Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005218.1 Hibiscus syriacus cultivar Beakdansim tig00011816_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: 87881
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:6647 original size:21 final size:22
Alignment explanation
Indices: 6623--6671 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
6613 CACCTAAGTG
6623 CCACATAT-TTATCCCAAATGA
1 CCACATATATTATCCCAAATGA
**
6644 CCACAT-TATTATCCTGAATGA
1 CCACATATATTATCCCAAATGA
6665 CCACATA
1 CCACATA
6672 AAACCCTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (22 bp):
CCACATATATTATCCCAAATGA
Found at i:7920 original size:12 final size:12
Alignment explanation
Indices: 7903--7936 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
7893 CGGTAAGAAG
*
7903 AAGAAGGAAATA
1 AAGAAGGAAAGA
7915 AAGAAGGAAAGA
1 AAGAAGGAAAGA
7927 AAGAAGGAAA
1 AAGAAGGAAA
7937 AGCTTTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (12 bp):
AAGAAGGAAAGA
Found at i:13479 original size:22 final size:22
Alignment explanation
Indices: 13457--13588 Score: 135
Period size: 23 Copynumber: 6.0 Consensus size: 22
13447 CAGCTCGTAA
13457 TTTGCACCGAAGTGCCACATA-
1 TTTGCACCGAAGTGCCACATAG
* *
13478 ATTGTC-CCGAAAG-ACCACATAG
1 TTTG-CACCG-AAGTGCCACATAG
* * *
13500 GTTACACCGAAGTGTCACATAG
1 TTTGCACCGAAGTGCCACATAG
* * *
13522 GTTACACCGAAGTGTCACATAGG
1 TTTGCACCGAAGTGCCACATA-G
13545 TTTGCACCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATA-G
13568 TTTGCACCGAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
13589 TTTATCCCGA
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
21 17 0.18
22 37 0.39
23 42 0.44
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (22 bp):
TTTGCACCGAAGTGCCACATAG
Found at i:13488 original size:21 final size:22
Alignment explanation
Indices: 13461--13588 Score: 145
Period size: 22 Copynumber: 5.8 Consensus size: 22
13451 TCGTAATTTG
*
13461 CACCGAAGTGCCACATA-ATTGT
1 CACCGAAGTGCCACATAGGTT-T
* *
13483 C-CCGAAAG-ACCACATAGGTTA
1 CACCG-AAGTGCCACATAGGTTT
* *
13504 CACCGAAGTGTCACATAGGTTA
1 CACCGAAGTGCCACATAGGTTT
*
13526 CACCGAAGTGTCACATAGGTTT
1 CACCGAAGTGCCACATAGGTTT
13548 GCACCGAAGTGCCACATAGGTTT
1 -CACCGAAGTGCCACATAGGTTT
13571 GCACCGAAGTGCCACATA
1 -CACCGAAGTGCCACATA
13589 TTTATCCCGA
Statistics
Matches: 94, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
21 14 0.15
22 41 0.44
23 39 0.41
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (22 bp):
CACCGAAGTGCCACATAGGTTT
Found at i:13556 original size:23 final size:22
Alignment explanation
Indices: 13492--13588 Score: 140
Period size: 23 Copynumber: 4.3 Consensus size: 22
13482 TCCCGAAAGA
13492 CCACATAGGTTACACCGAAGTG
1 CCACATAGGTTACACCGAAGTG
*
13514 TCACATAGGTTACACCGAAGTG
1 CCACATAGGTTACACCGAAGTG
* *
13536 TCACATAGGTTTGCACCGAAGTG
1 CCACATAGG-TTACACCGAAGTG
*
13559 CCACATAGGTTTGCACCGAAGTG
1 CCACATAGG-TTACACCGAAGTG
13582 CCACATA
1 CCACATA
13589 TTTATCCCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
22 30 0.42
23 41 0.58
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.22
Consensus pattern (22 bp):
CCACATAGGTTACACCGAAGTG
Found at i:13564 original size:45 final size:45
Alignment explanation
Indices: 13492--13588 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
13482 TCCCGAAAGA
*
13492 CCACATAGGTTACACCGAAGTGTCACATAGG-TTACACCGAAGTG
