Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014898.1 Kokia drynarioides strain JFW-HI SEQ_129941, 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: 1273188
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 233 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1152891 original size:12 final size:13
Alignment explanation
Indices: 1152856--1152891 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1152846 AGAAATTGGC
1152856 ATTGAATTTTGTT
1 ATTGAATTTTGTT
1152869 ATTGAATTTTGTT
1 ATTGAATTTTGTT
*
1152882 GTTG-ATTTTG
1 ATTGAATTTTG
1152892 CCGTGGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (13 bp):
ATTGAATTTTGTT
Found at i:1154896 original size:21 final size:21
Alignment explanation
Indices: 1154872--1154913 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1154862 TCCATTCACA
1154872 AGATGGGTGCATCATCATCTT
1 AGATGGGTGCATCATCATCTT
1154893 AGATGGGTGCATCATCATCTT
1 AGATGGGTGCATCATCATCTT
1154914 CCTTGCGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
AGATGGGTGCATCATCATCTT
Found at i:1160046 original size:12 final size:13
Alignment explanation
Indices: 1160024--1160052 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1160014 TTGTCGGGAA
1160024 TTGTCAAAATTAT
1 TTGTCAAAATTAT
1160037 TTGT-AAAATTAT
1 TTGTCAAAATTAT
1160049 TTGT
1 TTGT
1160053 TTTACATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.52
Consensus pattern (13 bp):
TTGTCAAAATTAT
Found at i:1170848 original size:17 final size:17
Alignment explanation
Indices: 1170826--1170875 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
1170816 ATTAACATTA
*
1170826 AAATGCGATGACAATGG
1 AAATGCAATGACAATGG
1170843 AAATGCAATGACAATGG
1 AAATGCAATGACAATGG
*
1170860 GAATGCAATGACAATG
1 AAATGCAATGACAATG
1170876 CTTACTAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.18
Consensus pattern (17 bp):
AAATGCAATGACAATGG
Found at i:1177742 original size:17 final size:17
Alignment explanation
Indices: 1177699--1177745 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1177689 ACATTATTAA
**
1177699 TGTCATTGCATTTTTAT
1 TGTCATTGCATTTACAT
*
1177716 TGT-TTCTGCATTTACAT
1 TGTCAT-TGCATTTACAT
1177733 TGTCATTGCATTT
1 TGTCATTGCATTT
1177746 CCATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.55
Consensus pattern (17 bp):
TGTCATTGCATTTACAT
Found at i:1194889 original size:21 final size:21
Alignment explanation
Indices: 1194864--1194910 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1194854 CTCCACAGGA
* * *
1194864 TCTTCCTCGGGATCTTTTTCT
1 TCTTCCTCAGGATCCTCTTCT
1194885 TCTTCCTCAGGATCCTCTTCT
1 TCTTCCTCAGGATCCTCTTCT
1194906 TCTTC
1 TCTTC
1194911 AGGGTCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.06, C:0.34, G:0.11, T:0.49
Consensus pattern (21 bp):
TCTTCCTCAGGATCCTCTTCT
Found at i:1194903 original size:18 final size:18
Alignment explanation
Indices: 1194881--1194945 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
1194871 CGGGATCTTT
*
1194881 TTCTTCTTCCTCAGGATC
1 TTCTTCTTCTTCAGGATC
* *
1194899 CTCTTCTTCTTCAGGGTC
1 TTCTTCTTCTTCAGGATC
*
1194917 TTCTTCTTCTTCAAGATC
1 TTCTTCTTCTTCAGGATC
