Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009266.1 Hibiscus syriacus cultivar Beakdansim tig00112921_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: 1543912
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1476805 original size:11 final size:10
Alignment explanation
Indices: 1476775--1476827 Score: 74
Period size: 9 Copynumber: 5.4 Consensus size: 10
1476765 TCGGGTCGTG
1476775 ACCGGTC-AA
1 ACCGGTCAAA
1476784 ACCGGTCAAA
1 ACCGGTCAAA
1476794 ACCGGTTCAAA
1 ACCGG-TCAAA
*
1476805 ACCGGT-TAA
1 ACCGGTCAAA
1476814 ACCGGTCAAA
1 ACCGGTCAAA
1476824 ACCG
1 ACCG
1476828 ATTTCCAGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
9 15 0.38
10 14 0.36
11 10 0.26
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1479750 original size:13 final size:13
Alignment explanation
Indices: 1479732--1479761 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1479722 GTCACGACCC
1479732 GACCCGACCCGTT
1 GACCCGACCCGTT
1479745 GACCCGACCCGTT
1 GACCCGACCCGTT
1479758 GACC
1 GACC
1479762 GGTGCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1479823 original size:29 final size:29
Alignment explanation
Indices: 1479791--1479858 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
1479781 ATTCGGTTTT
1479791 GGTGCTATTTTGGGAATTAATTCT-AAAAG
1 GGTGCTATTTTGGGAATT-ATTCTAAAAAG
* * *
1479820 GGTGCTATATTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTATTCTAAAAAG
1479849 GGTGCTATTT
1 GGTGCTATTT
1479859 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTATTCTAAAAAG
Found at i:1480593 original size:24 final size:24
Alignment explanation
Indices: 1480561--1480629 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
1480551 ATAGTTTATC
*
1480561 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
1480585 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
1480609 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
1480630 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:1484774 original size:24 final size:24
Alignment explanation
Indices: 1484742--1484810 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
1484732 ATAGTTTATC
*
1484742 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
1484766 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
1484790 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
1484811 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:1486125 original size:19 final size:19
Alignment explanation
Indices: 1486101--1486141 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1486091 TTGGGTTAAG
1486101 TAACTAACACATAAACTAT
1 TAACTAACACATAAACTAT
1486120 TAACTAACACATAAACTAT
1 TAACTAACACATAAACTAT
1486139 TAA
1 TAA
1486142 TTTATCGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (19 bp):
TAACTAACACATAAACTAT
Found at i:1490138 original size:48 final size:50
Alignment explanation
Indices: 1490073--1490166 Score: 165
Period size: 49 Copynumber: 1.9 Consensus size: 50
1490063 AAAAAATTTG
1490073 GGTTCGGGTCGGGTCAGG-TTTTTTAAGTGTGATATTCGGGTCGGGTTCA
1 GGTTCGGGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCA
*
1490122 GGTT-GGGTCGGGTCAGGTTTTTTTAAGTGTGATATTTGGGTCGGG
1 GGTTCGGGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1490167 GTCGGGGTCG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
48 13 0.30
49 30 0.70
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (50 bp):
GGTTCGGGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCA
Found at i:1490139 original size:15 final size:16
Alignment explanation
Indices: 1490110--1490140 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1490100 TGTGATATTC
1490110 GGGTCGGGTTCAGGTT
1 GGGTCGGGTTCAGGTT
1490126 GGGTCGGG-TCAGGTT
1 GGGTCGGGTTCAGGTT
1490141 TTTTTAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.06, C:0.13, G:0.52, T:0.29
Consensus pattern (16 bp):
GGGTCGGGTTCAGGTT
Found at i:1491097 original size:21 final size:21
Alignment explanation
Indices: 1491071--1491123 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1491061 GTTTCCAGAT
1491071 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
1491092 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
1491113 TCGCAATGCGA
1 TCGCAACGCGA
1491124 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1491162 original size:21 final size:21
Alignment explanation
Indices: 1491138--1491387 Score: 180
Period size: 21 Copynumber: 12.1 Consensus size: 21
1491128 CATATTCGAA
