Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003447.1 Hibiscus syriacus cultivar Beakdansim tig00007282_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: 97796
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:10644 original size:41 final size:41
Alignment explanation
Indices: 10587--10668 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
10577 GAGAAAAGAA
10587 GACCAATCCCCATTCTTCGTTTCAAACTAAGACAAACCGGT
1 GACCAATCCCCATTCTTCGTTTCAAACTAAGACAAACCGGT
10628 GACCAATCCCCATTCTTCGTTTCAAACTAAGACAAACCGGT
1 GACCAATCCCCATTCTTCGTTTCAAACTAAGACAAACCGGT
10669 TTTCCTTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (41 bp):
GACCAATCCCCATTCTTCGTTTCAAACTAAGACAAACCGGT
Found at i:13281 original size:18 final size:18
Alignment explanation
Indices: 13258--13292 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13248 ACATGTAAAT
*
13258 GGAGCAGTTGGAGGCGGC
1 GGAGCAGTTGAAGGCGGC
13276 GGAGCAGTTGAAGGCGG
1 GGAGCAGTTGAAGGCGG
13293 TGCCGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.54, T:0.11
Consensus pattern (18 bp):
GGAGCAGTTGAAGGCGGC
Found at i:13551 original size:3 final size:3
Alignment explanation
Indices: 13545--13616 Score: 126
Period size: 3 Copynumber: 24.0 Consensus size: 3
13535 AATTATTATT
13545 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
13593 TAA TAA TAA CAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
13617 AAATGAGACA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:13968 original size:119 final size:118
Alignment explanation
Indices: 13739--14407 Score: 862
Period size: 119 Copynumber: 5.6 Consensus size: 118
13729 GATTAAAACA
* * * * * * * * *
13739 AAAATGTTGCACAAGTTCTTCTCATTATGAACTTCTTATTCTTCTTCTTCGGATGAGTTTTTCTC
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTC-T-TTCGGACGAGTTCTTCTT
* * * * * ** * * *
13804 ATTATAAACTC-TCCACTGAGAATGATGATTTATTTGTTTCAGTGATGGAATCCAAC
64 ATTATGAACTCTTCCATTG-GAATGACGA-TCATCTCCTTCTGTGATGGAATCTATC
*
13860 AAAAGGTTGAACAAGCTCTTTTTATTATGAACTTCTTCTTCCTCTTTCGGACGAGTTCTTCTTAT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACGAGTTCTTCTTAT
*
13925 TATGAACTCTTCCACTGGAATGACGACTCATCTCCTTCTGTGATGGAATCTATC
66 TATGAACTCTTCCATTGGAATGACGA-TCATCTCCTTCTGTGATGGAATCTATC
* * *
13979 AAAAGGTTAAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACAAGTTCTTTTTAT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACGAGTTCTTCTTAT
14044 TATGAACTCTTCCATTGGAATGACGATCCATCTCCTTCTGTGATGGAATCTATC
66 TATGAACTCTTCCATTGGAATGACGAT-CATCTCCTTCTGTGATGGAATCTATC
*
14098 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTC-TTCGGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACGAGTTCTTCTTAT
* * *
14162 TATGAACTCTTTCATTGGAATGACGATCCATCTACTTCTGTGATGGAATCTAGC
66 TATGAACTCTTCCATTGGAATGACGAT-CATCTCCTTCTGTGATGGAATCTATC
* * *
14216 AAAAGGTTGAACAAGCTCTTTTTATTATGAACTTCTTCTTCCTTTTTCGGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACGAGTTCTTCTTAT
* * * *
14281 TATGAACTCTTTCATTGGAATGATGGTTCATGTCC-T-TGTGATGGAATCTATC
66 TATGAACTCTTCCATTGGAATGA-CGATCATCTCCTTCTGTGATGGAATCTATC
* * * * *
14333 AAAAGATTGAACAAACTCTTCTTATTATGAATTTTTTCTTTCTC-TTCGGACGAGTTCTTCTTAT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACGAGTTCTTCTTAT
*
14397 TGTGAACTCTT
66 TATGAACTCTT
14408 TCTGGAAATA
Statistics
