Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007795.1 Kokia drynarioides strain JFW-HI SEQ_122429, 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: 85186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:263 original size:117 final size:117
Alignment explanation
Indices: 48--266 Score: 258
Period size: 117 Copynumber: 1.9 Consensus size: 117
38 GAAATTTCAA
* * * * * * ** *
48 AAATAAAGCTCCAGTGGTCACACGATCTTGGAATAGGCTCGTGTGTGGTGGTCGTAGGCCTGTCT
1 AAATAAAGCTCCAATGGTCACACGATCTTGAAACACGCCCGTATGTGGTGACCGTAGGCCTATCT
* * * *
113 TCGCTTCTCCCACGCTCGTGTCTATAAATCGTGTGCTATTTCAACATTTTGG
66 TCACTTCTCCCACGCACATGTCTATAAACCGTGTGCTATTTCAACATTTTGG
* * * *
165 AAATAAGGCTCCAATGTTCACACGGTCTTGAAACACGCCCGTATGTGGTGACCGTGGGCCTATCT
1 AAATAAAGCTCCAATGGTCACACGATCTTGAAACACGCCCGTATGTGGTGACCGTAGGCCTATCT
* * *
230 TCACTTCTCCCATGCACATGTTTCTAAACCGTGTGCT
66 TCACTTCTCCCACGCACATGTCTATAAACCGTGTGCT
267 TTTTGATATT
Statistics
Matches: 82, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
117 82 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.31
Consensus pattern (117 bp):
AAATAAAGCTCCAATGGTCACACGATCTTGAAACACGCCCGTATGTGGTGACCGTAGGCCTATCT
TCACTTCTCCCACGCACATGTCTATAAACCGTGTGCTATTTCAACATTTTGG
Found at i:6602 original size:25 final size:23
Alignment explanation
Indices: 6574--6619 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
6564 GTAGGATCCA
6574 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
6599 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
6620 CCTTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:12768 original size:15 final size:15
Alignment explanation
Indices: 12748--12779 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12738 ACAACATTTC
12748 TGTTAGGCTACACGA
1 TGTTAGGCTACACGA
12763 TGTTAGGCTACACGA
1 TGTTAGGCTACACGA
12778 TG
1 TG
12780 CTGCTCACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (15 bp):
TGTTAGGCTACACGA
Found at i:27665 original size:33 final size:33
Alignment explanation
Indices: 27603--27667 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
27593 ATAGTACTCC
* * *
27603 ACTCCTTCTGGCCCATTATCATCGTAGTACAAA
1 ACTCCTTCTAGCCCATTACCATCGCAGTACAAA
27636 ACTCCTTCTAGCCCATTACCAAT-GCAGTACAA
1 ACTCCTTCTAGCCCATTACC-ATCGCAGTACAA
27668 CACTTCTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.28
Consensus pattern (33 bp):
ACTCCTTCTAGCCCATTACCATCGCAGTACAAA
Found at i:28073 original size:44 final size:44
Alignment explanation
Indices: 27981--28121 Score: 212
Period size: 44 Copynumber: 3.2 Consensus size: 44
27971 ACTATATAAT
* * * * *
27981 ATAGTAATTTAAATGAGAT-TGTTGGAACAAACTTGAAACAAAT
1 ATAGTAATTTAAAGGAGATGTATTGAAACAAACTTGGAACAAAC
*
28024 ATAGTAATTTAAAGGAGATGTATTGAAACAAACATGGAACAAAC
1 ATAGTAATTTAAAGGAGATGTATTGAAACAAACTTGGAACAAAC
*
28068 CTAGTAATTTAAAGGAGATGTATTGAAACAAACTTGGAACAAAC
1 ATAGTAATTTAAAGGAGATGTATTGAAACAAACTTGGAACAAAC
28112 ATAGTAATTT
1 ATAGTAATTT
28122 CATCATCGAG
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 18 0.20
44 70 0.80
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (44 bp):
