Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006601.1 Hibiscus syriacus cultivar Beakdansim tig00016192_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: 44635
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:41 original size:24 final size:23
Alignment explanation
Indices: 8--61 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1 TATTCAA
8 ATTTGATCTTGGTCAATACCCGG
1 ATTTGATCTTGGTCAATACCCGG
* *
31 ACTTTGATCTTGGTTAATACTCGG
1 A-TTTGATCTTGGTCAATACCCGG
55 ATTTGAT
1 ATTTGAT
62 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (23 bp):
ATTTGATCTTGGTCAATACCCGG
Found at i:2300 original size:18 final size:18
Alignment explanation
Indices: 2277--2312 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2267 AAGCAAAAGG
*
2277 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
2295 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
2313 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2603 original size:20 final size:20
Alignment explanation
Indices: 2578--2675 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 20
2568 ATGTTGCGAT
2578 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
2598 CAACGCGAAA-T--AA-GCG
1 CAACGCGAAAGTCAAATTCG
*** *
2614 TTGCG-GTA-GTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
2632 CAACGAGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
2652 CAACACGAAA-TCAAATTCG
1 CAACGCGAAAGTCAAATTCG
2671 CAACG
1 CAACG
2676 AAATAAGCGT
Statistics
Matches: 59, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
15 3 0.05
16 4 0.07
17 4 0.07
18 4 0.07
19 16 0.27
20 28 0.47
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:2667 original size:19 final size:20
Alignment explanation
Indices: 2621--2676 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2611 GCGTTGCGGT
2621 AGTCAAATTCGCAACGAGAA
1 AGTCAAATTCGCAACGAGAA
2641 AGTCAAATTCGCAAC-ACGAA
1 AGTCAAATTCGCAACGA-GAA
2661 A-TCAAATTCGCAACGA
1 AGTCAAATTCGCAACGA
2677 AATAAGCGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (20 bp):
AGTCAAATTCGCAACGAGAA
Found at i:2728 original size:18 final size:18
Alignment explanation
Indices: 2692--2728 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2682 GCGTTGCGAT
*
2692 AGTCAATTCGAAACGCAA
1 AGTCAATTCGAAACACAA
*
2710 AGTCAATTCGCAACACAA
1 AGTCAATTCGAAACACAA
2728 A
1 A
2729 TAAGCGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (18 bp):
AGTCAATTCGAAACACAA
Found at i:2767 original size:20 final size:20
Alignment explanation
Indices: 2732--2792 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
2722 ACACAAATAA
2732 GCGTTGCGAA-TTGACTATC
1 GCGTTGCGAATTTGACTATC
* *
2751 GCGTAGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
*
2771 GCGTTGCAAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
2791 GC
1 GC
2793 AACGCTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 9 0.25
20 27 0.75
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:3696 original size:39 final size:39
Alignment explanation
Indices: 3653--3739 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
3643 TCCGATGCTC
3653 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
3692 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
3731 ATCAAAATC
1 ATCAAAATC
3740 TACACTTGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:3933 original size:20 final size:20
Alignment explanation