1 CCACATAGGTTACACCGAAGTGCCACATAGGTTTACACCGAAGTG
* * *
13536 TCACATAGGTTTGCACCGAAGTGCCACATAGGTTTGCACCGAAGTG
1 CCACATAGG-TTACACCGAAGTGCCACATAGGTTTACACCGAAGTG
13582 CCACATA
1 CCACATA
13589 TTTATCCCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 8 0.17
45 20 0.43
46 18 0.39
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.22
Consensus pattern (45 bp):
CCACATAGGTTACACCGAAGTGCCACATAGGTTTACACCGAAGTG
Found at i:17934 original size:21 final size:22
Alignment explanation
Indices: 17909--17953 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
17899 GTCTATAAAG
17909 AGTCACAGGAGAAT-AAATATA
1 AGTCACAGGAGAATGAAATATA
* * *
17930 AGTCATATGATAATGAAATATA
1 AGTCACAGGAGAATGAAATATA
17952 AG
1 AG
17954 ACTATGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (22 bp):
AGTCACAGGAGAATGAAATATA
Found at i:25098 original size:30 final size:30
Alignment explanation
Indices: 25059--25138 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
25049 CAAAATGGTT
25059 TTTGGACTTGAATTGAATTTACAAAACGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
* * *
25089 TTTGAACTTGAATTAAATTTACAAAATGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
25119 TTTGGACTT-AATTGAATTTA
1 TTTGGACTTGAATTGAATTTA
25139 TTCAAAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 10 0.22
30 35 0.78
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (30 bp):
TTTGGACTTGAATTGAATTTACAAAACGTA
Found at i:26551 original size:30 final size:31
Alignment explanation
Indices: 26517--26575 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
26507 TCGAAGCTTG
*
26517 TTAAATTCCCCTTTTAT-CCCCTTTTATCTT
1 TTAAATTCCCCTATTATCCCCCTTTTATCTT
*
26547 TTAAATTCCCCTATTCTCCCCCTTTTATC
1 TTAAATTCCCCTATTATCCCCCTTTTATC
26576 GTATTAAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAAATTCCCCTATTATCCCCCTTTTATCTT
Found at i:29543 original size:18 final size:20
Alignment explanation
Indices: 29507--29543 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
29497 TTTCTTTAAA
*
29507 TTAATATAAGTATTTTCATT
1 TTAATATAAGTATTGTCATT
29527 TTAATAT-A-TATTGTCAT
1 TTAATATAAGTATTGTCAT
29544 ATTATGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAATATAAGTATTGTCATT
Found at i:29920 original size:191 final size:193
Alignment explanation
Indices: 29596--29994 Score: 488
Period size: 191 Copynumber: 2.1 Consensus size: 193
29586 TTGTATAAGG
*
29596 TGACGTTATGCATAATCATCATTCAAAATACTATTACATAACGTTATATTATGTCACTAAAAAAT
1 TGACGTTATGCATAATCATCATTCAAAATACTATTACATAACGTTATATTACGTCACTAAAAAAT
* * * *
29661 TGACAATATCTCTTTCGTAATATATAGGTTGATTTTATTGTAGTATTCGTGACGATATAAATTAT
66 TGACAATATCTCTTTCGTAATATATAGATTGATTATAATGTAGTATTCATGACGATATAAATTAT
* * *
29726 TAAT-A-AAAATATTATATAATTTAGTGATGTAATTAACTGTCA-TGCAATAT-AAGTTATAAAA
131 TAATAACAAAATATTATATAATTTAATGACGTAACTAACTGTCATTG-AATATCAA-TTATAAAA
* * ** *
29787 TGACGTTATGCATAAGT-GTCATTCATAATACTATTAGGTAACGTTATATTACGTCACT-GAAAA
1 TGACGTTATGCATAA-TCATCATTCAAAATACTATTACATAACGTTATATTACGTCACTAAAAAA
* * * * *
29850 TGTGACAATATCTCTTTTGT-CTCATATAGATTGATTATAATGTATTATTCATGACGATGTGAAT
65 T-TGACAATATCTCTTTCGTAAT-ATATAGATTGATTATAATGTAGTATTCATGACGATATAAAT
* ** *
29914 TATTAATAACAAAATTTTATATAATTTAATGACGTAACTAGTTGTCATTGAGTATCAATTATAAA
128 TATTAATAACAAAATATTATATAATTTAATGACGTAACTAACTGTCATTGAATATCAATTATAAA
*
29979 G
193 A
*
29980 TGACGTTATGTATAA
1 TGACGTTATGCATAA
29995 ACGTCATTTA
Statistics
