Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000788.1 Hibiscus syriacus cultivar Beakdansim tig00001527_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: 51612
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Found at i:731 original size:106 final size:106
Alignment explanation
Indices: 608--918 Score: 406
Period size: 106 Copynumber: 2.9 Consensus size: 106
598 ACTCGAAACA
* *
608 ACAAGTTCAACTCCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCG
1 ACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
673 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAAC
66 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAAC
*
714 ACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCC
1 ACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
* * * *
779 AATTTCAACTTCACAGCGAATGATATTGGACTTGAGACAGC
66 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAAC
* * * * * * * * * ** * *
820 ACAAGCTCCACTTTACAGCAAAGGGGCGGCTAGCTGTCAACAAACAATTTCTTAGTTCCAGAGCC
1 ACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
* * * *
885 AATTTTAACTTCACGACGGAGGAAATTGGACTCG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCG
919 GAAATACAAC
Statistics
Matches: 177, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 177 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
ACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAAC
Found at i:1319 original size:165 final size:162
Alignment explanation
Indices: 1071--1570 Score: 751
Period size: 163 Copynumber: 3.1 Consensus size: 162
1061 CCAAGTTTCC
* * * *
1071 CTTGAAACAAATATTTAAATCTGTTTTCATTGAAAC-TATTTCGTCTCCCTTGAGACATTTTCTT
1 CTTGAAACAAATCTTTGAATCTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTT
* *
1135 TTGGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCC
66 TTGGAACTAAGTTTTGTCT-CCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCC
1200 CTTGAATGAGTTTTGTCTCTCTTGAGATAGTTCT
130 CTTGAATGA-TTTTGTCTCTCTTGAGATAGTTCT
*
1234 CTTGAAACAAAATCTTTGAATCTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGATATTTTCT
1 CTTGAAAC-AAATCTTTGAATCTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGACATTTTCT
* *
1299 TTTGGAACTAAGTTTTGTCT-CTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATATTTCT
65 TTTGGAACTAAGTTTTGTCTCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCC
1363 CTTGAAATGATTTTGTCTCTCTTGAGATAGTTTCT
130 CTTG-AATGATTTTGTCTCTCTTGAGATAG-TTCT
*
1398 CTTGAAACAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTT
1 CTTGAAACAAATCTTTGAATCTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTT
* * *
1463 TTGGAACTAAGTTTTTTCTCTTTTGAGATAGTTTCTCTTGAAACATAAACATTTAAAACA-TTCC
66 TTGGAACTAAGTTTTGTCTC-CTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCC
*
1527 CTTGAGATGAATTTTGTCTCT-TT--GATAGGTTCC
130 CTTGA-ATG-ATTTTGTCTCTCTTGAGATA-GTTCT
1560 CTTGAAACAAA
1 CTTGAAACAAA
1571 ATTTTGTCTC
Statistics
Matches: 311, Mismatches: 17, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
162 18 0.06
163 148 0.48
164 54 0.17
165 91 0.29
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (162 bp):
CTTGAAACAAATCTTTGAATCTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTT
TTGGAACTAAGTTTTGTCTCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCC
TTGAATGATTTTGTCTCTCTTGAGATAGTTCT
Found at i:1387 original size:99 final size:100
Alignment explanation
Indices: 1208--1397 Score: 235
Period size: 99 Copynumber: 1.9 Consensus size: 100
1198 CCCTTGAATG
* ** *
1208 AGTTTTGTCTCTCTTGAGATAGTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCATTGAAACAA
1 AGTTTTG-CTCTCTTGAGATAGTTCTCTTGAAACAAAATCATTGAAAATATTTCCATTGAAACAA
*
1273 ATTTCGTCTCCCTTGAGATATTTTCTTTTGGAACTA
65 ATTTCGTCTCCCTTGAGATAGTTTCTTTTGGAACTA
1309 AGTTTTG-TCTCTTGAGATAGTTTCTCTTGAAACATAAA-CATTGAAAATATTTCTC-TTGAAA-
1 AGTTTTGCTCTCTTGAGATAG-TTCTCTTGAAACA-AAATCATTGAAAATATTTC-CATTGAAAC
** * *
1370 TGATTTTGTCTCTCTTGAGATAGTTTCT
63 AAATTTCGTCTCCCTTGAGATAGTTTCT
1398 CTTGAAACAA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
99 36 0.47
100 30 0.39
101 11 0.14
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (100 bp):
AGTTTTGCTCTCTTGAGATAGTTCTCTTGAAACAAAATCATTGAAAATATTTCCATTGAAACAAA
TTTCGTCTCCCTTGAGATAGTTTCTTTTGGAACTA
Found at i:1445 original size:64 final size:64
Alignment explanation
Indices: 1316--1453 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 64
1306 CTAAGTTTTG
* ** *
1316 TCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATATTTCTCTTGAAATGATTTTGTC
1 TCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAAAAATTTCGTC
* * ** *
1380 TCTCTTGAGATAGTTTCTCTTGAAACA-AATCTTTGAATCTGTTTCCCTTGAAACAAATTTCGTC
