Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005455.1 Hibiscus syriacus cultivar Beakdansim tig00012494_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: 111463
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:18626 original size:33 final size:33
Alignment explanation
Indices: 18589--18719 Score: 199
Period size: 33 Copynumber: 4.0 Consensus size: 33
18579 CAATGGAAGC
* * *
18589 CGTGGTGGTATGAGGGATGGTAGCTTTGGTGGA
1 CGTGGTGGAATGAGGGATGGTGGCTTTGGTGGG
18622 CGTGGTGGAATGAGGGATGGTGGCTTTGGTGGG
1 CGTGGTGGAATGAGGGATGGTGGCTTTGGTGGG
* * *
18655 CGTGGCGGTATTAGGGATGGTGGCTTTGGTGGG
1 CGTGGTGGAATGAGGGATGGTGGCTTTGGTGGG
*
18688 CGTGGTGGAATGAGGGATGGTGGTTTTGGTGG
1 CGTGGTGGAATGAGGGATGGTGGCTTTGGTGG
18720 CCCTGGAGGT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.12, C:0.06, G:0.52, T:0.30
Consensus pattern (33 bp):
CGTGGTGGAATGAGGGATGGTGGCTTTGGTGGG
Found at i:18693 original size:18 final size:18
Alignment explanation
Indices: 18639--18695 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
18629 GAATGAGGGA
18639 TGGTGGCTTTGGTGGGCG
1 TGGTGGCTTTGGTGGGCG
* * *
18657 TGGCGG-TATT--AGGG-A
1 TGGTGGCT-TTGGTGGGCG
18672 TGGTGGCTTTGGTGGGCG
1 TGGTGGCTTTGGTGGGCG
18690 TGGTGG
1 TGGTGG
18696 AATGAGGGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
15 7 0.25
16 4 0.14
17 4 0.14
18 13 0.46
ACGTcount: A:0.05, C:0.09, G:0.54, T:0.32
Consensus pattern (18 bp):
TGGTGGCTTTGGTGGGCG
Found at i:19295 original size:63 final size:61
Alignment explanation
Indices: 19148--19335 Score: 198
Period size: 63 Copynumber: 3.0 Consensus size: 61
19138 GAGAAGCCAA
* * * * * * *
19148 ACGAACAGAACGTTGAGCGGAAGGATGTTTCAAAGCGGGCATTTGACTCTCCTCCTGCCTCCT
1 ACGAACAGAAC-TTGAGCAGAAGGATG-TTAAAAGCGAGCATTCGATTCTCCTCCTGCTTCCC
* *
19211 ACAAACAGAACTTGGATCAGAAGGATGTTGAAAAGCGAGCATTCGATTCTCCTCCTGCTTCCC
1 ACGAACAGAACTT-GAGCAGAAGGATGTT-AAAAGCGAGCATTCGATTCTCCTCCTGCTTCCC
* * *
19274 ACGAACAGAACACTGAGCAGAAGGATATTACAAAGC-AGGCATTCGATTCTCCTCCTGTTTCC
1 ACGAACAGAAC-TTGAGCAGAAGGATGTTA-AAAGCGA-GCATTCGATTCTCCTCCTGCTTCC
19336 AGCATGTCTC
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
62 6 0.06
63 99 0.93
64 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (61 bp):
ACGAACAGAACTTGAGCAGAAGGATGTTAAAAGCGAGCATTCGATTCTCCTCCTGCTTCCC
Found at i:28411 original size:22 final size:22
Alignment explanation
Indices: 28386--28457 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
28376 AAGAAAGAAA
28386 GAGTAGATATCTATGGAACTTT
1 GAGTAGATATCTATGGAACTTT
*
28408 GAGTAGATATCTATCACGAGACTATTT
1 GAGTAGATATCTAT--GGA-AC--TTT
*
28435 GAGTA-ATATCCATGGAACTTT
1 GAGTAGATATCTATGGAACTTT
28456 GA
1 GA
28458 AATTTATGGC
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
21 5 0.12
22 14 0.33
23 2 0.05
24 4 0.10
25 2 0.05
26 7 0.17
27 8 0.19
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (22 bp):
GAGTAGATATCTATGGAACTTT
Found at i:32507 original size:26 final size:22
Alignment explanation
Indices: 32459--32504 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
32449 GCTTACTTTT
*
32459 TTTTATTTAATGAAAATCTAAC
1 TTTTATTTAAAGAAAATCTAAC
32481 TTTTATTTATAAGAACATATCTAA
1 TTTTATTTA-AAGAA-A-ATCTAA
32505 ACTCATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 1 0.05
25 6 0.30
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTTATTTAAAGAAAATCTAAC
Found at i:34355 original size:8 final size:8
Alignment explanation
Indices: 34344--34372 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
34334 AAAGAAACAA
34344 GAAGAAGG
1 GAAGAAGG
34352 GAAGAAGG
1 GAAGAAGG
34360 GAAGAA-G
1 GAAGAAGG
34367 GAAGAA
1 GAAGAA
34373 AACCCAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (8 bp):
GAAGAAGG
Found at i:38971 original size:21 final size:21
Alignment explanation
Indices: 38947--39012 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
38937 TTACGAGATG
38947 ATGCAACATTAAAACTGTATA
1 ATGCAACATTAAAACTGTATA
* * *
38968 ATGCATCA-TACAAC-GTATG
1 ATGCAACATTAAAACTGTATA
* ** *
38987 ATGCTATGTTAAAACTGTGTA
1 ATGCAACATTAAAACTGTATA
39008 ATGCA
1 ATGCA
39013 TCAGACAACA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 8 0.25
20 10 0.31
21 14 0.44
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
