Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009080.1 Hibiscus syriacus cultivar Beakdansim tig00112520_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: 74091
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3078 original size:2 final size:2
Alignment explanation
Indices: 3071--3111 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3061 ATCCTAACCT
3071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3112 TAATGAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3763 original size:14 final size:14
Alignment explanation
Indices: 3746--3786 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
3736 CTAGAATGCA
*
3746 AATGTATATTCCAT
1 AATGTATATTCCAG
3760 AATGTATATTCCAG
1 AATGTATATTCCAG
*
3774 AATGCATATTCCA
1 AATGTATATTCCA
3787 ATATTCTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (14 bp):
AATGTATATTCCAG
Found at i:3973 original size:35 final size:34
Alignment explanation
Indices: 3891--4002 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 34
3881 GTAAATCATC
*
3891 CGTTCTAGTTGAATCGAAAGTGCGATGCTTCCTT
1 CGTTCTAATTGAATCGAAAGTGCGATGCTTCCTT
* *
3925 CCATTCGAATTGAATCGAAAGTGCGATGCTTCCTT
1 -CGTTCTAATTGAATCGAAAGTGCGATGCTTCCTT
** * * *
3960 CTGTTCTTCTTGAATCAAAAGTGTGATGCCTCCCTT
1 C-GTTCTAATTGAATCGAAAGTGCGATG-CTTCCTT
3996 CGTTCTA
1 CGTTCTA
4003 TTATAGACGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.02
35 56 0.88
36 7 0.11
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (34 bp):
CGTTCTAATTGAATCGAAAGTGCGATGCTTCCTT
Found at i:5677 original size:14 final size:14
Alignment explanation
Indices: 5660--5700 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
5650 CTAGAATGCA
*
5660 AATGTATATTTCAG
1 AATGTATATTCCAG
5674 AATGTATATTCCAG
1 AATGTATATTCCAG
*
5688 AATGCATATTCCA
1 AATGTATATTCCA
5701 ATACGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (14 bp):
AATGTATATTCCAG
Found at i:8037 original size:40 final size:40
Alignment explanation
Indices: 7993--8223 Score: 167
Period size: 40 Copynumber: 5.8 Consensus size: 40
7983 ACCCAGTTTC
7993 CAAATTCGCAACGCAAATTTGT-AAATCGCAACACAGAAGT
1 CAAATTCGCAACGCAAA-TTGTCAAATCGCAACACAGAAGT
* * *
8033 CAAATTCGCAACACTGAA--GTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGC-AAATTGTCAAA-TCGCAACACAGAAGT
* * * ***
8073 CAAATTCACAACGC-GATAGTCAAAATCGCAA-GGTGATAGT
1 CAAATTCGCAACGCAAATTGTC-AAATCGCAACACAGA-AGT
* *
8113 CAAATTTGCAACGCGAATCTGT-AAATCGCAACACAGAAGT
1 CAAATTCGCAACGCAAAT-TGTCAAATCGCAACACAGAAGT
* * * *
8153 CAAATTCGCAACACAAA-AGTCAAATTCACAACGC-GATAGT
1 CAAATTCGCAACGCAAATTGTCAAA-TCGCAACACAGA-AGT
8193 CAAATTCGCAACGCGAAA--GTCAAATTCGCAA
1 CAAATTCGCAACGC-AAATTGTCAAA-TCGCAA
8224 AGCGCGTTTA
Statistics
Matches: 152, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
38 5 0.03
39 9 0.06
40 124 0.82
41 12 0.08
42 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACGCAAATTGTCAAATCGCAACACAGAAGT
Found at i:8041 original size:20 final size:19
Alignment explanation
Indices: 8018--8223 Score: 173
Period size: 20 Copynumber: 10.3 Consensus size: 19
8008 AATTTGTAAA
8018 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
8038 TCGCAACACTGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
8058 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* * *
8078 TCACAACGCGATAGTCAAAA
1 TCGCAACACGA-AGTCAAAT
***
8098 TCGCAAGGTGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* *
