Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005861.1 Hibiscus syriacus cultivar Beakdansim tig00013777_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: 44993
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:197 original size:21 final size:21
Alignment explanation
Indices: 171--227 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
161 CTCATGTTAT
171 GCAAAACCGAAGGCCACTAAA
1 GCAAAACCGAAGGCCACTAAA
192 GCAAAACCGAAGGCCACTAAA
1 GCAAAACCGAAGGCCACTAAA
213 GCAAAACCGAAGGCC
1 GCAAAACCGAAGGCC
228 TTTACTGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.46, C:0.30, G:0.21, T:0.04
Consensus pattern (21 bp):
GCAAAACCGAAGGCCACTAAA
Found at i:3280 original size:2 final size:2
Alignment explanation
Indices: 3273--3306 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3263 TACTATAAAT
3273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3307 GTCAGGTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3525 original size:22 final size:22
Alignment explanation
Indices: 3497--3540 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3487 TTTTTTTAAC
3497 TCCCCTAATGACTGACTACGAT
1 TCCCCTAATGACTGACTACGAT
*
3519 TCCCCTAATGACTGACTGCGAT
1 TCCCCTAATGACTGACTACGAT
3541 GATAAAAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (22 bp):
TCCCCTAATGACTGACTACGAT
Found at i:7147 original size:39 final size:39
Alignment explanation
Indices: 7103--7243 Score: 221
Period size: 39 Copynumber: 3.6 Consensus size: 39
7093 ATGTTGAACA
* * *
7103 AGTTCTTCTCATTATGAATTTATTCTTCCTCTTCAGAAG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGACG
*
7142 AGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGACG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGACG
**
7181 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGACG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGACG
7220 AGTTCTTCTCATTATGAAC-TCTTC
1 AGTTCTTCTCATTATGAACTTCTTC
7244 CACTGAGAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
38 5 0.05
39 90 0.95
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.46
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGACG
Found at i:7449 original size:123 final size:121
Alignment explanation
Indices: 7181--7599 Score: 544
Period size: 123 Copynumber: 3.4 Consensus size: 121
7171 TCTTCAGACG
* ** *
7181 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGACGAGTTCTTCTCATTATGAACTCTTCCA
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTCTTCCA
* * * * * *
7246 CTG-A-G--AATGTCGATCCATCTCCTTCTGTGATGGGATGT-AGCAAAATGTTAAACA
66 -TGAATGTTGATGTTGATCTATCTCCTTCTGTGAT-AGA-GTCAGCAAAAGGTTGAACA
* *
7300 AGTTCTTCTCATTATGAACTTCTTCTTCCTATTTAGATGAGTTCTTTTCATTATGAACTCTTCCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTCTTCC-
*
7365 TTGAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAACA
65 ATGAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTC-AGCAAAAGGTTGAACA
* * * *
7423 AGTTCTTCTCACTATGAACTTTTTCTTCCTATTCATATGAGTTTTTCTCATTATGAACTCCTT-C
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACT-CTTCC
* *
7487 AGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAACA
65 ATG-AATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTC-AGCAAAAGGTTGAACA
*
7546 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTAT
7600 TAATTCCTTC
Statistics
Matches: 265, Mismatches: 26, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
119 62 0.23
120 1 0.00
121 3 0.01
122 3 0.01
123 193 0.73
124 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (121 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTCTTCCA
TGAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAGCAAAAGGTTGAACA
Found at i:7717 original size:42 final size:42
Alignment explanation
Indices: 7666--7747 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
7656 AAGGACTTAT
* *
7666 CATCTTGCTCGAAAGGCTTACAGATGACCCAAAGGATTTAAG
1 CATCATGCTCGAAAGACTTACAGATGACCCAAAGGATTTAAG
* *
7708 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTA
1 CATCATGCTCGAAAGACTTACAGATGACCCAAAGGATTTA
7748 CAAATTCGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACAGATGACCCAAAGGATTTAAG
Found at i:10639 original size:86 final size:84
Alignment explanation
Indices: 10437--10660 Score: 276
Period size: 86 Copynumber: 2.6 Consensus size: 84
10427 TTGCCTCAAT
* * * * *
10437 CAGGCTAGTTGAA-ACTTAT-CTATAAAGACGAGGCTATTAACCAATTGCTCTAGAGGGACAACT
1 CAGGCTAGCTGAATA-TTATAC-ATAAAGACGGGGCGATTAACCAATTGCTTTAGGGGGACAACT
10500 TTATTGTATATAATAATATAA
64 TTATTGTATATAATAATATAA
*
10521 CAGGCTAGCTGAATATTATTCATAAAGACGGGGCGATTAACCAATTGCTTTAGGGGGACAAAAGC
1 CAGGCTAGCTGAATATTATACATAAAGACGGGGCGATTAACCAATTGCTTTAGGGGGAC--AA-C
10586 TTTATTGTATAT-ATAATA-ATA
63 TTTATTGTATATAATAATATA-A
* * * *
10607 TAGGTTAGCTGAATATTATACATAAAGTCGGGGTGATTAACCAATTGCTTTAGG
1 CAGGCTAGCTGAATATTATACATAAAGACGGGGCGATTAACCAATTGCTTTAGG
10661 ACGATAACTC
Statistics
Matches: 124, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
84 50 0.40
85 3 0.02
86 58 0.47
87 13 0.10
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (84 bp):
CAGGCTAGCTGAATATTATACATAAAGACGGGGCGATTAACCAATTGCTTTAGGGGGACAACTTT
ATTGTATATAATAATATAA
Found at i:14734 original size:17 final size:17
Alignment explanation
Indices: 14712--14753 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
14702 CTATGCCTGA
14712 CACGAAGAATAAATCCT
1 CACGAAGAATAAATCCT
14729 CACGAAGAATAAATCCT
1 CACGAAGAATAAATCCT
*
14746 CACAAAGA
1 CACGAAGA
14754 CATAGGGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.50, C:0.24, G:0.12, T:0.14
Consensus pattern (17 bp):
CACGAAGAATAAATCCT
Found at i:15013 original size:18 final size:17
Alignment explanation
Indices: 14990--15023 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
14980 ACATTAGTAT
14990 ATAAAGATATAAAAAATA
1 ATAAAGA-ATAAAAAATA
15008 ATAAAGAATAAAAAAT
1 ATAAAGAATAAAAAAT
15024 TGAAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
ATAAAGAATAAAAAATA
Found at i:15040 original size:26 final size:25
Alignment explanation
Indices: 15010--15059 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
15000 AAAAAATAAT
15010 AAAGAATAAAAAATTGAAAGAAATCA
1 AAAGAATAAAAAATT-AAAGAAATCA
* * *
15036 AAAGAATCATAAATTAAATAAATC
1 AAAGAATAAAAAATTAAAGAAATC
15060 TGAATTCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.66, C:0.06, G:0.08, T:0.20
Consensus pattern (25 bp):
AAAGAATAAAAAATTAAAGAAATCA
Found at i:15869 original size:2 final size:2
Alignment explanation
Indices: 15862--15913 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
15852 TGAATCTTTC
15862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15904 AT AT AT AT AT
1 AT AT AT AT AT
15914 TATTAATATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19105 original size:15 final size:15
Alignment explanation
Indices: 19078--19110 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
19068 ATTTACCATT
19078 TTTTAAGAAATTATAA
1 TTTTAAGAAATTA-AA
19094 TTTTAA-AAATTAAA
1 TTTTAAGAAATTAAA
19108 TTT
1 TTT
19111 ATCTTTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTTAAGAAATTAAA
Found at i:20681 original size:22 final size:22
Alignment explanation
Indices: 20656--20734 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
20646 CATTAAAATG
*
20656 CTACCTAAAATATTATTTTTTT
1 CTACCGAAAATATTATTTTTTT
* ****
20678 CTACCGAAAATGTTAATATTGAACA
1 CTACCGAAAATATT-AT-TT-TTTT
*
20703 CTACCTAAAATATTA-TTTTTT
1 CTACCGAAAATATTATTTTTTT
20724 CTACCGAAAAT
1 CTACCGAAAAT
20735 TAAGTAGCAA
Statistics
Matches: 41, Mismatches: 13, Indels: 7
0.67 0.21 0.11
Matches are distributed among these distances:
21 10 0.24
22 14 0.34
23 2 0.05
24 3 0.07
25 12 0.29
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (22 bp):
CTACCGAAAATATTATTTTTTT
Found at i:24153 original size:258 final size:255
Alignment explanation
Indices: 23660--24282 Score: 846
Period size: 258 Copynumber: 2.4 Consensus size: 255
23650 CTTATTCATA
*