1491138 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
1491159 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
1491180 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
* *
1491199 TTGCGATAGTCGAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
* *
1491220 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
* *
1491241 TTGCGATAGTCGAAGTTCGCA
1 TTGCGATAGTCCAAGTTCGCG
** *
1491262 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
* * *
1491281 TTGCAATAGTCGAAGTTTGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
1491302 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
1491323 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
1491344 TTGCGATTTA-TTTAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
1491364 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
1491385 TTG
1 TTG
1491388 TGATTTATTT
Statistics
Matches: 175, Mismatches: 37, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
18 2 0.01
19 49 0.28
20 8 0.05
21 93 0.53
22 5 0.03
23 18 0.10
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:1491275 original size:82 final size:82
Alignment explanation
Indices: 1491157--1491416 Score: 412
Period size: 82 Copynumber: 3.2 Consensus size: 82
1491147 TCCAAGTTCG
* *
1491157 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCACGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1491222 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* * *
1491239 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTTCCAAATTCGTTGCAATAGTCGAAGTTTGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1491304 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
** *
1491321 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTT-TCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* **
1491386 TGTGATTTATTTTAAATT
65 TGCGATTTATTCCAAATT
1491404 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1491417 CAAAATCGCA
Statistics
Matches: 163, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
82 108 0.66
83 55 0.34
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATT
Found at i:1491419 original size:42 final size:42
Alignment explanation
Indices: 1491157--1491416 Score: 395
Period size: 42 Copynumber: 6.3 Consensus size: 42
1491147 TCCAAGTTCG
*
1491157 CGTTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1491197 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1491239 CGTTGCGATAGTCGAAGTTCGCATTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
1491279 CGTTGCAATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1491321 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATT-TAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * **
1491362 CGTTGCGATAGTCCAAGTTCGCGTTGTGATTTATTTTAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1491404 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1491417 CAAAATCGCA
Statistics
Matches: 203, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
40 62 0.31
41 44 0.22
42 97 0.48
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:1504944 original size:19 final size:18
Alignment explanation
Indices: 1504920--1505063 Score: 83
Period size: 18 Copynumber: 8.1 Consensus size: 18
1504910 ATTTTGCTTG
1504920 AAGAAGAAATAAAAGAGAA
1 AAGAAGAAA-AAAAGAGAA
*
1504939 AAGAAGAAAAAATGAGAA
1 AAGAAGAAAAAAAGAGAA
*
1504957 AA-AAG-AAAAATGATGGAA
1 AAGAAGAAAAAAAGA--GAA
1504975 AA-AACGAAAAGGAAA-A-AA
1 AAGAA-GAAAA--AAAGAGAA
*
1504993 AAGAAGAAAAAATG-GAA
1 AAGAAGAAAAAAAGAGAA
*
1505010 AAGGGAAGAAAAAAA-TGAA
1 AA--GAAGAAAAAAAGAGAA
*
1505029 AA-ATG-AAAAAAGAGAA
1 AAGAAGAAAAAAAGAGAA
*
1505045 AA-ATGAAAAAAAAGAGAA
1 AAGAAG-AAAAAAAGAGAA
1505063 A
1 A
1505064 TAAAAGGAGG
Statistics
Matches: 104, Mismatches: 6, Indels: 31
0.74 0.04 0.22
Matches are distributed among these distances:
15 6 0.06
16 20 0.19
17 7 0.07
18 38 0.37
19 27 0.26
20 3 0.03
21 1 0.01
22 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.06
Consensus pattern (18 bp):
AAGAAGAAAAAAAGAGAA
Found at i:1505003 original size:27 final size:28
Alignment explanation
Indices: 1504973--1505031 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1504963 AAAATGATGG
1504973 AAAAAACGAAAA-GGAA-AAAAAAGAAGA
1 AAAAAACGAAAAGGGAAGAAAAAA-AAGA
** *
1505000 AAAAATGGAAAAGGGAAGAAAAAAATGA
1 AAAAAACGAAAAGGGAAGAAAAAAAAGA
1505028 AAAA
1 AAAA
1505032 TGAAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.37
28 11 0.41
29 6 0.22