8118 TTGCAACGCGAA-TCTGTAAA-
1 TCGCAACACGAAGTC---AAAT
8138 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
8158 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* *
8178 TCACAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
8198 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACG-AAGTCAAAT
8218 TCGCAA
1 TCGCAA
8224 AGCGCGTTTA
Statistics
Matches: 156, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 139 0.89
21 7 0.04
22 2 0.01
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:8057 original size:60 final size:59
Alignment explanation
Indices: 7993--8223 Score: 211
Period size: 60 Copynumber: 3.8 Consensus size: 59
7983 ACCCAGTTTC
7993 CAAATTCGCAACGCAAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACTGAAGT
1 CAAATTCGCAACGCAAA-TTGTAAATCGCAACACAGAAGTCAAATTCGCAACACTGAAGT
* * * * * **
8053 CAAATTCGCAACACAAA-AGTCAAATTCACAACGC-GATAGTCAAAATCGCAA-GGTGATAGT
1 CAAATTCGCAACGCAAATTGT-AAA-TCGCAACACAGA-AGTCAAATTCGCAACACTGA-AGT
* * **
8113 CAAATTTGCAACGCGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCAAAT-TGTAAATCGCAACACAGAAGTCAAATTCGCAACACTGAAGT
* * * *
8173 CAAATTCACAACGC-GATAGTCAAATTCGCAACGC-GAAAGTCAAATTCGCAA
1 CAAATTCGCAACGCAAATTGT-AAA-TCGCAACACAG-AAGTCAAATTCGCAA
8224 AGCGCGTTTA
Statistics
Matches: 137, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
58 4 0.03
59 14 0.10
60 111 0.81
61 6 0.04
62 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (59 bp):
CAAATTCGCAACGCAAATTGTAAATCGCAACACAGAAGTCAAATTCGCAACACTGAAGT
Found at i:8145 original size:100 final size:100
Alignment explanation
Indices: 8038--8223 Score: 318
Period size: 100 Copynumber: 1.9 Consensus size: 100
8028 GAAGTCAAAT
*
8038 TCGCAACACTGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAAATCGCA
1 TCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAAATCGCA
* * * *
8103 AGGTGATAGTCAAATTTGCAACGCGAATCTGTAAA
66 ACGCGAAAGTCAAATTCGCAACGCGAATCTGTAAA
*
8138 TCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGCA
1 TCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAAATCGCA
8203 ACGCGAAAGTCAAATTCGCAA
66 ACGCGAAAGTCAAATTCGCAA
8224 AGCGCGTTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 80 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (100 bp):
TCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACGCGATAGTCAAAATCGCA
ACGCGAAAGTCAAATTCGCAACGCGAATCTGTAAA
Found at i:8836 original size:14 final size:14
Alignment explanation
Indices: 8793--8836 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
8783 ACACGAAAAT
*
8793 GAAAATCGCAACAC
1 GAAAATCGCAACGC
*
8807 CAAAATCGCAACGC
1 GAAAATCGCAACGC
*
8821 GAAAATCGCAATGC
1 GAAAATCGCAACGC
8835 GA
1 GA
8837 TTTTAGTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:10366 original size:2 final size:2
Alignment explanation
Indices: 10359--10384 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10349 CATGCATAAG
10359 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
10385 GTTCATGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10574 original size:15 final size:15
Alignment explanation
Indices: 10556--10618 Score: 117
Period size: 15 Copynumber: 4.2 Consensus size: 15
10546 GAGGGTATAA
10556 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
10571 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
10586 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
