Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001870.1 Kokia drynarioides strain JFW-HI SEQ_113635, 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: 126866
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4426 original size:22 final size:22
Alignment explanation
Indices: 4398--4441 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4388 TCATTAAGCT
* * *
4398 TTAATTAACCCTTTTTTTACTC
1 TTAATTAAACCTATTTATACTC
4420 TTAATTAAACCTATTTATACTC
1 TTAATTAAACCTATTTATACTC
4442 ATTTTAACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATTAAACCTATTTATACTC
Found at i:9498 original size:24 final size:24
Alignment explanation
Indices: 9470--9553 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
9460 TGTACCAAGA
9470 TAAATATTATATTAAATTTAATAT
1 TAAATATTATATTAAATTTAATAT
* * *
9494 TAAATATTAT-TAAAATAATAAAATAA
1 TAAATATTATATTAAAT--T-TAATAT
* * *
9520 TAAGTTTTAAATTAAATTTAATAT
1 TAAATATTATATTAAATTTAATAT
9544 TAAACTATTA
1 TAAA-TATTA
9554 AAATAATAAG
Statistics
Matches: 44, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
23 5 0.11
24 17 0.39
25 6 0.14
26 11 0.25
27 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (24 bp):
TAAATATTATATTAAATTTAATAT
Found at i:9740 original size:41 final size:41
Alignment explanation
Indices: 9678--9771 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 41
9668 AATTTTCCAA
* * ***
9678 AAATCGAAGTAAATATGCTGGCACATAGTGCATCATTGGAT
1 AAATCGAAGTAAATATACTGGCACATAATGCATCACCAGAT
*
9719 AAATCGAAGTAAATATACTGGCACGTAATGCATCACCAGAT
1 AAATCGAAGTAAATATACTGGCACATAATGCATCACCAGAT
9760 AAATCGAAGTAA
1 AAATCGAAGTAA
9772 TTTGCGCTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (41 bp):
AAATCGAAGTAAATATACTGGCACATAATGCATCACCAGAT
Found at i:9948 original size:62 final size:62
Alignment explanation
Indices: 9733--9937 Score: 229
Period size: 62 Copynumber: 3.3 Consensus size: 62
9723 CGAAGTAAAT
* * * * * *
9733 ATACTGGCACGTAATGCATCACCAGATAAATCGAAGTAATTTGCGCTCA--ACTAACATGTC
1 ATACTGGCACATAGTGCATCACCAGATAAACCGAAGTAATCTGCGCTCAGGACTATCATATC
* * * * * *
9793 ATATTGGGACATAGTGCATCATC-GAATAAATCGAAGTAATCTGCGCTTAGGGCTATCATATC
1 ATACTGGCACATAGTGCATCACCAG-ATAAACCGAAGTAATCTGCGCTCAGGACTATCATATC
* * *
9855 ATATTGGCACATAGTGCATCACCAGATAAACCGAAGTAATCTGTGCTCAGGACTATCATTTC
1 ATACTGGCACATAGTGCATCACCAGATAAACCGAAGTAATCTGCGCTCAGGACTATCATATC
9917 ATACTGGCACATTA-TGCATCA
1 ATACTGGCACA-TAGTGCATCA
9938 TCGTATAAAC
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 40 0.33
62 78 0.64
63 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (62 bp):
ATACTGGCACATAGTGCATCACCAGATAAACCGAAGTAATCTGCGCTCAGGACTATCATATC
Found at i:15416 original size:2 final size:2
Alignment explanation
Indices: 15409--15438 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15399 TACTAGTATC
15409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15439 GGATGTCGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19875 original size:30 final size:30
Alignment explanation
Indices: 19809--19874 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
19799 GATTTTATTT
* *
19809 ATTTTTATAATTTTTAAAGGATTAAATTAA
