Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014610.1 Kokia drynarioides strain JFW-HI SEQ_129649, 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: 51404
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1770 original size:51 final size:51
Alignment explanation
Indices: 1651--1885 Score: 271
Period size: 51 Copynumber: 4.6 Consensus size: 51
1641 TTTCATTTAA
* * *
1651 TACTCACGATGACA-TATAGTCATCGGACCTCTTATTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * *
1704 TACTCACGATGACACTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * * *
1755 TATTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTTATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * * * *
1806 TACTCATGATGACACTTAATCATCGAACCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
1857 TACT--C-ATGACTCTTAGTCATCGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
1886 TCGTTTATAT
Statistics
Matches: 157, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
48 21 0.13
51 98 0.62
52 10 0.06
53 27 0.17
54 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:12417 original size:17 final size:17
Alignment explanation
Indices: 12362--12425 Score: 85
Period size: 17 Copynumber: 3.7 Consensus size: 17
12352 TTAATTTGAG
12362 TTTAAATTTATTGTAAA
1 TTTAAATTTATTGTAAA
* *
12379 TTTAAGACTTATT-TGAAG
1 TTTAA-ATTTATTGT-AAA
12397 TTTAAATTTATTGTAAA
1 TTTAAATTTATTGTAAA
12414 TTTAAATTTATT
1 TTTAAATTTATT
12426 TTGAAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 26 0.65
18 14 0.35
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTGTAAA
Found at i:12430 original size:35 final size:35
Alignment explanation
Indices: 12355--12426 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
12345 ATTTTAATTA
12355 ATTTG-AGTTTAAATTTATTGTAAATTTAAGACTT
1 ATTTGAAGTTTAAATTTATTGTAAATTTAAGACTT
*
12389 ATTTGAAGTTTAAATTTATTGTAAATTTAA-ATTT
1 ATTTGAAGTTTAAATTTATTGTAAATTTAAGACTT
12423 ATTT
1 ATTT
12427 TGAAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 12 0.33
35 24 0.67
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (35 bp):
ATTTGAAGTTTAAATTTATTGTAAATTTAAGACTT
Found at i:12845 original size:12 final size:12
Alignment explanation
Indices: 12828--12893 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
12818 AATGAATCAG
12828 TAATAATAATAT
1 TAATAATAATAT
*
12840 TAATAATAATAA
1 TAATAATAATAT
* *
12852 CAATAATAGTAAT
1 TAATAATAAT-AT
12865 TAATAAT-AT-T
1 TAATAATAATAT
* *
12875 TGATAATAACAT
1 TAATAATAATAT
12887 TAATAAT
1 TAATAAT
12894 CAAAGTTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
10 7 0.17
11 1 0.02
12 27 0.64
13 7 0.17
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:12883 original size:3 final size:3
Alignment explanation
Indices: 12828--12872 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
12818 AATGAATCAG
* * *
12828 TAA TAA TAA TAT TAA TAA TAA TAA CAA TAA TAG TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
12873 TTTGATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:14140 original size:58 final size:58
Alignment explanation
Indices: 14037--14554 Score: 484
Period size: 58 Copynumber: 8.9 Consensus size: 58
14027 TACCCTCATG
* * *
14037 CTTTCAAAAATTCCATTTTGACC-CTTATTTTTCC-AAAATTACCATTTTACCCCTAAA
1 CTTTCCAAAATTCCATTTTTACCTC-AATTTTTCCAAAAATTACCATTTTACCCCTAAA
* ** * *
14094 CTTTGCACCATTCTATTTTTACCTCAATTTTTCCAAAAATTACCATTTTACCCCTGAA
