Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007370.1 Hibiscus syriacus cultivar Beakdansim tig00019778_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: 114000
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1748 original size:2 final size:2
Alignment explanation
Indices: 1741--1777 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1731 AATGGTTATG
1741 TA TA TA TA 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 TA TA TA TA T
1778 TTTTTAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2226 original size:20 final size:20
Alignment explanation
Indices: 2203--2249 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2193 CACGGAATGT
2203 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
2223 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
2243 AAGATTA
1 AAGATTA
2250 ACAGGGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:2258 original size:18 final size:19
Alignment explanation
Indices: 2203--2259 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
2193 CACGGAATGT
*
2203 AAGATTACCAGTGGGAATAA
1 AAGATTAACAG-GGGAATAA
*
2223 AAGATTACCAGTGGGAATAA
1 AAGATTAACAG-GGGAATAA
2243 AAGATTAACA-GGGAATA
1 AAGATTAACAGGGGAATA
2260 GGATTACTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 7 0.19
20 29 0.81
ACGTcount: A:0.47, C:0.09, G:0.25, T:0.19
Consensus pattern (19 bp):
AAGATTAACAGGGGAATAA
Found at i:2439 original size:36 final size:35
Alignment explanation
Indices: 2406--2472 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2396 TACAAATTGT
*
2406 AAAATATTTATATATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTT-TTTACAAAATTAAATTC
*
2441 ATAATATTTATATAATTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTACAAAATTAAA
2473 AATATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (35 bp):
AAAATATTTATATAATTTTTTACAAAATTAAATTC
Found at i:3020 original size:12 final size:12
Alignment explanation
Indices: 3003--3028 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2993 TGTCGAATTT
3003 GATTTTATGTTA
1 GATTTTATGTTA
3015 GATTTTATGTTA
1 GATTTTATGTTA
3027 GA
1 GA
3029 GTGACGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (12 bp):
GATTTTATGTTA
Found at i:3120 original size:52 final size:53
Alignment explanation
Indices: 3026--3131 Score: 135
Period size: 52 Copynumber: 2.0 Consensus size: 53
3016 ATTTTATGTT
* * *
3026 AGAGTGACGAATTTGAGTTTTTTTAAATTTCATAGGACAAATTTAGA-TTATA
1 AGAGTGACGAATTTGAATTTTTTAAAATTTCATAGGACAAATTTAAATTTATA
* * *
3078 AGAGTGATGAATTTGAATTTTTTAAAATTTGATAAGG-TAAATTTAAATTTATA
1 AGAGTGACGAATTTGAATTTTTTAAAATTTCAT-AGGACAAATTTAAATTTATA
3131 A
1 A
3132 AAATTTAGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 37 0.80
53 9 0.20
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.42
Consensus pattern (53 bp):
AGAGTGACGAATTTGAATTTTTTAAAATTTCATAGGACAAATTTAAATTTATA
Found at i:3561 original size:140 final size:140
Alignment explanation
Indices: 3309--3588 Score: 382
Period size: 140 Copynumber: 2.0 Consensus size: 140
3299 TGTACTTCTC
* *
3309 GGTCTGTCTATATACACAAGGACACGACATTATCATACTATGGTAAACTACATATTATCTCTCCT
1 GGTCTATCTATATACACAAGAACACGACATTATCATACTATGGTAAACTACATATTATCTCTCCT
* * * * *
3374 CGGTCCATCCTACCCGTCTCCCTCGGTTTATCTCTGTACACAAAGACA-TGACATCCATCTCTAT
66 CGATCCATCCCACCCGCCTCCCTCGGTCTATCTCTATACACAAAGACACT-ACATCCATCTCTAT
*
3438 ACATAAGGACA
130 ACACAAGGACA
* * * *
3449 GGTCTATCTATGTACACAAGAACACGACATTATCATACTATGGTAAATTACATATTGTCTCTCTT
1 GGTCTATCTATATACACAAGAACACGACATTATCATACTATGGTAAACTACATATTATCTCTCCT
* * ** *
3514 CGATCTATCCCACTCGCCTCTTTCGGTCTATCTTTATACACAAAGACACTACATCCATCTCTATA
66 CGATCCATCCCACCCGCCTCCCTCGGTCTATCTCTATACACAAAGACACTACATCCATCTCTATA
*
3579 TACAAGGACA
131 CACAAGGACA