Indices: 3908--3984 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
3898 ATGTTGCGAT
3908 CAATGCGAAAGTCAAATTCG
1 CAATGCGAAAGTCAAATTCG
*
3928 CAATGC-AAAAT--AA---G
1 CAATGCGAAAGTCAAATTCG
**
3942 CGTTGCGAAAGTCAAATTCG
1 CAATGCGAAAGTCAAATTCG
3962 CAAAT-CGAAAGTCAAATTCG
1 C-AATGCGAAAGTCAAATTCG
3982 CAA
1 CAA
3985 ACCGAAAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
14 5 0.11
15 4 0.09
17 4 0.09
19 6 0.14
20 24 0.55
21 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.19
Consensus pattern (20 bp):
CAATGCGAAAGTCAAATTCG
Found at i:3985 original size:20 final size:20
Alignment explanation
Indices: 3947--3991 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3937 ATAAGCGTTG
*
3947 CGAAAGTCAAATTCGCAAAT
1 CGAAAGTCAAATTCGCAAAC
3967 CGAAAGTCAAATTCGCAAAC
1 CGAAAGTCAAATTCGCAAAC
3987 CGAAA
1 CGAAA
3992 ATCGCGTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.16
Consensus pattern (20 bp):
CGAAAGTCAAATTCGCAAAC
Found at i:5655 original size:42 final size:42
Alignment explanation
Indices: 5577--5676 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
5567 GGCGAGACCA
* * * * * *
5577 CTTGAACGATGACAGGGGCCTCTTGAATGGTGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
*
5619 CTTCG-ATGATGATAGGGGCCTCTTGAACGATAGGAGGTGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
5661 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
5677 TGCATCGGGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 47 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
Found at i:5679 original size:21 final size:21
Alignment explanation
Indices: 5577--5672 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
5567 GGCGAGACCA
* *
5577 CTTGAACGATGACAGGGGCCT
1 CTTGAATGATGAGAGGGGCCT
* * *
5598 CTTGAATGGTGGGAGGGGCTT
1 CTTGAATGATGAGAGGGGCCT
*
5619 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAATGATGAGAGGGGCCT
* *
5640 CTTGAACGAT-AGGAGGTGCCT
1 CTTGAATGATGA-GAGGGGCCT
5661 CTTGAATGATGA
1 CTTGAATGATGA
5673 TAGGTGCATC
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (21 bp):
CTTGAATGATGAGAGGGGCCT
Found at i:7936 original size:11 final size:12
Alignment explanation
Indices: 7908--7941 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
7898 TTTCTTCGAT
7908 AAAAGACAAAACA
1 AAAAGAC-AAACA
7921 AAAAGACAAA-A
1 AAAAGACAAACA
7932 AAAAGACAAA
1 AAAAGACAAA
7942 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 3 0.14
13 7 0.33
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAACA
Found at i:8177 original size:22 final size:22
Alignment explanation
Indices: 8149--8199 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
8139 GATGGAGATA
8149 GACGGATTTCGTCGAAAATGGG
1 GACGGATTTCGTCGAAAATGGG
* *
8171 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGAAAATGGG
8193 GACGGAT
1 GACGGAT
8200 GTCACCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGAAAATGGG
Found at i:8352 original size:20 final size:20
Alignment explanation
Indices: 8327--8430 Score: 108
Period size: 20 Copynumber: 5.2 Consensus size: 20
8317 GCGTAAAAAC
8327 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
8347 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
*
8366 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
8387 ATTTGACTTTCGCG-TGCGA
1 ATTTGACTTTCGCGTTGCGA
* * *
8406 ATTTTACTTTCGAGTTCCGA
1 ATTTGACTTTCGCGTTGCGA
8426 ATTTG
1 ATTTG
