Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004769.1 Hibiscus syriacus cultivar Beakdansim tig00010752_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: 69593
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:165 original size:29 final size:31
Alignment explanation
Indices: 133--192 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
123 AAACTTTGAA
133 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
162 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
193 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1457 original size:23 final size:23
Alignment explanation
Indices: 1417--1460 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1407 TTTGGCTTTC
*
1417 AAAATCTATTTTGTTTTTAAAAG
1 AAAATCTATTTTGATTTTAAAAG
1440 AAAATC-ATTTTCGATTTTAAA
1 AAAATCTATTTT-GATTTTAAA
1461 TTTTGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (23 bp):
AAAATCTATTTTGATTTTAAAAG
Found at i:3298 original size:29 final size:30
Alignment explanation
Indices: 3230--3288 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3220 AATTTAAGGC
*
3230 AAAATGGTTTTGGACTTGAATTGAATTTAT
1 AAAATGTTTTTGGACTTGAATTGAATTTAT
3260 AAAATGTTTTTGGACTT-AATTGAATTTAT
1 AAAATGTTTTTGGACTTGAATTGAATTTAT
3289 TCAAAGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAT
Found at i:8417 original size:21 final size:21
Alignment explanation
Indices: 8375--8418 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
8365 ACCCCGGGAA
* *
8375 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
8396 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
8417 CT
1 CT
8419 CCGGCACCGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:14003 original size:20 final size:21
Alignment explanation
Indices: 13978--14072 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 21
13968 TTGTGCTTCA
13978 TGCATCGATACACC-TAACA-G
1 TGCATCGATACACCTTAA-ATG
*
13998 TGCATCGATTCATCCTTAAATG
1 TGCATCGATACA-CCTTAAATG
* * *
14020 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTAAATG
* *
14041 TGCACCGATGTACACCTTGAATG
1 TGCATCGA--TACACCTTAAATG
14064 TGCATCGAT
1 TGCATCGAT
14073 GCACAAGGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
20 11 0.18
21 17 0.28
22 15 0.25
23 18 0.30
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (21 bp):
TGCATCGATACACCTTAAATG
Found at i:20756 original size:15 final size:16
Alignment explanation
Indices: 20736--20766 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20726 ACACAAAATC
20736 ATTAATT-AAAATTAA
1 ATTAATTCAAAATTAA
20751 ATTAATTCAAAATTAA
1 ATTAATTCAAAATTAA
20767 GATACCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAATTCAAAATTAA
Found at i:29564 original size:160 final size:168
Alignment explanation
Indices: 29347--29677 Score: 579
Period size: 161 Copynumber: 2.0 Consensus size: 168
29337 GCATTAGCTC
29347 CAAATCCCATATTTATTTAATGGAATAAAAAATCTAGGCCGTTGGTTATTCAACGAAAAA-AAGC
1 CAAATCCCATATTTATTTAATGGAATAAAAAATCTAGGCCGTTGGTTATTCAACGAAAAATAAGC
*
29411 AAAA-AG-TTTGTTATTCAGCAG-AAAACAAGTGCTGCAGTTGAAATGGTG-CGACTTGCCTTCC
66 AAAATAGTTTTGTAATTCAGCAGAAAAACAAGTGCTGCAGTTGAAATGGTGACGACTTGCCTTCC
29472 GAAAGAGACAAAGCATA-GCTCACACGTTGCGA-TCAG
131 GAAAGAGACAAAGCATATGCTCACACGTTGCGATTCAG
29508 CAAATCCCATATTTATTTAATGGAAT-AAAAATCTAGGCCGTTGGTTATTCAACGAAAAATAAGC
1 CAAATCCCATATTTATTTAATGGAATAAAAAATCTAGGCCGTTGGTTATTCAACGAAAAATAAGC
29572 AAAATTAGTTTTGTAATTCAGCAGAAAAACAAGTGCTGCAGTTGAAATGGTGATCGACTTGCCTT
66 AAAA-TAGTTTTGTAATTCAGCAGAAAAACAAGTGCTGCAGTTGAAATGGTGA-CGACTTGCCTT
29637 CCGAAAGAGACAAAGCATATGCTCACACGTTGCGATTCAG
129 CCGAAAGAGACAAAGCATATGCTCACACGTTGCGATTCAG
29677 C
1 C
29678 CGCCCGTTAA
Statistics
Matches: 160, Mismatches: 1, Indels: 10
0.94 0.01 0.06
