Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005418.1 Hibiscus syriacus cultivar Beakdansim tig00012430_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: 54273
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:14484 original size:31 final size:31
Alignment explanation
Indices: 14442--14606 Score: 168
Period size: 31 Copynumber: 5.3 Consensus size: 31
14432 CTAATGTGAC
* * *
14442 TCTTGGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTGGGTAGGCCCTGTGGCCCTGAGATCTT
* * *
14473 TCTTGGATAGGCCTTGTGGCCCTGAGATTTT
1 TCTTGGGTAGGCCCTGTGGCCCTGAGATCTT
* ** * * *
14504 TCTTGGGCAGGCCCCATGGACTTGAGATCAT
1 TCTTGGGTAGGCCCTGTGGCCCTGAGATCTT
* * ** *
14535 TCTTAGATAGGCCCTACGACCCTGAGATCTT
1 TCTTGGGTAGGCCCTGTGGCCCTGAGATCTT
*
14566 TCTTGGGTAGGCCCTGTGGCCCTGAGAACTT
1 TCTTGGGTAGGCCCTGTGGCCCTGAGATCTT
14597 TCTTGGGTAG
1 TCTTGGGTAG
14607 TCTCTCAAGC
Statistics
Matches: 104, Mismatches: 30, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (31 bp):
TCTTGGGTAGGCCCTGTGGCCCTGAGATCTT
Found at i:14600 original size:62 final size:62
Alignment explanation
Indices: 14442--14592 Score: 185
Period size: 62 Copynumber: 2.4 Consensus size: 62
14432 CTAATGTGAC
* * * * ** * *
14442 TCTTGGGTAGGCTCTGCGGCCCTGAGATCATTCTTGGATAGGCCTTGTGGCCCTGAGATTTT
1 TCTTGGGTAGGCCCTGTGGCCCTGAGATCATTCTTAGATAGGCCCTACGACCCTGAGATCTT
* ** * *
14504 TCTTGGGCAGGCCCCATGGACTTGAGATCATTCTTAGATAGGCCCTACGACCCTGAGATCTT
1 TCTTGGGTAGGCCCTGTGGCCCTGAGATCATTCTTAGATAGGCCCTACGACCCTGAGATCTT
14566 TCTTGGGTAGGCCCTGTGGCCCTGAGA
1 TCTTGGGTAGGCCCTGTGGCCCTGAGA
14593 ACTTTCTTGG
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (62 bp):
TCTTGGGTAGGCCCTGTGGCCCTGAGATCATTCTTAGATAGGCCCTACGACCCTGAGATCTT
Found at i:23771 original size:21 final size:21
Alignment explanation
Indices: 23732--23771 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23722 TCATTTATAT
*
23732 ATTATTTTTTTCAATTAAATC
1 ATTATTTTTTTCAAGTAAATC
23753 ATTATTTTTATT-AAGTAAA
1 ATTATTTTT-TTCAAGTAAA
23772 AATAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTATTTTTTTCAAGTAAATC
Found at i:25883 original size:22 final size:23
Alignment explanation
Indices: 25852--25898 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
25842 TATTTTATTT
25852 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
25875 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
25897 TA
1 TA
25899 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:25905 original size:30 final size:32
Alignment explanation
Indices: 25837--25925 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 32
25827 TATTAATTAT
* *
25837 TAAAAT-ATTTTAT-TTTATTAATATTTCTAA
1 TAAAATAATATTATATTTATTAATATTTATAA
*
25867 TAATATAATATTATATTT-TTAATA-TTATAA
1 TAAAATAATATTATATTTATTAATATTTATAA
*
25897 TAAAATAATCAATTATATTATAATAATAT
1 TAAAATAAT--ATTATATT-TATTAATAT
25926 AAGATATGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
30 18 0.38
31 12 0.26
32 11 0.23
33 1 0.02
34 5 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TAAAATAATATTATATTTATTAATATTTATAA
Found at i:28149 original size:22 final size:22
Alignment explanation
Indices: 28106--28146 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28096 AAAAAATTAT
28106 TTTTTATTAAATATTTTTAATA
1 TTTTTATTAAATATTTTTAATA
*
28128 TTTTTATTTAAT-TTTTTAA
1 TTTTTATTAAATATTTTTAA
28147 ATAATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTAAATATTTTTAATA
Found at i:28438 original size:11 final size:11
Alignment explanation
Indices: 28424--28458 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
28414 TATATTATTC
28424 ATATATTTAAA
1 ATATATTTAAA
28435 ATATA-TTAAA
1 ATATATTTAAA
*
28445 ATACATTTAAA
