Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007201.1 Hibiscus syriacus cultivar Beakdansim tig00019004_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: 79120
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:67 original size:39 final size:39
Alignment explanation
Indices: 1--78 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
1 CAATGCAAAATGACTATCGCAATGCGAAAATGACTATCG
1 CAATGCAAAATGACTATCGCAATGCGAAAATGACTATCG
**
40 CAATGCGAAAATGACTATCGCAA-GCGAATTTGACTATCG
1 CAATGC-AAAATGACTATCGCAATGCGAAAATGACTATCG
79 TAACGAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 20 0.56
40 16 0.44
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (39 bp):
CAATGCAAAATGACTATCGCAATGCGAAAATGACTATCG
Found at i:73 original size:19 final size:20
Alignment explanation
Indices: 1--78 Score: 124
Period size: 20 Copynumber: 4.0 Consensus size: 20
1 CAATGC-AAAATGACTATCG
1 CAATGCGAAAATGACTATCG
20 CAATGCGAAAATGACTATCG
1 CAATGCGAAAATGACTATCG
40 CAATGCGAAAATGACTATCG
1 CAATGCGAAAATGACTATCG
**
60 CAA-GCGAATTTGACTATCG
1 CAATGCGAAAATGACTATCG
79 TAACGAAAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.36
20 36 0.64
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
CAATGCGAAAATGACTATCG
Found at i:164 original size:20 final size:20
Alignment explanation
Indices: 126--183 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
116 GATTCTCTCG
*
126 TTGCGATAGTCA-ATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
145 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
165 TTGCGATAATCATTTTCGC
1 TTGCGATAGTCATTTTCGC
184 GTTGTGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.32
20 23 0.68
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:756 original size:21 final size:21
Alignment explanation
Indices: 666--769 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
656 ACTTCACCTG
*
666 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
688 T-ATCGTTC-AGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
707 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
728 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
749 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
770 CCAACATTCT
Statistics
Matches: 61, Mismatches: 19, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
19 3 0.05
20 12 0.20
21 45 0.74
22 1 0.02
ACGTcount: A:0.20, C:0.38, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:762 original size:42 final size:41
Alignment explanation
Indices: 663--772 Score: 107
Period size: 42 Copynumber: 2.7 Consensus size: 41
653 CCGACTTCAC
* * * *
663 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAGAGGCCA
* **
704 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTC-AGAGGCCA
*
746 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
773 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 24 0.44
42 27 0.49
43 2 0.04
ACGTcount: A:0.20, C:0.38, G:0.19, T:0.23
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAGAGGCCA
Found at i:2210 original size:20 final size:21
Alignment explanation
Indices: 2176--2272 Score: 119
Period size: 20 Copynumber: 4.8 Consensus size: 21
2166 TGTGCTTGTT
* *
2176 TATTTCGCATTGCGATAGTCA
1 TATTCCGCGTTGCGATAGTCA
2197 -ATTCCGCGTTGCGATAGTCA
1 TATTCCGCGTTGCGATAGTCA
*
2217 T-TTCCGTGTTGCGATAGTCA
1 TATTCCGCGTTGCGATAGTCA
* *
2237 TAGTCCGTGTTGCGATAGTCA
1 TATTCCGCGTTGCGATAGTCA
*
2258 TATT-CACGTTGCGAT
1 TATTCCGCGTTGCGAT
2273 TTCCGCGTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
20 46 0.69
21 21 0.31
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (21 bp):
TATTCCGCGTTGCGATAGTCA
Found at i:2245 original size:21 final size:21
Alignment explanation
Indices: 2185--2262 Score: 124
Period size: 20 Copynumber: 3.8 Consensus size: 21
2175 TTATTTCGCA
*
2185 TTGCGATAGTCA-ATTCCGCG
1 TTGCGATAGTCATATTCCGTG
2205 TTGCGATAGTCAT-TTCCGTG
1 TTGCGATAGTCATATTCCGTG
*
2225 TTGCGATAGTCATAGTCCGTG
1 TTGCGATAGTCATATTCCGTG
2246 TTGCGATAGTCATATTC
1 TTGCGATAGTCATATTC
2263 ACGTTGCGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 31 0.58
21 22 0.42
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTCATATTCCGTG
Found at i:2269 original size:41 final size:39
Alignment explanation
Indices: 2185--2272 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 39
2175 TTATTTCGCA
*
2185 TTGCGATAGTCAATTCCGCGTTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCAAGTCCGCGTTGCGATAGTCATTTCCG-G
*
2225 TTGCGATAGTCATAGTCCGTGTTGCGATAGTCATATTCAC-G
1 TTGCGATAGTCA-AGTCCGCGTTGCGATAGTCAT-TTC-CGG
2266 TTGCGAT
1 TTGCGAT
2273 TTCCGCGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
40 12 0.28
41 27 0.63
42 3 0.07
43 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (39 bp):
TTGCGATAGTCAAGTCCGCGTTGCGATAGTCATTTCCGG
Found at i:4137 original size:24 final size:24
Alignment explanation
Indices: 4103--4156 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4093 CTGAAAAATC
4103 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
4127 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4151 ATCAAA
1 ATCAAA
4157 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4170 original size:24 final size:24
Alignment explanation
Indices: 4103--4170 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
4093 CTGAAAAATC
* * *
4103 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
4127 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
4151 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
4171 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:5031 original size:20 final size:20
Alignment explanation
Indices: 5008--5104 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
4998 TTGCGATAGT
* *
5008 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
* *
5028 CAGATTCGCATTGTGATTTA
1 CAGAATCGCATTGCGATTTA
*
5048 C-GTAATCGCATTGCGATTTTC
1 CAG-AATCGCATTGCGA-TTTA
*
5069 CA-AATTCGCGTTGCGATTTA
1 CAGAA-TCGCATTGCGATTTA
* *
5089 CATATTCGCATTGCGA
1 CAGAATCGCATTGCGA
5105 ATTAGGAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
19 1 0.02
20 45 0.74
21 15 0.25
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:5082 original size:21 final size:20
Alignment explanation
Indices: 5018--5104 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
5008 CAGAATCTCG
*
5018 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAAATTCGCA
* *
5038 TTGTGATTTACGTAA-TCGCA
1 TTGCGATTTAC-AAATTCGCA
* *
5058 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACAAATTCGCA
*
5079 TTGCGATTTACATATTCGCA
1 TTGCGATTTACAAATTCGCA
5099 TTGCGA
1 TTGCGA
5105 ATTAGGAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:5087 original size:41 final size:40
Alignment explanation
Indices: 5018--5104 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
5008 CAGAATCTCG
* * *
5018 TTGCGATTTACAGATTCGCATTGTGATTTACGTAATCGCA
1 TTGCGATTTACAAATTCGCATTGCGATTTACATAATCGCA
* * *
5058 TTGCGATTTTCCAAATTCGCGTTGCGATTTACATATTCGCA
1 TTGCGA-TTTACAAATTCGCATTGCGATTTACATAATCGCA
5099 TTGCGA
1 TTGCGA
5105 ATTAGGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 6 0.15
41 34 0.85
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACAAATTCGCATTGCGATTTACATAATCGCA
Found at i:5124 original size:21 final size:21
Alignment explanation
Indices: 5094--5142 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5084 ATTTACATAT
*
5094 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
5115 TCGCAATGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
5136 TCGCAAT
1 TCGCAAT
5143 ACGATAGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:6025 original size:2 final size:2
Alignment explanation
Indices: 6018--6085 Score: 109
Period size: 2 Copynumber: 34.0 Consensus size: 2
6008 AAAAGAACAC
* *
6018 AT AT AT AT AT AC AT AT AT AT AT AT AC 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
*
6060 AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6086 GGTAAGCCTA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6037 original size:14 final size:14
Alignment explanation
Indices: 6018--6084 Score: 125
Period size: 14 Copynumber: 4.8 Consensus size: 14
6008 AAAAGAACAC
6018 ATATATATATACAT
1 ATATATATATACAT
6032 ATATATATATACAT
1 ATATATATATACAT
*
6046 ATATATATATATAT
1 ATATATATATACAT
6060 ATATATATATACAT
1 ATATATATATACAT
6074 ATATATATATA
1 ATATATATATA
