Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000894.1 Hibiscus syriacus cultivar Beakdansim tig00001756_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: 126325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3370 original size:7 final size:7
Alignment explanation
Indices: 3354--3388 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
3344 TTTTTTCAAA
*
3354 GTCAATG
1 GTCAACG
3361 GTCAACG
1 GTCAACG
3368 GTCAACG
1 GTCAACG
3375 GTCAACG
1 GTCAACG
*
3382 ATCAACG
1 GTCAACG
3389 TTGGATCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:4558 original size:2 final size:2
Alignment explanation
Indices: 4547--4588 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
4537 TTTAATTTAA
4547 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4587 AT
1 AT
4589 TTTACAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5084 original size:22 final size:22
Alignment explanation
Indices: 5052--5123 Score: 135
Period size: 22 Copynumber: 3.2 Consensus size: 22
5042 CGAAATAAAA
5052 ATAATGATTAGAATACTGAATGT
1 ATAAT-ATTAGAATACTGAATGT
5075 ATAATATTAGAATACTGAATGT
1 ATAATATTAGAATACTGAATGT
5097 ATAATATTAGAATACTGAATGT
1 ATAATATTAGAATACTGAATGT
5119 ATAAT
1 ATAAT
5124 TAGACTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 44 0.90
23 5 0.10
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (22 bp):
ATAATATTAGAATACTGAATGT
Found at i:5995 original size:12 final size:12
Alignment explanation
Indices: 5978--6002 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5968 TACTAATGAT
5978 TAAAAAATATTA
1 TAAAAAATATTA
5990 TAAAAAATATTA
1 TAAAAAATATTA
6002 T
1 T
6003 CTTATAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAATATTA
Found at i:7190 original size:2 final size:2
Alignment explanation
Indices: 7183--7236 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
7173 GTTTTTGTCA
7183 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT -T 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
7223 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
7237 TTATTTTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:12759 original size:17 final size:19
Alignment explanation
Indices: 12733--12774 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12723 TCACTAATTT
12733 TATTTAAAA-TA-AAAAAA
1 TATTTAAAATTACAAAAAA
* *
12750 TATTTCAAATTACAATAAA
1 TATTTAAAATTACAAAAAA
12769 TATTTA
1 TATTTA
12775 TAATCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTTAAAATTACAAAAAA
Found at i:16713 original size:171 final size:171
Alignment explanation
Indices: 16428--16866 Score: 704
Period size: 171 Copynumber: 2.6 Consensus size: 171
16418 CCCCTAGGCT
* * * * *
16428 CTCTGTAGAAGGTATTCATTTTAAACCTGAGGAGCCAGTTTCTGACAAAATGGAAAAGAAAGGTT
1 CTCTGTAGAAGGTATTCATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTT
*
16493 CATATGAAGCCTATTCCTGCAACGATATGGAGGAGGATGCCGGAAATATGAGTAAAAACAGCATC
66 CATATGAAGCTTATTCCTGCAACGATATGGAGGAGGATGCCGGAAATATGAGTAAAAACAGCAT-
* *
16558 AA-GCCTTCCTGTGAAGCTTTTCCAAATGAATTTGATTGGAA
130 AACACCTTCCTGTGAAGCTTTTCCAAATGAATTTGATCGGAA
*
16599 CTCTGTAGAAGGTATTCGA-TCTAAACCTGAAGAGCCAGCGTCTGAAAAAATGGAAAAGCAAGGT
1 CTCTGTAGAAGGTATTC-ATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGT
16663 TCATATGAAGCTTATTCCTGCAACGATATGGAGGAGGAT-CCTGGAAATATGAGTAAAAACAGCA
65 TCATATGAAGCTTATTCCTGCAACGATATGGAGGAGGATGCC-GGAAATATGAGTAAAAACAGCA
* *
16727 TAACACCTTCTTGTGAAGCTTTTCCTAATGAATTTGATCGGAA
129 TAACACCTTCCTGTGAAGCTTTTCCAAATGAATTTGATCGGAA
* *
16770 CTCTGTTGAAGGTATTCATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTG
1 CTCTGTAGAAGGTATTCATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTT
*
16835 CATATGAAGCTTATTCCTGCAACAATATGGAG
66 CATATGAAGCTTATTCCTGCAACGATATGGAG
16867 AGTAAGAACA
Statistics
Matches: 249, Mismatches: 15, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