Matches: 496, Mismatches: 48, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
116 29 0.06
117 52 0.10
118 112 0.23
119 256 0.52
120 10 0.02
121 37 0.07
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (118 bp):
AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACGAGTTCTTCTTAT
TATGAACTCTTCCATTGGAATGACGATCATCTCCTTCTGTGATGGAATCTATC
Found at i:14266 original size:237 final size:235
Alignment explanation
Indices: 13845--14498 Score: 864
Period size: 237 Copynumber: 2.7 Consensus size: 235
13835 ATTTGTTTCA
* * *
13845 GTGATGGAATCCAACAAAAGGTTGAACAAGCTCTTTTTATTATGAACTTCTTCTTCCTCTTTCGG
1 GTGATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTC-TTCGG
* *
13910 ACGAGTTCTTCTTATTATGAACTCTTCCACTGGAATGACGACTCATCTCCTTCTGTGATGGAATC
65 ACGAGTTCTTCTTATTATGAACTCTTTCACTGGAATGACGACTCATCTACTTCTGTGATGGAATC
* *
13975 TATCAAAAGGTTAAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACAAGTTCTTT
130 TAGCAAAAGGTTAAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACAAGTTCTTC
14040 TTATTATGAACTCTTCCATTGGAATGACGATCCATCTCCTTCT
195 TTATTATGAACTCTTCCATTGGAATGACGATCCATCTCC-T-T
14083 GTGATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGA
1 GTGATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGA
* *
14148 TGAGTTCTTCTTATTATGAACTCTTTCATTGGAATGACGA-TCCATCTACTTCTGTGATGGAATC
66 CGAGTTCTTCTTATTATGAACTCTTTCACTGGAATGACGACT-CATCTACTTCTGTGATGGAATC
* * * **
14212 TAGCAAAAGGTTGAACAAGCTCTTTTTATTATGAACTTCTTCTTCCTTTTTCGGATGAGTTCTTC
130 TAGCAAAAGGTTAAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACAAGTTCTTC
* * * * *
14277 TTATTATGAACTCTTTCATTGGAATGATGGTTCATGTCCTT
195 TTATTATGAACTCTTCCATTGGAATGACGATCCATCTCCTT
* * * * *
14318 GTGATGGAATCTATCAAAAGATTGAACAAACTCTTCTTATTATGAATTTTTTCTTTCTCTTCGGA
1 GTGATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGA
* * *
14383 CGAGTTCTTCTTATTGTGAACTCTTT--CTGGAAATATTGATGAAGCTCTATCTCCTTCTGTGAT
66 CGAGTTCTTCTTATTATGAACTCTTTCACTGG--A-A-TGACG-A-CTC-ATCTACTTCTGTGAT
* * * * * * * **
14446 AGAGTTTAGCAAAATGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCT
124 GGAATCTAGCAAAAGGTTAAACAAGCTCTTCTTATTATGAACTTCTTCTTCCT
14499 ATTAAGATGA
Statistics
Matches: 369, Mismatches: 38, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
233 3 0.01
235 86 0.23
236 3 0.01
237 160 0.43
238 57 0.15
239 1 0.00
240 59 0.16
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (235 bp):
GTGATGGAATCTATCAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGA
CGAGTTCTTCTTATTATGAACTCTTTCACTGGAATGACGACTCATCTACTTCTGTGATGGAATCT
AGCAAAAGGTTAAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACAAGTTCTTCT
TATTATGAACTCTTCCATTGGAATGACGATCCATCTCCTT
Found at i:14483 original size:123 final size:117
Alignment explanation
Indices: 13739--14777 Score: 851
Period size: 119 Copynumber: 8.7 Consensus size: 117
13729 GATTAAAACA
* * * * * * *
13739 AAAATGTTGCACAAGTTCTTCTCATTATGAACTTCTTATTCTTCTTCTTCGGATGAGTTTTTCTC
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTC---TTCTTCCTCTTCGGATGAGTTCTTCTT
* ** * * ** * * *
13804 ATTATAAACTCTCCACTGAGAATGATGA-TTTATTTGTTTCAGTGATGGAATCCAAC
63 ATTATGAACTCT-TTCTG-GAATGATGACTCTATCTCCTTCTGTGATGGAATCTAGC
* *
13860 AAAAGGTTGAACAAGCTCTTTTTATTATGAACTTCTTCTTCCTCTTTCGGACGAGTTCTTCTTAT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTC-TTCGGATGAGTTCTTCTTAT