6085 TGGTAAGCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 51 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:23874 original size:21 final size:22
Alignment explanation
Indices: 23850--23893 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
23840 AAACATTTTC
23850 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
23871 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
23893 T
1 T
23894 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:24235 original size:16 final size:16
Alignment explanation
Indices: 24182--24237 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
24172 ATTTAAACAT
24182 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
24199 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
24219 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
24235 ATA
1 ATA
24238 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:24252 original size:37 final size:37
Alignment explanation
Indices: 24182--24252 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
24172 ATTTAAACAT
* *
24182 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
24219 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
24253 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Found at i:25542 original size:3 final size:3
Alignment explanation
Indices: 25523--25575 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
25513 TTGTAATATT
** **
25523 TAA TAAA TAA TATA TAA TAA TAA TTT TAA TAA TAA TTT TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25570 TAA TAA
1 TAA TAA
25576 ATTTAAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:25554 original size:12 final size:13
Alignment explanation
Indices: 25516--25571 Score: 80
Period size: 12 Copynumber: 4.4 Consensus size: 13
25506 ATGGGCTTTG
25516 TAATATTTAATAAA
1 TAATATTTAAT-AA
*
25530 TAATATATAATAA
1 TAATATTTAATAA
25543 TAAT-TTTAATAA
1 TAATATTTAATAA
25555 TAAT-TTTAATAA
1 TAATATTTAATAA
25567 TAATA
1 TAATA
25572 ATAAATTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
12 23 0.59
13 6 0.15
14 10 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATATTTAATAA
Found at i:25564 original size:18 final size:18
Alignment explanation
Indices: 25549--25586 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25539 ATAATAATTT
*
25549 TAATAATAATTTTAATAA
1 TAATAATAAATTTAATAA
25567 TAATAATAAATTTAA-AA
1 TAATAATAAATTTAATAA
25584 TAA
1 TAA
25587 AAAAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATAATAAATTTAATAA
Found at i:29014 original size:31 final size:31
Alignment explanation
Indices: 28979--29040 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
28969 AGAAAAGAAA
28979 GCTCTTCCTGCATACATTGTAGGAGATGCTC
1 GCTCTTCCTGCATACATTGTAGGAGATGCTC
29010 GCTCTTCCTGCATACATTGTAGGAGATGCTC
1 GCTCTTCCTGCATACATTGTAGGAGATGCTC
29041 CTGAGGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (31 bp):
GCTCTTCCTGCATACATTGTAGGAGATGCTC
Found at i:31600 original size:15 final size:15
Alignment explanation
Indices: 31564--31602 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
31554 TAATAATGAC
*
31564 CATGTTAATGTTAAT
1 CATGTTGATGTTAAT
31579 CATGTTGATGTTAAT
1 CATGTTGATGTTAAT
31594 CATGTTGAT
1 CATGTTGAT
31603 ATATTTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (15 bp):
CATGTTGATGTTAAT
Found at i:37236 original size:31 final size:31
Alignment explanation
Indices: 37186--37261 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
37176 TAACTTTTTT
*
37186 ATTTGACCCTTAAATTTTAGATAAAATATCA
1 ATTTGACCCTTAAACTTTAGATAAAATATCA
*
37217 ATTTGATCCC-TAAACTTTAGATAATATATCA
1 ATTTGA-CCCTTAAACTTTAGATAAAATATCA
* *
37248 ATTTAACTCTTAAA
1 ATTTGACCCTTAAA
37262 TCCAACCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 2 0.05
31 34 0.87
32 3 0.08
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (31 bp):
ATTTGACCCTTAAACTTTAGATAAAATATCA
Found at i:40387 original size:12 final size:11
Alignment explanation
Indices: 40370--40437 Score: 56
Period size: 10 Copynumber: 6.5 Consensus size: 11
40360 TTAACACACA
40370 CATATATCATAT
1 CATATAT-ATAT
40382 CATATA-AT-T
1 CATATATATAT
* * *
40391 CATATCAGAAAA
1 CATAT-ATATAT
40403 CATATATATAT
