Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003049.1 Hibiscus syriacus cultivar Beakdansim tig00006352_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: 118299
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2887 original size:28 final size:29
Alignment explanation
Indices: 2856--2915 Score: 113
Period size: 28 Copynumber: 2.1 Consensus size: 29
2846 CCACAATGTC
2856 AAAGTGGTTCAATATTTAGCCTTGTTT-T
1 AAAGTGGTTCAATATTTAGCCTTGTTTGT
2884 AAAGTGGTTCAATATTTAGCCTTGTTTGT
1 AAAGTGGTTCAATATTTAGCCTTGTTTGT
2913 AAA
1 AAA
2916 AGGAGACCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.43
Consensus pattern (29 bp):
AAAGTGGTTCAATATTTAGCCTTGTTTGT
Found at i:5221 original size:19 final size:18
Alignment explanation
Indices: 5177--5211 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5167 ATCAAACCAC
5177 AATATATCTTTTTTGTAT
1 AATATATCTTTTTTGTAT
5195 AATATATC-TTTTTGTAT
1 AATATATCTTTTTTGTAT
5212 TACATTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (18 bp):
AATATATCTTTTTTGTAT
Found at i:8762 original size:18 final size:18
Alignment explanation
Indices: 8739--8776 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
8729 TTTCATAGTG
*
8739 TTTTCTATCATTAACGGA
1 TTTTCTACCATTAACGGA
8757 TTTTCTACCATTAACGGA
1 TTTTCTACCATTAACGGA
8775 TT
1 TT
8777 CACCAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTTCTACCATTAACGGA
Found at i:9543 original size:2 final size:2
Alignment explanation
Indices: 9536--9567 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9526 TAGACGGAAC
9536 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9568 AATAACAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9558 original size:15 final size:15
Alignment explanation
Indices: 9538--9568 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9528 GACGGAACAT
9538 ATATATATATATATA
1 ATATATATATATATA
9553 ATATATATATATATA
1 ATATATATATATATA
9568 A
1 A
9569 ATAACAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:9560 original size:19 final size:19
Alignment explanation
Indices: 9536--9572 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
9526 TAGACGGAAC
*
9536 ATATATATATATATATAAT
1 ATATATATATATAAATAAT
9555 ATATATATATATAAATAA
1 ATATATATATATAAATAA
9573 CAATCATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATATATATATAAATAAT
Found at i:10363 original size:18 final size:18
Alignment explanation
Indices: 10340--10380 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
10330 CCAGCACTTT
* *
10340 CAACAACATCATCATCAG
1 CAACAACAACATCAACAG
10358 CAACAACAACATCAACAG
1 CAACAACAACATCAACAG
10376 CAACA
1 CAACA
10381 GCTCTGGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.34, G:0.05, T:0.10
Consensus pattern (18 bp):
CAACAACAACATCAACAG
Found at i:19285 original size:2 final size:2
Alignment explanation
Indices: 19278--19302 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19268 TTTCTTAAAA
19278 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19303 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29231 original size:21 final size:21
Alignment explanation
Indices: 29205--29341 Score: 197
Period size: 21 Copynumber: 6.6 Consensus size: 21
29195 ATTTTCAGAT
*
29205 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTTGACTA
*
29226 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTTGACTA
* *
29247 TCGCAATACGAACTTGGACTA
1 TCGCAATGCGAACTTTGACTA
* *
29268 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACTTTG-ACTA
29288 TCGCAATGCGAACTTTGACTA
1 TCGCAATGCGAACTTTGACTA
29309 TCGCAATGCGAACTTTGACTA
1 TCGCAATGCGAACTTTGACTA
29330 TCGCAATGCGAA
1 TCGCAATGCGAA
29342 TATGTAAATC
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.15
21 88 0.85
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTTGACTA
Found at i:29291 original size:62 final size:62
Alignment explanation
Indices: 29225--29360 Score: 245
Period size: 62 Copynumber: 2.2 Consensus size: 62
29215 AACTTTGACT
29225 ATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACTATCGCAATGCGAATATGTAA
* * *