3589 CGACATTATC
Statistics
Matches: 121, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
140 120 0.99
141 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31
Consensus pattern (140 bp):
GGTCTATCTATATACACAAGAACACGACATTATCATACTATGGTAAACTACATATTATCTCTCCT
CGATCCATCCCACCCGCCTCCCTCGGTCTATCTCTATACACAAAGACACTACATCCATCTCTATA
CACAAGGACA
Found at i:3583 original size:27 final size:27
Alignment explanation
Indices: 3543--3594 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3533 CTTTCGGTCT
* *
3543 ATCTTTATACACAAAGACACTACATCC
1 ATCTCTATACACAAAGACACGACATCC
* *
3570 ATCTCTATATACAAGGACACGACAT
1 ATCTCTATACACAAAGACACGACAT
3595 TATCATACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (27 bp):
ATCTCTATACACAAAGACACGACATCC
Found at i:5489 original size:14 final size:14
Alignment explanation
Indices: 5470--5499 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5460 CGTTTAAAAT
5470 ATAAACGAACGCAA
1 ATAAACGAACGCAA
*
5484 ATAAACGAACGTAA
1 ATAAACGAACGCAA
5498 AT
1 AT
5500 CAATATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (14 bp):
ATAAACGAACGCAA
Found at i:5597 original size:20 final size:19
Alignment explanation
Indices: 5572--5619 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 19
5562 ATAATTTTAG
5572 GATTTATATTTTCTTTAATT
1 GATTTATATTTT-TTTAATT
*
5592 GATTTAAATATTTTTTTATTT
1 GATTT--ATATTTTTTTAATT
5613 GAGTTTA
1 GA-TTTA
5620 AAAATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 6 0.25
21 8 0.33
22 10 0.42
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (19 bp):
GATTTATATTTTTTTAATT
Found at i:5614 original size:21 final size:23
Alignment explanation
Indices: 5577--5621 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
5567 TTTAGGATTT
5577 ATATTTTCTTTAATTGA-TTTAA
1 ATATTTTCTTTAATTGAGTTTAA
*
5599 ATATTTT-TTTATTTGAGTTTAA
1 ATATTTTCTTTAATTGAGTTTAA
5621 A
1 A
5622 AATATTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (23 bp):
ATATTTTCTTTAATTGAGTTTAA
Found at i:15749 original size:22 final size:23
Alignment explanation
Indices: 15719--15763 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
15709 AGATCTATAT
15719 TTCTGAAAAATTT-AACAATGAA
1 TTCTGAAAAATTTGAACAATGAA
* *
15741 TTCTTAAAAATTTGATCAATGAA
1 TTCTGAAAAATTTGAACAATGAA
15764 AATGCATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (23 bp):
TTCTGAAAAATTTGAACAATGAA
Found at i:25339 original size:3 final size:3
Alignment explanation
Indices: 25310--25379 Score: 90
Period size: 3 Copynumber: 23.0 Consensus size: 3
25300 TATAAAAATG
*
25310 TTA TTA TT- TATA TTAA TTA AT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25355 TTA TTA TTAA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA
25380 CATTTTTTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
2 2 0.03
3 51 0.85
4 7 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:27019 original size:30 final size:30
Alignment explanation
Indices: 26937--27054 Score: 130
Period size: 30 Copynumber: 3.9 Consensus size: 30
26927 TTTGTAATTA
* *
26937 CTATTTTAGTCCTTTTAGATTCTGTTTTTT
1 CTATTTTAGTCCTTTAAGTTTCTGTTTTTT
* *
26967 ACTA-TTTAGTCCCTTAAGTTTCTATTTTTT
1 -CTATTTTAGTCCTTTAAGTTTCTGTTTTTT
* * **
26997 CTATTTTAGTCCTTTAACTTTCTGTCTTAG
1 CTATTTTAGTCCTTTAAGTTTCTGTTTTTT
* *
27027 CTACTTTAGTCCTTTAAGTTTTTGTTTT
1 CTATTTTAGTCCTTTAAGTTTCTGTTTT
27055 CTCCTTTTTG
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
29 3 0.04
30 66 0.92
31 3 0.04
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.58
Consensus pattern (30 bp):
CTATTTTAGTCCTTTAAGTTTCTGTTTTTT
Found at i:27215 original size:23 final size:22
Alignment explanation
Indices: 27189--27233 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27179 TATGTATAAC