1 ATATATTTAAA
28456 ATA
1 ATA
28459 AAAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATATTTAAA
Found at i:28690 original size:23 final size:24
Alignment explanation
Indices: 28660--28716 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
28650 TCTATTTGCT
28660 TTAATTAAATTAAAATAAAT-TAA
1 TTAATTAAATTAAAATAAATATAA
*
28683 TTAATTAAAATAAAATAAATATAA
1 TTAATTAAATTAAAATAAATATAA
*
28707 -TCATTAAATT
1 TTAATTAAATT
28717 GAATTGTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 27 0.90
24 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAATTAAATTAAAATAAATATAA
Found at i:29972 original size:16 final size:15
Alignment explanation
Indices: 29934--29973 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
29924 TTGGTTGATG
*
29934 TAAGTTTT-CTTCTT
1 TAAGTTTTGGTTCTT
29948 TAAGTTTTGGTTCTT
1 TAAGTTTTGGTTCTT
29963 TAATGTTTTGG
1 TAA-GTTTTGG
29974 ATAAGTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.35
15 8 0.35
16 7 0.30
ACGTcount: A:0.15, C:0.07, G:0.17, T:0.60
Consensus pattern (15 bp):
TAAGTTTTGGTTCTT
Found at i:30480 original size:17 final size:17
Alignment explanation
Indices: 30458--30501 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
30448 TCAAATACAA
30458 AACAAGCCCAGCAAAAC
1 AACAAGCCCAGCAAAAC
30475 AACAAGCCCAGCAAAAC
1 AACAAGCCCAGCAAAAC
*
30492 AACAAACCCA
1 AACAAGCCCA
30502 CGCTGACCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.55, C:0.36, G:0.09, T:0.00
Consensus pattern (17 bp):
AACAAGCCCAGCAAAAC
Found at i:31495 original size:8 final size:8
Alignment explanation
Indices: 31482--31552 Score: 53
Period size: 7 Copynumber: 9.5 Consensus size: 8
31472 AATCAATTCG
31482 TATTTTAT
1 TATTTTAT
31490 TATTTTAT
1 TATTTTAT
*
31498 T-TTTAAT
1 TATTTTAT
31505 T-TTTTAT
1 TATTTTAT
*
31512 TA-TTTAA
1 TATTTTAT
*
31519 TATATTA-
1 TATTTTAT
*
31526 CATTTTAT
1 TATTTTAT
31534 TA-TTTAT
1 TATTTTAT
* *
31541 TCTATTAT
1 TATTTTAT
31549 TATT
1 TATT
31553 ATGGTATATT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
7 29 0.60
8 19 0.40
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTTTAT
Found at i:31509 original size:14 final size:15
Alignment explanation
Indices: 31482--31519 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
31472 AATCAATTCG
*
31482 TATTTTATTATTTTAT
1 TATTTAATT-TTTTAT
31498 T-TTTAATTTTTTAT
1 TATTTAATTTTTTAT
31512 TATTTAAT
1 TATTTAAT
31520 ATATTACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 12 0.60
16 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTAATTTTTTAT
Found at i:31629 original size:11 final size:9
Alignment explanation
Indices: 31584--31675 Score: 60
Period size: 10 Copynumber: 9.3 Consensus size: 9
31574 TATATATTCC
31584 ATTATTTTT
1 ATTATTTTT
*
31593 ATTATTATT
1 ATTATTTTT
31602 ATTGATTTTT
1 ATT-ATTTTT
*
31612 TTCTATTTTT
1 AT-TATTTTT
31622 CATTTATTTATT
1 -A-TTATTT-TT
31634 ATTATTTTTT
1 ATTA-TTTTT
*
31644 CATACATTTTT
1 -AT-TATTTTT
*
31655 A-TATTTGT
1 ATTATTTTT
31663 ATATATTTTT
1 AT-TATTTTT
31673 ATT
1 ATT
31676 TTATTATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
8 6 0.09
9 12 0.18
10 26 0.40
11 17 0.26
12 4 0.06
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (9 bp):
ATTATTTTT
Found at i:31639 original size:21 final size:19
Alignment explanation
Indices: 31585--31689 Score: 70
Period size: 19 Copynumber: 5.3 Consensus size: 19
31575 ATATATTCCA
*
31585 TTATTTTTATTATTATTAT
1 TTATTTTTATTATTTTTAT
* *
31604 TGATTTTTTTCTATTTTTCAT
1 TTATTTTTAT-TATTTTT-AT
31625 TTATTTATTATTATTTTTTCAT
1 TTATTT-TTATTA-TTTTT-AT
** *
31647 ACATTTTTA-TATTTGTAT
1 TTATTTTTATTATTTTTAT
* *
31665 ATATTTTTATT-TTATTATT
1 TTATTTTTATTATTTTTA-T