29287 ATCGCAATGCGAACTTTGACTATCGCAATGCGAACTTTGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACTATCGCAATGCGAATATGTAA
29349 ATCGCAATGCGA
1 ATCGCAATGCGA
29361 TAGTCGAAGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (62 bp):
ATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:29380 original size:21 final size:21
Alignment explanation
Indices: 29350--29416 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
29340 AATATGTAAA
*
29350 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
29371 TCGCATTGCGATAATCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
29391 ATCGCATTGCGATAGTCCAAGT
1 -TCGCATTGCGATAGTCGAAGT
29413 TCGC
1 TCGC
29417 GTTGTGATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:29381 original size:83 final size:83
Alignment explanation
Indices: 29205--29360 Score: 244
Period size: 83 Copynumber: 1.9 Consensus size: 83
29195 ATTTTCAGAT
* *
29205 TCGCAACGCGAACTTTGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACTATC
1 TCGCAATGCGAACTTTGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACAATC
29270 GCAATGCGAATATGTAAA
66 GCAATGCGAATATGTAAA
* * *
29288 TCGCAATGCGAACTTTGACTATCGCAATGCGAACTTTGACTATCGCAATGCGAA-TATGTA-AAT
1 TCGCAATGCGAACTTTGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACT-TGGACAAT
29351 CGCAATGCGA
65 CGCAATGCGA
29361 TAGTCGAAGT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
82 13 0.19
83 54 0.81
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (83 bp):
TCGCAATGCGAACTTTGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACAATC
GCAATGCGAATATGTAAA
Found at i:29391 original size:62 final size:62
Alignment explanation
Indices: 29225--29402 Score: 200
Period size: 62 Copynumber: 2.9 Consensus size: 62
29215 AACTTTGACT
* * * * *
29225 ATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACGTCGACTATCGCAATGCGAACATCGACTATCGCAATGCGAATATGTAA
* * * *
29287 ATCGCAATGCGAACTTTGACTATCGCAATGCGAACTTTGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACGTCGACTATCGCAATGCGAACATCGACTATCGCAATGCGAATATGTAA
* * *
29349 ATCGCAATGCGATA-GTCGAAGT-TCGCATTGCGATA-ATCGACTATCGCATTGCGA
1 ATCGCAATGCGA-ACGTCG-ACTATCGCAATGCGA-ACATCGACTATCGCAATGCGA
29403 TAGTCCAAGT
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
62 99 0.96
63 4 0.04
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (62 bp):
ATCGCAATGCGAACGTCGACTATCGCAATGCGAACATCGACTATCGCAATGCGAATATGTAA
Found at i:29391 original size:83 final size:83
Alignment explanation
Indices: 29205--29402 Score: 208
Period size: 83 Copynumber: 2.4 Consensus size: 83
29195 ATTTTCAGAT
* * * *
29205 TCGCAACGCGAACTTTGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACTATC
1 TCGCAATGCGAACATCGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACAATC
29270 GCAATGCGAATATGTAAA
66 GCAATGCGAATATGTAAA
* * * * *
29288 TCGCAATGCGAACTTTGACTATCGCAATGCGAACTTTGACTATCGCAATGCGAA-TATGTA-AAT
1 TCGCAATGCGAACATCGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACT-TGGACAAT
*
29351 CGCAATGCG-ATA-GTCGAAGT
65 CGCAATGCGAATATGT--AA-A
* *
29371 TCGCATTGCGATA-ATCGACTATCGCATTGCGA
1 TCGCAATGCGA-ACATCGACTATCGCAATGCGA
29403 TAGTCCAAGT
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
80 2 0.02
81 3 0.03
82 14 0.14
83 80 0.80
84 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (83 bp):
TCGCAATGCGAACATCGACTATCGCAATGCGAACTTGGACTATCGCAATACGAACTTGGACAATC
GCAATGCGAATATGTAAA
Found at i:29552 original size:6 final size:6
Alignment explanation
Indices: 29541--29574 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
29531 AGACACGTAT
*
29541 GACCAC GACCAC GACCAC GACCAC GACAAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
29575 CGAGACGGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.35, C:0.47, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:30076 original size:6 final size:6
Alignment explanation
Indices: 30060--30088 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30050 TCTCGTCTCG
30060 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
30089 ACGTGTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:35634 original size:17 final size:17
