Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003103.1 Hibiscus syriacus cultivar Beakdansim tig00006477_pilon, 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: 65787
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8808 original size:16 final size:17
Alignment explanation
Indices: 8781--8813 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
8771 CTACGTGTAA
*
8781 GTGAACTATGTGCTAAT
1 GTGAACTATGTGATAAT
8798 GTGAA-TATGTGATAAT
1 GTGAACTATGTGATAAT
8814 TATAAAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
GTGAACTATGTGATAAT
Found at i:9043 original size:23 final size:23
Alignment explanation
Indices: 9017--9098 Score: 87
Period size: 23 Copynumber: 3.5 Consensus size: 23
9007 CAATCTTATA
9017 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
9040 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
9063 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTACGGTG-C-AATTCTACG
9087 TGGCACTACGGT
1 TGGCACTACGGT
9099 ACAAATTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.02
23 31 0.65
24 16 0.33
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:9829 original size:21 final size:21
Alignment explanation
Indices: 9803--9845 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9793 TTTACGAAGT
9803 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
*
9824 ACTGTAGCAGTGCCTCGATGC
1 ACTGTAGCAGTGCATCGATGC
9845 A
1 A
9846 TAATTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:9921 original size:21 final size:24
Alignment explanation
Indices: 9870--9916 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
9860 AAATTTTCAC
*
9870 TGTTCAT--GGTACTGTTCATTGT
1 TGTTCATACGGTACTATTCATTGT
9892 TGTTCATACGGTACTATTCATTGT
1 TGTTCATACGGTACTATTCATTGT
9916 T
1 T
9917 TATACCGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.32
24 15 0.68
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (24 bp):
TGTTCATACGGTACTATTCATTGT
Found at i:10384 original size:24 final size:24
Alignment explanation
Indices: 10302--10391 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 24
10292 TATGATAATA
* * *
10302 CACTCCTGTATTAGTGCGAATACG
1 CACTCCTGTATTAGTACAAATGCG
* * * *
10326 CACTCTTGTATTAGTGCAATTGTG
1 CACTCCTGTATTAGTACAAATGCG
* * *
10350 CATTCCCGTATTAGTACAAATGGG
1 CACTCCTGTATTAGTACAAATGCG
* *
10374 TACTCCTGTATTAATACA
1 CACTCCTGTATTAGTACA
10392 TTCGTGCACT
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (24 bp):
CACTCCTGTATTAGTACAAATGCG
Found at i:10467 original size:25 final size:25
Alignment explanation
Indices: 10375--10479 Score: 78
Period size: 24 Copynumber: 4.3 Consensus size: 25
10365 ACAAATGGGT
10375 ACTCCTGTATTA-A-TACATTCGTGC
1 ACTCCTG-ATTATAGTACATTCGTGC
* * *
10399 ACTCATGTATCAGT-GTA-ATT-TTGC
1 ACTCCTG-ATTA-TAGTACATTCGTGC
* * *
10423 ACTCCTTAAT-TAGTGCATTCGTGC
1 ACTCCTGATTATAGTACATTCGTGC
*
10447 ACTCCTGATTATAGTACATTCGTGT
1 ACTCCTGATTATAGTACATTCGTGC
10472 ACTCCTGA
1 ACTCCTGA
10480 CATTATGTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
21 1 0.02
22 2 0.03
23 4 0.07
24 29 0.48
25 23 0.38
26 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (25 bp):
ACTCCTGATTATAGTACATTCGTGC
Found at i:10536 original size:17 final size:18
Alignment explanation
Indices: 10516--10560 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
10506 ACAAGACAGT
*
10516 AAAAGGAATAGT-GCATA
1 AAAAGAAATAGTAGCATA
* *
10533 AAAAGAAACAGTAGGATA
1 AAAAGAAATAGTAGCATA
10551 AAAAGAAATA
1 AAAAGAAATA
10561 ATAAAGTACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.62, C:0.04, G:0.20, T:0.13