* * *
13925 TATGAACTCTTCCACTGGAATGACGACTC-ATCTCCTTCTGTGATGGAATCTATC
65 TATGAACTCTT--TCTGGAATGATGACTCTATCTCCTTCTGTGATGGAATCTAGC
* ** *
13979 AAAAGGTTAAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTTCGGACAAGTTCTTTTTAT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTC-TTCGGATGAGTTCTTCTTAT
* * * *
14044 TATGAACTCTTCCATTGGAATGACGA-TCCATCTCCTTCTGTGATGGAATCTATC
65 TATGAACTCTTTC--TGGAATGATGACTCTATCTCCTTCTGTGATGGAATCTAGC
14098 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTTATT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTTATT
* * *
14163 ATGAACTCTTTCATTGGAATGACGA-TCCATCTACTTCTGTGATGGAATCTAGC
66 ATGAACTCTTTC--TGGAATGATGACTCTATCTCCTTCTGTGATGGAATCTAGC
* *
14216 AAAAGGTTGAACAAGCTCTTTTTATTATGAACTTCTTCTTCCTTTTTCGGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCC-TCTTCGGATGAGTTCTTCTTAT
** * *
14281 TATGAACTCTTTCATTGGAATGATGGTTC-ATGTCC-T-TGTGATGGAATCTATC
65 TATGAACTCTTTC--TGGAATGATGACTCTATCTCCTTCTGTGATGGAATCTAGC
* * * * * *
14333 AAAAGATTGAACAAACTCTTCTTATTATGAATTTTTTCTTTCTCTTCGGACGAGTTCTTCTTATT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTTATT
* * * *
14398 GTGAACTCTTTCTGGAAATATTGATGAAGCTCTATCTCCTTCTGTGATAGAGTTTAGC
66 ATGAACTCTTTCTGG--A-A-TGATG-A-CTCTATCTCCTTCTGTGATGGAATCTAGC
* * * ** * **
14456 AAAATGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTATTAAGATGAG---TTCTTATT
1 AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTTATT
* * * * * * * * * **
14518 ACGGACTCCTTATGGAAATGTTGATGCTACTTTATCTCTTTCTGCGATAGAGTAGAGC
66 ATGAACTCTTTCTGG-AA---TGATG--ACTCTATCTCCTTCTGTGATGGAATCTAGC
* * * * *
14576 AAAAGGTTGAATAAGTTCTT-TAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTATTAT
1 AAAAGGTTGAACAAGCTCTTCT-TATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTTAT
* * ** * * * *
14640 TACGAACTCCTTCTAAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGAGC
65 TATGAACTCTTTCT-GGAA---TGATGA--CTCTATCTCCTTCTGTGATGGAATCTAGC
* * * * *** *
14699 AAAAGGTTGAATAAGTTCTT-TAGATTATGAACTTCTTTTTCCTCTTTAAATGAGTTCTTTTTAT
1 AAAAGGTTGAACAAGCTCTTCT-TATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTTAT
* *
14763 TACGAACTCCTTCTG
65 TATGAACTCTTTCTG
14778 AAAATGTTAA
Statistics
Matches: 794, Mismatches: 96, Indels: 55
0.84 0.10 0.06
Matches are distributed among these distances:
114 3 0.00
116 33 0.04
117 53 0.07
118 126 0.16
119 255 0.32
120 106 0.13
121 37 0.05
122 1 0.00
123 180 0.23
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (117 bp):
AAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTTATT
ATGAACTCTTTCTGGAATGATGACTCTATCTCCTTCTGTGATGGAATCTAGC
Found at i:14782 original size:123 final size:122
Alignment explanation
Indices: 14384--14785 Score: 531
Period size: 123 Copynumber: 3.3 Consensus size: 122
14374 CTCTTCGGAC
** * * * * *
14384 GAGTTCTTCTTATTGTGAACTCTTTCTGGAAATATTGATGAAGCTCTATCTCCTTCTGTGATAGA
1 GAGTTCTT-TTATTACGAACTCCTTCTGAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGA
** * * *
14449 GTTTAGCAAAATGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCT-ATTAAGAT
65 GTAGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTCTTTAA-AT
* * * * * * *
14507 GAGTTC--TTATTACGGACTCCTTATGGAAATGTTGATGCTACTTTATCTCTTTCTGCGATAGAG
1 GAGTTCTTTTATTACGAACTCCTTCTGAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAG
* *
14570 TAGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTCTTCAGAT
66 TAGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTCTTTAAAT
*
14627 GAGTTCTTATTATTACGAACTCCTTCTAAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGA
1 GAGTTCTT-TTATTACGAACTCCTTCTGAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGA
* *
14692 GTCGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTTTTCCTCTTTAAAT
65 GTAGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTCTTTAAAT
14750 GAGTTCTTTTTATTACGAACTCCTTCTGAAAATGTT
1 GAGTTC-TTTTATTACGAACTCCTTCTGAAAATGTT
14786 AATTCCTCGA
Statistics
Matches: 242, Mismatches: 32, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
120 98 0.40
121 2 0.01
123 140 0.58
124 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (122 bp):
GAGTTCTTTTATTACGAACTCCTTCTGAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAG
TAGAGCAAAAGGTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTCTTTAAAT
Found at i:17139 original size:24 final size:24
Alignment explanation
Indices: 17095--17144 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
17085 ATAAAGAACC
*
17095 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
17119 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
17143 AA
1 AA
17145 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:31904 original size:23 final size:23
Alignment explanation
Indices: 31841--31907 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
31831 CCACAGCTCA
* *
31841 TATAAATTCACCGAAGTACCACG
1 TATAAATGCACCGAAGTGCCACG
* * * *
31864 TAGAATTGCATCGTAGTGCCGA-G
1 TATAAATGCACCGAAGTGCC-ACG
31887 TATAAATGCACCGAAGTGCCA
1 TATAAATGCACCGAAGTGCCA
31908 TATAAGATGT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (23 bp):
TATAAATGCACCGAAGTGCCACG
Found at i:38187 original size:17 final size:18
Alignment explanation
Indices: 38165--38199 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
38155 ACCCTTTCTC
38165 ATATAATA-ACTTATACA
1 ATATAATAGACTTATACA
38182 ATATAATATGACTTATAC
1 ATATAATA-GACTTATAC
38200 TTGGTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (18 bp):
ATATAATAGACTTATACA
Found at i:38423 original size:18 final size:18
Alignment explanation
Indices: 38381--38423 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38371 TTATTCATGC
* *
38381 ATACATATAATTAATGTA
1 ATACATATAATCAATATA
38399 ATACATATAATCACATATA
1 ATACATATAATCA-ATATA
38418 AT-CATA
1 ATACATA
38424 ACAAACACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (18 bp):
ATACATATAATCAATATA
Found at i:42145 original size:29 final size:29
Alignment explanation
Indices: 42102--42159 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
42092 TCATGCTCAG
42102 GTGTGGAGTTCTCAATCTGTTTTAATTCT
1 GTGTGGAGTTCTCAATCTGTTTTAATTCT
*
42131 GTGTGGAGTTGTCAATCTGTTTTAATTCT
1 GTGTGGAGTTCTCAATCTGTTTTAATTCT
42160 CTCATGAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.12, G:0.22, T:0.48
Consensus pattern (29 bp):
GTGTGGAGTTCTCAATCTGTTTTAATTCT
Found at i:45707 original size:2 final size:2
Alignment explanation
Indices: 45700--45725 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45690 ATACTTATGA
45700 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
45726 TAGTGAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48340 original size:60 final size:60
