Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008455.1 Corchorus capsularis cultivar CVL-1 contig08476, 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: 53969
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2023 original size:20 final size:20
Alignment explanation
Indices: 1994--2036 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1984 AGCGGACACC
* *
1994 TAAGTTGTTGCCTTAGATCT
1 TAAGTCGTTGCCTTAGATAT
*
2014 TAAGTCGTTGCGTTAGATAT
1 TAAGTCGTTGCCTTAGATAT
2034 TAA
1 TAA
2037 ACAACGGAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (20 bp):
TAAGTCGTTGCCTTAGATAT
Found at i:2731 original size:30 final size:31
Alignment explanation
Indices: 2678--2736 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
2668 ATATTTTTCG
* *
2678 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCCTATTTTAAAAACATATTTCCA
2709 ATTGTACCCCT-TTTTAAAAACATATTTC
1 ATTGTACCCCTATTTTAAAAACATATTTC
2737 TAAATTGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTGTACCCCTATTTTAAAAACATATTTCCA
Found at i:2743 original size:31 final size:31
Alignment explanation
Indices: 2678--2743 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
2668 ATATTTTTCG
* * *
2678 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCCTATTTTAAAAACATATTTCAA
2709 ATTGTACCCCT-TTTTAAAAACATATTTCTAA
1 ATTGTACCCCTATTTTAAAAACATATTTC-AA
2740 ATTG
1 ATTG
2744 CCATTACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTGTACCCCTATTTTAAAAACATATTTCAA
Found at i:2773 original size:19 final size:19
Alignment explanation
Indices: 2746--2784 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2736 CTAAATTGCC
2746 ATTACTAAATAATATTTTA
1 ATTACTAAATAATATTTTA
* * *
2765 ATTATTAAATTATTTTTTA
1 ATTACTAAATAATATTTTA
2784 A
1 A
2785 CCATAAATTA
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:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTACTAAATAATATTTTA
Found at i:4018 original size:44 final size:43
Alignment explanation
Indices: 3979--4078 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 43
3969 TGGTTATTAT
*
3979 AATTTCATGAGGAGA-TTATCAAAATTCCATAGTGTGGTTACCAG
1 AATTTCAT-AGGA-ACTTACCAAAATTCCATAGTGTGGTTACCAG
* * *
4023 AATTTCATATGAACGTTACCAAAATTTCATAGTGTGGTTACCAA
1 AATTTCATAGGAAC-TTACCAAAATTCCATAGTGTGGTTACCAG
4067 AATTTCATAGGA
1 AATTTCATAGGA
4079 TCAGGTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.02
43 3 0.06
44 45 0.92
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (43 bp):
AATTTCATAGGAACTTACCAAAATTCCATAGTGTGGTTACCAG
Found at i:4092 original size:24 final size:23
Alignment explanation
Indices: 3948--4123 Score: 100
Period size: 22 Copynumber: 7.9 Consensus size: 23
3938 GTCTTTATGT
*
3948 GGTTATTAAAATTTCATAAGAT-
1 GGTTATTAAAATTTCATAGGATA
*
3970 GGTTATTATAATTTCATGAGG--A
1 GGTTATTAAAATTTCAT-AGGATA
* * *
3992 GATTATCAAAATTCCATAGTG-T-
1 GGTTATTAAAATTTCATAG-GATA
** * *
4014 GGTTACCAGAATTTCATATGA-A
1 GGTTATTAAAATTTCATAGGATA
* **
4036 CGTTACCAAAATTTCATAGTG-T-
1 GGTTATTAAAATTTCATAG-GATA
**
4058 GGTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGGAT-A
* *
4082 GGTTATTAAAATTTCTTA-GATT
1 GGTTATTAAAATTTCATAGGATA
*
4104 GGTTATTGAAATTTCATAGG
1 GGTTATTAAAATTTCATAGG
4124 GTGGTTAATT
Statistics
Matches: 121, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
21 4 0.03
22 95 0.79
23 7 0.06
24 15 0.12
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (23 bp):
GGTTATTAAAATTTCATAGGATA
Found at i:4191 original size:22 final size:22
Alignment explanation
Indices: 4166--4304 Score: 128
Period size: 22 Copynumber: 6.4 Consensus size: 22
4156 ATCAAAGAGA
*
4166 TTATCAAAATGTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
4188 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
4210 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* *
4232 TTA-CTAATATTTCAT-GGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* * *
4253 TTATAAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
4275 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
4297 TTAT-AAAA
1 TTATCAAAA
4305 GTCTCAATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 17
0.76 0.10 0.13
Matches are distributed among these distances:
20 1 0.01
21 25 0.26
22 65 0.68
23 5 0.05
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:4418 original size:22 final size:20
Alignment explanation
Indices: 4329--4420 Score: 57
Period size: 22 Copynumber: 4.5 Consensus size: 20
4319 AGGAGTACCA
* *
4329 AAATTTGATAGAAGGTTATC
1 AAATTTCATAGAAGATTATC
