Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005785.1 Hibiscus syriacus cultivar Beakdansim tig00013555_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: 46439
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5843 original size:23 final size:22
Alignment explanation
Indices: 5807--5874 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
5797 CATCTTATAT
5807 GACACTTCGATGTATTTCTACGC
1 GACACTTCG-TGTATTTCTACGC
* * *
5830 GGCACTTCAGTGTAATTCTACGT
1 GACACTTC-GTGTATTTCTACGC
*
5853 GACACTTCGGTGTATTTATACG
1 GACACTTC-GTGTATTTCTACG
5875 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (22 bp):
GACACTTCGTGTATTTCTACGC
Found at i:10366 original size:72 final size:70
Alignment explanation
Indices: 10258--10684 Score: 376
Period size: 72 Copynumber: 5.9 Consensus size: 70
10248 AAAACTTTTC
* * *
10258 GTTTATCTGTAAAC-AAAATTTCATCTTCCTTGAGATATTTTCCCTTGAAATGTTTAGTCTCACT
1 GTTTCTCT-TAAACGAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAAAT-TTTCGTCTCACT
* *
10322 GGAGAGA
64 CGAGACA
* * *
10329 GTTTCTCTTGAAACGAAAATTTCACCTCCCTTAAGATATTTTCCCTTGAATTTTTTTC-TCTCAC
1 GTTTCTCTT-AAACGAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAA--ATTTTCGTCTCAC
10393 TCGAGACA
63 TCGAGACA
* * * *
10401 ATTTCTCTTAAA-GAAAATTTTTTATCTCTCTTGAGAGATATTTTCTCTTGAAAATTTTCCGTCT
1 GTTTCTCTTAAACGAAAA--TTTCATCTCCCTT--GAGATATTTTCCCTTG-AAATTTT-CGTCT
*
10465 CGCTCGAGACA
60 CACTCGAGACA
* * * * * *
10476 GTTTCTATTGAAATGAAAATTACATCTCTCTTGAGATATTTTCCCTTGAAAATTTCGTCTCACTT
1 GTTTCTCTT-AAACGAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAAATTTTCGTCTCACTC
*
10541 GTGACA
65 GAGACA
* * **
10547 ATTTCTCTCTAAAC-ATAAATTTCATCTCCCTTGAGATATTTTTTCCTTGAAATTTATTTTCTCA
1 GTTTCTCT-TAAACGA-AAATTTCATCTCCCTTGAGATA-TTTTCCCTTGAAATTT-TCGTCTCA
**
10611 CTCGAGATG
62 CTCGAGACA
* * * * * *
10620 GTTTCCCTCAAATCCAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAAAATTTCGTCTCACT
1 GTTTCTCTTAAA-CGAAAATTTCATCTCCCTTGAGATATTTTCCCTTG-AAATTTTCGTCTCACT
10685 TAAGACATTT
Statistics
Matches: 289, Mismatches: 47, Indels: 39
0.77 0.13 0.10
Matches are distributed among these distances:
70 7 0.02
71 56 0.19
72 102 0.35
73 66 0.23
74 17 0.06
75 33 0.11
76 3 0.01
77 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (70 bp):
GTTTCTCTTAAACGAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAAATTTTCGTCTCACTCG
AGACA
Found at i:10494 original size:147 final size:145
Alignment explanation
Indices: 10267--10684 Score: 372
Period size: 147 Copynumber: 2.9 Consensus size: 145
10257 CGTTTATCTG
* * *
10267 TAAACA-AAATTTCATCTTCCTT--GAGATATTTTCCCTTG-AAATGTTTAGTCTCACTGGAGAG
1 TAAACATAAATTTCATCTCCCTTGAGAGATATTTT-CCTTGAAAATGTTTAGTCTCACTCGAGAC
* * **
10328 AGTTTCTCTTGAAACGAAAATTTCACCTCCCTTAAGATATTTTCCCTTGAATTTTTTTC-TCTCA
65 AGTTTCTATTGAAACGAAAATTACACCTCCCTTAAGATATTTTCCCTTGAA--AATTTCGTCTCA
10392 CTCGAGACAATTTCTCT-
128 CTCGAGACAATTTCTCTC
* * * * *
10409 TAAAGA-AAATTTTTTATCTCTCTTGAGAGATATTTTCTCTTGAAAAT-TTTCCGTCTCGCTCGA
1 TAAACATAAA--TTTCATCTCCCTTGAGAGATATTTTC-CTTGAAAATGTTT-AGTCTCACTCGA
* * * *
10472 GACAGTTTCTATTGAAATGAAAATTACATCTCTCTTGAGATATTTTCCCTTGAAAATTTCGTCTC
62 GACAGTTTCTATTGAAACGAAAATTACACCTCCCTTAAGATATTTTCCCTTGAAAATTTCGTCTC
* *
10537 ACTTGTGACAATTTCTCTC
127 ACTCGAGACAATTTCTCTC
* * ** *
10556 TAAACATAAATTTCATCTCCCTTGAGATATTTTTTCCTTG-AAAT-TTATTTTCTCACTCGAGAT
1 TAAACATAAATTTCATCTCCCTTGAGAGATATTTTCCTTGAAAATGTT-TAGTCTCACTCGAGAC
* ** * * * * * * *
10619 GGTTTC-CCTCAAATCCAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAAAATTTCGTCTCA
65 AGTTTCTATTGAAA-CGAAAATTACACCTCCCTTAAGATATTTTCCCTTG-AAAATTTCGTCTCA
10683 CT
128 CT
10685 TAAGACATTT
Statistics
Matches: 227, Mismatches: 36, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
142 8 0.04
143 4 0.02
144 62 0.27
145 26 0.11
146 59 0.26
147 65 0.29
148 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (145 bp):
TAAACATAAATTTCATCTCCCTTGAGAGATATTTTCCTTGAAAATGTTTAGTCTCACTCGAGACA
GTTTCTATTGAAACGAAAATTACACCTCCCTTAAGATATTTTCCCTTGAAAATTTCGTCTCACTC
