Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010115.1 Kokia drynarioides strain JFW-HI SEQ_124902, 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: 116968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:1005 original size:19 final size:19
Alignment explanation
Indices: 977--1014 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
967 TTCATCTTTT
* *
977 CTTTCCAACTTTTTTTAAA
1 CTTTCAAACTTGTTTTAAA
996 CTTTCAAACTTGTTTTAAA
1 CTTTCAAACTTGTTTTAAA
1015 TTCATTCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.03, T:0.50
Consensus pattern (19 bp):
CTTTCAAACTTGTTTTAAA
Found at i:2097 original size:29 final size:30
Alignment explanation
Indices: 2052--2137 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 30
2042 AACTTTGGTT
* *
2052 AAAATAATAAAACAATCACTAAACATT-GA
1 AAAATAACAAACCAATCACTAAACATTAGA
* * *
2081 AAAGTTAC-AACTCAATCACTAAACTTTAGA
1 AAAATAACAAAC-CAATCACTAAACATTAGA
2111 AAAATAACAAACCAATCACT-AACATTA
1 AAAATAACAAACCAATCACTAAACATTA
2138 TCGAAAAGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 2 0.04
29 25 0.54
30 16 0.35
31 3 0.07
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.22
Consensus pattern (30 bp):
AAAATAACAAACCAATCACTAAACATTAGA
Found at i:2820 original size:22 final size:21
Alignment explanation
Indices: 2788--2829 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2778 AAAACAGGTC
* *
2788 ATTTTATTTTATTTTACTTTAT
1 ATTTTAGTTTATGTTA-TTTAT
2810 ATTTTAGTTTATGTTATTTA
1 ATTTTAGTTTATGTTATTTA
2830 CATCACCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (21 bp):
ATTTTAGTTTATGTTATTTAT
Found at i:7535 original size:57 final size:54
Alignment explanation
Indices: 7416--7538 Score: 131
Period size: 57 Copynumber: 2.2 Consensus size: 54
7406 AAATCCAATC
* *
7416 AAGGCAAAATAACAAGTGATGGAAATAACACCTGTGTATGCCTAATAGAGTAACT
1 AAGG-AAAATAACAAGTGATGGAAATAACACATGTGTAAGCCTAATAGAGTAACT
* * * * *
7471 AATGAAAATACCATGTGATGGAAATAACGCCACATGTGTAAGCCTAATA-ATTTATCT
1 AAGGAAAATAACAAGTGATGGAAATAA---CACATGTGTAAGCCTAATAGA-GTAACT
7528 AAGGAAAATAA
1 AAGGAAAATAA
7539 GCTTATCATG
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
54 21 0.38
55 3 0.05
56 1 0.02
57 30 0.55
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (54 bp):
AAGGAAAATAACAAGTGATGGAAATAACACATGTGTAAGCCTAATAGAGTAACT
Found at i:16382 original size:19 final size:19
Alignment explanation
Indices: 16355--16395 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
16345 AATGTAGAGA
16355 TAAAAATGAGC-ATGCAAAT
1 TAAAAATGAGCTATGC-AAT
*
16374 TAAATATGAGCTATGCAAT
1 TAAAAATGAGCTATGCAAT
16393 TAA
1 TAA
16396 TGGTAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (19 bp):
TAAAAATGAGCTATGCAAT
Found at i:16641 original size:29 final size:29
Alignment explanation
Indices: 16609--16794 Score: 198
Period size: 30 Copynumber: 6.3 Consensus size: 29
16599 AGTTTTAGAG