1 CTTTCCAAAATTCCATTTTTACCTCAATTTTTCCAAAAATTACCATTTTACCCCTAAA
* *
14152 CTTTCCAAAATTCCATTTTTAACCACGATTTTTCCAAAAATTACCATTTTA-CCCTCAAA
1 CTTTCCAAAATTCCATTTTT-ACCTCAATTTTTCCAAAAATTACCATTTTACCCCT-AAA
** * *
14211 CTTTCCAAAATTGTATTTTTAACCCTTAA-TTTTCCAAAAATTACCATTTTATCCCTAAA
1 CTTTCCAAAATTCCATTTTT-A-CCTCAATTTTTCCAAAAATTACCATTTTACCCCTAAA
* * * * * **
14270 CATTCAAAAATTCCATTTTTTACCACAAATTTTCCAAAAATTTCCATTTTACCCCCGAA
1 CTTTCCAAAATTCCA-TTTTTACCTCAATTTTTCCAAAAATTACCATTTTACCCCTAAA
* * * ***
14329 C-TTCACAAAATTCAAATTTAACC-CTGGTTTTCCAAAAATTACCATTTTACCCCTAAA
1 CTTTC-CAAAATTCCATTTTTACCTCAATTTTTCCAAAAATTACCATTTTACCCCTAAA
* **
14386 CTTTCCAAAATTACC-TTTTTACC-CTAATTTTTTCAAAAATTACCATTTTACCCCCGAA
1 CTTTCCAAAATT-CCATTTTTACCTC-AATTTTTCCAAAAATTACCATTTTACCCCTAAA
* * * * *
14444 C-TCCCAAAAATTCCATTTTGACCTCGATTTTTCCAAAAGTTACCATTTTA-CCCTCGAA
1 CTTTCC-AAAATTCCATTTTTACCTCAATTTTTCCAAAAATTACCATTTTACCCCT-AAA
* * ** *
14502 C-TTCCTAAAATTCCATTTTGACCCCAATTTTT-GTAAAATTAACATTTTACCCC
1 CTTTCC-AAAATTCCATTTTTACCTCAATTTTTCCAAAAATTACCATTTTACCCC
14555 CGGATGTCTA
Statistics
Matches: 381, Mismatches: 63, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
57 89 0.23
58 157 0.41
59 123 0.32
60 12 0.03
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (58 bp):
CTTTCCAAAATTCCATTTTTACCTCAATTTTTCCAAAAATTACCATTTTACCCCTAAA
Found at i:14596 original size:29 final size:28
Alignment explanation
Indices: 14013--14609 Score: 169
Period size: 29 Copynumber: 20.5 Consensus size: 28
14003 CAAAAATTCT
* * *
14013 AAAAATTACATTTTTACCCTCATGCTTTC
1 AAAAATTACATTTTAACCCTGA-ACTTTC
* * * **
14042 AAAAATTCCATTTTGACCCTTATTTTTC
1 AAAAATTACATTTTAACCCTGAACTTTC
* * *
14070 CAAAATTACCATTTTACCCCTAAACTTTGC
1 AAAAATTA-CATTTTAACCCTGAACTTT-C
** * * *
14100 -ACCATT-CTATTTTTA-CCTCAATTTTTCC
1 AAAAATTAC-ATTTTAACCCTGAA-CTTT-C
*
14128 AAAAATTACCATTTTACCCCTGAACTTTC
1 AAAAATTA-CATTTTAACCCTGAACTTTC
* * **
14157 CAAAATTCCATTTTTAACCAC-GATTTTTCC
1 AAAAATTACA-TTTTAACC-CTGAACTTT-C
*
14187 AAAAATTACCATTTT-ACCCTCAAACTTTC
1 AAAAATTA-CATTTTAACCCT-GAACTTTC
* ** * *
14216 CAAAATTGTATTTTTAACCCTTAATTTTCC
1 AAAAATTACA-TTTTAACCCTGAACTTT-C
* * *
14246 AAAAATTACCATTTTATCCCTAAACATTC
1 AAAAATTA-CATTTTAACCCTGAACTTTC
* * * *
14275 AAAAATTCCATTTTTTACCAC-AAATTTTCC
1 AAAAATTACA-TTTTAACC-CTGAACTTT-C
* * *
14305 AAAAATTTCCATTTTACCCCCGAAC-TTC
1 AAAAA-TTACATTTTAACCCTGAACTTTC
* **
14333 ACAAAATT-CAAATTTAACCCTG-GTTTTCC
1 A-AAAATTAC-ATTTTAACCCTGAACTTT-C
* *
14362 AAAAATTACCATTTTACCCCTAAACTTTC
1 AAAAATTA-CATTTTAACCCTGAACTTTC
* * * *
14391 CAAAATTACCTTTTTACCCT-AATTTTTTC
1 AAAAATTACATTTTAACCCTGAA--CTTTC
* * **
14420 AAAAATTACCATTTTACCCCCGAACTCCC
1 AAAAATTA-CATTTTAACCCTGAACTTTC
* * **
14449 AAAAATTCCATTTTGA-CCTCGATTTTTCC
1 AAAAATTACATTTTAACCCT-GAACTTT-C
* *
14478 AAAAGTTACCATTTT-ACCCTCGAACTTCC
1 AAAAATTA-CATTTTAACCCT-GAACTTTC
* * * * * *
14507 TAAAATTCCATTTTGACCC-CAATTTTTG
1 AAAAATTACATTTTAACCCTGAA-CTTTC
* * * * *
14535 TAAAATTAACATTTTACCCCCGGA-TGTC
1 AAAAATT-ACATTTTAACCCTGAACTTTC
14563 TAAAAATTACATTTTAAACCCTGAACTTTC
1 -AAAAATTACATTTT-AACCCTGAACTTTC
14593 AAAAAATTATCATTTTA
1 -AAAAATTA-CATTTTA
14610 TCCTCGAATG
Statistics
Matches: 410, Mismatches: 112, Indels: 91
0.67 0.18 0.15
Matches are distributed among these distances:
27 13 0.03
28 88 0.21
29 183 0.45
30 104 0.25
31 22 0.05
