTTTAATTTGGGACTAAATTTAGTGAAATTAGTTTTATAT-T-TTATTT
29858 CTAAAAC
59 CTAAAAC
29865 CTTATAATAA
Statistics
Matches: 146, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
100 5 0.03
101 7 0.05
102 22 0.15
103 61 0.42
106 30 0.21
107 5 0.03
108 16 0.11
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (102 bp):
TAAAATAAAATTTTTAATTTGGGACTAAATTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
TCGATAACAATAAATAATTAATTTTAGAATTTACCCT
Found at i:30206 original size:15 final size:15
Alignment explanation
Indices: 30183--30212 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30173 TTCAGAAATT
*
30183 AATATATTATTAAAA
1 AATAAATTATTAAAA
30198 AATAAATTATTAAAA
1 AATAAATTATTAAAA
30213 GAAACTAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAAATTATTAAAA
Found at i:30250 original size:18 final size:18
Alignment explanation
Indices: 30227--30269 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
30217 CTAACAAGAG
*
30227 AAATCACTCTTGAAGCGT
1 AAATCAATCTTGAAGCGT
*
30245 AAATCAAATCTTGAAGTGT
1 AAATC-AATCTTGAAGCGT
30264 AAATCA
1 AAATCA
30270 GATCAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (18 bp):
AAATCAATCTTGAAGCGT
Found at i:34759 original size:44 final size:43
Alignment explanation
Indices: 34698--35146 Score: 211
Period size: 44 Copynumber: 10.2 Consensus size: 43
34688 TCTTATGAAA
34698 TTTGATAA-T-CACTATAAAATTTTGATAACCTCCATATAAAAT
1 TTTGATAACTACACTATAAAATTTTGATAACCTCC-TATAAAAT
* * * * * *
34740 TTTGATAATTACACTATAAAGTTTTTATGACGATACTATAAAAT
1 TTTGATAACTACACTATAAAATTTTGATAAC-CTCCTATAAAAT
* * * * * *
34784 TTCGAGAACCTCCA-TATAAAATTGTGTTAACTTCCCTATAAAAT
1 TTTGATAA-CTACACTATAAAATTTTGATAACCT-CCTATAAAAT
* * ** * *
34828 TTTGTTACACTATACCTATAAAATTTAAATAACCACCTAATGAAAT
1 TTTGATA-ACTACA-CTATAAAATTTTGATAACCTCCT-ATAAAAT
* * * * *
34874 TTTGATAACCACCCTATGAAATTTTGATAACCTCCCAATGAAAT
1 TTTGATAACTACACTATAAAATTTTGATAACCT-CCTATAAAAT
* * * * * *
34918 GTTGGTAAGCGCACATTATGAAATTTTGATAACCTTCCGATAAAAT
1 TTTGATAA-C-TACACTATAAAATTTTGATAACC-TCCTATAAAAT
* * * *
34964 ATT-AGTAA-TCACATTATAAAATTTTGATAACCAT-ATCATGAAAT
1 TTTGA-TAACT-ACACTATAAAATTTTGATAACC-TCCT-ATAAAAT
* * * * *
35008 TGTGATACCT-CACCATGAAAATTTT-ATAAACTTCCTTTTAAAAT
1 TTTGATAACTACACTAT-AAAATTTTGAT-AACCTCC-TATAAAAT
* * * *
35052 TTTGATAACTCCA-TTTGAAATTTTGATAACCATCTTAT-AAAT
1 TTTGATAACTACACTATAAAATTTTGATAACC-TCCTATAAAAT
* *
35094 TTTGATAACATAC-CTAT-AAATTTTCTATAACTTCCTTATAAAAT
1 TTTGATAAC-TACACTATAAAATTTT-GATAACCTCC-TATAAAAT
*
35138 TTTGTTAAC
1 TTTGATAAC
35147 CTCCTAGAGA
Statistics
Matches: 303, Mismatches: 74, Indels: 58
0.70 0.17 0.13
Matches are distributed among these distances:
42 30 0.10
43 33 0.11
44 160 0.53
45 20 0.07
46 59 0.19
47 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.38
Consensus pattern (43 bp):
TTTGATAACTACACTATAAAATTTTGATAACCTCCTATAAAAT
Found at i:34947 original size:46 final size:44
Alignment explanation
Indices: 34888--34995 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 44
34878 ATAACCACCC
* * *
34888 TATGAAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCACAT
1 TATGAAATTTTGATAACCTCCCAATAAAATATTAGTAA--GCACAT
* * *
34934 TATGAAATTTTGATAACCTTCCGATAAAATATTAGTAATCACAT
1 TATGAAATTTTGATAACCTCCCAATAAAATATTAGTAAGCACAT
*
34978 TATAAAATTTTGATAACC
1 TATGAAATTTTGATAACC
34996 ATATCATGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 22 0.40
46 33 0.60
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCAATAAAATATTAGTAAGCACAT
Found at i:35072 original size:21 final size:21
Alignment explanation
Indices: 35025--35102 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
35015 CCTCACCATG
*
35025 AAAATTTT-ATAAACTTCCTTTT
1 AAAATTTTGAT-AAC-TCCATTT
35047 AAAATTTTGATAACTCCATTT
1 AAAATTTTGATAACTCCATTT
*
35068 GAAATTTTGATAA--CCATCTT