*
27189 ATGTAATAAATGTTATTAGTTTT
1 ATGTAATAAATATT-TTAGTTTT
**
27212 ATGTTGTAAATATTTTAGTTTT
1 ATGTAATAAATATTTTAGTTTT
27234 CATTTATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (22 bp):
ATGTAATAAATATTTTAGTTTT
Found at i:27616 original size:17 final size:19
Alignment explanation
Indices: 27585--27623 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
27575 TTTATAATAT
27585 TATAGAACATTAAATA-TAA
1 TATAGAACA-TAAATATTAA
27604 TATAGAACA-AAATATTAA
1 TATAGAACATAAATATTAA
27622 TA
1 TA
27624 ATACAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
TATAGAACATAAATATTAA
Found at i:28761 original size:7 final size:7
Alignment explanation
Indices: 28749--28774 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28739 AAAATAGCAC
28749 CGGTCAA
1 CGGTCAA
28756 CGGTCAA
1 CGGTCAA
28763 CGGTCAA
1 CGGTCAA
28770 CGGTC
1 CGGTC
28775 GGGTCTGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:28797 original size:25 final size:24
Alignment explanation
Indices: 28757--28816 Score: 93
Period size: 25 Copynumber: 2.5 Consensus size: 24
28747 ACCGGTCAAC
*
28757 GGTCAACGGTCAACGGTCGGGTCT
1 GGTCAACGGTCAACGGTCGGGTCG
28781 GGTCAACGGGTCAACGGTCGGGTCG
1 GGTCAAC-GGTCAACGGTCGGGTCG
*
28806 GGTCAATGGTC
1 GGTCAACGGTC
28817 GGGTCAGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 11 0.33
25 22 0.67
ACGTcount: A:0.17, C:0.23, G:0.40, T:0.20
Consensus pattern (24 bp):
GGTCAACGGTCAACGGTCGGGTCG
Found at i:28839 original size:17 final size:17
Alignment explanation
Indices: 28789--28850 Score: 88
Period size: 17 Copynumber: 3.5 Consensus size: 17
28779 CTGGTCAACG
*
28789 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCA
*
28806 GGTCAATGGTCGGGTCA
1 GGTCAACGGTCGGGTCA
28823 GGTCAACGGTCGGGTCAA
1 GGTCAACGGTCGGGTC-A
28841 CGGTCAACGG
1 -GGTCAACGG
28851 GTCGTGACCG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 30 0.75
18 1 0.03
19 9 0.22
ACGTcount: A:0.18, C:0.23, G:0.42, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCA
Found at i:34567 original size:19 final size:21
Alignment explanation
Indices: 34526--34574 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
34516 TTTCAAAATT
34526 TATAATATTATAGAACATTAAA
1 TATAATATTATAGAACA-TAAA
34548 TATAATA-TATAGAACA-AAA
1 TATAATATTATAGAACATAAA
34567 TATTAATA
1 TA-TAATA
34575 ATACAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 9 0.35
22 7 0.27
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (21 bp):
TATAATATTATAGAACATAAA
Found at i:36639 original size:2 final size:2
Alignment explanation
Indices: 36632--36658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36622 CCACGTATTC
36632 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
36659 CAAACCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53672 original size:25 final size:22
Alignment explanation
Indices: 53643--53688 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
53633 TTTTTAACCC
53643 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
53668 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
53689 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:62501 original size:6 final size:6
Alignment explanation
Indices: 62492--62523 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
62482 TAAATATCGT
*
62492 GACAGA GACAGA GACAGA GACATA GACAGA GA
1 GACAGA GACAGA GACAGA GACAGA GACAGA GA
62524 GAATTCCAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.16, G:0.31, T:0.03
Consensus pattern (6 bp):
GACAGA
Found at i:74659 original size:14 final size:14
Alignment explanation
Indices: 74642--74694 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
74632 AATCCTAGAT
74642 TATAAACCCTAAAC
1 TATAAACCCTAAAC
* *
