Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009320.1 Hibiscus syriacus cultivar Beakdansim tig00113079_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: 50238
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1539 original size:26 final size:28
Alignment explanation
Indices: 1500--1575 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 28
1490 ATAGTTATTA
1500 TATTTATATT-AATATAATTATATAA-A-
1 TATTTAT-TTAAATATAATTATATAATAT
* *
1526 TATTTTTTTAAATA-ATATTTTATAATTAT
1 TATTTATTTAAATATA-ATTATATAA-TAT
1555 TATTTATTTAAATATTAATTA
1 TATTTATTTAAATA-TAATTA
1576 ATTAATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
25 3 0.08
26 18 0.46
28 1 0.03
29 13 0.33
30 3 0.08
31 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TATTTATTTAAATATAATTATATAATAT
Found at i:3419 original size:19 final size:20
Alignment explanation
Indices: 3377--3428 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3367 GAAACCCCTT
*
3377 TGAAAATACATGATTTTTTGA
1 TGAAAATACATGA-TTTTTAA
3398 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3417 TGAAGATACATG
1 TGAAAATACATG
3429 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:6783 original size:5 final size:5
Alignment explanation
Indices: 6773--6802 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
6763 TTTGAATTCT
6773 TTTTC TTTTC TTTTC TTTTC TTCTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTT
6803 GATTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:6809 original size:18 final size:16
Alignment explanation
Indices: 6772--6821 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
6762 TTTTGAATTC
6772 TTTTTCTT-TTCTTTT
1 TTTTTCTTCTTCTTTT
*
6787 CTTTTCTTCTTCTTTT
1 TTTTTCTTCTTCTTTT
6803 GATTTTT-TCTCTTCTTTT
1 --TTTTTCT-TCTTCTTTT
6821 T
1 T
6822 GCACTCCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
17 1 0.03
18 13 0.45
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTCTTCTTCTTTT
Found at i:7567 original size:18 final size:19
Alignment explanation
Indices: 7521--7570 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
7511 GAAACCCCTT
*
7521 TGAAAATACATGATTTTTGA
1 TGAAAATACATGA-TTTTAA
7541 TGAAAATACATGA-TTTAA
1 TGAAAATACATGATTTTAA
*
7559 TGAAGATACATG
1 TGAAAATACATG
7571 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:9220 original size:21 final size:21
Alignment explanation
Indices: 9194--9259 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 21
9184 TCATCTCCGA
*
9194 AGGGTTACTTTCCTAGCCCGC
1 AGGGTTACATTCCTAGCCCGC
9215 AGGGTTACATTCCTAGCCCGCC
1 AGGGTTACATTCCTAGCCCG-C
*
9237 A-GGTTACATGCCTAGCCCGC
1 AGGGTTACATTCCTAGCCCGC
9257 AGG
1 AGG
9260 TTTTATACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (21 bp):
AGGGTTACATTCCTAGCCCGC
Found at i:9843 original size:34 final size:33
Alignment explanation
Indices: 9774--9876 Score: 143
Period size: 34 Copynumber: 3.1 Consensus size: 33
9764 TAAATGTTTA
* *
9774 AAAATACAAATTATAGTATTCCAAATTCAAATT
1 AAAATACAAATTATAGTATTCGAAATTTAAATT
* *
9807 AAAATACAAATAATATTATTCGAAATTTAAATTT
1 AAAATACAAATTATAGTATTCGAAATTTAAA-TT
*
9841 AAAATATAAATTATAGTATTCGAAATTTAACATT
1 AAAATACAAATTATAGTATTCGAAATTTAA-ATT
9875 AA
1 AA
9877 TTCAACTTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
33 27 0.44
34 33 0.54
35 1 0.02
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (33 bp):
AAAATACAAATTATAGTATTCGAAATTTAAATT
Found at i:10586 original size:126 final size:127
Alignment explanation
Indices: 10276--10925 Score: 970
Period size: 126 Copynumber: 5.2 Consensus size: 127
10266 ATCTATAGTT
* ** * * *
10276 CCCCGGGAACGCG-CTTTAAAGTCCCCTAAGAAATAGTAGATATTGACATGAATAGTTCTCGGGG
