Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005986.1 Hibiscus syriacus cultivar Beakdansim tig00014074_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: 76193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2109 original size:16 final size:17
Alignment explanation
Indices: 2071--2111 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2061 GAATAATTTA
* *
2071 AATTATTTTATATTCTT
1 AATTATTTAATATTATT
2088 AA-TATTTAATA-TATT
1 AATTATTTAATATTATT
2103 AATTATTTA
1 AATTATTTA
2112 TAATTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTATTTAATATTATT
Found at i:4760 original size:20 final size:20
Alignment explanation
Indices: 4735--4772 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4725 AATATTATTA
4735 TTTCTATTC-GTTTTGTTACT
1 TTTCTA-TCAGTTTTGTTACT
4755 TTTCTATCAGTTTTGTTA
1 TTTCTATCAGTTTTGTTA
4773 TTATTGAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (20 bp):
TTTCTATCAGTTTTGTTACT
Found at i:5091 original size:32 final size:32
Alignment explanation
Indices: 5054--5141 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
5044 AGTCACCGAT
* *
5054 ATTATTAATTTATAACAAAAATATTAATTAAC
1 ATTATTAATTTGTAACAAAAATAGTAATTAAC
* * * *
5086 ATTATTAATTTGTAATAAAAATGGTCATTAGC
1 ATTATTAATTTGTAACAAAAATAGTAATTAAC
5118 ATTATTAATTTGTAAC-AAAATAGT
1 ATTATTAATTTGTAACAAAAATAGT
5142 CACTATATCT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 7 0.15
32 41 0.85
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.41
Consensus pattern (32 bp):
ATTATTAATTTGTAACAAAAATAGTAATTAAC
Found at i:11348 original size:21 final size:22
Alignment explanation
Indices: 11324--11405 Score: 69
Period size: 21 Copynumber: 3.7 Consensus size: 22
11314 TTGGTACAGA
*
11324 GGGAATCGATCCCCCCCATGA-
1 GGGAACCGATCCCCCCCATGAG
* **
11345 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATCCCCCCCATG-AG
*
11368 GGGAACCGATTCCCCCCCA-CAG
1 GGGAACCGA-TCCCCCCCATGAG
* *
11390 GGGAATCGATACCCCC
1 GGGAACCGATCCCCCC
11406 TGGGGTTCTG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
21 22 0.46
22 11 0.23
23 9 0.19
24 6 0.12
ACGTcount: A:0.23, C:0.38, G:0.24, T:0.15
Consensus pattern (22 bp):
GGGAACCGATCCCCCCCATGAG
Found at i:11391 original size:22 final size:22
Alignment explanation
Indices: 11321--11405 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
11311 ATTTTGGTAC
*
11321 AGAGGGAATCGA-TCCCCCCCA
1 AGAGGGAACCGATTCCCCCCCA
* **
11342 TGAGGGAACCGATTCCCCCTTTGA
1 AGAGGGAACCGATTCCCCC--CCA
11366 AG-GGGAACCGATTCCCCCCCA
1 AGAGGGAACCGATTCCCCCCCA
* *
11387 CAG-GGGAATCGATACCCCC
1 -AGAGGGAACCGATTCCCCC
11406 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 11 0.22
22 22 0.43
23 16 0.31
24 2 0.04
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.14
Consensus pattern (22 bp):
AGAGGGAACCGATTCCCCCCCA
Found at i:17197 original size:21 final size:21
Alignment explanation
Indices: 17172--17230 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
17162 GTCCGAGTTA
17172 CCCGCGATGGCCGCAATAGCGT
1 CCCGCGATGGCCGCAATAGC-T
* * *
17194 -CCGCGACGACCTCAATAGCT
1 CCCGCGATGGCCGCAATAGCT
17214 CCCGCGATGGCCGCAAT
1 CCCGCGATGGCCGCAAT
17231 CACGATAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.14
