Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006017.1 Hibiscus syriacus cultivar Beakdansim tig00014193_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: 82314
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:19202 original size:36 final size:36
Alignment explanation
Indices: 19161--19299 Score: 251
Period size: 36 Copynumber: 3.9 Consensus size: 36
19151 AGTTGAGTAT
*
19161 TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
19197 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
19233 TATCAGCTTTGGTACATTCGTATATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
19269 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
19300 CCAGCACCGT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:27233 original size:36 final size:36
Alignment explanation
Indices: 27192--27325 Score: 225
Period size: 36 Copynumber: 3.8 Consensus size: 36
27182 AGTTGAGTAT
27192 TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
*
27228 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
* *
27264 TATCAACTTTGGTACATTCATGTATCAATGTT-TCC
1 TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
*
27299 TATCAGCTTTGGTACATTCGTGTATCA
1 TATCAGCTTTGGTACATTCATGTATCA
27326 TTGTCCATCA
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 27 0.29
36 65 0.71
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCATGTATCAATGTTATCA
Found at i:29755 original size:21 final size:20
Alignment explanation
Indices: 29729--29782 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
29719 TAATATCGAC
29729 TCTTTAGATCCTGGTACAACT
1 TCTTTAGA-CCTGGTACAACT
* *
29750 TCTTTATACCTGGTACATCT
1 TCTTTAGACCTGGTACAACT
*
29770 TCTTTATACCTGG
1 TCTTTAGACCTGG
29783 ATGCATAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 24 0.77
21 7 0.23
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (20 bp):
TCTTTAGACCTGGTACAACT
Found at i:29763 original size:20 final size:20
Alignment explanation
Indices: 29738--29782 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
29728 CTCTTTAGAT
29738 CCTGGTACAACTTCTTTATA
1 CCTGGTACAACTTCTTTATA
*
29758 CCTGGTACATCTTCTTTATA
1 CCTGGTACAACTTCTTTATA
29778 CCTGG
1 CCTGG
29783 ATGCATAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (20 bp):
CCTGGTACAACTTCTTTATA
Found at i:40703 original size:6 final size:6
Alignment explanation
Indices: 40692--40752 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
40682 GACACGTATT
* *
40692 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
40740 ACCACG ACCACG A
1 ACCACG ACCACG A
40753 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:40760 original size:5 final size:5
Alignment explanation
Indices: 40750--40803 Score: 81
Period size: 5 Copynumber: 10.8 Consensus size: 5
40740 ACCACGACCA
* * *
40750 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
40800 CGAG
1 CGAG
40804 ACAGACGGAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.15, C:0.39, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:46678 original size:6 final size:6
Alignment explanation
Indices: 46667--46705 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
46657 GACACGTATT
46667 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
46706 TCGAGCCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:46717 original size:5 final size:5
Alignment explanation
Indices: 46707--46770 Score: 85
Period size: 5 Copynumber: 12.8 Consensus size: 5
46697 ACCACGACCT
* *
46707 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGTA-C CGTGC CGTGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CG-AGC CGAGC CGAGC
*
46757 CGTGC CGAGC CGAG
1 CGAGC CGAGC CGAG
46771 ACGGACAGAC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 54 0.98
6 1 0.02
ACGTcount: A:0.16, C:0.39, G:0.39, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:47347 original size:36 final size:35
Alignment explanation
Indices: 47288--47357 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
