Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013867.1 Kokia drynarioides strain JFW-HI SEQ_128895, 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: 111038
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:961 original size:15 final size:13
Alignment explanation
Indices: 949--981 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
939 TAGGTGTCAA
949 GTATTTTTTTGTC
1 GTATTTTTTTGTC
962 GTA-TTTTTT-TC
1 GTATTTTTTTGTC
973 GTATTTTTT
1 GTATTTTTT
982 GAAAAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.26
12 11 0.58
13 3 0.16
ACGTcount: A:0.09, C:0.06, G:0.12, T:0.73
Consensus pattern (13 bp):
GTATTTTTTTGTC
Found at i:974 original size:11 final size:12
Alignment explanation
Indices: 953--982 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
943 TGTCAAGTAT
953 TTTTTTGTCGTA
1 TTTTTTGTCGTA
965 TTTTTT-TCGTA
1 TTTTTTGTCGTA
976 TTTTTTG
1 TTTTTTG
983 AAAAAAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.73
Consensus pattern (12 bp):
TTTTTTGTCGTA
Found at i:1638 original size:21 final size:21
Alignment explanation
Indices: 1600--1639 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1590 TGTTCACTCC
* * *
1600 ATTGCAATTTTTATTTTCAGT
1 ATTGAAATTTTAAATTTCAGT
1621 ATTGAAATTTTAAATTTCA
1 ATTGAAATTTTAAATTTCA
1640 AAACATCAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTGAAATTTTAAATTTCAGT
Found at i:2106 original size:144 final size:144
Alignment explanation
Indices: 1910--2199 Score: 519
Period size: 144 Copynumber: 2.0 Consensus size: 144
1900 TGTTATAAAT
*
1910 AATTGTATACCTGAAATAAATATTACATAAAATATATTAAATTATAAATAAAAATGATCTTTCTA
1 AATTGTATACCTGAAATAAATATTACATAAAATATATTAAATTATAAATAAAAATCATCTTTCTA
*
1975 AAAGTAAAAGTTAAAAAAATGTTTTTACTTTTAGGTTTAAAAACACTTTTAACTCAAAAATTTAT
66 AAAGTAAAAGTTAAAAAAATGTTTTTACTTTTAGGTTCAAAAACACTTTTAACTCAAAAATTTAT
*
2040 GGGTTTATTTGGAC
131 GGATTTATTTGGAC
2054 AATTGTATA-CTGGAAATAAATATTACATAAAATATATTAAATTATAAATAAAAATCATCTTTCT
1 AATTGTATACCT-GAAATAAATATTACATAAAATATATTAAATTATAAATAAAAATCATCTTTCT
* *
2118 AAAAGTAAAAGTTAAAAAAATGTTTTTACTTTTAGGTTCAAAAATACTTTTAACTTAAAAATTTA
65 AAAAGTAAAAGTTAAAAAAATGTTTTTACTTTTAGGTTCAAAAACACTTTTAACTCAAAAATTTA
2183 TGGATTTATTTGGAC
130 TGGATTTATTTGGAC
2198 AA
1 AA
2200 CACAAAGTAA
Statistics
Matches: 140, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
143 2 0.01
144 138 0.99
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (144 bp):
AATTGTATACCTGAAATAAATATTACATAAAATATATTAAATTATAAATAAAAATCATCTTTCTA
AAAGTAAAAGTTAAAAAAATGTTTTTACTTTTAGGTTCAAAAACACTTTTAACTCAAAAATTTAT
GGATTTATTTGGAC
Found at i:10183 original size:20 final size:19
Alignment explanation
Indices: 10151--10193 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
10141 ACCCTTAAAC
10151 TTAAGTTTAAATTTAAAGT
1 TTAAGTTTAAATTTAAAGT
* *
10170 TTAAGGTTTGAATTTAGAGT
1 TTAA-GTTTAAATTTAAAGT
10190 TTAA
1 TTAA
10194 AATATGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (19 bp):
TTAAGTTTAAATTTAAAGT
Found at i:10185 original size:26 final size:26
Alignment explanation
Indices: 10156--10212 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
10146 TAAACTTAAG
* *
10156 TTTA-AATTTAAAGTTTAAGGTTTGAA
1 TTTAGAATTTAAAATATAA-GTTTGAA
* *
10182 TTTAGAGTTTAAAATATGAGTTTGAA
1 TTTAGAATTTAAAATATAAGTTTGAA
10208 TTTAG
1 TTTAG