Matches are distributed among these distances:
160 33 0.21
161 34 0.21
163 2 0.01
164 14 0.09
165 27 0.17
167 30 0.19
168 15 0.09
169 5 0.03
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (168 bp):
CAAATCCCATATTTATTTAATGGAATAAAAAATCTAGGCCGTTGGTTATTCAACGAAAAATAAGC
AAAATAGTTTTGTAATTCAGCAGAAAAACAAGTGCTGCAGTTGAAATGGTGACGACTTGCCTTCC
GAAAGAGACAAAGCATATGCTCACACGTTGCGATTCAG
Found at i:31085 original size:40 final size:40
Alignment explanation
Indices: 31033--31113 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
31023 GATAACGTAA
31033 GTGAACAATTTATGACTTTTGAAACATTAGTGGTAAAAAC
1 GTGAACAATTTATGACTTTTGAAACATTAGTGGTAAAAAC
31073 GTGAACAATTTATGACTTTTGAAACATTAGTGGTAAAAAC
1 GTGAACAATTTATGACTTTTGAAACATTAGTGGTAAAAAC
31113 G
1 G
31114 AAAACTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (40 bp):
GTGAACAATTTATGACTTTTGAAACATTAGTGGTAAAAAC
Found at i:31570 original size:10 final size:10
Alignment explanation
Indices: 31555--31595 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
31545 GTGTTTGTGT
31555 TGTTCGTTTA
1 TGTTCGTTTA
**
31565 TGTTCGTTCG
1 TGTTCGTTTA
31575 TGTTCGTTTA
1 TGTTCGTTTA
*
31585 TATTCGTTTA
1 TGTTCGTTTA
31595 T
1 T
31596 TATTTAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:31580 original size:20 final size:20
Alignment explanation
Indices: 31555--31592 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31545 GTGTTTGTGT
*
31555 TGTTCGTTTATGTTCGTTCG
1 TGTTCGTTTATATTCGTTCG
31575 TGTTCGTTTATATTCGTT
1 TGTTCGTTTATATTCGTT
31593 TATTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.13, G:0.21, T:0.58
Consensus pattern (20 bp):
TGTTCGTTTATATTCGTTCG
Found at i:35669 original size:30 final size:30
Alignment explanation
Indices: 35635--35696 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
35625 GCATACTTTT
35635 AAGCATAAATATTACGTTAAATAAGCAAAC
1 AAGCATAAATATTACGTTAAATAAGCAAAC
*
35665 AAGCATAAATATTACGTTAAATAAGTAAAC
1 AAGCATAAATATTACGTTAAATAAGCAAAC
35695 AA
1 AA
35697 AATATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.24
Consensus pattern (30 bp):
AAGCATAAATATTACGTTAAATAAGCAAAC
Found at i:37883 original size:22 final size:21
Alignment explanation
Indices: 37851--37911 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
37841 AGGTCTTATG
*
37851 GATGGCCCGGAGGACTTACGCAT
1 GATGGCTCGGAGGACTTAC-C-T
*
37874 GAT-GCTCGGAAGACTTA-CT
1 GATGGCTCGGAGGACTTACCT
*
37893 GATGGCTTGGAGGACTTAC
1 GATGGCTCGGAGGACTTAC
37912 AAATCAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.12
20 13 0.41
22 12 0.38
23 3 0.09
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (21 bp):
GATGGCTCGGAGGACTTACCT
Found at i:37942 original size:132 final size:132
Alignment explanation
Indices: 37690--38400 Score: 1068
Period size: 132 Copynumber: 5.4 Consensus size: 132
37680 ATCGAAAATG
* * * * *
37690 TTGAAAACACCCTGC-CTGAATGTCTTATAGATGGCCTGAAGGACTTACGCATCATGCTCGGAAG
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAG
* * *
37754 ACTTACTGATGGCCTGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTTGTTTCTAAAATCTC
66 ACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
37819 AT
131 AT
*
37821 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATGATGCTCGGAAG
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAG
** * * *
37886 ACTTACTGATGGCTTGGAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTCTAAAATTTT
66 ACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
37951 AT
131 AT
* * * *
37953 TTGAAAACATCATGCACTGAAGGTCTTATGGATCGCCCGGAGGACTTACGTATGATGCTCGGAAG
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAG
* *
38018 ACTTACCGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGTCTTAGTTTCTAAAATCTC
66 ACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
38083 AT
131 AT
* ** ** *
38085 TTGAAAACATTCTGCACTGAAGGTCTTATGGATGGCCAAGAAAACTTACTCATCATGCTCGGAAG
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAG
* * * *
38150 ACTTACTGATGGCCCAGAGGACTTACAAATAAAGAAA-CCCCAAAGGCTTTGTTTCTAAAATCTC
66 ACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
38214 AT
131 AT
* *
38216 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCAGAGGACTTACGAAT-ATTGCTCGGAA
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCA-TGCTCGGAA
* *
38280 GAGTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACTCCCGAAGGCTTAGTTTCTAAAATCT
65 GACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCT
38345 CAT
130 CAT
* *
38348 TTGAAAAAATCCTGCACTGAAGGTCTTATGGATGGCCCGGATGACTTACGCAT
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCAT
38401 TAAGAAACTC
Statistics
Matches: 523, Mismatches: 54, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
130 1 0.00
131 131 0.25
132 391 0.75
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (132 bp):
TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAG
ACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
AT
Found at i:38040 original size:20 final size:22
Alignment explanation
Indices: 37987--38043 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
37977 CTTATGGATC
37987 GCCCGGAGGACTTA-CGTATGA
1 GCCCGGAGGACTTACCGTATGA
* *
38008 TGCTCGGAAGACTTACCG-ATG-
1 -GCCCGGAGGACTTACCGTATGA
38029 GCCCGGAGGACTTAC
1 GCCCGGAGGACTTAC
38044 AAATCAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.43
22 15 0.50
23 2 0.07
ACGTcount: A:0.23, C:0.26, G:0.32, T:0.19
Consensus pattern (22 bp):
GCCCGGAGGACTTACCGTATGA
Found at i:38187 original size:264 final size:262
Alignment explanation
Indices: 37690--38384 Score: 1059
Period size: 263 Copynumber: 2.6 Consensus size: 262
37680 ATCGAAAATG
* * * * * *
37690 TTGAAAACACCCTGC-CTGAATGTCTTATAGATGGCCTGAAGGACTTACGCATCATGCTCGGAAG
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGAAT-ATGCTCGGAAG
* * *
37754 ACTTACTGATGGCCTGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTTGTTTCTAAAATCTC
65 ACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
** ** *
37819 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGCATGATGCTCGGA
130 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCAAGAAAACTTACGCATCATGCTCGGA
*** * *
37884 AGACTTACTGATGGCTTGGAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTCTAAAATT
195 AGACTTACTGATGGCCCAGAGGACTTACAAATAAAGAAA-CCCCAAAGGCTTAGTTTCTAAAATC
*
37949 TTAT
259 TCAT
* * *
37953 TTGAAAACATCATGCACTGAAGGTCTTATGGATCGCCCGGAGGACTTACGTATGATGCTCGGAAG
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGAAT-ATGCTCGGAAG
* *
38018 ACTTACCGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGTCTTAGTTTCTAAAATCTC
65 ACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
* *
38083 ATTTGAAAACATTCTGCACTGAAGGTCTTATGGATGGCCAAGAAAACTTACTCATCATGCTCGGA
130 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCAAGAAAACTTACGCATCATGCTCGGA
*
38148 AGACTTACTGATGGCCCAGAGGACTTACAAATAAAGAAACCCCAAAGGCTTTGTTTCTAAAATCT
195 AGACTTACTGATGGCCCAGAGGACTTACAAATAAAGAAACCCCAAAGGCTTAGTTTCTAAAATCT
38213 CAT
260 CAT
*
38216 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCAGAGGACTTACGAATATTGCTCGGAAG
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGAATA-TGCTCGGAAG
* *
38281 AGTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACTCCCGAAGGCTTAGTTTCTAAAATCTC
65 ACTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
*
38346 ATTTGAAAAAATCCTGCACTGAAGGTCTTATGGATGGCC
130 ATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCC
38385 CGGATGACTT
Statistics
Matches: 392, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