1 CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGG
* *
10340 GACATAAGTGACATAATAGGGAAATGATAACATATTCTCTGACAAAATAATGAAAGGCGCGC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
* * * *
10402 CACCGGGAACGCGTCTTCACGATCTCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGG
1 CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGG
* * *
10467 GACATACGTGACATAATAGGGCAATGATAACATATTCTCTGA-TAAATAATGGAAGGCGTGC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
* * *
10528 CCCCGGGAACGCACCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATAAATAGTTCT-TGGG
1 CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGG
10592 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
* * * ** **
10654 CCCTGGGAACACGCCTTCACAGTCCCCTAAGGAATAATATATATTGACATGAATAGTTC-CAATG
1 CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTC-GGG
* *
10718 GGACATAAGTGACATAATAGGG-AATGATAACAT-TTCTCTGACAAAAAAATGGAAGGCACGC
65 GGACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
* *
10779 CCCCGGGAACGCGCCTTCACGGTCCTCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGG
1 CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGG
*
10844 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
*
10906 CCCCGGGAATGCGCCTTCAC
1 CCCCGGGAACGCGCCTTCAC
10926 ATGAATAGTA
Statistics
Matches: 470, Mismatches: 47, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
125 146 0.31
126 174 0.37
127 150 0.32
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (127 bp):
CCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGG
GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
Found at i:15122 original size:56 final size:56
Alignment explanation
Indices: 15058--15174 Score: 216
Period size: 56 Copynumber: 2.1 Consensus size: 56
15048 AATTGCGGCA
*
15058 ACAGCGAGCGGAACGATACCGGCTTCAGCTTTGGTAGCAGCTGGAGGCTTACTTTC
1 ACAGCGAGCGGAACGATACCGGCTTCAGCTTTGGCAGCAGCTGGAGGCTTACTTTC
15114 ACAGCGAGCGGAACGATACCGGCTTCAGCTTTGGCAGCAGCTGGAGGCTTACTTTC
1 ACAGCGAGCGGAACGATACCGGCTTCAGCTTTGGCAGCAGCTGGAGGCTTACTTTC
*
15170 GCAGC
1 ACAGC
15175 AATAGGCGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.21
Consensus pattern (56 bp):
ACAGCGAGCGGAACGATACCGGCTTCAGCTTTGGCAGCAGCTGGAGGCTTACTTTC
Found at i:17997 original size:23 final size:24
Alignment explanation
Indices: 17970--18026 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
17960 TATTAAATAC
*
17970 AATAACATATTAGGTACCGCTTAT
1 AATAAAATATTAGGTACCGCTTAT
** * *
17994 -ATAATGTAATAGGTAGCGCTTAT
1 AATAAAATATTAGGTACCGCTTAT
18017 AATAAAATAT
1 AATAAAATAT
18027 GTTAATTACT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (24 bp):
AATAAAATATTAGGTACCGCTTAT
Found at i:18124 original size:23 final size:23
Alignment explanation
Indices: 18065--18127 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
18055 AATATTATAT
* *
18065 TAGGTACCACTTATATAATGTAA
1 TAGGTAGCACTTATATAACGTAA
*
18088 TAGGTTGCACTTATATAACGTAA
1 TAGGTAGCACTTATATAACGTAA
**
18111 TAGGTAGCTTTTATATA
1 TAGGTAGCACTTATATA
18128 TTAAATATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (23 bp):
TAGGTAGCACTTATATAACGTAA
Found at i:18712 original size:111 final size:111
Alignment explanation
Indices: 18518--18987 Score: 674
Period size: 111 Copynumber: 4.2 Consensus size: 111
18508 TAGTGCTTAT
* * * *
18518 AAAGTATCGATAC-TTTATAAAAATG-TATCGATATTTTACAATGTAACAGGTAAAAATATGACA
1 AAAGTATCGATCCTTTTATAAAAAGGATAT--ATACTTTACAATATAACAGGTAAAAATATGACA
* * * * *
18581 AAACCAATTTCATAATGACAAAACCGGTAAAATTTACTTGATATGTTG
64 AAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
* *
18629 AAAGTATCTATCCTTTTATAAAAAGGATATATACTTTACAATATAACAGGTAAAAATATGAAAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATATATACTTTACAATATAACAGGTAAAAATATGACAAA
