Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001133.1 Hibiscus syriacus cultivar Beakdansim tig00002260_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: 49759
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1056 original size:23 final size:22
Alignment explanation
Indices: 1008--1056 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
998 ACAGAATGTC
1008 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
1029 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
1052 AAGGA
1 AAGGA
1057 AAATTGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:2810 original size:103 final size:103
Alignment explanation
Indices: 2627--3053 Score: 738
Period size: 103 Copynumber: 4.2 Consensus size: 103
2617 GTTGAGGGTC
* *
2627 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2692 TTGATCCTCGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTCGGCATATGTATATGATTCTTAAGGAATGA
*
2730 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACACGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2795 TTGATCCTCGACATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTCGGCATATGTATATGATTCTTAAGGAATGA
2833 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2898 TTGATCCTCGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTCGGCATATGTATATGATTCTTAAGGAATGA
* *
2936 TA--TGGTCATTC-GGAC--ATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
2996 TTGATCCTTGGCATATTTATATGATTCTTAAGGAATGA
66 TTGATCCTCGGCATATGTATATGATTCTTAAGGAATGA
*
3034 TATGTGGTCCTTCAGGACAT
1 TATGTGGTCCTTCGGGACAT
3054 TATTATATGG
Statistics
Matches: 308, Mismatches: 11, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
98 82 0.27
100 12 0.04
101 12 0.04
103 202 0.66
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTCGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3101 original size:23 final size:23
Alignment explanation
Indices: 3061--3129 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
3051 CATTATTATA
* **
3061 TGGCACTACGGTGCAATTCTACG
1 TGGCACTCCGGTATAATTCTACG
* *
3084 TGGTACTCCGGTATAATTCTATG
1 TGGCACTCCGGTATAATTCTACG
* * *
3107 TGGCACTTCGGTGTAATTATACG
1 TGGCACTCCGGTATAATTCTACG
3130 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTCCGGTATAATTCTACG
Found at i:19121 original size:27 final size:27
Alignment explanation
Indices: 19079--19173 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
19069 TTGTAGGAAT
19079 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
**
19104 TATAGAGATATGATTTGTTTTCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
19131 TATAGAGATATGATTTGTTACCATTCT
1 TATAGAGATATGATTTGTTACCATTCC
19158 TATAGAGATATGATTT
1 TATAGAGATATGATTT
19174 TGTAAATAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 7 0.11
27 56 0.89
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:22904 original size:27 final size:27
Alignment explanation
Indices: 22867--22988 Score: 203
Period size: 27 Copynumber: 4.6 Consensus size: 27
22857 GTGTAGGAAT
22867 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
22892 TATAGAGAGATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
22919 TATAGAGATATGATTTGTTTCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
22946 TATAGAGATATGATTTGTTACCATTCT
1 TATAGAGATATGATTTGTTACCATTCC
22973 TATAGAGATATGATTT
1 TATAGAGATATGATTT
22989 TGTAAATAGA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
25 7 0.08
27 84 0.92
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:32942 original size:29 final size:24