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (28 bp):
AAAAAACGAAAAGGGAAGAAAAAAAAGA
Found at i:1505047 original size:54 final size:54
Alignment explanation
Indices: 1504930--1505063 Score: 131
Period size: 54 Copynumber: 2.6 Consensus size: 54
1504920 AAGAAGAAAT
*
1504930 AAAAGAG--AAAAGAAGAAAAAATGAGAAAAAAGAAAAATGATGGAAAAAACGA
1 AAAAGAGAAAAAAGAAGAAAAAATGAGAAAAAAGAAAAATAATGGAAAAAACGA
* * *
1504982 AAAGGAAAAAAAAGAAGAAAAAATG-GAAAAGGGAAGAAAAA-AAT-G-AAAAATGAA
1 AAAAGAGAAAAAAGAAGAAAAAATGAGAAAA---AAGAAAAATAATGGAAAAAACG-A
*
1505036 AAAAGAGAAAAATGAA-AAAAAA-GAGAAA
1 AAAAGAGAAAAAAGAAGAAAAAATGAGAAA
1505064 TAAAAGGAGG
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
52 6 0.09
53 21 0.31
54 31 0.46
55 2 0.03
56 8 0.12
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (54 bp):
AAAAGAGAAAAAAGAAGAAAAAATGAGAAAAAAGAAAAATAATGGAAAAAACGA
Found at i:1505057 original size:27 final size:25
Alignment explanation
Indices: 1504930--1505057 Score: 84
Period size: 27 Copynumber: 4.9 Consensus size: 25
1504920 AAGAAGAAAT
1504930 AAAAGAG-AAAAGAAGAAAAAATGA
1 AAAAGAGAAAAAGAAGAAAAAATGA
* * *
1504954 GAAAAAAGAAAAATGATGGAAAAAACGA
1 -AAAAGAGAAAAA-GA-AGAAAAAATGA
* *
1504982 AAAGGAAAAAAAAGAAGAAAAAATGGA
1 AAAAG-AGAAAAAGAAGAAAAAAT-GA
*
1505009 AAAGGGAAGAAAAA-AATG-AAAAATGAA
1 AAA-AG-AGAAAAAGAA-GAAAAAATG-A
1505036 AAAAGAGAAAAATGAA-AAAAAA
1 AAAAGAGAAAAA-GAAGAAAAAA
1505058 GAGAAATAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 21
0.73 0.09 0.19
Matches are distributed among these distances:
25 13 0.16
26 18 0.22
27 26 0.32
28 25 0.30
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.05
Consensus pattern (25 bp):
AAAAGAGAAAAAGAAGAAAAAATGA
Found at i:1505064 original size:16 final size:16
Alignment explanation
Indices: 1505017--1505068 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
1505007 GAAAAGGGAA
*
1505017 GAAAAAAATGAAAAAT
1 GAAAAAAAAGAAAAAT
*
1505033 GAAAAAAGAGAAAAAT
1 GAAAAAAAAGAAAAAT
*
1505049 GAAAAAAAAGAGAAAT
1 GAAAAAAAAGAAAAAT
1505065 -AAAA
1 GAAAA
1505069 GGAGGGTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 4 0.12
16 28 0.88
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (16 bp):
GAAAAAAAAGAAAAAT
Found at i:1506443 original size:51 final size:51
Alignment explanation
Indices: 1506382--1506904 Score: 821
Period size: 51 Copynumber: 10.1 Consensus size: 51
1506372 AAGCAAATTC
1506382 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
1506433 GTTTGTTGAAGATTGAGTCATATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* *
1506484 GTTTGTTGAAGATTGAGTCTTATACTCTCTGAAGGAATAGGGAACGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1506535 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
**
1506586 GTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1506637 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
1506688 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* *
1506739 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * **
1506790 GTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCC
1 GTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * * *
1506845 GTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACAC
1 GTTTGTTGAAG---ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1506900 GTTTG
1 GTTTG
1506905 CCAAAAATTG
Statistics
Matches: 441, Mismatches: 24, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
51 357 0.81
54 2 0.00
55 81 0.18
58 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
Found at i:1509610 original size:42 final size:42
Alignment explanation
Indices: 1509544--1509816 Score: 397
Period size: 42 Copynumber: 6.5 Consensus size: 42
1509534 TGCTATTTTG
* *
1509544 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1509586 GACTATTGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1509628 GACTATCGCAACGAATTTGGAATAAATCGTAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1509670 GACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
1509712 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
1509754 GACTATCGCAACGAA-TTTGAA-AAATCGCAACGCGAATTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1509794 GACTATCGCAACGCAAACTTGGA
1 GACTATCGCAACG--AACTTGGA
1509817 CTATCGCAAT
Statistics
Matches: 210, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
40 30 0.14
41 5 0.02
42 171 0.81
43 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1509801 original size:21 final size:21
Alignment explanation
