Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000231.1 Hibiscus syriacus cultivar Beakdansim tig00000401_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: 46158
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:496 original size:33 final size:36
Alignment explanation
Indices: 436--521 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 36
426 TATTACTGGT
*
436 TGTATTTTAGATTCCAACAAATTCTCGTT-GAATTTTC
1 TGTATTTT--ATTACAACAAATTCTCGTTAGAATTTTC
473 TGTATTTTA-TACAAC-AATTCTCGTTAGAATTTTC
1 TGTATTTTATTACAACAAATTCTCGTTAGAATTTTC
507 TGTATTTTATTACAA
1 TGTATTTTATTACAA
522 ATTTCAGCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
33 10 0.22
34 22 0.48
35 6 0.13
37 8 0.17
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (36 bp):
TGTATTTTATTACAACAAATTCTCGTTAGAATTTTC
Found at i:21154 original size:25 final size:25
Alignment explanation
Indices: 21120--21167 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
21110 GTTCTGGTTC
*
21120 TAGTTCTAGTTCATGTCTTTCAATA
1 TAGTTCTAGTTCATGTCTCTCAATA
*
21145 TAGTTCTAGTTCTTGTCTCTCAA
1 TAGTTCTAGTTCATGTCTCTCAA
21168 CAGGCCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (25 bp):
TAGTTCTAGTTCATGTCTCTCAATA
Found at i:23990 original size:228 final size:226
Alignment explanation
Indices: 23589--24035 Score: 788
Period size: 228 Copynumber: 2.0 Consensus size: 226
23579 GTAAATTATC
* * *
23589 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
23654 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
23719 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
23783 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAAC-TAAATTACATAACTTT-AAAAAAGTATA
*
23816 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
23881 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
*
23946 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
24011 GAAACTAAATTACATAACTTTAAAA
195 GAAACTAAATTACATAACTTTAAAA
24036 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
227 40 0.19
228 160 0.76
229 10 0.05
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACTAAATTACATAACTTTAAAAAAGTATA
Found at i:24124 original size:20 final size:19
Alignment explanation
Indices: 24101--24146 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
24091 CGATATACCA
24101 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
24121 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
24141 GGTAAA
1 GGTAAA
24147 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:24289 original size:20 final size:19
Alignment explanation
Indices: 24266--24311 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
24256 CGATATAACA
24266 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
24286 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
24306 GGTAAA
1 GGTAAA
24312 TGATACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:25219 original size:20 final size:20
Alignment explanation
Indices: 25194--25232 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25184 GGTTATATTG
* *
25194 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
25214 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
25233 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:25578 original size:23 final size:23
Alignment explanation
Indices: 25547--25610 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
25537 ATAGGTAAAC
*
25547 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
25570 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
25593 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
25611 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:25617 original size:23 final size:23
Alignment explanation
Indices: 25547--25619 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
25537 ATAGGTAAAC
* **
25547 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
25570 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
25593 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
25616 ATAT
1 ATAT
25620 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:25921 original size:25 final size:25
Alignment explanation
Indices: 25887--25937 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
25877 ACAACAAATC
*
25887 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
25912 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