262 1 0.00
263 196 0.50
264 195 0.50
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (262 bp):
TTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGGAGGACTTACGAATATGCTCGGAAGA
CTTACTGATGGCCCGGAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCA
TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCAAGAAAACTTACGCATCATGCTCGGAA
GACTTACTGATGGCCCAGAGGACTTACAAATAAAGAAACCCCAAAGGCTTAGTTTCTAAAATCTC
AT
Found at i:39826 original size:28 final size:28
Alignment explanation
Indices: 39785--39847 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
39775 TATAAAAGGC
* *
39785 TCAGGCTAACTTGGGAAGGTAGTGTGTT
1 TCAGGTTAACTTGGGAAGGTAATGTGTT
* *
39813 TCAGGTTAATTTGGGGAGGTAATGTGTT
1 TCAGGTTAACTTGGGAAGGTAATGTGTT
39841 TCAGGTT
1 TCAGGTT
39848 GGCTTATTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.21, C:0.08, G:0.35, T:0.37
Consensus pattern (28 bp):
TCAGGTTAACTTGGGAAGGTAATGTGTT
Found at i:40502 original size:8 final size:7
Alignment explanation
Indices: 40484--40573 Score: 88
Period size: 6 Copynumber: 13.4 Consensus size: 7
40474 GATCTGTCTA
40484 TTTTCTTC
1 TTTT-TTC
40492 TTTCTTTC
1 TTT-TTTC
40500 TTTTTT-
1 TTTTTTC
40506 TTTTTT-
1 TTTTTTC
40512 TTTTTT-
1 TTTTTTC
40518 TTTTTTC
1 TTTTTTC
40525 TTTTTT-
1 TTTTTTC
40531 TTCTTTTC
1 TT-TTTTC
40539 -TTTTT-
1 TTTTTTC
40544 TTTTTT-
1 TTTTTTC
40550 TTTTTTC
1 TTTTTTC
40557 -TTTTTC
1 TTTTTTC
40563 TCTTTTTC
1 T-TTTTTC
40571 TTT
1 TTT
40574 CTTTTTGTGT
Statistics
Matches: 74, Mismatches: 0, Indels: 17
0.81 0.00 0.19
Matches are distributed among these distances:
6 41 0.55
7 16 0.22
8 16 0.22
9 1 0.01
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:40568 original size:14 final size:12
Alignment explanation
Indices: 40496--40579 Score: 102
Period size: 11 Copynumber: 7.0 Consensus size: 12
40486 TTCTTCTTTC
40496 TTTCTTTTTTTT
1 TTTCTTTTTTTT
40508 TTT-TTTTTTTT
1 TTTCTTTTTTTT
*
40519 TTT-TTCTTTTT
1 TTTCTTTTTTTT
*
40530 TTTCTTTTCTTT
1 TTTCTTTTTTTT
40542 TTT-TTTTTTTT
1 TTTCTTTTTTTT
40553 TTTCTTTTTCTCTT
1 TTTCTTTTT-T-TT
40567 TTTCTTTCTTTTT
1 TTTCTTT-TTTTT
40580 GTGTTTTTCC
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
11 31 0.49
12 17 0.27
13 3 0.05
14 10 0.16
15 2 0.03
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:40568 original size:18 final size:16
Alignment explanation
Indices: 40484--40579 Score: 106
Period size: 16 Copynumber: 5.8 Consensus size: 16
40474 GATCTGTCTA
*
40484 TTTTCTTCTTTCTTTCTT
1 TTTTTTTCTTT-TTT-TT
40502 TTTTTTT-TTTTTTTT
1 TTTTTTTCTTTTTTTT
40517 TTTTTTTCTTTTTTTT
1 TTTTTTTCTTTTTTTT
*
40533 CTTTTCTT-TTTTTTTT
1 -TTTTTTTCTTTTTTTT
40549 TTTTTTTCTTTTTCTCTT
1 TTTTTTTCTTTTT-T-TT
*
40567 TTTCTTTCTTTTT
1 TTTTTTTCTTTTT
40580 GTGTTTTTCC
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
15 15 0.22
16 24 0.35
17 10 0.14
18 20 0.29
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTCTTTTTTTT
Found at i:40579 original size:1 final size:1
Alignment explanation
Indices: 40500--40561 Score: 88
Period size: 1 Copynumber: 62.0 Consensus size: 1
40490 TCTTTCTTTC
* * * *
40500 TTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTCTTTTCTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40562 CTCTTTTTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:40597 original size:32 final size:32
Alignment explanation
Indices: 40534--40598 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
40524 CTTTTTTTTC
* * * ** *
40534 TTTTCTTTTTTTTTTTTTTTTTCTTTTTCTCT
1 TTTTCTTTCTTTTTGTGTTTTTCCATATCTCT
40566 TTTTCTTTCTTTTTGTGTTTTTCCATATCTCT
1 TTTTCTTTCTTTTTGTGTTTTTCCATATCTCT
40598 T
1 T
40599 CCTTTTCTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (32 bp):