1 ATTTTTATAATTTTTAAAGGATCAAAGTAA
*
19839 ATTTTTATCATTTTTAAGAGG-TCAAAGTATA
1 ATTTTTATAATTTTTAA-AGGATCAAAGTA-A
19870 ATTTT
1 ATTTT
19875 ACTTTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAGGATCAAAGTAA
Found at i:21833 original size:29 final size:30
Alignment explanation
Indices: 21801--21858 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
21791 AAGGAAAAAT
21801 GAGG-TAAAAACAAAATTTTAGAAAGTTTG
1 GAGGCTAAAAACAAAATTTTAGAAAGTTTG
***
21830 GAGGCTAAATTTAAAATTTTAGAAAGTTT
1 GAGGCTAAAAACAAAATTTTAGAAAGTTT
21859 AGGGGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.33
Consensus pattern (30 bp):
GAGGCTAAAAACAAAATTTTAGAAAGTTTG
Found at i:21886 original size:30 final size:30
Alignment explanation
Indices: 21811--22015 Score: 154
Period size: 30 Copynumber: 6.9 Consensus size: 30
21801 GAGGTAAAAA
* *
21811 CAAAATTTTAGAAAGTTT-GGAGG-CTAAATT
1 CAAATTTTTGGAAAGTTTAGG-GGTC-AAATT
* * * *
21841 TAAAATTTTAGAAAGTTTAGGGGTTAAATT
1 CAAATTTTTGGAAAGTTTAGGGGTCAAATT
* * * *
21871 CTAATTTTTGTAAAGTTCA-AGGTCAAATT
1 CAAATTTTTGGAAAGTTTAGGGGTCAAATT
** **
21900 -GGATTTTTCAAAAAGTTT-GAGGGTCAAATT
1 CAAATTTTT-GGAAAGTTTAG-GGGTCAAATT
*
21930 CAAATTTTTGGAAAG--TATGGGTCAAATT
1 CAAATTTTTGGAAAGTTTAGGGGTCAAATT
** * *
21958 TGAATTTATGGAAAGTTTAGGGGTCAAACT
1 CAAATTTTTGGAAAGTTTAGGGGTCAAATT
21988 CAAATTTTTGGAAAGTTTAGGGGTCAAA
1 CAAATTTTTGGAAAGTTTAGGGGTCAAA
22016 ACATTAATTT
Statistics
Matches: 137, Mismatches: 29, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
28 29 0.21
29 14 0.10
30 86 0.63
31 8 0.06
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (30 bp):
CAAATTTTTGGAAAGTTTAGGGGTCAAATT
Found at i:21899 original size:59 final size:58
Alignment explanation
Indices: 21844--22008 Score: 185
Period size: 58 Copynumber: 2.8 Consensus size: 58
21834 CTAAATTTAA
* * * *
21844 AATTTTAGAAAGTTTAGGGGTTAAATTCTAATTTTTGTAAAGTTCA-AGGTCAAATTGG
1 AATTTTAGAAAGTTTAGGGGTCAAATTCAAATTTTTGGAAAGTT-ATAGGTCAAATTTG
* * *
21902 ATTTTTCAAAAAGTTT-GAGGGTCAAATTCAAATTTTTGGAAAG-TATGGGTCAAATTTG
1 AATTTT-AGAAAGTTTAG-GGGTCAAATTCAAATTTTTGGAAAGTTATAGGTCAAATTTG
* *
21960 AATTTATGGAAAGTTTAGGGGTCAAACTCAAATTTTTGGAAAGTT-TAGG
1 AATTT-TAGAAAGTTTAGGGGTCAAATTCAAATTTTTGGAAAGTTATAGG
22009 GGTCAAAACA
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
57 1 0.01
58 55 0.62
59 33 0.37
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.38
Consensus pattern (58 bp):
AATTTTAGAAAGTTTAGGGGTCAAATTCAAATTTTTGGAAAGTTATAGGTCAAATTTG
Found at i:22740 original size:20 final size:19
Alignment explanation
Indices: 22697--22746 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
22687 TTTATTTTCG
*
22697 ATATATATAA-AAAAGAAA
1 ATATATATAACATAAGAAA
22715 A-A-ATATAACATAAGAAA
1 ATATATATAACATAAGAAA
*
22732 TATATATATTACATA
1 -ATATATATAACATA
22747 TACGAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 6 0.23
17 8 0.31
18 2 0.08
19 1 0.04
20 9 0.35
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
ATATATATAACATAAGAAA
Found at i:32072 original size:4 final size:4
Alignment explanation
Indices: 32063--32194 Score: 67
Period size: 4 Copynumber: 31.8 Consensus size: 4