8431 GAAAATCGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.03
19 24 0.34
20 35 0.50
21 7 0.10
22 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:8446 original size:60 final size:60
Alignment explanation
Indices: 8327--8446 Score: 136
Period size: 60 Copynumber: 2.0 Consensus size: 60
8317 GCGTAAAAAC
* * * **
8327 ATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGAATTTGACTTCTGAGTTCCGATTTACAAAATCGCAATGCGA
* **
8387 ATTTGACTTTCGCG-TGCGAATTTTACTT-TCGAGTTCCGAATTTGGAAAATCGCAATGCGA
1 ATTTGACTTTCGCGTTGCGAATTTGACTTCT-GAGTTCCG-ATTTACAAAATCGCAATGCGA
8447 TTTACATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.02
59 19 0.38
60 30 0.60
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (60 bp):
ATTTGACTTTCGCGTTGCGAATTTGACTTCTGAGTTCCGATTTACAAAATCGCAATGCGA
Found at i:8503 original size:20 final size:20
Alignment explanation
Indices: 8460--8507 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
8450 ACATATTAGT
*
8460 GTTGCGAAATTGGAAACTGG
1 GTTGCGAAATTGGAAACTGC
*
8480 GTTGCGAAATTGG-AATTCGC
1 GTTGCGAAATTGGAAACT-GC
8500 GTTGCGAA
1 GTTGCGAA
8508 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (20 bp):
GTTGCGAAATTGGAAACTGC
Found at i:10082 original size:19 final size:19
Alignment explanation
Indices: 10058--10101 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
10048 TATTTGAATT
* *
10058 TTATAATTTATTTTTGAAA
1 TTATAATATATTTTTCAAA
10077 TTATAAATATATTTTTCAAA
1 TTAT-AATATATTTTTCAAA
10097 TTATA
1 TTATA
10102 CTTAAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATAATATATTTTTCAAA
Found at i:12258 original size:2 final size:2
Alignment explanation
Indices: 12243--12453 Score: 98
Period size: 2 Copynumber: 115.0 Consensus size: 2
12233 TCGTCTGGGG
*
12243 AT AT AT -T AT A- AT AT AT AT AT AT -T A- AT -T AT GT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12279 AGT TT AT -T AT ACT AT AT AGT AT AT AT -T AT -T AT AT AT AT -T
1 A-T AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
12318 AT AT AGT -T AT AT AT -T AT AT AT -T AT -T AT -T AT -T AT -T AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
12354 -T AT -T AT -T TT CT A- AT AT AT AT -T TT AT AT AT AT -T AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
12391 AT AT AT TT AT CAT AT AGT AT AT AT AT AT AT AT AT -T AT CAT AT
1 AT AT AT AT AT -AT AT A-T AT AT AT AT AT AT AT AT AT AT -AT AT
*
12433 AT -T AT AT -T AT TT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
12454 TATTATTTTT
Statistics
Matches: 164, Mismatches: 10, Indels: 70
0.67 0.04 0.29
Matches are distributed among these distances:
1 27 0.16
2 123 0.75
3 14 0.09
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (2 bp):
AT
Found at i:12301 original size:7 final size:7
Alignment explanation
Indices: 12286--12493 Score: 141
Period size: 7 Copynumber: 31.4 Consensus size: 7
12276 TATAGTTTAT
*
12286 TATACTA
1 TATATTA
*
12293 TATAGTA
1 TATATTA
12300 TATATTA
1 TATATTA
12307 T-TA-TA
1 TATATTA
12312 TATATTA
1 TATATTA
12319 TATAGTTA
1 TATA-TTA
12327 TATATTA
1 TATATTA
12334 TATATTA
1 TATATTA
12341 T-TATTA
1 TATATTA
12347 T-TATTA
1 TATATTA
12353 T-TATTA
1 TATATTA
*
12359 T-T-TTC
1 TATATTA
12364 TA-A-TA
1 TATATTA
12369 TATATT-
1 TATATTA
12375 T-TA-TA
1 TATATTA
12380 TATATTA
1 TATATTA
12387 TAGTA-TA
1 TA-TATTA
12394 TAT-TTA
1 TATATTA
12400 TCATA-TA
1 T-ATATTA
12407 GTATA-TA
1 -TATATTA
12414 TATA-TA