Consensus pattern (18 bp):
AAAAGAAATAGTAGCATA
Found at i:11904 original size:24 final size:24
Alignment explanation
Indices: 11863--11912 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
11853 ATAAACATCA
*
11863 AATACAATAAATAATATTATTTATT
1 AATAAAATAAATAATATTATTT-TT
11888 AATAAAAT-AATAATATTATTTTT
1 AATAAAATAAATAATATTATTTTT
11911 AA
1 AA
11913 AATATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
24 13 0.54
25 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATAAAATAAATAATATTATTTTT
Found at i:12014 original size:31 final size:31
Alignment explanation
Indices: 11978--12036 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
11968 ATATCTACAA
11978 TTTTATAAATAAAAGT-ATTA-AAATTATAATC
1 TTTTATAAA-AAAA-TAATTAGAAATTATAATC
*
12009 TTTTATTAAAAAATAATTAGAAATTATA
1 TTTTATAAAAAAATAATTAGAAATTATA
12037 TTAGTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 1 0.04
30 8 0.32
31 16 0.64
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (31 bp):
TTTTATAAAAAAATAATTAGAAATTATAATC
Found at i:12109 original size:17 final size:16
Alignment explanation
Indices: 12056--12114 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 16
12046 TATTAAAACA
12056 AAAATAATATATTATT
1 AAAATAATATATTATT
12072 AACTATATTAAT-TACTTATT
1 AA--A-A-TAATATA-TTATT
12092 AAAATAATAGTATTATT
1 AAAATAATA-TATTATT
12109 AAAATA
1 AAAATA
12115 TTAAAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
16 6 0.17
17 12 0.33
18 4 0.11
19 3 0.08
20 11 0.31
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (16 bp):
AAAATAATATATTATT
Found at i:12128 original size:14 final size:15
Alignment explanation
Indices: 12111--12145 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
12101 GTATTATTAA
12111 AATATTAAAAATA-T
1 AATATTAAAAATATT
12125 AATATT-AAAATATT
1 AATATTAAAAATATT
12139 AATATTA
1 AATATTA
12146 TTTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATTAAAAATATT
Found at i:15018 original size:31 final size:32
Alignment explanation
Indices: 14980--15045 Score: 125
Period size: 31 Copynumber: 2.1 Consensus size: 32
14970 CTACATAGGG
14980 TCTGTAACAAGAGTCCGACTC-GTAGAAATCA
1 TCTGTAACAAGAGTCCGACTCGGTAGAAATCA
15011 TCTGTAACAAGAGTCCGACTCGGTAGAAATCA
1 TCTGTAACAAGAGTCCGACTCGGTAGAAATCA
15043 TCT
1 TCT
15046 TTCGAGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.62
32 13 0.38
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (32 bp):
TCTGTAACAAGAGTCCGACTCGGTAGAAATCA
Found at i:15294 original size:15 final size:15
Alignment explanation
Indices: 15274--15304 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15264 TATCAATGAA
15274 TTTTATATAAATAAT
1 TTTTATATAAATAAT
*
15289 TTTTATTTAAATAAT
1 TTTTATATAAATAAT
15304 T
1 T
15305 AAAATTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTATATAAATAAT
Found at i:23643 original size:34 final size:34
Alignment explanation
Indices: 23605--23671 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
23595 TAGTTGTTAC
23605 CTTTT-TAAATTTGAATATTAAAGATAAT-TATATA
1 CTTTTGTAAATTTGAA-ATTAAA-ATAATATATATA
* *
23639 CTTTTGTATATTTTAAATTAAAATAATATATAT
1 CTTTTGTAAATTTGAAATTAAAATAATATATAT
23672 TTAAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 16 0.55
35 8 0.28
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (34 bp):
CTTTTGTAAATTTGAAATTAAAATAATATATATA
Found at i:23676 original size:21 final size:20
Alignment explanation
Indices: 23645--23684 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
23635 TATACTTTTG
23645 TATATTTTAAATTAAAATAA
1 TATATTTTAAATTAAAATAA
*
23665 TATATATTTAAATTTAAATA