10601 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
10616 TAG
1 TAG
10619 GAGTCCTACG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:17281 original size:12 final size:12
Alignment explanation
Indices: 17263--17298 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
17253 TATATATGTT
17263 CATGTGATATGA
1 CATGTGATATGA
*
17275 TATGTGATATGA
1 CATGTGATATGA
*
17287 CCTGTGATATGA
1 CATGTGATATGA
17299 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:17461 original size:15 final size:15
Alignment explanation
Indices: 17443--17485 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
17433 GAGGGTATAA
17443 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
17458 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
17473 TAGTCCTTCGGGA
1 TAGTCCTTCGGGA
17486 TGTAAGAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.14, C:0.26, G:0.33, T:0.28
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:25070 original size:105 final size:104
Alignment explanation
Indices: 24888--25103 Score: 261
Period size: 105 Copynumber: 2.1 Consensus size: 104
24878 GGGTCTACGC
* * * *
24888 GGTCCTTTGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGCGACACATATTTGGT
1 GGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACATACTTGAT
* *
24953 CATTAGCATATGTATATGATTCTTAAGGAATTTTCTATGT
66 CATTAGCATATGTATATGATTCTTAA-GAAATTTATATGT
* * * * * * *
24993 GGTCCTTCGGGACGTATATGTATTCTTTGGAGCATGTATGAGGTCTTTTGAGACACTTACTTGAT
1 GGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACATACTTGAT
* * * *
25058 CCTTGGTATATGTATATGGTTCTTAAGAAATTTATATGT
66 CATTAGCATATGTATATGATTCTTAAGAAATTTATATGT
*
25097 GCTCCTT
1 GGTCCTT
25104 ATGGACAATC
Statistics
Matches: 93, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
104 17 0.18
105 76 0.82
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (104 bp):
GGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACATACTTGAT
CATTAGCATATGTATATGATTCTTAAGAAATTTATATGT
Found at i:25152 original size:24 final size:24
Alignment explanation
Indices: 25120--25169 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
25110 AATCTTATAT
*
25120 GGCACTACGGTGTAAATTCTACGC
1 GGCACTACGGTGCAAATTCTACGC
25144 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACGGTGCAAATTCTACGC
25168 GG
1 GG
25170 TACTTCAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (24 bp):
GGCACTACGGTGCAAATTCTACGC
Found at i:25189 original size:23 final size:24
Alignment explanation
Indices: 25120--25182 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
25110 AATCTTATAT
* *
25120 GGCACTACGGTGTAAATTCTACGC
1 GGCACTACAGTGCAAATTCTACGC
*
25144 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACAGTGCAAATTCTACGC
* *
25168 GGTACTTCAGTGCAA
1 GGCACTACAGTGCAA
25183 TTATACGAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (24 bp):
GGCACTACAGTGCAAATTCTACGC
Found at i:25999 original size:19 final size:19
Alignment explanation
Indices: 25975--26034 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
25965 CCAGATTCGA
25975 GTATGAAGTTTGCAAGGGT
1 GTATGAAGTTTGCAAGGGT
* *
25994 GTATGAACGCTT---A--TT
1 GTATGAA-GTTTGCAAGGGT
26009 GTATGAAGTTTGCAAGGGT
1 GTATGAAGTTTGCAAGGGT
26028 GTATGAA
1 GTATGAA
26035 TGCTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
14 3 0.10
15 8 0.26
17 2 0.06
19 15 0.48
20 3 0.10
ACGTcount: A:0.28, C:0.07, G:0.32, T:0.33