170 5 0.02
171 243 0.98
172 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (171 bp):
CTCTGTAGAAGGTATTCATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTT
CATATGAAGCTTATTCCTGCAACGATATGGAGGAGGATGCCGGAAATATGAGTAAAAACAGCATA
ACACCTTCCTGTGAAGCTTTTCCAAATGAATTTGATCGGAA
Found at i:20381 original size:24 final size:25
Alignment explanation
Indices: 20354--20414 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
20344 TTGACACGAT
20354 AATTAATTTATTGAATT-AAATTAA
1 AATTAATTTATTGAATTAAAATTAA
*
20378 AATT-ATTGAATTGAATTAAAATTAA
1 AATTAATT-TATTGAATTAAAATTAA
*
20403 GATTAAATTTAT
1 AATT-AATTTAT
20415 AAAATATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.10
24 12 0.40
25 10 0.33
26 2 0.07
27 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (25 bp):
AATTAATTTATTGAATTAAAATTAA
Found at i:20385 original size:19 final size:19
Alignment explanation
Indices: 20361--20401 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
20351 GATAATTAAT
20361 TTATTGAATTAAATTAAAA
1 TTATTGAATTAAATTAAAA
*
20380 TTATTGAATTGAATTAAAA
1 TTATTGAATTAAATTAAAA
20399 TTA
1 TTA
20402 AGATTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (19 bp):
TTATTGAATTAAATTAAAA
Found at i:27715 original size:28 final size:28
Alignment explanation
Indices: 27683--27739 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
27673 TTGTCGTTGC
* *
27683 TTTCAAGCACTGATTCGACGTCATAATG
1 TTTCAAGCACTGACTCGACGACATAATG
*
27711 TTTCAAGCACTGGCTCGACGACATAATG
1 TTTCAAGCACTGACTCGACGACATAATG
27739 T
1 T
27740 AAACAGAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (28 bp):
TTTCAAGCACTGACTCGACGACATAATG
Found at i:36945 original size:23 final size:23
Alignment explanation
Indices: 36915--36961 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
36905 TCTAGCGCCG
36915 CCTAGGCACCGAGGACGTAAGCA
1 CCTAGGCACCGAGGACGTAAGCA
36938 CCTAGGCACCGAGGACGTAAGCA
1 CCTAGGCACCGAGGACGTAAGCA
36961 C
1 C
36962 ATTGCCGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.30, T:0.09
Consensus pattern (23 bp):
CCTAGGCACCGAGGACGTAAGCA
Found at i:37966 original size:60 final size:61
Alignment explanation
Indices: 37855--37984 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 61
37845 GTACATACGT
* * * * * *
37855 ATAGTTT-GAGATGAAATTGGAATGTTTAAACACTTTGAGGACCAATTTAGAATGA-AGGTC
1 ATAGTTTAGGGATAAAATTGAAATGTTCAAACACTTTAAGGACCAATATAGAATGATA-GTC
* * *
37915 GTAGTTTAGGGATAAAATTGAAATGTTCAAA-AGTTTAAGGACTAATATAGAATGATAGTC
1 ATAGTTTAGGGATAAAATTGAAATGTTCAAACACTTTAAGGACCAATATAGAATGATAGTC
37975 ATAGTTTAGG
1 ATAGTTTAGG
37985 AATGGAATTG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
60 38 0.66
61 20 0.34
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (61 bp):
ATAGTTTAGGGATAAAATTGAAATGTTCAAACACTTTAAGGACCAATATAGAATGATAGTC
Found at i:37994 original size:60 final size:59
Alignment explanation
Indices: 37868--38011 Score: 139
Period size: 60 Copynumber: 2.4 Consensus size: 59
37858 GTTTGAGATG
* * * * * *
37868 AAATTGGAATGTTTAAACACTTTGAGGACCAATTTAGAATGAAGGTCGTAGTTTAGGGATA
1 AAATTGAAATG-TTAAA-AGTTTAAGGACCAATATAGAATGAAGGTCATAGTTTAGGAATA
* *
37929 AAATTGAAATGTTCAAAAGTTTAAGGACTAATATAGAATGATA-GTCATAGTTTAGGAATG
1 AAATTGAAATGTT-AAAAGTTTAAGGACCAATATAGAATGA-AGGTCATAGTTTAGGAATA
*
37989 GAATTGTAAAAT-TTAAAAGTTTA
1 AAATTG--AAATGTTAAAAGTTTA
38012 TGGTCAAGAT
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
60 50 0.71
61 16 0.23
62 4 0.06
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.33
Consensus pattern (59 bp):
AAATTGAAATGTTAAAAGTTTAAGGACCAATATAGAATGAAGGTCATAGTTTAGGAATA
Found at i:38634 original size:30 final size:30
Alignment explanation
Indices: 38598--38656 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
38588 ACGGTAGTCC
*
38598 AATTTTTATTTATTTTAAATAATTTTTATA