ATAGTAATTTAAAGGAGATGTATTGAAACAAACTTGGAACAAAC
Found at i:29988 original size:19 final size:19
Alignment explanation
Indices: 29964--30046 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 19
29954 ATTCCAAAAA
*
29964 TAATATTATTTTAATTGTT
1 TAATATTATTTTAATTATT
**
29983 TAATATTAAATTAA--ATT
1 TAATATTATTTTAATTATT
*
30000 TAATACTTACTTTAATAATATT
1 TAATA-TTATTTTAAT--TATT
*
30022 T--TATTATTTTAATTGTT
1 TAATATTATTTTAATTATT
30039 TAATATTA
1 TAATATTA
30047 AATTTATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
17 11 0.22
18 7 0.14
19 26 0.52
20 2 0.04
22 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TAATATTATTTTAATTATT
Found at i:29995 original size:24 final size:25
Alignment explanation
Indices: 29971--30059 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 25
29961 AAATAATATT
29971 ATTTTAATTGTTTAATATTAAATTAA
1 ATTTTAATTGTTTAATATTAAATT-A
* * * **
29997 ATTTAATACTTACTTTAATAATATTTTA
1 ATTT--TAATT-GTTTAATATTAAATTA
*
30025 TTATTTTAATTGTTTAATATTAAATTT
1 --ATTTTAATTGTTTAATATTAAATTA
30052 ATTTTAAT
1 ATTTTAAT
30060 ACTTACTTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
25 8 0.17
26 4 0.09
27 11 0.23
28 9 0.19
29 11 0.23
30 4 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTAATTGTTTAATATTAAATTA
Found at i:30013 original size:29 final size:29
Alignment explanation
Indices: 29981--30072 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
29971 ATTTTAATTG
29981 TTTAATATTAAATTAAATTTAATACTTAC
1 TTTAATATTAAATTAAATTTAATACTTAC
* ** * * *
30010 TTTAATAATATTTTATTATTT--TAATT-G
1 TTTAATATTAAATTA-AATTTAATACTTAC
* *
30037 TTTAATATTAAATTTATTTTAATACTTAC
1 TTTAATATTAAATTAAATTTAATACTTAC
30066 TTTAATA
1 TTTAATA
30073 GTATTTTATT
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
26 3 0.07
27 11 0.24
28 8 0.18
29 19 0.42
30 4 0.09
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTAATATTAAATTAAATTTAATACTTAC
Found at i:30036 original size:56 final size:56
Alignment explanation
Indices: 29967--30090 Score: 212
Period size: 56 Copynumber: 2.2 Consensus size: 56
29957 CCAAAAATAA
29967 TATTATTTTAATTGTTTAATATTAAATTAAATTTAATACTTACTTTAATAATATTT
1 TATTATTTTAATTGTTTAATATTAAATTAAATTTAATACTTACTTTAATAATATTT
* * *
30023 TATTATTTTAATTGTTTAATATTAAATTTATTTTAATACTTACTTTAATAGTATTT
1 TATTATTTTAATTGTTTAATATTAAATTAAATTTAATACTTACTTTAATAATATTT
*
30079 TATTAATTTAAT
1 TATTATTTTAAT
30091 ATTAAAATGA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (56 bp):
TATTATTTTAATTGTTTAATATTAAATTAAATTTAATACTTACTTTAATAATATTT
Found at i:30225 original size:130 final size:124
Alignment explanation
Indices: 29982--30217 Score: 264
Period size: 128 Copynumber: 1.9 Consensus size: 124
29972 TTTTAATTGT
**
29982 TTAATATTAAATTAAATTTAATACTTACTTTAATAATATTTTATTATTTTAATTGTTTAATATTA
1 TTAATATTAAATTAAATTTAATACTTACTTTAATAATATTTTATTATTTTAATAATTTAATATTA
* * * * * *
30047 AATTTATTTTAATACTTACTTTAATAGTATTTTATTAATTTAATATTAAAATGATTATC
66 AATTTAATCTAATACTAAATTTAATAGTAATTTAATAATTTAATATTAAAATGATTATC
* ** *
30106 TTAATATTAAATTTAATTTAATGTTTATCTTTTCGATAAATATTTTATTATTTTAATAAAATTTA