GAGACAATTTCTCTC
Found at i:11537 original size:3 final size:3
Alignment explanation
Indices: 11529--11572 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
11519 TATTTTACGG
*
11529 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTGA TTA ATA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA T
11573 ATTTCTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:11710 original size:20 final size:20
Alignment explanation
Indices: 11687--11733 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
11677 TATTTGATTG
11687 CTATATATAATA-GATTATTA
1 CTAT-TATAATATGATTATTA
* *
11707 CTATTATATTATTATTATTA
1 CTATTATAATATGATTATTA
*
11727 CTTTTAT
1 CTATTAT
11734 TTTATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (20 bp):
CTATTATAATATGATTATTA
Found at i:11719 original size:3 final size:3
Alignment explanation
Indices: 11700--11748 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
11690 TATATAATAG
*
11700 ATT ATT ACT ATT A-T ATT ATT ATT ATT ACTT -TT ATT -TT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
11742 ATT ATT A
1 ATT ATT A
11749 ATTTATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 8 0.21
3 29 0.74
4 2 0.05
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:11738 original size:20 final size:19
Alignment explanation
Indices: 11700--11745 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
11690 TATATAATAG
11700 ATTATTACTATTATATTATT
1 ATTATTACTATTATATTA-T
* *
11720 ATTATTACTTTTATTTTAT
1 ATTATTACTATTATATTAT
11739 ATTATTA
1 ATTATTA
11746 TTAATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTATTACTATTATATTAT
Found at i:14072 original size:5 final size:5
Alignment explanation
Indices: 14045--14083 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
14035 ATTTTAAACA
*
14045 AAATT AAATT GAATT GAAA-T AAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT -AAATT AAATT AAATT AAATT AAAT
14084 AAAGACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.10
5 25 0.83
6 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:16493 original size:16 final size:17
Alignment explanation
Indices: 16462--16494 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16452 AAGTTCCTCT
*
16462 ATTTTCTCTTTTTCTTC
1 ATTTTCTCTATTTCTTC
16479 ATTTTCTC-ATTTCTTC
1 ATTTTCTCTATTTCTTC
16495 TCTCTCTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTCTCTATTTCTTC
Found at i:19204 original size:36 final size:36
Alignment explanation
Indices: 19163--19256 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
19153 TCCGATATGG
19163 TGTATAACATCGTATAATTTTTGAGGTCAAATACCT
1 TGTATAACATCGTATAATTTTTGAGGTCAAATACCT
*
19199 TGTATAACATCGTAAAATTTTTGAGGTCAAATACCT
1 TGTATAACATCGTATAATTTTTGAGGTCAAATACCT
19235 TGTATAACATCGTATAATTTTT
1 TGTATAACATCGTATAATTTTT
19257 ATCCTATTCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (36 bp):
TGTATAACATCGTATAATTTTTGAGGTCAAATACCT
Found at i:21116 original size:24 final size:22
Alignment explanation
Indices: 21085--21134 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
21075 GACCTGAAAT
*
21085 TAAAAAAATAAAAAGAAAATTAA
1 TAAAAAAAGAAAAAGAAAATT-A
*
21108 TAAACAAAAGAAAAATAAAATTA
1 TAAA-AAAAGAAAAAGAAAATTA
21131 TAAA
1 TAAA
21135 TAATAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (22 bp):
TAAAAAAAGAAAAAGAAAATTA
Found at i:21172 original size:2 final size:2
Alignment explanation
Indices: 21165--21244 Score: 53
Period size: 2 Copynumber: 42.0 Consensus size: 2
21155 TTTCAAAAAT
* * * * * *
21165 TA TA TA TA TA TA TA TA TA TA TA TT TA AA AA AA TA TA TA AA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
21207 TA T- TA TA -A TA CA TA -A TA TA -A TA CTA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
21245 CACACAAATG
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
1 5 0.08
2 57 0.89
3 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (2 bp):
TA
Found at i:21180 original size:32 final size:31
Alignment explanation
Indices: 21132--21216 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