1 TATATTA
12420 TATATTA
1 TATATTA
12427 TCATA-TA
1 T-ATATTA
12434 TTATATTA
1 -TATATTA
*
12442 TTTATTA
1 TATATTA
12449 TATATTA
1 TATATTA
*
12456 T-TATTTT
1 TATA-TTA
12463 TATATTA
1 TATATTA
*
12470 TCTATGTA
1 TATAT-TA
12478 T-TATTA
1 TATATTA
*
12484 TTTATTA
1 TATATTA
12491 TAT
1 TAT
12494 TTTTATTATT
Statistics
Matches: 168, Mismatches: 10, Indels: 46
0.75 0.04 0.21
Matches are distributed among these distances:
4 1 0.01
5 12 0.07
6 46 0.27
7 88 0.52
8 21 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (7 bp):
TATATTA
Found at i:12310 original size:3 final size:3
Alignment explanation
Indices: 12302--12510 Score: 101
Period size: 3 Copynumber: 65.3 Consensus size: 3
12292 ATATAGTATA
12302 TAT TAT TA- TAT ATAT TAT ATAGT TAT ATAT TAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT -TA-T TAT -TAT TAT -TAT TAT TAT TAT
* * *
12348 TAT TAT TAT TAT TTT CTAA TAT ATAT T-T TA- TAT ATAT TA- TAG TAT
1 TAT TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT
* * *
12393 ATATT TAT CAT ATAG TA- TAT ATAT ATAT ATAT TAT CAT ATAT TA- TAT
1 -TA-T TAT TAT -TAT TAT TAT -TAT -TAT -TAT TAT TAT -TAT TAT TAT
*
12440 TATT TAT TAT ATAT TAT TAT TTT TA- TAT TAT CTAT GTAT TAT TATT
1 TA-T TAT TAT -TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TA-T
*
12486 TAT TA- TAT TTT TAT TAT TAT CTAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT T
12511 TATTTATTTA
Statistics
Matches: 165, Mismatches: 15, Indels: 52
0.71 0.06 0.22
Matches are distributed among these distances:
2 16 0.10
3 91 0.55
4 56 0.34
5 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:12381 original size:120 final size:113
Alignment explanation
Indices: 12256--12470 Score: 283
Period size: 115 Copynumber: 1.8 Consensus size: 113
12246 TATTATAATA
12256 TATATATATTAATTATGTTATATAGTTTAT-TATACTATATAGTATATAT-TATTAT-ATATATT
1 TATATATATT-A-TA-G-TATATA-TTTATATATACTATATA-TATATATATATTATCATATA-T
12318 ATATAGTTATATATTATATATTATTATTATTATTATTATTATTTTCTAATATATATTT
59 -TATA-TTATATATTATATATTATTATTATTA-TATTATTATTTTCTAATATATATTT
*
12376 TATATATATTATAGTATATATTTATCATATAGTATATATATATATATATTATCATATATTATATT
1 TATATATATTATAGTATATATTTAT-ATATACTATATATATATATATATTATCATATATTATATT
* *
12441 ATTTATTATATATTATTATTTTTATATTAT
65 ATATATTATATATTATTATTATTATATTAT
12471 CTATGTATTA
Statistics
Matches: 88, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
114 6 0.07
115 29 0.33
116 17 0.19
117 18 0.20
118 7 0.08
119 1 0.01
120 10 0.11
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (113 bp):
TATATATATTATAGTATATATTTATATATACTATATATATATATATATTATCATATATTATATTA
TATATTATATATTATTATTATTATATTATTATTTTCTAATATATATTT
Found at i:12406 original size:27 final size:28
Alignment explanation
Indices: 12300--12456 Score: 120
Period size: 27 Copynumber: 5.8 Consensus size: 28
12290 CTATATAGTA
12300 TATATTAT-TATATATATTAT-ATAGTTA-
1 TATATTATATATATATATTATCATA--TAG
* *
12327 TATATTATATAT-TATTATTATTAT-TAT
1 TATATTATATATATA-TATTATCATATAG
* *
12354 TATTATTTTCTAATATATATT-T--TATA-
1 TA-TATTATAT-ATATATATTATCATATAG
12380 TATATTATAGTATATAT-TTATCATATAG
1 TATATTATA-TATATATATTATCATATAG
*
12408 TATA-TATATATATATATTATCATATAT
1 TATATTATATATATATATTATCATATAG
*
12435 TATATTATTTATTATATATTAT
1 TATATTATATA-TATATATTAT
12457 TATTTTTATA
Statistics
Matches: 108, Mismatches: 6, Indels: 30
0.75 0.04 0.21
Matches are distributed among these distances:
24 2 0.02
25 12 0.11
26 13 0.12
27 36 0.33
28 25 0.23
29 18 0.17
30 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
TATATTATATATATATATTATCATATAG
Found at i:12482 original size:14 final size:13
Alignment explanation
Indices: 12243--12510 Score: 146
Period size: 14 Copynumber: 19.5 Consensus size: 13
12233 TCGTCTGGGG
12243 ATATATTATAATATAT
1 ATATATTAT--TAT-T
12259 ATATATTAATTATGTT
1 ATATATT-ATTA--TT
*
12275 ATATAGT-TTATT
1 ATATATTATTATT
*
12287 ATACTA-TA-TAGT
1 ATA-TATTATTATT
12299 ATATATTATTA-T
1 ATATATTATTATT
12311 ATATATTATATAGTT
1 ATATATTAT-TA-TT
12326 ATATATTATATATT
1 ATATATTAT-TATT
12340 AT-TATTATTATT
1 ATATATTATTATT
12352 AT-TATTATT-TT
1 ATATATTATTATT
*
12363 CTAATATATATT-TT
1 AT-ATAT-TATTATT
12377 ATATA-TATTA-T
1 ATATATTATTATT
*
12388 AGTATA-TATTTATC
1 A-TATATTA-TTATT
12402 ATATAGTATATATATAT
1 ATATA-T-TAT-TAT-T
*
12419 ATATATTATCATAT
1 ATATATTATTAT-T
12433 ATTATATTATTTATT
1 A-TATATTA-TTATT
12448 ATATATTATTATTT
1 ATATATTATTA-TT
*
12462 TTATATTATCTATGT
1 ATATATTAT-TAT-T
12477 AT-TATTATTTATT
1 ATATATTA-TTATT
*
12490 ATATTTTTATTATT
1 ATA-TATTATTATT
*
12504 ATCTATT
1 ATATATT
12511 TATTTATTTA
Statistics
Matches: 209, Mismatches: 13, Indels: 63
0.73 0.05 0.22
Matches are distributed among these distances:
11 11 0.05
12 43 0.21
13 34 0.16
14 53 0.25
15 37 0.18
16 23 0.11
17 8 0.04
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (13 bp):
ATATATTATTATT
Found at i:12482 original size:35 final size:34
Alignment explanation
Indices: 12243--12510 Score: 150
Period size: 35 Copynumber: 7.8 Consensus size: 34
12233 TCGTCTGGGG
* * *
12243 ATATATTATAATATATATA-TAT-TAATTA-TGTT
1 ATATATTATTATTTATATATTATCT-ATTATTATT
* * *
12275 ATATAGTTTATTATACTATATAGTATATATTATTA-T
1 ATATA--TTATTAT-TTATATATTATCTATTATTATT
* *
12311 ATATATTATATAGTTATATATTATATATTATTATT
1 ATATATTAT-TATTTATATATTATCTATTATTATT
* * *
12346 ATTATTATTATTATTT-TCTAATATATATT-TTA-T
1 A-TA-TATTATTATTTATATATTATCTATTATTATT
*
12379 ATATATTA-TA-GTATATATTTATC-ATATAGTATATAT
1 ATATATTATTATTTATATA-TTATCTAT-TA-T-TAT-T
*
12415 ATATATATATTA-TCATATATTA--TATTATTTATT
1 ATATAT-TATTATTTATATATTATCTATTA-TTATT
*
12448 ATATATTATTATTTTTATATTATCTATGTATTATT
1 ATATATTATTATTTATATATTATCTAT-TATTATT
* *
12483 ATTTATTA-TATTTTTATTATTATCTATT
1 ATATATTATTATTTATA-TATTATCTATT
12511 TATTTATTTA
Statistics
Matches: 191, Mismatches: 19, Indels: 50
0.73 0.07 0.19
Matches are distributed among these distances:
29 1 0.01
30 7 0.04
31 9 0.05
32 12 0.06
33 18 0.09
34 45 0.24
35 49 0.26
36 30 0.16
37 13 0.07
38 7 0.04
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (34 bp):
ATATATTATTATTTATATATTATCTATTATTATT
Found at i:13683 original size:13 final size:13
Alignment explanation
Indices: 13665--13712 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
13655 TTTATGAATA
*
13665 GTGAACAGTATCC
1 GTGAACAGTAACC
*
13678 GTGAACAGTAACA
1 GTGAACAGTAACC
*
13691 GTGAACAGTACCC
1 GTGAACAGTAACC
13704 GTGAACAGT
1 GTGAACAGT
13713 GGGGGAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (13 bp):
GTGAACAGTAACC
Found at i:14242 original size:45 final size:47
Alignment explanation
Indices: 14193--14281 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
14183 CATAAAATCT
* * *
14193 CTTACCATTT-ATCCCATAATCTTGTAGGCTTA-TTTTACCAAAATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTTACCAAAATA
*