Consensus pattern (19 bp):
GTATGAAGTTTGCAAGGGT
Found at i:26018 original size:34 final size:34
Alignment explanation
Indices: 25975--26042 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
25965 CCAGATTCGA
25975 GTATGAAGTTTGCAAGGGTGTATGAACGCTTATT
1 GTATGAAGTTTGCAAGGGTGTATGAACGCTTATT
*
26009 GTATGAAGTTTGCAAGGGTGTATGAATGCTTATT
1 GTATGAAGTTTGCAAGGGTGTATGAACGCTTATT
26043 TTTAAATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.07, G:0.29, T:0.37
Consensus pattern (34 bp):
GTATGAAGTTTGCAAGGGTGTATGAACGCTTATT
Found at i:32739 original size:145 final size:145
Alignment explanation
Indices: 32476--32765 Score: 580
Period size: 145 Copynumber: 2.0 Consensus size: 145
32466 GCGAAATCGG
32476 ATATCACCATTAAAGCAACGGCTTGGTGTTTGGCAGCACCGGCGGTGTTTTCGATCCCGATGTTT
1 ATATCACCATTAAAGCAACGGCTTGGTGTTTGGCAGCACCGGCGGTGTTTTCGATCCCGATGTTT
32541 TTAGCATAGAAGAAGTCGCCATGAACGGCTGCATTGATTGAACAATATACATGAATGAACAAAAA
66 TTAGCATAGAAGAAGTCGCCATGAACGGCTGCATTGATTGAACAATATACATGAATGAACAAAAA
32606 AAGAAACAACTACAT
131 AAGAAACAACTACAT
32621 ATATCACCATTAAAGCAACGGCTTGGTGTTTGGCAGCACCGGCGGTGTTTTCGATCCCGATGTTT
1 ATATCACCATTAAAGCAACGGCTTGGTGTTTGGCAGCACCGGCGGTGTTTTCGATCCCGATGTTT
32686 TTAGCATAGAAGAAGTCGCCATGAACGGCTGCATTGATTGAACAATATACATGAATGAACAAAAA
66 TTAGCATAGAAGAAGTCGCCATGAACGGCTGCATTGATTGAACAATATACATGAATGAACAAAAA
32751 AAGAAACAACTACAT
131 AAGAAACAACTACAT
32766 TTGTATTTTA
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (145 bp):
ATATCACCATTAAAGCAACGGCTTGGTGTTTGGCAGCACCGGCGGTGTTTTCGATCCCGATGTTT
TTAGCATAGAAGAAGTCGCCATGAACGGCTGCATTGATTGAACAATATACATGAATGAACAAAAA
AAGAAACAACTACAT
Found at i:33145 original size:21 final size:21
Alignment explanation
Indices: 33116--33161 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33106 CTAGTACGGA
* *
33116 AATATAATCGTCATGTCCATC
1 AATAAAATCGTAATGTCCATC
*
33137 AATAAAATCGTAATGTCCGTC
1 AATAAAATCGTAATGTCCATC
33158 AATA
1 AATA
33162 TTGGATTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (21 bp):
AATAAAATCGTAATGTCCATC
Found at i:33234 original size:90 final size:88
Alignment explanation
Indices: 33081--33727 Score: 502
Period size: 90 Copynumber: 7.3 Consensus size: 88
33071 TCGAGGATCA
* * * * * * *
33081 TTTTCTTGGAGTAAACTACGTTTATCTAGTACGGAAATATAATCGTCATGTCCATCAATAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
* *
33146 GTAATGTCCGTCAATATTGGATTCT
66 ATAATG-CC-TCAATATTGGGTTCT
* * * * *
33171 TTTTCTTGAAGTAGACGACGTTTATCTAACACGGTAATATAATCATCATGCCCGTCAACAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
*
33236 ATAATGCC-CATTACCTTGAGGTTCT
66 ATAATGCCTCAATA--TTG-GGTTCT
* * * *
33261 TTTTCTTGAAGTAGACGACGTTTATCTAGTATGGTAGA-ATAATCGCCATGTCCGTCAACACTAA
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTA-ATATAATCGTCATGTCCGTCAACA-AAA
* ** ** *
33325 -CATAAGGCCT-ACCACGGGGTTGT
64 TCATAATGCCTCAATATTGGGTTCT
** * * * * ** * * *
33348 ACTTCTTGGACTAGAGGGCGTTTATCTAGCATAGTAGCATAATCATCATGTCCATCAATAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
* * *
33413 GTAATGCCCATCCATATTGAGTTCT
66 ATAATG-CC-TCAATATTGGGTTCT
* ** *
33438 TTTTCTTGGAGTAGACGGCGTTTATCTAGCATGGTACCATAATCGTCATGTCCGTCAACACTAA-
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACA-AAAT
* **
33502 CA-AATGGCCT-ATTACGGGGCTT-T
65 CATAAT-GCCTCAATATTGGG-TTCT
* * ** * * ** * *
33525 ATTTCTTGGAGTAGAGGGTGATTATCTAGCATGGTAGTGGAATCGTCATGTCCATCAATAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