1 AATTTTTATATATTTTAAATAATTTTTATA
38628 AATTTTTATATATTTTAAATAATTTTTAT
1 AATTTTTATATATTTTAAATAATTTTTAT
38657 TGATAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
AATTTTTATATATTTTAAATAATTTTTATA
Found at i:54079 original size:15 final size:16
Alignment explanation
Indices: 54050--54079 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54040 ATATAAATAT
54050 TTTAAAACAATAATTG
1 TTTAAAACAATAATTG
54066 TTTAAAAC-ATAATT
1 TTTAAAACAATAATT
54080 TCAAAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (16 bp):
TTTAAAACAATAATTG
Found at i:54273 original size:31 final size:32
Alignment explanation
Indices: 54207--54279 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
54197 GGCCCGAGAA
* * **
54207 CCTACCCAAGAAAGTTACTCTGGGCCACGTGG
1 CCTACCCAAGAAAGATACTCGGGGCCACGAAG
*
54239 CCTACCCAAGAAAGAT-CTCGGGGCCTCGAAG
1 CCTACCCAAGAAAGATACTCGGGGCCACGAAG
54270 CCTACCCAAG
1 CCTACCCAAG
54280 GGTCACCTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 21 0.58
32 15 0.42
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.15
Consensus pattern (32 bp):
CCTACCCAAGAAAGATACTCGGGGCCACGAAG
Found at i:56768 original size:23 final size:24
Alignment explanation
Indices: 56726--56770 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
56716 ACTCAGTCAA
* *
56726 AGTCAAAGCTTAACGTGTTGACAC
1 AGTCAAAGCTCAACGAGTTGACAC
56750 AGTCAAAG-TCAACGAGTTGAC
1 AGTCAAAGCTCAACGAGTTGAC
56771 CCGGTGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (24 bp):
AGTCAAAGCTCAACGAGTTGACAC
Found at i:58552 original size:23 final size:23
Alignment explanation
Indices: 58526--58598 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
58516 AAACAAACGA
**
58526 TAAACGAACATGTTCGTGAATGC
1 TAAACGAACATGTTCGTGAACAC
* * * *
58549 TAAATGAACACGTTTGTGAACAT
1 TAAACGAACATGTTCGTGAACAC
* *
58572 TAAACGAACATGTTCGCGAACAA
1 TAAACGAACATGTTCGTGAACAC
58595 TAAA
1 TAAA
58599 TAAACGAACA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (23 bp):
TAAACGAACATGTTCGTGAACAC
Found at i:58641 original size:26 final size:30
Alignment explanation
Indices: 58593--58650 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
58583 GTTCGCGAAC
*
58593 AATAAATAAACGAACACGGACAA-CTTAAAA
1 AATAAATAAACGAACAC-GACAATATTAAAA
58623 AATAAATAAACG-A-AC-ACAATATTAAAA
1 AATAAATAAACGAACACGACAATATTAAAA
58650 A
1 A
58651 TTTAAACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.15
27 7 0.27
28 2 0.08
29 1 0.04
30 12 0.46
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.16
Consensus pattern (30 bp):
AATAAATAAACGAACACGACAATATTAAAA
Found at i:63175 original size:16 final size:18
Alignment explanation
Indices: 63135--63177 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
63125 AATTTTTTTC
63135 TCTTTTCTTCTCTCTTTA
1 TCTTTTCTTCTCTCTTTA
63153 TC--TTCTTCTC-CTTT-
1 TCTTTTCTTCTCTCTTTA
63167 TCTTTTCTTCT
1 TCTTTTCTTCT
63178 GTCTGAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.09
15 4 0.17
16 15 0.65
18 2 0.09
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTTCTTCTCTCTTTA
Found at i:64918 original size:13 final size:13
Alignment explanation
Indices: 64902--64929 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
64892 TTATAAATTA
64902 AATATATATATAT
1 AATATATATATAT
64915 AATATATATATAT
1 AATATATATATAT
64928 AA
1 AA
64930 ACTTAACCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATATATATATAT
Found at i:65284 original size:2 final size:2
Alignment explanation
Indices: 65279--65326 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
65269 TATCGTTATG
* *
65279 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT CG CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
65321 CT CT CT
1 CT CT CT
65327 GTTAAATGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.04, T:0.46
Consensus pattern (2 bp):
CT