14238 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTACCAA
1 CTTACCATTT-AATCCCATAAGCTCGTAAGCTTATTTTTACCAA
14282 TACACTTGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 10 0.27
47 18 0.49
48 9 0.24
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (47 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTTACCAAAATA
Found at i:16419 original size:46 final size:46
Alignment explanation
Indices: 16350--16671 Score: 430
Period size: 46 Copynumber: 7.0 Consensus size: 46
16340 AAATGAATGA
* *
16350 ATAAATGAAAATGTATAACGGTGCATTATCGGCATGAAACGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
16396 ATAAATGAAAATGCATAAAGGTGCATTATTGGCATAAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
16442 ATAAATGAAATTGTATAATGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
16488 ATAAAAGAAAATGCATAACAGTGCATTATCAGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
16534 ATAAACGAAAATGCATAACGATGCATTATAGGCATGAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
16580 ATAAATGAAAATGCATAACGGTGAATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * * *
16626 ACAAATGAAAATGCATAACAGTGTATTAACGACATAAAAGG-TGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
16671 A
1 A
16672 CTCATTGTAT
Statistics
Matches: 243, Mismatches: 33, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
45 5 0.02
46 238 0.98
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:18091 original size:32 final size:31
Alignment explanation
Indices: 18016--18114 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 31
18006 TTTATTATTA
*
18016 TTTTTCTATTTATATTTTTTATTTTTAACATG
1 TTTTTCTATTT-TATTTTTTATTTTAAACATG
* *
18048 TTCTTCAATTTT-TTATTATTATTGTTAAACAT-
1 TTTTTCTATTTTATT-TT-TTATT-TTAAACATG
* * *
18080 TTTTTCTATTTTATTTTCTCTTTT-AACATT
1 TTTTTCTATTTTATTTTTTATTTTAAACATG
18110 TTTTT
1 TTTTT
18115 GTTATTTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
29 5 0.09
30 9 0.16
31 6 0.11
32 26 0.47
33 9 0.16
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (31 bp):
TTTTTCTATTTTATTTTTTATTTTAAACATG
Found at i:28474 original size:23 final size:22
Alignment explanation
Indices: 28447--28576 Score: 98
Period size: 23 Copynumber: 6.0 Consensus size: 22
28437 AATGAATCAT
28447 TTATATATATATTATATTTATTA
1 TTATATATATATTATATTTA-TA
* *
28470 TTATA-ATTATATTTTATATATA
1 TTATATA-TATATTATATTTATA
28492 TTATAGTATATATT-TA-TTATA
1 TTATA-TATATATTATATTTATA
*
28513 -TAGAATATATATTATATCATT-TA
1 TTA-TATATATATTATAT--TTATA
28536 TTATATAT-TATT-T-TTTATA
1 TTATATATATATTATATTTATA
28555 TTATATA-AGTATTATTATTTAT
1 TTATATATA-TATTA-TATTTAT
28577 TATAGTTTTA
Statistics
Matches: 87, Mismatches: 5, Indels: 30
0.71 0.04 0.25
Matches are distributed among these distances:
18 2 0.02
19 9 0.10
20 15 0.17
21 8 0.09
22 15 0.17
23 33 0.38
24 5 0.06
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATATATATATTATATTTATA
Found at i:28506 original size:41 final size:42
Alignment explanation
Indices: 28448--28555 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 42
28438 ATGAATCATT
* *
28448 TATATA-TATAT-TATATTTATTAT-TATAAT-TATATTTTA
1 TATATATTATATATATATTTATTATATAGAATATATATTATA
28486 TATATATTATAGTATATATTTATTATATAGAATATATATTATA
1 TATATATTATA-TATATATTTATTATATAGAATATATATTATA
* *
28529 TCATTTATTATATAT-TATTTTTTATAT
1 T-ATATATTATATATATATTTATTATAT
28556 TATATAAGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