47278 CAATCTAAAT
* *
47288 ATTTTAATCTTAATCTATCTTACAATCCATATTTG
1 ATTTTAATCTTAATCTATATTACAATCAATATTTG
* *
47323 ATTTTGAATTTTAATTTATATTACAATCAATATTT
1 ATTTT-AATCTTAATCTATATTACAATCAATATTT
47358 TAATTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 5 0.17
36 25 0.83
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.51
Consensus pattern (35 bp):
ATTTTAATCTTAATCTATATTACAATCAATATTTG
Found at i:47423 original size:36 final size:36
Alignment explanation
Indices: 47368--47440 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
47358 TAATTTAAAT
* * * *
47368 CTAATCCTAAACCATTATAACATAAAAACCCTAACC
1 CTAACCCTAAACCACTATAACACAAAAAACCTAACC
*
47404 CTAACCCTAAACCACTATAACCCAAAAAACCTAACC
1 CTAACCCTAAACCACTATAACACAAAAAACCTAACC
47440 C
1 C
47441 AAAAACCTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.18
Consensus pattern (36 bp):
CTAACCCTAAACCACTATAACACAAAAAACCTAACC
Found at i:47446 original size:13 final size:14
Alignment explanation
Indices: 47421--47450 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
47411 TAAACCACTA
47421 TAACCCAAAAAACC
1 TAACCCAAAAAACC
47435 TAACCC-AAAAACC
1 TAACCCAAAAAACC
47448 TAA
1 TAA
47451 ATCGAATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.57, C:0.33, G:0.00, T:0.10
Consensus pattern (14 bp):
TAACCCAAAAAACC
Found at i:48663 original size:17 final size:17
Alignment explanation
Indices: 48638--48676 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
48628 AATATCATTT
* *
48638 AAAACAATTTTAAGAAA
1 AAAATAATTTAAAGAAA
48655 AAAATAATTTAAAGAAA
1 AAAATAATTTAAAGAAA
48672 AAAAT
1 AAAAT
48677 TAGATTGCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (17 bp):
AAAATAATTTAAAGAAA
Found at i:52434 original size:17 final size:16
Alignment explanation
Indices: 52392--52435 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
52382 GAAGTTGTTC
*
52392 GAAAGAAAAAGAGAGA
1 GAAAGAAAAAGAGACA
*
52408 GAGAAAAAAAAGAGACA
1 GA-AAGAAAAAGAGACA
52425 TGAAAGAAAAA
1 -GAAAGAAAAA
52436 ATGGAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.02
Consensus pattern (16 bp):
GAAAGAAAAAGAGACA
Found at i:59732 original size:27 final size:27
Alignment explanation
Indices: 59701--59766 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
59691 AGATGTCAAA
*
59701 AATCTATAATTCCTGAAGAATTAAAAT
1 AATCTATAATTCCTGAAGAATTAAAAG
* *
59728 AATCTATATTTCCTTAAGAATTAAAAG
1 AATCTATAATTCCTGAAGAATTAAAAG
59755 AATCTATAATTC
1 AATCTATAATTC
59767 AATCGATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (27 bp):
AATCTATAATTCCTGAAGAATTAAAAG
Found at i:68032 original size:41 final size:41
Alignment explanation
Indices: 67987--68086 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
67977 TCGATCTTGG
* * *
67987 CAACATATATTACTTCACAATTCAATTTAATTCAATCATGA
1 CAACATGTAATACTTCACAATTCAATTCAATTCAATCATGA
* * * *
68028 CAACATGCAATAGTTCACCATTCAATTCAATTCAATCATGG
1 CAACATGTAATACTTCACAATTCAATTCAATTCAATCATGA
*
68069 CACCATGTAATACTTCAC
1 CAACATGTAATACTTCAC
68087 TAGTCAACTT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (41 bp):
CAACATGTAATACTTCACAATTCAATTCAATTCAATCATGA
Found at i:68139 original size:41 final size:41
Alignment explanation
Indices: 68035--68372 Score: 410
Period size: 41 Copynumber: 8.3 Consensus size: 41
68025 TGACAACATG
* * * * * *
68035 CAATAGTTCACCATTCAA-TTCAATTCAATCATGGCACCATG
1 CAATAATTCACCATTCAACTT-GATTCGATCATGGTAGCATA
* * * * * *
68076 TAATACTTCACTAGTCAACTTGATTCGGTCATGGTAGAATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* * *
68117 CAATAATTTACCATTCATCTTGATTCAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* * *
68158 CAATAATTCACCAATCAACTTGATTCGATCATTGTATCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* *
68199 C-ATTATTCACCATTCAACTTGATTCGATCATGATAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
*
68239 CAATAATTCACCATTCAACTTGATTCAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* * *