Alignment explanation
Indices: 35612--35671 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
35602 ATTTTTTAAT
35612 AAAGTAAAAGTAATTAC
1 AAAGTAAAAGTAATTAC
*
35629 AAAGTAATA-TATATT-C
1 AAAGTAAAAGTA-ATTAC
35645 TAAGTAGTAAAAGTAATTAC
1 -AA--AGTAAAAGTAATTAC
35665 AAAGTAA
1 AAAGTAA
35672 TATATATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.28
Consensus pattern (17 bp):
AAAGTAAAAGTAATTAC
Found at i:35655 original size:36 final size:36
Alignment explanation
Indices: 35614--35686 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
35604 TTTTTAATAA
35614 AGTAAAAGTAATTACAAAGTAATATATATTCTAAGT
1 AGTAAAAGTAATTACAAAGTAATATATATTCTAAGT
35650 AGTAAAAGTAATTACAAAGTAATATATATTCTAAGT
1 AGTAAAAGTAATTACAAAGTAATATATATTCTAAGT
35686 A
1 A
35687 TTCTTAAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (36 bp):
AGTAAAAGTAATTACAAAGTAATATATATTCTAAGT
Found at i:36930 original size:26 final size:27
Alignment explanation
Indices: 36877--36930 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
36867 AAGAATGTAA
*
36877 AATATTTTTATTATATTATAACTATTT
1 AATATTTTTATTATATTATAAATATTT
*
36904 AATA-TTTTATTATTTTATTAAAT-TTT
1 AATATTTTTATTATATTA-TAAATATTT
36930 A
1 A
36931 TTATACTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
AATATTTTTATTATATTATAAATATTT
Found at i:37166 original size:80 final size:80
Alignment explanation
Indices: 37077--37236 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
37067 ATTTTATTTA
37077 CTTAATTTTTTAGTATTAGTTTATATTTTAATTTGTGTACTATTTATTAAATTAAGAGAGAGACT
1 CTTAATTTTTTAGTATTAGTTTATATTTTAATTTGTGTACTATTTATTAAATTAAGAGAGAGACT
37142 GTATATTAGATCCAT
66 GTATATTAGATCCAT
37157 CTTAATTTTTTAGTATTAGTTTATATTTTAATTTGTGTACTATTTATTAAATTAAGAGAGAGACT
1 CTTAATTTTTTAGTATTAGTTTATATTTTAATTTGTGTACTATTTATTAAATTAAGAGAGAGACT
37222 GTATATTAGATCCAT
66 GTATATTAGATCCAT
37237 TCATTAGTAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (80 bp):
CTTAATTTTTTAGTATTAGTTTATATTTTAATTTGTGTACTATTTATTAAATTAAGAGAGAGACT
GTATATTAGATCCAT
Found at i:38668 original size:21 final size:21
Alignment explanation
Indices: 38643--38696 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
38633 TGTATATTCC
*
38643 ACAACCATTTCAGATGGTAAT
1 ACAACCATTTCAGATGATAAT
* * * *
38664 GCAACCGTATCAGATGATACT
1 ACAACCATTTCAGATGATAAT
38685 ACAACCATTTCA
1 ACAACCATTTCA
38697 TATGTCACCG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (21 bp):
ACAACCATTTCAGATGATAAT
Found at i:42125 original size:14 final size:14
Alignment explanation
Indices: 42103--42136 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42093 TACAACCGTA
* *
42103 AAAAATAATATAAT
1 AAAATTAATACAAT
42117 AAAATTAATACAAT
1 AAAATTAATACAAT
42131 AAAATT
1 AAAATT
42137 TGTTCAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTAATACAAT
Found at i:50074 original size:5 final size:5
Alignment explanation
Indices: 50064--50112 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
50054 TATTAGTTTA
50064 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
50113 ACCTCTTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
TTCCC
Found at i:62248 original size:8 final size:9
Alignment explanation
Indices: 62222--62260 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
62212 TTTTAAAAAC
62222 ACACTTAAA
1 ACACTTAAA
62231 ACACTTAAA
1 ACACTTAAA
62240 ACA-TTAAA
1 ACACTTAAA
62248 ACACTTAAA
1 ACACTTAAA
62257 ACAC
1 ACAC
62261 ACTTCTCCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (9 bp):
ACACTTAAA
Found at i:62248 original size:17 final size:17
Alignment explanation
Indices: 62226--62259 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
62216 AAAAACACAC
62226 TTAAAACACTTAAAACA
1 TTAAAACACTTAAAACA
62243 TTAAAACACTTAAAACA
1 TTAAAACACTTAAAACA
62260 CACTTCTCCC
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:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TTAAAACACTTAAAACA
Found at i:64590 original size:20 final size:21
Alignment explanation
Indices: 64536--64598 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