25937 A
1 A
25938 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:26252 original size:18 final size:18
Alignment explanation
Indices: 26231--26265 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26221 GTAATTGGAG
26231 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
26249 TTTGAGTTTGAATTTCA
1 TTTGAATTTAAATTTCA
26266 TATATATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:26571 original size:38 final size:38
Alignment explanation
Indices: 26528--26606 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
26518 ATGCTCATCA
*
26528 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATC
1 AAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAATC
*
26566 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
1 AAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAATC
26604 AAA
1 AAA
26607 ATCTACAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.16
Consensus pattern (38 bp):
AAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAATC
Found at i:27038 original size:23 final size:23
Alignment explanation
Indices: 27007--27070 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
26997 ATAGGTAAAC
*
27007 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
27030 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
27053 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
27071 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:27077 original size:23 final size:23
Alignment explanation
Indices: 27007--27079 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
26997 ATAGGTAAAC
* **
27007 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
27030 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
27053 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
27076 ATAT
1 ATAT
27080 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:28298 original size:32 final size:32
Alignment explanation
Indices: 28237--28298 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
28227 GACTCCCTCA
* *
28237 TCAAAACGATGTCGTTTTGATGTTCAAAAAGC
1 TCAAAACGACGTCGTTTTGATGATCAAAAAGC
* *
28269 TCAAAACGACGTCGTTTTGTTGATGAAAAA
1 TCAAAACGACGTCGTTTTGATGATCAAAAA
28299 AATGTTTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (32 bp):
TCAAAACGACGTCGTTTTGATGATCAAAAAGC
Found at i:32432 original size:17 final size:17
Alignment explanation
Indices: 32400--32433 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32390 AGCTTGTTAA
*
32400 AAACTCGAGTTAAATTC
1 AAACTCGAATTAAATTC
*
32417 AAACTCGAATTGAATTC
1 AAACTCGAATTAAATTC
32434 GTTCAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
AAACTCGAATTAAATTC
Found at i:35721 original size:34 final size:33
Alignment explanation
Indices: 35670--35736 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
35660 TAGAATATGC
* *
35670 AATACATTTTCTCAATCAAGGAATTCTTGGTAAT
1 AATACATTCTCTCAATCAAGGAAATCTT-GTAAT
*
35704 AATACATTCTCTTAATCAAGGAAATCTTGTAAT
1 AATACATTCTCTCAATCAAGGAAATCTTGTAAT
35737 TAACTTAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (33 bp):
AATACATTCTCTCAATCAAGGAAATCTTGTAAT
Found at i:38580 original size:38 final size:37
Alignment explanation
Indices: 38529--38606 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 37
38519 CAACTTAGAC
*
38529 TTATTTAATGAAAGCCAAATCTGAAACTGAGGGTATTT
1 TTATTTAATGAAAGCCAAATCTAAAACTGA-GGTATTT
38567 TTATTTAATGAAAGCCAAATCTAAAACTGAGGTATTT
1 TTATTTAATGAAAGCCAAATCTAAAACTGAGGTATTT
38604 TTA
1 TTA
38607 CAACATTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 10 0.26
38 29 0.74
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (37 bp):
TTATTTAATGAAAGCCAAATCTAAAACTGAGGTATTT
Found at i:39229 original size:24 final size:24
Alignment explanation
Indices: 39172--39229 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
39162 CTTTACCACA
*
39172 ACCCAAAATTGAGCCTACTTCTAT
1 ACCCAAAATTCAGCCTACTTCTAT
**
39196 ACCCGGAATTCAGCCTACTTCTAT
1 ACCCAAAATTCAGCCTACTTCTAT
39220 ACCCAAAATT
1 ACCCAAAATT
39230 GCTCCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.28
Consensus pattern (24 bp):
ACCCAAAATTCAGCCTACTTCTAT
Found at i:40194 original size:147 final size:147
Alignment explanation
Indices: 39927--40221 Score: 581
Period size: 147 Copynumber: 2.0 Consensus size: 147
39917 ATTATTTTTG
39927 CAAAAACCACCTGGCTTATCTTTGACTTCGAATACAGGGCAGGTTTGCAAGCTTCTCTTTATACG