1 TCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAA-AAATTTCGTC
*
1444 TCCCTTGAGA
1 TCTCTTGAGA
1454 CATTTTCTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 20 0.32
64 43 0.68
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (64 bp):
TCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAAAAATTTCGTC
Found at i:1673 original size:36 final size:36
Alignment explanation
Indices: 1619--1704 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 36
1609 ATTGAAAACA
* ** * *
1619 TTTCCCTTGAAATGAATTTTATCACTCATGAGATAG
1 TTTCACTTGAAACAAATTTTATCACCCATGAGACAG
* * *
1655 TTTCACTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCACTTGAAACAAATTTTATCACCCATGAGACAG
*
1691 TTTCTCTTGAAACA
1 TTTCACTTGAAACA
1705 TAAACTTTGA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
TTTCACTTGAAACAAATTTTATCACCCATGAGACAG
Found at i:1686 original size:99 final size:99
Alignment explanation
Indices: 1372--1732 Score: 345
Period size: 101 Copynumber: 3.6 Consensus size: 99
1362 TCTTGAAATG
* * * * * * **
1372 ATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATCTTTG-AATCTGTTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACATTGAAAAC-ATTTCCCTTGAAATGA
* * * * ** * *
1436 ATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAA
65 ATTTTGTC-CTC-TGAGATAGTTTCACTTGAAACAAA
* * ** * * *
1473 GTTTTTTCTCTTTTGAGATAGTTTCTCTTGAAACATAAACATTTAAAACA-TTCCCTTGAGATGA
1 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAACATTGAAAACATTTCCCTTGAAATGA
** * *
1537 ATTTTGT-CTCTTTGATAGGTTCCCTTGAAACAAA
65 ATTTTGTCCTCTGAGATAGTTTCACTTGAAACAAA
1571 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAACATTGAAAACATTTCCCTTGAAATGAA
1 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACATTGAAAACATTTCCCTTGAAATGAA
*
1635 TTTTATCACTCATGAGATAGTTTCACTTGAAAC-AA
66 TTTTGTC-CTC-TGAGATAGTTTCACTTGAAACAAA
* *
1670 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACAGTTTCCTTTGAAA
1 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAACATTGAAAACA-TTTCCCTTGAAA
1733 CAAAATCTTT
Statistics
Matches: 215, Mismatches: 36, Indels: 17
0.80 0.13 0.06
Matches are distributed among these distances:
96 13 0.06
97 19 0.09
98 44 0.20
99 41 0.19
100 17 0.08
101 62 0.29
102 16 0.07
103 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (99 bp):
ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACATTGAAAACATTTCCCTTGAAATGAA
TTTTGTCCTCTGAGATAGTTTCACTTGAAACAAA
Found at i:1721 original size:30 final size:30
Alignment explanation
Indices: 1687--1745 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1677 CTCCCTTGAG
1687 ACAGTTT-CTCTTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCT-TTGAAACA-AAATCTTTGAAA
1717 ACAGTTTCCTTTGAAACAAAATCTTTGAA
1 ACAGTTTCCTTTGAAACAAAATCTTTGAA
1746 TATGTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 3 0.11
30 22 0.81
31 2 0.07
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (30 bp):
ACAGTTTCCTTTGAAACAAAATCTTTGAAA
Found at i:1821 original size:21 final size:21
Alignment explanation
Indices: 1797--1858 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1787 TTCTTTTGGA
1797 AGTTTTTGTCTCTCTTGAGAC
1 AGTTTTTGTCTCTCTTGAGAC
*
1818 AG----T-T-TCTCTTGAAAC
1 AGTTTTTGTCTCTCTTGAGAC
**
1833 AAATTTTGTCTCTCTTGAGAC
1 AGTTTTTGTCTCTCTTGAGAC
1854 AGTTT
1 AGTTT
1859 CCCTTGAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 11 0.37
16 1 0.03
17 1 0.03
19 1 0.03
20 1 0.03
21 15 0.50
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (21 bp):
AGTTTTTGTCTCTCTTGAGAC
Found at i:1847 original size:36 final size:36
Alignment explanation
Indices: 1800--1868 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1790 TTTTGGAAGT
*
1800 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1836 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1869 TTCAATCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1926 original size:33 final size:33
Alignment explanation
Indices: 1886--1971 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 33
1876 TTTGAATACA
*
1886 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
*
1919 GTTTCTCTTGAAACATAAAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAAC----ACAAAAAACCTTTGAAAAT
1956 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
1972 CAAACCCTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
33 15 0.33
37 31 0.67
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
Found at i:3223 original size:17 final size:16
Alignment explanation
Indices: 3159--3225 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 16
3149 CCTATATATA
*
3159 TTTTTAATTATATTTAT
1 TTTTTTATTATA-TTAT
* *
3176 TTATTTATTATATTCCGCT
1 TTTTTTATTATATT---AT
3195 TTTTTTATTTATATTAT
1 TTTTTTA-TTATATTAT