31684 TTATTT
1 TTATTT
31690 ATACTATGTA
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
18 14 0.21
19 19 0.28
20 8 0.12
21 12 0.18
22 15 0.22
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (19 bp):
TTATTTTTATTATTTTTAT
Found at i:31652 original size:22 final size:20
Alignment explanation
Indices: 31617--31660 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
31607 TTTTTTTCTA
**
31617 TTTTTCATTTATTTATTATTAT
1 TTTTTCATACATTT-TTA-TAT
31639 TTTTTCATACATTTTTATAT
1 TTTTTCATACATTTTTATAT
31659 TT
1 TT
31661 GTATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
22 12 0.60
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTCATACATTTTTATAT
Found at i:31700 original size:36 final size:35
Alignment explanation
Indices: 31652--31722 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
31642 TTCATACATT
* *
31652 TTTATATTTGTATATATTTTTATTTTATTATTTTA
1 TTTATATATGTATATATTTTCATTTTATTATTTTA
* * *
31687 TTTATACTATGTATTTATTTTCATTTTGTTTTTTTA
1 TTTATA-TATGTATATATTTTCATTTTATTATTTTA
31723 GTTTCTTTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.70
Consensus pattern (35 bp):
TTTATATATGTATATATTTTCATTTTATTATTTTA
Found at i:35730 original size:95 final size:97
Alignment explanation
Indices: 35558--35818 Score: 327
Period size: 95 Copynumber: 2.7 Consensus size: 97
35548 ATTATTTATA
* * * * *
35558 TATATATACACAATAAAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAAGATCCCGACTTTATG
1 TATATCTATACAAT-AAACTTGAGTTATCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATG
*
35623 GATAAGAGTCAGCTAGCCTGATAAAG-G-TGAT
65 GATAAGAGTCAGCTAGCCTGATAAAGAGATAAT
35654 TATA-CTATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATG
1 TATATCTATACAATAAA-CTTGAGTTATCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATG
* *
35718 GATAATATTCAGCTAGCCTGATAAAGATGATAAT
65 GATAAGAGTCAGCTAGCCTGATAAAGA-GATAAT
* * *
35752 TATATTTATACAATAATA-TTGAGTTTTCCCTCTAGAA-CAATTGGTTAAACGCCCC-AGCTTTA
1 TATATCTATACAATAA-ACTTGAGTTATCCCTCTA-AAGCAATTGGTTAAACACCCCGA-CTTTA
35814 TGGAT
63 TGGAT
35819 TCAACTAGCC
Statistics
Matches: 146, Mismatches: 11, Indels: 14
0.85 0.06 0.08
Matches are distributed among these distances:
94 3 0.02
95 75 0.51
96 4 0.03
97 2 0.01
98 49 0.34
99 12 0.08
100 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (97 bp):
TATATCTATACAATAAACTTGAGTTATCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATGG
ATAAGAGTCAGCTAGCCTGATAAAGAGATAAT
Found at i:36915 original size:110 final size:110
Alignment explanation
Indices: 36726--37028 Score: 434
Period size: 110 Copynumber: 2.8 Consensus size: 110
36716 ATGGTGGTTT
** *
36726 GCTCAACTTCACAAAGAAGGGGCGACT-G---TCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGGCTATCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* ** ** *
36787 AATTTCAACTTCACAACGAAGGATATTGGACTTGAGGCAACATAA
66 AATTTCAACTTCACAACGAAGGATATTAGACTCAAGAAAACACAA
* *
36832 GCTCAACTTCGCAGCGAAGGGGCGACTGGCTATCAATAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGGCTATCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
36897 AATTTCAACTTCACAACGAAGAATATTAGACTCAAGAAAACACAA
66 AATTTCAACTTCACAACGAAGGATATTAGACTCAAGAAAACACAA
* *
36942 GCTCAACTTCACAGCGAAGGGGCAACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGGCTATCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
37007 AATTTTAACTTCACAGCGAAGG
66 AATTTCAACTTCACAACGAAGG
37029 GGCGACTGGC
Statistics
Matches: 174, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
106 24 0.14
107 1 0.01
110 149 0.86
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGGCTATCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAACGAAGGATATTAGACTCAAGAAAACACAA