Consensus pattern (21 bp):
CCCGCGATGGCCGCAATAGCT
Found at i:28238 original size:17 final size:17
Alignment explanation
Indices: 28216--28251 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
28206 GACTACAATT
28216 ATTTTAAATATTT-TAAA
1 ATTTTAAAT-TTTATAAA
28233 ATTTTAAATTTTATAAA
1 ATTTTAAATTTTATAAA
28250 AT
1 AT
28252 ACATATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAAATTTTATAAA
Found at i:31293 original size:21 final size:18
Alignment explanation
Indices: 31242--31291 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
31232 CATTATGCAC
31242 AACATGATATTATTCATT
1 AACATGATATTATTCATT
31260 AACATGATATTATTCATT
1 AACATGATATTATTCATT
31278 AACATGATATTATT
1 AACATGATATTATT
31292 ATCTCTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (18 bp):
AACATGATATTATTCATT
Found at i:33197 original size:12 final size:12
Alignment explanation
Indices: 33171--33225 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
33161 ATATACAAAT
*
33171 ACCTAATTC-TC
1 ACCTAACTCTTC
33182 ACCTAACTCTTC
1 ACCTAACTCTTC
* *
33194 ACCTAATTCTTA
1 ACCTAACTCTTC
*
33206 ACCAAACTCTTC
1 ACCTAACTCTTC
*
33218 ACCAAACT
1 ACCTAACT
33226 AAATTGATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
11 8 0.22
12 29 0.78
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:33201 original size:23 final size:24
Alignment explanation
Indices: 33171--33220 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
33161 ATATACAAAT
* *
33171 ACCTAATTC-TCACCTAACTCTTC
1 ACCTAATTCTTAACCAAACTCTTC
33194 ACCTAATTCTTAACCAAACTCTTC
1 ACCTAATTCTTAACCAAACTCTTC
33218 ACC
1 ACC
33221 AAACTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (24 bp):
ACCTAATTCTTAACCAAACTCTTC
Found at i:37896 original size:12 final size:12
Alignment explanation
Indices: 37870--37912 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
37860 ATATATAAAT
37870 ACCTAACTC-TC
1 ACCTAACTCTTC
*
37881 ACCTACCTCTTC
1 ACCTAACTCTTC
*
37893 ACCTAATTCTTC
1 ACCTAACTCTTC
37905 ACCTAACT
1 ACCTAACT
37913 AAATTGATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.26, C:0.42, G:0.00, T:0.33
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:45506 original size:36 final size:36
Alignment explanation
Indices: 45466--45540 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
45456 CCGATCCAAA
45466 AATTTGGATATCCGATCAATTTTTTGATTTTCAGAT
1 AATTTGGATATCCGATCAATTTTTTGATTTTCAGAT
*
45502 AATTTGGATATCCGATCAATTTTTTGATTTTCGGAT
1 AATTTGGATATCCGATCAATTTTTTGATTTTCAGAT
45538 AAT
1 AAT
45541 CAAATTGGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (36 bp):
AATTTGGATATCCGATCAATTTTTTGATTTTCAGAT
Found at i:45915 original size:16 final size:16
Alignment explanation
Indices: 45894--45935 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
45884 ACATATCACT
45894 ATTTTTTG-TATCCAAA
1 ATTTTTTGATATCC-AA
* *
45910 ATTTTTGGATATCCGA
1 ATTTTTTGATATCCAA
45926 ATTTTTTGAT
1 ATTTTTTGAT
45936 CGAATCGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (16 bp):
ATTTTTTGATATCCAA
Found at i:53607 original size:13 final size:13
Alignment explanation
Indices: 53589--53627 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