Matches: 177, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
190 6 0.03
191 109 0.62
192 2 0.01
193 56 0.32
194 4 0.02
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (193 bp):
TGACGTTATGCATAATCATCATTCAAAATACTATTACATAACGTTATATTACGTCACTAAAAAAT
TGACAATATCTCTTTCGTAATATATAGATTGATTATAATGTAGTATTCATGACGATATAAATTAT
TAATAACAAAATATTATATAATTTAATGACGTAACTAACTGTCATTGAATATCAATTATAAAA
Found at i:37860 original size:17 final size:20
Alignment explanation
Indices: 37825--37864 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
37815 AGTCGACGGA
37825 AAATAATAATGTAATTTTTT
1 AAATAATAATGTAATTTTTT
37845 AAATAATAAT-T-ATTTTTT
1 AAATAATAATGTAATTTTTT
37863 AA
1 AA
37865 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATAATAATGTAATTTTTT
Found at i:37967 original size:26 final size:25
Alignment explanation
Indices: 37925--37973 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
37915 ATTCTTTTAA
*
37925 TCGAATCAAAAATAATATATAATTT
1 TCGAATCAAAAATAATAAATAATTT
**
37950 TCGAATCAAATTTAAATAAATAAT
1 TCGAATCAAAAAT-AATAAATAAT
37974 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (25 bp):
TCGAATCAAAAATAATAAATAATTT
Found at i:38594 original size:5 final size:5
Alignment explanation
Indices: 38586--38745 Score: 230
Period size: 5 Copynumber: 32.0 Consensus size: 5
38576 ATAATTATAT
* * * * * * * * * *
38586 TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
38636 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
38686 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
38736 TATTA TATTA
1 TATTA TATTA
38746 AGAGGCATGC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 154 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:39996 original size:2 final size:2
Alignment explanation
Indices: 39989--40023 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39979 AAGAAAAATA
39989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40024 AATGTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40061 original size:24 final size:24
Alignment explanation
Indices: 40015--40061 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40005 ATATATATAT
**
40015 ATATATATAAATGTTAAATAAAAA
1 ATATATATAAATGAAAAATAAAAA
40039 ATATATATAAA-GAAAAATAAAAA
1 ATATATATAAATGAAAAATAAAAA
40062 TAGAATGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
ATATATATAAATGAAAAATAAAAA
Found at i:40114 original size:2 final size:2
Alignment explanation
Indices: 40107--40137 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40097 AATAAAGAAA
40107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40138 ATTGTTAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40869 original size:16 final size:16
Alignment explanation
Indices: 40848--40880 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40838 GCTGATTCAA
40848 GTCTAGACCGGTTCGG
1 GTCTAGACCGGTTCGG
40864 GTCTAGACCGGTTCGG
1 GTCTAGACCGGTTCGG
40880 G
1 G
40881 CTACTGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.39, T:0.24
Consensus pattern (16 bp):
GTCTAGACCGGTTCGG
Found at i:41051 original size:22 final size:22
Alignment explanation
Indices: 41018--41059 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41008 GTAAATGAAA
*
41018 TGAATAATATATATATATATAT
1 TGAATAATATATATAAATATAT
41040 TGAAT-ATAATATATAAATAT
1 TGAATAAT-ATATATAAATAT
41060 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TGAATAATATATATAAATATAT