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAAATTACATTTTAACCCTGAACTTTC
Found at i:14626 original size:59 final size:59
Alignment explanation
Indices: 14536--14671 Score: 164
Period size: 59 Copynumber: 2.3 Consensus size: 59
14526 CAATTTTTGT
* * *
14536 AAAATTAACATTTTACCCCCGGATGTCTAAAAATTACATTTTAAACCCTGAACTTTCAA
1 AAAATTAACATTTTACCCCCGAATGTATAAAAATTACATTTTAAACCATGAACTTTCAA
* * * * ** **
14595 AAAATTATCATTTTATCCTCGAATGTATAAAAATTCCATTTTCGACCATGAACTTTCTC
1 AAAATTAACATTTTACCCCCGAATGTATAAAAATTACATTTTAAACCATGAACTTTCAA
*
14654 AAAATTACCATTTTACCC
1 AAAATTAACATTTTACCC
14672 ACAAGTGTCG
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAATTAACATTTTACCCCCGAATGTATAAAAATTACATTTTAAACCATGAACTTTCAA
Found at i:21784 original size:18 final size:19
Alignment explanation
Indices: 21758--21800 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
21748 AAATGTGAAG
21758 GAAAAGAAGAAAGAGAT-A
1 GAAAAGAAGAAAGAGATGA
* **
21776 GAAAGGAAGCGAGAGATGA
1 GAAAAGAAGAAAGAGATGA
21795 GAAAAG
1 GAAAAG
21801 CACAACTGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.58, C:0.02, G:0.35, T:0.05
Consensus pattern (19 bp):
GAAAAGAAGAAAGAGATGA
Found at i:25271 original size:18 final size:18
Alignment explanation
Indices: 25248--25282 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25238 CATCTAACAC
*
25248 TGTTCCTTGTAATTATTG
1 TGTTCCTTGTAAATATTG
25266 TGTTCCTTGTAAATATT
1 TGTTCCTTGTAAATATT
25283 CGGCAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.14, T:0.54
Consensus pattern (18 bp):
TGTTCCTTGTAAATATTG
Found at i:25885 original size:98 final size:97
Alignment explanation
Indices: 25697--26209 Score: 501
Period size: 98 Copynumber: 5.3 Consensus size: 97
25687 CTACAGGTCT
* * * * *
25697 CAGTACAACGAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCC-AGTA-C-CATGAAG
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTAGTACCTCA-GAAC
* *
25758 ATATAGAGGGAAAGG-TTTAAGTCGCAACGGCGAA-C
64 AT-GA-AGGG-AAGGATTTAAGCCGCAACGGCGAATC
* *
25793 CGTGTACCTCAGAAG-CATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGA
1 C-AGTACCAC-GAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGA-A
*
25857 CATGAAGGGAAGGATTTAAGCCGTAACGGCGAATC
63 CATGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
* *
25892 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCTCAATGACGAACCTAGTACCTCAGAAACA
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAG-AACA
25957 TGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
65 TGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
* ** * *
25990 CAGTA-C-CGAAGACA-AGAGGAGAAAGGTTTAAGTCGCAACAGCAAACCTTGTACCTCAGAAGC
1 CAGTACCACGAAGACATAAAGG-GAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAA-C
* * * *
26052 ATAAAGGGAAAGATTTAAGCCGTAAAGGCGAATC
64 ATGAAGGGAAGGATTTAAGCCGCAACGGCGAATC
** ** *
26086 CAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCATAATGGCGAACCTTA-TAACTCAGAAGC
1 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACC-TAGTACCTCAGAA-C
* * **
26150 ATGAAAGGGAAAGATTT-AGCCACAACGTTGAATC
64 ATG-AAGGGAAGGATTTAAGCCGCAACGGCGAATC
** * * *
26184 TGGTACCATGAAAACACAAAGGGAAA
1 CAGTACCACGAAGACATAAAGGGAAA
26210 TATTAAAGCA
Statistics
Matches: 353, Mismatches: 46, Indels: 34
0.82 0.11 0.08
Matches are distributed among these distances:
95 6 0.02
96 77 0.22
97 17 0.05
98 224 0.63
99 24 0.07
100 5 0.01
