Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006269.1 Hibiscus syriacus cultivar Beakdansim tig00014948_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: 80758
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:629 original size:28 final size:28
Alignment explanation
Indices: 531--630 Score: 76
Period size: 28 Copynumber: 3.4 Consensus size: 28
521 AATTAGAAAT
* *
531 AATAAATAAATATTGAATAAATCAAAGGA
1 AATAAATAAAAATTGAATAAATCAAA-AA
* * **
560 AA-AAATAAAAAATAAATCAAAGGAACAAA
1 AATAAATAAAAATTGAAT-AAATCAA-AAA
* *
589 AGATGAAAAAAAAATTGAATAACTCAAAAA
1 A-AT-AAATAAAAATTGAATAAATCAAAAA
619 AATAAATAAAAA
1 AATAAATAAAAA
631 ACATACTATA
Statistics
Matches: 53, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
28 20 0.38
29 11 0.21
30 6 0.11
31 4 0.08
32 12 0.23
ACGTcount: A:0.70, C:0.05, G:0.08, T:0.17
Consensus pattern (28 bp):
AATAAATAAAAATTGAATAAATCAAAAA
Found at i:2405 original size:31 final size:29
Alignment explanation
Indices: 2350--2419 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
2340 AAAAAAGAAA
2350 AAATAATTAATAATTAATAAAATAAAAAC
1 AAATAATTAATAATTAATAAAATAAAAAC
* *
2379 AAATAA-TATTAATGTAATATATAATAAAAAT
1 AAATAATTAATAAT-TAATA-A-AATAAAAAC
2410 AAA-AATTAAT
1 AAATAATTAAT
2420 TTTAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 6 0.18
29 11 0.32
30 3 0.09
31 14 0.41
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (29 bp):
AAATAATTAATAATTAATAAAATAAAAAC
Found at i:2509 original size:32 final size:33
Alignment explanation
Indices: 2419--2544 Score: 102
Period size: 34 Copynumber: 3.8 Consensus size: 33
2409 TAAAAATTAA
*
2419 TTTT-AAAATTATATAT-TATATATGCTTCAAAATCGT
1 TTTTAAAAACTATATATATATATAT--TTC-AAAT--T
*
2455 TTTTAAAAGC-ATATA-ATATATATTT-AAATAT
1 TTTTAAAAACTATATATATATATATTTCAAAT-T
*
2486 TTTTAAAAACTATATATAT-TATATTTTCAAATG
1 TTTTAAAAACTATATATATATATA-TTTCAAATT
*
2519 TTTCAAAAACATATATATATATATAT
1 TTTTAAAAAC-TATATATATATATAT
2545 ATATATATAT
Statistics
Matches: 76, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
31 10 0.13
32 13 0.17
33 14 0.18
34 16 0.21
35 4 0.05
36 16 0.21
37 3 0.04
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (33 bp):
TTTTAAAAACTATATATATATATATTTCAAATT
Found at i:2536 original size:2 final size:2
Alignment explanation
Indices: 2529--2554 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2519 TTTCAAAAAC
2529 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2555 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2636 original size:37 final size:37
Alignment explanation
Indices: 2581--2694 Score: 160
Period size: 37 Copynumber: 3.1 Consensus size: 37
2571 GTGTTTTGAG
* *
2581 AATGTTTTCAAAACTATATAATATATATATTTTCAAA
1 AATGATTTCAAAACTATATATTATATATATTTTCAAA
2618 AATGATTTCAAAACTATATATTATATAT-TTTTCAAAA
1 AATGATTTCAAAACTATATATTATATATATTTTC-AAA
*
2655 AAT-ATTTTCAAAAACTATATATTATATATATATTCAAA
1 AATGA-TTTC-AAAACTATATATTATATATATTTTCAAA
2693 AA
1 AA
2695 CTATATATCA
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
36 6 0.09
37 36 0.51
38 24 0.34
39 4 0.06
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (37 bp):
AATGATTTCAAAACTATATATTATATATATTTTCAAA
Found at i:2711 original size:75 final size:74
Alignment explanation
Indices: 2585--2776 Score: 175
Period size: 75 Copynumber: 2.6 Consensus size: 74
2575 TTTGAGAATG
* *
2585 TTTTC-AAAACTATATAATATATATATTTTCAAAAATGATTTCAAAACTATATATTAT-ATAT-T
1 TTTTCAAAAACTATAT-ATATATATATATTCAAAAATGATTTC-AAACTATAT-TTATAAAATGT
2647 TTTCAAAAAATA
63 TTTCAAAAAATA
** *
2659 TTTTCAAAAACTATATATTATATATATATTCAAAAACT-ATATATC-ATGTATATTTTTAAAATG
1 TTTTCAAAAACTATATA-TATATATATATTCAAAAA-TGAT-T-TCAAACTATATTTATAAAATG
*
2722 TTTTCAAAAACTA
62 TTTTCAAAAAATA
* * * *
2735 TATT-ATATA-TATATATATATATATATTC-AAAATGGTTTCAAA