Found at i:41058 original size:13 final size:13
Alignment explanation
Indices: 41021--41067 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
41011 AATGAAATGA
*
41021 ATAATATATATAT
1 ATAATATATAAAT
*
41034 AT-ATAT-TGAAT
1 ATAATATATAAAT
41045 ATAATATATAAAT
1 ATAATATATAAAT
*
41058 ATTATATATA
1 ATAATATATA
41068 TAGTGATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 5 0.18
12 8 0.29
13 15 0.54
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:41067 original size:31 final size:30
Alignment explanation
Indices: 41023--41082 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
41013 TGAAATGAAT
*
41023 AATATATATATATATATTGAATATAATATATA
1 AATATATATATATATAGTG-ATATAA-ATATA
41055 AATAT-TATATATATAGTGATATAAATAT
1 AATATATATATATATAGTGATATAAATAT
41083 GTAACACATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 6 0.22
31 12 0.44
32 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (30 bp):
AATATATATATATATAGTGATATAAATATA
Found at i:41979 original size:57 final size:54
Alignment explanation
Indices: 41843--41993 Score: 184
Period size: 57 Copynumber: 2.8 Consensus size: 54
41833 GTAAAGTTGA
41843 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATAC-A-AGTATTGTTTTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATACAATAGTATTGTTTTG
* * *
41895 ACTTTGCA-TTGGACATCCTTCGTTGTGAAGTTGAAATCCAATATTGAATATTG-TTTG
1 GCTTTG-AGTTGGATATCCTTCGTTGTGAAGTTGAAATACAATA--G--TATTGTTTTG
* *
41952 GCTTTGAGTTGGATATCCTTCATTGTGAAGTTGAAATTCAAT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATACAAT
41994 CTTGTATAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
52 34 0.40
53 2 0.02
54 1 0.01
56 2 0.02
57 40 0.48
58 5 0.06
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (54 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATACAATAGTATTGTTTTG
Found at i:44137 original size:19 final size:18
Alignment explanation
Indices: 44099--44176 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 18
44089 CTTGAACCTA
*
44099 CCTTATTTCTTTTCTATTT
1 CCTTATTTCTTTT-TTTTT
44118 CCTTATTTCTTTTTCTTTT
1 CCTTATTTCTTTTT-TTTT
*
44137 CTTTTACTTTTCTTTTTTTCTT
1 C-CTTA--TTTCTTTTTTT-TT
* *
44159 CTTTTTTTCTTTTTTTTT
1 CCTTATTTCTTTTTTTTT
44177 TATTTAGGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
18 3 0.06
19 28 0.55
20 3 0.06
21 5 0.10
22 12 0.24
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (18 bp):
CCTTATTTCTTTTTTTTT
Found at i:44140 original size:30 final size:30
Alignment explanation
Indices: 44104--44171 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
44094 ACCTACCTTA
44104 TTTCTTTT-CTATTTCCTTATTTCTT-TTTCT
1 TTTCTTTTACT-TTTCCTTATTTCTTCTTT-T
* *
44134 TTTCTTTTACTTTTCTTTTTTTCTTCTTTT
1 TTTCTTTTACTTTTCCTTATTTCTTCTTTT
44164 TTTCTTTT
1 TTTCTTTT
44172 TTTTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (30 bp):
TTTCTTTTACTTTTCCTTATTTCTTCTTTT
Found at i:44165 original size:24 final size:23
Alignment explanation
Indices: 44104--44177 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
44094 ACCTACCTTA
* *
44104 TTTCTTTTCTATTTCCTTATTTCTT
1 TTTCTTTTCT-TTTACTT-TTTTTT
44129 TTTCTTTTCTTTTACTTTTCTTTT
1 TTTCTTTTCTTTTACTTTT-TTTT
*
44153 TTTCTTCTT-TTTTTCTTTTTTTT
1 TTTCTT-TTCTTTTACTTTTTTTT
44176 TT
1 TT
44178 ATTTAGGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 8 0.18
24 24 0.55
25 12 0.27