10213 GGTAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.46
Consensus pattern (26 bp):
TTTAGAATTTAAAATATAAGTTTGAA
Found at i:13392 original size:13 final size:12
Alignment explanation
Indices: 13367--13396 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
13357 TTTATTTATA
13367 ATTTATTTTGTT
1 ATTTATTTTGTT
13379 ATTTATTGTTGTT
1 ATTTATT-TTGTT
13392 ATTTA
1 ATTTA
13397 AAACATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (12 bp):
ATTTATTTTGTT
Found at i:22458 original size:5 final size:5
Alignment explanation
Indices: 22448--22479 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
22438 AACAAGAAAT
22448 AAAA- AAAA- AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
22480 ACAAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:22485 original size:10 final size:10
Alignment explanation
Indices: 22426--22486 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
22416 ATGCAAAATT
*
22426 AAAAAAATG-
1 AAAAAAAAGA
*
22435 AAAAACAAGA
1 AAAAAAAAGA
*
22445 AATAAAAAAAA
1 AA-AAAAAAGA
22456 AAAAGAAAAGA
1 AAAA-AAAAGA
*
22467 AAAGAAAAGA
1 AAAAAAAAGA
*
22477 AAAACAAAGA
1 AAAAAAAAGA
22487 TAAATTCCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
9 7 0.17
10 18 0.44
11 16 0.39
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:22485 original size:15 final size:14
Alignment explanation
Indices: 22429--22486 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
22419 CAAAATTAAA
*
22429 AAAATGAAAAACAAG
1 AAAA-GAAAAAAAAG
*
22444 -AAATAAAAAAAA-
1 AAAAGAAAAAAAAG
22456 AAAAGAAAAGAAAAG
1 AAAAGAAAA-AAAAG
22471 AAAAGAAAAACAAAG
1 AAAAGAAAAA-AAAG
22486 A
1 A
22487 TAAATTCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 14 0.39
14 8 0.22
15 14 0.39
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:26303 original size:6 final size:6
Alignment explanation
Indices: 26292--26320 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
26282 ATTTAGATAT
26292 AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAAT
26321 TGTTTACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:29071 original size:19 final size:19
Alignment explanation
Indices: 29047--29086 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
29037 GTACTAAGAG
29047 TTTGATTGTATTTTGCTTC
1 TTTGATTGTATTTTGCTTC
29066 TTTGATTGTATTTTGCTTC
1 TTTGATTGTATTTTGCTTC
29085 TT
1 TT
29087 CTACTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.65
Consensus pattern (19 bp):
TTTGATTGTATTTTGCTTC
Found at i:33453 original size:2 final size:2
Alignment explanation
Indices: 33446--33472 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33436 TCTAGGGTTT
33446 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
33473 TTATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38861 original size:17 final size:17
Alignment explanation
Indices: 38835--38875 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
38825 AAAACCAAAT
*
38835 CAGTTTATTAGAAATAA
1 CAGTTCATTAGAAATAA
*
38852 CAGTTCATTAGACATAA
1 CAGTTCATTAGAAATAA
*
38869 CAATTCA
1 CAGTTCA
38876 CACACACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (17 bp):
CAGTTCATTAGAAATAA
Found at i:46723 original size:15 final size:15
Alignment explanation
Indices: 46684--46727 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
46674 ATATTTGATA
*
46684 TTTTTT-AAATTATT