68280 TAATAATTAACCATTCAACTTCATTCGATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* **
68321 CAATAATTCACTATTCAACTTGATTAAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
68362 CAATAATTCAC
1 CAATAATTCAC
68373 AAACCAATTC
Statistics
Matches: 251, Mismatches: 44, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
40 35 0.14
41 214 0.85
42 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (41 bp):
CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
Found at i:68245 original size:122 final size:123
Alignment explanation
Indices: 68000--68727 Score: 606
Period size: 123 Copynumber: 6.0 Consensus size: 123
67990 CATATATTAC
* * * ** * * * * * *
68000 TTCACAATTCAATTTAATTCAATCATGACAACATGCAATAGTTCACCATTCAA-TTCAATTCAAT
1 TTCACCATTCAACTTGATTCAATCATGGTAGCATACAATAATTAACCAATCAACTTC-ATTCGAT
* * ** * * * * *
68064 CATGGCACCATGTAATACTTCACTAGTCAACTTGATTCGGTCATGGTAGAATACAATAA
65 CATGGTAGCATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAA
* * * *
68123 TTTACCATTCATCTTGATTCAATCATGGTAGCATACAATAATTCACCAATCAACTTGATTCGATC
1 TTCACCATTCAACTTGATTCAATCATGGTAGCATACAATAATTAACCAATCAACTTCATTCGATC
* * * *
68188 ATTGTATCATAC-ATTATTCACCATTCAACTTGATTCGATCATGATAGCATACAATAA
66 ATGGTAGCATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAA
* *
68245 TTCACCATTCAACTTGATTCAATCATGGTAGCATATAATAATTAACCATTCAACTTCATTCGATC
1 TTCACCATTCAACTTGATTCAATCATGGTAGCATACAATAATTAACCAATCAACTTCATTCGATC
* **
68310 ATGGTAGCATACAATAATTCACTATTCAACTTGATTAAATCATGGTAGCATACAATAA
66 ATGGTAGCATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAA
* ** * * * *
68368 TTCACAAACCAA-TTCAATT-AGATCA---TAG-ATCCAATTCAATTTA--AATCAA----A-GC
1 TTCACCATTCAACTT-GATTCA-ATCATGGTAGCATACAA-T-AATTAACCAATCAACTTCATTC
* * * *
68420 -AACAT-GCA--ATAGC--TAATTTACCAATT-AACTTGATTCGATCATGGTAGCATACATTAA
62 GATCATGGTAGCATA-CAATAATTCACC-ATTCAACTTGATTCGATCATGGTAGCATACAATAA
* * ** * * * * *
68477 TTCA-CTTCTCAAGTTGATTTGATCATGTTAGCATACAATAATTCACCATTCAACTTGATTTGAT
1 TTCACCAT-TCAACTTGATTCAATCATGGTAGCATACAATAATTAACCAATCAACTTCATTCGAT
* * *
68541 CATGGTAGAATACAATAATTCACCAATT-AACTTGAAGT-GATCATGGTAGCATACATTAA
65 CATGGTAGCATACAATAATTCACC-ATTCAACTTG-ATTCGATCATGGTAGCATACAATAA
* * * *
68600 TTCACCATTCGACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCAACTTGATTCGATC
1 TTCACCATTCAACTTGATTCAATCATGGTAGCATACAATAATTAACCAATCAACTTCATTCGATC
* * * * *
68665 ATGGTAGCATACAATAATTCACCATTCAACATGATTTGATCATGGTGGAAAACAATAA
66 ATGGTAGCATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAA
68723 TTCAC
1 TTCAC
68728 AAACCAATTG
Statistics
Matches: 490, Mismatches: 83, Indels: 64
0.77 0.13 0.10
Matches are distributed among these distances:
109 49 0.10
110 8 0.02
111 6 0.01
112 6 0.01
113 14 0.03
114 1 0.00
115 1 0.00
117 1 0.00
119 13 0.03
120 6 0.01
121 6 0.01
122 118 0.24
123 255 0.52
124 6 0.01
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (123 bp):
TTCACCATTCAACTTGATTCAATCATGGTAGCATACAATAATTAACCAATCAACTTCATTCGATC
ATGGTAGCATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAA
Found at i:68494 original size:41 final size:41
Alignment explanation
Indices: 68433--68727 Score: 373
Period size: 41 Copynumber: 7.2 Consensus size: 41
68423 ATGCAATAGC
* *
68433 TAATTTACCAATT-AACTTGATTCGATCATGGTAGCATACAT
1 TAATTCACC-ATTCAACTTGATTCGATCATGGTAGCATACAA
* * * *
68474 TAATTCA-CTTCTCAAGTTGATTTGATCATGTTAGCATACAA
1 TAATTCACCAT-TCAACTTGATTCGATCATGGTAGCATACAA
* *
68515 TAATTCACCATTCAACTTGATTTGATCATGGTAGAATACAA
1 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
* *
68556 TAATTCACCAATT-AACTTGAAGT-GATCATGGTAGCATACAT
1 TAATTCACC-ATTCAACTTG-ATTCGATCATGGTAGCATACAA
* *
68597 TAATTCACCATTCGACTTGATTCAATCATGGTAGCATACAA
1 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
68638 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
1 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
* * * * *
68679 TAATTCACCATTCAACATGATTTGATCATGGTGGAAAACAA
1 TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