Alignment explanation
Indices: 32877--32936 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
32867 CCATCCATTT
*
32877 TTTGATGGAATTCACTTTCTCTCA
1 TTTGATAGAATTCACTTTCTCTCA
32901 TTTGATAGAATTCACTTTCTCTCA
1 TTTGATAGAATTCACTTTCTCTCA
32925 TTTGATAGAATT
1 TTTGATAGAATT
32937 AAATTCCATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.47
Consensus pattern (24 bp):
TTTGATAGAATTCACTTTCTCTCA
Found at i:42178 original size:22 final size:22
Alignment explanation
Indices: 42137--42177 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
42127 ATTTTGTTCG
*
42137 TATTTATTATATAATAAAAACA
1 TATTTATTATAAAATAAAAACA
42159 TATTTATT-TAAAATAAAAA
1 TATTTATTATAAAATAAAAA
42178 ATAAAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTTATTATAAAATAAAAACA
Found at i:43361 original size:16 final size:15
Alignment explanation
Indices: 43333--43366 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
43323 AATTAAAAAA
*
43333 ATATAATATAAATAT
1 ATATAATACAAATAT
43348 ATATAAATACAAATAT
1 ATAT-AATACAAATAT
43364 ATA
1 ATA
43367 ATATATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAATACAAATAT
Found at i:43382 original size:11 final size:11
Alignment explanation
Indices: 43368--43403 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
43358 AAATATATAA
*
43368 TATATATAGTT
1 TATATGTAGTT
43379 TATATGTAGTT
1 TATATGTAGTT
*
43390 TACATGTAGTT
1 TATATGTAGTT
43401 TAT
1 TAT
43404 TAATAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (11 bp):
TATATGTAGTT
Found at i:43577 original size:9 final size:9
Alignment explanation
Indices: 43563--43595 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
43553 GTGTAAACAA
*
43563 TATATAAAC
1 TATATAAAG
43572 TATATAAAG
1 TATATAAAG
43581 TAT-TAAAG
1 TATATAAAG
43589 TATATAA
1 TATATAA
43596 TTTATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (9 bp):
TATATAAAG
Found at i:43616 original size:17 final size:16
Alignment explanation
Indices: 43590--43623 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
43580 GTATTAAAGT
*
43590 ATATAATTTATTTATA
1 ATATAATTTATATATA
43606 ATATAAGTTTATATATA
1 ATATAA-TTTATATATA
43623 A
1 A
43624 ATTATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATATAATTTATATATA
Found at i:43710 original size:74 final size:72
Alignment explanation
Indices: 43591--43766 Score: 221
Period size: 74 Copynumber: 2.4 Consensus size: 72
43581 TATTAAAGTA
* * *
43591 TATAATTTATTTATAATATA-AGTTTATATATAAATTATGTATATAAACTATAAAAAGTATATAG
1 TATAATTTATAT-TAATATAGA-TATATATATAAATTATATATATAAACTATAAAAAGTATATAG
43655 ATTATAAAC
64 ATTATAAAC
* *
43664 TATAATTTATATTAATATAGATATATATATAAACTATATATGTATAAACTATATAAAGTATATAG
1 TATAATTTATATTAATATAGATATATATATAAA-T-TATATATATAAACTATAAAAAGTATATAG
* *
43729 TTTATAAAT
64 ATTATAAAC
* *
43738 TCTAATCTATATTAATATAG-TATATATAT
1 TATAATTTATATTAATATAGATATATATAT
43767 GTATGTATAA
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
72 18 0.20
73 22 0.24
74 51 0.56
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (72 bp):
TATAATTTATATTAATATAGATATATATATAAATTATATATATAAACTATAAAAAGTATATAGAT
TATAAAC
Found at i:43863 original size:2 final size:2
Alignment explanation
Indices: 43678--43846 Score: 102
Period size: 2 Copynumber: 85.5 Consensus size: 2
43668 ATTTATATTA
* * * * *
43678 AT AT AG AT AT AT AT AT AA ACT AT AT AT GT AT AA ACT AT AT AA AGT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T
* * * *