23660 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGAGTCAGGTTTCTAATTCATATATTCGGGC
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCG-GTC-GGTTTCTAATTCATATATTCGGGT
* *
23725 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTTA
64 CGGGTC-GGTAAAACTTTATTTTGGTC--GT---GTCGGGTCGGTTTTTTTAAGTGTGATATTCA
* * *
23790 GGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCTACCCGAAAACATATATAATTTTACCTT
123 GGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTT
23855 ATATATTTAGGAATAATTACAATAATACCCCTCTCTATATACAT-T-TTTTCAATTAAGTCACTG
188 ATATATTTAGGAATAATTACAATAATA-CCCTCTCTATATACATATATTTTCAATTAAGTCACTG
23918 TTTT
252 TTTT
*
23922 TATTGAATAAAAATATTTTTATTATTATTTCGGGTCAGGTCGGATTTCTGATTCATATATTCGGG
1 TATTGAATAAAAATATTTTT-TTATTATTTCGGGTC-GGTCGG-TTTCTAATTCATATATTCGGG
*
23987 TCGGGTCAGGTAAAACTTTATTTTGGTCGTGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
63 TCGGGTC-GGTAAAACTTTATTTTGGTCGTGTCGGGTCGGTTTTTTTAAGTGTGATATTCAGGTC
*
24052 GGGTCGGGTTCGAGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATTTTACCGT
127 GGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCG----AAAAAATATATAATTTTACC-T
* * *
24117 T-TATATTTAGGAATAATTATAATAATA-CC-C-CTATATATATATATTTTCAATTAAGTCATTG
187 TATATATTTAGGAATAATTACAATAATACCCTCTCTATATACATATATTTTCAATTAAGTCACTG
24178 TTTT
252 TTTT
* * *
24182 TGTTGAATAAAAATAATTTTTTATTATTTTC-AGTCGGGTCGGTTTTCTAATTCATATATTCGGG
1 TATTGAATAAAAATATTTTTTTATTA-TTTCGGGTC-GGTCGG-TTTCTAATTCATATATTCGGG
* *
24246 TCGGGTCGAGTAAAATTTTATTTTGGTCGGGTCGGGT
63 TCGGGTCG-GTAAAACTTTATTTTGGTCGTGTCGGGT
24283 ATAGGATGAA
Statistics
Matches: 328, Mismatches: 21, Indels: 27
0.87 0.06 0.07
Matches are distributed among these distances:
258 79 0.24
259 70 0.21
260 45 0.14
261 2 0.01
262 66 0.20
263 65 0.20
264 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (255 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGTCGGTTTCTAATTCATATATTCGGGTCG
GGTCGGTAAAACTTTATTTTGGTCGTGTCGGGTCGGTTTTTTTAAGTGTGATATTCAGGTCGGGT
CGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTT
AGGAATAATTACAATAATACCCTCTCTATATACATATATTTTCAATTAAGTCACTGTTTT
Found at i:24671 original size:17 final size:18
Alignment explanation
Indices: 24649--24695 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
24639 TATGGAATTG
24649 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTGACA
* *
24666 GATTCCAATTCCTTTACT
1 GATTCCAATTCCTTGACA
24684 GATTCCAATTCC
1 GATTCCAATTCC
24696 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTGACA
Found at i:25476 original size:18 final size:17
Alignment explanation
Indices: 25432--25482 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
25422 TATGAAATTG
*
25432 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
* *
25449 TATTCTAATTCCTTCACA
1 GATTCCAATTCC-TCACA
25467 GATTCCAATTCTCTCA
1 GATTCCAATTC-CTCA
25483 TAAACATTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 10 0.37
18 16 0.59
19 1 0.04
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.37
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:26297 original size:39 final size:40
Alignment explanation
Indices: 26253--26354 Score: 138
Period size: 39 Copynumber: 2.6 Consensus size: 40
26243 TTTGAACAAG
*
26253 GTACTAAAATGAAATAAAAACTAAAGTTTTTAAC-GATGA
1 GTACTAAAATGAAATAAAAACTAAAGGTTTTAACGGATGA
* * *
26292 GTACTAAAATGAAACAAAAATTAAAGGTTTTAACGGCTGA
1 GTACTAAAATGAAATAAAAACTAAAGGTTTTAACGGATGA
*
26332 -TACTCAAATGAAAT-AAAACTAAA
1 GTACTAAAATGAAATAAAAACTAAA
26355 ATTTAGGTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
38 8 0.15
39 43 0.78
40 4 0.07
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (40 bp):
GTACTAAAATGAAATAAAAACTAAAGGTTTTAACGGATGA
Found at i:30096 original size:26 final size:26
Alignment explanation
Indices: 30060--30111 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
30050 TATCTTATCT
30060 CACTAGACAAACTAATTGTCAGTTAA
1 CACTAGACAAACTAATTGTCAGTTAA
* * *
30086 CACTAGACAAATTAGTTGTCCGTTAA
1 CACTAGACAAACTAATTGTCAGTTAA