Found at i:69469 original size:26 final size:21
Alignment explanation
Indices: 69419--69475 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
69409 ATAAAATTCG
69419 ATTTGATTTGATTAATTTTAT
1 ATTTGATTTGATTAATTTTAT
69440 ATTTGATTTGATTAATTTTAT
1 ATTTGATTTGATTAATTTTAT
*
69461 ATTTAATTTGATTAA
1 ATTTGATTTGATTAA
69476 AAAATACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
ATTTGATTTGATTAATTTTAT
Found at i:69588 original size:2 final size:2
Alignment explanation
Indices: 69581--69618 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
69571 TAGCCTCTCG
69581 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
69619 TACATATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73118 original size:2 final size:2
Alignment explanation
Indices: 73111--73225 Score: 230
Period size: 2 Copynumber: 57.5 Consensus size: 2
73101 TTTTTAAAAC
73111 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
73153 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
73195 AT AT AT 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 AT AT AT A
73226 CACCCCCATC
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 113 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84326 original size:21 final size:21
Alignment explanation
Indices: 84300--84339 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
84290 CCCCCTTTGA
*
84300 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
84321 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
84340 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:91744 original size:28 final size:29
Alignment explanation
Indices: 91703--91762 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
91693 TATCATCTCC
* * *
91703 AATGTTTTCAAGCACTGACTTGATGACAT
1 AATGTTTTCAAGCACTAACTCGACGACAT
91732 AATG-TTTCAAGCACTAACTCGACGACAT
1 AATGTTTTCAAGCACTAACTCGACGACAT
91760 AAT
1 AAT
91763 ATAAACGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (29 bp):
AATGTTTTCAAGCACTAACTCGACGACAT
Found at i:92070 original size:13 final size:13
Alignment explanation
Indices: 92052--92076 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92042 AAATATTAAC
92052 AAATATTTATATT
1 AAATATTTATATT
92065 AAATATTTATAT
1 AAATATTTATAT
92077 AATTAATCTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATATTTATATT
Found at i:92814 original size:23 final size:23
Alignment explanation
Indices: 92788--92833 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
92778 TTGGAACAAA
92788 CTACTATTAATGCTATTAAACCT
1 CTACTATTAATGCTATTAAACCT
*
92811 CTACTATTAATGTTATTAAACCT
1 CTACTATTAATGCTATTAAACCT
92834 TTCATAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (23 bp):
CTACTATTAATGCTATTAAACCT
Found at i:96549 original size:53 final size:53
Alignment explanation
Indices: 96469--96572 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
96459 CAAGCTTTGT
96469 TTTCAATTCCAAAGTAGACGAGGTTGCTACATGATTAGGGAATATGTGCTCGG
1 TTTCAATTCCAAAGTAGACGAGGTTGCTACATGATTAGGGAATATGTGCTCGG
* * * * * *
96522 TTTCAATTCCGAAGTCGACTAGGTTGCTCCATGATTAGGTAGTATGTGCTC
1 TTTCAATTCCAAAGTAGACGAGGTTGCTACATGATTAGGGAATATGTGCTC
96573 TCGGTTTAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (53 bp):
TTTCAATTCCAAAGTAGACGAGGTTGCTACATGATTAGGGAATATGTGCTCGG
Found at i:97061 original size:29 final size:29
Alignment explanation
Indices: 97024--97089 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
97014 AAACATTAAG
97024 ATTAA-TATATTATTAAAAT-ATAAATATT
1 ATTAATTATATTATTAAAATAAT-AATATT
97052 ATTAATTATATTATTAAAATAATAATATT
1 ATTAATTATATTATTAAAATAATAATATT
*
97081 TTTATATTA
1 ATTA-ATTA
97090 AAATATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.15
29 23 0.68
30 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTAATTATATTATTAAAATAATAATATT
Found at i:97099 original size:21 final size:22
Alignment explanation