43723 AT AT AGT TT AT AA AT -T CT A- AT CT AT AT -T A- AT AT AGT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * * *
43763 AT AT GT AT GT AT A- ACT A- AT AT AT GT A- AT CT AT AG AT -T AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
43802 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
43844 AT A
1 AT A
43847 AAGTAATAAA
Statistics
Matches: 126, Mismatches: 27, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
1 8 0.06
2 111 0.88
3 7 0.06
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:43936 original size:48 final size:48
Alignment explanation
Indices: 43841--43942 Score: 136
Period size: 48 Copynumber: 2.1 Consensus size: 48
43831 TATATATATA
* **
43841 TATATAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAAC
1 TATATAAAGTAATAAAGTATATAATTTATAGAAACACTAACCATAAAC
*
43889 TATATAAAGTAAT-AAGTATATAATTTATAGAAAC-CTTAAACCCTAAAC
1 TATATAAAGTAATAAAGTATATAATTTATAGAAACAC-T-AACCATAAAC
43937 TATATA
1 TATATA
43943 TGTATAGACA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 1 0.02
47 21 0.44
48 26 0.54
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (48 bp):
TATATAAAGTAATAAAGTATATAATTTATAGAAACACTAACCATAAAC
Found at i:44175 original size:314 final size:315
Alignment explanation
Indices: 43831--44451 Score: 1025
Period size: 321 Copynumber: 2.0 Consensus size: 315
43821 TATATATATA
43831 TATATATATATATATAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAACTATATAA
1 TATATATATATATATAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAAC--TATAA
*
43896 AGTAAT-AAGTATATAATTTATAGAAACCTTAAA-CC-C-TAAACTATATATGTATAGACACAGT
64 AGTAATAAAGTATATAATTTATAGAAA-CATAAACCCACATAAACTATATATGTATAGACACAGT
* *
43957 TGATAATTCATATATAGTTTATATAAAAAATAGTTTATATAAATTATATATGTAACCTTAACCTA
128 TGACAATTCATATATAGTTTATATAAAAAATAGTTTATATAAATTATAAATGTAACCTTAACCTA
* * * *
44022 TAGTCTATAAACGATGGTTAATATATGTAACCTATAGTATATGTATACATGTAAACTATATATTT
193 TAGTCTATAAACAATAGTTAATATATATAACCTATAGTATATGTATACATGTAAACTATATATGT
44087 AACTTATAGTACATATATGCATAAACTATGTATAGTATATATAACCTCTCTCTCTCTC
258 AACTTATAGTACATATATGCATAAACTATGTATAGTATATATAACCTCTCTCTCTCTC
*
44145 TATATATATATATATAAAGTAATAAAGTATATAGTTTATAGAAATACTATGCATAAACTATAAAG
1 TATATATATATATATAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAACTATAAAG
44210 TAATAAAGTATATAATTTATAGAAACATAAACCCTAAACTATATAAACTATATATGTATAGACAC
66 TAATAAAGTATATAATTTATAGAAACATAAACCC---AC---ATAAACTATATATGTATAGACAC
*
44275 AGTTGACAATTCATATATAGTTTATATAAACAATAGTTTATATAAATTATAAATGTAACCTTAAC
125 AGTTGACAATTCATATATAGTTTATATAAAAAATAGTTTATATAAATTATAAATGTAACCTTAAC
*
44340 CTATAGTCTATAAACAATAGTTAATATATATAACCTATAGTATATGTATACATGTAAATTATATA
190 CTATAGTCTATAAACAATAGTTAATATATATAACCTATAGTATATGTATACATGTAAACTATATA
* *
44405 TGTAACTTATAGTACATGTATGTATAAACTATGTATAGTATATATAA
255 TGTAACTTATAGTACATATATGCATAAACTATGTATAGTATATATAA
44452 ACTATATATA
Statistics
Matches: 285, Mismatches: 12, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
312 16 0.06
313 22 0.08
314 57 0.20
317 1 0.00
321 189 0.66
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (315 bp):
TATATATATATATATAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAACTATAAAG
TAATAAAGTATATAATTTATAGAAACATAAACCCACATAAACTATATATGTATAGACACAGTTGA
CAATTCATATATAGTTTATATAAAAAATAGTTTATATAAATTATAAATGTAACCTTAACCTATAG
TCTATAAACAATAGTTAATATATATAACCTATAGTATATGTATACATGTAAACTATATATGTAAC
TTATAGTACATATATGCATAAACTATGTATAGTATATATAACCTCTCTCTCTCTC
Found at i:44248 original size:46 final size:46
Alignment explanation