Alignment explanation
Indices: 48259--48403 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 60
48249 GTATCATATG
* * * *
48259 TCCCTAAACTATGAC-CATCATTTTAAATTAATCCTTAAACTTTTAAGCATTATAATTTCA
1 TCCCCAAACTATGACTC-TCATTTTAAATTAATCCTTAAACATTTAAGCATCACAATTTCA
* * * * *
48319 TCCTCAAACTATGACTCTCATTTTAAATTAGTTCTTAAACATTTGAGCATCCCAATTTCA
1 TCCCCAAACTATGACTCTCATTTTAAATTAATCCTTAAACATTTAAGCATCACAATTTCA
*
48379 TCCCCAAACTATGAATCTCATTTTA
1 TCCCCAAACTATGACTCTCATTTTA
48404 TTGGTCCCTA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 72 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.39
Consensus pattern (60 bp):
TCCCCAAACTATGACTCTCATTTTAAATTAATCCTTAAACATTTAAGCATCACAATTTCA
Found at i:48675 original size:60 final size:60
Alignment explanation
Indices: 48568--48728 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 60
48558 CGTATAATTT
* * *
48568 AGGAT-AAAACTGAAATA-TTCAAAAAGTTTATGAACCAATTTAGAATGA-AGATCATAATTGG
1 AGGATGAAAA-TGAAA-AGTTC-AAAAGTTTAAGGACCAATTTAGAATGATAG-TCATAATTGA
* * * * * *
48629 AGGATGAAAATGAAATGTTCAAAATTTTGAGGACTAATTTAGAATGATAGTCATAGTTTA
1 AGGATGAAAATGAAAAGTTCAAAAGTTTAAGGACCAATTTAGAATGATAGTCATAATTGA
* *
48689 AGGATGAAAATTAAAAGTTTAAAAGTTTAAGGACCAATTT
1 AGGATGAAAATGAAAAGTTCAAAAGTTTAAGGACCAATTT
48729 GAAAATGAGG
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
60 63 0.77
61 15 0.18
62 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (60 bp):
AGGATGAAAATGAAAAGTTCAAAAGTTTAAGGACCAATTTAGAATGATAGTCATAATTGA
Found at i:49017 original size:2 final size:2
Alignment explanation
Indices: 49010--49051 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
49000 ACTTTAGTGG
49010 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
49052 TTCATAATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49838 original size:26 final size:26
Alignment explanation
Indices: 49800--49850 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
49790 TCATTTAAAC
*
49800 AAATTATTAT-AAAAAAAATTAAATG
1 AAATAATTATAAAAAAAAATTAAATG
49825 AAATAATTGATAAAAAAAAATTAAAT
1 AAATAATT-ATAAAAAAAAATTAAAT
49851 ATGAAGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 2 0.09
27 14 0.61
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (26 bp):
AAATAATTATAAAAAAAAATTAAATG
Found at i:56258 original size:13 final size:13
Alignment explanation
Indices: 56228--56252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56218 TATTTACAAA
56228 ATTAAAGAATCAG
1 ATTAAAGAATCAG
56241 ATTAAAGAATCA
1 ATTAAAGAATCA
56253 ATTTAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
ATTAAAGAATCAG
Found at i:56504 original size:2 final size:2
Alignment explanation
Indices: 56497--56614 Score: 170
Period size: 2 Copynumber: 60.0 Consensus size: 2
56487 GATAAAAATA
*
56497 AT AT AT AT AT AT -T AT AT AT AT A- AT AT AT AT GAT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
* *
56538 AA AT AT AT A- AT AA 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
*
56579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56615 CTTAATAATA
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
1 3 0.03
2 99 0.95
3 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57676 original size:65 final size:64
Alignment explanation
Indices: 57566--57693 Score: 247