3212 TATTTTTATTATAT
1 T-TTTTTATTATAT
3226 ATATCTTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.05
17 18 0.45
18 6 0.15
19 7 0.17
20 7 0.17
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (16 bp):
TTTTTTATTATATTAT
Found at i:3260 original size:19 final size:18
Alignment explanation
Indices: 3218--3260 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
3208 TTATTATTTT
*
3218 TATTATATATATCTTATA
1 TATTATATATATATTATA
3236 TCATTATATATATATATATA
1 T-ATTATATATATAT-TATA
3256 TATTA
1 TATTA
3261 ATTTTTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATATATATATTATA
Found at i:19983 original size:32 final size:32
Alignment explanation
Indices: 19931--20017 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
19921 TGATGTAACT
* * *
19931 CATAACATATCATCACTTTAGGTTACATGATA
1 CATAATATGTCATCACTTTAGGTAACATGATA
* * **
19963 CATACTATGTCATCATTTTAGGTAATTTGATA
1 CATAATATGTCATCACTTTAGGTAACATGATA
* *
19995 CATAATATGTTATCGCTTTAGGT
1 CATAATATGTCATCACTTTAGGT
20018 GAAGCAACAT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (32 bp):
CATAATATGTCATCACTTTAGGTAACATGATA
Found at i:22440 original size:31 final size:31
Alignment explanation
Indices: 22405--22472 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
22395 AAAAACAAAC
*
22405 GATTTGGCCACTTTCATTTAATTTTAATTAA
1 GATTTGGCCACTTACATTTAATTTTAATTAA
* * **
22436 GATTTGGTCACTTACGTTTCGTTTTAATTAA
1 GATTTGGCCACTTACATTTAATTTTAATTAA
22467 GATTTG
1 GATTTG
22473 ATCACTAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.49
Consensus pattern (31 bp):
GATTTGGCCACTTACATTTAATTTTAATTAA
Found at i:23331 original size:31 final size:31
Alignment explanation
Indices: 23293--23351 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
23283 TCTCATTTCC
23293 AAGTGACCAAAACTAAATAAAAAGATAACGT
1 AAGTGACCAAAACTAAATAAAAAGATAACGT
* * * *
23324 AAGTGACCGAAATTTAATAAAACGATAA
1 AAGTGACCAAAACTAAATAAAAAGATAA
23352 TTGAGCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.14, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTAAATAAAAAGATAACGT
Found at i:26484 original size:20 final size:21
Alignment explanation
Indices: 26459--26502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
26449 TTTTATTTTA
*
26459 TAATTATATA-TTATTTAAAT
1 TAATTATAAACTTATTTAAAT
*
26479 TAATTATAAACTTTTTTAAAT
1 TAATTATAAACTTATTTAAAT
26500 TAA
1 TAA
26503 AAAATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTATAAACTTATTTAAAT
Found at i:26557 original size:182 final size:184
Alignment explanation
Indices: 26322--26708 Score: 654
Period size: 182 Copynumber: 2.1 Consensus size: 184
26312 ATTAAATTTT
* * *
26322 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
26387 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATGAATTAATT-AAATTTTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATGAATTAATTAAAAATTTTATATAAAATTT
*
26451 TTATTTTATAATTATATATTATTTAAATTAATTATAAAC-TTTTTTAAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTAGAAACGTTTTTTAAATTAAA
*
26504 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
* *
26569 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATGAATTAATTAAAAATTTTATATAAAATTT
26634 TTATTTTATAATTATATATTATTTAAATTAATTAGAAACTGTTTTTTAAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTAGAAAC-GTTTTTTAAATTAAA
* *
26689 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
26709 AATTAGAAAA
Statistics
Matches: 192, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
182 104 0.54
183 56 0.29
184 8 0.04
185 24 0.12
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATGAATTAATTAAAAATTTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTAGAAACGTTTTTTAAATTAAA
Found at i:28646 original size:29 final size:29
Alignment explanation
Indices: 28602--28670 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 29
28592 CCGGAGTTTC
* *
28602 AAAAAATGACCGAAAATATTATTATACGTT
1 AAAAAATGACCAAAAATATTATTAGAC-TT
*
28632 AAAAAATGACCAAAAATATTATTAGGCTT
1 AAAAAATGACCAAAAATATTATTAGACTT
28661 AAAAAATGAC
1 AAAAAATGAC
28671 TGAATTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 12 0.33
30 24 0.67
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (29 bp):
AAAAAATGACCAAAAATATTATTAGACTT
Found at i:40145 original size:3 final size:3
Alignment explanation
Indices: 40137--40237 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
40127 AATATATATT
* * *
40137 TAA TAA TAA TAA TAA TGA TGA TGA 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
* * *
40185 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAT TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40233 TAA TA
1 TAA TA
40238 TGGATAAAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40784 original size:113 final size:113