1 CAAAAACCACCTGGCTTATCTTTGACTTCGAATACAGGGCAGGTTTGCAAGCTTCTCTTTATACG
39992 GCCTTAAGCAGTCGTCGCGTGCTTGGTTAGAGAGGTTTACCAAAGGCATTCTACAATTTGGCTAT
66 GCCTTAAGCAGTCGTCGCGTGCTTGGTTAGAGAGGTTTACCAAAGGCATTCTACAATTTGGCTAT
40057 CTTCAGTGCCAGGCTGA
131 CTTCAGTGCCAGGCTGA
*
40074 CAAAAACCACCTGGCTTATCTTTGACTTCGAATACAGGGCAGGTTTGCAAGCTTCTCTTTATACT
1 CAAAAACCACCTGGCTTATCTTTGACTTCGAATACAGGGCAGGTTTGCAAGCTTCTCTTTATACG
40139 GCCTTAAGCAGTCGTCGCGTGCTTGGTTAGAGAGGTTTACCAAAGGCATTCTACAATTTGGCTAT
66 GCCTTAAGCAGTCGTCGCGTGCTTGGTTAGAGAGGTTTACCAAAGGCATTCTACAATTTGGCTAT
40204 CTTCAGTGCCAGGCTGA
131 CTTCAGTGCCAGGCTGA
40221 C
1 C
40222 CACACGCTAT
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (147 bp):
CAAAAACCACCTGGCTTATCTTTGACTTCGAATACAGGGCAGGTTTGCAAGCTTCTCTTTATACG
GCCTTAAGCAGTCGTCGCGTGCTTGGTTAGAGAGGTTTACCAAAGGCATTCTACAATTTGGCTAT
CTTCAGTGCCAGGCTGA
Found at i:42524 original size:12 final size:13
Alignment explanation
Indices: 42502--42537 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
42492 AGATGCAATT
42502 TTTGATTTATTTA
1 TTTGATTTATTTA
42515 TTTG-TTTATTTA
1 TTTGATTTATTTA
42527 TTT-ATTT-TTTA
1 TTTGATTTATTTA
42538 AATGTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.18
12 14 0.64
13 4 0.18
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTGATTTATTTA
Found at i:42527 original size:16 final size:15
Alignment explanation
Indices: 42499--42537 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
42489 GTCAGATGCA
*
42499 ATTTTTGATTTATTT
1 ATTTTTTATTTATTT
42514 ATTTGTTTATTTATTT
1 ATTT-TTTATTTATTT
42530 ATTTTTTA
1 ATTTTTTA
42538 AATGTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (15 bp):
ATTTTTTATTTATTT
Found at i:44545 original size:26 final size:26
Alignment explanation
Indices: 44516--44566 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
44506 TTTTCTGTAT
*
44516 AATATACTAATTAGTGTTATAATTAA
1 AATATACTAATTAGTGCTATAATTAA
* *
44542 AATATATTAATTAGTGCTATGATTA
1 AATATACTAATTAGTGCTATAATTA
44567 GTTATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (26 bp):
AATATACTAATTAGTGCTATAATTAA
Found at i:44607 original size:19 final size:19
Alignment explanation
Indices: 44583--44632 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
44573 AAATTAAATA
*
44583 AAATTACAATATTATTTAT
1 AAATTATAATATTATTTAT
*
44602 AAATTATAATATTGTTTAT
1 AAATTATAATATTATTTAT
44621 AAATTATAATAT
1 AAATTATAATAT
44633 GATTGATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
AAATTATAATATTATTTAT
Found at i:45566 original size:20 final size:20
Alignment explanation
Indices: 45543--45701 Score: 148
Period size: 20 Copynumber: 8.0 Consensus size: 20
45533 AATATGTAAA
45543 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
45563 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
45583 TCACAACACA-AAGTCAAAT
1 TCGCAACACATAAGTCAAAT
* *
45602 TCGCTACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
45622 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
* **
45642 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACAC--ATAAGTCAAAT
45662 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
* * *
45682 TCGTAACGCAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
45702 GTTTACACGA
Statistics
Matches: 111, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
18 4 0.04
19 19 0.17
20 80 0.72
21 5 0.05
22 3 0.03
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:45611 original size:39 final size:40
Alignment explanation
Indices: 45522--45701 Score: 226
Period size: 40 Copynumber: 4.5 Consensus size: 40
45512 AGTTTCCAAT
45522 TTCGCAACGCGAATATGT-AAA-TCGCAACACATAAGTCAAA
1 TTCGCAACGCG-ATA-GTCAAATTCGCAACACATAAGTCAAA
*
45562 TTCGCAACGCGATAGTCAAATTCACAACACA-AAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACATAAGTCAAA
* *
45601 TTCGCTACGCGATAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACATAAGTCAAA
*
45641 TTCGCAACGCGAATTTGT-AAA-TCGCAACACATAAGTCAAA
1 TTCGCAACGCG-A-TAGTCAAATTCGCAACACATAAGTCAAA
* * *
45681 TTCGTAACGCAAAAGTCAAAT
1 TTCGCAACGCGATAGTCAAAT
45702 GTTTACACGA
Statistics
Matches: 123, Mismatches: 10, Indels: 14
0.84 0.07 0.10
Matches are distributed among these distances:
38 4 0.03
39 47 0.38
40 65 0.53
41 4 0.03
42 3 0.02
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (40 bp):
TTCGCAACGCGATAGTCAAATTCGCAACACATAAGTCAAA
Done.