Period size: 65 Copynumber: 2.0 Consensus size: 64
57556 GATGTGCCTT
57566 GCATTGACTGGGATATCCAACTGCTGTCGTGTTCTACTAGAGAGACTCGGGTGTCCTAGTTGTG
1 GCATTGACTGGGATATCCAACTGCTGTCGTGTTCTACTAGAGAGACTCGGGTGTCCTAGTTGTG
57630 GCATTGACTGGGATATCCAACTGACTGTCGTGTTCTACTAGAGAGACTCGGGTGTCCTAGTTGT
1 GCATTGACTGGGATATCCAACTG-CTGTCGTGTTCTACTAGAGAGACTCGGGTGTCCTAGTTGT
57694 TTCCCGAGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 23 0.37
65 40 0.63
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (64 bp):
GCATTGACTGGGATATCCAACTGCTGTCGTGTTCTACTAGAGAGACTCGGGTGTCCTAGTTGTG
Found at i:63060 original size:59 final size:59
Alignment explanation
Indices: 62968--63100 Score: 239
Period size: 59 Copynumber: 2.3 Consensus size: 59
62958 TTTACCTTTC
* * *
62968 ATAAATCTTTTGGGTCCAACTTAGCCCAATTCCAAATATACTTAGTCCAAGCTATTTTA
1 ATAAATCTTTTGGGCCCAACTTAGCCCAATTCCAAATAAACTTAGTCCAAGATATTTTA
63027 ATAAATCTTTTGGGCCCAACTTAGCCCAATTCCAAATAAACTTAGTCCAAGATATTTTA
1 ATAAATCTTTTGGGCCCAACTTAGCCCAATTCCAAATAAACTTAGTCCAAGATATTTTA
63086 ATAAATCTTTTGGGC
1 ATAAATCTTTTGGGC
63101 TCTAAAATGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 71 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (59 bp):
ATAAATCTTTTGGGCCCAACTTAGCCCAATTCCAAATAAACTTAGTCCAAGATATTTTA
Found at i:71755 original size:36 final size:36
Alignment explanation
Indices: 71708--71789 Score: 164
Period size: 36 Copynumber: 2.3 Consensus size: 36
71698 TTTCTATTTA
71708 AATTTAATTGTAAATATTATAATATTATTTGATTCC
1 AATTTAATTGTAAATATTATAATATTATTTGATTCC
71744 AATTTAATTGTAAATATTATAATATTATTTGATTCC
1 AATTTAATTGTAAATATTATAATATTATTTGATTCC
71780 AATTTAATTG
1 AATTTAATTG
71790 GATTTCTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (36 bp):
AATTTAATTGTAAATATTATAATATTATTTGATTCC
Found at i:73443 original size:43 final size:43
Alignment explanation
Indices: 73386--73469 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
73376 TCTTATTAAA
* *
73386 AGTTATTTAGAATATTATGAATAATTCTAGCGTGGAATCTATT
1 AGTTATTTAGAATATTATGAACAATTCTAACGTGGAATCTATT
*
73429 AGTTATTTAGAATATTATGAACAATTCTAACTTGGAATCTA
1 AGTTATTTAGAATATTATGAACAATTCTAACGTGGAATCTA
73470 AGATCTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (43 bp):
AGTTATTTAGAATATTATGAACAATTCTAACGTGGAATCTATT
Found at i:74075 original size:27 final size:24
Alignment explanation
Indices: 74016--74077 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 24
74006 GTCAGTAATA
74016 TTATTAAAATATAATTTTTACAAT
1 TTATTAAAATATAATTTTTACAAT
* * *
74040 TTATAAAAATATTAATATTATTATATT
1 TTATTAAAATA-TAAT-TT-TTACAAT
74067 TTATTAAAATA
1 TTATTAAAATA
74078 AAAATACTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 10 0.32
25 4 0.13
26 2 0.06
27 15 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATTAAAATATAATTTTTACAAT
Found at i:74131 original size:33 final size:31
Alignment explanation
Indices: 74042--74137 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 31
74032 TTTACAATTT
* *
74042 ATAAAAATATTAATATTATTATATTTTATTAAA
1 ATAAAAATATTAATATTAAT-TA-TTCATTAAA
74075 ATAAAAATACTATAAATTATATTAATTATTCATTAAA
1 ATAAAAATA-T-T--A--ATATTAATTATTCATTAAA
74112 ATAAAAATATTAAGCTATTAATTATT
1 ATAAAAATATTAA--TATTAATTATT
74138 AAATAAGAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
31 1 0.02
33 21 0.40
34 1 0.02
35 2 0.04
36 1 0.02
37 18 0.34
