Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010492.1 Kokia drynarioides strain JFW-HI SEQ_125400, 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: 36134
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:650 original size:20 final size:20
Alignment explanation
Indices: 597--650 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
587 CAATCTCATT
597 AAAAAATTTC-CTTCTGAACA
1 AAAAAATTTCTC-TCTGAACA
*
617 AAAAAATCTT-TCTCTGAATA
1 AAAAAAT-TTCTCTCTGAACA
637 AAAAAATTTCTCTC
1 AAAAAATTTCTCTC
651 AATCTTATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAAAATTTCTCTCTGAACA
Found at i:1411 original size:49 final size:49
Alignment explanation
Indices: 1312--1644 Score: 192
Period size: 49 Copynumber: 6.8 Consensus size: 49
1302 ACTGTCATGG
* * * * * * **
1312 CTTCAA-TCTATCTCTCTTCATTTTTAAGGTATTAGGTCTGCCGTCACGA
1 CTTCAACT-TATCCCTCTTCAATTTTAAGGTGTAAGATCCGCCGTTGCGA
* * * *
1361 CTTCAACTTATTCCTTTTCTATTTTAAGGTGTAAGATCCGTCGTTGCGA
1 CTTCAACTTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCCGTTGCGA
* * ** * * * *
1410 CTTCAATCTT-TCACTCATCGTGTTTTAGGGTGCT-AGGTTCGCCGTTGTGA
1 CTTCAA-CTTATCCCTCTTC-AATTTTAAGGTG-TAAGATCCGCCGTTGCGA
* * * *
1460 CTTTAACCTATCCCTCTTCAATTTTAAGGTGTAAGGTCCACCGTTGCGA
1 CTTCAACTTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCCGTTGCGA
* * * * ** *
1509 CTTCAACCTT-TCCCTATTTAATTTTAGGGTGTTAGATCTACCGTTGCGG
1 CTTCAA-CTTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCCGTTGCGA
* * * * * * * *
1558 CTTCAA-TCTATTCCTCTTCAATTTTAGGGTATTAGGTCCGTCATTACGA
1 CTTCAACT-TATCCCTCTTCAATTTTAAGGTGTAAGATCCGCCGTTGCGA
* * *
1607 CTTCAAC-CATCCCTATTCGATTTTAAGGTGTAAGATCC
1 CTTCAACTTATCCCTCTTCAATTTTAAGGTGTAAGATCC
1645 ATTATTGCGA
Statistics
Matches: 214, Mismatches: 60, Indels: 21
0.73 0.20 0.07
Matches are distributed among these distances:
47 1 0.00
48 25 0.12
49 147 0.69
50 40 0.19
51 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.39
Consensus pattern (49 bp):
CTTCAACTTATCCCTCTTCAATTTTAAGGTGTAAGATCCGCCGTTGCGA
Found at i:1666 original size:146 final size:147
Alignment explanation
Indices: 1458--1765 Score: 343
Period size: 146 Copynumber: 2.1 Consensus size: 147
1448 TCGCCGTTGT
* * * *
1458 GACTTTAACCTATCCCTCTTCAATTTTAAGGTGTAAGGTCCACCGTTGCGACTTCAACCTTTCCC
1 GACTTCAACCTATCCCTATTCAATTTTAAGGTGTAAGATCCACCATTGCGACTTCAACCTTTCCC
* * * *
1523 TATTT-AATTTTAGGGTGTTAGATCTACCGTTGCGGCTTCAATCTATT-CCTCTTCAATTTTAGG
66 TATTTGAATTTT-GGGTGTTAGATCCACCGCTACGGCTTCAACCT-TTCCCTCTTCAATTTTAGG
*
1586 GTATTAGGTCCGTCATTAC
129 ATATTAGGTCCGTCATTAC
* ** * * *
1605 GACTTCAACC-ATCCCTATTCGATTTTAAGGTGTAAGATCCATTATTGCGACTTTAATCTTTCTC
1 GACTTCAACCTATCCCTATTCAATTTTAAGGTGTAAGATCCACCATTGCGACTTCAACCTTTCCC
* * * * * *
1669 TTTTTGACTTTTGGGTGTTAGGTCCGCTGCTACGGCTTCAACCTTTCCCTCTTCGATTTTAGGAT
66 TATTTGAATTTTGGGTGTTAGATCCACCGCTACGGCTTCAACCTTTCCCTCTTCAATTTTAGGAT