Indices: 44157--44252 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
44147 TATATATATA
* * **
44157 TATAAAGTAATAAAGTATATAGTTTATAGAAATACTATGCATAAAC
1 TATAAAGTAATAAAGTATATAATTTATAGAAACACTAACCATAAAC
*
44203 TATAAAGTAATAAAGTATATAATTTATAGAAACA-TAAACCCTAAAC
1 TATAAAGTAATAAAGTATATAATTTATAGAAACACT-AACCATAAAC
44249 TATA
1 TATA
44253 TAAACTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 1 0.02
46 43 0.98
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (46 bp):
TATAAAGTAATAAAGTATATAATTTATAGAAACACTAACCATAAAC
Found at i:44439 original size:52 final size:54
Alignment explanation
Indices: 44382--44525 Score: 161
Period size: 55 Copynumber: 2.7 Consensus size: 54
44372 ACCTATAGTA
* * * *
44382 TATGTATACATGTAAATTATATATGTAACTTATAGTACATGTATGTATA-AA-C
1 TATGTATATATGTAAACTATATATGTAACCTATAGTACATGTATATATACAATC
* * *
44434 TATGTATAGTATATATAAACTATATATATAACCTATAGTATATGTATATATACAATC
1 TATG--TA-TATATGTAAACTATATATGTAACCTATAGTACATGTATATATACAATC
*
44491 TAT-T-TATATGTGAACTATATATGTAACCTATAGTA
1 TATGTATATATGTAAACTATATATGTAACCTATAGTA
44526 TATATTATGT
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
52 32 0.42
54 3 0.04
55 36 0.47
56 2 0.03
57 4 0.05
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (54 bp):
TATGTATATATGTAAACTATATATGTAACCTATAGTACATGTATATATACAATC
Found at i:44445 original size:20 final size:20
Alignment explanation
Indices: 44422--44461 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44412 TATAGTACAT
* *
44422 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
44442 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
44462 TAACCTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:44461 original size:13 final size:13
Alignment explanation
Indices: 44443--44566 Score: 51
Period size: 13 Copynumber: 9.5 Consensus size: 13
44433 CTATGTATAG
44443 TATATATAAACTA
1 TATATATAAACTA
*
44456 TATATATAACCTA
1 TATATATAAACTA
*
44469 TAGTATAT---GTA
1 TA-TATATAAACTA
* *
44480 TATATACAATCTA
1 TATATATAAACTA
* *
44493 TTTATATGTGAACTA
1 --TATATATAAACTA
* *
44508 TATATGTAACCTA
1 TATATATAAACTA
*
44521 TAGTATAT--ATTA
1 TA-TATATAAACTA
* * *
44533 TGTATATATATTA
1 TATATATAAACTA
44546 TATATATACAATCTA
1 TATATATA-AA-CTA
44561 TATATA
1 TATATA
44567 GTTTATATAA
Statistics
Matches: 83, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
10 4 0.05
11 9 0.11
12 3 0.04
13 40 0.48
14 10 0.12
15 17 0.20
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:44538 original size:92 final size:89
Alignment explanation
Indices: 44363--44597 Score: 225
Period size: 92 Copynumber: 2.6 Consensus size: 89
44353 ACAATAGTTA
* *
44363 ATATATATAACCTATAGTATATGTATACATGTAAATTATATATGTAACTTATAGTACATGTATGT
1 ATATATATAACCTATAGTATATGTAT--ATATAAATTATATATGTAACTTATAGTACATATATGT
44428 ATAAACTATGTATAGTATATATA-AACT
64 AT-AACTATGTATAGTATATATATAA-T
*
44455 ATATATATAACCTATAGTATATGTATATATACAATCTATTTATATGTGAACTATATATGTAACCT
1 ATATATATAACCTATAGTATATGTATATATA-AAT-TA--TATATGT-AACT-TATA-GT-ACAT
*
44520 ATA-GTAT-A-TAT-TAT-GTATATATATTAT
58 ATATGTATAACTATGTATAGTATATATATAAT
* * * * *
44547 ATATATACAATCTATA-TATA-GTTTATATAAACTATATATGTAACCTATAGT
1 ATATATATAACCTATAGTATATGTATATATAAATTATATATGTAACTTATAGT
44598 TTATAAACAA
Statistics
Matches: 125, Mismatches: 9, Indels: 27
0.78 0.06 0.17
Matches are distributed among these distances:
83 2 0.02
84 4 0.03
85 3 0.02
86 7 0.06
88 2 0.02
89 2 0.02
90 12 0.10
91 7 0.06
92 52 0.42
93 4 0.03
94 10 0.08
95 5 0.04
96 4 0.03
97 6 0.05
98 5 0.04