* **
4349 AAATCTCATAGGGTGATTATC
1 AAATTTCATA-GAAGATTATC
4370 GAAATTTCATA-AAG---ATC
1 -AAATTTCATAGAAGATTATC
*
4387 AGATTATCATAGGAAGATTATC
1 AAATT-TCATA-GAAGATTATC
4409 AAAATTTCATAG
1 -AAATTTCATAG
4421 TGTTGTTATC
Statistics
Matches: 53, Mismatches: 10, Indels: 17
0.66 0.12 0.21
Matches are distributed among these distances:
16 4 0.08
17 8 0.15
19 3 0.06
20 9 0.17
21 8 0.15
22 17 0.32
23 4 0.08
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (20 bp):
AAATTTCATAGAAGATTATC
Found at i:4429 original size:22 final size:21
Alignment explanation
Indices: 4404--4573 Score: 92
Period size: 22 Copynumber: 7.8 Consensus size: 21
4394 CATAGGAAGA
*
4404 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAATG-TG
* * *
4426 TTATCAAAATTTCAAAACGAGG
1 TTATCAAAATTTCATAATG-TG
*
4448 TTATCAAAATTGCATAATGTG
1 TTATCAAAATTTCATAATGTG
* * *
4469 ATTATCAGAATTTCATAGAGGGG
1 -TTATCAAAATTTCATA-ATGTG
* * * * *
4492 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAATG-TG
* *
4514 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAATG-TG
* *
4536 TTATCAAATTTTCGA-AATGTTA
1 TTATCAAAATTTC-ATAATG-TG
4558 TTA-CAAAAATTTCATA
1 TTATC-AAAATTTCATA
4574 GTGGTATTTC
Statistics
Matches: 115, Mismatches: 27, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
21 5 0.04
22 106 0.92
23 4 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAATGTG
Found at i:4474 original size:44 final size:43
Alignment explanation
Indices: 4404--4573 Score: 148
Period size: 44 Copynumber: 3.9 Consensus size: 43
4394 CATAGGAAGA
*
4404 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAACGAGG
1 TTATCAAAATTTCATAATG-TGTTATCAAAATTTCATAAA-GAGG
* * * *
4448 TTATCAAAATTGCATAATGTGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGTG-TTATCAAAATTTCATAAAGAGG
* * * * *
4492 TCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAATG-TGTTATCAAAATTTCATAAAGAGG
* *
4536 TTATCAAATTTTCGA-AATGTTATTA-CAAAAATTTCATA
1 TTATCAAAATTTC-ATAATG-TGTTATC-AAAATTTCATA
4574 GTGGTATTTC
Statistics
Matches: 99, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
43 3 0.03
44 92 0.93
45 4 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (43 bp):
TTATCAAAATTTCATAATGTGTTATCAAAATTTCATAAAGAGG
Found at i:4481 original size:66 final size:66
Alignment explanation
Indices: 4402--4548 Score: 170
Period size: 66 Copynumber: 2.2 Consensus size: 66
4392 ATCATAGGAA
* ** * *
4402 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAACGAGGTTATCAAAATTGCATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAA-GAGGTTATCAAAATTGCATAAT
4466 GT
65 GT
* * * *
4468 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTGCATAATG
*
4533 A
66 T
* *
4534 GGTTATCAAATTTTC
1 GATTATCAAAATTTC
4549 GAAATGTTAT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
66 64 0.96
67 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTGCATAATG
T
Found at i:4702 original size:22 final size:22
Alignment explanation
Indices: 4674--4930 Score: 130
Period size: 22 Copynumber: 11.7 Consensus size: 22
4664 TCAGGGAGGA
4674 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
4696 TATCAAAATTTCATAATTTA-GT
1 TATCAAAATTTCAT-ATGAAGGT
* *
4718 TTTCAAAATTTCATAAG-AGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
4740 TATCAAAATTTCAT-TGTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
4761 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
4784 TAACAAAATTTCATAATG-AGTT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
4806 TATCAAAAAATCATAGGGTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
4828 TATCAAGATTTCGTAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* **
4850 TATCAAAATTTTATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * ***
4872 TCTCGAAATTAT-ATATTATCAT
1 TATCAAAATT-TCATATGAAGGT
* * *
4894 TATTAAAATTTCATAGGAAAGT
1 TATCAAAATTTCATATGAAGGT
4916 TATCAAAATTTCATA
1 TATCAAAATTTCATA
4931 ATGGGATCAT
Statistics
Matches: 174, Mismatches: 49, Indels: 24
0.70 0.20 0.10
Matches are distributed among these distances:
20 1 0.01
21 8 0.05
22 155 0.89
23 10 0.06
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:4726 original size:44 final size:44
Alignment explanation
Indices: 4676--4932 Score: 154
Period size: 44 Copynumber: 5.8 Consensus size: 44
4666 AGGGAGGATA
*
4676 TCAAAATTTCATATGAAGGTTATCAAAATTTCATAATTTAGTTT
1 TCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATTTAGTTT
* * **
4720 TCAAAATTTCATAAG-AGGTTTATCAAAATTTCAT--TGTATGTAGA