38 6 0.10
39 4 0.07
40 1 0.02
41 12 0.20
42 16 0.27
43 12 0.20
44 9 0.15
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (42 bp):
TATATATTATATATATATTTATTATATAGAATATATATTATA
Found at i:28511 original size:25 final size:24
Alignment explanation
Indices: 28447--28543 Score: 87
Period size: 28 Copynumber: 4.0 Consensus size: 24
28437 AATGAATCAT
28447 TTATATATATATTATATT-TAT-TA
1 TTATATATATATT-TATTATATATA
28470 TTATA-AT-TATATT-TTATATATA
1 TTATATATATAT-TTATTATATATA
*
28492 TTATAGTATATATTTATTATATAGAA
1 TTATA-TATATATTTATTATATA-TA
28518 TATATATTATATCATTTATTATATAT
1 T-TATA-TATAT-ATTTATTATATAT
28544 TATTTTTTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
20 2 0.03
21 7 0.11
22 10 0.16
23 5 0.08
24 4 0.07
25 10 0.16
26 2 0.03
27 9 0.15
28 12 0.20
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATATATATTTATTATATATA
Found at i:28528 original size:7 final size:7
Alignment explanation
Indices: 28448--28598 Score: 78
Period size: 7 Copynumber: 22.9 Consensus size: 7
28438 ATGAATCATT
28448 TATA-TA
1 TATATTA
28454 TATATTA
1 TATATTA
28461 TAT-TTA
1 TATATTA
28467 T-TATTA
1 TATATTA
28473 TA-ATTA
1 TATATTA
*
28479 TATTTTA
1 TATATTA
28486 TATA-TA
1 TATATTA
*
28492 TTATAGTA
1 -TATATTA
28500 TATATT-
1 TATATTA
28506 TAT-TATA
1 TATAT-TA
* *
28513 TAGAATA
1 TATATTA
28520 TATATTA
1 TATATTA
28527 TATCA-T-
1 TAT-ATTA
28533 T-TATTA
1 TATATTA
28539 TATATTA
1 TATATTA
*
28546 T-T-TTT
1 TATATTA
28551 TATATTA
1 TATATTA
*
28558 TATAAGTA
1 TAT-ATTA
28566 T-TATTA
1 TATATTA
*
28572 TTTATTA
1 TATATTA
*
28579 TAGTTTTA
1 TA-TATTA
28587 T-TATTA
1 TATATTA
*
28593 TTTATT
1 TATATT
28599 TATTTATTTT
Statistics
Matches: 112, Mismatches: 14, Indels: 37
0.69 0.09 0.23
Matches are distributed among these distances:
4 1 0.01
5 7 0.06
6 37 0.33
7 55 0.49
8 12 0.11
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.60
Consensus pattern (7 bp):
TATATTA
Found at i:28570 original size:33 final size:32
Alignment explanation
Indices: 28520--28610 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 32
28510 ATATAGAATA
* *
28520 TATATTATATCATTTATTATATATTAT-TTTT
1 TATATTATATAATTTATTATATATTATAGTTT
*
28551 TATATTATATAAGTATTATTATTTATTATAGTTT
1 TATATTATATAA-T-TTATTATATATTATAGTTT
* *
28585 TATTATTAT-TTATTTATT-TATTTTAT
1 TA-TATTATATAATTTATTATATATTAT
28611 TTTTAATAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
31 17 0.34
32 6 0.12
33 14 0.28
34 7 0.14
35 6 0.12
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (32 bp):
TATATTATATAATTTATTATATATTATAGTTT
Found at i:28581 original size:66 final size:65
Alignment explanation
Indices: 28451--28614 Score: 169
Period size: 66 Copynumber: 2.5 Consensus size: 65
28441 AATCATTTAT
* *
28451 ATATATATTATATTTATTATTATA-ATTATATTTTATATATATTATAGTATATATTTATTATATA
1 ATATATATTATATAT-TTATTATATATTATTTTTTATATATATTATAGTATATATTTATTATATA
28515 G
65 G
28516 AATATATATTATATCATTTATTATATATTATTTTTTATAT-TA-TATAAGTAT-TA-TTATTTAT
1 -ATATATATTATAT-ATTTATTATATATTATTTTTTATATATATTAT-AGTATATATTTA-TTA-
28577 TATAG
61 TATAG
* * * *
28582 TTTTATTATTATTTATTTATT-TATTTTATTTTT
1 ATATA-TATTATATATTTATTATATATTATTTTT
28615 AATAGGTCCA
Statistics
Matches: 86, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
64 14 0.16
65 18 0.21
66 40 0.47
67 14 0.16
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (65 bp):