* *
33590 GTAATATCCGTCAATATTGGGTTCT
66 ATAAT-GCC-TCAATATTGGGTTCT
* * *
33615 TTTTCTTGGAGTAGACGACGTTTATCTAACACGGTAATATAATCATCATGTCCGTCAACAAAATC
1 TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
*
33680 ATAATGCC-CATTACCTTGGGGTTCT
66 ATAATGCCTCAATA--TT-GGGTTCT
* *
33705 TTTTCTTGAAGTAAACGACGTTT
1 TTTTCTTGGAGTAGACGACGTTT
33728 CCATTGGTTA
Statistics
Matches: 435, Mismatches: 100, Indels: 44
0.75 0.17 0.08
Matches are distributed among these distances:
86 4 0.01
87 120 0.28
88 11 0.03
89 18 0.04
90 277 0.64
91 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (88 bp):
TTTTCTTGGAGTAGACGACGTTTATCTAGCATGGTAATATAATCGTCATGTCCGTCAACAAAATC
ATAATGCCTCAATATTGGGTTCT
Found at i:33390 original size:87 final size:86
Alignment explanation
Indices: 33262--33582 Score: 286
Period size: 87 Copynumber: 3.7 Consensus size: 86
33252 TGAGGTTCTT
* * * * * *
33262 TTTCTTGAAGTAGACGACGTTTATCTAGTATGGTAGAATAATCGCCATGTCCGTCAACACTAACA
1 TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAACACTAACA
33327 TAAGGCCTACCACGGGGTTGTA
66 TAAGGCCTACCACGGGGTT-TA
* * * * * * *
33349 CTTCTTGGACTAGAGGGCGTTTATCTAGCATAGTAGCATAATCATCATGTCCATCAATA-AAATC
1 TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAACACTAA-C
* * * ** * *
33413 GTAATGCCCATCCATATTGAGTTCTT
65 ATAAGGCCTA-CC--ACGGGGTT-TA
* *
33439 TTTCTTGGAGTAGACGGCGTTTATCTAGCATGGTACCATAATCGTCATGTCCGTCAACACTAACA
1 TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAACACTAACA
**
33504 -AATGGCCTATTACGGGGCTTTA
66 TAA-GGCCTACCACGGGG-TTTA
* * *** *
33526 TTTCTTGGAGTAGAGGGTGATTATCTAGCATGGTAGTGGAATCGTCATGTCCATCAA
1 TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAA
33583 TAAAATCGTA
Statistics
Matches: 180, Mismatches: 47, Indels: 14
0.75 0.20 0.06
Matches are distributed among these distances:
86 2 0.01
87 108 0.60
88 4 0.02
89 2 0.01
90 62 0.34
91 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (86 bp):
TTTCTTGGAGTAGAGGGCGTTTATCTAGCATGGTAGCATAATCGTCATGTCCGTCAACACTAACA
TAAGGCCTACCACGGGGTTTA
Found at i:33439 original size:177 final size:176
Alignment explanation
Indices: 33209--33674 Score: 578
Period size: 177 Copynumber: 2.6 Consensus size: 176
33199 ACACGGTAAT
* * * * * ** *
33209 ATAATCATCATGCCCGTCAACAAAATCATAATGCCCAT-TACCTTGAGGTTCTTTTTCTTGAAGT
1 ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCAATATTGA-GTTCTTTTTCTTGGAGT
* *
33273 AGACGACGTTTATCTAGTATGGTAGAATAATCGCCATGTCCGTCAACACTAACATAA-GGCCTAC
65 AGACGACGTTTATCTAGCATGGTA-AATAATCGTCATGTCCGTCAACACTAACA-AATGGCCTAC
*
33337 CACGGGG-TTGTACTTCTTGGACTAGAGGGCGTTTATCTAGCATAGTAGC
128 CACGGGGCTT-TACTTCTTGGACTAGAGGGCGATTATCTAGCATAGTAGC
*
33386 ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCCATATTGAGTTCTTTTTCTTGGAGTA
1 ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCAATATTGAGTTCTTTTTCTTGGAGTA
* * **
33451 GACGGCGTTTATCTAGCATGGTACCATAATCGTCATGTCCGTCAACACTAACAAATGGCCTATTA
66 GACGACGTTTATCTAGCATGGTA-AATAATCGTCATGTCCGTCAACACTAACAAATGGCCTACCA
* * * * *
33516 CGGGGCTTTATTTCTTGGAGTAGAGGGTGATTATCTAGCATGGTAGT
130 CGGGGCTTTACTTCTTGGACTAGAGGGCGATTATCTAGCATAGTAGC
** * ** * *
33563 GGAATCGTCATGTCCATCAATAAAATCGTAATATCCGTCAATATTGGGTTCTTTTTCTTGGAGTA
1 ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCAATATTGAGTTCTTTTTCTTGGAGTA
* * *
33628 GACGACGTTTATCTAACACGGTAATATAATCATCATGTCCGTCAACA