*
16609 AGTTTGGGGTCAAAATGTGATTTTTGGAA
1 AGTTCGGGGTCAAAATGTGATTTTTGGAA
**
16638 AGTTCAAGGTCAAAATGTGATTTTT-GAA
1 AGTTCGGGGTCAAAATGTGATTTTTGGAA
*
16666 AGTTCGGAGGTC-AAATGTAATTTTTTTGG-A
1 AGTTCGG-GGTCAAAATGTGA--TTTTTGGAA
** *
16696 AGTTTAGGGTTAAAATGTGATTTTTGGAA
1 AGTTCGGGGTCAAAATGTGATTTTTGGAA
* * *
16725 AGTTCGAGGGTTAAAATGTAATTTTTAGAA
1 AGTTCG-GGGTCAAAATGTGATTTTTGGAA
*
16755 AGTTCGAGGGTCAAAAGGTGATTTTTGGAA
1 AGTTCG-GGGTCAAAATGTGATTTTTGGAA
16785 AGTTCAGGGG
1 AGTTC-GGGG
16795 CTTACTAGGC
Statistics
Matches: 131, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
28 22 0.17
29 34 0.26
30 73 0.56
31 2 0.02
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (29 bp):
AGTTCGGGGTCAAAATGTGATTTTTGGAA
Found at i:16679 original size:58 final size:59
Alignment explanation
Indices: 16615--16793 Score: 224
Period size: 60 Copynumber: 3.1 Consensus size: 59
16605 AGAGAGTTTG
* *
16615 GGGTCAAAATGTGATTTTTGGAAAGTTCAAGGTCAAAATGTGATTTTT-GAAAGTTCG-
1 GGGTCAAAATGTAATTTTTGGAAAGTTCAGGGTCAAAATGTGATTTTTGGAAAGTTCGA
* *
16672 GAGGTC-AAATGTAATTTTTTTGG-AAGTTTAGGGTTAAAATGTGATTTTTGGAAAGTTCGA
1 G-GGTCAAAATGTAA--TTTTTGGAAAGTTCAGGGTCAAAATGTGATTTTTGGAAAGTTCGA
* * *
16732 GGGTTAAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAGGTGATTTTTGGAAAGTTC-A
1 GGGTCAAAATGTAATTTTTGGAAAGTTC-AGGGTCAAAATGTGATTTTTGGAAAGTTCGA
16791 GGG
1 GGG
16794 GCTTACTAGG
Statistics
Matches: 105, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
57 8 0.08
58 33 0.31
59 28 0.27
60 36 0.34
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTCAGGGTCAAAATGTGATTTTTGGAAAGTTCGA
Found at i:18910 original size:78 final size:76
Alignment explanation
Indices: 18779--19182 Score: 407
Period size: 78 Copynumber: 5.2 Consensus size: 76
18769 TCTACCCCGA
* * * * * *
18779 TCGGGGTAAAAGAT-TAGATGGCTGCAATCTGCCCCATGATCAGGGTAAAAGATTGGCTGATGAT
1 TCGGGGTAAAAGATCGA-ATGGCTGCAATCT-ACCCAGGCTCAGGGTAAGAGATTGGCTGATGGT
18843 GATTTGCCCCAAGC
64 GATTT-CCCCAAGC
* * *
18857 TCGGGGTAAAAGATCGAATGGCTGTAATCTACCTCAGGCTCAAGGTAAGAGATTGGTTGATGGTG
1 TCGGGGTAAAAGATCGAATGGCTGCAATCTACC-CAGGCTCAGGGTAAGAGATTGGCTGATGGTG
* **
18922 ATCTACCAGAAGC
65 AT-TTCCCCAAGC
* * * *
18935 TC-GGGTAAAAGATCGAATAGCTGCAATCTATCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
1 TCGGGGTAAAAGATCGAATGGCTGCAATCTA-CCCAGGCTCAGGGTAAGAGATTGGCTGATGGTG
*
18999 ATATGCCCCAAGC
65 AT-TTCCCCAAGC
* * * *
19012 TCGGGGTAAAAGATAGAATGGCTGCAATCTGCCCTAGGCTCAGGGTAAGAGATTGGCTGGTAGTG
1 TCGGGGTAAAAGATCGAATGGCTGCAATCTACCC-AGGCTCAGGGTAAGAGATTGGCTGATGGTG
* *
19077 ATTTACCCTAGAC
65 ATTTCCCCAAG-C
* * * ** * * *
19090 TCAGGGTAAAAGATCGGATGGTTGTGATCTGTCCAAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 TCGGGGTAAAAGATCGAATGGCTGCAATCT-ACCCAGGCTCAGGGTAAGAGATTGGCTGATGGTG
19155 ATCTTCCCCAAGC
65 AT-TTCCCCAAGC
*
19168 TCGAGGTAAAAGATC
1 TCGGGGTAAAAGATC
19183 CGATGGTTAT
Statistics