32053 TATGACATAC
*
32063 AAAT AAAT AAA- AAAT AAAT AAAT AAAATT AAAT -AAT GAAT AAAT ATAATT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAA-T AAAT AAAT AAAT AAAT A-AA-T
* * * * * *
32113 AAAT AAAGGT AAAG ATAT AAAT AGCAT AAA- AACT AAAA AAAT ATAT AAAAT
1 AAAT AAA--T AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT -AAAT
*
32164 ACAT -AA- AAAT AAAT AAAT AAAGT CAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAA-T -AAAT AAA
32195 GGCAAAAAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
3 11 0.11
4 59 0.60
5 18 0.18
6 10 0.10
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:32094 original size:14 final size:15
Alignment explanation
Indices: 32063--32266 Score: 65
Period size: 17 Copynumber: 12.3 Consensus size: 15
32053 TATGACATAC
32063 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
32078 AAATAAATAAAATTAA-
1 AAATAAATAAAA--AAT
*
32094 ATAATGAATAAATATAATT
1 A-AATAAATAAA-A-AA-T
*
32113 AAATAAAGGTAAAGATAT
1 AAATAAA--TAAA-AAAT
* *
32131 AAATAGCATAAAAACT
1 AAATA-AATAAAAAAT
*
32147 AAAAAAATATATAAAAT
1 AAATAAATA-A-AAAAT
* *
32164 ACATAAA-AATAAAT
1 AAATAAATAAAAAAT
*
32178 AAATAAAGTCAAATAAAGGC
1 AAATAAA-T-AAA-AAA--T
32198 AAA-AAA-AAAAACAT
1 AAATAAATAAAAA-AT
* *
32212 AAAAATGAATAACAAAT
1 --AAATAAATAAAAAAT
*
32229 AAATAAATAAAAGAAGAA
1 AAATAAAT-AAA-AA-AT
*
32247 AAATAAATAAAAATT
1 AAATAAATAAAAAAT
32262 AAATA
1 AAATA
32267 CTAAATAAAA
Statistics
Matches: 140, Mismatches: 24, Indels: 50
0.65 0.11 0.23
Matches are distributed among these distances:
14 10 0.07
15 30 0.21
16 20 0.14
17 38 0.27
18 28 0.20
19 6 0.04
20 8 0.06
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (15 bp):
AAATAAATAAAAAAT
Found at i:32103 original size:21 final size:21
Alignment explanation
Indices: 32063--32118 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
32053 TATGACATAC
*
32063 AAAT-AAA-TAAAAAATAAAT
1 AAATAAAATTAAATAATAAAT
*
32082 AAATAAAATTAAATAATGAAT
1 AAATAAAATTAAATAATAAAT
*
32103 AAATATAATTAAATAA
1 AAATAAAATTAAATAA
32119 AGGTAAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 25 0.78
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAAAATTAAATAATAAAT
Found at i:32119 original size:25 final size:24
Alignment explanation
Indices: 32063--32119 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
32053 TATGACATAC
32063 AAATAAATAAAAAATAAATAAATA
1 AAATAAATAAAAAATAAATAAATA
** *
32087 AAATTAAATAATGAATAAATATAATT
1 AAA-TAAATAAAAAATAAATA-AATA
32113 AAATAAA
1 AAATAAA
32120 GGTAAAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 19 0.68
26 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (24 bp):
AAATAAATAAAAAATAAATAAATA
Found at i:32158 original size:28 final size:27
Alignment explanation
Indices: 32127--32182 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
32117 AAAGGTAAAG
32127 ATAT-AAATAGCATAAAAACTAAAAAAAT
1 ATATAAAATA-CATAAAAA-TAAAAAAAT
*
32155 ATATAAAATACATAAAAATAAATAAAT
1 ATATAAAATACATAAAAATAAAAAAAT
32182 A
1 A
32183 AAGTCAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
28 12 0.46
29 5 0.19
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (27 bp):