ATGCAACATTAAAACTGTATA
Found at i:44608 original size:15 final size:16
Alignment explanation
Indices: 44573--44626 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
44563 TTCAATAATA
44573 CAAAATAATCAAAATC
1 CAAAATAATCAAAATC
* *
44589 CAAAATGATCAACA-C
1 CAAAATAATCAAAATC
**
44604 CAAAATTGTC-AAAT-
1 CAAAATAATCAAAATC
44618 CAAAATAAT
1 CAAAATAAT
44627 TTGAGAATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 9 0.30
15 9 0.30
16 12 0.40
ACGTcount: A:0.57, C:0.19, G:0.04, T:0.20
Consensus pattern (16 bp):
CAAAATAATCAAAATC
Found at i:47628 original size:27 final size:28
Alignment explanation
Indices: 47588--47647 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
47578 ATGATTAAAA
* *
47588 TTAAAATTTTAAAAGTTTT-GGGTTTTT
1 TTAAAATTTGAAAAGTTTTAAGGTTTTT
*
47615 TTAATATTTGAAAAGTTTTAAGGTTTTT
1 TTAAAATTTGAAAAGTTTTAAGGTTTTT
47643 TTAAA
1 TTAAA
47648 TATATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (28 bp):
TTAAAATTTGAAAAGTTTTAAGGTTTTT
Found at i:52145 original size:128 final size:128
Alignment explanation
Indices: 51934--52559 Score: 1150
Period size: 128 Copynumber: 4.9 Consensus size: 128
51924 TAATCGGAGT
*
51934 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGTCTTCCATTA--TT-TCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
51996 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
52059 ACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
52124 CATTGCCCTATTACGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
52187 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
52252 CATTGCCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
52315 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
52380 CATTGTCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTC
66 CATTGCCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
52443 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGATAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
52508 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
52560 AATCAGGTAA
Statistics
Matches: 485, Mismatches: 13, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
125 42 0.09
127 2 0.00
128 441 0.91
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:52833 original size:14 final size:14
Alignment explanation
Indices: 52814--52843 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52804 CATAAGTTGA
*
52814 TTTTAATGTATATG
1 TTTTAATATATATG
52828 TTTTAATATATATG
1 TTTTAATATATATG
52842 TT
1 TT
52844 AATGATAAAA
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:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:52997 original size:34 final size:34
Alignment explanation
Indices: 52959--53059 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
52949 AAATTTAATG
*
52959 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
52993 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* *
53027 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
53060 AACATTTATC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:53609 original size:21 final size:21
Alignment explanation
Indices: 53579--53672 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
53569 TATGGTATAA
*
53579 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
53600 AA-CCTGGCGGGCAAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
53621 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
53642 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
53663 AACCCTGCGG
1 AACCCTGCGG
53673 AGATGGCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 3 0.04
21 61 0.91
22 3 0.04
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:55408 original size:15 final size:15
Alignment explanation
Indices: 55390--55444 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 15
55380 TAATAATTAT
55390 ATAAATATTATTTTA
1 ATAAATATTATTTTA
*
55405 ATAAAAAAAATTATATTTA
1 AT---AAATATTAT-TTTA
55424 CATAAATATTATTTTA
1 -ATAAATATTATTTTA
55440 ATAAA
1 ATAAA
55445 AAATAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 8 0.24
18 8 0.24
19 4 0.12
20 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAATATTATTTTA
Found at i:55436 original size:35 final size:34
Alignment explanation