1 TTAATATTAAATTAAATTTAATACTTA-C-TTT-AAT-AATATTTTATTATTTTAAT--AATTTA
30171 ATATTAAATTTAATCTAATA-TAAATATT-AT-GTTAATTTAAT-ATTTAA
60 ATATTAAATTTAATCTAATACTAAAT-TTAATAG-TAATTTAATAATTTAA
30218 GTGATTAAGT
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
124 24 0.26
125 1 0.01
126 3 0.03
127 2 0.02
128 26 0.28
129 12 0.13
130 24 0.26
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (124 bp):
TTAATATTAAATTAAATTTAATACTTACTTTAATAATATTTTATTATTTTAATAATTTAATATTA
AATTTAATCTAATACTAAATTTAATAGTAATTTAATAATTTAATATTAAAATGATTATC
Found at i:39653 original size:19 final size:17
Alignment explanation
Indices: 39623--39657 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
39613 TTTAACATAA
39623 TTTTTTTCTTTTTCTTC
1 TTTTTTTCTTTTTCTTC
39640 TTTTTTCTCATTTTTCTT
1 TTTTTT-TC-TTTTTCTT
39658 TTTCAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTCTTTTTCTTC
Found at i:41190 original size:273 final size:273
Alignment explanation
Indices: 40703--41245 Score: 944
Period size: 273 Copynumber: 2.0 Consensus size: 273
40693 GGTTTTCTTC
* *
40703 AGCAGCTTCCGCCTAACTCTCTCCATCTTGTGACAAGCCTTCAGTTATTGCAACCACAACTTCAG
1 AGCAGCTTCCGCCTAACTCGCTCCATCTTGTGACAAGCCTTCAATTATTGCAACCACAACTTCAG
* *
40768 GTGCAGGGACAAATTTCTCAGCTAAATATGCCTTGACATCTATTTTTTTTCAACTTTTTCTTACT
66 GTGCAGGGACAAATTTCTCAGCTAAATATGCCTTGACATATATTTTTTTTCAACTTTTGCTTACT
40833 CCACATGAACTTCGTCCATTTTCAGCATTAAGTCAGTAGGTGCAGTACAACTGTACAAAATTGCG
131 CCACATGAACTTCGTCCATTTTCAGCATTAAGTCAGTAGGTGCAGTACAACTGTACAAAATTGCG
*
40898 TTGACAATGGAATCCTAATGCGACGAAAATAGTGTTTACTTATACCTCAATTGGTGCAGACATAA
196 TTGACAATGGAATCCTAATGCGACGAAAATAGTGTTTACTTATACCTCAATTGGTGCAGACACAA
40963 TATGTGTTTCATT
261 TATGTGTTTCATT
* * *
40976 AGCAGCTTTCGCCTAACTCGCTCCATCTTGTGACAAGCCTTCAATTATTGCACCCATAACTTCAG
1 AGCAGCTTCCGCCTAACTCGCTCCATCTTGTGACAAGCCTTCAATTATTGCAACCACAACTTCAG
*
41041 GTGCAGGGACAAATTTCTCAGCTAAATATGCCTTGACATATATTTTTTTTTCAAC-TTTGCTTCC
66 GTGCAGGGACAAATTTCTCAGCTAAATATGCCTTGACATATA-TTTTTTTTCAACTTTTGCTTAC
*
41105 TCCGCATGAACTTCGTCCATTTTCAGCATTAAGTCAGTAGGTGCAGTACAACTGTACAAAATTGC
130 TCCACATGAACTTCGTCCATTTTCAGCATTAAGTCAGTAGGTGCAGTACAACTGTACAAAATTGC
* * * *
41170 GTTGATAATGGAATCCTAATGCGAGGATAATAGTGTTTACTTATTCCTCAATTGGTGCAGACACA
195 GTTGACAATGGAATCCTAATGCGACGAAAATAGTGTTTACTTATACCTCAATTGGTGCAGACACA
41235 ATATGTGTTTC
260 ATATGTGTTTC
41246 TTCTTCTTCA
Statistics
Matches: 255, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
273 243 0.95
274 12 0.05
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (273 bp):
AGCAGCTTCCGCCTAACTCGCTCCATCTTGTGACAAGCCTTCAATTATTGCAACCACAACTTCAG
GTGCAGGGACAAATTTCTCAGCTAAATATGCCTTGACATATATTTTTTTTCAACTTTTGCTTACT
CCACATGAACTTCGTCCATTTTCAGCATTAAGTCAGTAGGTGCAGTACAACTGTACAAAATTGCG
TTGACAATGGAATCCTAATGCGACGAAAATAGTGTTTACTTATACCTCAATTGGTGCAGACACAA
TATGTGTTTCATT
Found at i:53403 original size:20 final size:21
Alignment explanation
Indices: 53365--53404 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
53355 TAAACCTAGC
53365 ATTACTAAGTTAGAAAATGCA
1 ATTACTAAGTTAGAAAATGCA
53386 ATTACTAAGTTA-AAAATGC
1 ATTACTAAGTTAGAAAATGC