ATATAAAATACATAAAAATAAAAAAAT
Found at i:32275 original size:11 final size:10
Alignment explanation
Indices: 32067--32266 Score: 75
Period size: 11 Copynumber: 18.9 Consensus size: 10
32057 ACATACAAAT
*
32067 AAATAAAAAA
1 AAATAAATAA
32077 TAAATAAATAA
1 -AAATAAATAA
*
32088 AATTAAATAA
1 AAATAAATAA
* *
32098 TGAATAAATAT
1 -AAATAAATAA
*
32109 AATTAAATAA
1 AAATAAATAA
** *
32119 AGGTAAAGATAT
1 AAAT-AA-ATAA
*
32131 AAATAGCATAA
1 AAATA-AATAA
32142 AAACT-AA-AA
1 AAA-TAAATAA
*
32151 AAATATAT-A
1 AAATAAATAA
*
32160 AAATACATAA
1 AAATAAATAA
32170 AAATAAATAAA
1 AAATAAAT-AA
32181 TAAAGTCAAATAA
1 -AAA-T-AAATAA
***
32194 AGGCAAA-AA
1 AAATAAATAA
*
32203 AAAAAACATAA
1 AAATAA-ATAA
*
32214 AAATGAATAA
1 AAATAAATAA
32224 CAAATAAATAA
1 -AAATAAATAA
* *
32235 ATAAAAGAAGAA
1 A-AATA-AATAA
32247 AAATAAATAA
1 AAATAAATAA
32257 AAATTAAATA
1 AAA-TAAATA
32267 CTAAATAAAA
Statistics
Matches: 139, Mismatches: 32, Indels: 36
0.67 0.15 0.17
Matches are distributed among these distances:
8 1 0.01
9 19 0.14
10 43 0.31
11 54 0.39
12 15 0.11
13 3 0.02
14 4 0.03
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.20
Consensus pattern (10 bp):
AAATAAATAA
Found at i:32275 original size:44 final size:48
Alignment explanation
Indices: 32170--32275 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 48
32160 AAATACATAA
* *
32170 AAATAAATAAATAAAGTCAAATAAAGGCAAAAAAAAAAACATAAAAAT
1 AAATAACTAAATAAAGTCAAATAAAAGCAAAAAAAAAAACATAAAAAT
* * *
32218 GAATAAC-AAATAAA-T-AAATAAAAG-AAGAAAAATAA-ATAAAAATT
1 AAATAACTAAATAAAGTCAAATAAAAGCAAAAAAAAAAACATAAAAA-T
32262 AAAT-ACTAAATAAA
1 AAATAACTAAATAAA
32276 ATAATGCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
43 9 0.18
44 20 0.40
45 8 0.16
46 1 0.02
47 7 0.14
48 5 0.10
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.17
Consensus pattern (48 bp):
AAATAACTAAATAAAGTCAAATAAAAGCAAAAAAAAAAACATAAAAAT
Found at i:32455 original size:16 final size:15
Alignment explanation
Indices: 32416--32469 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
32406 AATTAAAGGT
*
32416 ATAAATTAAAATTAGAA
1 ATAAAATAAAA-TA-AA
32433 ATAAAATAAAATAAA
1 ATAAAATAAAATAAA
**
32448 ACTAAAATCGAATAAA
1 A-TAAAATAAAATAAA
32464 ATAAAA
1 ATAAAA
32470 ATTACAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 8 0.24
16 15 0.45
17 10 0.30
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (15 bp):
ATAAAATAAAATAAA
Found at i:32471 original size:6 final size:5
Alignment explanation
Indices: 32416--32469 Score: 54
Period size: 5 Copynumber: 10.2 Consensus size: 5
32406 AATTAAAGGT
* **
32416 ATAAA TTAAA ATTAGAA ATAAA ATAAA ATAAA ACTAAA ATCGA ATAAA
1 ATAAA ATAAA A-TA-AA ATAAA ATAAA ATAAA A-TAAA ATAAA ATAAA
32464 ATAAA A
1 ATAAA A
32470 ATTACAAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 28 0.70
6 9 0.22
7 3 0.08
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:35084 original size:20 final size:20
Alignment explanation
Indices: 35059--35097 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35049 ATTATAAACA
35059 TTGGTAAAAAATAGCAAATG
1 TTGGTAAAAAATAGCAAATG
35079 TTGGTAAAAAATAGCAAAT
1 TTGGTAAAAAATAGCAAAT