1 TTTTTTAAAAATATT
46698 TTTTATGTAAAAATATT
1 TTTT-T-TAAAAATATT
46715 TTTTTTAAAAATA
1 TTTTTTAAAAATA
46728 ATACATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 2 0.08
17 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TTTTTTAAAAATATT
Found at i:46857 original size:27 final size:28
Alignment explanation
Indices: 46823--46879 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
46813 ACACTTCCAT
*
46823 AAAAAT-AATAAATGTTTTGTAATATTA
1 AAAAATAAATAAATATTTTGTAATATTA
**
46850 AAAAATAAATAAATATTTTGTTGTATTA
1 AAAAATAAATAAATATTTTGTAATATTA
46878 AA
1 AA
46880 TATAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (28 bp):
AAAAATAAATAAATATTTTGTAATATTA
Found at i:48794 original size:201 final size:201
Alignment explanation
Indices: 48449--49363 Score: 1433
Period size: 201 Copynumber: 4.6 Consensus size: 201
48439 ATTAATAGTT
* *
48449 TTTTTAATCCGGGGAAGACGATTGAAATATGTTAATGGTAACATCCTGTATAAGCATCTTTAGTT
1 TTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTTAGTT
* *
48514 GTTTGTATAGCTATATACAAATCCGGATTGAAAACTTGTGTTATAAAGTCGTATATTAGTTGCTC
66 GTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAAAGTTGTATATTAGTTGCTC
* * *
48579 GAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCTGGTGATCGAGCATACATCGTTTTCAAG
131 GAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGATCATACATCGTTTTAAAG
48644 CAAGTG
196 CAAGTG
* * *
48650 TTTTTAATCCGGGGAAGATGATTGAAAGACGTTAATGGTAACATCTTGTGTAAGCATCTTTAGTT
1 TTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTTAGTT
* *
48715 GTTTGTATAGCTATATACACATCCGGATCGAAAACTTGTGTTATAAAGTTGTATATTAGATGCTC
66 GTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAAAGTTGTATATTAGTTGCTC
* * *
48780 GAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATTGACCATACATCATTTTAAAG
131 GAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGATCATACATCGTTTTAAAG
48845 CAAGT-
196 CAAGTG
48850 TTCTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTTAGT
1 TT-TTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTTAGT
* * * * *
48915 T-ATAGTATAGCTATATACAAATCTGGATAGAAAACTTGTGTTATAAAGTTGTGTATTAGTTGCT
65 TGTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAAAGTTGTATATTAGTTGCT
* * * *
48979 CAAAAACTCTGATTTAGTGAAAGGCAAAGAAATTTCTCTGGTGATCGATCATACATCGTTTTAAA
130 CGAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGATCATACATCGTTTTAAA
49044 GCAAGTG
195 GCAAGTG
* * *
49051 TTTTTAATCCAGGGAAGACGATTGAAAGATGTTAATGTTAACATCTTGTATGAGCATCTTTAGTT
1 TTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTTAGTT
*
49116 GTTTGTATAGCTATATACAAATCCGTATCGAAAACTTGTGTTATAAAGTTGTATATTAGTTGCGT
66 GTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAAAGTTGTATATTAGTTGC-T
49181 -GAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGATCATACATCGTTTTAAA
130 CGAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGATCATACATCGTTTTAAA
*
49245 GCAAGTTTT
195 GCAAG--TG
* *
49254 TTTTTAATCTGGGGAAGACGATTGAAAGATGTTAATGATAACATCTTGTATAAGCATCTTTAGTT
1 TTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTTAGTT
* * ** * *
49319 -ATTGTTTAGCTATATACAAATTGGGATTGAAAACTTTTGTTATAA
66 GTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAA
49364 GGGGTAAAAG
Statistics
Matches: 652, Mismatches: 56, Indels: 11
0.91 0.08 0.02
Matches are distributed among these distances:
200 182 0.28