1 TTTTCAAAAACTATATATATATATATATTCAAAAATGATTTCAAA
2777 AACTATATAA
Statistics
Matches: 98, Mismatches: 11, Indels: 21
0.75 0.08 0.16
Matches are distributed among these distances:
70 2 0.02
71 3 0.03
72 5 0.05
73 13 0.13
74 15 0.15
75 41 0.42
76 17 0.17
77 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (74 bp):
TTTTCAAAAACTATATATATATATATATTCAAAAATGATTTCAAACTATATTTATAAAATGTTTT
CAAAAAATA
Found at i:2719 original size:26 final size:26
Alignment explanation
Indices: 2656--2719 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
2646 TTTTCAAAAA
*
2656 ATATTTTCAAAAACTATATATTATAT
1 ATATTTTCAAAAACTATATATCATAT
* *
2682 ATATATTCAAAAACTATATATCATGT
1 ATATTTTCAAAAACTATATATCATAT
*
2708 ATATTTTTAAAA
1 ATATTTTCAAAA
2720 TGTTTTCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (26 bp):
ATATTTTCAAAAACTATATATCATAT
Found at i:2730 original size:63 final size:64
Alignment explanation
Indices: 2627--2752 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 64
2617 AAATGATTTC
2627 AAAACTATATATTATATATTTTTCAAAAAATATTTTCAAAAACTATA-TAT-TATATATATATTC
1 AAAACTATATATTATATATTTTT--AAAAATATTTTCAAAAACTATATTATATATATATATATTC
2690 A
64 A
* *
2691 AAAACTATATATCATGTATATTTTT-AAAATGTTTTCAAAAACTATATTATATATATATATAT
1 AAAACTATATAT--TATATATTTTTAAAAATATTTTCAAAAACTATATTATATATATATATAT
2753 ATATATATTC
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
63 20 0.36
64 15 0.27
65 11 0.20
66 10 0.18
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (64 bp):
AAAACTATATATTATATATTTTTAAAAATATTTTCAAAAACTATATTATATATATATATATTCA
Found at i:2774 original size:47 final size:48
Alignment explanation
Indices: 2696--2791 Score: 140
Period size: 47 Copynumber: 2.0 Consensus size: 48
2686 ATTCAAAAAC
* * * * *
2696 TATATATCATGTATATTTTTAAAATGTTTTCAAAAACTATATTATATA
1 TATATATCATATATATATTCAAAATGGTTTCAAAAACTATATAATATA
2744 TATATAT-ATATATATATTCAAAATGGTTTCAAAAACTATATAATATA
1 TATATATCATATATATATTCAAAATGGTTTCAAAAACTATATAATATA
2791 T
1 T
2792 TTTCAAAACC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 36 0.84
48 7 0.16
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (48 bp):
TATATATCATATATATATTCAAAATGGTTTCAAAAACTATATAATATA
Found at i:4890 original size:32 final size:30
Alignment explanation
Indices: 4830--4899 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 30
4820 TATCAATTGT
4830 AATTAAAAGTATAAAAATGCAATAAAAAAG
1 AATTAAAAGTATAAAAATGCAATAAAAAAG
*
4860 AATTAAAAGTGA-ATAAAATTCAATACAAAAAG
1 AATTAAAAGT-ATA-AAAATGCAATA-AAAAAG
4892 AATATAAA
1 AAT-TAAA
4900 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
30 11 0.31
31 11 0.31
32 9 0.26
33 4 0.11
ACGTcount: A:0.66, C:0.04, G:0.09, T:0.21
Consensus pattern (30 bp):
AATTAAAAGTATAAAAATGCAATAAAAAAG
Found at i:7660 original size:17 final size:17
Alignment explanation
Indices: 7640--7673 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
7630 ATTGGCTGCT
7640 GGATAGCATTAGCAACC
1 GGATAGCATTAGCAACC
7657 GGATAGCATTAGCAACC
1 GGATAGCATTAGCAACC
7674 AAGCTTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (17 bp):
GGATAGCATTAGCAACC
Found at i:13596 original size:22 final size:24
Alignment explanation
Indices: 13566--13618 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
13556 GAAACATGCC
*
13566 AAAAGACAGAAG-AATTATGTCAT
1 AAAAGACAGAAGAAAATATGTCAT
*
13589 AAAA-ACAGAGGAAAATATGTCAT
1 AAAAGACAGAAGAAAATATGTCAT
13612 -AAAGACA
1 AAAAGACA
13619 AAACTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (24 bp):
AAAAGACAGAAGAAAATATGTCAT
Found at i:18956 original size:21 final size:21
Alignment explanation
Indices: 18930--18976 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
18920 TAATAAAAAA
18930 TTTTATTTAAAATATTATTAT
1 TTTTATTTAAAATATTATTAT
*
18951 TTTTATTTAAAATATTATTTT
1 TTTTATTTAAAATATTATTAT