35098 TTCAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (20 bp):
TTGGTAAAAAATAGCAAATG
Found at i:51903 original size:24 final size:24
Alignment explanation
Indices: 51876--51923 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
51866 TAAAAAGGGT
51876 GAAAATGTAAATAAACAAATTATA
1 GAAAATGTAAATAAACAAATTATA
51900 GAAAATGTAAATAAACAAATTATA
1 GAAAATGTAAATAAACAAATTATA
51924 ATATGACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.25
Consensus pattern (24 bp):
GAAAATGTAAATAAACAAATTATA
Found at i:58422 original size:30 final size:31
Alignment explanation
Indices: 58361--58419 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
58351 ACGTATCGCT
58361 AGATGTCACAATCTAAACCAGTTTGGGGGAA
1 AGATGTCACAATCTAAACCAGTTTGGGGGAA
58392 AGATGTCACAATCTAAACCAGTTTGGGG
1 AGATGTCACAATCTAAACCAGTTTGGGG
58420 AAATGGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (31 bp):
AGATGTCACAATCTAAACCAGTTTGGGGGAA
Found at i:59500 original size:24 final size:22
Alignment explanation
Indices: 59464--59507 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
59454 AACATGATAA
59464 TAGAGCAATTTCACTAGTTCAGAG
1 TAGAGCAATTTCA--AGTTCAGAG
59488 TAGAGGCAA-TTCAAGTTCAG
1 TAGA-GCAATTTCAAGTTCAG
59508 TAGGTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 7 0.37
24 8 0.42
25 4 0.21
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (22 bp):
TAGAGCAATTTCAAGTTCAGAG
Found at i:65990 original size:27 final size:27
Alignment explanation
Indices: 65960--66012 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
65950 TGTGTTTGAT
65960 AAATTTAGATCTTATTTAGTTGGTACA
1 AAATTTAGATCTTATTTAGTTGGTACA
65987 AAATTTAGATCTTATTTAGTTGGTAC
1 AAATTTAGATCTTATTTAGTTGGTAC
66013 TATGGTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (27 bp):
AAATTTAGATCTTATTTAGTTGGTACA
Found at i:68344 original size:3 final size:3
Alignment explanation
Indices: 68336--68388 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
68326 ATATATATCT
*
68336 TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
68383 TTA TTA
1 TTA TTA
68389 AGGGATATCG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:69395 original size:15 final size:15
Alignment explanation
Indices: 69377--69411 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
69367 CCTCAGCTAA
69377 TTCTTTCTCAGCATC
1 TTCTTTCTCAGCATC
**
69392 TTCTTTCTTGGCATC
1 TTCTTTCTCAGCATC
69407 TTCTT
1 TTCTT
69412 CCTTCTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.29, G:0.09, T:0.54
Consensus pattern (15 bp):
TTCTTTCTCAGCATC
Found at i:71549 original size:92 final size:92
Alignment explanation
Indices: 71392--71579 Score: 376
Period size: 92 Copynumber: 2.0 Consensus size: 92
71382 GTAAATCCTT
71392 AATTAGGACCGCACAATGAGGAAATACTTCGACCACTTCGAAAGGTCCAAACCAACATGAGCATA
1 AATTAGGACCGCACAATGAGGAAATACTTCGACCACTTCGAAAGGTCCAAACCAACATGAGCATA
71457 ATTTACCTGGGTGCAATTTCAGTCTAG
66 ATTTACCTGGGTGCAATTTCAGTCTAG
71484 AATTAGGACCGCACAATGAGGAAATACTTCGACCACTTCGAAAGGTCCAAACCAACATGAGCATA
1 AATTAGGACCGCACAATGAGGAAATACTTCGACCACTTCGAAAGGTCCAAACCAACATGAGCATA
71549 ATTTACCTGGGTGCAATTTCAGTCTAG
66 ATTTACCTGGGTGCAATTTCAGTCTAG
71576 AATT