1 TCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAATTTA-GT-TT
* * * *
4764 TCAAAATTTCATAGGGAGATTAACAAAATTTCATAA-TGAGTTT
1 TCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATTTAGTTT
** * * * *** *
4807 ATCAAAAAATCATAGGGTA-GTTATCAAGATTTCGTAAGAAAGTTA
1 -TCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAATTTAGTTT
* ** * *
4852 TCAAAATTTTATAAAAAGGTTCTCGAAA-TT-ATATATTATCA-TTAT
1 TCAAAATTTCATAGGAAGGTTATCAAAATTTCATA-ATT-T-AGTT-T
*
4897 T-AAAATTTCATAGGAAAGTTATCAAAATTTCATAAT
1 TCAAAATTTCATAGGAAGGTTATCAAAATTTCATAAT
4933 GGGATCATAA
Statistics
Matches: 156, Mismatches: 41, Indels: 31
0.68 0.18 0.14
Matches are distributed among these distances:
42 5 0.03
43 9 0.06
44 123 0.79
45 16 0.10
46 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (44 bp):
TCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATTTAGTTT
Found at i:7387 original size:15 final size:17
Alignment explanation
Indices: 7340--7387 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
7330 AACCGAAGTA
*
7340 ATATATAATTA-TTTAT
1 ATATATTATTATTTTAT
*
7356 ATATATTATTATATTAT
1 ATATATTATTATTTTAT
7373 ATAT-TTA-TATTTTAT
1 ATATATTATTATTTTAT
7388 TTAATAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.25
16 13 0.46
17 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATTATTATTTTAT
Found at i:8794 original size:6 final size:6
Alignment explanation
Indices: 8772--8829 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
8762 TAAATTTCTT
* * * *
8772 CTCGGA CT-GGTA CTCGGA CTCGGA CTCGGA CCCGGA CCCCGA CTTGGA
1 CTCGGA CTCGG-A CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA
8820 CTCGGA CTCG
1 CTCGGA CTCG
8830 AGAGTAGGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
5 2 0.05
6 40 0.91
7 2 0.05
ACGTcount: A:0.16, C:0.36, G:0.31, T:0.17
Consensus pattern (6 bp):
CTCGGA
Found at i:9433 original size:185 final size:185
Alignment explanation
Indices: 9121--9491 Score: 600
Period size: 185 Copynumber: 2.0 Consensus size: 185
9111 AGGGTTCTTT
* *
9121 TAGTTTAATTTTGATTATTCGTGTTGGGAGAGGAACCCGAGCCCTGACTGCTTCGGCAAAGCCCA
1 TAGTTTAATTTTGATTATTCGTGTTGGGAGAGGAACCCAAGCCCTGACTGCTTCAGCAAAGCCCA
* *
9186 TCGAGCAGCCCATATACATGTCAGAAACTAATCCGAACCCAAAAGTCTAGATTGATGGTTTCTTG
66 TCGAGCAGCCCATATACATGTCAGAAACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTG
* *
9251 GGTCCTTCATGTATATATGGCACTCAAACAACCCATCCTTTTCTGATGTGAGATG
131 GATCCTTCATGTATATATGGCACTCAAACAACCCATCCTTTTATGATGTGAGATG
* * *
9306 TAGTTTAATTTTGATTATTTGTGTTGGGAGAGGAACCCAAGCCCTGACTGCTTCAGCAAGGCTCA
1 TAGTTTAATTTTGATTATTCGTGTTGGGAGAGGAACCCAAGCCCTGACTGCTTCAGCAAAGCCCA
* *
9371 -CGGAGCAGCCCATATACATGTTAGACACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTT
66 TC-GAGCAGCCCATATACATGTCAGAAACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTT
* * *
9435 GGATTCTTCATGTATATATGTCACTCAAACAACCCATCCTTTTATGATGTGGGATG
130 GGATCCTTCATGTATATATGGCACTCAAACAACCCATCCTTTTATGATGTGAGATG
9491 T
1 T
9492 TTCCTTGCAT
Statistics
Matches: 171, Mismatches: 14, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
184 1 0.01
185 170 0.99
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (185 bp):
TAGTTTAATTTTGATTATTCGTGTTGGGAGAGGAACCCAAGCCCTGACTGCTTCAGCAAAGCCCA
TCGAGCAGCCCATATACATGTCAGAAACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTG
GATCCTTCATGTATATATGGCACTCAAACAACCCATCCTTTTATGATGTGAGATG
Found at i:9532 original size:40 final size:40
Alignment explanation
Indices: 9477--9557 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
9467 CCCATCCTTT
* * ** *
9477 TATGATGTGGGATGTTTCCTTGCATGTAAATGCTCAACAA
1 TATGATGCGGAATGTTTCCTCACATGTAAATCCTCAACAA
9517 TATGATGCGGAATGTTTCCTCACATGTAAATCCTCAACAA
1 TATGATGCGGAATGTTTCCTCACATGTAAATCCTCAACAA
9557 T
1 T
9558 CTCCCTCGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (40 bp):
TATGATGCGGAATGTTTCCTCACATGTAAATCCTCAACAA
Found at i:9931 original size:40 final size:40
Alignment explanation
Indices: 9872--9952 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
9862 CCCATCCTTT
* * ** *
9872 TATGATGTGGGATGTTTCCTTGCATGTAAATGCTCAACAA
1 TATGATGTGGAATGCTTCCTCACATGTAAATCCTCAACAA
9912 TATGATGTGGAATGCTTCCTCACATGTAAATCCTCAACAA
1 TATGATGTGGAATGCTTCCTCACATGTAAATCCTCAACAA
9952 T
1 T
9953 CTACATGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (40 bp):
TATGATGTGGAATGCTTCCTCACATGTAAATCCTCAACAA
Found at i:10167 original size:381 final size:384
Alignment explanation
Indices: 9327--10333 Score: 1615
Period size: 381 Copynumber: 2.6 Consensus size: 384