53579 TAGTTGAACA
53589 GTCTTCTTATGCG
1 GTCTTCTTATGCG
*
53602 GTCTTCTTATGCA
1 GTCTTCTTATGCG
*
53615 GTCTTCATATGCG
1 GTCTTCTTATGCG
53628 AGTTTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (13 bp):
GTCTTCTTATGCG
Found at i:56803 original size:59 final size:60
Alignment explanation
Indices: 56710--56837 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 60
56700 ATAGTCAGAT
* * * *
56710 GACCATTTTTGTAATTTTTAATAGTCAATGGACTCAACAAAGTA--ATACCTATAGTTAGGG
1 GACCA-TTTTATAACTTTTAACAGTCAATGGACTCAACAAAATATCAT-CCTATAGTTAGGG
*
56770 GACCATTTTATAACTTTTAACAGTCAA-GTGACTCAACAAAATATCATCCTATAGTTTGGG
1 GACCATTTTATAACTTTTAACAGTCAATG-GACTCAACAAAATATCATCCTATAGTTAGGG
56830 GACCATTT
1 GACCATTT
56838 GTGGATTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.02
59 32 0.53
60 25 0.42
61 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAACAGTCAATGGACTCAACAAAATATCATCCTATAGTTAGGG
Found at i:56847 original size:59 final size:59
Alignment explanation
Indices: 56710--56837 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 59
56700 ATAGTCAGAT
* * * *
56710 GACCATTTTTGTAATTTTTAATAGTCAATGGACTCAACAAAGTAATACCTATAGTTAGGG
1 GACCATTTTAG-AACTTTTAACAGTCAATGGACTCAACAAAATAATACCTATAGTTAGGG
* *
56770 GACCATTTTATAACTTTTAACAGTCAA-GTGACTCAACAAAAT-ATCATCCTATAGTTTGGG
1 GACCATTTTAGAACTTTTAACAGTCAATG-GACTCAACAAAATAAT-A-CCTATAGTTAGGG
56830 GACCATTT
1 GACCATTT
56838 GTGGATTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
58 3 0.05
59 27 0.46
60 29 0.49
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (59 bp):
GACCATTTTAGAACTTTTAACAGTCAATGGACTCAACAAAATAATACCTATAGTTAGGG
Found at i:57657 original size:39 final size:38
Alignment explanation
Indices: 57614--57729 Score: 123
Period size: 37 Copynumber: 3.1 Consensus size: 38
57604 TAATATATAG
* *
57614 TTTTTGAAAGTATATATAATATATATAGTTTTAAAAATA
1 TTTTTGAAA-TATATATAATATATATAATTTTAAAAACA
* *
57653 TTTTT-AAATATATAT-ATATAATATAATTTTGAAAACG
1 TTTTTGAAATATATATAATAT-ATATAATTTTAAAAACA
*
57690 TTTTAGAAAATATATATAATATATAT--TTTTAGAAAACA
1 TTTTTG-AAATATATATAATATATATAATTTTA-AAAACA
57728 TT
1 TT
57730 CGGAAATTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
36 4 0.06
37 28 0.43
38 10 0.15
39 19 0.29
40 4 0.06
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (38 bp):
TTTTTGAAATATATATAATATATATAATTTTAAAAACA
Found at i:57663 original size:26 final size:27
Alignment explanation
Indices: 57593--57666 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 27
57583 TTTTTTTAAA
57593 AAAAATATATAT-AATATATAGTTTTT
1 AAAAATATATATAAATATATAGTTTTT
* *
57619 GAAAGTATATATAATATATATAG-TTTT
1 AAAAATATATATAA-ATATATAGTTTTT
* *
57646 AAAAATATTTTTAAATATATA
1 AAAAATATATATAAATATATA
57667 TATATAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 17 0.43
27 15 0.38
28 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (27 bp):
AAAAATATATATAAATATATAGTTTTT
Found at i:59923 original size:39 final size:37
Alignment explanation
Indices: 59824--60243 Score: 374
Period size: 37 Copynumber: 11.4 Consensus size: 37
59814 ATAATAATAC
*
59824 TATATTATATATA---T-AAAAATATTTTCAAAAA-TA
1 TATATTATATATATTTTCAAAAAT-TTTTTAAAAACTA