1 AATT
71580 GAATAATAAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 96 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (92 bp):
AATTAGGACCGCACAATGAGGAAATACTTCGACCACTTCGAAAGGTCCAAACCAACATGAGCATA
ATTTACCTGGGTGCAATTTCAGTCTAG
Found at i:93505 original size:7 final size:7
Alignment explanation
Indices: 93493--93519 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
93483 ATTGCTAATT
93493 AATTTTA
1 AATTTTA
93500 AATTTTA
1 AATTTTA
93507 AATTTTA
1 AATTTTA
93514 AATTTT
1 AATTTT
93520 TGCATTATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:94501 original size:42 final size:42
Alignment explanation
Indices: 94455--94562 Score: 216
Period size: 42 Copynumber: 2.6 Consensus size: 42
94445 ACAAATTTAC
94455 ATATTCATCCATAAAATCTTTTATATTTGAATCCATGCTACA
1 ATATTCATCCATAAAATCTTTTATATTTGAATCCATGCTACA
94497 ATATTCATCCATAAAATCTTTTATATTTGAATCCATGCTACA
1 ATATTCATCCATAAAATCTTTTATATTTGAATCCATGCTACA
94539 ATATTCATCCATAAAATCTTTTAT
1 ATATTCATCCATAAAATCTTTTAT
94563 TTGTCACTCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.42
Consensus pattern (42 bp):
ATATTCATCCATAAAATCTTTTATATTTGAATCCATGCTACA
Found at i:105737 original size:24 final size:24
Alignment explanation
Indices: 105692--105737 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
105682 TACTTCTACA
** * *
105692 GTTTAATTTTTTTTTTTCTTATAT
1 GTTTAATACTTTTTATTATTATAT
105716 GTTTAATACTTTTTATTATTAT
1 GTTTAATACTTTTTATTATTAT
105738 TTTTTTTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (24 bp):
GTTTAATACTTTTTATTATTATAT
Found at i:106771 original size:16 final size:16
Alignment explanation
Indices: 106723--106771 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
106713 TTTAAAAATT
106723 TATTTTTTATAAATAA
1 TATTTTTTATAAATAA
* *
106739 -ATTATGTTAAAAAATAA
1 TATT-T-TTTATAAATAA
106756 TATTTTTTATAAATAA
1 TATTTTTTATAAATAA
106772 ATATATTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 10 0.38
18 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TATTTTTTATAAATAA
Found at i:106774 original size:17 final size:17
Alignment explanation
Indices: 106723--106775 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
106713 TTTAAAAATT
106723 TATTTTTTATAAATAAA
1 TATTTTTTATAAATAAA
* * *
106740 T-TATGTTA-AAAAATAA
1 TATTTTTTATAAATA-AA
106756 TATTTTTTATAAATAAA
1 TATTTTTTATAAATAAA
106773 TAT
1 TAT
106776 ATTGTTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
15 4 0.15
16 8 0.30
17 11 0.41
18 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATTTTTTATAAATAAA
Found at i:112507 original size:52 final size:52
Alignment explanation
Indices: 112212--112490 Score: 312
Period size: 52 Copynumber: 5.4 Consensus size: 52
112202 GATTCACTTC
* * * * * *
112212 ATTCATATACTAACGATGACACATA-TCCACCAGACC-TTATAATTCGTAAGGG
1 ATTCATATACTCACGATGACACTTAGT-CATCGGACCGTT-TAATCCGTAAAGG
* * ** *
112264 ATTCGTATACTCACAATGACACAGAGTCATCGAACC-TCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCGT-TTAATCCGTAAAGG
* * * * *
112316 ATCCATATACACACGATGACACTTAGCCATTGGACCATTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGG
* **