9317 TGATTATTTG
* * *
9327 TGTTGGGAGAGGAACCCAAGCCCTGACTGCTTCAGCAAGGCTCACGGAGCAGCCCATATACATGT
1 TGTTGGGAGAGGAACCCGAGCCCTGACTGCTTCAGCAAGGCCCACCGAGCAGCCCATATACATGT
* * *
9392 TAGACACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGATTCTTCATGTATATATGTC
66 CAGACACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGTC
9457 ACTCAAACAACCCATCCTTTTATGATGTGGGATGTTTCCTTGCATGTAAATGCTCAACAATATGA
131 ACTCAAACAACCCATCCTTTTATGATGTGGGATGTTTCCTTGCATGTAAATGCTCAACAATATGA
*
9522 TGCGGAATGTTTCCTCACATGTAAATCCTCAACAATCTCCCTCGATTTACATGTGAGTCCTCATC
196 TGTGGAATGTTTCCTCACATGTAAATCCTCAACAA------TC---TTACATGTGAGTCCTCATC
* * *
9587 TCTCCCCTGTGCGGCTCAACCCATCAAGTTTTAAGCCAGTTACCGGCTATCGAAGACTTAACCTC
252 TCT--CCTGTGCGGCACAACCCATCAAGTCTTAAGCCAGTTACCGGCTATCGAAGACTTAACCCC
*
9652 TAGAGTGGTGCAAGCTACGAACACTCCAAAATCGCAAGCCCCTCGAGTCCAACCAGACTCTGATA
315 TAGAGTGGTGCAAGCTACCAACACTCCAAAATCGCAAGCCCCTCGAGTCCAACCAGACTCTGATA
*
9717 CCAGT
380 CCACT
* *
9722 TGTTGGGAGAGGAACTCGAGCCCTGACTGCTTCAACAAGGCCCACCGAGCAGCCCATATACATGT
1 TGTTGGGAGAGGAACCCGAGCCCTGACTGCTTCAGCAAGGCCCACCGAGCAGCCCATATACATGT
* *
9787 CAGACACCAAACCGAACCCAAAAGTCTAGACTGAAGGTTTCTTGGGTCCTTCATGTATATATGTC
66 CAGACACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGTC
9852 ACTCAAACAACCCATCCTTTTATGATGTGGGATGTTTCCTTGCATGTAAATGCTCAACAATATGA
131 ACTCAAACAACCCATCCTTTTATGATGTGGGATGTTTCCTTGCATGTAAATGCTCAACAATATGA
* *
9917 TGTGGAATGCTTCCTCACATGTAAATCCTCAACAATC-TACATGTGAGTCCTTATCTCT-C-GTG
196 TGTGGAATGTTTCCTCACATGTAAATCCTCAACAATCTTACATGTGAGTCCTCATCTCTCCTGTG
* *
9979 CGGCACAACCCATCATGTCTTAAGCCAGTTACCGGCTATCGAAGACTTAACCCCTGGAGTGGTGC
261 CGGCACAACCCATCAAGTCTTAAGCCAGTTACCGGCTATCGAAGACTTAACCCCTAGAGTGGTGC
* * *
10044 AAGCTACCAACACTCCACAATCGCACGCTCCTCGAGTCCAACCAGACTCTGATACCACT
326 AAGCTACCAACACTCCAAAATCGCAAGCCCCTCGAGTCCAACCAGACTCTGATACCACT
*
10103 TGTTGGGAGAGGAACCCGAGCCCTGACTGCTTCAGCAAGGCCCACCGAGCAGTCCATATACATGT
1 TGTTGGGAGAGGAACCCGAGCCCTGACTGCTTCAGCAAGGCCCACCGAGCAGCCCATATACATGT
* *
10168 CAAACACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGTA
66 CAGACACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGTC
* * * *
10233 ACTCAAACAACCCATCCTTTTATGATGTGAGATGTTTCCTCGCATGTAAATCCTCAACAATATAA
131 ACTCAAACAACCCATCCTTTTATGATGTGGGATGTTTCCTTGCATGTAAATGCTCAACAATATGA
*
10298 TGTGGGATGTTTCCTCACATGTAAATCCTCAACAAT
196 TGTGGAATGTTTCCTCACATGTAAATCCTCAACAAT
10334 TTGAACTGTT
Statistics
Matches: 576, Mismatches: 36, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
381 335 0.58
382 1 0.00
385 20 0.03
389 2 0.00
395 218 0.38
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (384 bp):
TGTTGGGAGAGGAACCCGAGCCCTGACTGCTTCAGCAAGGCCCACCGAGCAGCCCATATACATGT
CAGACACCAATCCGAACCCAAAAGTCTAGACTGATGGTTTCTTGGGTCCTTCATGTATATATGTC
ACTCAAACAACCCATCCTTTTATGATGTGGGATGTTTCCTTGCATGTAAATGCTCAACAATATGA
TGTGGAATGTTTCCTCACATGTAAATCCTCAACAATCTTACATGTGAGTCCTCATCTCTCCTGTG
CGGCACAACCCATCAAGTCTTAAGCCAGTTACCGGCTATCGAAGACTTAACCCCTAGAGTGGTGC
AAGCTACCAACACTCCAAAATCGCAAGCCCCTCGAGTCCAACCAGACTCTGATACCACT
Found at i:10301 original size:40 final size:40
Alignment explanation
Indices: 10257--10333 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
10247 TCCTTTTATG
*
10257 ATGTGAGATGTTTCCTCGCATGTAAATCCTCAACAATATA
1 ATGTGAGATGTTTCCTCACATGTAAATCCTCAACAATATA
*
10297 ATGTGGGATGTTTCCTCACATGTAAATCCTCAACAAT
1 ATGTGAGATGTTTCCTCACATGTAAATCCTCAACAAT
10334 TTGAACTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (40 bp):
ATGTGAGATGTTTCCTCACATGTAAATCCTCAACAATATA
Found at i:10659 original size:6 final size:6
Alignment explanation
Indices: 10648--10690 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
10638 ATTTCTTCTT
* * * *
10648 GGACTC GGACTC GGACCC CGACTT GGACTT GGACTC GGACTC G
1 GGACTC GGACTC GGACTC GGACTC GGACTC GGACTC GGACTC G
10691 AGAGTAGGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.19
Consensus pattern (6 bp):
GGACTC
Found at i:16584 original size:50 final size:50
Alignment explanation
Indices: 16523--16951 Score: 596
Period size: 50 Copynumber: 8.7 Consensus size: 50
16513 CAAATTTTGT
* *
16523 TTTTCCCAAAATACCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
* *
16573 TTTTCCAAAAATACCCTTCCCGGATGGAAGGTATTTACTTTTACCTGCTA
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
*
16623 TTTTCCAAAAATGCCCTTCCCGGATGGAAGACATTTACTTTTACCTGCTA
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
16673 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
16723 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