Matches: 268, Mismatches: 49, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
77 74 0.28
78 183 0.68
79 11 0.04
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (76 bp):
TCGGGGTAAAAGATCGAATGGCTGCAATCTACCCAGGCTCAGGGTAAGAGATTGGCTGATGGTGA
TTTCCCCAAGC
Found at i:19009 original size:39 final size:39
Alignment explanation
Indices: 18805--19181 Score: 178
Period size: 39 Copynumber: 9.7 Consensus size: 39
18795 GATGGCTGCA
* * * *
18805 ATCTGCCCCATGATCAGGGTAAAAGATTGGCTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* * ** * *
18844 ATTTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCT-GTA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCT-GATGGTG
* * * ** * *
18883 ATCTACCTCAGGCTCAAGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* ** * ** *
18922 ATCTACCAGAAGCTC-GGGTAAAAGATCGAAT-A-GCTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
** * *
18958 CAATCTATCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
* * *
18999 ATATGCCCCAAGCTCGGGGTAAAAGA-TAG--AATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGG-TG
* * * * * *
19036 CAATCTGCCCTAGGCTCAGGGTAAGAGATTGGCTGGTAGTG
1 --ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
** * * * * * *
19077 AT-TTACCCTAGACTCAGGGTAAAAGATCGGATGGTTGTG
1 ATCTGCCCCAAG-CTCGGGGTAAAAGATTGGCTGATGGTG
* *
19116 ATCTG-TCCAAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAA-GCTCGGGGTAAAAGATTGGCTGATGGTG
* *
19155 ATCTTCCCCAAGCTCGAGGTAAAAGAT
1 ATCTGCCCCAAGCTCGGGGTAAAAGAT
19182 CCGATGGTTA
Statistics
Matches: 246, Mismatches: 75, Indels: 34
0.69 0.21 0.10
Matches are distributed among these distances:
36 8 0.03
37 3 0.01
38 31 0.13
39 186 0.76
40 11 0.04
41 5 0.02
42 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTGATGGTG
Found at i:19064 original size:155 final size:156
Alignment explanation
Indices: 18821--19181 Score: 462
Period size: 155 Copynumber: 2.3 Consensus size: 156
18811 CCCATGATCA
* * * * *
18821 GGGTAAAAGATTGGCTGATGATGATTTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTGTAATC
1 GGGTAAGAGATTGGCTGATGGTGATATGCCCCAAGCTCGGGGTAAAAGATAGAATGGCTGCAATC
* *
18886 TACCTCAGGCTCAAGGTAAGAGATTGGTTGATGGTGATCTA-CC-AGAAGCTC-GGGTAAAAGAT
66 TACCTCAGGCTCAAGGTAAGAGATTGGCTGATAGTGATCTACCCTAG-A-CTCAGGGTAAAAGAT
18948 CGAATAGCTGCAATCTATCCCAA-GCTCG
129 CGAATAGCTGCAATCTAT-CCAAGGCTCG
*
18976 GGGTAAGAGATTGGCTAATGGTGATATGCCCCAAGCTCGGGGTAAAAGATAGAATGGCTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATATGCCCCAAGCTCGGGGTAAAAGATAGAATGGCTGCAATC
* * * *
19041 TGCC-CTAGGCTCAGGGTAAGAGATTGGCTGGTAGTGATTTACCCTAGACTCAGGGTAAAAGATC
66 TACCTC-AGGCTCAAGGTAAGAGATTGGCTGATAGTGATCTACCCTAGACTCAGGGTAAAAGATC
* * * ** *
19105 GGATGGTTGTGATCTGTCCAAGGCTCG
130 GAATAGCTGCAATCTATCCAAGGCTCG
* * *
19132 GGGTAAGAGATTGGCTGATGGTGATCTTCCCCAAGCTCGAGGTAAAAGAT
1 GGGTAAGAGATTGGCTGATGGTGATATGCCCCAAGCTCGGGGTAAAAGAT