** * *
18694 ATTAGTTTCATTATGACAAAAACGGTAAAATTTATCTGATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
* *
18740 AAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAACTATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATATATACTTTACAATATAACAGGTAAAAATATGACAAA
* *
18805 ATCAGTTTCATTATGACAAAAATGGTAAAATTTACCTAATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
**
18851 AAAGTATCGATCCTTTTATAAAAAATATATATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATATATACTTTACAATATAACAGGTAAAAATATGACAAA
*
18916 ACCAGTTTCATTATGACAAAACCGGTAAAATTTACCTAATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
** *
18962 AAAGTATAAATACTTTTTATAAAAAG
1 AAAGTATCGAT-CCTTTTATAAAAAG
18988 AATCGATCTT
Statistics
Matches: 324, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
111 298 0.92
112 23 0.07
113 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (111 bp):
AAAGTATCGATCCTTTTATAAAAAGGATATATACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTAATATGTTG
Found at i:19446 original size:18 final size:19
Alignment explanation
Indices: 19423--19462 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
19413 TAATAGTGCC
19423 TATAAAA-TATCGATACTT
1 TATAAAAGTATCGATACTT
*
19441 TATAAAATGTATCGATATTT
1 TATAAAA-GTATCGATACTT
19461 TA
1 TA
19463 CAATATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (19 bp):
TATAAAAGTATCGATACTT
Found at i:19629 original size:111 final size:111
Alignment explanation
Indices: 19430--19789 Score: 542
Period size: 111 Copynumber: 3.2 Consensus size: 111
19420 GCCTATAAAA
* * *
19430 TATCGATAC-TTTATAAAATGTATCGATATTTTACAATATAACAGGTAAAAAATATGACAAAATC
1 TATCGATCCTTTTATAAAAAGGATCGATATTTTACAATATAACAGGT-AAAAATATGACAAAATC
* *
19494 AGTTTCATTATGACAAAAATGGTAAAATTTACCTGATATGTTGAAAT
65 AGTTTCATTATGACAAAAAAGGTAAAATTTACCTGATATGTTGAAAG
*
19541 TATCGATCCTTTTATAAAAAGGATAGATATTTTACAATATAACAGGTAAAAATATGACAAAATCA
1 TATCGATCCTTTTATAAAAAGGATCGATATTTTACAATATAACAGGTAAAAATATGACAAAATCA
19606 GTTTCATTATGACAAAAAAGGTAAAATTTACCTGATATGTTGAAAG
66 GTTTCATTATGACAAAAAAGGTAAAATTTACCTGATATGTTGAAAG
* * * *
19652 TATCGATCCTTTTATAAAAATGATCGATATTTTACAATATAACATGTATAAATATGACAAAACCA
1 TATCGATCCTTTTATAAAAAGGATCGATATTTTACAATATAACAGGTAAAAATATGACAAAATCA
* **
19717 GATTCATTATGACAAAACCGGTAAAAATTTACCTGATATGTTGAAAG
66 GTTTCATTATGACAAAAAAGGT-AAAATTTACCTGATATGTTGAAAG
* *
19764 TATAGATACTTTTTAATAAAAAGGAT
1 TATCGAT-CCTTTT-ATAAAAAGGAT
19790 TAATACTTTT
Statistics
Matches: 228, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
111 149 0.65
112 64 0.28
113 5 0.02
114 10 0.04
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (111 bp):
TATCGATCCTTTTATAAAAAGGATCGATATTTTACAATATAACAGGTAAAAATATGACAAAATCA
GTTTCATTATGACAAAAAAGGTAAAATTTACCTGATATGTTGAAAG
Found at i:20704 original size:21 final size:20
Alignment explanation
Indices: 20672--20712 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
20662 ATCCTAAGCC
20672 CTAAAACCTAAACCATAAAT
1 CTAAAACCTAAACCATAAAT
*
20692 CTAAAACCCTAAACCCTAAAT
1 CTAAAA-CCTAAACCATAAAT
20713 ATTAAATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (20 bp):
CTAAAACCTAAACCATAAAT
Found at i:23286 original size:23 final size:23
Alignment explanation
Indices: 23255--23310 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
23245 GTCGAGCACA
*
23255 GAATCGAGCTCAAAATCGAGCTT
1 GAATCGAGCTCAAAATCAAGCTT
*
23278 GAATTGAGCTCAAAATCAAGCTT
1 GAATCGAGCTCAAAATCAAGCTT
*
23301 TAATCGAGCT
1 GAATCGAGCT
23311 TCAATCGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (23 bp):
GAATCGAGCTCAAAATCAAGCTT
Found at i:23472 original size:27 final size:29