53405 TAAAAATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (21 bp):
ATTACTAAGTTAGAAAATGCA
Found at i:53419 original size:13 final size:13
Alignment explanation
Indices: 53401--53425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53391 TAAGTTAAAA
53401 ATGCTAAAAATGC
1 ATGCTAAAAATGC
53414 ATGCTAAAAATG
1 ATGCTAAAAATG
53426 ATAAAATAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:56759 original size:38 final size:38
Alignment explanation
Indices: 56708--56783 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
56698 TTGATCGAGG
56708 AGCTCATCCTAGACGAATCGAAAATTTAAAATTTTGGT
1 AGCTCATCCTAGACGAATCGAAAATTTAAAATTTTGGT
*
56746 AGCTCATCCTAGACGAATCGAAAATTTACAATTTTGGT
1 AGCTCATCCTAGACGAATCGAAAATTTAAAATTTTGGT
56784 TAAGTGTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (38 bp):
AGCTCATCCTAGACGAATCGAAAATTTAAAATTTTGGT
Found at i:60720 original size:21 final size:21
Alignment explanation
Indices: 60696--60738 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
60686 TTGATACTTA
*
60696 TGACAATTCTACCGATACAAG
1 TGACAATACTACCGATACAAG
** *
60717 TGACTCTACTATCGATACAAG
1 TGACAATACTACCGATACAAG
60738 T
1 T
60739 CTTACTTCTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (21 bp):
TGACAATACTACCGATACAAG
Found at i:61605 original size:53 final size:53
Alignment explanation
Indices: 61481--61672 Score: 284
Period size: 52 Copynumber: 3.7 Consensus size: 53
61471 ATTCATTTTC
* *
61481 ATTTA-ATACTCACGATGACACATAGTTATCGGACCTCATAA-CC-CACAAAGG
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAC-AAGG
* * *
61532 ATTCATATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTACAATG
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTACAAGG
*
61585 ATTTATATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTA-AAGG
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTACAAGG
*
61637 ATTTATATACTCACAATGACACATAGTCATCGGACC
1 ATTTATATACTCACGATGACACATAGTCATCGGACC
61673 CTTTTCATTT
Statistics
Matches: 127, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
51 4 0.03
52 71 0.56
53 50 0.39
54 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (53 bp):
ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTACAAGG
Found at i:61668 original size:105 final size:104
Alignment explanation
Indices: 61481--61672 Score: 303
Period size: 105 Copynumber: 1.8 Consensus size: 104
61471 ATTCATTTTC
* *
61481 ATTTAATACTCACGATGACACATAGTTATCGGACCTCATAACCCACAAAGGATTCATATACTCAC
1 ATTTAATACTCACGATGACACATAGTCATCAGACCTCATAACCCACAAAGGATTCATATACTCAC
* *
61546 GATGACACGTAGTCATCGGACCTCATAATCCGTACAATG
66 AATGACACATAGTCATCGGACCTCATAATCCGTACAATG
* ** *
61585 ATTTATATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTTATATACTCA
1 ATTTA-ATACTCACGATGACACATAGTCATCAGACCTCATAACCCACAAAGGATTCATATACTCA
61650 CAATGACACATAGTCATCGGACC
65 CAATGACACATAGTCATCGGACC
61673 CTTTTCATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
104 5 0.06
105 74 0.94
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (104 bp):
ATTTAATACTCACGATGACACATAGTCATCAGACCTCATAACCCACAAAGGATTCATATACTCAC