1 TATAT-TTTAAATTAAAATA
23685 GTAAAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATTTTAAATTAAAATAA
Found at i:23864 original size:189 final size:189
Alignment explanation
Indices: 23451--23896 Score: 567
Period size: 189 Copynumber: 2.4 Consensus size: 189
23441 ATCTTTTTAA
* ** * * * **
23451 TTTTGTATATTTTAAATTAAAATAATATTTGCTTAAGTTTAAATAGTAAAATGAATTTACCTTTT
1 TTTTGTATATTTTAAATTAAAATAATATATATTTAAATTTAAATAGTAAAAAGAGTTTATTTTTT
* * * *
23516 CACCATTACAAATTAAATATATTATTTAATTTTAATATTTGTATGATAATTACTCTTTGAATATC
66 GACAATTACAAATTAAATATATTATTTAATTTGAATATTAGTATGATAATTACTCTTTGAATATC
23581 TCAATTTAAAAAGGTAGTTGTTACCTTTTTAAATTTGAATATTAAAGATAATTATATAC
131 TCAATTTAAAAAGGTAGTTGTTACCTTTTTAAATTTGAATATTAAAGATAATTATATAC
23640 TTTTGTATATTTTAAATTAAAATAATATATATTTAAATTTAAATAGTAAAAAGAGTTTATTTTTT
1 TTTTGTATATTTTAAATTAAAATAATATATATTTAAATTTAAATAGTAAAAAGAGTTTATTTTTT
* * * * *
23705 GACAATTGCAAATTAAATCTATTATTTAATTTGAATATTAGTA-GAATAATTATTCTTTTAGTAT
66 GACAATTACAAATTAAATATATTATTTAATTTGAATATTAGTATG-ATAATTACTCTTTGAATAT
* * * *
23769 GTCAATTTAAAAATGTA-TCT-TATACCTTTTTAACTTTGAATATTAAAGATAATTATATAT
130 CTCAATTTAAAAAGGTAGT-TGT-TACCTTTTTAAATTTGAATATTAAAGATAATTATATAC
* * * * * **
23829 TTTTATATATTTTTAATTAAAATAATATCTATTT-AAGTTATAATGGTAAAGGGAGTTTTATTTT
1 TTTTGTATATTTTAAATTAAAATAATATATATTTAAATTTA-AATAGTAAAAAGAG-TTTATTTT
23893 TTGA
64 TTGA
23897 ATATTTTAAA
Statistics
Matches: 224, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
188 8 0.04
189 204 0.91
190 12 0.05
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (189 bp):
TTTTGTATATTTTAAATTAAAATAATATATATTTAAATTTAAATAGTAAAAAGAGTTTATTTTTT
GACAATTACAAATTAAATATATTATTTAATTTGAATATTAGTATGATAATTACTCTTTGAATATC
TCAATTTAAAAAGGTAGTTGTTACCTTTTTAAATTTGAATATTAAAGATAATTATATAC
Found at i:29325 original size:60 final size:60
Alignment explanation
Indices: 29247--29396 Score: 237
Period size: 60 Copynumber: 2.5 Consensus size: 60
29237 TAATTTATAT
* * * *
29247 ACTTTTGAATATTTTAATTTAATCCCCAAGCTATGACTCTCATTCTAAATTAGTCTTTAA
1 ACTTTTGAATATTCTAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAA
*
29307 ACTTTTGAATATTCTAATTTCATCCCCAAACTATGACTCTCATTTTAAATTAGTCCTTAA
1 ACTTTTGAATATTCTAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAA
* *
29367 ACTTTTGAATCTTCCAATTTCATCCCCAAA
1 ACTTTTGAATATTCTAATTTCATCCCCAAA
29397 ATATCCAAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 83 1.00
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (60 bp):
ACTTTTGAATATTCTAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAA
Found at i:29717 original size:14 final size:17
Alignment explanation
Indices: 29677--29719 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
29667 CTTAATTTTA
29677 TAAATATTTTTATTATAT
1 TAAATA-TTTTATTATAT
29695 TAAATATTTTATT-T-T
1 TAAATATTTTATTATAT
29710 TAAA-ATTTTA
1 TAAATATTTTA
29720 AATTATTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 1 0.04
17 7 0.28
18 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAAATATTTTATTATAT
Found at i:30685 original size:21 final size:20
Alignment explanation
Indices: 30623--30690 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
30613 GATTCGCAAC
30623 GCGATAGTCGAAGTTTGCGTT
1 GCGATAGTCGAAG-TTGCGTT
* *
30644 GCGATTCATTTC-AAATT-CGTT
1 GCGA-T-A-GTCGAAGTTGCGTT
30665 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCGAAGTT-GCGTT
30686 GCGAT
1 GCGAT
30691 TCAGTCCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 2 0.05
19 5 0.14
20 1 0.03
21 21 0.57
22 3 0.08
23 3 0.08
24 2 0.05
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.34