Alignment explanation
Indices: 23412--23470 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 29
23402 TAGGCTTGCG
23412 AGTTTTCGAG-TCGAGTCGAGCTTAGATTTAT
1 AGTTTTCGAGTTCGAGTCGAGCTTA-A--TAT
23443 AGTTTTCGAGTTCGAGTCGAGCTTAATA
1 AGTTTTCGAGTTCGAGTCGAGCTTAATA
23471 GTAATCGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 2 0.07
31 11 0.41
32 14 0.52
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (29 bp):
AGTTTTCGAGTTCGAGTCGAGCTTAATAT
Found at i:24623 original size:99 final size:99
Alignment explanation
Indices: 24452--24651 Score: 382
Period size: 99 Copynumber: 2.0 Consensus size: 99
24442 TAGAAACTCG
24452 AGAAAAATAATAGGCCAAGTATTCGATTTGAAAAATCAAATATTTTTATTATAAGTACTTGATAT
1 AGAAAAATAATAGGCCAAGTATTCGATTTGAAAAATCAAATATTTTTATTATAAGTACTTGATAT
24517 TTTTTAACCGATTCAGCTGATCAACGGATTAAAT
66 TTTTTAACCGATTCAGCTGATCAACGGATTAAAT
*
24551 AGAAAAATAGTAGGCCAAGTATTCGATTTGAAAAATCAAATATTTTTATTATAAGTACTTGATAT
1 AGAAAAATAATAGGCCAAGTATTCGATTTGAAAAATCAAATATTTTTATTATAAGTACTTGATAT
*
24616 TTTTTAACCGATTGAGCTGATCAACGGATTAAAT
66 TTTTTAACCGATTCAGCTGATCAACGGATTAAAT
24650 AG
1 AG
24652 TTTAAATAGA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (99 bp):
AGAAAAATAATAGGCCAAGTATTCGATTTGAAAAATCAAATATTTTTATTATAAGTACTTGATAT
TTTTTAACCGATTCAGCTGATCAACGGATTAAAT
Found at i:37629 original size:15 final size:15
Alignment explanation
Indices: 37609--37659 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
37599 TAATTTGATT
37609 TTATTATTTTATTTA
1 TTATTATTTTATTTA
* *
37624 TTATTATTTGA-TTG
1 TTATTATTTTATTTA
*
37638 TTAATATTTTATTTA
1 TTATTATTTTATTTA
37653 TTTATTA
1 -TTATTA
37660 ATATTAGTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 11 0.39
15 12 0.43
16 5 0.18
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (15 bp):
TTATTATTTTATTTA
Found at i:37649 original size:29 final size:29
Alignment explanation
Indices: 37601--37659 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
37591 TGACACAATA
*
37601 ATTTGATTTTATTATTTTATTTA-TTATT
1 ATTTGATTTTAATATTTTATTTATTTATT
37629 ATTTGATTGTTAATATTTTATTTATTTATT
1 ATTTGATT-TTAATATTTTATTTATTTATT
37659 A
1 A
37660 ATATTAGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 8 0.29
29 14 0.50
30 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (29 bp):
ATTTGATTTTAATATTTTATTTATTTATT
Found at i:37651 original size:19 final size:20
Alignment explanation
Indices: 37622--37665 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
37612 TTATTTTATT
*
37622 TATTATTATTTGA-TTGTTAA
1 TATTATTATTT-ATTTATTAA
37642 TATT-TTATTTATTTATTAA
1 TATTATTATTTATTTATTAA
37661 TATTA
1 TATTA
37666 GTCTTGCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TATTATTATTTATTTATTAA
Found at i:41422 original size:16 final size:17
Alignment explanation
Indices: 41401--41434 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41391 ATCGGCCGTT
*
41401 AAATATTT-TATTTAAA
1 AAATATTTAAATTTAAA
41417 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
41434 A
1 A
41435 TATACAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:50231 original size:21 final size:21
Alignment explanation
Indices: 50150--50231 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
50140 CGCAAATCAG
50150 TTTCC-AAATCGCAACGCGAT
1 TTTCCAAAATCGCAACGCGAT
* *
50170 TCTT-GAAAATCGCAATGCGAT
1 T-TTCCAAAATCGCAACGCGAT
** * * **
50191 AGTACAAATTCGCATTGCGAT
1 TTTCCAAAATCGCAACGCGAT
50212 TTTCCAAAATCGCAACGCGA
1 TTTCCAAAATCGCAACGCGA
50232 ATATGAA
Statistics
Matches: 46, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
20 2 0.04
21 44 0.96
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
TTTCCAAAATCGCAACGCGAT
Done.