* * * * *
59857 TGTAATATATAAATTTCCAAAATGTTTTTTAAAAACTA
1 TATATTATATATATTTTCAAAA-ATTTTTTAAAAACTA
* **
59895 TATATTATACATATTTTCAAAAACGTTTTAAAAACTA
1 TATATTATATATATTTTCAAAAATTTTTTAAAAACTA
* * * *
59932 TATAATATATATTTTTTAAAAAATGTTTTAAAAACTA
1 TATATTATATATATTTTCAAAAATTTTTTAAAAACTA
59969 TATATTATATATATTTTC-AAAATATTTTTAAAAACTA
1 TATATTATATATATTTTCAAAAAT-TTTTTAAAAACTA
* * * ** *
60006 TATAATATATAAATGTTTTCATAAACGTTTTCAAAACTA
1 TAT-AT-TATATATATTTTCAAAAATTTTTTAAAAACTA
* *
60045 TATATTATATAAATTTTC-AAAATAATTTTAAAAA-TA
1 TATATTATATATATTTTCAAAAAT-TTTTTAAAAACTA
* *
60081 TATATTATATATATTTTCTAAAATGTTTTAAAAACTA
1 TATATTATATATATTTTCAAAAATTTTTTAAAAACTA
* *
60118 TATATTATATA-GTTTTCAAAAATATTTTAAAAACTA
1 TATATTATATATATTTTCAAAAATTTTTTAAAAACTA
* *
60154 TATATTATGTACATTTTC-AAAATATTTTTAAAAACTA
1 TATATTATATATATTTTCAAAAAT-TTTTTAAAAACTA
* * ** **
60191 TATATAATATACGTGTTTTCAAAAACCGTTTTGCAAACTA
1 TATATTATATA--TATTTTCAAAAA-TTTTTTAAAAACTA
*
60231 TATAATATATATA
1 TATATTATATATA
60244 GATATATATG
Statistics
Matches: 313, Mismatches: 55, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
33 10 0.03
36 73 0.23
37 149 0.48
38 25 0.08
39 30 0.10
40 26 0.08
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATTATATATATTTTCAAAAATTTTTTAAAAACTA
Found at i:59924 original size:37 final size:36
Alignment explanation
Indices: 59883--60243 Score: 384
Period size: 37 Copynumber: 9.7 Consensus size: 36
59873 CCAAAATGTT
*
59883 TTTTAAAAACTATATATTATACATATTTTCAAAAACG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAA-G
* * *
59920 TTTTAAAAACTATATAATATATATTTTTTAAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAA-G
*
59957 TTTTAAAAACTATATATTATATATATTTTCAAAATAT
1 TTTTAAAAACTATATATTATATATATTTTCAAAA-AG
* * *
59994 TTTTAAAAACTATATAATATATAAATGTTTTCATAAACG
1 TTTTAAAAACTATAT-AT-TATATATATTTTCA-AAAAG
* * *
60033 TTTTCAAAACTATATATTATATAAATTTTCAAAATAA
1 TTTTAAAAACTATATATTATATATATTTTCAAAA-AG
*
60070 TTTTAAAAA-TATATATTATATATATTTTCTAAAATG
1 TTTTAAAAACTATATATTATATATATTTTC-AAAAAG
* *
60106 TTTTAAAAACTATATATTATATA-GTTTTCAAAAATA
1 TTTTAAAAACTATATATTATATATATTTTCAAAAA-G
* * *
60142 TTTTAAAAACTATATATTATGTACATTTTCAAAATAT
1 TTTTAAAAACTATATATTATATATATTTTCAAAA-AG
* *
60179 TTTTAAAAACTATATATAATATACGTGTTTTCAAAAACCG
1 TTTTAAAAACTATATATTATATA--TATTTTCAAAAA--G
** *
60219 TTTTGCAAACTATATAATATATATA
1 TTTTAAAAACTATATATTATATATA
60244 GATATATATG
Statistics
Matches: 271, Mismatches: 39, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
35 4 0.01
36 58 0.21
37 144 0.53
38 8 0.03
39 35 0.13
40 22 0.08
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAAAG
Found at i:60109 original size:149 final size:148
Alignment explanation
Indices: 59824--60243 Score: 462
Period size: 149 Copynumber: 2.8 Consensus size: 148
59814 ATAATAATAC
* * * *
59824 TATATTATATATA---TAAAAATATTTTCAAAAA-TATGTAATATATAAATTTCCAAAATGTTTT
1 TATATTATATATATTTTCAAAATATTTTTAAAAACTATATAATATATAAATTTCCAAAACG-TTT
* * *
59885 TTAAAAACTATATATTATACATATTTTCAAAAACGTTTTAAAAACTATATAATATATATTTTTTA
65 TTAAAAACTATATATTATACAAATTTTCAAAAACATTTTAAAAACTATATAATATATATATTTTA
59950 AAAAATGTTTTAAAAACTA
130 AAAAATGTTTTAAAAACTA
*