* * * *
1734 GTTAGGTCCGCCGTTGC
131 ATTAGGTCCGTCATTAC
*
1751 GGCTTCAACCTATCC
1 GACTTCAACCTATCC
1766 TTCTTCAAAC
Statistics
Matches: 132, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
145 2 0.02
146 112 0.85
147 18 0.14
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (147 bp):
GACTTCAACCTATCCCTATTCAATTTTAAGGTGTAAGATCCACCATTGCGACTTCAACCTTTCCC
TATTTGAATTTTGGGTGTTAGATCCACCGCTACGGCTTCAACCTTTCCCTCTTCAATTTTAGGAT
ATTAGGTCCGTCATTAC
Found at i:6110 original size:15 final size:15
Alignment explanation
Indices: 6090--6118 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6080 AATATACATA
6090 CAATAAAATGCAAAG
1 CAATAAAATGCAAAG
6105 CAATAAAATGCAAA
1 CAATAAAATGCAAA
6119 AGATCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.10, T:0.14
Consensus pattern (15 bp):
CAATAAAATGCAAAG
Found at i:6843 original size:4 final size:4
Alignment explanation
Indices: 6834--6871 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
6824 ATAATGACAA
*
6834 AAAT AAAT AAAT AAAT AAAT AAAT ATAT AAATT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT A
6872 TAATTAAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:8260 original size:33 final size:34
Alignment explanation
Indices: 8201--8269 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
8191 AAAAAAAATT
8201 CTCTCAATCTTATTCAAAAAGAAAAAAAAACCTC
1 CTCTCAATCTTATTCAAAAAGAAAAAAAAACCTC
8235 CTCTCAATCTTATTCAAAAAG-AAAAAAAACCTC
1 CTCTCAATCTTATTCAAAAAGAAAAAAAAACCTC
8268 CT
1 CT
8270 TCTATTACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 14 0.40
34 21 0.60
ACGTcount: A:0.48, C:0.25, G:0.03, T:0.25
Consensus pattern (34 bp):
CTCTCAATCTTATTCAAAAAGAAAAAAAAACCTC
Found at i:9017 original size:49 final size:49
Alignment explanation
Indices: 8808--9341 Score: 249
Period size: 49 Copynumber: 10.9 Consensus size: 49
8798 TTTTTATTTC
* * ** * * *
8808 AAGGTGTTAGATCTACCGTTGTGGCTTCAATCTATCCCTATTCATTTTT
1 AAGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCAGTTTT
* ** * * * *
8857 AAGGTATTAGGTCCACCGTCACGGCTTCAACCTATTCCTTTTCTGTTTT
1 AAGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCAGTTTT
* * *** * * * * * * *
8906 AAGGTGTAAGATCCATCATTACGACTTTAATCTTTCCTTCGTCATGTTTT
1 AAGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCA-GTTTT
* * *
8956 ACA-GTGATAGGTCTGCCGTTGCGGCTTTAACCTATCCCTCTTCAGTTTT
1 A-AGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCAGTTTT
* * * * **
9005 AAGGTGTAAGGTCCGTCGTTACGGCTTCAACCTTTCCCTCTTTGGTTTT
1 AAGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCAGTTTT
* * * ** * *
9054 AAGGTGTTAGATCCGTCGTTGA-AACTTCAATCTATTCCTCTTC-GATTTT
1 AAGGTGTTAGGTCTGCCGTT-ACGGCTTCAACCTATCCCTCTTCAG-TTTT
* * * * * *
9103 AGGGTATTAGGTCTGTCATTACGACTTCAACCTATCCCCCTTC-GATTTT
1 AAGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCAG-TTTT
* * * * * * * * *