Indices: 55372--55484 Score: 135
Period size: 35 Copynumber: 3.4 Consensus size: 34
55362 TTAATAATTC
* * *
55372 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATATTTACATAAATATTATTTTAA
*
55406 TAAAAAAAATTATATTTACATAAATATTATTTTAA
1 T-AAAAAAATAATATTTACATAAATATTATTTTAA
*
55441 T-AAAAAATAATATTTATATAAATA-TA--TTAA
1 TAAAAAAATAATATTTACATAAATATTATTTTAA
55471 TATAAAAAATAATA
1 TA-AAAAAATAATA
55485 ACTATTTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.07
32 13 0.19
33 21 0.30
34 1 0.01
35 30 0.43
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (34 bp):
TAAAAAAATAATATTTACATAAATATTATTTTAA
Found at i:55454 original size:18 final size:18
Alignment explanation
Indices: 55392--55455 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
55382 ATAATTATAT
*
55392 AAATATTATTTTAATAAA
1 AAATAATATTTTAATAAA
55410 AAA-AATTATATTTACAT---
1 AAATAA-TAT-TTTA-ATAAA
*
55427 AAATATTATTTTAATAAA
1 AAATAATATTTTAATAAA
55445 AAATAATATTT
1 AAATAATATTT
55456 ATATAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
15 2 0.06
16 4 0.11
17 7 0.19
18 17 0.47
19 4 0.11
20 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATAATATTTTAATAAA
Found at i:55463 original size:15 final size:15
Alignment explanation
Indices: 55375--55481 Score: 54
Period size: 15 Copynumber: 6.7 Consensus size: 15
55365 ATAATTCTAA
*
55375 ATAAATAATAATTAT
1 ATAAATAATATTTAT
*
55390 ATAAATATTATTTTAAT
1 ATAAATAATA-TTT-AT
* * *
55407 AAAAAAAATTATATTTAC
1 ---ATAAATAATATTTAT
*
55425 ATAAATATTATTTTAAT
1 ATAAATAATA-TTT-AT
*
55442 AAAAAATAATATTTAT
1 -ATAAATAATATTTAT
*
55458 ATAAAT-ATATTAAT
1 ATAAATAATATTTAT
*
55472 ATAAAAAATA
1 ATAAATAATA
55482 ATAACTATTT
Statistics
Matches: 68, Mismatches: 15, Indels: 18
0.67 0.15 0.18
Matches are distributed among these distances:
14 12 0.18
15 24 0.35
16 7 0.10
17 6 0.09
18 9 0.13
19 3 0.04
20 7 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAATAATATTTAT
Found at i:55485 original size:35 final size:33
Alignment explanation
Indices: 55377--55484 Score: 130
Period size: 33 Copynumber: 3.2 Consensus size: 33
55367 AATTCTAAAT
*
55377 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATATTTATATAAATATTA-TTT-ATAAAAA
* *
55412 AAATTATATTTACATAAATATTATTT-TAATAAA
1 AAATAATATTTATATAAATATTATTTATAA-AAA
* *
55445 AAATAATATTTATATAAATA-TATTAATATAAA
1 AAATAATATTTATATAAATATTATTTATAAAAA
55477 AAATAATA
1 AAATAATA
55485 ACTATTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
32 18 0.28
33 23 0.36
34 3 0.05
35 20 0.31
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATAATATTTATATAAATATTATTTATAAAAA
Found at i:55792 original size:51 final size:51
Alignment explanation
Indices: 55694--55793 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
55684 TAATGGAAGG
* * * *
55694 CGCGTCCCCGGGGATGCGCTTTTCACACGTGGCAGTCGAGCTGGCGAAAGA
1 CGCGTCCCCGGGGATGCGCCTTCCACACGTGGCAGTCGAACTAGCGAAAGA
*
55745 CGCGTCCCCGGGGATGCGCCTTCCACACGTGGCA-TCTAACTCAGCGAAA
1 CGCGTCCCCGGGGATGCGCCTTCCACACGTGGCAGTCGAACT-AGCGAAA
55794 ACACGGATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 5 0.12
51 38 0.88
ACGTcount: A:0.19, C:0.33, G:0.31, T:0.17
Consensus pattern (51 bp):
CGCGTCCCCGGGGATGCGCCTTCCACACGTGGCAGTCGAACTAGCGAAAGA
Found at i:56596 original size:21 final size:21
Alignment explanation
Indices: 56557--56596 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56547 TTTTTTTCCA
* *
56557 ATGATGATATGACATTATCTT
1 ATGATGACATGACAATATCTT
*
56578 ATGATGACATGTCAATATC
1 ATGATGACATGACAATATC
56597 ACTATTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (21 bp):
ATGATGACATGACAATATCTT
Found at i:64177 original size:21 final size:21
Alignment explanation
Indices: 64153--64194 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
64143 AGTTTATTTT
64153 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
64174 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
64195 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:64242 original size:33 final size:33
Alignment explanation
Indices: 64189--64287 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
64179 TTTGTTTCAA
64189 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