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (89 bp):
ATATATATAACCTATAGTATATGTATATATAAATTATATATGTAACTTATAGTACATATATGTAT
AACTATGTATAGTATATATATAAT
Found at i:44710 original size:22 final size:21
Alignment explanation
Indices: 44635--44714 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 21
44625 CTATATAGTT
* *
44635 TATAACCTATAGTATATAATTTA
1 TATAA-CTATAGTTTAT-ATTAA
44658 TA-AACTATAGTTTATATTAA
1 TATAACTATAGTTTATATTAA
44678 TAT-ACTATATAGTTTATATTAA
1 TATAAC--TATAGTTTATATTAA
*
44700 TGTTAACTATA-TTTA
1 T-ATAACTATAGTTTA
44715 ACTTATATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
20 8 0.16
21 14 0.29
22 22 0.45
23 3 0.06
24 2 0.04
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (21 bp):
TATAACTATAGTTTATATTAA
Found at i:44816 original size:24 final size:25
Alignment explanation
Indices: 44733--44830 Score: 87
Period size: 25 Copynumber: 4.0 Consensus size: 25
44723 TTATAGTTTA
*
44733 TATAGT-ATATAGTATAATATTAT-T
1 TATAGTAATATA-AATAATATTATAT
* * *
44757 AATAGTAACATATATAACTATTA-AT
1 TATAGTAATATAAATAA-TATTATAT
*
44782 TATAGTAATATTAAT-ATATTATAT
1 TATAGTAATATAAATAATATTATAT
* *
44806 TATAGTTATATAAATAATACTATAT
1 TATAGTAATATAAATAATATTATAT
44831 AATTTATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
23 5 0.08
24 26 0.43
25 29 0.48
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (25 bp):
TATAGTAATATAAATAATATTATAT
Found at i:44884 original size:33 final size:32
Alignment explanation
Indices: 44832--44895 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
44822 ATACTATATA
44832 ATTTATAAAATATAGTTTATATTTTAATATTAT
1 ATTTATAAAATATAGTTTATA-TTTAATATTAT
*
44865 ATTTAT-AACTATAGTTTTATATTTAATATTA
1 ATTTATAAAATATAG-TTTATATTTAATATTA
44896 ATTAACTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (32 bp):
ATTTATAAAATATAGTTTATATTTAATATTAT
Found at i:44904 original size:76 final size:76
Alignment explanation
Indices: 44835--44975 Score: 175
Period size: 76 Copynumber: 1.9 Consensus size: 76
44825 CTATATAATT
* * *
44835 TATAA-AATATAGT-TTATATT-TTA-ATATTATATTTATAACTA-TAGTTTTATATTTAATATT
1 TATAACAATATA-TATTATATTATTACAAATTATATATATAA-TATTA-ATTTATA-TTAATATT
44895 AATTAACTATATTTA
62 AATTAACTATATTTA
*
44910 TATAACTATATATATTATATTATTACAAATTATATATATAATATTAATTTATATTAATATTAATT
1 TATAACAATATATATTATATTATTACAAATTATATATATAATATTAATTTATATTAATATTAATT
44975 A
66 A
44976 TAATTATAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
75 6 0.11
76 25 0.44
77 11 0.19
78 15 0.26
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (76 bp):
TATAACAATATATATTATATTATTACAAATTATATATATAATATTAATTTATATTAATATTAATT
AACTATATTTA
Found at i:45020 original size:49 final size:46
Alignment explanation
Indices: 44940--45032 Score: 118
Period size: 47 Copynumber: 1.9 Consensus size: 46
44930 TATTACAAAT
44940 TATATATATAATATTAATTTATATTAATATTAAT-TATAATTATAATA
1 TATATATATAATATTAATTTATATT-ATATTAATATA-AATTATAATA
44987 TATATATATAATATTAATTATAAATAGTT-TATTAATATAAATTATA
1 TATATATATAATATTAATT-T--ATA-TTATATTAATATAAATTATA
45033 TAGGGATGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
47 19 0.46
48 1 0.02
49 14 0.34
50 5 0.12
51 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (46 bp):
TATATATATAATATTAATTTATATTATATTAATATAAATTATAATA
Found at i:45025 original size:31 final size:32
Alignment explanation
Indices: 44917--45012 Score: 104
Period size: 34 Copynumber: 2.9 Consensus size: 32
44907 TTATATAACT
* ** *
44917 ATATATATTATATTATTACAAATTATATATATA
1 ATATATA-TATATTAATATTAATTATAAATATA