Consensus pattern (20 bp):
GCGATAGTCGAAGTTGCGTT
Found at i:30783 original size:6 final size:6
Alignment explanation
Indices: 30772--30798 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30762 GACACGTATT
30772 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
30799 CGAGACGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:31568 original size:21 final size:21
Alignment explanation
Indices: 31544--31698 Score: 99
Period size: 21 Copynumber: 7.4 Consensus size: 21
31534 TTTGGAATGA
31544 ATCGCAACGCGAACTTCGCCT
1 ATCGCAACGCGAACTTCGCCT
* * **
31565 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGCCT
*
31584 GAATCTCAACGCGAACTTCGCCT
1 --ATCGCAACGCGAACTTCGCCT
* * **
31607 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGCCT
31626 GAATCGCAACGCGAACTTCGCCT
1 --ATCGCAACGCGAACTTCGCCT
* **
31649 ATCGCAA--CGAA-TTGGAAT
1 ATCGCAACGCGAACTTCGCCT
31667 GAATCGCAACGCGAACTTCGCCT
1 --ATCGCAACGCGAACTTCGCCT
31690 ATCGCAACG
1 ATCGCAACG
31699 AATTGGAATG
Statistics
Matches: 97, Mismatches: 24, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
18 4 0.04
19 20 0.21
20 7 0.07
21 42 0.43
22 4 0.04
23 20 0.21
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGCCT
Found at i:31676 original size:41 final size:42
Alignment explanation
Indices: 31521--31818 Score: 503
Period size: 42 Copynumber: 7.2 Consensus size: 42
31511 AATATTTGGA
*
31521 CTATCGCAATGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
31563 CTATCGCAACGAATTTGGAATGAATCTCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
31605 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
31647 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* *
31688 CTATCGCAACGAA-TTGGAATGAATCGCAACGTGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
31729 CTATTGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
31770 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
31812 CTATCGC
1 CTATCGC
31819 GTTGCGAATC
Statistics
Matches: 242, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
40 1 0.00
41 113 0.47
42 128 0.53
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:33519 original size:18 final size:19
Alignment explanation
Indices: 33496--33549 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
33486 GACTCGATTT
*
33496 AATATTTATT-TAATAAAA
1 AATATTTATTAAAATAAAA
*
33514 AATATTTTATTAAAATGAAA
1 AATA-TTTATTAAAATAAAA
33534 AATATGTTATTAAAAT
1 AATAT-TTATTAAAAT
33550 GTAATAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.13
19 7 0.23
20 20 0.65
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
AATATTTATTAAAATAAAA
Found at i:33536 original size:20 final size:20
Alignment explanation
Indices: 33511--33550 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
33501 TTATTTAATA
*
33511 AAAAATATTTTATTAAAATG
1 AAAAATATGTTATTAAAATG
33531 AAAAATATGTTATTAAAATG
1 AAAAATATGTTATTAAAATG
33551 TAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
AAAAATATGTTATTAAAATG
Found at i:33566 original size:22 final size:20
Alignment explanation
Indices: 33511--33568 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
33501 TTATTTAATA
**
33511 AAAAATATTTTATTAAAATG
1 AAAAATATGATATTAAAATG
*
33531 AAAAATATGTTATTAAAATG
1 AAAAATATGATATTAAAATG
33551 TAATAAATAAT-ATATTAA
1 -AA-AAAT-ATGATATTAA
33569 TGTATAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 19 0.58
21 2 0.06
22 10 0.30
23 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAATATGATATTAAAATG
Found at i:35740 original size:32 final size:32
Alignment explanation