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.17
Consensus pattern (97 bp):
CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAACAT
GAAGGGAAGGATTTAAGCCGCAACGGCGAATC
Found at i:25980 original size:147 final size:147
Alignment explanation
Indices: 25709--26070 Score: 416
Period size: 147 Copynumber: 2.5 Consensus size: 147
25699 GTACAACGAA
* * * *
25709 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCATGAAGATATAGAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAAGGT
* * * *
25774 TTAAGTCGCAACGGCGAACCGTGTACCTCAGAAGCATAAAGGGAAAGGTTTAAGTCGCAATGGCG
66 TTAAGTCGCAACGACGAACCGTGTACCTCAGAAACATAAAGGGAAAGGTTTAAGCCGCAACGGCG
25839 AA-CCTAGTACCTCAGAG
131 AATCC-AGTACCTCAGAG
* *
25856 ACATGAAGGGAAGGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAAGGT
* * *
25921 TTAAGTCTCAATGACGAACC-TAGTACCTCAGAAACATGAAGGG-AAGGATTTAAGCCGCAACGG
66 TTAAGTCGCAACGACGAACCGT-GTACCTCAGAAACATAAAGGGAAAGG-TTTAAGCCGCAACGG
*
25984 CGAATCCAGTACC-GA-AG
129 CGAATCCAGTACCTCAGAG
* * * * * * *
26001 ACAAG-AGGAGAAAGGTTTAAGTCGCAACAGC-AAACCTTGTACCTCAGAAG-CATAAAGGGAAA
1 ACATGAAGG-GAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAGACATAAAGGGAAA
*
26063 GATTTAAG
63 GGTTTAAG
26071 CCGTAAAGGC
Statistics
Matches: 185, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
144 7 0.04
145 48 0.26
146 10 0.05
147 118 0.64
148 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.17
Consensus pattern (147 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAAGGT
TTAAGTCGCAACGACGAACCGTGTACCTCAGAAACATAAAGGGAAAGGTTTAAGCCGCAACGGCG
AATCCAGTACCTCAGAG
Found at i:26047 original size:194 final size:194
Alignment explanation
Indices: 25816--26176 Score: 532
Period size: 194 Copynumber: 1.9 Consensus size: 194
25806 AGCATAAAGG
** * * *
25816 GAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAG-AGACATGAAGGGAAGGATTTAAGCCG
1 GAAAGGTTTAAGTCGCAACAGCAAACCTAGTACCTCAGAAG-CATAAAGGGAAAGATTTAAGCCG
* *
25880 TAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTC-TCAATGACGAACC-TA
65 TAAAGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCAT-AATGACGAACCTTA
* * *
25943 GTACCTCAGAAACATG-AAGGGAAGGATTTAAGCCGCAACGGCGAATCCAGTACCGAAGACAAGA
129 -TAACTCAGAAACATGAAAGGGAAAGATTT-AGCCACAACGGCGAATCCAGTACCGAAGACAAGA
26007 GGA
192 GGA
*
26010 GAAAGGTTTAAGTCGCAACAGCAAACCTTGTACCTCAGAAGCATAAAGGGAAAGATTTAAGCCGT
1 GAAAGGTTTAAGTCGCAACAGCAAACCTAGTACCTCAGAAGCATAAAGGGAAAGATTTAAGCCGT
* *
26075 AAAGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCATAATGGCGAACCTTATA
66 AAAGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCATAATGACGAACCTTATA
*
26140 ACTCAGAAGCATGAAAGGGAAAGATTTAGCCACAACG
131 ACTCAGAAACATGAAAGGGAAAGATTTAGCCACAACG
26177 TTGAATCTGG
Statistics
Matches: 149, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
194 132 0.89
195 17 0.11
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (194 bp):
GAAAGGTTTAAGTCGCAACAGCAAACCTAGTACCTCAGAAGCATAAAGGGAAAGATTTAAGCCGT
AAAGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCATAATGACGAACCTTATA
ACTCAGAAACATGAAAGGGAAAGATTTAGCCACAACGGCGAATCCAGTACCGAAGACAAGAGGA
Found at i:26132 original size:49 final size:49
Alignment explanation
Indices: 25697--26121 Score: 367
Period size: 49 Copynumber: 8.7 Consensus size: 49
25687 CTACAGGTCT
* * * *
25697 CAGTACAACGAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
1 CAGTACCACGAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATC
* *
25745 CAGTACCATGAAGATAT-AGAGGGAAAGGTTTAAGTCGCAACGGCGAA-C
1 CAGTACCACGAAGACATGA-AGGGAAAGGTTTAAGTCGCAACGGCGAATC
* * * *
25793 CGTGTACCTCAGAAG-CATAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-C
1 C-AGTACCAC-GAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATC
* * *
25842 CTAGTACCTC-AGAGACATGAAGGG-AAGGATTTAAGCCGTAACGGCGAATC
1 C-AGTACCACGA-AGACATGAAGGGAAAGG-TTTAAGTCGCAACGGCGAATC
* * * *
25892 CAGTACCACGAAGACATAAAGGGAAAGGTTTAAGTCTCAATGACGAA-C
1 CAGTACCACGAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATC
* *
25940 CTAGTACCTCAGAA-ACATGAAGGG-AAGGATTTAAGCCGCAACGGCGAATC
1 C-AGTACCAC-GAAGACATGAAGGGAAAGG-TTTAAGTCGCAACGGCGAATC
* * *
25990 CAGTA-C-CGAAGACAAG-AGGAGAAAGGTTTAAGTCGCAACAGC-AAAC
1 CAGTACCACGAAGACATGAAGG-GAAAGGTTTAAGTCGCAACGGCGAATC
* * * * * * *
26036 CTTGTACCTCAGAAG-CATAAAGGGAAAGATTTAAGCCGTAAAGGCGAATC
1 C-AGTACCAC-GAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATC
*
26086 CAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTC
1 CAGTACCACGAAGACATGAAGGGAAAGGTTTAAGTC
26122 ATAATGGCGA
Statistics
Matches: 303, Mismatches: 49, Indels: 49
0.76 0.12 0.12
Matches are distributed among these distances:
46 10 0.03
47 24 0.08
48 35 0.12
49 206 0.68
50 28 0.09
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.16
Consensus pattern (49 bp):
CAGTACCACGAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATC
Found at i:26667 original size:35 final size:34
Alignment explanation
Indices: 26628--26694 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
26618 AATTCATTTA
26628 AGTTTAAATTTATTGTAAATTTAAGACTTATTTGG
1 AGTTTAAATTTATTGTAAATTTAA-ACTTATTTGG
*
26663 AGTTTAAATTTATTGTAAATTTAAATTTATTT
1 AGTTTAAATTTATTGTAAATTTAAACTTATTT
26695 TGAAATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 7 0.23
35 24 0.77
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.52
Consensus pattern (34 bp):
AGTTTAAATTTATTGTAAATTTAAACTTATTTGG
Found at i:26685 original size:17 final size:17
Alignment explanation
Indices: 26630--26693 Score: 76
Period size: 17 Copynumber: 3.7 Consensus size: 17
26620 TTCATTTAAG
26630 TTTAAATTTATTGTAAA
1 TTTAAATTTATTGTAAA
* * *
26647 TTTAAGACTTATT-TGGAG
1 TTTAA-ATTTATTGT-AAA
26665 TTTAAATTTATTGTAAA
1 TTTAAATTTATTGTAAA
26682 TTTAAATTTATT
1 TTTAAATTTATT
26694 TTGAAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 25 0.66
18 13 0.34
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTGTAAA
Found at i:28614 original size:30 final size:27
Alignment explanation
Indices: 28580--28649 Score: 68
Period size: 30 Copynumber: 2.5 Consensus size: 27
28570 TTGACCCCTA
28580 AACTTTTCCAAAACCGCATTTTTAACCTT
1 AACTTTTCCAAAACCGCATTTTT-ACC-T
** **
28609 GAACTTTTTGAAAATTGCATTTTTACCT
1 -AACTTTTCCAAAACCGCATTTTTACCT
*
28637 AATTTTTCCAAAA
1 AACTTTTCCAAAA
28650 AATACCATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
27 10 0.30
28 1 0.03
29 3 0.09
30 19 0.58
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (27 bp):
AACTTTTCCAAAACCGCATTTTTACCT
Found at i:28709 original size:59 final size:58
Alignment explanation
Indices: 28619--29158 Score: 456
Period size: 59 Copynumber: 9.2 Consensus size: 58
28609 GAACTTTTTG
* * *
28619 AAAATTGCATTTTT-ACCTAATTTTTCCAAAAAATACCATTTTACCCTTGAACTTTCC
1 AAAATTCCATTTTTGACCTAATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTCC
* * *
28676 AAAATTCCATTTTTGATCCTAATTTTTCAAAAAATTACCATTTTACCCTCAAACTATCC
1 AAAATTCCATTTTTGA-CCTAATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTCC
* * **
28735 AAAATTCTATTTTTGACCCCT-ATTTTTCCAAAAAATTACCATTTTACCCTTGAACTTTTT
1 AAAATTCCATTTTTGA--CCTAATTTTTCC-AAAAATTACCATTTTACCCTCGAACTTTCC
* * * *
28795 AAAATTCCATATTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCTCAAACTTTCT
1 AAAATTCCATTTTTGACCT-AATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTCC
* * * * * * *
28854 AAAATTCCATATATGACATTGATTTTTCTAAAAATTACCATTTTACCCTAGAAC-TCCC
1 AAAATTCCATTTTTGAC-CTAATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTCC
* *
28912 AAAAATTCCA-TTTTGACCCAGATTTTTCCAAAAGTTACCATTTTACCCTCGAAC-TTCC
1 -AAAATTCCATTTTTGACCTA-ATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTCC
* * * * *
28970 TAAAATTCCA-TTTTGACCCTAA-TTTTCCCAATATTACCATTTTACCCCCGAA-TGTCTA
1 -AAAATTCCATTTTTGA-CCTAATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTC-C
* * * ** * * * *
29028 AAAATTCCATTTTAAGCCCCAAACTTTCCAAAAATTACCATTTTATCCTCGGA-TGTCTA
1 AAAATTCCATTTT-TGACCTAATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTC-C
* * * * * *
29087 AAAATTCTATTTTTGACCTCGAA-CTTTCCCAAAACTACCATTTTGTCCC-C-AAGTTTCC
1 AAAATTCCATTTTTGACCT--AATTTTTCCAAAAATTACCATTTT-ACCCTCGAACTTTCC
29145 AAAATTACCATTTT
1 AAAATT-CCATTTT
29159 ACCCCCGGGT
Statistics
Matches: 399, Mismatches: 64, Indels: 38
0.80 0.13 0.08
Matches are distributed among these distances:
57 50 0.13
58 77 0.19
59 217 0.54
60 55 0.14
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTAATTTTTCCAAAAATTACCATTTTACCCTCGAACTTTCC
Found at i:29009 original size:29 final size:28
Alignment explanation
Indices: 28629--29016 Score: 131
Period size: 29 Copynumber: 13.3 Consensus size: 28
28619 AAAATTGCAT
* *
28629 TTTTA-CCTAATTTTTCCAAAAAATACCA
1 TTTTACCCTAA-TTTTCCCAAAATTACCA
*
28657 TTTTACCCTTGAACTTT-CCAAAATT-CCA
1 TTTTACCC-T-AATTTTCCCAAAATTACCA
* **
28685 TTTTTGATCCTAATTTTTCAAAAAATTACCA
1 -TTTT-ACCCTAA-TTTTCCCAAAATTACCA
* * *
28716 TTTTACCCTCAAACTAT-CCAAAATT-CTA
1 TTTTACCCT--AATTTTCCCAAAATTACCA
* *
28744 TTTTTGACCCCTATTTTTCCAAAAAATTACCA
1 -TTTT-A-CCCTAATTTTCC-CAAAATTACCA
*
28776 TTTTACCCTTGAACTTTT--TAAAATT-CCA
1 TTTTACCC-T-AA-TTTTCCCAAAATTACCA
* * *
28804 TATTTGACCTCGATTTTTCCAAAAATTACCA
1 T-TTT-ACC-CTAATTTTCCCAAAATTACCA
* *
28835 TTTTACCCTCAAACTTT-CTAAAATT-CCA
1 TTTTACCCT--AATTTTCCCAAAATTACCA
* ** * **
28863 TATATGACATTGATTTTTCTAAAAATTACCA
1 T-T-TTACCCT-AATTTTCCCAAAATTACCA
**
28894 TTTTACCCTAGA-ACTCCCAAAAATT-CCA
1 TTTTACCCTA-ATTTTCCC-AAAATTACCA
*
28922 TTTTGACCC-AGATTTTTCCAAAAGTTACCA
1 TTTT-ACCCTA-ATTTTCCCAAAA-TTACCA
* *
28952 TTTTACCCTCGAA-CTTCCTAAAATT-CCA
1 TTTTACCCT--AATTTTCCCAAAATTACCA
*
28980 TTTTGACCCTAATTTTCCCAATATTACCA
1 TTTT-ACCCTAATTTTCCCAAAATTACCA
29009 TTTTACCC
1 TTTTACCC
29017 CCGAATGTCT
Statistics
Matches: 265, Mismatches: 52, Indels: 86
0.66 0.13 0.21
Matches are distributed among these distances:
27 2 0.01
28 62 0.23
29 98 0.37
30 64 0.24
31 32 0.12
32 7 0.03
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (28 bp):
TTTTACCCTAATTTTCCCAAAATTACCA
Found at i:29164 original size:28 final size:27
Alignment explanation
Indices: 28936--29164 Score: 97
Period size: 29 Copynumber: 7.9 Consensus size: 27
28926 GACCCAGATT
*
28936 TTTCCAAAAGTTACCATTTTACCCTCGAA
1 TTTCCAAAA-TTACCATTTTACCC-CCAA