* * *
16773 TTTTCCAAAAATACCCTTCCCGGACGGAAGGCATTTACTTTTACTTGCT-
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
* * * * * *
16822 TTTTCCCAAAGTGCCCTTCCCGGACGGAAGGCACTAACTTTTACTTGCT-
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
* * * * * * *
16871 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGC-GTTAGTTTTGCCCGCT-
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
** * * *
16919 TTTTCTTAAAATGCCCTTTCCAGATGAAAGGCA
1 TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCA
16952 AGTTCACTTT
Statistics
Matches: 349, Mismatches: 29, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
48 36 0.10
49 73 0.21
50 240 0.69
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (50 bp):
TTTTCCAAAAATGCCCTTCCCGGATGGAAGGCATTTACTTTTACCTGCTA
Found at i:19600 original size:15 final size:16
Alignment explanation
Indices: 19569--19601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19559 CCGAATCCGA
*
19569 GAACCCGCCCGAACCC
1 GAACCCACCCGAACCC
19585 GAACCCACCC-AACCC
1 GAACCCACCCGAACCC
19600 GA
1 GA
19602 TTTGACCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.55, G:0.15, T:0.00
Consensus pattern (16 bp):
GAACCCACCCGAACCC
Found at i:19686 original size:16 final size:16
Alignment explanation
Indices: 19643--19748 Score: 92
Period size: 16 Copynumber: 6.6 Consensus size: 16
19633 GCTCGTCCTA
19643 AGACCCGAATGACCC-
1 AGACCCGAATGACCCG
* * *
19658 ACAACCTAGATGACCCG
1 AGACCCGA-ATGACCCG
19675 AGACCCGAATGACCCG
1 AGACCCGAATGACCCG
19691 TA-ACCC-AGATGACCCG
1 -AGACCCGA-ATGACCCG
* *
19707 AAACCCGAATGACCTG
1 AGACCCGAATGACCCG
* *
19723 AGACCCGTATGACCAG
1 AGACCCGAATGACCCG
*
19739 AAACCCGAAT
1 AGACCCGAAT
19749 AAACCGAGAA
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
15 7 0.10
16 59 0.81
17 7 0.10
ACGTcount: A:0.35, C:0.35, G:0.20, T:0.10
Consensus pattern (16 bp):
AGACCCGAATGACCCG
Found at i:19735 original size:32 final size:32
Alignment explanation
Indices: 19645--19748 Score: 122
Period size: 32 Copynumber: 3.2 Consensus size: 32
19635 TCGTCCTAAG
** * *
19645 ACCCGAATGACCCACAACCTAGATGACCCGAG
1 ACCCGAATGACCCGTAACCCAGATGACCCGAA
19677 ACCCGAATGACCCGTAACCCAGATGACCCGAA
1 ACCCGAATGACCCGTAACCCAGATGACCCGAA
* *
19709 ACCCGAATGACCTG-AGACCC-GTATGACCAGAA
1 ACCCGAATGACCCGTA-ACCCAG-ATGACCCGAA
19741 ACCCGAAT
1 ACCCGAAT
19749 AAACCGAGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
31 2 0.03
32 62 0.97
ACGTcount: A:0.35, C:0.36, G:0.19, T:0.11
Consensus pattern (32 bp):
ACCCGAATGACCCGTAACCCAGATGACCCGAA
Found at i:21834 original size:42 final size:42
Alignment explanation
Indices: 21770--21851 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
21760 TGTTGACACA
*
21770 TACCCCACCTGATAATTAATTATGTATTTAATATTCAAAACC
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAACC
*
21812 TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAA
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAA
21852 TTAATATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (42 bp):
TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAACC
Found at i:22128 original size:32 final size:31
Alignment explanation
Indices: 22095--22205 Score: 98
Period size: 32 Copynumber: 3.5 Consensus size: 31
22085 CCCGGTAGAT
*
22095 CCGAAACCCGAATGACACGGAACCCGAATGAT
1 CCGAAACCCGAATGAC-CGGAACCCGAATGAC
* * * * * *
22127 CCGAGACCCAAATTATCCGAAACCTGTATGAC
1 CCGAAACCCGAATGA-CCGGAACCCGAATGAC
* * *
22159 CCGAGACCCGAATAACCCGAACCC-AGATGAC
1 CCGAAACCCGAATGACCGGAACCCGA-ATGAC
22190 CCGAAACCCGAATGAC
1 CCGAAACCCGAATGAC
22206 GAATGACCCG
Statistics
Matches: 62, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
31 25 0.40
32 36 0.58
33 1 0.02
ACGTcount: A:0.36, C:0.34, G:0.19, T:0.11
Consensus pattern (31 bp):
CCGAAACCCGAATGACCGGAACCCGAATGAC
Found at i:22135 original size:16 final size:16
Alignment explanation
Indices: 22077--22205 Score: 86
Period size: 16 Copynumber: 8.1 Consensus size: 16
22067 AACCCGCCCA
*
22077 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAAT-G
* *
22093 ATCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
*
22109 ACACG-GAACCCGAATG
1 ACCCGAG-ACCCGAATG
* * *
22125 ATCCGAGACCCAAATT
1 ACCCGAGACCCGAATG
* * * *
22141 ATCCGAAACCTGTATG
1 ACCCGAGACCCGAATG
*
22157 ACCCGAGACCCGAATA
1 ACCCGAGACCCGAATG
22173 ACCCGA-ACCC-AGATG
1 ACCCGAGACCCGA-ATG
*
22188 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
22204 AC
1 AC
22206 GAATGACCCG
Statistics
Matches: 86, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