66 GACGACGTTTATCTAGCATGGTAA-ATAATCGTCATGTCCGTCAACA
33675 AAATCATAAT
Statistics
Matches: 251, Mismatches: 34, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
176 2 0.01
177 242 0.96
178 7 0.03
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (176 bp):
ATAATCATCATGTCCATCAATAAAATCGTAATGCCCATCAATATTGAGTTCTTTTTCTTGGAGTA
GACGACGTTTATCTAGCATGGTAAATAATCGTCATGTCCGTCAACACTAACAAATGGCCTACCAC
GGGGCTTTACTTCTTGGACTAGAGGGCGATTATCTAGCATAGTAGC
Found at i:33591 original size:21 final size:21
Alignment explanation
Indices: 33565--33605 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33555 ATGGTAGTGG
* *
33565 AATCGTCATGTCCATCAATAA
1 AATCGTAATATCCATCAATAA
*
33586 AATCGTAATATCCGTCAATA
1 AATCGTAATATCCATCAATA
33606 TTGGGTTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (21 bp):
AATCGTAATATCCATCAATAA
Found at i:35505 original size:24 final size:24
Alignment explanation
Indices: 35456--35506 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
35446 TGAATTAATA
*
35456 TATTTATTAAACTATTTTTAGTAT
1 TATTTATTAAACTATTTTTAGCAT
* *
35480 TATTTATTTACCTA-TTTTAGACAT
1 TATTTATTAAACTATTTTTAG-CAT
35504 TAT
1 TAT
35507 AGTCTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTTATTAAACTATTTTTAGCAT
Found at i:37934 original size:15 final size:15
Alignment explanation
Indices: 37914--37951 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
37904 TTGAGAGGAC
*
37914 GAGAAGGGGCTTATG
1 GAGAAGGGGCTGATG
*
37929 GAGAAGGGGCTGATT
1 GAGAAGGGGCTGATG
37944 GAGAAGGG
1 GAGAAGGG
37952 AGAGGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.50, T:0.16
Consensus pattern (15 bp):
GAGAAGGGGCTGATG
Found at i:43938 original size:31 final size:30
Alignment explanation
Indices: 43869--43958 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
43859 GATGATATTT
* *
43869 TTTATTTTATTAATCTTTTATATGATATAA
1 TTTATTTTATTAATATTTTATATAATATAA
* * *
43899 CTTGTTTTATTAAAATTTTACTATAATATAA
1 TTTATTTTATTAATATTTTA-TATAATATAA
* *
43930 TTTATTTTACTAATA-TTTATATCATATAA
1 TTTATTTTATTAATATTTTATATAATATAA
43959 ATTTTAGAGT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 9 0.18
30 20 0.41
31 20 0.41
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTATTTTATTAATATTTTATATAATATAA
Found at i:48517 original size:105 final size:103
Alignment explanation
Indices: 48314--48571 Score: 326
Period size: 105 Copynumber: 2.5 Consensus size: 103
48304 AAAACTCAAA
* ** * * * *
48314 CAATCTTC-ATAAAACAAGTCTGTTCTCTATTCCTTCAGAGAGTATAGGAC-TAAATCTTCAACA
1 CAATCTTCAATCAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTTAAACCTTCAACA
* *
48377 AATGTGTCCGCTCCCCATTCCTTCAGAGAGTATAGGACT
66 AA-GCGTCCGCTCCCCATTCCTTCAGAAAGTATAGGACT
* *
48416 CAATCTTCAATCAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATATGACTTAAACAACCTTCA
1 CAATCTTCAATCAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTT--A-AACCTTCA
* *
48481 ACAAA-CGTCCTCTCCCTATTCCTTCAGAAAGTATAGGACT
63 ACAAAGCGTCCGCTCCCCATTCCTTCAGAAAGTATAGGACT
*
48521 CAATCTTCAA-CAAATGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACT
1 CAATCTTCAATCAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACT
48572 CGAATAATTT
Statistics
Matches: 136, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
102 8 0.06
103 35 0.26
104 39 0.29
105 41 0.30
106 1 0.01
107 12 0.09
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (103 bp):
CAATCTTCAATCAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTTAAACCTTCAACA
AAGCGTCCGCTCCCCATTCCTTCAGAAAGTATAGGACT
Found at i:48612 original size:55 final size:55
Alignment explanation
Indices: 48291--48749 Score: 421
Period size: 55 Copynumber: 8.6 Consensus size: 55
48281 CTCTTTTTTG
* * * * ** * *
48291 CTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAACAAGTCTGTTCTCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAATCGTGTCTGCTCCCTATTC
* * *
48346 CTTCAGAGAGTATAGGACT---A-AATCTTCAACAAAT-GTGTCCGCTCCCCATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCCTATTC
* * *
48397 CTTCAGAGAGTATAGGACT----CAATCTTCAATCAAACGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAA-CAATCGTGTCTGCTCCCTATTC
* ** * * *
48449 CTTCAGAGAGTATATGACTTAAACAACCTTCAACAAACGT-CCT-CTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* *
48502 CTTCAGAAAGTATAGGACT----CAATCTTCAACAAAT-GTGTCTGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCCTATTC
* * * *
48553 CTTCAGAGAGTATAAGACTCGAATAATTTTCAACATTCGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * * * * *
48608 CTTCAGAGAGTATTAGACTCGAACAATTTTCAATATTCATGTCTGCTCCCTATTG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
* * * * *
48663 CTTAAGAGAGTATGAGACTTGAACAATCTTCAACAATCGTGTCTGCTCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
*
48718 GTTCAGAGAGTATAAGACTCGAACAATCTTCA
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCA
48750 TTTGCTTCAC
Statistics
Matches: 340, Mismatches: 47, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
49 12 0.04
50 5 0.01
51 76 0.22
52 36 0.11
53 26 0.08
54 4 0.01
55 172 0.51
56 9 0.03
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
Found at i:48736 original size:165 final size:159
Alignment explanation
Indices: 48340--48749 Score: 458
Period size: 156 Copynumber: 2.6 Consensus size: 159
48330 AGTCTGTTCT
* * * * *
48340 CTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCCCCATTCCTTCAGAG
1 CTATTCCTTAAGAAAGTATAGGACTCAATCTTCAACAAATGTGTCTGCTCCCTATTCCTTCAGAG
* **
48405 AGTATAGGACT----CAATCTTCAATCAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATATGA
66 AGTATAAGACTCGAACAATCTTCAA-CATTCGTGTCTGCTCCCTATTTCTTCAGAGAGTATATGA
*
48466 CTTAAACAACCTTCAACAAACGTCCTCTCC
130 CTCAAACAACCTTCAACAAACGTCCTCTCC
*
48496 CTATTCCTTCAGAAAGTATAGGACTCAATCTTCAACAAATGTGTCTGCTCCCTATTCCTTCAGAG
1 CTATTCCTTAAGAAAGTATAGGACTCAATCTTCAACAAATGTGTCTGCTCCCTATTCCTTCAGAG
* *
48561 AGTATAAGACTCGAATAATTTTCAACATTCGTGTCTGCTCCCTATTTCTTCAGAGAGTAT-TAGA
66 AGTATAAGACTCGAACAATCTTCAACATTCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAT-GA
* ** * * *
48625 CTCGAACAATTTTCAATATTCATGT-CTGCTCC
130 CTCAAACAACCTTCAACA--AACGTCCT-CTCC
* * * **
48657 CTATTGCTTAAGAGAGTAT-GAGACTTGAACAATCTTCAAC-AATCGTGTCTGCTCTCTATTTGT
1 CTATTCCTTAAGAAAGTATAG-GAC-T---CAATCTTCAACAAAT-GTGTCTGCTCCCTATTCCT
48720 TCAGAGAGTATAAGACTCGAACAATCTTCA
60 TCAGAGAGTATAAGACTCGAACAATCTTCA
48750 TTTGCTTCAC
Statistics
Matches: 216, Mismatches: 24, Indels: 19
0.83 0.09 0.07
Matches are distributed among these distances:
156 71 0.33
158 1 0.00
159 48 0.22
160 11 0.05
161 26 0.12
162 1 0.00
164 3 0.01
165 55 0.25
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (159 bp):
CTATTCCTTAAGAAAGTATAGGACTCAATCTTCAACAAATGTGTCTGCTCCCTATTCCTTCAGAG
AGTATAAGACTCGAACAATCTTCAACATTCGTGTCTGCTCCCTATTTCTTCAGAGAGTATATGAC
TCAAACAACCTTCAACAAACGTCCTCTCC
Done.