9152 AGGGTGTAAGAT-T-CATCGTTATGACTTCAATCTTTCCTTTTTC-GATTTT
1 AAGGTGTTAGGTCTGC--CGTTACGGCTTCAACCTATCCCTCTTCAG-TTTT
** ** * *
9201 TGGGTGTTAGGTCCACCGTTACAGCTTCAACCTATCCCTCTTTAGTTTT
1 AAGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCAGTTTT
* * * * * * * * *
9250 AAGGAGTAAGGTTTGTCGTTGCGGTTTTAACCTTTCCCTCTTCAATTTT
1 AAGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCAGTTTT
** *
9299 -AGGATGTTAGGTCTGCCGTTGTGG-TTCAACCTATCCTTCTTCA
1 AAGG-TGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCA
9342 AACTTCATGA
Statistics
Matches: 362, Mismatches: 111, Indels: 25
0.73 0.22 0.05
Matches are distributed among these distances:
48 23 0.06
49 301 0.83
50 36 0.10
51 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (49 bp):
AAGGTGTTAGGTCTGCCGTTACGGCTTCAACCTATCCCTCTTCAGTTTT
Found at i:9115 original size:98 final size:98
Alignment explanation
Indices: 8987--9259 Score: 291
Period size: 98 Copynumber: 2.8 Consensus size: 98
8977 CGGCTTTAAC
* * * *
8987 CTATCCCTCTTC-AGTTTTAAGGTGTAAGGTCCGTCGTTACGGCTTCAACCTTTCCCTCTTTGGT
1 CTATTCCTCTTCGA-TTTTAGGGTGTTAGGTCCGTCGTTACGGCTTCAACCTATCCCTCTTTGGT
* *
9051 TTTAAGGTGTTAGATCCGTCGTTGA-AACTTCAAT
65 TTTAAGGTGTAAGATCCATCGTT-ATAACTTCAAT
* * * * * * *
9085 CTATTCCTCTTCGATTTTAGGGTATTAGGTCTGTCATTACGACTTCAACCTATCCCCCTTCGATT
1 CTATTCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTTACGGCTTCAACCTATCCCTCTTTGGTT
* * *
9150 TTAGGGTGTAAGATTCATCGTTATGACTTCAAT
66 TTAAGGTGTAAGATCCATCGTTATAACTTCAAT
* * ** * *
9183 CT-TTCCTTTTTCGATTTTTGGGTGTTAGGTCCACCGTTACAGCTTCAACCTATCCCTCTTTAGT
1 CTATTCC-TCTTCGATTTTAGGGTGTTAGGTCCGTCGTTACGGCTTCAACCTATCCCTCTTTGGT
*
9247 TTTAAGGAGTAAG
65 TTTAAGGTGTAAG
9260 GTTTGTCGTT
Statistics
Matches: 141, Mismatches: 31, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
97 5 0.04
98 135 0.96
99 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (98 bp):
CTATTCCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTTACGGCTTCAACCTATCCCTCTTTGGTT
TTAAGGTGTAAGATCCATCGTTATAACTTCAAT
Found at i:9318 original size:98 final size:97
Alignment explanation
Indices: 8972--9339 Score: 290
Period size: 98 Copynumber: 3.8 Consensus size: 97
8962 ATAGGTCTGC
* * * * * * *
8972 CGTTGCGGCTTTAACCTATCCCTCTTCAGTTTTAAGGTGTAAGGTCCGTCGTTACGGCTTCAACC
1 CGTTGCGACTTCAACCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCGCCGTTAC-GCTTCAACC
* * * *
9037 TTTCCCTCTTTGGTTTTAAGGTGTTAGATCCGT
65 TATCCCTCTTTAGTTTTAAGGTGTAAGATTCGT
** * * * * * *
9070 CGTTGAAACTTCAATCTATT-CCTCTTCGATTTTAGGGTATTAGGTCTGTCATTACGACTTCAAC
1 CGTTGCGACTTCAACCT-TTCCCTCTTCAATTTTAGGGTGTTAGGTCCGCCGTTACG-CTTCAAC
* * * *
9134 CTATCCC-CCTTCGATTTTAGGGTGTAAGATTCAT
64 CTATCCCTCTTTAG-TTTTAAGGTGTAAGATTCGT
** * * * * * *
9168 CGTTATGACTTCAATCTTTCCTTTTTCGATTTTTGGGTGTTAGGTCCACCGTTACAGCTTCAACC
1 CGTTGCGACTTCAACCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCGCCGTTAC-GCTTCAACC