19182 CCGATGGTTA
Statistics
Matches: 179, Mismatches: 22, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
154 1 0.01
155 99 0.55
156 77 0.43
157 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (156 bp):
GGGTAAGAGATTGGCTGATGGTGATATGCCCCAAGCTCGGGGTAAAAGATAGAATGGCTGCAATC
TACCTCAGGCTCAAGGTAAGAGATTGGCTGATAGTGATCTACCCTAGACTCAGGGTAAAAGATCG
AATAGCTGCAATCTATCCAAGGCTCG
Found at i:20221 original size:3 final size:3
Alignment explanation
Indices: 20213--20238 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20203 TATCTTGATT
20213 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
20239 GATTTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30980 original size:19 final size:19
Alignment explanation
Indices: 30956--30992 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
30946 AGAGATAAAA
30956 ATGAGC-ATGCAAATTAATT
1 ATGAGCTATGC-AATTAATT
30975 ATGAGCTATGCAATTAAT
1 ATGAGCTATGCAATTAAT
30993 GATAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGAGCTATGCAATTAATT
Found at i:31242 original size:30 final size:30
Alignment explanation
Indices: 31207--31350 Score: 163
Period size: 30 Copynumber: 4.8 Consensus size: 30
31197 GAGTTTGGTA
31207 TTAAAATGTGATTTTTGAAAAGTTT-GAGGG
1 TTAAAATGTGATTTTTGAAAAGTTTAG-GGG
*
31237 TTAAAATGTGATTTTTGGAAAGTTTAGGGG
1 TTAAAATGTGATTTTTGAAAAGTTTAGGGG
31267 TTAAAATGTGATTTTTTTGGAAAA-TTTAGGGG
1 TTAAAATGTGA--TTTTT-GAAAAGTTTAGGGG
* *
31299 TTAAAATG-CATTTTT-AAAAG-TTCGAGGG
1 TTAAAATGTGATTTTTGAAAAGTTTAG-GGG
* *
31327 TCAAAAGGTGATTTTTGAAAAGTT
1 TTAAAATGTGATTTTTGAAAAGTT
31351 CGGGGGCTTA
Statistics
Matches: 98, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
27 7 0.07
28 9 0.09
29 11 0.11
30 43 0.44
31 3 0.03
32 21 0.21
33 4 0.04
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (30 bp):
TTAAAATGTGATTTTTGAAAAGTTTAGGGG
Found at i:31312 original size:31 final size:32
Alignment explanation
Indices: 31218--31313 Score: 112
Period size: 32 Copynumber: 3.1 Consensus size: 32
31208 TAAAATGTGA
*
31218 TTTTT-GAAAAGTTT-GAGGGTTAAAATGTGA--
1 TTTTTGGAAAA-TTTAG-GGGTTAAAATGTCATT
* *
31248 TTTTTGGAAAGTTTAGGGGTTAAAATGTGATT
1 TTTTTGGAAAATTTAGGGGTTAAAATGTCATT
31280 TTTTTGGAAAATTTAGGGGTTAAAATG-CATT
1 TTTTTGGAAAATTTAGGGGTTAAAATGTCATT
31311 TTT
1 TTT
31314 AAAAGTTCGA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
30 22 0.37
31 11 0.19
32 26 0.44
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.44
Consensus pattern (32 bp):
TTTTTGGAAAATTTAGGGGTTAAAATGTCATT
Found at i:32972 original size:23 final size:22
Alignment explanation
Indices: 32932--32979 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
32922 AGGACATTAA
* *
32932 TAAATTTAAATGATTTTAAACT
1 TAAATTTAAATAAATTTAAACT
*
32954 TAAATTTAAAATAAATTTAAATT
1 TAAATTT-AAATAAATTTAAACT
32977 TAA
1 TAA
32980 GTTTTATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAATTTAAATAAATTTAAACT
Found at i:36250 original size:18 final size:17
Alignment explanation
Indices: 36229--36326 Score: 70
Period size: 18 Copynumber: 5.5 Consensus size: 17
36219 TGTCTTTAGG
36229 TGAGCTCGCAACTTCCAA
1 TGAGCTCGCAACTT-CAA
* * **
36247 TGAGCTTGCAAATTTGGA
1 TGAGCTCGC-AACTTCAA
*
36265 TGAGCTCACAACTTCAA
1 TGAGCTCGCAACTTCAA
* * *
36282 GTGAGCTTGCAAGTGCAGA
1 -TGAGCTCGCAACTTCA-A
*
36301 TGAGCTCGCAGCTTCAA
1 TGAGCTCGCAACTTCAA
36318 GTGAGCTCG
1 -TGAGCTCG
36327 TGACTTGGCA
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
17 6 0.10
18 48 0.81
19 5 0.08
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (17 bp):
TGAGCTCGCAACTTCAA
Found at i:36269 original size:36 final size:36
Alignment explanation
Indices: 36229--36324 Score: 122
Period size: 36 Copynumber: 2.7 Consensus size: 36
36219 TGTCTTTAGG
***
36229 TGAGCTCGCAACTTCCAA-TGAGCTTGCAAATTTGGA
1 TGAGCTCGCAACTT-CAAGTGAGCTTGCAAATGCAGA
* *
36265 TGAGCTCACAACTTCAAGTGAGCTTGCAAGTGCAGA
1 TGAGCTCGCAACTTCAAGTGAGCTTGCAAATGCAGA
*
36301 TGAGCTCGCAGCTTCAAGTGAGCT
1 TGAGCTCGCAACTTCAAGTGAGCT
36325 CGTGACTTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
35 3 0.06
36 49 0.94
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (36 bp):
TGAGCTCGCAACTTCAAGTGAGCTTGCAAATGCAGA
Found at i:41635 original size:19 final size:19
Alignment explanation
Indices: 41613--41687 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
41603 TAAATTTCAT
41613 TATTTATTAGAAATTTTGG
1 TATTTATTAGAAATTTTGG
* *
41632 TA-TTGTTAGAAATATTGG
1 TATTTATTAGAAATTTTGG
* *
41650 TATTCAATAGAAATTTTGG
1 TATTTATTAGAAATTTTGG
*
41669 TATTTAGTTACAAATTTTG
1 TATTTA-TTAGAAATTTTG
41688 ATATCCGGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
18 16 0.36
19 19 0.42
20 10 0.22
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (19 bp):
TATTTATTAGAAATTTTGG
Found at i:41642 original size:18 final size:19
Alignment explanation
Indices: 41619--41687 Score: 79
Period size: 18 Copynumber: 3.6 Consensus size: 19
41609 TCATTATTTA
41619 TTAGAAATTTTGGTATT-G
1 TTAGAAATTTTGGTATTAG
*
41637 TTAGAAATATTGGTATTCA-
1 TTAGAAATTTTGGTATT-AG
*
41656 ATAGAAATTTTGGTATTTAG
1 TTAGAAATTTTGGTA-TTAG
*
41676 TTACAAATTTTG
1 TTAGAAATTTTG
41688 ATATCCGGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
18 16 0.38
19 14 0.33
20 12 0.29
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.46
Consensus pattern (19 bp):
TTAGAAATTTTGGTATTAG
Found at i:42595 original size:60 final size:62
Alignment explanation
Indices: 42499--42616 Score: 152
Period size: 60 Copynumber: 1.9 Consensus size: 62
42489 TTGGCATAAT
* * * *
42499 AATAAATTTAGCCCTTCAATGTTTACAGATTCTATCAATTT-GATCTTAATTCTAAAAATTTC
1 AATAAATTTAGACCTTCAATCTTTACACATTATATCAATTTAG-TCTTAATTCTAAAAATTTC
* *
42561 AATAAATTTA-ACCTTCAA-CTTTACACATTATATCAATTTAGTGTTGATTCTAAAAA
1 AATAAATTTAGACCTTCAATCTTTACACATTATATCAATTTAGTCTTAATTCTAAAAA