TTTTCTTTCTTTTTGTGTTTTTCCATATCTCT
Found at i:43131 original size:6 final size:6
Alignment explanation
Indices: 43120--43151 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
43110 AAATAAATAC
43120 ATGCAA ATGCAA ATGCTAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGC-AA ATGCAA ATGCAA A
43152 AATGTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:43142 original size:13 final size:12
Alignment explanation
Indices: 43120--43151 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
43110 AAATAAATAC
43120 ATGCAAATGCAA
1 ATGCAAATGCAA
43132 ATGCTAAATGCAA
1 ATGC-AAATGCAA
43145 ATGCAAA
1 ATGCAAA
43152 AATGTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (12 bp):
ATGCAAATGCAA
Found at i:50948 original size:20 final size:21
Alignment explanation
Indices: 50909--50948 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
50899 TCGTTTGGAT
* *
50909 TTATATAATTATATTTTATAA
1 TTATATAATTAAATTATATAA
50930 TTAT-TAATTAAATTATATA
1 TTATATAATTAAATTATATA
50949 TATGTGTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATATAATTAAATTATATAA
Found at i:52562 original size:16 final size:16
Alignment explanation
Indices: 52541--52572 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52531 TTACTGGCTA
52541 ATTTTCTTTTTCTTTT
1 ATTTTCTTTTTCTTTT
*
52557 ATTTTCTTTTTGTTTT
1 ATTTTCTTTTTCTTTT
52573 TGCATTGCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.81
Consensus pattern (16 bp):
ATTTTCTTTTTCTTTT
Found at i:53653 original size:21 final size:24
Alignment explanation
Indices: 53628--53682 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 24
53618 GCTATGACAA
53628 AATGAAATGGAT-GT-TGAT-TGG
1 AATGAAATGGATAGTGTGATGTGG
53649 AATGAAAT-GATAGTGTGATGTGG
1 AATGAAATGGATAGTGTGATGTGG
53672 AA-GTAAATGGA
1 AATG-AAATGGA
53683 GATATTGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.10
21 10 0.34
22 5 0.17
23 9 0.31
24 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (24 bp):
AATGAAATGGATAGTGTGATGTGG
Found at i:54233 original size:21 final size:21
Alignment explanation
Indices: 54199--54242 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54189 AACCTCAAGG
*
54199 AATTAAACATCATAAACAAAAC
1 AATTAAACAACATAAA-AAAAC
*
54221 AATT-AACAACATACAAAAAC
1 AATTAAACAACATAAAAAAAC
54241 AA
1 AA
54243 CCATCAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.66, C:0.18, G:0.00, T:0.16
Consensus pattern (21 bp):
AATTAAACAACATAAAAAAAC
Found at i:54781 original size:32 final size:32
Alignment explanation
Indices: 54740--54816 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
54730 CCAGGACAGT
54740 TGGGTGTGGTCCCCTCCTGGGTAGCTTGCAGC
1 TGGGTGTGGTCCCCTCCTGGGTAGCTTGCAGC
54772 TGGGTGTGGTCCCCTCCTGGGTAGCTTGCAGC
1 TGGGTGTGGTCCCCTCCTGGGTAGCTTGCAGC
54804 TGGGTGTGGTCCC
1 TGGGTGTGGTCCC
54817 GACAGAATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.05, C:0.27, G:0.39, T:0.29
Consensus pattern (32 bp):
TGGGTGTGGTCCCCTCCTGGGTAGCTTGCAGC
Found at i:61793 original size:108 final size:109
Alignment explanation
Indices: 61681--61897 Score: 244
Period size: 109 Copynumber: 2.0 Consensus size: 109
61671 GTATAGACCA
* * * ** * * *
61681 AAGTTGTCATTTGCCCGTTTTTATGTATGCTTTAT-TTTTTTTGGATATTTG-TTGTTTAGTCCC
1 AAGTTGTCATTTACCCATTTTTATGCATAATATATGTTTGTTCGGATATTTGCTT-TTTAGT-CC
61744 CTATA-GTTTAGCGTGTTTTTGCATGTTT-GTCACATGTAGGGACTG
64 CTATATGTTTAGCGTGTTTTTGCAT-TTTGGTCACATGTAGGGACTG
* * * *
61789 AAGTTGTTATTTACCCATTTTTATGCCTAATATGTGTTTGTTCGGTTATTTGCTTTTTAGTCCCT
1 AAGTTGTCATTTACCCATTTTTATGCATAATATATGTTTGTTCGGATATTTGCTTTTTAGTCCCT
* * *
61854 ATATGTTTAGTGTGTTTTTGCATTTTGGTCATATGTAGTGACTG
66 ATATGTTTAGCGTGTTTTTGCATTTTGGTCACATGTAGGGACTG
61898 TTTAATTTTA
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