59969 TATATTATATATATTTTCAAAATATTTTTAAAAACTATATAATATATAAATGTTTTCATAAACG-
1 TATATTATATATATTTTCAAAATATTTTTAAAAACTATATAATATATAAA--TTTCCA-AAACGT
* * *
60033 TTTTCAAAACTATATATTATATAAATTTTCAAAATA-ATTTTAAAAA-TATATATTATATATATT
63 TTTTAAAAACTATATATTATACAAATTTTCAAAA-ACATTTTAAAAACTATATAATATATATATT
**
60096 TTCTAAAATGTTTTAAAAACTA
127 TTAAAAAATGTTTTAAAAACTA
* * * * * **
60118 TATATTATATA-GTTTTCAAAA-ATATTTTAAAAACTATATATTATGTACATTTTCAAAATATTT
1 TATATTATATATATTTTCAAAATAT-TTTTAAAAACTATATAATATATAAATTTCCAAAACGTTT
*** * **
60181 TTAAAAACTATATATAATATACGTGTTTTCAAAAACCGTTTTGCAAACTATATAATATATATA
65 TTAAAAACTATATAT--TATACAAATTTTCAAAAA-CATTTTAAAAACTATATAATATATATA
60244 GATATATATG
Statistics
Matches: 232, Mismatches: 28, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
145 16 0.07
146 22 0.09
147 3 0.01
148 60 0.26
149 67 0.29
150 54 0.23
151 6 0.03
152 4 0.02
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (148 bp):
TATATTATATATATTTTCAAAATATTTTTAAAAACTATATAATATATAAATTTCCAAAACGTTTT
TAAAAACTATATATTATACAAATTTTCAAAAACATTTTAAAAACTATATAATATATATATTTTAA
AAAATGTTTTAAAAACTA
Found at i:60457 original size:13 final size:13
Alignment explanation
Indices: 60435--60469 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
60425 AAATTAAATT
60435 AAAAAT-AAATAA
1 AAAAATAAAATAA
60447 AAAAATAAAATAA
1 AAAAATAAAATAA
*
60460 AAATATAAAA
1 AAAAATAAAA
60470 ATTAAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:62733 original size:3 final size:3
Alignment explanation
Indices: 62727--62783 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
62717 ATATTTATAC
*
62727 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A AT- ATA A-A ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
62772 ATTA AAA ATA AT
1 A-TA ATA ATA AT
62784 GAAATTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.13
3 38 0.81
4 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:62771 original size:27 final size:27
Alignment explanation
Indices: 62741--62806 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
62731 TAATAATAAT
*
62741 AATAA-TAATAATAATAAAATATAAAAC
1 AATAATTAAAAATAATAAAAT-TAAAAC
*
62768 AATAATTAAAAATAATGAAATTAAAAC
1 AATAATTAAAAATAATAAAATTAAAAC
* *
62795 TATAAATAAAAA
1 AATAATTAAAAA
62807 AAACTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.26
Consensus pattern (27 bp):
AATAATTAAAAATAATAAAATTAAAAC
Found at i:62807 original size:28 final size:28
Alignment explanation
Indices: 62738--62807 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
62728 TAATAATAAT
62738 AATAATAATAATAATAATAAAATATAAAAC
1 AATAATAA-AA-AATAATAAAATATAAAAC
* *
62768 AATAATTAAAAATAATGAAAT-TAAAAC
1 AATAATAAAAAATAATAAAATATAAAAC
*
62795 TATAAATAAAAAA
1 AAT-AATAAAAAA
62808 AACTAGTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.23
28 18 0.51
29 2 0.06
30 7 0.20
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (28 bp):
AATAATAAAAAATAATAAAATATAAAAC
Found at i:64001 original size:3 final size:3
Alignment explanation
Indices: 63990--64051 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
63980 TTGTATTATT
* *
63990 TAA TAAA TAA TATA TAA TAT TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