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTTTTCTTTTACTTTTTTTT
Found at i:44177 original size:11 final size:11
Alignment explanation
Indices: 44123--44177 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
44113 TATTTCCTTA
*
44123 TTTCTTTTTCT
1 TTTCTTTTTTT
**
44134 TTTCTTTTACT
1 TTTCTTTTTTT
44145 TTTCTTTTTTT
1 TTTCTTTTTTT
*
44156 CTTCTTTTTTT
1 TTTCTTTTTTT
44167 CTTT-TTTTTTT
1 -TTTCTTTTTTT
44178 ATTTAGGGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
11 36 0.95
12 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:54580 original size:18 final size:18
Alignment explanation
Indices: 54559--54596 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
54549 TAAAAAAACT
54559 AAAAAACAAATT-AAAGA
1 AAAAAACAAATTAAAAGA
*
54576 AAAAAGCAAATTAAAAGA
1 AAAAAACAAATTAAAAGA
54594 AAA
1 AAA
54597 TAATAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (18 bp):
AAAAAACAAATTAAAAGA
Found at i:54703 original size:45 final size:49
Alignment explanation
Indices: 54603--54707 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 49
54593 AAAATAATAG
* *
54603 AAATATA-AAAAAACAGAAACAAAAGAAGGCAAATAAAATGTAATAAAA
1 AAATATATATAAAACAGAAACAAAAGAAAGCAAATAAAATGTAATAAAA
*
54651 AAGATATATATAAAACAGAAAGAAAAGAAAG-AAA-AAAAT-TAA-AAAA
1 AA-ATATATATAAAACAGAAACAAAAGAAAGCAAATAAAATGTAATAAAA
*
54697 TAATATATATA
1 AAATATATATA
54708 TATATATGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
45 9 0.18
46 5 0.10
47 3 0.06
48 7 0.14
49 8 0.16
50 19 0.37
ACGTcount: A:0.70, C:0.04, G:0.10, T:0.16
Consensus pattern (49 bp):
AAATATATATAAAACAGAAACAAAAGAAAGCAAATAAAATGTAATAAAA
Found at i:56043 original size:22 final size:23
Alignment explanation
Indices: 55995--56044 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
55985 GAAATGAATA
*
55995 ATATAT-ATATATATAGATATTG
1 ATATATAATATATATAAATATTG
56017 A-ATATAATATATATAAATATT-
1 ATATATAATATATATAAATATTG
56038 ATATATA
1 ATATATA
56045 TGGTGATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATATAATATATATAAATATTG
Found at i:57666 original size:23 final size:22
Alignment explanation
Indices: 57643--57710 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
57633 TGGCATGTGA
*
57643 AATATATCCTGAAGGACCTATG
1 AATATATCCAGAAGGACCTATG
*
57665 AATATGTCCAGAAGGACC-AGTG
1 AATATATCCAGAAGGACCTA-TG
** * *
57687 TCTATATCCCGAAGGATCTATG
1 AATATATCCAGAAGGACCTATG
57709 AA
1 AA
57711 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (22 bp):
AATATATCCAGAAGGACCTATG
Found at i:63546 original size:22 final size:22
Alignment explanation
Indices: 63516--63582 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
63506 AGTAGAGGGT
63516 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
* * *
63538 TACACAGGTCATTCGAGACATA
1 TACATAGGTCCTTCGGGACATA
*
63560 TGCATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
63582 T
1 T
63583 TTCACATGCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:63919 original size:16 final size:17
Alignment explanation
Indices: 63888--63920 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
63878 AAGATATAGA
63888 ATATGAACATAAGAGATC
1 ATATGAACA-AAGAGATC
63906 ATATGAAC-AAGAGAT
1 ATATGAACAAAGAGAT
63921 AAGAGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (17 bp):
ATATGAACAAAGAGATC
Found at i:69409 original size:13 final size:13
Alignment explanation