Found at i:37054 original size:67 final size:67
Alignment explanation
Indices: 36944--37095 Score: 234
Period size: 67 Copynumber: 2.3 Consensus size: 67
36934 AAACACAAGC
36944 TCAACTTCACAGCGAAGGGGCAACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAGCGAAGGGGCAACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
37009 TT
66 TT
* * * * **
37011 TTAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTTGGAGTCAA
1 TCAACTTCACAGCGAAGGGGCAACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
37076 TT
66 TT
37078 TCAACTTCAC-GACGAAGG
1 TCAACTTCACAG-CGAAGG
37096 ATATTGGACT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
66 1 0.01
67 76 0.99
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (67 bp):
TCAACTTCACAGCGAAGGGGCAACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
TT
Found at i:37062 original size:177 final size:177
Alignment explanation
Indices: 36836--37205 Score: 578
Period size: 177 Copynumber: 2.1 Consensus size: 177
36826 ACATAAGCTC
* *
36836 AACTTCGCAGCGAAGGGGCGACTGGCTATCAATAAACAACTTTTCAGTTTCATTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGGCTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
36901 TCAACTTCACAACGAAGAATATTAGACTCAAGAAAACACAAGCTCAACTTCACAGCGAAGGGGCA
66 TCAACTTCACAACGAAGAATATTAGACTCAAGAAAACACAAGCTCAACTTCACAGCGAAGGGGCA
** *
36966 ACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTT
131 ACTGACTATCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATTTT
* **
37013 AACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTTGGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGGCTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
* * * * * * * *
37078 TCAACTTCACGACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTTACAGCGAATGGGCG
66 TCAACTTCACAACGAAGAATATTAGACTCAAGAAAACACAAGCTCAACTTCACAGCGAAGGGGCA
* *
37143 ACTGACTGTCAACAAACAACTTCCCAGTTTTATTCAGAGCCAATTTT
131 ACTGACTATCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATTTT
37190 AACTTCACAGCGAAGG
1 AACTTCACAGCGAAGG
37206 ATATTGGACT
Statistics
Matches: 175, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
177 175 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (177 bp):
AACTTCACAGCGAAGGGGCGACTGGCTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
TCAACTTCACAACGAAGAATATTAGACTCAAGAAAACACAAGCTCAACTTCACAGCGAAGGGGCA
ACTGACTATCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATTTT
Found at i:37157 original size:110 final size:110
Alignment explanation
Indices: 37013--37215 Score: 300
Period size: 110 Copynumber: 1.8 Consensus size: 110
37003 AGTCAATTTT
* ** ** *
37013 AACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTTGGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATT
37078 TCAACTTCAC-GACGAAGGATATTGGACTCGAGACAACACAAGCTC
66 TCAACTTCACAG-CGAAGGATATTGGACTCGAGACAACACAAGCTC
* * *
37123 AACTTTACAGCGAATGGGCGACTGACTGTCAACAAACAACTTCCCAGTTTTATTCAGAGCCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATT
*
37188 TTAACTTCACAGCGAAGGATATTGGACT
66 TCAACTTCACAGCGAAGGATATTGGACT
37216 TGAAACAGTA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 81 0.99
111 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (110 bp):
AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATT
TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
Found at i:37742 original size:36 final size:36
Alignment explanation
Indices: 37689--37838 Score: 239
Period size: 36 Copynumber: 4.1 Consensus size: 36
37679 ATTTACTCAA
37689 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
37726 AAAC-AATTTACGTCTCTCTTGAGACAGTTTCCCTGG
1 AAACAAATTT-TGTCTCTCTTGAGACAGTTTCCCTTG