68720 TAATTCAC
1 TAATTCAC
68728 AAACCAATTG
Statistics
Matches: 223, Mismatches: 24, Indels: 14
0.85 0.09 0.05
Matches are distributed among these distances:
39 1 0.00
40 7 0.03
41 208 0.93
42 7 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (41 bp):
TAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAA
Found at i:68768 original size:123 final size:123
Alignment explanation
Indices: 68508--68756 Score: 306
Period size: 123 Copynumber: 2.0 Consensus size: 123
68498 ATCATGTTAG
* *
68508 CATACAATAATTCACCATTCAACTTGATTTGATCATGGTAGAATACAATAATTCACCAATTAACT
1 CATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGAATACAATAATTCACCAATTAACA
* * * ** * * * * *
68573 TGAAGTGATCATGGTAGCATACATTAATTCACCATTCGACTTGATTCAATCATGGTAG
66 TGAAGTGATCATGGTAGAAAACAATAATTCACCAAACCAATTGATTCAATCATAGAAA
*
68631 CATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCACC-ATTCAAC
1 CATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGAATACAATAATTCACCAATT-AAC
** *
68695 ATGATTTGATCATGGTGGAAAACAATAATTCA-CAAACCAATTGAATT-AAGTCATAGAAA
65 ATGAAGTGATCATGGTAGAAAACAATAATTCACCAAACCAATTG-ATTCAA-TCATAGAAA
68754 CAT
1 CAT
68757 GTATTAATTC
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
122 12 0.11
123 95 0.89
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (123 bp):
CATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGAATACAATAATTCACCAATTAACA
TGAAGTGATCATGGTAGAAAACAATAATTCACCAAACCAATTGATTCAATCATAGAAA
Found at i:76799 original size:41 final size:41
Alignment explanation
Indices: 76744--77034 Score: 339
Period size: 41 Copynumber: 7.2 Consensus size: 41
76734 TCATGGTATG
* * *
76744 CAATACTTCGCCATTCAAGTTGATTC-AGTCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGA-TCATGGTAGCATA
* ** *
76785 CAATAATTCACCATTTAACTTGATTTAATCATGGTA-AATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* *
76825 CAAT--TTCAACAATCAACTTGATTCGATCATGGTAGCA-A
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
* *
76863 CATTAATTCACTATTCAACTTGATTCGATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
*
76904 CAATAA-TCAACCATTCAACTTGGTTCGATCATGGTAGCATA
1 CAATAATTC-ACCATTCAACTTGATTCGATCATGGTAGCATA
* *
76945 CAATAATTCACCATTCAGCTTGATTCGATCATGGTATC-TGA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCAT-A
* * *
76986 CAATCATTAACCATTCAACTTGATTTGATCAT-GTAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
77026 C-ATAATTCA
1 CAATAATTCA
77035 AAAACCAATT
Statistics
Matches: 212, Mismatches: 29, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
38 29 0.14
39 7 0.03
40 46 0.22
41 127 0.60
42 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (41 bp):
CAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATA
Found at i:76895 original size:119 final size:122
Alignment explanation
Indices: 76754--77034 Score: 342
Period size: 119 Copynumber: 2.3 Consensus size: 122
76744 CAATACTTCG
* * *
76754 CCATTCAAGTTGATTC-AGTCATGGTAGCATACAATAATTCACCATTTAACTTGATTTAATCATG
1 CCATTCAACTTGATTCGA-TCATGGTAGCATACAATAATTCACCATTCAACTTGATTCAATCATG
* *
76818 GTA-AATACAAT-TTCAACAATCAACTTGATTCGATCATGGTAGC-AACATTAATTCA
65 GTAGAATACAATATTCAACAATCAACTTGATTCGATCATGGTAGCTAACAATAATTAA
* * *
76873 CTATTCAACTTGATTCGATCATGGTAGCATACAATAA-TCAACCATTCAACTTGGTTCGATCATG
1 CCATTCAACTTGATTCGATCATGGTAGCATACAATAATTC-ACCATTCAACTTGATTCAATCATG
* * * * * * *
76937 GTAGCATACAATAATTCACCATTCAGCTTGATTCGATCATGGTATCTGACAATCATTAA
65 GTAGAATACAAT-ATTCAACAATCAACTTGATTCGATCATGGTAGCTAACAATAATTAA
*
76996 CCATTCAACTTGATTTGATCAT-GTAGCATAC-ATAATTCA
1 CCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCA
77035 AAAACCAATT
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
118 2 0.01
119 56 0.41
120 8 0.06
121 5 0.04
122 39 0.28
123 28 0.20
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (122 bp):
CCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCATTCAACTTGATTCAATCATGG
TAGAATACAATATTCAACAATCAACTTGATTCGATCATGGTAGCTAACAATAATTAA
Done.