64037 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
64052 ATTTAAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:66344 original size:20 final size:20
Alignment explanation
Indices: 66306--66365 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
66296 AAAAATATTT
*
66306 TATGAATAGTAT-TGTACTG
1 TATGAATAGTATCGGTACTG
66325 TATGAATAGTATCGGTACTG
1 TATGAATAGTATCGGTACTG
* * *
66345 TATAAATAGTACCGATACTG
1 TATGAATAGTATCGGTACTG
66365 T
1 T
66366 GTAAACAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 12 0.33
20 24 0.67
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (20 bp):
TATGAATAGTATCGGTACTG
Found at i:66370 original size:20 final size:20
Alignment explanation
Indices: 66320--66375 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
66310 AATAGTATTG
* * *
66320 TACTGTATGAATAGTATCGG
1 TACTGTATAAATAGTACCGA
66340 TACTGTATAAATAGTACCGA
1 TACTGTATAAATAGTACCGA
* *
66360 TACTGTGTAAACAGTA
1 TACTGTATAAATAGTA
66376 ATGAACGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
TACTGTATAAATAGTACCGA
Found at i:66603 original size:20 final size:22
Alignment explanation
Indices: 66565--66604 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
66555 TTTGAGCAAA
66565 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
66587 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
66605 ATATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:66861 original size:34 final size:33
Alignment explanation
Indices: 66822--66886 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
66812 AAGGGGTTTT
*
66822 GGTTCTAGCTTAGCCCGTGTAAAAGCTAGGGAAA
1 GGTTCTAGCTTAGCCCGTG-AAAAACTAGGGAAA
*
66856 GGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 GGTTCTAGCTTAGCCCGTGAAAAACTAGGGA
66887 GTTGTAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (33 bp):
GGTTCTAGCTTAGCCCGTGAAAAACTAGGGAAA
Found at i:67757 original size:6 final size:6
Alignment explanation
Indices: 67735--67776 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
67725 CAAATTAAAT
* *
67735 TAAAAA TAAATA CAAAAA T-AAAA TAAAAA TAAAAA TATAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA-AAAA
67777 ATTAAATCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
5 5 0.17
6 21 0.70
7 4 0.13
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:67759 original size:17 final size:17
Alignment explanation
Indices: 67737--67771 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
67727 AATTAAATTA
*
67737 AAAATAAATACAAAAAT
1 AAAATAAAAACAAAAAT
*
67754 AAAATAAAAATAAAAAT
1 AAAATAAAAACAAAAAT
67771 A
1 A
67772 TAAAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATAAAAACAAAAAT
Found at i:67783 original size:19 final size:20
Alignment explanation
Indices: 67731--67783 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
67721 TTATCAAATT
67731 AAAT-TAAAAA-TAAATACA
1 AAATATAAAAATTAAATACA
*
67749 AAA-AT-AAAATAAAAATA-A
1 AAATATAAAAAT-TAAATACA
67767 AAATATAAAAATTAAAT
1 AAATATAAAAATTAAAT
67784 CTATCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
17 4 0.14
18 8 0.29
19 11 0.39
20 5 0.18
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATATAAAAATTAAATACA
Done.