*
37762 GAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
37798 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
37834 AAACA
1 AAACA
37839 TCAATCTTTG
Statistics
Matches: 104, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
35 3 0.03
36 92 0.88
37 9 0.09
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:37893 original size:67 final size:67
Alignment explanation
Indices: 37788--37938 Score: 207
Period size: 67 Copynumber: 2.2 Consensus size: 67
37778 TCTTGAGACA
* * * *
37788 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATC-AATCTTTGAA
1 GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACA-CAAACCTTTGAA
*
37851 TAT
65 AAT
37854 GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACACGAAAAACCTTTG
1 GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACAC---AAACCTTTG
37919 AAAAT
63 AAAAT
37924 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
37939 CAAAACTTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
66 14 0.19
67 35 0.47
70 26 0.35
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (67 bp):
GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACACAAACCTTTGAAA
AT
Found at i:39093 original size:2 final size:2
Alignment explanation
Indices: 39086--39133 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
39076 TTGAGAAATA
39086 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
39128 AT AT AT
1 AT AT AT
39134 CGCCACCGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39560 original size:19 final size:18
Alignment explanation
Indices: 39531--39576 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
39521 TCAATTCGTA
39531 TTTTA-TTATTTTA-ATT
1 TTTTATTTATTTTACATT
39547 TTATATATTTA-TTTACATT
1 TT-T-TATTTATTTTACATT
39566 TTTTATTTATT
1 TTTTATTTATT
39577 ATATTACGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 7 0.28
18 8 0.32
19 8 0.32
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATTTATTTTACATT
Found at i:39571 original size:21 final size:21
Alignment explanation
Indices: 39545--39603 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
39535 ATTATTTTAA
*
39545 TTTTATATATTTATTTACATT
1 TTTTATTTATTTATTTACATT
*
39566 TTTTATTTA-TTATATTACGTT
1 TTTTATTTATTTAT-TTACATT
39587 TTATTATTTATTCTATT
1 TT-TTATTTATT-TATT
39604 ATTATTATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 16 0.50
22 7 0.22
23 2 0.06
24 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTATTTATTTATTTACATT
Found at i:39593 original size:3 final size:3
Alignment explanation
Indices: 39587--39703 Score: 58
Period size: 3 Copynumber: 35.7 Consensus size: 3
39577 ATATTACGTT
*
39587 TTA TTA TTTA TT- CTA TTA TTA TTA TGGTA -TA TTA TATA TATA TTCCA
1 TTA TTA -TTA TTA TTA TTA TTA TTA T--TA TTA TTA T-TA T-TA TT--A
* * * * *
39634 TTC TTT TTA TTA TTA TTA TTA TTA TTTA TTT TTT TCTA TTT TTCA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TT-A -TTA
39683 TTTA TTA TTA TTA TTA TTA TT
1 -TTA TTA TTA TTA TTA TTA TT
39704 TTAGTATTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
2 3 0.03
3 63 0.68
4 20 0.22
5 7 0.08
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39593 original size:22 final size:21
Alignment explanation
Indices: 39532--39604 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 21
39522 CAATTCGTAT
* *
39532 TTTATTATTTTA-ATTTTATA
1 TTTATTATATTACATTTTTTA
*
39552 TAT-TTAT-TTACATTTTTTA
1 TTTATTATATTACATTTTTTA
*
39571 TTTATTATATTACGTTTTATTA
1 TTTATTATATTACATTTT-TTA
*
39593 TTTATTCTATTA
1 TTTATTATATTA
39605 TTATTATGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.07
19 13 0.30
20 6 0.14
21 8 0.18
22 14 0.32