1194935 TTCTTCTTCTT
1 TTCTTCTTCTT
1194946 TTTCAGCTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.09, C:0.31, G:0.09, T:0.51
Consensus pattern (18 bp):
TTCTTCTTCTTCAGGATC
Found at i:1215965 original size:17 final size:17
Alignment explanation
Indices: 1215942--1215980 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1215932 TCCTTGCATT
1215942 TTTCA-TTGTCACTGCA
1 TTTCATTTGTCACTGCA
*
1215958 TCTTCATTTGTCATTGCA
1 T-TTCATTTGTCACTGCA
1215976 TTTCA
1 TTTCA
1215981 ATATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 8 0.40
18 11 0.55
ACGTcount: A:0.18, C:0.23, G:0.10, T:0.49
Consensus pattern (17 bp):
TTTCATTTGTCACTGCA
Found at i:1219862 original size:20 final size:20
Alignment explanation
Indices: 1219816--1219863 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1219806 TCTTCTTTAT
**
1219816 ATTTTCTTGTTATTTCTCAA
1 ATTTTCTTACTATTTCTCAA
* **
1219836 ATATTCTTACTATTTCTCGG
1 ATTTTCTTACTATTTCTCAA
1219856 ATTTTCTT
1 ATTTTCTT
1219864 GAGAACTAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTCTTACTATTTCTCAA
Found at i:1223448 original size:17 final size:17
Alignment explanation
Indices: 1223409--1223453 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1223399 ATTGAATTTA
*
1223409 ATTTAATTTTTATTTAAT
1 ATTT-ATTTTTATTAAAT
1223427 ATTTATGTTTTATTAAAT
1 ATTTAT-TTTTATTAAAT
1223445 -TTTATTTTT
1 ATTTATTTTT
1223454 GTAATTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 7 0.28
18 14 0.56
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTTATTTTTATTAAAT
Found at i:1235486 original size:14 final size:14
Alignment explanation
Indices: 1235469--1235498 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1235459 TTTAAACTCT
1235469 AAAAGATAAATATA
1 AAAAGATAAATATA
1235483 AAAAGATAAATATA
1 AAAAGATAAATATA
1235497 AA
1 AA
1235499 TTAAATACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAGATAAATATA
Found at i:1235505 original size:11 final size:11
Alignment explanation
Indices: 1235489--1235521 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1235479 TATAAAAAGA
1235489 TAAATATAAAT
1 TAAATATAAAT
*
1235500 TAAATACAAAT
1 TAAATATAAAT
1235511 TAAATATAAAT
1 TAAATATAAAT
1235522 AATATCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:1237396 original size:28 final size:28
Alignment explanation
Indices: 1237351--1237664 Score: 259
Period size: 28 Copynumber: 11.5 Consensus size: 28
1237341 TTAATACGCA
*
1237351 TTTACGCTCGCCATCTTATACTTATGCG
1 TTTACGCTCGCCAGCTTATACTTATGCG
** *
1237379 TTTACGCTCGTTAGCTTATACTTAAGCG
1 TTTACGCTCGCCAGCTTATACTTATGCG
1237407 TTTACGCTCGCCAGCTTATACTTATGCG
1 TTTACGCTCGCCAGCTTATACTTATGCG
* *
1237435 TTTACGCTCGCTAGCTTATACTTATGCA
1 TTTACGCTCGCCAGCTTATACTTATGCG
* * * *
1237463 TTTATGCTCACCAGC-T-TGCATAT--G
1 TTTACGCTCGCCAGCTTATACTTATGCG
* * * * **
1237487 TTTACACTCGTCAGCTTATTCATATTTG
1 TTTACGCTCGCCAGCTTATACTTATGCG
* **
1237515 TTTACGCTCGCCAGC-T-TGCAAAT--G
1 TTTACGCTCGCCAGCTTATACTTATGCG
** * * *
1237539 TTTACGCTCTTCAGCTTATTCTTCTGCT
1 TTTACGCTCGCCAGCTTATACTTATGCG
* * *
1237567 TTTACGCTAGCTAGCTTATACTTATACG
1 TTTACGCTCGCCAGCTTATACTTATGCG