Indices: 69378--69402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69368 GATGTACTAT
69378 TTATTTATCTCAA
1 TTATTTATCTCAA
69391 TTATTTATCTCA
1 TTATTTATCTCA
69403 TTCATTTCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTTATCTCAA
Found at i:73645 original size:16 final size:16
Alignment explanation
Indices: 73624--73654 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73614 CATTTCACGG
*
73624 AAAAAAAAATTCTCAC
1 AAAAAAAAACTCTCAC
73640 AAAAAAAAACTCTCA
1 AAAAAAAAACTCTCA
73655 AACACTCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAAAAACTCTCAC
Found at i:74583 original size:33 final size:34
Alignment explanation
Indices: 74539--74669 Score: 111
Period size: 33 Copynumber: 3.8 Consensus size: 34
74529 AACTAACTAA
* * * *
74539 AAAAATATATATTATACGTTTTCAAAGTCGTTTT
1 AAAAACATATATTATACATTTTCAAAATCATTTT
* * *
74573 TAAAACTATATATTATACATTTTTAAAATTATTTT
1 AAAAAC-ATATATTATACATTTTCAAAATCATTTT
* * *
74608 AAAAAC-TTTATTATACATTTTTAAAATTATTTT
1 AAAAACATATATTATACATTTTCAAAATCATTTT
* **
74641 AAAATACTATATACTATATGTTTTCAAAA
1 AAAA-AC-ATATATTATACATTTTCAAAA
74670 CCGCTTCAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
33 30 0.38
34 6 0.08
35 28 0.35
36 15 0.19
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (34 bp):
AAAAACATATATTATACATTTTCAAAATCATTTT
Found at i:74584 original size:35 final size:35
Alignment explanation
Indices: 74538--74669 Score: 142
Period size: 35 Copynumber: 3.8 Consensus size: 35
74528 TAACTAACTA
* * * **
74538 AAAAAATATATATTATACGTTTTCAAAGTCGTTTT
1 AAAAACTATATATTATACATTTTCAAAATTATTTT
* *
74573 TAAAACTATATATTATACATTTTTAAAATTATTTT
1 AAAAACTATATATTATACATTTTCAAAATTATTTT
*
74608 AAAAACT-T-TATTATACATTTTTAAAATTATTTT
1 AAAAACTATATATTATACATTTTCAAAATTATTTT
* **
74641 AAAATACTATATACTATATGTTTTCAAAA
1 AAAA-ACTATATATTATACATTTTCAAAA
74670 CCGCTTCAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
33 29 0.35
34 4 0.05
35 35 0.43
36 14 0.17
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (35 bp):
AAAAACTATATATTATACATTTTCAAAATTATTTT
Found at i:74704 original size:45 final size:46
Alignment explanation
Indices: 74631--74717 Score: 167
Period size: 45 Copynumber: 1.9 Consensus size: 46
74621 TACATTTTTA
74631 AAATTATTTTAAAATACTATATACTATATGTTTTCAAAACCGCTTC
1 AAATTATTTTAAAATACTATATACTATATGTTTTCAAAACCGCTTC
74677 AAATTATTTTAAAA-ACTATATACTATATGTTTTCAAAACCG
1 AAATTATTTTAAAATACTATATACTATATGTTTTCAAAACCG
74718 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 27 0.66
46 14 0.34
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (46 bp):
AAATTATTTTAAAATACTATATACTATATGTTTTCAAAACCGCTTC
Found at i:74732 original size:37 final size:36
Alignment explanation
Indices: 74683--74752 Score: 122
Period size: 37 Copynumber: 1.9 Consensus size: 36
74673 CTTCAAATTA
*
74683 TTTTAAAAACTATATACTATATGTTTTCAAAACCGT
1 TTTTAAAAACTATATAATATATGTTTTCAAAACCGT
74719 TTTTAAAAAACTATATAATATATGTTTTCAAAAC
1 TTTT-AAAAACTATATAATATATGTTTTCAAAAC
74753 TATATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATATGTTTTCAAAACCGT
Found at i:74751 original size:25 final size:25
Alignment explanation
Indices: 74717--74775 Score: 86
Period size: 23 Copynumber: 2.4 Consensus size: 25
74707 TTTCAAAACC
*
74717 GTTTTTAAAAAACTATATAATATAT
1 GTTTTCAAAAAACTATATAATATAT
*
74742 GTTTTC--AAAACTATATAATATGT
1 GTTTTCAAAAAACTATATAATATAT
74765 GTTTTCAAAAA
1 GTTTTCAAAAA