* *
44950 ATATTAATTTATATTAATATTAATTATAATTATA
1 ATA-TA-TATATATTAATATTAATTATAAATATA
44984 ATATATATATA-TAATATTAATTATAAATA
1 ATATATATATATTAATATTAATTATAAATA
45013 GTTTATTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
31 17 0.32
32 5 0.09
33 5 0.09
34 25 0.47
35 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
ATATATATATATTAATATTAATTATAAATATA
Found at i:45774 original size:6 final size:6
Alignment explanation
Indices: 45712--45759 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
45702 CATCTTCTAT
* *
45712 CCCAAA CCCAAA CCCAAA CCCAAA CTCAAA CCCAAA CCCGAA CCCAAA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA
45760 TATGAACCCG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.48, C:0.48, G:0.02, T:0.02
Consensus pattern (6 bp):
CCCAAA
Found at i:46434 original size:80 final size:80
Alignment explanation
Indices: 46187--46426 Score: 464
Period size: 80 Copynumber: 3.0 Consensus size: 80
46177 TTCGTTGGGA
46187 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTTGTAGTCC
1 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTTGTAGTCC
46252 TTGTTTGTGTAGCTG
66 TTGTTTGTGTAGCTG
46267 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTTGTAGTCC
1 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTTGTAGTCC
46332 TTGTTTGTGTAGCTG
66 TTGTTTGTGTAGCTG
46347 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTA-TTGTTTCCTTTGTAGTCC
1 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTTGTAGTCC
46411 TTGTTTTGTGTAGCTG
66 TTG-TTTGTGTAGCTG
46427 TTTGTTGTTC
Statistics
Matches: 159, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
79 21 0.13
80 138 0.87
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.47
Consensus pattern (80 bp):
ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTTGTAGTCC
TTGTTTGTGTAGCTG
Found at i:47240 original size:22 final size:20
Alignment explanation
Indices: 47190--47237 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
47180 CTTTAAGTTT
47190 GTGAAAAAGATGACATGTGA
1 GTGAAAAAGATGACATGTGA
*
47210 GTGAAAAAGATGACATGTGT
1 GTGAAAAAGATGACATGTGA
47230 GTGAAAAA
1 GTGAAAAA
47238 AAGCATTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.29, T:0.21
Consensus pattern (20 bp):
GTGAAAAAGATGACATGTGA
Found at i:48914 original size:19 final size:19
Alignment explanation
Indices: 48890--48932 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
48880 TTCTGTAAGG
*
48890 GTTTGGTAAAGTTAGAAAT
1 GTTTGGTAAAGTCAGAAAT
48909 GTTTGGTAAAGTCAGAAAT
1 GTTTGGTAAAGTCAGAAAT
48928 GTTTG
1 GTTTG
48933 ACACTGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (19 bp):
GTTTGGTAAAGTCAGAAAT
Found at i:49598 original size:20 final size:20
Alignment explanation
Indices: 49575--49618 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
49565 TATTATTTTG
*
49575 TATTTACATAAATTAAATTA
1 TATTTACATAAATTAAACTA
49595 TATTTACATAAATTAAACTA
1 TATTTACATAAATTAAACTA
49615 TATT
1 TATT
49619 AAAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTACATAAATTAAACTA
Found at i:49721 original size:30 final size:30
Alignment explanation
Indices: 49685--49753 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
49675 AAATGATTTT
* *
49685 ATAATTTTATTAA-ATAATTTTTATTAATAA
1 ATAATTTTATTAATATAATTATCA-TAATAA
*
49715 ATAA-TTTATTAATTTAATTATCATAATAA
1 ATAATTTTATTAATATAATTATCATAATAA
*
49744 ATATTTTTAT
1 ATAATTTTAT
49754 AACATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (30 bp):
ATAATTTTATTAATATAATTATCATAATAA
Done.