* *
28965 CTTCCTAAAATT-CCATTTTGA-CCCTAA
1 TTTCC-AAAATTACCATTTT-ACCCCCAA
*
28992 TTTTCCCAATATTACCATTTTACCCCCGAA
1 -TTT-CCAAAATTACCATTTTACCCCC-AA
* * *
29022 TGTCTAAAAATT-CCATTTTAAGCCCCAAA
1 TTTC-CAAAATTACCATTTT-A-CCCCCAA
* **
29051 CTTTCCAAAAATTACCATTTTATCCTCGGA
1 -TTTCC-AAAATTACCATTTTA-CCCCCAA
* * * * *
29081 TGTCTAAAAATT-CTATTTTTGACCTCGAA
1 TTTC-CAAAATTACCA-TTTT-ACCCCCAA
* **
29110 CTTTCCCAAAACTACCATTTTGTCCCCAA
1 -TTT-CCAAAATTACCATTTTACCCCCAA
29139 GTTTCCAAAATTACCATTTTACCCCC
1 -TTTCCAAAATTACCATTTTACCCCC
29165 GGGTATCCAA
Statistics
Matches: 150, Mismatches: 31, Indels: 39
0.68 0.14 0.18
Matches are distributed among these distances:
27 3 0.02
28 46 0.31
29 55 0.37
30 36 0.24
31 10 0.07
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.35
Consensus pattern (27 bp):
TTTCCAAAATTACCATTTTACCCCCAA
Found at i:29173 original size:28 final size:28
Alignment explanation
Indices: 29115--29176 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
29105 TCGAACTTTC
** *
29115 CCAAAACTACCATTTTGTCCCCAAGTTT
1 CCAAAACTACCATTTTACCCCCAAGTAT
* **
29143 CCAAAATTACCATTTTACCCCCGGGTAT
1 CCAAAACTACCATTTTACCCCCAAGTAT
29171 CCAAAA
1 CCAAAA
29177 ATCTCATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.27
Consensus pattern (28 bp):
CCAAAACTACCATTTTACCCCCAAGTAT
Found at i:32863 original size:51 final size:50
Alignment explanation
Indices: 32785--32950 Score: 215
Period size: 51 Copynumber: 3.3 Consensus size: 50
32775 ATAGTTTCGT
* * * * *
32785 TCATCGGACCTTTAATCCATCATGGATTCATTTACTCATGATGACACTTAG
1 TCATCGAACCTTTAAT-CGTAAAGGATTCATTTACTCACGATGACACTTAG
*
32836 TCATCGAACCTTTAATCTGTAAAGGATTCATTTACTCACGATAACACTTAG
1 TCATCGAACCTTTAATC-GTAAAGGATTCATTTACTCACGATGACACTTAG
* * *
32887 TCATCGAACCTTTAATCGATAAAGGATTCATTTACTTACGACGACTCTTAG
1 TCATCGAACCTTTAATCG-TAAAGGATTCATTTACTCACGATGACACTTAG
*
32938 TCATCGGACCTTT
1 TCATCGAACCTTT
32951 TCGTTTATAG
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
50 2 0.02
51 100 0.98
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (50 bp):
TCATCGAACCTTTAATCGTAAAGGATTCATTTACTCACGATGACACTTAG
Found at i:40626 original size:34 final size:34
Alignment explanation
Indices: 40588--40653 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
40578 CTGTAGTATA
*
40588 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
40622 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
40654 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:40627 original size:17 final size:17
Alignment explanation
Indices: 40596--40653 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
40586 TAATTGTCCC
* *
40596 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
40613 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
40630 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
40647 TGCATTT
1 TGCATTT
40654 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:44048 original size:33 final size:33
Alignment explanation
Indices: 44011--44446 Score: 387
Period size: 33 Copynumber: 13.2 Consensus size: 33
44001 GCATACACAT
* * *
44011 CCTCCCCATCAGCTTGTACCCCTCCTACATCAC
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
* *
44044 CCTCCCCA-CAAGCTTTTACCCC-TCAACAGCAC
1 CCTCCCCATC-AGCTTCTACCCCTTCAACATCAC
* * * * * * *
44076 CCTTCCCAACAGCGTGTACCCC-TCTAATAACAA
1 CCTCCCCATCAGCTTCTACCCCTTC-AACATCAC
* * * * *