* * *
9233 TATCCCTCTTTAGTTTTAAGGAGTAAGGTTTGT
65 TATCCCTCTTTAGTTTTAAGGTGTAAGATTCGT
** * * * ** *
9266 CGTTGCGGTTTTAACCTTTCCCTCTTCAATTTTAGGATGTTAGGTCTGCCGTTGTGGTTCAACCT
1 CGTTGCGACTTCAACCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCGCCGTTACGCTTCAACCT
*
9331 ATCCTTCTT
66 ATCCCTCTT
9340 CAAACTTCAT
Statistics
Matches: 209, Mismatches: 55, Indels: 13
0.75 0.20 0.05
Matches are distributed among these distances:
97 24 0.11
98 179 0.86
99 6 0.03
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (97 bp):
CGTTGCGACTTCAACCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCGCCGTTACGCTTCAACCT
ATCCCTCTTTAGTTTTAAGGTGTAAGATTCGT
Found at i:10455 original size:50 final size:49
Alignment explanation
Indices: 10399--10495 Score: 149
Period size: 50 Copynumber: 2.0 Consensus size: 49
10389 TTTTTTTTTG
* * *
10399 CTAGTTTGAGCCGCCTTTTCAGGTTTTCAACCCGAACTTGTTTTTTAGTT
1 CTAGTTTGAGCCCCCATTTCAGGTTTTCAACCCAAACTT-TTTTTTAGTT
*
10449 CTAGTTTGAGCCCCCATTTCAGGTTTTCAACTCAAACTTTTTTTTAG
1 CTAGTTTGAGCCCCCATTTCAGGTTTTCAACCCAAACTTTTTTTTAG
10496 GCGAAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 8 0.19
50 35 0.81
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (49 bp):
CTAGTTTGAGCCCCCATTTCAGGTTTTCAACCCAAACTTTTTTTTAGTT
Found at i:15837 original size:15 final size:13
Alignment explanation
Indices: 15816--15857 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
15806 CAATATACAT
15816 ACAATAAAATGCGA
1 ACAATAAAATGC-A
15830 AGCAATAAAATGCA
1 A-CAATAAAATGCA
*
15844 AAAATAAAATGCA
1 ACAATAAAATGCA
15857 A
1 A
15858 ATGATCACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14
Consensus pattern (13 bp):
ACAATAAAATGCA
Found at i:17001 original size:15 final size:17
Alignment explanation
Indices: 16972--17003 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16962 AACAACAACT
16972 TACATATAAATAATAAA
1 TACATATAAATAATAAA
16989 TACATA-AAA-AATAAA
1 TACATATAAATAATAAA
17004 AAGAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (17 bp):
TACATATAAATAATAAA
Found at i:17728 original size:30 final size:32
Alignment explanation
Indices: 17691--17752 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
17681 TTTTCTGAAT
17691 AAAAAAAA-TCCTCTCAATCTTATTAAAAATG
1 AAAAAAAACTCCTCTCAATCTTATTAAAAATG
*
17722 AAAAAAAACCTCCTTTCAATCTTATTAAAAA
1 AAAAAAAA-CTCCTCTCAATCTTATTAAAAA
17753 AAAATCTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 8 0.29
33 20 0.71
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.29
Consensus pattern (32 bp):
AAAAAAAACTCCTCTCAATCTTATTAAAAATG
Found at i:22712 original size:14 final size:14
Alignment explanation
Indices: 22693--22721 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22683 AAGAAAAATC
22693 ATGTTGTCACGACG
1 ATGTTGTCACGACG
22707 ATGTTGTCACGACG
1 ATGTTGTCACGACG
22721 A
1 A
22722 GAGGCTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (14 bp):