Indices: 97063--97117 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
97053 TTAATTATAT
97063 TATTAAAATAATAATATTTTTA
1 TATTAAAATAATAATATTTTTA
97085 TATTAAAAT-ATAATATTTTTA
1 TATTAAAATAATAATATTTTTA
* *
97106 TTTTAATATAAT
1 TATTAAAATAAT
97118 TGAGCATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTAAAATAATAATATTTTTA
Found at i:97107 original size:19 final size:20
Alignment explanation
Indices: 97062--97117 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
97052 ATTAATTATA
97062 TTATTAAAATAATAATATTTT
1 TTATTAAAAT-ATAATATTTT
97083 TATATTAAAATATAATA-TTT
1 T-TATTAAAATATAATATTTT
**
97103 TTATTTTAATATAAT
1 TTATTAAAATATAAT
97118 TGAGCATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.38
20 4 0.12
21 7 0.22
22 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTAAAATATAATATTTT
Found at i:100188 original size:18 final size:18
Alignment explanation
Indices: 100165--100214 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
100155 TCTCATTCGT
100165 CTTCATCTTCATCCTCCG
1 CTTCATCTTCATCCTCCG
* * * *
100183 CTTCATCATCGTCATCGG
1 CTTCATCTTCATCCTCCG
*
100201 CTTCTTCTTCATCC
1 CTTCATCTTCATCC
100215 AACGGAAGCG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.40, G:0.08, T:0.40
Consensus pattern (18 bp):
CTTCATCTTCATCCTCCG
Found at i:101264 original size:27 final size:27
Alignment explanation
Indices: 101234--101290 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
101224 GTTGTCAGGA
*
101234 TATTTCACATGTTTTATTTTGTTTATG
1 TATTTCACATGTTTTATTTAGTTTATG
101261 TATTTCACATGTTTTATTTAGTTTATG
1 TATTTCACATGTTTTATTTAGTTTATG
101288 TAT
1 TAT
101291 ATTTTTATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.07, G:0.11, T:0.61
Consensus pattern (27 bp):
TATTTCACATGTTTTATTTAGTTTATG
Found at i:102282 original size:48 final size:49
Alignment explanation
Indices: 102123--102317 Score: 320
Period size: 49 Copynumber: 4.0 Consensus size: 49
102113 ATGACTTGAA
102123 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
*
102172 TTACACAAGCATAGAGAATCTATGTTCATCTTTCTTTTACTCTTGTATG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
* *
102221 TTACACAAGCATAGAGAATCTATGTTCATCTTTC-TTTACTCTTTTATG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
* * * *
102269 TTACACAACCATAGAGTATCTATGTTCATCTGTCTTTTATTCTTATATG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
102318 AACATCTTCA
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
48 44 0.32
49 94 0.68
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (49 bp):
TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
Found at i:102293 original size:97 final size:98
Alignment explanation
Indices: 102123--102317 Score: 320
Period size: 97 Copynumber: 2.0 Consensus size: 98
102113 ATGACTTGAA
*
102123 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATGTTACACAAGCATAGAG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATGTTACACAACCATAGAG
* *
102188 AATCTATGTTCATCTTTCTTTTACTCTTGTATG
66 AATCTATGTTCATCTGTCTTTTACTCTTATATG
* *
102221 TTACACAAGCATAGAGAATCTATGTTCATCTTTC-TTTACTCTTTTATGTTACACAACCATAGAG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATGTTACACAACCATAGAG
* *
102285 TATCTATGTTCATCTGTCTTTTATTCTTATATG
66 AATCTATGTTCATCTGTCTTTTACTCTTATATG
102318 AACATCTTCA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
97 57 0.63
98 33 0.37
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (98 bp):
TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATGTTACACAACCATAGAG
AATCTATGTTCATCTGTCTTTTACTCTTATATG
Found at i:104865 original size:2 final size:2
Alignment explanation
Indices: 104858--104891 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
104848 CGTATTCCCA
* *
104858 CT CT CT CT CG CT TT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