108 36 0.40
109 52 0.58
110 2 0.02
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.51
Consensus pattern (109 bp):
AAGTTGTCATTTACCCATTTTTATGCATAATATATGTTTGTTCGGATATTTGCTTTTTAGTCCCT
ATATGTTTAGCGTGTTTTTGCATTTTGGTCACATGTAGGGACTG
Found at i:62249 original size:24 final size:24
Alignment explanation
Indices: 62222--62271 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
62212 TATAGTCTTA
* *
62222 TTTGCATTTTG-TTTTATTTTAATT
1 TTTGCATGTTGCTTTTATGTT-ATT
62246 TTTGCATGTTGCTTTTATGTTATT
1 TTTGCATGTTGCTTTTATGTTATT
62270 TT
1 TT
62272 ATTTTAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.14, C:0.06, G:0.12, T:0.68
Consensus pattern (24 bp):
TTTGCATGTTGCTTTTATGTTATT
Found at i:62894 original size:21 final size:21
Alignment explanation
Indices: 62865--62911 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
62855 ATTCTGACTA
*
62865 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCAATTTCCCAAAT
* * *
62886 TCGCGTTGCAATTTTCCTAAT
1 TCGCATTGCAATTTCCCAAAT
62907 TCGCA
1 TCGCA
62912 ATGCGAATAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTGCAATTTCCCAAAT
Found at i:63673 original size:20 final size:20
Alignment explanation
Indices: 63630--63697 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
63620 CGATTCTTGC
** **
63630 GTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTCATTTTCGT
63650 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
63670 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
63690 GTTGCGAT
1 GTTGCGAT
63698 TTAAAATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.43
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:63707 original size:20 final size:20
Alignment explanation
Indices: 63664--63707 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
63654 CGATAGTCAT
** *
63664 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAA
63684 TTTCGTGTTGCGATTTAAAA
1 TTTCGTGTTGCGATTTAAAA
63704 TTTC
1 TTTC
63708 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAA
Found at i:65596 original size:20 final size:20
Alignment explanation
Indices: 65571--65679 Score: 148
Period size: 20 Copynumber: 5.5 Consensus size: 20
65561 AGAATAGTTT
65571 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
65591 ACTATCGCAACGCG-AAATG
1 ACTATCGCAATGCGAAAATG
*
65610 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
65630 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
**
65650 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
*
65670 GCTATCGCAA
1 ACTATCGCAA
65680 CGAAAGAATC
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
19 19 0.23
20 64 0.77
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:65625 original size:39 final size:40
Alignment explanation
Indices: 65571--65681 Score: 161
Period size: 39 Copynumber: 2.8 Consensus size: 40
65561 AGAATAGTTT
65571 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAA-ATG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAATATG
* * *
65610 ACTATCGCAACGCGAAAATGACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAATATG
** *
65650 ACTATCGCAATGCGAATTTGGCTATCGCAACG
1 ACTATCGCAATGCGAAAATGACTATCGCAACG
65682 AAAGAATCGC
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 34 0.54
40 29 0.46
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGCGAATATG
Found at i:65748 original size:20 final size:20
Alignment explanation
Indices: 65723--65809 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
65713 GATTCTCTCG
**
65723 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
65743 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
65763 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
65783 TTGCAATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