Indices: 1509569--1509831 Score: 186
Period size: 21 Copynumber: 12.6 Consensus size: 21
1509559 TTTGAAATAA
*
1509569 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
1509590 ATTGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
1509609 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
* *
1509632 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
* *
1509651 AAATCGTAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
*
1509674 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
1509693 AAATCACAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
* *
1509716 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
* *
1509735 AAATCGCAACGCAAACTTTGACT
1 --ATCGCAACGCGAACTTGGACT
* * **
1509758 ATCGCAA--CGAATTTGAAAA
1 ATCGCAACGCGAACTTGGACT
* *
1509777 ATCGCAACGCGAATTTTGACT
1 ATCGCAACGCGAACTTGGACT
*
1509798 ATCGCAACGCAAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
1509819 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1509832 TATGTAAATC
Statistics
Matches: 184, Mismatches: 40, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
19 52 0.28
21 94 0.51
23 38 0.21
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:1511771 original size:28 final size:29
Alignment explanation
Indices: 1511740--1511799 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
1511730 ATGATCATTT
* * *
1511740 CAGTTAATAAATTTTTAAAC-TTATAAAA
1 CAGTCAATAAATTATCAAACATTATAAAA
*
1511768 CAGTCATTAAATTATCAAACTATTATAAAA
1 CAGTCAATAAATTATCAAAC-ATTATAAAA
1511798 CA
1 CA
1511800 ATCACTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 16 0.62
30 10 0.38
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (29 bp):
CAGTCAATAAATTATCAAACATTATAAAA
Found at i:1514064 original size:7 final size:7
Alignment explanation
Indices: 1514052--1514082 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1514042 GTCAAAGAAA
1514052 GTCAACG
1 GTCAACG
1514059 GTCAACG
1 GTCAACG
1514066 GTCAACG
1 GTCAACG
1514073 GTCAACG
1 GTCAACG
1514080 GTC
1 GTC
1514083 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1514094 original size:17 final size:17
Alignment explanation
Indices: 1514072--1514129 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
1514062 AACGGTCAAC
*
1514072 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1514089 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1514106 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1514123 GGTCAAC
1 GGTCAAC
1514130 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1514147 original size:19 final size:19
Alignment explanation
Indices: 1514123--1514192 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
1514113 AGTCGGGTCG
* *
1514123 GGTCAACCCGGTTCAGACT
1 GGTCAAACCGGTTCAGACC
1514142 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1514161 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
1514180 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1514193 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
18 1 0.02
19 47 0.98
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1514172 original size:9 final size:9
Alignment explanation
Indices: 1514123--1514191 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
1514113 AGTCGGGTCG
*
1514123 GGTCAACCC
1 GGTCAAACC
* *
1514132 GGTTCAGACT
1 GG-TCAAACC
1514142 GGTCAAACC
1 GGTCAAACC
*
1514151 GGTTCAGACC
1 GG-TCAAACC
1514161 GGTCAAACC
1 GGTCAAACC
*
1514170 GGTTCGAACC
1 GG-TCAAACC
1514180 GGTCAAACC
1 GGTCAAACC
1514189 GGT
1 GGT
1514192 TTTCCAGCAG
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 26 0.54
10 22 0.46
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1521376 original size:7 final size:7
Alignment explanation
Indices: 1521364--1521400 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1521354 GTCAAAGAAA
1521364 GTCAACG
1 GTCAACG
1521371 GTCAACG
1 GTCAACG
1521378 GTC-ACG
1 GTCAACG
1521384 GTCAACG
1 GTCAACG
*
1521391 GTCAATG
1 GTCAACG
1521398 GTC
1 GTC
1521401 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:1521386 original size:13 final size:13
Alignment explanation
Indices: 1521368--1521394 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1521358 AAGAAAGTCA
1521368 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1521381 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1521394 A
1 A
1521395 ATGGTCGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:1523483 original size:23 final size:21