30112 AAATAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (26 bp):
CACTAGACAAACTAATTGTCAGTTAA
Found at i:36141 original size:14 final size:14
Alignment explanation
Indices: 36122--36149 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36112 GATTCACATT
36122 CAATTAATTAAATA
1 CAATTAATTAAATA
36136 CAATTAATTAAATA
1 CAATTAATTAAATA
36150 TGAATGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
CAATTAATTAAATA
Found at i:36310 original size:29 final size:30
Alignment explanation
Indices: 36243--36312 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
36233 GAGATTTTGA
*
36243 TTAAATTTAAAGATTAAAATAATATTTTAT
1 TTAAATTTAAAGATTAAAATAATATATTAT
*
36273 TTAAAATTTAGAGATT-AAAT-ATATATTAT
1 TT-AAATTTAAAGATTAAAATAATATATTAT
36302 TTAATATTTAA
1 TTAA-ATTTAA
36313 TACTCAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 15 0.43
30 6 0.17
31 12 0.34
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (30 bp):
TTAAATTTAAAGATTAAAATAATATATTAT
Found at i:36338 original size:36 final size:34
Alignment explanation
Indices: 36255--36435 Score: 115
Period size: 30 Copynumber: 5.6 Consensus size: 34
36245 AAATTTAAAG
* * * *
36255 ATTAAAATAATATTTTATTTAAAATT--TA-GAG
1 ATTAAATTAATATTTTATTTAATATTAATATCAA
*
36286 ATTAAA-T-ATATATTATTTAATATTTAATACTCAA
1 ATTAAATTAATATTTTATTTAATA-TTAATA-TCAA
*
36320 ATTAAATTAATATTTTATTTAA-A--AATAT-AG
1 ATTAAATTAATATTTTATTTAATATTAATATCAA
* *
36350 ATTAAATTAATAATTTACCTT--TATTAATATCAA
1 ATTAAATTAATATTTTA-TTTAATATTAATATCAA
*
36383 ATT-AA-T-ATA--TTATTTAATATTTAAAACTCAA
1 ATTAAATTAATATTTTATTTAATA-TTAATA-TCAA
*
36414 ACTAAATTAATATTTTATTTAA
1 ATTAAATTAATATTTTATTTAA
36436 AATCCCTTCT
Statistics
Matches: 117, Mismatches: 12, Indels: 37
0.70 0.07 0.22
Matches are distributed among these distances:
27 2 0.02
28 3 0.03
29 15 0.13
30 29 0.25
31 16 0.14
32 15 0.13
33 5 0.04
34 10 0.09
35 2 0.02
36 20 0.17
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (34 bp):
ATTAAATTAATATTTTATTTAATATTAATATCAA
Found at i:40562 original size:18 final size:18
Alignment explanation
Indices: 40535--40585 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
40525 GTAGAATTTG
*
40535 TCCCGTAGGACCACTATA
1 TCCCGAAGGACCACTATA
* *
40553 TCCCGAAGGACCACTGTG
1 TCCCGAAGGACCACTATA
40571 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
40586 CTTAATCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.18
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:43140 original size:69 final size:69
Alignment explanation
Indices: 43029--43161 Score: 221
Period size: 69 Copynumber: 1.9 Consensus size: 69
43019 TACTAAAGAT
* * **
43029 AGAACCACATTGTCATGCAAACCATAAAACACGTAGACACTCCACATGGCTTACGCACTCAAACG
1 AGAACCACATTGTCATGCAAACCATAAAACACATAGACACTCCACATGCCCAACGCACTCAAACG
43094 ACCA
66 ACCA
*
43098 AGAACCACATTGTCATGCAAACCATAAAGCACATAGACACTCCACATGCCCAACGCACTCAAAC
1 AGAACCACATTGTCATGCAAACCATAAAACACATAGACACTCCACATGCCCAACGCACTCAAAC
43162 TGCCAATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.40, C:0.33, G:0.12, T:0.15
Consensus pattern (69 bp):
AGAACCACATTGTCATGCAAACCATAAAACACATAGACACTCCACATGCCCAACGCACTCAAACG
ACCA
Found at i:43522 original size:44 final size:44
Alignment explanation
Indices: 43459--43542 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
43449 TATGAGCAAA
43459 CTTCACAAGCTTACATTTGTTAAAATATATATTCTCTTTGTAAG
1 CTTCACAAGCTTACATTTGTTAAAATATATATTCTCTTTGTAAG
** *
43503 CTTCACAAGCTTGTATTTGTTCAAATATATATTCTCTTTG
1 CTTCACAAGCTTACATTTGTTAAAATATATATTCTCTTTG
43543 CTTTTGTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (44 bp):
CTTCACAAGCTTACATTTGTTAAAATATATATTCTCTTTGTAAG
Found at i:44815 original size:2 final size:2
Alignment explanation
Indices: 44808--44854 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
44798 TTTATTTATT
44808 TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44848 TA -A TA TA
1 TA TA TA TA
44855 ATAGTAATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.