18972 TTTTA
1 TTTTA
18977 AACATTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATTTAAAATATTATTAT
Found at i:19308 original size:23 final size:24
Alignment explanation
Indices: 19282--19327 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
19272 ATAATATATT
*
19282 TTTACGC-CTTTAAATTTTATAAA
1 TTTACGCTCTTAAAATTTTATAAA
**
19305 TTTATTCTCTTAAAATTTTATAA
1 TTTACGCTCTTAAAATTTTATAA
19328 TTTCGTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTACGCTCTTAAAATTTTATAAA
Found at i:20563 original size:16 final size:16
Alignment explanation
Indices: 20542--20572 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20532 ATAAATAAGT
20542 GAACATAAACGAACAC
1 GAACATAAACGAACAC
20558 GAACATAAACGAACA
1 GAACATAAACGAACA
20573 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:20652 original size:10 final size:10
Alignment explanation
Indices: 20637--20679 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
20627 CATTTAATAA
20637 ATAAACGAAC
1 ATAAACGAAC
20647 ATAAACGAAC
1 ATAAACGAAC
20657 ----ACGAAC
1 ATAAACGAAC
20663 ATAAACGAAC
1 ATAAACGAAC
20673 ATAAACG
1 ATAAACG
20680 TTGGAGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 23 0.79
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:20662 original size:16 final size:16
Alignment explanation
Indices: 20641--20673 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20631 TAATAAATAA
20641 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
20657 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
20673 A
1 A
20674 TAAACGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:21968 original size:27 final size:29
Alignment explanation
Indices: 21902--21968 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 29
21892 GAAAGGAAAG
21902 AGATGAAGCTCCGTCGAATCGTTGCAGTTGA
1 AGATGAAGCTCCGTCGAATCGTTGCA--TGA
*
21933 AGACTTGAAGCTCCGTCGAATTGTTGCA-GA
1 AGA--TGAAGCTCCGTCGAATCGTTGCATGA
21963 A-ATGAA
1 AGATGAA
21969 AATTGTGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 4 0.12
29 1 0.03
30 3 0.09
31 3 0.09
33 22 0.67
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (29 bp):
AGATGAAGCTCCGTCGAATCGTTGCATGA
Found at i:22254 original size:24 final size:24
Alignment explanation
Indices: 22193--22254 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
22183 TATTAGGTTA
*
22193 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
22217 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
22241 AACATAACCGAACG
1 AACATAACTGAACG
22255 TTCATGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:23797 original size:2 final size:2
Alignment explanation
Indices: 23790--23865 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
23780 TATGAATTGA
23790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23866 TAACGTTAAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29132 original size:2 final size:2
Alignment explanation
Indices: 29121--29194 Score: 66
Period size: 2 Copynumber: 38.5 Consensus size: 2
29111 CCATTGTTAT
*
29121 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
29160 TT TA TT TA CA AA CTA TA T- 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 T
29195 TTACTTATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
1 4 0.07
2 54 0.92
3 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:30474 original size:20 final size:21
Alignment explanation
Indices: 30437--30488 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
30427 TTTATTTCAT
**
30437 TTACTTTATTTCTTTTTGTGA
1 TTACTTTATTTCCCTTTGTGA
*
30458 TTACTTT-TTTCCCTTTGTTA
1 TTACTTTATTTCCCTTTGTGA
30478 TTTA-TTTATTT
1 -TTACTTTATTT
30489 ATTTAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.13, C:0.12, G:0.06, T:0.69
Consensus pattern (21 bp):
TTACTTTATTTCCCTTTGTGA