44109 CTTCACCATCAACTGCTACACCTTCAACATCAC
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
* *
44142 CCTCCCCAAT-AGCTTCTATCCCTTCAACAACAC
1 CCTCCCC-ATCAGCTTCTACCCCTTCAACATCAC
* ** * * *
44175 CTTTACCATTAACTTCTACCTCTTCAACATCAC
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
* * *
44208 CCTCCCCAACAACTTCTACCCCTTTAACATCAC
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
* *
44241 CCTCCCCATCAGCTTCTACCCCTTCAACAACAG
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
* * *
44274 CTTCACCATCAACTTCTACCCCTTCAACATCAC
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
* * * * *
44307 CCTCCGCAACAACTTCTGCCCTTTCAACATCAC
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
*
44340 CCTCCTCATCAGCTTCTACCCCTTCAACATCAC
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
*** * * *
44373 CCTTCTTAAT-AACTTTTACCCTTTCAACATCAC
1 CC-TCCCCATCAGCTTCTACCCCTTCAACATCAC
*
44406 CCTCCCCATCAGCTTCTACCCCTTTAACATCAC
1 CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
44439 CCTCCCCA
1 CCTCCCCA
44447 ACATTCAATA
Statistics
Matches: 319, Mismatches: 76, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
32 33 0.10
33 277 0.87
34 9 0.03
ACGTcount: A:0.25, C:0.45, G:0.03, T:0.26
Consensus pattern (33 bp):
CCTCCCCATCAGCTTCTACCCCTTCAACATCAC
Found at i:44241 original size:99 final size:98
Alignment explanation
Indices: 44118--44446 Score: 430
Period size: 99 Copynumber: 3.3 Consensus size: 98
44108 ACTTCACCAT
* * * *
44118 CAACTGCTACACCTTCAACATCACCCTCCCCAAT-AGCTTCTATCCCTTCAACAACACCTTTACC
1 CAACTTCTACCCCTTTAACATCACCCTCCCC-ATCAGCTTCTACCCCTTCAACAACACCTTTACC
44182 ATTAACTTCTACCTCTTCAACATCACCCTCCCCAA
65 ATTAACTTCTACC-CTTCAACATCACCCTCCCCAA
* *
44217 CAACTTCTACCCCTTTAACATCACCCTCCCCATCAGCTTCTACCCCTTCAACAACAGCTTCACCA
1 CAACTTCTACCCCTTTAACATCACCCTCCCCATCAGCTTCTACCCCTTCAACAACACCTTTACCA
* *
44282 TCAACTTCTACCCCTTCAACATCACCCTCCGCAA
66 TTAACTTCTA-CCCTTCAACATCACCCTCCCCAA
* * * *
44316 CAACTTCT-GCCCTTTCAACATCACCCTCCTCATCAGCTTCTACCCCTTCAACATCACCCTT-CT
1 CAACTTCTACCCCTTT-AACATCACCCTCCCCATCAGCTTCTACCCCTTCAACAACACCTTTAC-
* * * *
44379 TAATAACTTTTACCCTTTCAACATCACCCTCCCCAT
64 CATTAACTTCTACCC-TTCAACATCACCCTCCCCAA
*
44415 CAGCTTCTACCCCTTTAACATCACCCTCCCCA
1 CAACTTCTACCCCTTTAACATCACCCTCCCCA
44447 ACATTCAATA
Statistics
Matches: 201, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
98 12 0.06
99 181 0.90
100 8 0.04
ACGTcount: A:0.26, C:0.45, G:0.02, T:0.27
Consensus pattern (98 bp):
CAACTTCTACCCCTTTAACATCACCCTCCCCATCAGCTTCTACCCCTTCAACAACACCTTTACCA
TTAACTTCTACCCTTCAACATCACCCTCCCCAA
Found at i:47686 original size:20 final size:20
Alignment explanation
Indices: 47661--47702 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
47651 ACAACTTTAA
*
47661 AATCAAATTAAAATGATTTT
1 AATCAAATCAAAATGATTTT
*
47681 AATCAAGTCAAAATGATTTT
1 AATCAAATCAAAATGATTTT
47701 AA
1 AA
47703 CTAAGGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (20 bp):
AATCAAATCAAAATGATTTT
Found at i:47712 original size:20 final size:20
Alignment explanation
Indices: 47670--47726 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
47660 AAATCAAATT
*
47670 AAAATGATTTTAA-TCAAGTC
1 AAAATGATTTTAACT-AAGGC
47690 AAAATGATTTTAACTAAGGC
1 AAAATGATTTTAACTAAGGC
*
47710 AAAATCATTTTAACTAA
1 AAAATGATTTTAACTAA
47727 TCAAATTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (20 bp):
AAAATGATTTTAACTAAGGC
Done.