Alignment explanation
Indices: 40554--41450 Score: 1532
Period size: 113 Copynumber: 8.0 Consensus size: 113
40544 AGAATTATGC
* * *
40554 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
40618 TATGAAC-TTCTCCGG-AAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
*
40664 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
40729 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
40777 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
40842 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
40890 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
40955 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAA-ATGATGGATTCAGGT
41004 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
41068 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
41116 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
41181 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
41229 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
41294 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAA-ATGATGGATTCAGGT
*
41343 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
41408 TATGAACTTTCTCTGGAAAAGCTGATCTTTCAAATGATAGATT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATT
41451 TGAATCTTTG
Statistics
Matches: 748, Mismatches: 33, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
110 37 0.05
111 31 0.04
112 60 0.08
113 461 0.62
114 159 0.21
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
Found at i:42351 original size:165 final size:164
Alignment explanation
Indices: 42077--42546 Score: 752
Period size: 165 Copynumber: 2.9 Consensus size: 164
42067 CCTACTGAAT
* * *
42077 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATGTTACGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACACATTCATCTTCCAAATTCAA
*
42142 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTGGCAA
65 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TTGACAA
42207 ATTCATC-TTCTAAATTCACTGATTGGTTCTGCCAAAC
129 ATTCATCTTTC-AAATTCA-TGATTGGTTCTGCCAAAC
42244 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA-ACATTCATCTTCCAAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGACACATTCATCTTCCAAATTCAAT
* *
42308 GATTGGTTCTGCCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACA
66 GATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAA
42372 TTCATCTTTCAAATTCATGATTGGTTCTGCCAAAC
130 TTCATCTTTCAAATTCATGATTGGTTCTGCCAAAC
* * * *
42407 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGACACATTCATCTTCCAAATTCAA
42472 TGATT-GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
65 TGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
42535 ATTCATCTTTCA
129 ATTCATCTTTCA
42547 TTTAATTGTT
Statistics
Matches: 285, Mismatches: 12, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
163 58 0.20
164 81 0.28
165 104 0.36
166 1 0.00
167 41 0.14
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (164 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGACACATTCATCTTCCAAATTCAAT
GATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAAT
TCATCTTTCAAATTCATGATTGGTTCTGCCAAAC
Found at i:42432 original size:82 final size:83
Alignment explanation
Indices: 42077--42546 Score: 715
Period size: 82 Copynumber: 5.7 Consensus size: 83
42067 CCTACTGAAT
* * * *
42077 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATGTTACGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTTCAAATTCA
42141 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
*
42160 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTGGCAAATTCATC-TTCTAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TTGACAAATTCATCTTTC-AAATTC
*
42224 ACTGATTGGTTCTGCCAAAC
64 AATGATTGGTTCTGCCAAAC
* *
42244 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGA-ACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTTCAAATTCAA
42307 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
* *
42325 TAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTTCAAATTC-
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTTCAAATTCA
42388 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
* *
42407 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTGACAAATTCATC-TTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTTC-AAATTCA
42471 ATGATT-GTTCTGTCC-AAC
65 ATGATTGGTTCTG-CCAAAC
42489 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTTCA
42547 TTTAATTGTT
Statistics
Matches: 359, Mismatches: 17, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
81 76 0.21
82 138 0.38
83 72 0.20
84 71 0.20
85 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTTCAAATTCAA
TGATTGGTTCTGCCAAAC
Done.