ATGTTGTCACGACG
Found at i:27590 original size:52 final size:52
Alignment explanation
Indices: 27503--27736 Score: 280
Period size: 52 Copynumber: 4.6 Consensus size: 52
27493 TTCATTTAAG
*
27503 ACTCACGATGACACATAGTCATCGAACCTCTTAATTCGTAAAAGAATCATAT
1 ACTCACGATGACACATAGTCATCGAACCTCATAATTCGTAAAAGAATCATAT
* * * * *
27555 ACTCACGATGACATATAATCATC-AGATCTCATAATTCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGA-ACCTCATAATTCGTAAAAGAATCATAT
* * *
27607 ACTCACGATGACACATAATCATCGAACCTCATAA-TCTGT-AAAGGAT--TCT
1 ACTCACGATGACACATAGTCATCGAACCTCATAATTC-GTAAAAGAATCATAT
* * * * *
27656 ACTCACGATGACAAATAGTCATCGGACCTCATAATCCATAAAAGATTCATAT
1 ACTCACGATGACACATAGTCATCGAACCTCATAATTCGTAAAAGAATCATAT
*
27708 ACTCACGATGACACATAGTCATCGGACCT
1 ACTCACGATGACACATAGTCATCGAACCT
27737 TTTTCATTTA
Statistics
Matches: 154, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
49 34 0.22
50 6 0.04
51 7 0.05
52 106 0.69
53 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCGAACCTCATAATTCGTAAAAGAATCATAT
Found at i:27705 original size:101 final size:103
Alignment explanation
Indices: 27503--27736 Score: 321
Period size: 101 Copynumber: 2.3 Consensus size: 103
27493 TTCATTTAAG
*
27503 ACTCACGATGACACATAGTCATCGAACCTCTTAATTCGTAAAAGAATCATATACTCACGATGACA
1 ACTCACGATGACACATAGTCATCGAACCTCATAATTCGTAAAAGAAT-ATATACTCACGATGACA
* * * * *
27568 TATAATCATCAGATCTCATAATTCGTAAAGGATTCATAT
65 AATAATCATCAGACCTCATAATCCATAAAAGATTCATAT
* * *
27607 ACTCACGATGACACATAATCATCGAACCTCATAA-TCTGT-AAAGGAT-TCTACTCACGATGACA
1 ACTCACGATGACACATAGTCATCGAACCTCATAATTC-GTAAAAGAATATATACTCACGATGACA
* *
27669 AATAGTCATCGGACCTCATAATCCATAAAAGATTCATAT
65 AATAATCATCAGACCTCATAATCCATAAAAGATTCATAT
*
27708 ACTCACGATGACACATAGTCATCGGACCT
1 ACTCACGATGACACATAGTCATCGAACCT
27737 TTTTCATTTA
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
101 74 0.64
103 8 0.07
104 34 0.29
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
ACTCACGATGACACATAGTCATCGAACCTCATAATTCGTAAAAGAATATATACTCACGATGACAA
ATAATCATCAGACCTCATAATCCATAAAAGATTCATAT
Found at i:32147 original size:21 final size:21
Alignment explanation
Indices: 32121--32197 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
32111 AATAATATAG
*
32121 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGAAACAAGTGAC
*
32142 ACTTCTACTGAAACAAGT---
1 ACTTCTACCGAAACAAGTGAC
*
32160 -CTTAC-ACCGATACAAGTGAC
1 ACTT-CTACCGAAACAAGTGAC
*
32180 ACTTCTACTGAAACAAGT
1 ACTTCTACCGAAACAAGT
32198 CTTACTTCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
17 13 0.30
18 1 0.02
20 1 0.02
21 29 0.66
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (21 bp):
ACTTCTACCGAAACAAGTGAC
Found at i:32178 original size:38 final size:38
Alignment explanation
Indices: 32127--32202 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
32117 ATAGACTTCT