64221 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
64254 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
64287 T
1 T
64288 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:65112 original size:21 final size:21
Alignment explanation
Indices: 65060--65113 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
65050 AAACCATTCA
*
65060 GGGGGAATCGATACCCCCTTG
1 GGGGGAATCGGTACCCCCTTG
65081 GGGGGAATCGGTACCCCCTTG
1 GGGGGAATCGGTACCCCCTTG
65102 GGGGGAATCGGT
1 GGGGGAATCGGT
65114 TCCCTCTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTTG
Found at i:65585 original size:15 final size:17
Alignment explanation
Indices: 65559--65590 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
65549 TTCTATGGGA
65559 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
65575 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
65591 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:75677 original size:15 final size:16
Alignment explanation
Indices: 75631--75680 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
75621 ATTATATAAT
*
75631 TATATAATT-TTTTTA
1 TATATTATTCTTTTTA
* * *
75646 CATATTATTCATGTTA
1 TATATTATTCTTTTTA
75662 TAT-TTATTCTTTTTA
1 TATATTATTCTTTTTA
75677 TATA
1 TATA
75681 ATGTATAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (16 bp):
TATATTATTCTTTTTA
Found at i:83339 original size:28 final size:29
Alignment explanation
Indices: 83273--83327 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
83263 ATTAGATATC
*
83273 GTAAATGTTTATTATCTTATTTTTTTTGA
1 GTAAATGTTTATTATCTTATTTTTTATGA
83302 GTAAATGTTTATTATC-TATTTTTTAT
1 GTAAATGTTTATTATCTTATTTTTTAT
83328 ATTTACATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.62
Consensus pattern (29 bp):
GTAAATGTTTATTATCTTATTTTTTATGA
Found at i:83984 original size:32 final size:32
Alignment explanation
Indices: 83948--84012 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
83938 GTCTTTTATA
83948 TGCTGAAATTTAAGATCATATGAAAATCCAAT
1 TGCTGAAATTTAAGATCATATGAAAATCCAAT
83980 TGCTGAAATTTAAGATCATATGAAAATCCAAT
1 TGCTGAAATTTAAGATCATATGAAAATCCAAT
84012 T
1 T
84013 AACTCTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (32 bp):
TGCTGAAATTTAAGATCATATGAAAATCCAAT
Found at i:84927 original size:21 final size:21
Alignment explanation
Indices: 84888--84927 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
84878 ACCCGACCCG
*
84888 AAATAAAAAAATATTTTTATT
1 AAATAAAAAAATATATTTATT
84909 AAATAAAAATAAT-TATTTA
1 AAATAAAAA-AATATATTTA
84928 ATTGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAAAAAAATATATTTATT
Found at i:88796 original size:31 final size:31
Alignment explanation
Indices: 88745--88812 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
88735 CACATGTCCT
* * *
88745 CAAATTATGACCCTTGTTTTAATTTCATCCC
1 CAAACTATGACCCTTATTTTAAATTCATCCC
* **
88776 CAAACTATGACCTTTATTTTAAATTGGTCCC
1 CAAACTATGACCCTTATTTTAAATTCATCCC
88807 CAAACT
1 CAAACT
88813 GTTTTAACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (31 bp):
CAAACTATGACCCTTATTTTAAATTCATCCC
Found at i:89109 original size:60 final size:59
Alignment explanation
Indices: 88965--89134 Score: 200
Period size: 60 Copynumber: 2.9 Consensus size: 59
88955 TTTGGATGAC
* * * * ** *
88965 TTTAAGGATGAACTTGGAATGTTCAAAAGTTTGGGGACTAATTTAGAAAGAGGTCATAG
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGGTCATAG
*
89024 TTTAGGGATGAAATTA-AAAATTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
1 TTTAGGGATGAAATTAGAATA-TTCAAAAGTTTAAGGACTAATTTAGAATGAG-GTCATAG
* * *
89084 TTTTGGGATGAAATTAGAATATTCAAAAGTTTAAAGA-TCAATTTAAAATGA
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACT-AATTTAGAATGA
89135 AAGTTATAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
58 2 0.02
59 42 0.44
60 48 0.51
61 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.32
Consensus pattern (59 bp):
TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGGTCATAG
Found at i:98774 original size:2 final size:2
Alignment explanation
Indices: 98767--98795 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
98757 TGTCAGTAAT
98767 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 T
98796 TAGCGGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.