64526 ATTCCCCCTG
64536 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
64560 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
64580 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
64599 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:70912 original size:24 final size:24
Alignment explanation
Indices: 70885--70959 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
70875 GTTCGTGAAC
*
70885 GTTCGGTTATGTTCATTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
*
70909 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
**
70933 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
70957 GTT
1 GTT
70960 TAACCCAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCGGTTAT
Found at i:70937 original size:14 final size:14
Alignment explanation
Indices: 70884--70939 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
70874 CGTTCGTGAA
70884 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
70898 CATTCGGTTATGTT
1 CGTTCGGTTATGTT
70912 CG-T---TTATGTT
1 CGTTCGGTTATGTT
70922 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
70936 CGTT
1 CGTT
70940 TATGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 25 0.69
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:71510 original size:18 final size:18
Alignment explanation
Indices: 71489--71534 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
71479 CTTGTGTGAC
* *
71489 CTTTAGTTATGGAGTAGA
1 CTTTAGTTATGGAGAAAA
71507 CTTTAGTTATGGAGAAAA
1 CTTTAGTTATGGAGAAAA
*
71525 CTTTTGTTAT
1 CTTTAGTTAT
71535 TGCCTTGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (18 bp):
CTTTAGTTATGGAGAAAA
Found at i:71939 original size:16 final size:16
Alignment explanation
Indices: 71918--71968 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
71908 GTCTCCAACG
71918 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
71934 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
71950 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
71964 TTTAT
1 TTTAT
71969 TAAATGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:72581 original size:59 final size:60
Alignment explanation
Indices: 72454--72588 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 60
72444 ATTATTTTGT
* * **
72454 TCGAGTATTAAAAGTTACAAACTGATACTTTACTTATATAGTGTTATTTTGTTGAGTCAC
1 TCGACTATTAAAAGTTACAAAATGATACTCAACTTATATAGTGTTATTTTGTTGAGTCAC
* * * * *
72514 -CGATTATTAAAAGTTACAAAATGATCCTCAAC-TCTATAGTGTTGTTTTGTTGAGTCCC
1 TCGACTATTAAAAGTTACAAAATGATACTCAACTTATATAGTGTTATTTTGTTGAGTCAC
*
72572 TCGACTATTAGAAGTTA
1 TCGACTATTAAAAGTTA
72589 TAGAATGGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 23 0.36
59 41 0.64
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (60 bp):
TCGACTATTAAAAGTTACAAAATGATACTCAACTTATATAGTGTTATTTTGTTGAGTCAC
Found at i:78561 original size:20 final size:20
Alignment explanation
Indices: 78520--78561 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
78510 TAGTAAAAAA
* * *
78520 TTACTTAAAATATTATTGTT
1 TTACCTAAAATATTAATATT
78540 TTACCTAAAATATTAATATT
1 TTACCTAAAATATTAATATT
78560 TT
1 TT
78562 TTTAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (20 bp):
TTACCTAAAATATTAATATT
Found at i:89999 original size:17 final size:16
Alignment explanation
Indices: 89966--89999 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
89956 GACTAAAGTG
*
89966 TAATTTTAAAAAGTTA
1 TAATTTTAAAAAATTA
89982 TAATTTTAAAAAAATTA
1 TAATTTT-AAAAAATTA
89999 T
1 T
90000 GTAATATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TAATTTTAAAAAATTA
Found at i:91620 original size:20 final size:20
Alignment explanation
Indices: 91597--91666 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
91587 GAACTCCAAT
91597 TTCGCAACACAGTTTCTAGA
1 TTCGCAACACAGTTTCTAGA
* *
91617 TTCGCAACACGAATTTCCCAGA
1 TTCGCAACAC-AGTTT-CTAGA
* *
91639 TTCGCAACTCAGTTT-TGAAA
1 TTCGCAACACAGTTTCT-AGA
91659 TTCGCAAC
1 TTCGCAAC
91667 TCGAATTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
20 20 0.49
21 8 0.20
22 13 0.32
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (20 bp):