Found at i:30534 original size:24 final size:25
Alignment explanation
Indices: 30504--30551 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
30494 ATATATGTTT
*
30504 TAATTTT-ATTTCTTTGTTTTTATA
1 TAATTTTCATTTCTTTGTTCTTATA
30528 TAATTTTCATTTCTTTGTTCTTAT
1 TAATTTTCATTTCTTTGTTCTTAT
30552 GTTTGCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (25 bp):
TAATTTTCATTTCTTTGTTCTTATA
Found at i:30642 original size:12 final size:12
Alignment explanation
Indices: 30625--30651 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30615 TAGTATATGT
30625 TTTTTTCCTTTA
1 TTTTTTCCTTTA
30637 TTTTTTCCTTTA
1 TTTTTTCCTTTA
30649 TTT
1 TTT
30652 ATCCTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTCCTTTA
Found at i:31679 original size:21 final size:20
Alignment explanation
Indices: 31655--31700 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
31645 CTTTTCGTTT
* *
31655 TTTTCTTTCATTATTTATTTA
1 TTTTATTTCATCATTT-TTTA
*
31676 TTTTATTTTATCATTTTTTA
1 TTTTATTTCATCATTTTTTA
31696 TTTTA
1 TTTTA
31701 CTAACTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTCATCATTTTTTA
Found at i:33960 original size:13 final size:13
Alignment explanation
Indices: 33942--33970 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
33932 TACTTTGCAT
33942 TTTATATTTCATG
1 TTTATATTTCATG
33955 TTTATATTTCATG
1 TTTATATTTCATG
33968 TTT
1 TTT
33971 TCCATGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TTTATATTTCATG
Found at i:41170 original size:7 final size:7
Alignment explanation
Indices: 41158--41197 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
41148 CTAAATTGAA
41158 AAAAAAG
1 AAAAAAG
41165 AAAAAAG
1 AAAAAAG
*
41172 TAAAAAG
1 AAAAAAG
*
41179 AAAAATG
1 AAAAAAG
*
41186 AGAAAAG
1 AAAAAAG
41193 AAAAA
1 AAAAA
41198 TAAGGTGGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:43132 original size:16 final size:16
Alignment explanation
Indices: 43076--43146 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
43066 TATTATAATA
43076 TATATATATATTATTATT
1 TATATATATA-T-TTATT
* * *
43094 TACAAACTATATTATATA
1 TATATA-TATATT-TATT
*
43112 CATATATATATTTATT
1 TATATATATATTTATT
*
43128 TATATATATATTTACT
1 TATATATATATTTATT
43144 TAT
1 TAT
43147 TTGGGTTCTA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
16 20 0.48
17 7 0.17
18 11 0.26
19 4 0.10
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATATATTTATT
Found at i:45768 original size:21 final size:21
Alignment explanation
Indices: 45743--45799 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 21
45733 CATAGCATTA
45743 TTATTTTACTTTTTTATTTA-
1 TTATTTTACTTTTTTATTTAG
*
45763 TT-TATTA--TTTTT-TTTAG
1 TTATTTTACTTTTTTATTTAG
*
45780 ATAGTTTTACTTTTTTATTT
1 TTA-TTTTACTTTTTTATTT
45800 TCCTTATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
16 4 0.14
17 6 0.21
19 8 0.29
20 2 0.07
21 5 0.18
22 3 0.11
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (21 bp):
TTATTTTACTTTTTTATTTAG
Found at i:47168 original size:24 final size:24
Alignment explanation
Indices: 47124--47173 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
47114 ATAAAGAACC
*
47124 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
47148 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
47172 AA
1 AA
47174 TCAACCACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:56906 original size:17 final size:16
Alignment explanation
Indices: 56884--56917 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
56874 TAAAGACAGT
56884 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
56901 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
56917 A
1 A
56918 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:57436 original size:24 final size:24
Alignment explanation