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (21 bp):
TTTATTATATTACATTTTTTA
Found at i:39725 original size:44 final size:44
Alignment explanation
Indices: 39637--39758 Score: 117
Period size: 44 Copynumber: 2.7 Consensus size: 44
39627 TATTCCATTC
* ** *
39637 TTTTTATTATTATTATTATTA-TTTATTTTTTTCTATTTTTCAT
1 TTTTTATTATTATTATTATTATTTTATATTTTTCTATCATACAT
39680 TTATTTATTATTATTATTATTATTTTAGTATTTTT-TA-CATACAT
1 TT-TTTATTATTATTATTATTATTTTA-TATTTTTCTATCATACAT
*
39724 TTTTATATT-TGTATATATTTTTATTTTATTATTTT
1 TTTT-TATTAT-TAT-TATTATTATTTTA-TATTTT
39759 ATTTATACTA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.07
44 32 0.48
45 24 0.36
46 6 0.09
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (44 bp):
TTTTTATTATTATTATTATTATTTTATATTTTTCTATCATACAT
Found at i:41769 original size:20 final size:20
Alignment explanation
Indices: 41744--41783 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41734 CCTCAATATC
41744 GGGTTAGTGACCAAATTGTG
1 GGGTTAGTGACCAAATTGTG
41764 GGGTTAGTGACCAAATTGTG
1 GGGTTAGTGACCAAATTGTG
41784 AGATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.30
Consensus pattern (20 bp):
GGGTTAGTGACCAAATTGTG
Found at i:48685 original size:23 final size:22
Alignment explanation
Indices: 48659--48724 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
48649 TCTTATACGA
48659 CACTTCGTTGCATTTCTACGCGG
1 CACTTCG-TGCATTTCTACGCGG
* ** *
48682 CACTTCGGTACAAATCTACGTGG
1 CACTTC-GTGCATTTCTACGCGG
*
48705 CACTTCAGTGCATTTATACG
1 CACTTC-GTGCATTTCTACG
48725 AGCTGTGGTG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (22 bp):
CACTTCGTGCATTTCTACGCGG
Found at i:50480 original size:43 final size:42
Alignment explanation
Indices: 50410--50588 Score: 214
Period size: 43 Copynumber: 4.2 Consensus size: 42
50400 ATGGTAATTA
* *
50410 CGGCGTTTGTTTCAAAAACGCCACTACAGATCTGACCTTTTG
1 CGGCGTTTGTTACAAAAACGCCGCTACAGATCTGACCTTTTG
* * * * *
50452 CGGCATTTGTATCCAAAAACGCTGCTACAAATCTGAACTTTTG
1 CGGCGTTTGT-TACAAAAACGCCGCTACAGATCTGACCTTTTG
*
50495 CGGCGTTTGTCTACAAAAACGCCGCTATAGATCTGACCTTTTG
1 CGGCGTTTGT-TACAAAAACGCCGCTACAGATCTGACCTTTTG
* * * * *
50538 CGGCGTTTGTTTCAAAAAAGCCTCTATAGATCTTGACTTTTTG
1 CGGCGTTTGTTACAAAAACGCCGCTACAGATC-TGACCTTTTG
50581 CGGCGTTT
1 CGGCGTTT
50589 TTATTTCACA
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
42 28 0.24
43 90 0.76
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (42 bp):
CGGCGTTTGTTACAAAAACGCCGCTACAGATCTGACCTTTTG
Found at i:52481 original size:12 final size:12
Alignment explanation
Indices: 52464--52488 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52454 GAGCTATGGC
52464 AAAATCAATAAA
1 AAAATCAATAAA
52476 AAAATCAATAAA
1 AAAATCAATAAA
52488 A
1 A
52489 TAGATGATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATCAATAAA
Found at i:52867 original size:81 final size:83
Alignment explanation
Indices: 52729--52891 Score: 296
Period size: 81 Copynumber: 2.0 Consensus size: 83
52719 CCATACAAGA
52729 ATGCAATCAATAAAAAGTTCCTTCCACAATGGGGCGAGCTTTGCACAAAGCCTTCAAGGGATTAG
1 ATGCAATCAATAAAAAGTTCCTTCCACAATGGGGCGAGCTTTGCACAAAGCCTTCAAGGGATTAG
52794 CTTTAGGCATGGTGCCTCG
66 C-TTAGGCATGGTGCCTCG
52813 ATGCAATCAAT-AAAAGTTCCTT-C-CAATGGGGCGAGCTTTGCACAAAGCCTTCAAGGGATTAG
1 ATGCAATCAATAAAAAGTTCCTTCCACAATGGGGCGAGCTTTGCACAAAGCCTTCAAGGGATTAG
52875 CTTAGGCATGGTGCCTC
66 CTTAGGCATGGTGCCTC
52892 CTGTTTCGTT
Statistics
Matches: 79, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
80 16 0.20
81 40 0.51
82 1 0.01
83 11 0.14
84 11 0.14
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (83 bp):
ATGCAATCAATAAAAAGTTCCTTCCACAATGGGGCGAGCTTTGCACAAAGCCTTCAAGGGATTAG
CTTAGGCATGGTGCCTCG
Done.