201 369 0.57
202 39 0.06
203 62 0.10
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (201 bp):
TTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTTAGTT
GTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAAAGTTGTATATTAGTTGCTC
GAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGATCATACATCGTTTTAAAG
CAAGTG
Found at i:49195 original size:401 final size:401
Alignment explanation
Indices: 48445--49363 Score: 1509
Period size: 401 Copynumber: 2.3 Consensus size: 401
48435 TTATATTAAT
* *
48445 AGTTTTTTTAATCCGGGGAAGACGATTGAAATATGTTAATGGTAACATCCTGTATAAGCATCTTT
1 AGTTTTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTT
* *
48510 AGTTGTTTGTATAGCTATATACAAATCCGGATTGAAAACTTGTGTTATAAAGTCGTATATTAGTT
66 AGTT-ATTGTATAGCTATATACAAATCTGGATTGAAAACTTGTGTTATAAAGTCGTATATTAGTT
* *
48575 GCTCGAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCTGGTGATCGAGCATACATCGTTTT
130 GCTCAAAAACTCTGATTTAGTGAAAGGAAAAGAAATTTCTCTGGTGATCGAGCATACATCGTTTT
* * * *
48640 CAAGCAAGTGTTTTTAATCCGGGGAAGATGATTGAAAGACGTTAATGGTAACATCTTGTGTAAGC
195 AAAGCAAGTGTTTTTAATCCAGGGAAGACGATTGAAAGACGTTAATGGTAACATCTTGTATAAGC
*
48705 ATCTTTAGTTGTTTGTATAGCTATATACACATCCGGATCGAAAACTTGTGTTATAAAGTTGTATA
260 ATCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAAAGTTGTATA
*
48770 TTAGATGCTCGAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATTGACCATACAT
325 TTAGATGCTCGAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGACCATACAT
48835 CATTTTAAAGCA
390 CATTTTAAAGCA
*
48847 AGTTTCTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTT
1 AGTTTTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTT
* * * *
48912 AGTTATAGTATAGCTATATACAAATCTGGATAGAAAACTTGTGTTATAAAGTTGTGTATTAGTTG
66 AGTTATTGTATAGCTATATACAAATCTGGATTGAAAACTTGTGTTATAAAGTCGTATATTAGTTG
* *
48977 CTCAAAAACTCTGATTTAGTGAAAGGCAAAGAAATTTCTCTGGTGATCGATCATACATCGTTTTA
131 CTCAAAAACTCTGATTTAGTGAAAGGAAAAGAAATTTCTCTGGTGATCGAGCATACATCGTTTTA
* * *
49042 AAGCAAGTGTTTTTAATCCAGGGAAGACGATTGAAAGATGTTAATGTTAACATCTTGTATGAGCA
196 AAGCAAGTGTTTTTAATCCAGGGAAGACGATTGAAAGACGTTAATGGTAACATCTTGTATAAGCA
*
49107 TCTTTAGTTGTTTGTATAGCTATATACAAATCCGTATCGAAAACTTGTGTTATAAAGTTGTATAT
261 TCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAAAGTTGTATAT
* *
49172 TAGTTGCGT-GAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGATCATACAT
326 TAGATGC-TCGAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGACCATACAT
*
49236 CGTTTTAAAGCA
390 CATTTTAAAGCA
* *
49248 AGTTTTTTTTTAATCTGGGGAAGACGATTGAAAGATGTTAATGATAACATCTTGTATAAGCATCT
1 AG--TTTTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCT
* *
49313 TTAGTTATTGTTTAGCTATATACAAAT-TGGGATTGAAAACTTTTGTTATAA
64 TTAGTTATTGTATAGCTATATACAAATCT-GGATTGAAAACTTGTGTTATAA
49364 GGGGTAAAAG
Statistics
Matches: 480, Mismatches: 33, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
401 309 0.64
402 68 0.14
403 103 0.21
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (401 bp):
AGTTTTTTTAATCCGGGGAAGACGATTGAAAGATGTTAATGGTAACATCTTGTATAAGCATCTTT
AGTTATTGTATAGCTATATACAAATCTGGATTGAAAACTTGTGTTATAAAGTCGTATATTAGTTG
CTCAAAAACTCTGATTTAGTGAAAGGAAAAGAAATTTCTCTGGTGATCGAGCATACATCGTTTTA
AAGCAAGTGTTTTTAATCCAGGGAAGACGATTGAAAGACGTTAATGGTAACATCTTGTATAAGCA
TCTTTAGTTGTTTGTATAGCTATATACAAATCCGGATCGAAAACTTGTGTTATAAAGTTGTATAT