14 1 0.01
15 12 0.14
16 70 0.81
17 3 0.03
ACGTcount: A:0.35, C:0.34, G:0.20, T:0.11
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:22145 original size:48 final size:47
Alignment explanation
Indices: 22092--22205 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 47
22082 AGACCCGGTA
* * *
22092 GATCCGAAACCCGAATGACACG-GAACCCGAATGATCCGAGACCCAAAT
1 GATCCGAAACCCGAATGACCCGAG-ACCCGAATAACCCGA-ACCCAAAT
* * * *
22140 TATCCGAAACCTGTATGACCCGAGACCCGAATAACCCGAACCCAGAT
1 GATCCGAAACCCGAATGACCCGAGACCCGAATAACCCGAACCCAAAT
*
22187 GACCCGAAACCCGAATGAC
1 GATCCGAAACCCGAATGAC
22206 GAATGACCCG
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
47 22 0.41
48 31 0.57
49 1 0.02
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.11
Consensus pattern (47 bp):
GATCCGAAACCCGAATGACCCGAGACCCGAATAACCCGAACCCAAAT
Found at i:23449 original size:31 final size:28
Alignment explanation
Indices: 23381--23458 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 28
23371 CCCAAATCGA
*
23381 AAAGTTCAGGCACTAATTTGACCTTTTC
1 AAAGTTTAGGCACTAATTTGACCTTTTC
* *
23409 ATAGTTTAGGCACTTATTTGACCCTTTTGGC
1 AAAGTTTAGGCACTAATTTGA-CCTTTT--C
*
23440 AAAGTTTAGGACCCTAATT
1 AAAGTTTAGG-CACTAATT
23459 GAGATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 18 0.45
29 6 0.15
31 10 0.25
32 6 0.15
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (28 bp):
AAAGTTTAGGCACTAATTTGACCTTTTC
Found at i:24877 original size:47 final size:47
Alignment explanation
Indices: 24803--24927 Score: 205
Period size: 47 Copynumber: 2.7 Consensus size: 47
24793 TGGAGTGGTA
* *
24803 CAAGCTACGAACACTCCACGATCGCACGCCTCTGGCCAGCGGCCAAC
1 CAAGTTACGAACACTCCACGATCGCACGCCCCTGGCCAGCGGCCAAC
**
24850 CAAGTTACGAACACTCCACGATCGCACGCCCCTGGTTAGCGGCCAAC
1 CAAGTTACGAACACTCCACGATCGCACGCCCCTGGCCAGCGGCCAAC
*
24897 CAAGTTACGAACACTCCACGATCCCACGCCC
1 CAAGTTACGAACACTCCACGATCGCACGCCC
24928 AACCAGGTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.26, C:0.42, G:0.19, T:0.13
Consensus pattern (47 bp):
CAAGTTACGAACACTCCACGATCGCACGCCCCTGGCCAGCGGCCAAC
Found at i:25074 original size:74 final size:74
Alignment explanation
Indices: 24953--25100 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
24943 GCTCATGGGC
* **
24953 CACACTGATCGATCGCCCCTGGTTAGCGGCCAACCAGGTCACGAACACTCCACGATCGCATGCCC
1 CACACTGATCAATCGCCCCTGGCCAGCGGCCAACCAGGTCACGAACACTCCACGATCGCATGCCC
25018 AACCAGGTT
66 AACCAGGTT
*
25027 CACACTGATCAATCGCCCCTGGCCAGCGGCCAACCAGGTTACGAACACTCCACGATCGCATGCCC
1 CACACTGATCAATCGCCCCTGGCCAGCGGCCAACCAGGTCACGAACACTCCACGATCGCATGCCC
25092 AACCAGGTT
66 AACCAGGTT
25101 TACCGTGCTC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.25, C:0.39, G:0.21, T:0.16
Consensus pattern (74 bp):
CACACTGATCAATCGCCCCTGGCCAGCGGCCAACCAGGTCACGAACACTCCACGATCGCATGCCC
AACCAGGTT
Found at i:25100 original size:34 final size:34
Alignment explanation
Indices: 24982--25100 Score: 98
Period size: 34 Copynumber: 3.3 Consensus size: 34
24972 TGGTTAGCGG
*
24982 CCAACCAGGTCACGAACACTCCACGATCGCATGC
1 CCAACCAGGTTACGAACACTCCACGATCGCATGC
* * ** *
25016 CCAACCAGGTTCACACTGATCAATCGC-CCCTGGCCA-GC
1 CCAACCAGGTT---AC-GAACACTC-CACGATCG-CATGC
25054 GGCCAACCAGGTTACGAACACTCCACGATCGCATGC
1 --CCAACCAGGTTACGAACACTCCACGATCGCATGC
25090 CCAACCAGGTT
1 CCAACCAGGTT
25101 TACCGTGCTC
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
34 21 0.33
35 3 0.05
36 11 0.17
37 4 0.06
38 11 0.17
39 3 0.05
40 11 0.17
ACGTcount: A:0.27, C:0.39, G:0.19, T:0.14
Consensus pattern (34 bp):
CCAACCAGGTTACGAACACTCCACGATCGCATGC
Found at i:25127 original size:43 final size:43
Alignment explanation
Indices: 25080--25205 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 43
25070 AACACTCCAC
25080 GATCGCATGCCCAACCAGGTTTACCGTGCTCATGGGTCACACT
1 GATCGCATGCCCAACCAGGTTTACCGTGCTCATGGGTCACACT
** *
25123 GATCG-ATCGCCCCAACCAGG-TTA-C--GAACAT---T-TCAC-
1 GATCGCAT-G-CCCAACCAGGTTTACCGTGCTCATGGGTCACACT
* *
25158 GATCGCACGCCCAACCAGGTTTACCGTGCTCATGGGCCACACT
1 GATCGCATGCCCAACCAGGTTTACCGTGCTCATGGGTCACACT
25201 GATCG
1 GATCG
25206 ATCGCCCCTG
Statistics
Matches: 63, Mismatches: 8, Indels: 24
0.66 0.08 0.25
Matches are distributed among these distances:
34 10 0.16
35 9 0.14
36 5 0.08
37 1 0.02
38 4 0.06
40 4 0.06
42 6 0.10
43 14 0.22
44 10 0.16
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (43 bp):
GATCGCATGCCCAACCAGGTTTACCGTGCTCATGGGTCACACT
Found at i:25144 original size:44 final size:44
Alignment explanation