Indices: 57392--57441 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
57382 ATAAAGAACC
57392 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAATATACCATTA
*
57416 AAAATAAAGTTTAAATA-ACCATTA
1 AAAATAAA-CTTAAATATACCATTA
57440 AA
1 AA
57442 TCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAATATACCATTA
Found at i:61159 original size:7 final size:8
Alignment explanation
Indices: 61140--61165 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
61130 CCTCTTTGTA
61140 AAAAAATG
1 AAAAAATG
61148 AAAAAATG
1 AAAAAATG
61156 AAAAAATG
1 AAAAAATG
61164 AA
1 AA
61166 GTTGTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:69006 original size:37 final size:38
Alignment explanation
Indices: 68913--69069 Score: 226
Period size: 37 Copynumber: 4.0 Consensus size: 38
68903 AGTAAGCTTG
* * * *
68913 AGCTTTGTGCAATCATTTTCCAGAAATTTGCTTATGAGG
1 AGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTA-T
68952 AGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTAT
1 AGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTAT
68990 AGC-TTGTGCAATCATTTTCCAGAAATTTGGTTCTTAT
1 AGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTAT
69027 AAGGAGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTAT
1 ----AGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTAT
69069 A
1 A
69070 AGATCCTGCT
Statistics
Matches: 109, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
37 34 0.31
38 4 0.04
39 34 0.31
41 3 0.03
42 34 0.31
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.41
Consensus pattern (38 bp):
AGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTAT
Found at i:69048 original size:42 final size:42
Alignment explanation
Indices: 68912--69071 Score: 255
Period size: 42 Copynumber: 4.0 Consensus size: 42
68902 GAGTAAGCTT
*
68912 GAGCTTTGTGCAATCATTTTCCAGAAATTT-G--CTTATGAG
1 GAGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTATAAG
68951 GAGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTAT---
1 GAGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTATAAG
68990 -AGC-TTGTGCAATCATTTTCCAGAAATTTGGTTCTTATAAG
1 GAGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTATAAG
69030 GAGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTATAAG
1 GAGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTATAAG
69072 ATCCTGCTTA
Statistics
Matches: 113, Mismatches: 0, Indels: 13
0.90 0.00 0.10
Matches are distributed among these distances:
37 34 0.30
38 3 0.03
39 30 0.27
40 1 0.01
41 3 0.03
42 42 0.37
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (42 bp):
GAGCTTTGTGCAATCATTTTCCAGAAATTTGGTTCTTATAAG
Found at i:69048 original size:79 final size:76
Alignment explanation
Indices: 68917--69069 Score: 270
Period size: 79 Copynumber: 2.0 Consensus size: 76
68907 AGCTTGAGCT
*
68917 TTGTGCAATCATTTTCCAGAAATTTGCTTATGAGGAGCTTTGTGCAATCATTTTCCAGAAATTTG
1 TTGTGCAATCATTTTCCAGAAATTTGCTTATAAGGAGCTTTGTGCAATCATTTTCCAGAAATTTG
68982 GTTCTTATAGC
66 GTTCTTATAGC
68993 TTGTGCAATCATTTTCCAGAAATTTGGTTCTTATAAGGAGCTTTGTGCAATCATTTTCCAGAAAT
1 TTGTGCAATCATTTTCCAGAAATTT-G--CTTATAAGGAGCTTTGTGCAATCATTTTCCAGAAAT
69058 TTGGTTCTTATA
63 TTGGTTCTTATA
69070 AGATCCTGCT
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
76 25 0.34
77 1 0.01
79 47 0.64
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (76 bp):
TTGTGCAATCATTTTCCAGAAATTTGCTTATAAGGAGCTTTGTGCAATCATTTTCCAGAAATTTG
GTTCTTATAGC
Found at i:75076 original size:26 final size:27
Alignment explanation
Indices: 75042--75093 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
75032 TAAATTTATC
75042 TTTTGGTCAAAATAG-TACATAAAGTT
1 TTTTGGTCAAAATAGATACATAAAGTT
* *
75068 TTTTTGTCAAAATAGATACCTAAAGT
1 TTTTGGTCAAAATAGATACATAAAGT
75094 ATTCAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (27 bp):