TAGATGCTCGAAAACTTTGATTTAGTGAAAGGAAAAGAAATTTCTCCGGTGATCGACCATACATC
ATTTTAAAGCA
Found at i:50863 original size:22 final size:24
Alignment explanation
Indices: 50833--50883 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
50823 TAACAGTAAT
*
50833 TAAATAAATA-ATT-ATAAAATTA
1 TAAAAAAATATATTAATAAAATTA
**
50855 TAAAAAAATATATTAATAATTTTA
1 TAAAAAAATATATTAATAAAATTA
50879 TAAAA
1 TAAAA
50884 TTTATTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
23 3 0.12
24 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAAAAATATATTAATAAAATTA
Found at i:56792 original size:12 final size:12
Alignment explanation
Indices: 56777--56802 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56767 TCTCACATTT
56777 ATTTTTCTCAAA
1 ATTTTTCTCAAA
56789 ATTTTTCTCAAA
1 ATTTTTCTCAAA
56801 AT
1 AT
56803 CAGAAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTTCTCAAA
Found at i:57281 original size:45 final size:45
Alignment explanation
Indices: 57208--57300 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
57198 TATAGAAGCT
57208 CTAGGAAAAATGAAGAGTTCGGGAAAAAAAATAAGGGATTTTGTG
1 CTAGGAAAAATGAAGAGTTCGGGAAAAAAAATAAGGGATTTTGTG
* *
57253 CTAGGAAAAATGAAGAGTTTGGGGAAAAAAATAAGGGATTTTGTG
1 CTAGGAAAAATGAAGAGTTCGGGAAAAAAAATAAGGGATTTTGTG
57298 CTA
1 CTA
57301 CATATAGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.24
Consensus pattern (45 bp):
CTAGGAAAAATGAAGAGTTCGGGAAAAAAAATAAGGGATTTTGTG
Found at i:62469 original size:21 final size:21
Alignment explanation
Indices: 62445--62485 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62435 TGTTCTTGTA
62445 GTTGTAGTTGTAGCTGTTCTT
1 GTTGTAGTTGTAGCTGTTCTT
* *
62466 GTTGTGGTTGTTGCTGTTCT
1 GTTGTAGTTGTAGCTGTTCT
62486 GGCTCGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.10, G:0.32, T:0.54
Consensus pattern (21 bp):
GTTGTAGTTGTAGCTGTTCTT
Found at i:63952 original size:12 final size:12
Alignment explanation
Indices: 63937--63980 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
63927 CTTATTAAGA
63937 TAAATATTAA-AT
1 TAAAT-TTAATAT
63949 TAAATTTAATAT
1 TAAATTTAATAT
63961 TAAATTT--TAT
1 TAAATTTAATAT
63971 TAAA-TTAATA
1 TAAATTTAATA
63981 GAATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.07
10 7 0.24
11 6 0.21
12 14 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATTTAATAT
Found at i:63988 original size:21 final size:22
Alignment explanation
Indices: 63947--63988 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
63937 TAAATATTAA
*
63947 ATTAAATTTAATATTAAATTTT
1 ATTAAATTTAATATGAAATTTT
63969 ATTAAA-TTAATA-GAATATTT
1 ATTAAATTTAATATGAA-ATTT
63989 ATCTACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATATGAAATTTT
Found at i:64968 original size:24 final size:26
Alignment explanation
Indices: 64939--64988 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
64929 AAAATTTGAA
64939 TTAAAAAAT-AAAA-AATTAAATTCT
1 TTAAAAAATAAAAATAATTAAATTCT
64963 TTAAAAAATAAAAATAATTAAATTCT
1 TTAAAAAATAAAAATAATTAAATTCT
64989 AGATATACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 9 0.38
25 4 0.17
26 11 0.46
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (26 bp):
TTAAAAAATAAAAATAATTAAATTCT
Found at i:66934 original size:35 final size:35
Alignment explanation
Indices: 66882--66949 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
66872 AATGTAGTTA