32127 ACCGATACAAGTGACACTTCTACTGAAACAAGTCTTAC
1 ACCGATACAAGTGACACTTCTACTGAAACAAGTCTTAC
32165 ACCGATACAAGTGACACTTCTACTGAAACAAGTCTTAC
1 ACCGATACAAGTGACACTTCTACTGAAACAAGTCTTAC
32203 TTCTATTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (38 bp):
ACCGATACAAGTGACACTTCTACTGAAACAAGTCTTAC
Found at i:32204 original size:21 final size:21
Alignment explanation
Indices: 32142--32207 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
32132 TACAAGTGAC
32142 ACTTCTACTGAAACAAGTCTT
1 ACTTCTACTGAAACAAGTCTT
* * ***
32163 A---C-ACCGATACAAGTGAC
1 ACTTCTACTGAAACAAGTCTT
32180 ACTTCTACTGAAACAAGTCTT
1 ACTTCTACTGAAACAAGTCTT
32201 ACTTCTA
1 ACTTCTA
32208 TTAATACTAA
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
17 11 0.35
18 1 0.03
20 1 0.03
21 18 0.58
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.29
Consensus pattern (21 bp):
ACTTCTACTGAAACAAGTCTT
Found at i:33132 original size:101 final size:103
Alignment explanation
Indices: 32948--33181 Score: 337
Period size: 101 Copynumber: 2.3 Consensus size: 103
32938 TTCATTTAAG
* * * *
32948 ACTCACGATAACACATAGTCATCGAACCTCTTAATTCGTAAAAGAATCATATACTCACGATGACA
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGAAT-ATATACTCACGATGACA
* * * *
33013 CATAGTCATCAGATCTCATAATCCGTAAAGGATTCATAT
65 AATAGTCATCAGACCTCATAATCCATAAAAGATTCATAT
* * *
33052 ACTCACGATGACACATAGTTATCGGACCTCATAATCCGT-AAAGGAT-TTTACTCACGATGACAA
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGAATATATACTCACGATGACAA
33115 ATAGTCATCAGACCTCATAATCCATAAAAGATTCATAT
66 ATAGTCATCAGACCTCATAATCCATAAAAGATTCATAT
*
33153 ACTCACGATGACACATAGTCACCGGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
33182 TTTTCATTTA
Statistics
Matches: 117, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
101 77 0.66
103 6 0.05
104 34 0.29
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGAATATATACTCACGATGACAA
ATAGTCATCAGACCTCATAATCCATAAAAGATTCATAT
Found at i:33181 original size:52 final size:52
Alignment explanation
Indices: 32948--33181 Score: 321
Period size: 52 Copynumber: 4.6 Consensus size: 52
32938 TTCATTTAAG
* * * * *
32948 ACTCACGATAACACATAGTCATCGAACCTCTTAATTCGTAAAAGAATCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCATAT
* * *
33000 ACTCACGATGACACATAGTCATCAGATCTCATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCATAT
* *
33052 ACTCACGATGACACATAGTTATCGGACCTCATAATCCGTAAAGGATT--T-T
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCATAT
* * *
33101 ACTCACGATGACAAATAGTCATCAGACCTCATAATCCATAAAAGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCATAT
*
33153 ACTCACGATGACACATAGTCACCGGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
33182 TTTTCATTTA
Statistics
Matches: 160, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
49 43 0.27
50 1 0.01
51 1 0.01
52 115 0.72
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCATAT
Done.