AATGACACATAGTCATCGGACCTCATAATCCGTACAATG
Found at i:61792 original size:2 final size:2
Alignment explanation
Indices: 61785--61825 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
61775 AGAATATGAA
*
61785 AT AT AT AT AT AT AT AT AT AGG A- AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A
61826 GGAATTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:61809 original size:22 final size:22
Alignment explanation
Indices: 61784--61830 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
61774 AAGAATATGA
61784 AATATATATATATATATATAGG
1 AATATATATATATATATATAGG
61806 AATATATATATATATATATAGG
1 AATATATATATATATATATAGG
61828 AAT
1 AAT
61831 TTAATAGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (22 bp):
AATATATATATATATATATAGG
Found at i:65582 original size:21 final size:21
Alignment explanation
Indices: 65558--65601 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
65548 GATGATTCAA
65558 GCTTGAGCTATAGGAGGTCTT
1 GCTTGAGCTATAGGAGGTCTT
65579 GCTTGAGCTATAGGAGGTCTT
1 GCTTGAGCTATAGGAGGTCTT
65600 GC
1 GC
65602 AGGGAAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (21 bp):
GCTTGAGCTATAGGAGGTCTT
Found at i:66924 original size:13 final size:13
Alignment explanation
Indices: 66860--66926 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
66850 TTCGAAATCA
* *
66860 AATCTTAAACTTC
1 AATCTTGAACTTG
*
66873 AAACTTGTAACATTG
1 AATCTTG-AAC-TTG
* *
66888 AATTTTGAATCTTA
1 AATCTTGAA-CTTG
*
66902 AATCTCGAACTTG
1 AATCTTGAACTTG
66915 AATCTTGAACTT
1 AATCTTGAACTT
66927 TAAATCACAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
13 19 0.46
14 14 0.34
15 8 0.20
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (13 bp):
AATCTTGAACTTG
Found at i:67153 original size:34 final size:34
Alignment explanation
Indices: 67110--67179 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
67100 ACTTTATTAT
67110 GTTTAAAATTTAATGATGTGGTACGATTTTATTG
1 GTTTAAAATTTAATGATGTGGTACGATTTTATTG
67144 GTTTAAAATTTAATGATGTGGTACGATTTTATTG
1 GTTTAAAATTTAATGATGTGGTACGATTTTATTG
67178 GT
1 GT
67180 GCCTAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (34 bp):
GTTTAAAATTTAATGATGTGGTACGATTTTATTG
Found at i:68865 original size:22 final size:22
Alignment explanation
Indices: 68818--68875 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
68808 CAAGAGCTGC
**
68818 ATGTCTAGAGACATTGCGCAGT
1 ATGTCTAGAGACATTGCGCAAA
*
68840 ATGTCTAGGGACATTTG-GCAAA
1 ATGTCTAGAGACA-TTGCGCAAA
*
68862 ATGTCTCGAGACAT
1 ATGTCTAGAGACAT
68876 AGATTGCCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 1 0.03
22 26 0.87
23 3 0.10
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (22 bp):
ATGTCTAGAGACATTGCGCAAA
Found at i:80754 original size:20 final size:20
Alignment explanation
Indices: 80715--80754 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
80705 TATTGATTAC
*
80715 TAATTTTTGCTAGTTCTTTT
1 TAATTTTTGCTAGGTCTTTT
* *
80735 TAATTTTTGTTAGGTGTTTT
1 TAATTTTTGCTAGGTCTTTT
80755 ATGTCCATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.15, T:0.65
Consensus pattern (20 bp):
TAATTTTTGCTAGGTCTTTT
Done.