112368 ATTCATATACTCACGATGACACTTAGTCATCGGATCGTTTAATCTATAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGG
* *
112420 ATTCATATACTCATGATGACACTTAGTCATCGGACCGTTTAATCTGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGG
*
112472 ATTCATATACTCATGATGA
1 ATTCATATACTCACGATGA
112491 TTCATAATCA
Statistics
Matches: 195, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
52 192 0.98
53 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGG
Found at i:118081 original size:52 final size:51
Alignment explanation
Indices: 117986--118263 Score: 299
Period size: 52 Copynumber: 5.4 Consensus size: 51
117976 GATTTACTTC
* ** * * *
117986 ATTCATATACTCACGATGACACATAACCA-CCGAACCTTATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCAG-ACCTT-TAATCCGTAAAGG
* **
118038 ATTCGTATACTCACGATGACACAGAGTCATCAGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCAGACCT-TTAATCCGTAAAGG
* * * *
118090 ATCCATATACTCACAATGACACTTAGTTATCGGACCGTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCAGACC-TTTAATCCGTAAAGG
* *
118142 ATTCATATACTCAC-ATGAAACTTAGTCATCAGACTGTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCAGAC-CTTTAATCCGTAAAGG
* * * **
118193 ATTCATATACTTACAATGACACTTAGTCATCGGACCGTTTAATTTGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCAGACC-TTTAATCCGTAAAGG
*
118245 ATTCATATACTCATGATGA
1 ATTCATATACTCACGATGA
118264 TTCATAATCA
Statistics
Matches: 192, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
51 45 0.23
52 143 0.74
53 4 0.02
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGG
Found at i:118209 original size:103 final size:104
Alignment explanation
Indices: 117989--118263 Score: 340
Period size: 103 Copynumber: 2.7 Consensus size: 104
117979 TTACTTCATT
* * ** * * * * *
117989 CATATACTCACGATGACACATAACCACCGAACC-TTATAATCCGCAAGGGATTCGTATACTCACG
1 CATATACTCACAATGACACTTAGTCATCGGACCGTT-TAATCCGTAAAGGATTCATATACTCACG
*
118053 ATGACACAGAGTCATCAGACCTCTTAATCCGTAAAGGATC
65 ATGAAACAGAGTCATCAGACCTCTTAATCCGTAAAGGATC
*
118093 CATATACTCACAATGACACTTAGTTATCGGACCGTTTAATCCGTAAAGGATTCATATACTCAC-A
1 CATATACTCACAATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGGATTCATATACTCACGA
** * *
118157 TGAAACTTAGTCATCAGA-CTGTTTAATCCGTAAAGGATT
66 TGAAACAGAGTCATCAGACCT-CTTAATCCGTAAAGGATC
* ** *
118196 CATATACTTACAATGACACTTAGTCATCGGACCGTTTAATTTGTAAAGGATTCATATACTCATGA
1 CATATACTCACAATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGGATTCATATACTCACGA
118261 TGA
66 TGA
118264 TTCATAATCA
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
102 2 0.01
103 90 0.61
104 54 0.36
105 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (104 bp):
CATATACTCACAATGACACTTAGTCATCGGACCGTTTAATCCGTAAAGGATTCATATACTCACGA
TGAAACAGAGTCATCAGACCTCTTAATCCGTAAAGGATC
Found at i:124124 original size:18 final size:18
Alignment explanation
Indices: 124101--124145 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
124091 TGTGCAGCCT
*
124101 AACCAGATGCGATCATAA
1 AACCAGATGCAATCATAA
*
124119 AACCAGATGCAATCATAT
1 AACCAGATGCAATCATAA
*
124137 AATCAGATG
1 AACCAGATG
124146 TAACCACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (18 bp):
AACCAGATGCAATCATAA
Done.