* * *
1237595 TTTACGCTCGTCAACTTATTA-TTATGCA
1 TTTACGCTCGCCAGCTTA-TACTTATGCG
* *
1237623 TTTACGCTCGCCATCTTATACTTATGTG
1 TTTACGCTCGCCAGCTTATACTTATGCG
*
1237651 TTTACACTCGCCAG
1 TTTACGCTCGCCAG
1237665 GTTGCACACG
Statistics
Matches: 225, Mismatches: 51, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
24 25 0.11
25 2 0.01
26 19 0.08
27 4 0.02
28 173 0.77
29 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (28 bp):
TTTACGCTCGCCAGCTTATACTTATGCG
Found at i:1237501 original size:24 final size:24
Alignment explanation
Indices: 1237474--1237555 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 24
1237464 TTATGCTCAC
*
1237474 CAGCTTGCATATGTTTACACTCGT
1 CAGCTTGCATATGTTTACGCTCGT
* *
1237498 CAGCTTATTCATATTTGTTTACGCTCGC
1 CAGC-T-TGCATA--TGTTTACGCTCGT
* *
1237526 CAGCTTGCAAATGTTTACGCTCTT
1 CAGCTTGCATATGTTTACGCTCGT
1237550 CAGCTT
1 CAGCTT
1237556 ATTCTTCTGC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 21 0.45
25 1 0.02
26 9 0.19
27 1 0.02
28 15 0.32
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.39
Consensus pattern (24 bp):
CAGCTTGCATATGTTTACGCTCGT
Found at i:1237687 original size:188 final size:188
Alignment explanation
Indices: 1237351--1237695 Score: 451
Period size: 188 Copynumber: 1.8 Consensus size: 188
1237341 TTAATACGCA
* * *
1237351 TTTACGCTCGCCATCTTATACTTATGCGTTTACGCTCGTTAGCTTATACTTAAGCGTTTACGCTC
1 TTTACGCTCGCCAGCTTATACTTATGCGTTTACGCTAGCTAGCTTATACTTAAGCGTTTACGCTC
* * * **
1237416 GCCAGCTTATACTTATGCGTTTACGCTCGCTAGCTTATACTTATGCATTTATGCTCACCAGCTTG
66 GCCAACTTATACTTATGCATTTACGCTCGCCAGCTTATACTTATGCATTTACACTCACCAGCTTG
* *
1237481 CATATGTTTACACTCGTCAGCTTATTCATATTTGTTTACGCTCGCCAGCTTGCAAATG
131 CACACGTTTACACTCGTCAGCTTATTCATATTTGTTTACGCTCGCCAGCTTGCAAATG
** * * *
1237539 TTTACGCTCTTCAGCTTATTCTTCTGCTTTTACGCTAGCTAGCTTATACTTATA-CGTTTACGCT
1 TTTACGCTCGCCAGCTTATACTTATGCGTTTACGCTAGCTAGCTTATACTTA-AGCGTTTACGCT
* * ** * *
1237603 CGTCAACTTATTA-TTATGCATTTACGCTCGCCATCTTATACTTATGTGTTTACACTCGCCAGGT
65 CGCCAACTTA-TACTTATGCATTTACGCTCGCCAGCTTATACTTATGCATTTACACTCACCAGCT
**
1237667 TGCACACGTTTATGCTCGTCAGCTTATTC
129 TGCACACGTTTACACTCGTCAGCTTATTC
1237696 TTATGCATTT
Statistics
Matches: 132, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
188 129 0.98
189 3 0.02
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.40
Consensus pattern (188 bp):
TTTACGCTCGCCAGCTTATACTTATGCGTTTACGCTAGCTAGCTTATACTTAAGCGTTTACGCTC
GCCAACTTATACTTATGCATTTACGCTCGCCAGCTTATACTTATGCATTTACACTCACCAGCTTG
CACACGTTTACACTCGTCAGCTTATTCATATTTGTTTACGCTCGCCAGCTTGCAAATG
Found at i:1243383 original size:3 final size:3
Alignment explanation
Indices: 1243375--1243413 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1243365 CTGGGCAACG
*
1243375 TCT TCT TCT TTT TCT TCT TCT T-T TCT CTCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT
1243414 GTCTCTATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:1243395 original size:15 final size:16
Alignment explanation
Indices: 1243375--1243419 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1243365 CTGGGCAACG
*
1243375 TCTTCTTCTT-TTTCT
1 TCTTCTTCTTCTCTCT