74656 TATAATCTCTAAA-
1 TATAAACCCTAAAC
74669 TCATAAACCCTAAAC
1 T-ATAAACCCTAAAC
*
74684 T-TAAACTCTAA
1 TATAAACCCTAA
74695 CTTAAGATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 10 0.31
14 21 0.66
15 1 0.03
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
TATAAACCCTAAAC
Found at i:74989 original size:31 final size:34
Alignment explanation
Indices: 74913--74991 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 34
74903 GATTTAAATT
* * *
74913 AAATTTAAATAATAAATATATTTTAAGATTATGC
1 AAATTTAAATAATAAAGATATTTTAAAAATATGC
* * *
74947 TATTTTTAATAA-AAAGAT-TTTTAAAAATAT-C
1 AAATTTAAATAATAAAGATATTTTAAAAATATGC
74978 AAATTTAAATAATA
1 AAATTTAAATAATA
74992 TAATATTCCA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
31 10 0.29
32 11 0.31
33 5 0.14
34 9 0.26
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (34 bp):
AAATTTAAATAATAAAGATATTTTAAAAATATGC
Found at i:77907 original size:20 final size:20
Alignment explanation
Indices: 77882--77922 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
77872 TTTTGAGAAC
77882 TGATCTCATGTCATTTTAGA
1 TGATCTCATGTCATTTTAGA
77902 TGATCTCATGTCATTTTAGA
1 TGATCTCATGTCATTTTAGA
77922 T
1 T
77923 CTTTCAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
TGATCTCATGTCATTTTAGA
Found at i:86615 original size:4 final size:4
Alignment explanation
Indices: 86590--86937 Score: 490
Period size: 4 Copynumber: 88.2 Consensus size: 4
86580 GTGTAAGTGC
* * * *
86590 ATGT ATGC ATGT ATGC ATGT ATGT ATGC ATGT ATGT ATGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * * * * *
86638 ATGT ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
86686 ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
86734 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
86782 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
86830 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
86878 ATGT ATGT ATGT ATGT ATGT ATG- -TGT GTGT AT-T GTGT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
86923 ATGT A--T ATGT ATGT A
1 ATGT ATGT ATGT ATGT A
86938 CTAAAATGGG
Statistics
Matches: 324, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
2 4 0.01
3 2 0.01
4 318 0.98
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:111294 original size:37 final size:36
Alignment explanation
Indices: 111222--111295 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
111212 GTTAAAAAAT
* *
111222 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
*
111258 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTAAAAATCATAAA
111295 A
1 A
111296 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 15 0.45
38 10 0.30
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:111297 original size:38 final size:37
Alignment explanation
Indices: 111217--111297 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
111207 AACAAGTTAA
* *
111217 AAAATATTTATATATTTTCTTTAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAATTAAAAATCAT
*
111255 -AAAATTTATATAATTTTTTTTACAAAATTAAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTA-AAAATTAAAAATCAT
111292 AAAAAT
1 AAAAAT
111298 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 8 0.22
37 14 0.38
38 15 0.41
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (37 bp):
AAAAATTTATATATTTTCTTTAAAAATTAAAAATCAT
Found at i:112202 original size:15 final size:15
Alignment explanation
Indices: 112182--112214 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
112172 TCTCCTCTCG
112182 TCACCCCACATCCGA
1 TCACCCCACATCCGA
*
112197 TCACCCCACCTCCGA
1 TCACCCCACATCCGA
112212 TCA
1 TCA
112215 GCGGTGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.55, G:0.06, T:0.15
Consensus pattern (15 bp):
TCACCCCACATCCGA
Done.