TTTTGGTCAAAATAGATACATAAAGTT
Found at i:75204 original size:31 final size:31
Alignment explanation
Indices: 75129--75204 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
75119 AAAAATTGAA
* * *
75129 TACTTTAGGTAAC-TATTTTGACCAAAAAGAT
1 TACTTTAGAT-ACTTATTTTGACAAAAAAAAT
* *
75160 AAATTTA-AGTACTTATTTTGACAAAAAAAAT
1 TACTTTAGA-TACTTATTTTGACAAAAAAAAT
75191 TACTTTAGATACTT
1 TACTTTAGATACTT
75205 GAAAAAATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
30 2 0.06
31 32 0.91
32 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (31 bp):
TACTTTAGATACTTATTTTGACAAAAAAAAT
Found at i:77881 original size:168 final size:167
Alignment explanation
Indices: 77604--77908 Score: 540
Period size: 168 Copynumber: 1.8 Consensus size: 167
77594 GACGTCAACC
*
77604 AAAAGGGCGTAGATATAAGCTAAGTAACGGCATAAATGAATAAGTACTCACCCTAATATCCGATT
1 AAAAGGGCGTAGATATAAGCTAAGTAACGGCAGAAATGAATAAGTACTCACCCTAATATCCGATT
77669 TTTAAGCATTATATATAGAATGGAAAATGAAGAAAGAAATGTCATAAAATATGACACTT-TCAAC
66 TTTAAGCATTATATATAGAATGGAAAATGAAGAAAGAAATGTCATAAAATATGACACTTCT-AAC
77733 AAATCATTATATATAGAATGGAAATGAATAAGCTAAGT
130 AAATCATTATATATAGAATGGAAATGAATAAGCTAAGT
* * *
77771 AAAAGGGTGTAGATATAAGCTAAGTAATGGCAGAAATGAATAAGATTCTCACCCTAATATCCGAT
1 AAAAGGGCGTAGATATAAGCTAAGTAACGGCAGAAATGAATAAG-TACTCACCCTAATATCCGAT
77836 TTTTAAGCATTATATATAGAATGGAAAATGAAGAAAGAAATGTCATAAAATATGACACTTCTAAC
65 TTTTAAGCATTATATATAGAATGGAAAATGAAGAAAGAAATGTCATAAAATATGACACTTCTAAC
*
77901 ATATCATT
130 AAATCATT
77909 GTCGTTTATA
Statistics
Matches: 131, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
167 41 0.31
168 89 0.68
169 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (167 bp):
AAAAGGGCGTAGATATAAGCTAAGTAACGGCAGAAATGAATAAGTACTCACCCTAATATCCGATT
TTTAAGCATTATATATAGAATGGAAAATGAAGAAAGAAATGTCATAAAATATGACACTTCTAACA
AATCATTATATATAGAATGGAAATGAATAAGCTAAGT
Found at i:80612 original size:20 final size:19
Alignment explanation
Indices: 80589--80635 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
80579 CGATATACCA
80589 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
80609 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
80629 GGTAAAA
1 GGTAAAA
80636 CGTTACTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:80694 original size:181 final size:176
Alignment explanation
Indices: 80382--80754 Score: 475
Period size: 181 Copynumber: 2.1 Consensus size: 176
80372 GATCCAAATT
* * ***
80382 AAAAATGTGTCGATCC-AAACGATATAAAATGTAAAAATGAAAAACCGGTATTGAAAGATAAAAC
1 AAAAATGTATCGATCCAAAACGATATAAAAGGTAAAAATGAAAAACCGGTAACAAAAGATAAAAC
* *
80446 CGGTAAAGCGCTACCGGATACATTTAAAGTGTCAGTACTTTAATATAAGGATCGACACTTCGTGA
66 CGGTAAAACGCTACCGGATACATTGAAAGTGTCAGTACTTTAATATAAGGATCGACACTTCGTGA
* *
80511 ATTTAAAAGAGTAGCAGTTTTAAATCCTATAAAGTGT-CGATACTTTTA
131 ATTTAAAAGAGAAGCAGTTTTAAAGCCTAT-AA-TGTACGATAC-TTTA
* **
80559 AAAAATGTATTGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAAAAGGT-AAAA-ATGA-AAAACCGGTAACAAAA-GATA
* * *
80624 AAACCGGTAAAACGTTACTGGATATATTGAAAGTGTC-GATACTTT-ATATAAGGATCGACACTT
62 AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCAG-TACTTTAATATAAGGATCGACACTT
* **
80687 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTACGATACTTTA
126 CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAATGTACGATACTTTA
*
80738 AAAAATATATCGATCCA
1 AAAAATGTATCGATCCA
80755 CAAC
Statistics
Matches: 169, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
177 14 0.08
178 13 0.08
179 26 0.15
180 12 0.07
181 62 0.37
182 42 0.25
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (176 bp):
AAAAATGTATCGATCCAAAACGATATAAAAGGTAAAAATGAAAAACCGGTAACAAAAGATAAAAC
CGGTAAAACGCTACCGGATACATTGAAAGTGTCAGTACTTTAATATAAGGATCGACACTTCGTGA
ATTTAAAAGAGAAGCAGTTTTAAAGCCTATAATGTACGATACTTTA
Done.