ATATATATTATATATTTATTATATATTATTTTTTATATATATTATAGTATATATTTATTATATAG
Found at i:28600 original size:14 final size:14
Alignment explanation
Indices: 28445--28612 Score: 61
Period size: 14 Copynumber: 12.0 Consensus size: 14
28435 CGAATGAATC
28445 ATTTATATATATATTAT
1 ATTTAT-TAT-TATT-T
*
28462 ATTTATTATTA-TA
1 ATTTATTATTATTT
*
28475 ATTATATT-TTATAT
1 ATT-TATTATTATTT
* *
28489 ATATTA-TAGTATAT
1 AT-TTATTATTATTT
**
28503 ATTTATTATATAGAAT
1 ATTTATTAT-TA-TTT
*
28519 ATATATTATATCATTT
1 ATTTATTAT-T-ATTT
28535 A-TTATATATTATTT
1 ATTTAT-TATTATTT
*
28549 -TTTA-TATTATAT
1 ATTTATTATTATTT
**
28561 AAGTATTATTATTT
1 ATTTATTATTATTT
*
28575 A-TTA-TAGT-TTT
1 ATTTATTATTATTT
28586 A-TTATTATTTATTT
1 ATTTATTA-TTATTT
28600 ATTTATT-TTATTT
1 ATTTATTATTATTT
28613 TTAATAGGTC
Statistics
Matches: 118, Mismatches: 17, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
11 7 0.06
12 12 0.10
13 21 0.18
14 37 0.31
15 14 0.12
16 20 0.17
17 7 0.06
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (14 bp):
ATTTATTATTATTT
Found at i:28604 original size:18 final size:20
Alignment explanation
Indices: 28564--28612 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
28554 ATTATATAAG
28564 TATTATTATTTATTATAGTTT
1 TATTATTATTTATTATAG-TT
28585 TATTATTATTTATT-TA-TT
1 TATTATTATTTATTATAGTT
28603 TATT-TTATTT
1 TATTATTATTT
28613 TTAATAGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
20 2 0.07
21 14 0.50
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTATTATTTATTATAGTT
Found at i:29749 original size:18 final size:18
Alignment explanation
Indices: 29715--29759 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
29705 AATTTGATCC
29715 TTTATTATTTTTATTTCTT
1 TTTATT-TTTTTATTTCTT
29734 TTTATTTTTTGT-TTTCTT
1 TTTATTTTTT-TATTTCTT
*
29752 TTAATTTT
1 TTTATTTT
29760 AACATGTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTATTTTTTTATTTCTT
Found at i:36097 original size:22 final size:22
Alignment explanation
Indices: 36040--36105 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
36030 CTGAATAGAG
*
36040 ATTTAAATTAATGGAATT--AA
1 ATTTAAATTAATTGAATTGAAA
*
36060 A-TAAAGATCTAATTGAATTGAAA
1 ATTTAA-AT-TAATTGAATTGAAA
36083 ATTTAAATTAATTGAATTGAAA
1 ATTTAAATTAATTGAATTGAAA
36105 A
1 A
36106 AAAAAGACCC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 9 0.24
22 15 0.39
23 5 0.13
24 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (22 bp):
ATTTAAATTAATTGAATTGAAA
Found at i:37976 original size:41 final size:41
Alignment explanation
Indices: 37826--38035 Score: 142
Period size: 41 Copynumber: 5.1 Consensus size: 41
37816 ATTGAATCAG
* * * * *
37826 ATTGTGAATTAATACATGTTACCATGATCTAATTGAATTGG
1 ATTGTGAATTATTGCATGCTGCCATGATCTAATTGAATTGA
* * * * *
37867 TTTGTGAATAAATT-CATGTTTCCATGA-CTGAATTAAATTGAA
1 ATTGTGAAT-TATTGCATGCTGCCATGATCT-AATTGAATTG-A
** * **
37909 ATTAAGGATTATTGCATGCTTACATGATCTAATT-AAGTTGA
1 ATTGTGAATTATTGCATGCTGCCATGATCTAATTGAA-TTGA
* *
37950 ATTGTGAATTATTGCATGCTGCCATGAAT-GAATTGAATCGA
1 ATTGTGAATTATTGCATGCTGCCATG-ATCTAATTGAATTGA
* * * *
37991 ATGGTGAATTACTGCATGATGCCATGATCGAATTTG-ATTGA
1 ATTGTGAATTATTGCATGCTGCCATGATCTAA-TTGAATTGA
38032 ATTG
1 ATTG
38036 AAATCTTGAA
Statistics
Matches: 134, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
40 4 0.03
41 96 0.72
42 32 0.24
43 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTGTGAATTATTGCATGCTGCCATGATCTAATTGAATTGA
Done.