21122 ATAAAATTAT
* *
21132 AAATA-AT-AATATATATAATATGTTTTCAAA
1 AAATATATAAATATATATAATAT-ATTTAAAA
* *
21162 AATTATATATATATATATATATATATTTAAAA
1 AAATATATAAATATATATA-ATATATTTAAAA
*
21194 AAATATATAAAAATATTATAATA
1 AAATATATAAATATA-TATAATA
21217 CATAATATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
30 4 0.09
31 2 0.05
32 30 0.68
33 8 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
AAATATATAAATATATATAATATATTTAAAA
Found at i:21641 original size:25 final size:25
Alignment explanation
Indices: 21607--21655 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
21597 ATAGTCCATG
21607 TTAAATTCTACCATTTTAAGACATT
1 TTAAATTCTACCATTTTAAGACATT
21632 TTAAATTCTACCATTTTAAGACAT
1 TTAAATTCTACCATTTTAAGACAT
21656 GAAAATGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (25 bp):
TTAAATTCTACCATTTTAAGACATT
Found at i:24266 original size:2 final size:2
Alignment explanation
Indices: 24259--24290 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24249 TTACAGGAGA
24259 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
24291 TGAGTTGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31155 original size:3 final size:3
Alignment explanation
Indices: 31147--31227 Score: 117
Period size: 3 Copynumber: 27.0 Consensus size: 3
31137 TTAATATATT
* * *
31147 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
31195 TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31228 ATAAATCGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:32242 original size:113 final size:113
Alignment explanation
Indices: 31462--32207 Score: 1008
Period size: 113 Copynumber: 6.7 Consensus size: 113
31452 TAGAGTCATC
* * * * * *
31462 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTCTT--TTCTTCAAATGGGTTCTTCTCA
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
31523 TTATGAACTTTCTCT-GTAAAGGTTGATCCATTAAGTGATGAATTTGAA-
66 TTATGAACTCTCTCTGGCAAA-GCTGATCCATCAAATGATGAATTT-AAG
31571 CAAAAGGGTTAAACAAGTTCTTCTCATTATGAAC-T-TTCTT--TTCTTCAGATGAGTTCTTCTC
1 CAAAA-GGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *** * *
31632 ATTATGAACTCTCTTTGGCGCTGATGATCCATCAAATGATGAATTCAAG
65 ATTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAAG
*
31681 CAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
31746 TTATGAACTTTCTCTGGCAAAACTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAAG
*
31794 CAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
31859 TTATGAACTTTCTCTGGCAAAGCTGATCTATCAAATGATGAATTCAAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAAG
* *
31907 CAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
31972 TTATGAACTCTTTCTGGAAAAGCTAATCCATCAAATGATGAATTTGAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAAG
* *
32020 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*** * * * * *
32085 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAAG
* *
32133 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
32198 TTATGAACTC
66 TTATGAACTC
32208 GAACTGGCAC
Statistics
Matches: 585, Mismatches: 45, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
109 35 0.06
110 88 0.15
111 6 0.01
113 456 0.78
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCTCTGGCAAAGCTGATCCATCAAATGATGAATTTAAG
Found at i:33194 original size:83 final size:83
Alignment explanation
Indices: 33055--33360 Score: 594
Period size: 83 Copynumber: 3.7 Consensus size: 83
33045 CTGTGGTTCA
*
33055 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATATTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
33120 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
33138 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
33203 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
33221 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
33286 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
*
33304 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
33361 GCATTTGTTC
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 221 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