TTCGCAACACAGTTTCTAGA
Found at i:91642 original size:22 final size:20
Alignment explanation
Indices: 91597--91646 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
91587 GAACTCCAAT
* *
91597 TTCGCAACACAGTTTCTAGA
1 TTCGCAACACAATTTCCAGA
91617 TTCGCAACACGAATTTCCCAGA
1 TTCGCAACAC-AATTT-CCAGA
91639 TTCGCAAC
1 TTCGCAAC
91647 TCAGTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 10 0.38
21 4 0.15
22 12 0.46
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (20 bp):
TTCGCAACACAATTTCCAGA
Found at i:91971 original size:20 final size:22
Alignment explanation
Indices: 91933--91979 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
91923 CACGTTGATG
*
91933 TTATATAAAAAATTCAATT-ATT
1 TTATATAAAAAA-TAAATTCATT
91955 TTATATAAAAAA-AAATTCATT
1 TTATATAAAAAATAAATTCATT
91976 TTAT
1 TTAT
91980 TCTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 7 0.30
22 12 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATATAAAAAATAAATTCATT
Found at i:92040 original size:26 final size:26
Alignment explanation
Indices: 91989--92045 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
91979 TTCTTTTTTA
* ***
91989 ATTTCAAGATAATTAAAAATTCAATT
1 ATTTTAAGATAATTAAAAAAAAAATT
92015 ATTTTAAGATAATTAAAAAAAAAATT
1 ATTTTAAGATAATTAAAAAAAAAATT
*
92041 CTTTT
1 ATTTT
92046 TATTCTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTTTAAGATAATTAAAAAAAAAATT
Found at i:99107 original size:29 final size:29
Alignment explanation
Indices: 99065--99150 Score: 163
Period size: 29 Copynumber: 3.0 Consensus size: 29
99055 AGTGTTGGCC
99065 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
99094 GTAGGTCGCCATGCACTCCTGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
99123 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
99151 ACTCTTGCTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.14, C:0.35, G:0.30, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:99309 original size:33 final size:33
Alignment explanation
Indices: 99268--99342 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
99258 GCGATCTACC
* *
99268 CTCGCTCGGCTT-CCATCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCATCAGATGCCCTCGCATAG
*
99301 CTCGCTCGGTTGCCCTCAGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCATCAGATGCCCTCGCATAG
*
99334 CTCGTTCGG
1 CTCGCTCGG
99343 ATGGTCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.11, C:0.39, G:0.24, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCATCAGATGCCCTCGCATAG
Found at i:99446 original size:29 final size:29
Alignment explanation
Indices: 99409--99466 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
99399 GCAATCTCTT
*
99409 GTAGCTCGCCGGGAAGACATGACGACCTA
1 GTAGCTCGCCCGGAAGACATGACGACCTA
* * *
99438 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGACGACCTA
99467 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGACGACCTA
Found at i:106677 original size:33 final size:34
Alignment explanation
Indices: 106619--106684 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
106609 TACCTAACTC
*
106619 TCACCTAACTAATTTGATGTAAGCAATAACATCT
1 TCACCTAACAAATTTGATGTAAGCAATAACATCT
*
106653 TCACCTAACAAATTT-ATGTAAGCAATGACATC
1 TCACCTAACAAATTTGATGTAAGCAATAACATC
106685 AAATTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (34 bp):
TCACCTAACAAATTTGATGTAAGCAATAACATCT
Found at i:108466 original size:12 final size:12
Alignment explanation
Indices: 108449--108474 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
108439 AGTTTCAAGC
108449 TCTTGTTGAGGT
1 TCTTGTTGAGGT
108461 TCTTGTTGAGGT
1 TCTTGTTGAGGT
108473 TC
1 TC
108475 ACCTAGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.12, G:0.31, T:0.50
Consensus pattern (12 bp):
TCTTGTTGAGGT
Found at i:112410 original size:11 final size:11
Alignment explanation
Indices: 112394--112423 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
112384 ACAAACAAGC
112394 AAAAAAGAAAA
1 AAAAAAGAAAA
112405 AAAAAAGAAAA
1 AAAAAAGAAAA
*
112416 AAGAAAGA
1 AAAAAAGA
112424 CCAGTCTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Done.