38 2 0.04
39 7 0.13
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (31 bp):
ATAAAAATATTAATATTAATTATTCATTAAA
Found at i:79398 original size:3 final size:3
Alignment explanation
Indices: 79390--79457 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
79380 TTTCTCTCGA
79390 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
79438 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
79458 AGTTTATTGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:82347 original size:34 final size:34
Alignment explanation
Indices: 82309--82391 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
82299 TTCTTGAGAG
*
82309 TTGTTTTCTCCTTTTTATCAAGAGAAAATTATCA
1 TTGTTTTCTCCTTTTTATCAAAAGAAAATTATCA
*
82343 TTGTTTTCTCCTTTTTATCAAAAGAGAATTATCA
1 TTGTTTTCTCCTTTTTATCAAAAGAAAATTATCA
82377 TTGTTTTCTCCTTTT
1 TTGTTTTCTCCTTTT
82392 CAGATCGAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTTATCAAAAGAAAATTATCA
Found at i:90533 original size:32 final size:32
Alignment explanation
Indices: 90498--90642 Score: 112
Period size: 32 Copynumber: 4.5 Consensus size: 32
90488 CTGACGTTCT
*
90498 TGTGCATTATCTGAATGTAACACTAACTCTGT
1 TGTGCATTATCTGAATGTAACACTAACTCTGC
* * * * *
90530 TGTGCATCATCTAAATGTAACGCTGACTCTAC
1 TGTGCATTATCTGAATGTAACACTAACTCTGC
* ** * * * *
90562 TGTGCATTATTTGAATACAATATTGACTCTGA
1 TGTGCATTATCTGAATGTAACACTAACTCTGC
* * * *
90594 TATGCATTATCTGAATGTGATACTAAATCTGC
1 TGTGCATTATCTGAATGTAACACTAACTCTGC
*
90626 TATGCATTA-CATGAATG
1 TGTGCATTATC-TGAATG
90643 CAATGTTGAT
Statistics
Matches: 87, Mismatches: 25, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
31 1 0.01
32 86 0.99
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTGCATTATCTGAATGTAACACTAACTCTGC
Found at i:97396 original size:22 final size:21
Alignment explanation
Indices: 97366--97421 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 21
97356 AAAATAATTA
97366 AAACATAAATAATAATATTTTAT
1 AAAC-TAAATAATAA-ATTTTAT
97389 -AACGTAAATAAT-AATTTTAT
1 AAAC-TAAATAATAAATTTTAT
97409 AAACTAAATAATA
1 AAACTAAATAATA
97422 TTAAGATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 15 0.50
21 4 0.13
22 11 0.37
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (21 bp):
AAACTAAATAATAAATTTTAT
Found at i:97407 original size:20 final size:20
Alignment explanation
Indices: 97366--97421 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 20
97356 AAAATAATTA
97366 AAACATAAATAATAATATTT-T
1 AAAC-TAAATAATAAT-TTTAT
97387 ATAACGTAAATAATAATTTTAT
1 A-AAC-TAAATAATAATTTTAT
97409 AAACTAAATAATA
1 AAACTAAATAATA
97422 TTAAGATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 9 0.28
21 7 0.22
22 16 0.50
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
AAACTAAATAATAATTTTAT
Found at i:97505 original size:31 final size:31
Alignment explanation
Indices: 97433--97514 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
97423 TAAGATAAAT
*
97433 ATATATTAATTATAAAATAATTATAACACACA
1 ATATATTAA-TATAAAATATTTATAACACACA
** *
97465 ATATA-TAATATAATAATATTTATAGTATA-A
1 ATATATTAATATAA-AATATTTATAACACACA
97495 ATATATTAATATAACAATAT
1 ATATATTAATATAA-AATAT
97515 ATTTGTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 11 0.26
31 27 0.63
32 5 0.12
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (31 bp):
ATATATTAATATAAAATATTTATAACACACA
Done.