Indices: 25089--25213 Score: 128
Period size: 44 Copynumber: 3.1 Consensus size: 44
25079 CGATCGCATG
25089 CCCAACCAGGTTTACCGTGCTCATGGGTCACACTGATCGATCGC
1 CCCAACCAGGTTTACCGTGCTCATGGGTCACACTGATCGATCGC
** *
25133 CCCAACCAGG-TTA-C--GAACAT---T-TCAC-GATCGCA-CG-
1 CCCAACCAGGTTTACCGTGCTCATGGGTCACACTGATCG-ATCGC
*
25167 CCCAACCAGGTTTACCGTGCTCATGGGCCACACTGATCGATCGC
1 CCCAACCAGGTTTACCGTGCTCATGGGTCACACTGATCGATCGC
25211 CCC
1 CCC
25214 TGGCCAGCGG
Statistics
Matches: 62, Mismatches: 7, Indels: 24
0.67 0.08 0.26
Matches are distributed among these distances:
34 10 0.16
35 10 0.16
36 5 0.08
37 1 0.02
38 4 0.06
40 4 0.06
42 5 0.08
43 10 0.16
44 13 0.21
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.20
Consensus pattern (44 bp):
CCCAACCAGGTTTACCGTGCTCATGGGTCACACTGATCGATCGC
Found at i:25171 original size:78 final size:78
Alignment explanation
Indices: 24982--25213 Score: 287
Period size: 78 Copynumber: 3.0 Consensus size: 78
24972 TGGTTAGCGG
* * * * *
24982 CCAACCAGGTCACGAACACTCCACGATCGCATGCCCAACCAGGTTCACAC-TGATCAAT-CGCC-
1 CCAACCAGGTTACGAACACTCCACGATCGCACGCCCAACCAGGTTTAC-CGTGCTC-ATGGGCCA
* * * *
25044 C-CTG-GCCAGCG-G
64 CACTGATCGATCGCC
* *
25056 CCAACCAGGTTACGAACACTCCACGATCGCATGCCCAACCAGGTTTACCGTGCTCATGGGTCACA
1 CCAACCAGGTTACGAACACTCCACGATCGCACGCCCAACCAGGTTTACCGTGCTCATGGGCCACA
25121 CTGATCGATCGCC
66 CTGATCGATCGCC
* *
25134 CCAACCAGGTTACGAACATTTCACGATCGCACGCCCAACCAGGTTTACCGTGCTCATGGGCCACA
1 CCAACCAGGTTACGAACACTCCACGATCGCACGCCCAACCAGGTTTACCGTGCTCATGGGCCACA
25199 CTGATCGATCGCC
66 CTGATCGATCGCC
25212 CC
1 CC
25214 TGGCCAGCGG
Statistics
Matches: 139, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
73 3 0.02
74 52 0.37
75 1 0.01
76 3 0.02
77 4 0.03
78 76 0.55
ACGTcount: A:0.25, C:0.38, G:0.20, T:0.17
Consensus pattern (78 bp):
CCAACCAGGTTACGAACACTCCACGATCGCACGCCCAACCAGGTTTACCGTGCTCATGGGCCACA
CTGATCGATCGCC
Found at i:25266 original size:47 final size:47
Alignment explanation
Indices: 25208--25324 Score: 197
Period size: 43 Copynumber: 2.6 Consensus size: 47
25198 ACTGATCGAT
25208 CGCCCCTGGCCAGCGGCCAACCAGGTTACGAACACTCCACGATCGCA
1 CGCCCCTGGCCAGCGGCCAACCAGGTTACGAACACTCCACGATCGCA
*
25255 CGCCTCTGGCCAGCGGCC-A--A-GTTACGAACACTCCACGATCGCA
1 CGCCCCTGGCCAGCGGCCAACCAGGTTACGAACACTCCACGATCGCA
25298 CGCCCCTGGCCAGCGGCCAACCAGGTT
1 CGCCCCTGGCCAGCGGCCAACCAGGTT
25325 TACCGTGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
43 40 0.62
44 2 0.03
46 2 0.03
47 20 0.31
ACGTcount: A:0.21, C:0.42, G:0.25, T:0.12
Consensus pattern (47 bp):
CGCCCCTGGCCAGCGGCCAACCAGGTTACGAACACTCCACGATCGCA
Found at i:29826 original size:25 final size:25
Alignment explanation
Indices: 29779--29827 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29769 TGAGCTGTCA
* *
29779 TTTGGAACAATTAAGCTCTTTCAAT
1 TTTGGAACAATTAAGCCCCTTCAAT
*
29804 TTTGGAACAATTTAGCCCCTTCAA
1 TTTGGAACAATTAAGCCCCTTCAA
29828 AGAACATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (25 bp):
TTTGGAACAATTAAGCCCCTTCAAT
Found at i:30884 original size:20 final size:20
Alignment explanation
Indices: 30859--30917 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
30849 AGATATGTTT
30859 TACTAATAAATAATAATATA
1 TACTAATAAATAATAATATA
*
30879 TACTAATAAAT-A-AATATT
1 TACTAATAAATAATAATATA
* *
30897 TACTAATTTACTAATAATATA
1 TACTAA-TAAATAATAATATA
30918 AATATATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.34
19 4 0.12
20 12 0.38
21 5 0.16
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (20 bp):
TACTAATAAATAATAATATA
Found at i:33217 original size:2 final size:2
Alignment explanation
Indices: 33210--33250 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
33200 AAATTCCGAG
*
33210 TA TA TA TA TA TA TA TA TA TA T- TA TA TA CT- TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
33251 AGTTATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.91
3 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:34086 original size:60 final size:59
Alignment explanation
Indices: 33964--34093 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
33954 TTCTTGGGGA
* * * * * *
33964 GAAAATATCCTGATTTTGATAGTTTAAGAGTAAAAGTTTCAAATTAAAAGTTAAAGAGG
1 GAAAATGTCCCGATTTTGATAGTTAAAGAGTAAAAGTTCCAAAATAAAAATTAAAGAGG
* * * *
34023 GAAATTGTCCCGATTTTGATAGATTAAAGATTGAAAGTTCCAAAATAAAAATT-CAGAGTG
1 GAAAATGTCCCGATTTTGATAG-TTAAAGAGTAAAAGTTCCAAAATAAAAATTAAAGAG-G
34083 GAAAATGTCCC
1 GAAAATGTCCC
34094 TTTTGAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 23 0.40
60 35 0.60