1 AAAATTTTGATAACTCCAT-TT
35088 ATAAATTTTGATAAC
1 A-AAATTTTGATAAC
35103 ATACCTATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.08
20 2 0.04
21 30 0.61
22 11 0.22
23 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (21 bp):
AAAATTTTGATAACTCCATTT
Found at i:35111 original size:21 final size:20
Alignment explanation
Indices: 35048--35152 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 20
35038 CTTCCTTTTA
*
35048 AAATTTTGATAAC-TCCATTT
1 AAATTTTGATAACATCC-TAT
*
35068 GAAATTTTGATAACCATCTTAT
1 -AAATTTTGATAA-CATCCTAT
35090 AAATTTTGATAACATACCTAT
1 AAATTTTGATAACAT-CCTAT
* *
35111 AAATTTTCTATAACTTCCTTAT
1 AAATTTT-GATAACATCC-TAT
* *
35133 AAAATTTTGTTAACCTCCTA
1 -AAATTTTGATAACATCCTA
35153 GAGAACTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
20 3 0.04
21 39 0.56
22 19 0.27
23 9 0.13
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (20 bp):
AAATTTTGATAACATCCTAT
Found at i:35151 original size:22 final size:22
Alignment explanation
Indices: 34710--35151 Score: 169
Period size: 22 Copynumber: 20.0 Consensus size: 22
34700 TGATAATCAC
*
34710 TATAAAATTTTGATAACCTCCA
1 TATAAAATTTTGATAACCTCCT
*
34732 TATAAAATTTTGATAA-TTACAC-
1 TATAAAATTTTGATAACCT-C-CT
* * * * *
34754 TATAAAGTTTTTATGACGATAC-
1 TATAAAATTTTGATAAC-CTCCT
* * *
34776 TATAAAATTTCGAGAACCTCCA
1 TATAAAATTTTGATAACCTCCT
* * * *
34798 TATAAAATTGTGTTAACTTCCC
1 TATAAAATTTTGATAACCTCCT
* *
34820 TATAAAATTTTGTTACACTATACC-
1 TATAAAATTTTGATA-AC-CT-CCT
** *
34844 TATAAAATTTAAATAACCACCT
1 TATAAAATTTTGATAACCTCCT
* * * *
34866 AATGAAATTTTGATAACCACCC
1 TATAAAATTTTGATAACCTCCT
* *
34888 TATGAAATTTTGATAACCTCCC
1 TATAAAATTTTGATAACCTCCT
* * * * * *
34910 AATGAAATGTTGGTAAGCGCACAT
1 TATAAAATTTTGATAA-C-CTCCT
*
34934 TATGAAATTTTGATAACCTTCC-
1 TATAAAATTTTGATAACC-TCCT
* * * * *
34956 GATAAAATATT-AGTAATCACAT
1 TATAAAATTTTGA-TAACCTCCT
*
34978 TATAAAATTTTGATAACCAT-AT
1 TATAAAATTTTGATAACC-TCCT
* * *
35000 CATGAAATTGTGAT-ACCTCAC-
1 TATAAAATTTTGATAACCTC-CT
* *
35021 CATGAAAATTTT-ATAAACTTCCT
1 TAT-AAAATTTTGAT-AACCTCCT
*
35044 TTTAAAATTTTGATAA-CTCCAT
1 TATAAAATTTTGATAACCTCC-T
*
35066 T-TGAAATTTTGATAACCAT-CT
1 TATAAAATTTTGATAACC-TCCT
*
35087 TAT-AAATTTTGATAACATACC-
1 TATAAAATTTTGATAACCT-CCT
* *
35108 TAT-AAATTTTCTATAACTTCCT
1 TATAAAATTTT-GATAACCTCCT
*
35130 TATAAAATTTTGTTAACCTCCT
1 TATAAAATTTTGATAACCTCCT
35152 AGAGAACTAT
Statistics
Matches: 317, Mismatches: 71, Indels: 64
0.70 0.16 0.14
Matches are distributed among these distances:
20 2 0.01
21 58 0.18
22 202 0.64
23 24 0.08
24 29 0.09
25 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCCT
Found at i:35783 original size:26 final size:27
Alignment explanation
Indices: 35712--35808 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
35702 TTAGGATCAC
* * * *
35712 CTAGGGGCATTTTGGTCTTTTTCTTCA-
1 CTAGGGGTATTTTGGTCATTTGC-ACAT
* * *
35739 CTAAGGGCATTTTGGTCATTTGCACGT
1 CTAGGGGTATTTTGGTCATTTGCACAT
*
35766 CT-GGGGTATTTTGGTCATTTGTACAT
1 CTAGGGGTATTTTGGTCATTTGCACAT
*
35792 TTAGGGGTATTTTGGTC
1 CTAGGGGTATTTTGGTC
35809 CTTTTCGTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
26 22 0.38
27 36 0.62
ACGTcount: A:0.14, C:0.14, G:0.27, T:0.44
Consensus pattern (27 bp):
CTAGGGGTATTTTGGTCATTTGCACAT
Found at i:35806 original size:27 final size:26
Alignment explanation
Indices: 35747--35808 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
35737 CACTAAGGGC
*
35747 ATTTTGGTCATTTGCACGTCTGGGGT
1 ATTTTGGTCATTTGCACATCTGGGGT
* *
35773 ATTTTGGTCATTTGTACATTTAGGGGT
1 ATTTTGGTCATTTGCACATCT-GGGGT
35800 ATTTTGGTC
1 ATTTTGGTC
35809 CTTTTCGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 18 0.56
27 14 0.44
ACGTcount: A:0.15, C:0.11, G:0.27, T:0.47
Consensus pattern (26 bp):
ATTTTGGTCATTTGCACATCTGGGGT
Done.