1 CATATATATAT
40414 -ATATATATAT
1 CATATATATAT
40424 -ATATATATAT
1 CATATATATAT
40434 -ATAT
1 CATAT
40438 CACATATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
9 6 0.12
10 27 0.56
11 4 0.08
12 11 0.23
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (11 bp):
CATATATATAT
Found at i:40446 original size:2 final size:2
Alignment explanation
Indices: 40404--40437 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40394 ATCAGAAAAC
40404 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
40438 CACATATATT
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):
AT
Found at i:40994 original size:2 final size:2
Alignment explanation
Indices: 40987--41068 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
40977 ACATATGTTC
40987 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
41029 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
41069 CACATAACAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63969 original size:3 final size:3
Alignment explanation
Indices: 63961--63988 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
63951 TGGTCTCAAC
63961 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
63989 TCACTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:64000 original size:2 final size:2
Alignment explanation
Indices: 63993--64022 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
63983 ATTATTTCAC
63993 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64023 CTCACTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67537 original size:18 final size:17
Alignment explanation
Indices: 67510--67544 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
67500 GATAAGTAAA
*
67510 TAAATTTATTATTTAAT
1 TAAATTTATTAATTAAT
67527 TAAATTTTATTAATTAAT
1 TAAA-TTTATTAATTAAT
67545 ATTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAATTTATTAATTAAT
Found at i:67541 original size:14 final size:15
Alignment explanation
Indices: 67522--67555 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
67512 AATTTATTAT
*
67522 TTAATTAA-ATTTTA
1 TTAATTAATATTTAA
67536 TTAATTAATATTTAA
1 TTAATTAATATTTAA
67551 TTAAT
1 TTAAT
67556 ATTATACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATTAATATTTAA
Found at i:77486 original size:60 final size:60
Alignment explanation
Indices: 77412--77578 Score: 160
Period size: 60 Copynumber: 2.8 Consensus size: 60
77402 TTAGACTTTT
* * * *
77412 TAAACTATAACTCTCAGTT-TAAATT-GGTCACTAAATTTTTTAATATTTCAATTTCATCCC
1 TAAACTATGACTCTCA-TTCTAAATTAGGTC-CTAAACTTTTGAATATTTCAATTTCATCCA
* * *
77472 TAAACTATGACTCTCATTCTAAATTAGTTCTTAAACTTTTGAATATTTTAATTTCATCCA
1 TAAACTATGACTCTCATTCTAAATTAGGTCCTAAACTTTTGAATATTTCAATTTCATCCA
* * ** * * *
77532 TAAATTATGACCCTTTTTCTAAATCA-GTCCCCAAACATTTGAATATT
1 TAAACTATGACTCTCATTCTAAATTAGGT-CCTAAACTTTTGAATATT
77579 CTAAATTTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 3 0.03
60 82 0.93
61 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.43
Consensus pattern (60 bp):
TAAACTATGACTCTCATTCTAAATTAGGTCCTAAACTTTTGAATATTTCAATTTCATCCA
Found at i:77811 original size:60 final size:59
Alignment explanation
Indices: 77747--77908 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 59
77737 GGAATGTGAA
* *
77747 AAAAGCTTGAGGACCAATTTAGAATGAATATCATAGTTTGAGGATGAAATTAAAATATT
1 AAAAGCTTGAGGACCAATTTAAAATGAATATCATAATTTGAGGATGAAATTAAAATATT
* * * *
77806 CAAAAGTTTGAGGACTAATTTAAAAT-AATAGTCTTAATTT-AGGGATGAAATTAGAATATT
1 -AAAAGCTTGAGGACCAATTTAAAATGAATA-TCATAATTTGA-GGATGAAATTAAAATATT
* * * *
77866 AAAAGGTTTAGGGACCAGTTTAAAATGACA-ATCATATTTTGAG
1 AAAAGCTTGA-GGACCAATTTAAAATGA-ATATCATAATTTGAG
77909 ACATGTGTGT
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
59 13 0.15
60 67 0.80
61 3 0.04
62 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.32
Consensus pattern (59 bp):
AAAAGCTTGAGGACCAATTTAAAATGAATATCATAATTTGAGGATGAAATTAAAATATT
Found at i:77993 original size:3 final size:3
Alignment explanation
Indices: 77985--78014 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
77975 AATATTAAAA
77985 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
78015 GCCTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.