74776 TTGTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 22 0.73
25 8 0.27
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (25 bp):
GTTTTCAAAAAACTATATAATATAT
Found at i:74755 original size:23 final size:23
Alignment explanation
Indices: 74725--74774 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
74715 CCGTTTTTAA
74725 AAAACTATATAATATATGTTTTC
1 AAAACTATATAATATATGTTTTC
*
74748 AAAACTATATAATATGTGTTTTC
1 AAAACTATATAATATATGTTTTC
74771 AAAA
1 AAAA
74775 ATTGTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (23 bp):
AAAACTATATAATATATGTTTTC
Found at i:74756 original size:60 final size:60
Alignment explanation
Indices: 74683--74811 Score: 179
Period size: 60 Copynumber: 2.1 Consensus size: 60
74673 CTTCAAATTA
* * *
74683 TTTTAAAAACTATATACTATATGTTTTC-AAAACCGTTTTTAAAAAACTATATAATATATG
1 TTTTCAAAACTATATAATATATGTTTTCAAAAACCGTTTTT-AAAAACTATATAATATACG
* ** *
74743 TTTTCAAAACTATATAATATGTGTTTTCAAAAATTGTTTTTCAAAACTATATAATATACG
1 TTTTCAAAACTATATAATATATGTTTTCAAAAACCGTTTTTAAAAACTATATAATATACG
74803 TTTTCAAAA
1 TTTTCAAAA
74812 ATGTGTTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 51 0.84
61 10 0.16
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (60 bp):
TTTTCAAAACTATATAATATATGTTTTCAAAAACCGTTTTTAAAAACTATATAATATACG
Found at i:74784 original size:37 final size:37
Alignment explanation
Indices: 74741--74925 Score: 169
Period size: 37 Copynumber: 4.9 Consensus size: 37
74731 ATATAATATA
*
74741 TGTTTTCAAAACTATATAATATGTGTTTTCAAAAAT-
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAATG
*
74777 TGTTTTTCAAAACTATATAATATACGTTTTCAAAAATG
1 TG-TTTTCAAAACTATATAATATATGTTTTCAAAAATG
* * *
74815 TGTTTTCAAAATTATATAATATATGTTTT--TAAATCA
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAAT-G
* * * ** *
74851 TATTTTCAAAACCATATTATATACATTTTCAAAAATCAA
1 TGTTTTCAAAACTATATAATATATGTTTTCAAAAAT--G
* * * *
74890 TTTTTTAAAAAACTATATATTATATGTTTTTAAAAA
1 TGTTTT-CAAAACTATATAATATATGTTTTCAAAAA
74926 ATCGTTTTCT
Statistics
Matches: 120, Mismatches: 22, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
35 4 0.03
36 25 0.21
37 57 0.47
38 6 0.05
39 6 0.05
40 22 0.18
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (37 bp):
TGTTTTCAAAACTATATAATATATGTTTTCAAAAATG
Found at i:74946 original size:39 final size:38
Alignment explanation
Indices: 74748--74983 Score: 152
Period size: 37 Copynumber: 6.2 Consensus size: 38
74738 ATATGTTTTC
* *
74748 AAAACTATATA--ATATGTGTTTTCAAAAAT-TGTTTTTC
1 AAAACTATATATTATATGT-TTTTCAAAAATAT-TTTCTA
* * * *
74785 AAAACTATATAATATACG-TTTTCAAAAATGTGTTT-TC
1 AAAACTATATATTATATGTTTTTCAAAAATAT-TTTCTA
* * *
74822 AAAATTATATAATATATGTTTTT-AAATCATATTTTC--
1 AAAACTATATATTATATGTTTTTCAAA-AATATTTTCTA
* ** *
74858 AAAAC--CATATTATATACATTTTCAAAAATCAATTTTTTAA
1 AAAACTATATATTATAT-GTTTTTCAAAAAT--ATTTTCT-A
* *
74898 AAAACTATATATTATATGTTTTTAAAAAATCGTTTTCTA
1 AAAACTATATATTATATGTTTTTCAAAAAT-ATTTTCTA
* *
74937 AAAACTATATGTTATACGTTTTTTCAAAAATATTTTC-A
1 AAAACTATATATTATATG-TTTTTCAAAAATATTTTCTA
74975 AAAACTATA
1 AAAACTATA
74984 CTATATTATT
Statistics
Matches: 160, Mismatches: 23, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
34 8 0.05
35 6 0.04
36 7 0.04
37 51 0.32
38 22 0.14
39 26 0.16
40 21 0.13
41 10 0.06
42 9 0.06
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (38 bp):
AAAACTATATATTATATGTTTTTCAAAAATATTTTCTA