AAATTCAATGATTGGTTT
Found at i:33276 original size:166 final size:172
Alignment explanation
Indices: 32966--33360 Score: 640
Period size: 166 Copynumber: 2.3 Consensus size: 172
32956 GGTTTTATAT
* * * *
32966 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
*
33031 TTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 TTC-A-AACTGG-TATGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
33096 ATGCTATGAGCACATTCATATTTCAAATTCAATGATTGGTTTTAC
128 ATGCTATGAGCACATTCATATTTCAAATTCAATGATTGGTTTTAC
*
33141 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
*
33206 TTC-AA-T-G-AT-TGGTT-TTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
66 TTCAAACTGGTATGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
33265 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
131 CTATGAGCACATTCATATTTCAAATTCAATGATTGGTTTTAC
*
33307 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
33361 GCATTTGTTC
Statistics
Matches: 211, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
166 138 0.65
167 5 0.02
168 1 0.00
170 1 0.00
171 1 0.00
172 2 0.01
175 63 0.30
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (172 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
TTCAAACTGGTATGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
CTATGAGCACATTCATATTTCAAATTCAATGATTGGTTTTAC
Found at i:34520 original size:8 final size:8
Alignment explanation
Indices: 34507--34555 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 8
34497 TTGACCCCCC
34507 TTTTTCTT
1 TTTTTCTT
34515 TTTTTCTT
1 TTTTTCTT
*
34523 TTCTCTTTTT
1 TT-T-TTCTT
34533 TTCTTTCTT
1 TT-TTTCTT
34542 TTTTCTCTT
1 TTTT-TCTT
34551 TTTTT
1 TTTTT
34556 TAAGCATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 13 0.36
9 15 0.42
10 8 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:34526 original size:13 final size:13
Alignment explanation
Indices: 34508--34556 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
34498 TGACCCCCCT
34508 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
34521 TTTTCTCTTTTTT-
1 TTTTCT-TTTTTTC
34534 TCTTTCTTTTTTCTC
1 T-TTTCTTTTTT-TC
34549 TTTT-TTTT
1 TTTTCTTTT
34557 AAGCATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 16 0.50
14 15 0.47
15 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:34536 original size:10 final size:10
Alignment explanation
Indices: 34521--34555 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
34511 TCTTTTTTTC
34521 TTTTCTCTTT
1 TTTTCTCTTT
*
34531 TTTTCTTTCTT
1 TTTTCTCT-TT
34542 TTTTCTCTTT
1 TTTTCTCTTT
34552 TTTT
1 TTTT
34556 TAAGCATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:34555 original size:21 final size:23
Alignment explanation
Indices: 34507--34555 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
34497 TTGACCCCCC
*
34507 TTTTTCTTTTTTTCTTTTCTCTT
1 TTTTTCTTTTCTTCTTTTCTCTT
34530 TTTTTC-TTTCTT-TTTTCTCTT
1 TTTTTCTTTTCTTCTTTTCTCTT
34551 TTTTT
1 TTTTT
34556 TAAGCATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.56
22 5 0.20
23 6 0.24
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTTCTTCTTTTCTCTT
Found at i:34556 original size:23 final size:23
Alignment explanation
Indices: 34507--34556 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
34497 TTGACCCCCC
*
34507 TTTTTCTTTTTTTCTTTTCTCTT
1 TTTTTCTTTTTTTCTTCTCTCTT
34530 TTTTTCTTTCTTTT-TTCTCT-TT
1 TTTTTCTTT-TTTTCTTCTCTCTT
34552 TTTTT
1 TTTTT
34557 AAGCATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 14 0.56
24 4 0.16
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTTTTTCTTCTCTCTT
Found at i:45225 original size:23 final size:24
Alignment explanation
Indices: 45190--45239 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
45180 ACTTGCAAAT
* *
45190 AAAATGAACATATAAATATTATGA
1 AAAATGAAAATATAAAAATTATGA
*
45214 AAAAT-AAAATATAAAAATTTTGA
1 AAAATGAAAATATAAAAATTATGA
45237 AAA
1 AAA
45240 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (24 bp):
AAAATGAAAATATAAAAATTATGA
Done.