1243390 TCTTCTT-TTCTCTCT
1 TCTTCTTCTTCTCTCT
1243405 TCTTCTTCTGTCTCT
1 TCTTCTTCT-TCTCT
1243420 ATACCCACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 18 0.69
16 1 0.04
17 5 0.19
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (16 bp):
TCTTCTTCTTCTCTCT
Found at i:1248921 original size:54 final size:54
Alignment explanation
Indices: 1248839--1248944 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
1248829 CTGCGGTGAC
1248839 ATTGCAATTAGCAGATAGATCTCAAGCACAACCGGAGGGACAAATCAAAGACAT
1 ATTGCAATTAGCAGATAGATCTCAAGCACAACCGGAGGGACAAATCAAAGACAT
* *
1248893 ATTGCAATTAGCGGATAGATCTCTAGCACAACCGGAGGGACAAATCAAAGAC
1 ATTGCAATTAGCAGATAGATCTCAAGCACAACCGGAGGGACAAATCAAAGAC
1248945 GTTCTTGTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.17
Consensus pattern (54 bp):
ATTGCAATTAGCAGATAGATCTCAAGCACAACCGGAGGGACAAATCAAAGACAT
Found at i:1272840 original size:28 final size:28
Alignment explanation
Indices: 1272772--1273081 Score: 108
Period size: 28 Copynumber: 11.5 Consensus size: 28
1272762 ATACGCGTTT
*
1272772 ACGCTTGCCAGCTTATACTTATGCATTC
1 ACGCTCGCCAGCTTATACTTATGCATTC
* * *
1272800 ACGTTCGCCAGCTTATAGTTATGCATTT
1 ACGCTCGCCAGCTTATACTTATGCATTC
* * * ** *
1272828 ATGCTCTCTAGCTTGCAC--A--CATTT
1 ACGCTCGCCAGCTTATACTTATGCATTC
** * * * * *
1272852 ACGCTCGTTAGATTATTCATATACATTT
1 ACGCTCGCCAGCTTATACTTATGCATTC
* * * *
1272880 ACGCTCGCCAACTTATATTTATGCGTTT
1 ACGCTCGCCAGCTTATACTTATGCATTC
* * * * *
1272908 ACACTCGCCAAC-T-TGC--ATTCATTT
1 ACGCTCGCCAGCTTATACTTATGCATTC
* * * *
1272932 ACGCTCGTCAACTTATTCTTATG-AGTTT
1 ACGCTCGCCAGCTTATACTTATGCA-TTC
* * *
1272960 ACACTCGCCAGCTTATACTTATGCGTTT
1 ACGCTCGCCAGCTTATACTTATGCATTC
*
1272988 ACGCTCGCCAGCTTGA-AC--ATG--TTT
1 ACGCTCGCCAGCTT-ATACTTATGCATTC
* * * * *
1273012 ATGCTCGTCAGCTTATTCTTATGCGTTT
1 ACGCTCGCCAGCTTATACTTATGCATTC
* * *
1273040 ACGCTCACCAGCTTATACTTATGCGTTT
1 ACGCTCGCCAGCTTATACTTATGCATTC
**
1273068 ATACTCGCCAGCTT
1 ACGCTCGCCAGCTT
1273082 GCACATGTTT
Statistics
Matches: 214, Mismatches: 52, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
23 1 0.00
24 48 0.22
25 1 0.00
26 11 0.05
27 2 0.01
28 150 0.70
29 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.38
Consensus pattern (28 bp):
ACGCTCGCCAGCTTATACTTATGCATTC
Found at i:1272902 original size:80 final size:80
Alignment explanation
Indices: 1272769--1273133 Score: 340
Period size: 80 Copynumber: 4.6 Consensus size: 80
1272759 TTAATACGCG
* * * * * * * * * **
1272769 TTTACGCTTGCCAGCTTATACTTATGCATTCACGTTCGCCAGCTTATAGTTATGCATTTATGCTC
1 TTTACGCTCGTCAGATTATTCTTATACATTTACGCTCGCCAGCTTATACTTATGCGTTTACACTC
* *
1272834 TCTAGCTTGCACACA
66 GCCAGCTTGCACACA
* * * *
1272849 TTTACGCTCGTTAGATTATTCATATACATTTACGCTCGCCAACTTATATTTATGCGTTTACACTC
1 TTTACGCTCGTCAGATTATTCTTATACATTTACGCTCGCCAGCTTATACTTATGCGTTTACACTC
* **
1272914 GCCAACTTGCATTCA
66 GCCAGCTTGCACACA
* * *
1272929 TTTACGCTCGTCA-ACTTATTCTTATGA-GTTTACACTCGCCAGCTTATACTTATGCGTTTACGC
1 TTTACGCTCGTCAGA-TTATTCTTAT-ACATTTACGCTCGCCAGCTTATACTTATGCGTTTACAC
* **
1272992 TCGCCAGCTTGAACATG
64 TCGCCAGCTTGCACACA
* * * * * *