42617 ATTAAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 31 0.63
61 8 0.16
62 10 0.20
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (62 bp):
AATAAATTTAGACCTTCAATCTTTACACATTATATCAATTTAGTCTTAATTCTAAAAATTTC
Found at i:43826 original size:19 final size:20
Alignment explanation
Indices: 43804--43845 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
43794 AAGAATACCC
*
43804 AAATTTGTAA-TTGATACAA
1 AAATTTGTAACATGATACAA
43823 AAATTTGTAACATGATACAA
1 AAATTTGTAACATGATACAA
43843 AAA
1 AAA
43846 AACTCTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATTTGTAACATGATACAA
Found at i:51380 original size:14 final size:13
Alignment explanation
Indices: 51342--51384 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
51332 ATTTACAAAA
51342 ATAAATATA-AAT
1 ATAAATATATAAT
51354 ATAAATATATAAT
1 ATAAATATATAAT
*
51367 ATTAAATCTATAAT
1 A-TAAATATATAAT
51381 -TAAA
1 ATAAA
51385 ATAAAATAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 13 0.46
13 4 0.14
14 11 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAATATATAAT
Found at i:52600 original size:14 final size:14
Alignment explanation
Indices: 52578--52660 Score: 82
Period size: 14 Copynumber: 6.0 Consensus size: 14
52568 AAGTCAAAGT
52578 CAGTCAACGGTCAA
1 CAGTCAACGGTCAA
* *
52592 CAGTTAACGG-CAG
1 CAGTCAACGGTCAA
*
52605 CAGTCAA-AGTCAA
1 CAGTCAACGGTCAA
* *
52618 CAATCAATGGTCAA
1 CAGTCAACGGTCAA
52632 C-GATCAACGGTCAA
1 CAG-TCAACGGTCAA
52646 CAGTCAACGGGTCAA
1 CAGTCAAC-GGTCAA
52661 GTTCGGGTGG
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
12 1 0.02
13 16 0.29
14 31 0.56
15 7 0.13
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (14 bp):
CAGTCAACGGTCAA
Found at i:64304 original size:21 final size:21
Alignment explanation
Indices: 64280--64321 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
64270 ATACTTATTA
*
64280 TTTGTTTAACACGAATTACCT
1 TTTGTCTAACACGAATTACCT
64301 TTTGTCTAACACGAATTACCT
1 TTTGTCTAACACGAATTACCT
64322 AATGTTCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (21 bp):
TTTGTCTAACACGAATTACCT
Found at i:65109 original size:24 final size:25
Alignment explanation
Indices: 65056--65102 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
65046 GTCTGTTTCA
65056 TATTTTTCTTCCAATTAAACTTTGC
1 TATTTTTCTTCCAATTAAACTTTGC
*
65081 TATTTTT-TT-CAGTTAAACTTTG
1 TATTTTTCTTCCAATTAAACTTTG
65103 ATTATTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 2 0.10
25 7 0.33
ACGTcount: A:0.23, C:0.15, G:0.06, T:0.55
Consensus pattern (25 bp):
TATTTTTCTTCCAATTAAACTTTGC
Found at i:69566 original size:22 final size:23
Alignment explanation
Indices: 69535--69583 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
69525 TTGATTCTTC
69535 AAACCCTAAAACCAAAA-CTAAA
1 AAACCCTAAAACCAAAACCTAAA
* * *
69557 AAACCTTAAACCCAAAACCTTAA
1 AAACCCTAAAACCAAAACCTAAA
69580 AAAC