Indices: 35700--35770 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
35690 CATATCACCC
35700 GTTGTTCGTAAATGGTCCGTGCTCAATTTTCT
1 GTTGTTCGTAAATGGTCCGTGCTCAATTTTCT
*
35732 GTTGTTCGTAAATGGTCCGTGCTCGATTTTCT
1 GTTGTTCGTAAATGGTCCGTGCTCAATTTTCT
*
35764 GTGGTTC
1 GTTGTTC
35771 TTAACGGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.13, C:0.18, G:0.25, T:0.44
Consensus pattern (32 bp):
GTTGTTCGTAAATGGTCCGTGCTCAATTTTCT
Found at i:44138 original size:44 final size:44
Alignment explanation
Indices: 44088--44176 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
44078 AACTTTCCAG
44088 GTGTTCTAGTTAAAGGTCAGAGTGAAGTTCCGAGTATGAAAGGA
1 GTGTTCTAGTTAAAGGTCAGAGTGAAGTTCCGAGTATGAAAGGA
44132 GTGTTCTAGTTAAAGGTCAGAGTGAAGTTCCGAGTATGAAAGGA
1 GTGTTCTAGTTAAAGGTCAGAGTGAAGTTCCGAGTATGAAAGGA
44176 G
1 G
44177 AAATACATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.09, G:0.33, T:0.27
Consensus pattern (44 bp):
GTGTTCTAGTTAAAGGTCAGAGTGAAGTTCCGAGTATGAAAGGA
Found at i:44302 original size:2 final size:2
Alignment explanation
Indices: 44295--44324 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44285 GCTTAAACTT
44295 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
44325 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:48295 original size:20 final size:21
Alignment explanation
Indices: 48266--48319 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
48256 AAATTAAGGC
*
48266 AGTATTGATACT-CTAGTA-TG
1 AGTATCGATACTAC-AGTATTG
*
48286 AGTATCGATACTACGGTATTG
1 AGTATCGATACTACAGTATTG
48307 AGGTATCGATACT
1 A-GTATCGATACT
48320 TGACTAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 4 0.14
22 11 0.38
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (21 bp):
AGTATCGATACTACAGTATTG
Found at i:48439 original size:21 final size:21
Alignment explanation
Indices: 48391--48444 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
48381 CCCCTATGAG
**
48391 GAGTATCGATACTCATGCTTT
1 GAGTATCGATACTCATGCAAT
48412 G-GTATCGATACTCAATG-AAT
1 GAGTATCGATACTC-ATGCAAT
48432 GAGTATCGATACT
1 GAGTATCGATACT
48445 ACCCTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (21 bp):
GAGTATCGATACTCATGCAAT
Found at i:53398 original size:24 final size:24
Alignment explanation
Indices: 53328--53398 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
53318 AAATCTTATA
*
53328 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* * *
53351 CGGCACTTTGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
53375 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
53399 AGATGTGGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 11 0.28
24 28 0.72
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:54075 original size:12 final size:12
Alignment explanation
Indices: 54058--54101 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
54048 AGAATTTTCC
**
54058 ACTGTTCATTGT
1 ACTGTTCACGGT
54070 ACTGTTCACGGT
1 ACTGTTCACGGT
54082 ACTGTTCACGGT
1 ACTGTTCACGGT
*
54094 ATTGTTCA
1 ACTGTTCA
54102 TACCATATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (12 bp):
ACTGTTCACGGT
Found at i:62186 original size:19 final size:17
Alignment explanation
Indices: 62162--62218 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 17
62152 CCGAAACTGG
62162 TTTTTTCGGTTCGGTTCAT
1 TTTTTTCGGTTCGGTT--T
*
62181 TTTTTTAACGGTTCGATTT
1 TTTTTT--CGGTTCGGTTT
62200 TTTTGATTCGGTTCGGTTT
1 TTTT--TTCGGTTCGGTTT
62219 ATCGGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 21 0.66
21 11 0.34
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (17 bp):
TTTTTTCGGTTCGGTTT
Done.