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (59 bp):
GAAAATGTCCCGATTTTGATAGTTAAAGAGTAAAAGTTCCAAAATAAAAATTAAAGAGG
Found at i:37334 original size:15 final size:15
Alignment explanation
Indices: 37285--37335 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
37275 ATAATATATT
37285 TTAATTATTCCATTA
1 TTAATTATTCCATTA
** *
37300 TTTTTTATACCA-TA
1 TTAATTATTCCATTA
37314 --AATTATTCCATTA
1 TTAATTATTCCATTA
37327 TTAATTATT
1 TTAATTATT
37336 AGATCATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 16 0.59
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTATTCCATTA
Found at i:37441 original size:37 final size:37
Alignment explanation
Indices: 37385--37469 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
37375 TTACTTTTTA
*
37385 TTTCCAACATCCTATTTAATTTTG-TCTTTTGTCTTTG
1 TTTCCAACATCCTAGTTAATTTTGCT-TTTTGTCTTTG
* *
37422 TTTCCAACGTCGTAGTTAATTTTGCTTTTTGTCTTTG
1 TTTCCAACATCCTAGTTAATTTTGCTTTTTGTCTTTG
*
37459 TCTCCAACATC
1 TTTCCAACATC
37470 TTATTTGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 41 0.98
38 1 0.02
ACGTcount: A:0.16, C:0.21, G:0.11, T:0.52
Consensus pattern (37 bp):
TTTCCAACATCCTAGTTAATTTTGCTTTTTGTCTTTG
Found at i:37705 original size:2 final size:2
Alignment explanation
Indices: 37700--37728 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37690 AAAAACAATT
37700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37729 TACACTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49380 original size:200 final size:202
Alignment explanation
Indices: 48564--49501 Score: 1213
Period size: 199 Copynumber: 4.7 Consensus size: 202
48554 CTTTATAATA
* * * *
48564 AGGATTATTATATAAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTGA
1 AGGATTATTATA-CAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGA
* * *
48629 CACATACCCACATTTCATAATTAATT--AGATATTTGATATTAATACATATTCCCTAAGATGACA
65 CACATA-CCACATTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGAGGACA
* * * * *
48692 CATGTCAACCCTTAAACCAT-GCACGTGCAGTCTGCTAAATTCCACTGGCGGTGTACTGTATAAT
129 CATGTCAACCCTTAAACCCTAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAAT
48756 TTTGT-TTAT
194 TTT-TCTTAT
* * * *
48765 TGGATTATTATACAATACAATGTCAGTGTAAATTTTGAACTCCATAACCAGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* * * **
48830 ACATACCATATTTCATAATTAATTAGATATA--AAATATTAATACATATTCCCTAAGATAACACA
66 ACATACCACATTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGAGGACACA
* * * * ** * *
48893 TATAAATCCTTAAACCCTACGCA--TGCAGTTTGCTAAACTTTATTGACAGTGTATTGTATAATT
131 TGTCAACCCTTAAACCCTA-GCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATT
*
48956 TTTTTTAT
195 TTTCTTAT
* *
48964 ATGG-TTATTATACAATACACTGTCAGTATAAATTTTGAACTCCAAAAGCGGGTTAAGAAGTTGA
1 A-GGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGA
* * * *
49028 CACATATCTCATTTCATAATTACTT-AA-ATATTTAATATTAATACATATTCCCTAAGGGGACAC
65 CACATACCACATTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGAGGACAC
49091 ATGTCAACCCTTAAA-CCTAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATT
130 ATGTCAACCCTTAAACCCTAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATT
49155 TTTCTTAT
195 TTTCTTAT
* * * *
49163 AGGATTATTATACAATACATTGTTAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAG
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* *
49228 ACATACCACATTTCATAATTAATTAAATATATTTAATATTAATACATATTTCCTAAGGGGACACA
66 ACATACCACATTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGAGGACACA
* * * * **
49293 TGTCAA-CCTCAAACCCT-GCATGTGCAGTCTGTTAAACTCTACTGACGGTATATTGTGCAATTT
131 TGTCAACCCTTAAACCCTAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTT
*
49356 TTCTTGT
196 TTCTTAT
* * * * * *
49363 AGAATTATTACACAATACACTGTCAATGCAAATTTTGTACTCCATTAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
*
49428 ACATACCTCATTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGCA-GACAC
66 ACATACCACATTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAG-AGGACAC
49492 ATGTCAACCC
130 ATGTCAACCC
49502 GCACGTGCAA
Statistics
Matches: 643, Mismatches: 78, Indels: 32
0.85 0.10 0.04
Matches are distributed among these distances:
197 6 0.01
198 8 0.01
199 333 0.52
200 231 0.36
201 65 0.10
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (202 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCACATTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGAGGACACA
TGTCAACCCTTAAACCCTAGCATGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTT
TTCTTAT
Done.