Alignment explanation
Indices: 1523457--1523506 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
1523447 CTTATTTTAA
1523457 ATTTTACAACAATAAATAAAAAT
1 ATTTTA-AACAAT-AATAAAAAT
**
1523480 ATTTTTAATTAATAATAAAAAT
1 A-TTTTAAACAATAATAAAAAT
1523502 ATTTT
1 ATTTT
1523507 TAATAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 5 0.21
24 5 0.21
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTTAAACAATAATAAAAAT
Found at i:1524533 original size:18 final size:18
Alignment explanation
Indices: 1524496--1524563 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
1524486 TTTATTTTTA
1524496 TTTTATTTAGAAGAGTTTT
1 TTTTATTTAGAAGAG-TTT
1524515 TTTTATTTAGAAGAGTTT
1 TTTTATTTAGAAGAGTTT
1524533 TTTTATTTAGAAGAG-TT
1 TTTTATTTAGAAGAGTTT
1524550 TTTTATTTAGAAGA
1 TTTTATTTAGAAGA
1524564 AAGTTTAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.33
18 18 0.37
19 15 0.31
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.54
Consensus pattern (18 bp):
TTTTATTTAGAAGAGTTT
Found at i:1528901 original size:20 final size:20
Alignment explanation
Indices: 1528876--1528924 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1528866 TGTTTATATA
1528876 TGTTTGTGTATTTTTGAAGG
1 TGTTTGTGTATTTTTGAAGG
1528896 TGTTTGTGTATTTTTGAAGG
1 TGTTTGTGTATTTTTGAAGG
*
1528916 TGTTCGTGT
1 TGTTTGTGT
1528925 TTGGTCCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.02, G:0.31, T:0.55
Consensus pattern (20 bp):
TGTTTGTGTATTTTTGAAGG
Found at i:1529877 original size:28 final size:28
Alignment explanation
Indices: 1529845--1529918 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
1529835 GGCACGTAGA
1529845 ATATGTCCCGAAGGACCACATATAACAC
1 ATATGTCCCGAAGGACCACATATAACAC
* * *
1529873 ATATGACTCAAAGGACCACATATAACAC
1 ATATGTCCCGAAGGACCACATATAACAC
*
1529901 ATATATCCCGAAGGACCA
1 ATATGTCCCGAAGGACCA
1529919 TGTAGAACCC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.18
Consensus pattern (28 bp):
ATATGTCCCGAAGGACCACATATAACAC
Found at i:1534222 original size:28 final size:28
Alignment explanation
Indices: 1534179--1534247 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
1534169 GACCACTATG
*
1534179 TCCCGAAGGAGCACATATAACACATATA
1 TCCCGAAGGACCACATATAACACATATA
* *
1534207 TCTCGAAGGACCACATATAACACATATG
1 TCCCGAAGGACCACATATAACACATATA
1534235 TCCCGAAGGACCA
1 TCCCGAAGGACCA
1534248 TGTAGAACCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.17
Consensus pattern (28 bp):
TCCCGAAGGACCACATATAACACATATA
Found at i:1536536 original size:3 final size:3
Alignment explanation
Indices: 1536528--1536597 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
1536518 TTTTTTCATT
* * * *
1536528 TTA TTA TTA TTA TAA TT- TT- TTT TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1536574 TTA TTA TAA ATA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1536598 CAAGCCAAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 4 0.07
3 51 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1540044 original size:14 final size:13
Alignment explanation
Indices: 1540025--1540072 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
1540015 GAGTAACACC
*
1540025 TTTTCATACATGCA
1 TTTTCAT-CTTGCA
*
1540039 TTTTCATTTTGCA
1 TTTTCATCTTGCA
1540052 TTTTGCATCTTGCA
1 TTTT-CATCTTGCA
1540066 TTTTCAT
1 TTTTCAT
1540073 TTATACTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 11 0.37
14 19 0.63
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTTCATCTTGCA
Found at i:1540055 original size:7 final size:7
Alignment explanation
Indices: 1540035--1540074 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
1540025 TTTTCATACA
1540035 TGCATTT
1 TGCATTT
1540042 T-CATTT
1 TGCATTT
1540048 TGCATTT
1 TGCATTT
*
1540055 TGCATCT
1 TGCATTT
1540062 TGCATTT
1 TGCATTT
1540069 T-CATTT
1 TGCATTT
1540075 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 11 0.37
7 19 0.63
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (7 bp):
TGCATTT
Found at i:1543396 original size:32 final size:32
Alignment explanation
Indices: 1543356--1543422 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
1543346 AGAGTCTGGA
** *
1543356 AACAAGAAGTATCTCTAGGAGATGAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
1543388 AACAAGAAGTATCTCTACCAGATAAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
1543420 AAC
1 AAC
1543423 CATTTCTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.18
Consensus pattern (32 bp):
AACAAGAAGTATCTCTACCAGATAAGCATAAC
Done.