* *
66882 ACGGAATAACTATAGAGTTACACATGGTATGCCAC
1 ACGGAATAACTAGAGAGTTACACATGGCATGCCAC
*
66917 ACGGAATAACTGGAGAGTTACACATGGCATGCC
1 ACGGAATAACTAGAGAGTTACACATGGCATGCC
66950 GCATGTACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (35 bp):
ACGGAATAACTAGAGAGTTACACATGGCATGCCAC
Found at i:73857 original size:2 final size:2
Alignment explanation
Indices: 73852--73881 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73842 TTATATACGA
73852 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
73882 TCTACTTTGA
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:75086 original size:189 final size:188
Alignment explanation
Indices: 74691--75188 Score: 666
Period size: 189 Copynumber: 2.6 Consensus size: 188
74681 AGCAATTAGA
* *
74691 GGCCGAGAGAAGAATCATAAATTATTTA--AGGTTTAAAGTGTAATTTTGTCATTATACTAACAA
1 GGCC-AGAGAAGAATCATAAATTA-TTAGGAGG-TTAAAGTGTAATTTTATCATTATACTAACAT
*
74754 ATAATTTCATAAAAATTAAGAAGTTAAATGACAAATTTACCATTTTTGAGGGGCCAA-ACATCTA
63 ATAATTTCATAAAAATTAAGAAGTTAAATGACAAATCTACCATTTTTGAGGGGCCAAGACATCTA
* * *
74818 CTTGCACCTTTTGTCTTCGTCTCTATTCATCCAAGGACGAGGTTAGAAAATTGTTGTAGGG
128 CTTGCACCTTTTGTCTTCGTCTCCATTCAGCCAAGGACGAGGCTAGAAAATTGTTGTAGGG
* * * * * *
74879 GGCCAAAGAAGAATCATAAATTATTAGGAGGTCAAAGTGTAATTTTACCATTATATTGACATGTA
1 GGCCAGAGAAGAATCATAAATTATTAGGAGGTTAAAGTGTAATTTTATCATTATACTAACATATA
* * * *
74944 ATTTCATAAAAATTTAAGAAGTTAAATGACAAATCTATCATTTTTTAGGGACCAAGGC-TCCTAG
66 ATTTCATAAAAA-TTAAGAAGTTAAATGACAAATCTACCATTTTTGAGGGGCCAAGACAT-CTA-
* * *
75008 C-TGCCCCTTTTGTCTTCGTCTCCGTTCAGCCAAGGACGAGGCTAGAAATTTGTTGTAGGG
128 CTTGCACCTTTTGTCTTCGTCTCCATTCAGCCAAGGACGAGGCTAGAAAATTGTTGTAGGG
* * *
75068 GGGCAGAGAAGAATCATAAATTATTAGGAGGTTAAAGTGGAATTTTATCATTATACTAACCTATA
1 GGCCAGAGAAGAATCATAAATTATTAGGAGGTTAAAGTGTAATTTTATCATTATACTAACATATA
**
75133 ATTTCATAAAAAATTAA-AGAGTTAAATGGTAAATCTACCATTTTTGAGGGGCCAAG
66 ATTTCAT-AAAAATTAAGA-AGTTAAATGACAAATCTACCATTTTTGAGGGGCCAAG
75189 CCCTCTGCCT
Statistics
Matches: 269, Mismatches: 33, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
186 3 0.01
187 57 0.21
188 47 0.17
189 156 0.58
190 6 0.02
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (188 bp):
GGCCAGAGAAGAATCATAAATTATTAGGAGGTTAAAGTGTAATTTTATCATTATACTAACATATA
ATTTCATAAAAATTAAGAAGTTAAATGACAAATCTACCATTTTTGAGGGGCCAAGACATCTACTT
GCACCTTTTGTCTTCGTCTCCATTCAGCCAAGGACGAGGCTAGAAAATTGTTGTAGGG
Found at i:77693 original size:37 final size:36
Alignment explanation
Indices: 77652--77723 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
77642 TTAGTTAAGT
77652 TCAAATATTTTTACTTTACCTC-ATTTTCCCCTAAAAC
1 TCAAA-ATTTTTACTTTACC-CAATTTTCCCCTAAAAC
* *
77689 TCAAACTTTTTACTTTACCCAATTTTTCCCTAAAA
1 TCAAAATTTTTACTTTACCCAATTTTCCCCTAAAA
77724 GTTAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 1 0.03
36 26 0.81
37 5 0.16
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (36 bp):
TCAAAATTTTTACTTTACCCAATTTTCCCCTAAAAC
Found at i:87826 original size:20 final size:21
Alignment explanation
Indices: 87788--87833 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
87778 ATATTCATAG
* *
87788 TAATTTAAGATTCTCTTTA-T
1 TAATTTAAAATTCTATTTATT
*
87808 TAATTTAAAATTTTATTTATT
1 TAATTTAAAATTCTATTTATT
87829 TAATT
1 TAATT
87834 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TAATTTAAAATTCTATTTATT