104892 TATTCTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:107954 original size:19 final size:19
Alignment explanation
Indices: 107930--108002 Score: 146
Period size: 19 Copynumber: 3.8 Consensus size: 19
107920 ATTAAAACAT
107930 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
107949 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
107968 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
107987 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
108003 AAACTGCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.22
Consensus pattern (19 bp):
GAGTGCATCGATGCATGGA
Found at i:107959 original size:65 final size:64
Alignment explanation
Indices: 107822--107960 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 64
107812 TGCACTAAGT
* * * * * * *
107822 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAATAAGCCTAAGTGCATTGATGCATGGTGT
1 GTGCATCGATACATAAAATGCATTCGATGTTTTCAATAAACATAAGTGCATCGATGCATGGAGA
* * * *
107886 GTGCATCGATACATAAAATGTATTTGATGTTTTCATTAAAACATGAGTGCATCGATGCATGGAGA
1 GTGCATCGATACATAAAATGCATTCGATGTTTTCAAT-AAACATAAGTGCATCGATGCATGGAGA
107951 GTGCATCGAT
1 GTGCATCGAT
107961 GCATGGAGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 32 0.51
65 31 0.49
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGCATCGATACATAAAATGCATTCGATGTTTTCAATAAACATAAGTGCATCGATGCATGGAGA
Found at i:108055 original size:20 final size:20
Alignment explanation
Indices: 108030--108067 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
108020 CAATTTATTC
*
108030 ATTGGTGTATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
108050 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
108068 CCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:110697 original size:23 final size:21
Alignment explanation
Indices: 110671--110713 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
110661 TTGATGCATA
110671 TTCAAGGAGTACATCGATGCACC
1 TTCAAGGAGT--ATCGATGCACC
* *
110694 TTCATGGTGTATCGATGCAC
1 TTCAAGGAGTATCGATGCAC
110714 TGTGAAGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
TTCAAGGAGTATCGATGCACC
Found at i:116310 original size:20 final size:20
Alignment explanation
Indices: 116285--116322 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
116275 CAATTTATTC
116285 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
116305 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
116323 CCATTTGAAA
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:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:121476 original size:3 final size:3
Alignment explanation
Indices: 121470--121539 Score: 52
Period size: 3 Copynumber: 23.3 Consensus size: 3
121460 CGACAACAAC
* * * * * * * *
121470 AGG AGG AGG AAG AGG AGG AGG AGA AGA AGA AGA AGA AGA AGA AGAG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG-G
121516 AGG AGG AGG AGG AGG AGG A-G AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
121540 AGATGAAATG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.93
4 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:122660 original size:16 final size:16
Alignment explanation
Indices: 122636--122669 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
122626 TATGTTTATA
*
122636 TTATTTTTGAATGTGT
1 TTATGTTTGAATGTGT
*
122652 TTATGTTTGATTGTGT
1 TTATGTTTGAATGTGT
122668 TT
1 TT
122670 GTCTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.65
Consensus pattern (16 bp):
TTATGTTTGAATGTGT
Found at i:122758 original size:22 final size:22
Alignment explanation
Indices: 122732--122775 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
122722 GTGTTCATTC
*
122732 GTTTAGCGATCGTGAACATGTT
1 GTTTAACGATCGTGAACATGTT
* *
122754 GTTTAACGTTTGTGAACATGTT
1 GTTTAACGATCGTGAACATGTT
122776 CAAGTAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (22 bp):
GTTTAACGATCGTGAACATGTT
Done.