1273009 TTTATGCTCGTCAGCTTATTCTTATGCGTTTACGCTCACCAGCTTATACTTATGCGTTTATACTC
1 TTTACGCTCGTCAGATTATTCTTATACATTTACGCTCGCCAGCTTATACTTATGCGTTTACACTC
**
1273074 GCCAGCTTGCACATG
66 GCCAGCTTGCACACA
* * * *
1273089 TTTACGCTCGTCA-ACTTATTCTTATGCGTTTACGCTTGCTAGCTT
1 TTTACGCTCGTCAGA-TTATTCTTATACATTTACGCTCGCCAGCTT
1273134 GCACACATTT
Statistics
Matches: 235, Mismatches: 45, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.00
80 233 0.99
81 1 0.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.39
Consensus pattern (80 bp):
TTTACGCTCGTCAGATTATTCTTATACATTTACGCTCGCCAGCTTATACTTATGCGTTTACACTC
GCCAGCTTGCACACA
Found at i:1273064 original size:160 final size:159
Alignment explanation
Indices: 1272804--1273121 Score: 422
Period size: 160 Copynumber: 2.0 Consensus size: 159
1272794 GCATTCACGT
* * * * * *
1272804 TCGCCAGCTTATAGTTATGCATTTATGCTCTCTAGCTTGCACACATTTACGCTCGTTAGATTATT
1 TCGCCAGCTTATACTTATGCATTTACGCTCGCCAGCTTGAACACATTTACGCTCGTCAGATTATT
* *
1272869 CATATACATTTACGCTCGCCAACTTATATTTATGCGTTTACACTCGCCAACTTGCATTCA-TTTA
66 CATATACATTTACGCTCACCAACTTATACTTATGCGTTTACACTCGCCAACTTGCA--CAGTTTA
1272933 CGCTCGTCAACTTATTCTTATGAGTTTACAC
129 CGCTCGTCAACTTATTCTTATGAGTTTACAC
* ** * *
1272964 TCGCCAGCTTATACTTATGCGTTTACGCTCGCCAGCTTGAACATGTTTATGCTCGTCAGCTTATT
1 TCGCCAGCTTATACTTATGCATTTACGCTCGCCAGCTTGAACACATTTACGCTCGTCAGATTATT
* * * * * *
1273029 CTTATGCGTTTACGCTCACCAGCTTATACTTATGCGTTTATACTCGCCAGCTTGCACATGTTTAC
66 CATATACATTTACGCTCACCAACTTATACTTATGCGTTTACACTCGCCAACTTGCACA-GTTTAC
*
1273094 GCTCGTCAACTTATTCTTATGCGTTTAC
130 GCTCGTCAACTTATTCTTATGAGTTTAC
1273122 GCTTGCTAGC
Statistics
Matches: 136, Mismatches: 20, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
158 2 0.01
160 134 0.99
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (159 bp):
TCGCCAGCTTATACTTATGCATTTACGCTCGCCAGCTTGAACACATTTACGCTCGTCAGATTATT
CATATACATTTACGCTCACCAACTTATACTTATGCGTTTACACTCGCCAACTTGCACAGTTTACG
CTCGTCAACTTATTCTTATGAGTTTACAC
Found at i:1273092 original size:52 final size:52
Alignment explanation
Indices: 1272877--1273138 Score: 151
Period size: 52 Copynumber: 5.0 Consensus size: 52
1272867 TTCATATACA
* * *
1272877 TTTACGCTCGCCAACTTATATTTATGCGTTTACACTCGCCAACTTGCATTCA--
1 TTTACGCTCACCAACTTATACTTATGCGTTTACACTCGCCAGCTTGCA--CATG
** * * **
1272929 TTTACGCTCGTCAACTTATTCTTATGAGTTTACACTCGCCAGCTTATACTTATGCG
1 TTTACGCTCACCAACTTATACTTATGCGTTTACACTCGCCAGCTTGCAC--AT--G
* * ** * * **
1272985 TTTACGCTCGCCAGCTTGA-AC--AT--GTTTATGCTCGTCAGCTTATTCTTATGCG
1 TTTACGCTCACCAACTT-ATACTTATGCGTTTACACTCGCCAGC-T-TGCACAT--G
* *
1273037 TTTACGCTCACCAGCTTATACTTATGCGTTTATACTCGCCAGCTTGCACATG
1 TTTACGCTCACCAACTTATACTTATGCGTTTACACTCGCCAGCTTGCACATG
** * * * *
1273089 TTTACGCTCGTCAACTTATTCTTATGCGTTTACGCTTGCTAGCTTGCACA
1 TTTACGCTCACCAACTTATACTTATGCGTTTACACTCGCCAGCTTGCACA
1273139 CATTTACCAA
Statistics
Matches: 165, Mismatches: 31, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 121 0.73
53 1 0.01
54 9 0.05
55 1 0.01
56 30 0.18
57 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.38
Consensus pattern (52 bp):
TTTACGCTCACCAACTTATACTTATGCGTTTACACTCGCCAGCTTGCACATG
Done.