65803 TTGCGAT
1 TTGCGAT
65810 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:66383 original size:21 final size:21
Alignment explanation
Indices: 66292--66396 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
66282 GACTCACCTG
*
66292 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
66314 T-ATCATTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
66334 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
66355 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
66376 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
66397 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:66389 original size:42 final size:42
Alignment explanation
Indices: 66319--66399 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
66309 TCCCCTATCA
*
66319 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCG
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACCG
* ** *
66361 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
66400 ACATTCTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACCG
Found at i:67217 original size:19 final size:19
Alignment explanation
Indices: 67172--67293 Score: 173
Period size: 19 Copynumber: 6.6 Consensus size: 19
67162 GAAGAAACTA
*
67172 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
67191 ATTTTCGCATTGCGATTTTC
1 A-TTTCGCATTGCGATTTTC
67211 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
67230 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
* *
67247 A-CTCG--TTGCGATTTTT
1 ATTTCGCATTGCGATTTTC
67263 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
67282 ATTTCGCATTGC
1 ATTTCGCATTGC
67294 AATTCTCTCG
Statistics
Matches: 92, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
14 6 0.07
16 6 0.07
17 7 0.08
19 55 0.60
20 18 0.20
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:67256 original size:33 final size:34
Alignment explanation
Indices: 67178--67278 Score: 132
Period size: 33 Copynumber: 2.9 Consensus size: 34
67168 ACTAATTTCG
*
67178 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCATTT
1 CGTTGCGATTTTCA-TTTCGCATTGCGA--TTCATCT
67215 CGCATTGCGATTTTCATTTCGCATTGCGATTCA-CT
1 CG--TTGCGATTTTCATTTCGCATTGCGATTCATCT
*
67250 CGTTGCGATTTTTATTTCGCATTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
67279 TTCATTTCGC
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
33 26 0.43
35 3 0.05
36 4 0.07
37 2 0.03
38 13 0.22
39 12 0.20
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCATCT
Found at i:67278 original size:52 final size:52
Alignment explanation
Indices: 67200--67330 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 52
67190 CATTTTCGCA
*
67200 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATTCACTCG
* *
67252 TTGCGATTTTTATTTCGCATTGCGATTTTCATTTCGCATTGCAATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATTCACTCG
** *
67304 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
67331 AGTCAATTCC
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 61 0.86
53 10 0.14
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCAATTCACTCG
Found at i:67327 original size:20 final size:20
Alignment explanation
Indices: 67302--67395 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
67292 GCAATTCTCT
67302 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
67322 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
67342 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
67362 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
67382 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
67396 AATTAATGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 65 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Done.