Found at i:78079 original size:18 final size:18
Alignment explanation
Indices: 78047--78121 Score: 98
Period size: 18 Copynumber: 4.2 Consensus size: 18
78037 CAATGAACAC
78047 TTGTCCC-AGAGGACCACT
1 TTGTCCCGA-AGGACCACT
* *
78065 TTGTCTCGAATGACCACT
1 TTGTCCCGAAGGACCACT
78083 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
* *
78101 ATATCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
78119 TTG
1 TTG
78122 AACCCTCGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
18 47 0.98
19 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (18 bp):
TTGTCCCGAAGGACCACT
Found at i:78096 original size:36 final size:36
Alignment explanation
Indices: 78038--78121 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
78028 CACTAGGGGC
* * * *
78038 AATGAACAC-TTGTCCCAGAGGACCACTTTGTCTCG
1 AATGACCACTTTGTCCCAGAGGACCACTATATCCCG
78073 AATGACCACTTTGTCCC-GAAGGACCACTATATCCCG
1 AATGACCACTTTGTCCCAG-AGGACCACTATATCCCG
*
78109 AAGGACCACTTTG
1 AATGACCACTTTG
78122 AACCCTCGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 9 0.21
36 33 0.79
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (36 bp):
AATGACCACTTTGTCCCAGAGGACCACTATATCCCG
Found at i:80218 original size:30 final size:31
Alignment explanation
Indices: 80184--80256 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
80174 AAAGTATCAT
* * *
80184 TTTGGTCCCTAAACTTTTCAAAGT-TTATAC
1 TTTGGTCCCTAAACTTTACAAAATCTTATAA
*
80214 TTTGGTTACC-AAACTTTACAAAATCTTATAA
1 TTTGG-TCCCTAAACTTTACAAAATCTTATAA
*
80245 TTTGGTCACTAA
1 TTTGGTCCCTAA
80257 CTAAATCCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.41
Consensus pattern (31 bp):
TTTGGTCCCTAAACTTTACAAAATCTTATAA
Found at i:83578 original size:18 final size:18
Alignment explanation
Indices: 83549--83621 Score: 112
Period size: 18 Copynumber: 4.1 Consensus size: 18
83539 GGGCACTGAA
83549 CACT-TGTCCCGAAGGAC
1 CACTATGTCCCGAAGGAC
*
83566 CACTATATCCCGAAGGAC
1 CACTATGTCCCGAAGGAC
*
83584 CACTTTGTCCCGAAGGAC
1 CACTATGTCCCGAAGGAC
*
83602 CACTATGTCTCGAAGGAC
1 CACTATGTCCCGAAGGAC
83620 CA
1 CA
83622 TTTTGAACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 4 0.08
18 46 0.92
ACGTcount: A:0.27, C:0.33, G:0.21, T:0.19
Consensus pattern (18 bp):
CACTATGTCCCGAAGGAC
Found at i:85743 original size:30 final size:31
Alignment explanation
Indices: 85702--85781 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
85692 CTTTTTGAAA
* * *
85702 TTATAATTTTGGTCTCTAAACTTTTCAAAGT-
1 TTATAA-TTTGGTCACTAAACTTTACAAAATC
* *
85733 TTATACTTTGGTCACCAAACTTTACAAAATC
1 TTATAATTTGGTCACTAAACTTTACAAAATC
85764 TTATAATTTGGTCACTAA
1 TTATAATTTGGTCACTAA
85782 CTAAATCCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 20 0.49
31 21 0.51
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (31 bp):
TTATAATTTGGTCACTAAACTTTACAAAATC
Found at i:85774 original size:31 final size:30
Alignment explanation
Indices: 85702--85778 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
85692 CTTTTTGAAA
* * * *
85702 TTATAATTTTGGTCTCTAAACTTTTCAAAGT
1 TTATAA-TTTGGTCACCAAACTTTACAAAAT
*
85733 TTATACTTTGGTCACCAAACTTTACAAAAT
1 TTATAATTTGGTCACCAAACTTTACAAAAT
85763 CTTATAATTTGGTCAC
1 -TTATAATTTGGTCAC
85779 TAACTAAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 20 0.51
31 19 0.49
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (30 bp):
TTATAATTTGGTCACCAAACTTTACAAAAT
Done.