Found at i:92143 original size:31 final size:31
Alignment explanation
Indices: 92112--92185 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
92102 ACGCTATAAT
*
92112 TTTTTGTATTTTTG-TAAATTTGTATTTTAA
1 TTTTTGTATTTTTGATAAATTTGTACTTTAA
*
92142 TTTTT-T-TTTTAGAAATAAATTTGTACTTTAA
1 TTTTTGTATTTTTG--ATAAATTTGTACTTTAA
92173 TTTTTGTATTTTT
1 TTTTTGTATTTTT
92186 ATTTTTAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 5 0.14
29 1 0.03
30 5 0.14
31 20 0.56
32 1 0.03
33 4 0.11
ACGTcount: A:0.24, C:0.01, G:0.08, T:0.66
Consensus pattern (31 bp):
TTTTTGTATTTTTGATAAATTTGTACTTTAA
Found at i:96883 original size:31 final size:30
Alignment explanation
Indices: 96848--96926 Score: 122
Period size: 31 Copynumber: 2.6 Consensus size: 30
96838 ATAATCTAAT
96848 ATTTGGTACTTAAACTTGACACTTTTTCTTA
1 ATTTGGTACTTAAACTTGACACTTTTT-TTA
* *
96879 ATTTGGTACCTAAACTTGACACTTTTTTTT
1 ATTTGGTACTTAAACTTGACACTTTTTTTA
96909 ATGTTGGTACTTAAACTT
1 AT-TTGGTACTTAAACTT
96927 TTTGCGGTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 4 0.09
31 40 0.91
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (30 bp):
ATTTGGTACTTAAACTTGACACTTTTTTTA
Found at i:97169 original size:32 final size:31
Alignment explanation
Indices: 97133--97232 Score: 89
Period size: 32 Copynumber: 3.3 Consensus size: 31
97123 TAAATTTAGG
97133 TACCAAATTAGAAAAAAAATATCAAGTTTAAA
1 TACCAAATTAGAAAAAAAATAT-AAGTTTAAA
**** **
97165 TACCAAATT-GGGTTAAAA-A-AAGTTTAGG
1 TACCAAATTAGAAAAAAAATATAAGTTTAAA
* *
97193 TACTAAATTAGAAAAAAAATGTTAAGTTTAAA
1 TACCAAATTAGAAAAAAAAT-ATAAGTTTAAA
97225 TACCAAAT
1 TACCAAAT
97233 GTTATATTAA
Statistics
Matches: 49, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
28 15 0.31
29 5 0.10
30 1 0.02
31 5 0.10
32 23 0.47
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (31 bp):
TACCAAATTAGAAAAAAAATATAAGTTTAAA
Found at i:100874 original size:40 final size:40
Alignment explanation
Indices: 100830--100910 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
100820 AATTCCTGAA
100830 AATAAAAATACAGGGACTAAATTCCAAATTTATGAAGAAT
1 AATAAAAATACAGGGACTAAATTCCAAATTTATGAAGAAT
100870 AATAAAAATACAGGGACTAAATTCCAAATTTATGAAGAAT
1 AATAAAAATACAGGGACTAAATTCCAAATTTATGAAGAAT
100910 A
1 A
100911 GAGGGATCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (40 bp):
AATAAAAATACAGGGACTAAATTCCAAATTTATGAAGAAT
Found at i:103047 original size:30 final size:32
Alignment explanation
Indices: 103013--103081 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
103003 AGTTAGGTCC
* *
103013 TGAACTTGATAATTTTTC-CACACTGGAGC-T
1 TGAACTTGACAATTATTCTCACACTGGAGCTT
* * *
103043 TGAACTAGACAATTATTCTCATATTGGAGCTT
1 TGAACTTGACAATTATTCTCACACTGGAGCTT
103075 TGAACTT
1 TGAACTT
103082 TTTTTCGTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 15 0.48
31 9 0.29
32 7 0.23
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (32 bp):
TGAACTTGACAATTATTCTCACACTGGAGCTT
Found at i:107555 original size:18 final size:17
Alignment explanation
Indices: 107532--107566 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
107522 GGCTTGGTTG
107532 CCTCAGGATCATCTATCT
1 CCTCAGGATCATC-ATCT
*
107550 CCTCAGGCTCATCATCT
1 CCTCAGGATCATCATCT
107567 AACCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.37, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTCAGGATCATCATCT
Done.