1 AAAC
69584 AAACATAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.59, C:0.29, G:0.00, T:0.12
Consensus pattern (23 bp):
AAACCCTAAAACCAAAACCTAAA
Found at i:69601 original size:22 final size:22
Alignment explanation
Indices: 69576--69649 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
69566 ACCCAAAACC
*
69576 TTAAAAACAAACATAAACATAA
1 TTAAAAACAAAAATAAACATAA
*
69598 TTAAATACAAAAATAAAAACTATTAA
1 TTAAAAACAAAAAT--AAAC-A-TAA
*
69624 TTAAATAA-AAATATAAACATAA
1 TTAAA-AACAAAAATAAACATAA
69646 TTAA
1 TTAA
69650 TTTCTAATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 19 0.44
23 1 0.02
24 8 0.19
25 1 0.02
26 13 0.30
27 1 0.02
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (22 bp):
TTAAAAACAAAAATAAACATAA
Found at i:70045 original size:18 final size:18
Alignment explanation
Indices: 70030--70093 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
70020 GCTCATATGA
70030 CTCGAGCTCAAGAT-ATTG
1 CTCGAGCTCAAGATCA-TG
*
70048 CTCGAGGTCAAGATCATG
1 CTCGAGCTCAAGATCATG
* * *
70066 CTTGGGCTCAAGATCGTG
1 CTCGAGCTCAAGATCATG
70084 CTCGAGCTCA
1 CTCGAGCTCA
70094 TGCTCAAGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 37 0.97
19 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (18 bp):
CTCGAGCTCAAGATCATG
Found at i:71875 original size:21 final size:21
Alignment explanation
Indices: 71836--71875 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
71826 TATGCAAATT
*
71836 AATCAAAAAAATAAGCATACC
1 AATCAAAAAAATAAACATACC
71857 AATC-AAAAAATAAAACATA
1 AATCAAAAAAAT-AAACATA
71876 AACATACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.68, C:0.15, G:0.03, T:0.15
Consensus pattern (21 bp):
AATCAAAAAAATAAACATACC
Found at i:71881 original size:27 final size:27
Alignment explanation
Indices: 71841--71893 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
71831 AAATTAATCA
*
71841 AAAAAATAAGCATACCAATCAAAAAAT
1 AAAAAATAAACATACCAATCAAAAAAT
* **
71868 AAAACATAAACATACCTTTCAAAAAA
1 AAAAAATAAACATACCAATCAAAAAA
71894 CCTTCTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.64, C:0.17, G:0.02, T:0.17
Consensus pattern (27 bp):
AAAAAATAAACATACCAATCAAAAAAT
Found at i:71999 original size:18 final size:18
Alignment explanation
Indices: 71968--72012 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
71958 TCAAAAAGCA
71968 AAAAAAAAATAACAT-AT
1 AAAAAAAAATAACATAAT
*
71985 AAAAAAATATGAACATAAT
1 AAAAAAAAAT-AACATAAT
72004 AAACAAAAA
1 AAA-AAAAA
72013 CTACTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 5 0.22
19 5 0.22
20 4 0.17
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAAAAAAATAACATAAT
Found at i:88476 original size:95 final size:95
Alignment explanation
Indices: 88351--88552 Score: 377
Period size: 95 Copynumber: 2.1 Consensus size: 95
88341 AGAATCCATA
88351 CTTGTATCGGTACAAGTACAGAGTAGGAGAGAGGTTGCTCATTGACTTGGGTTGTATCAATAGTT
1 CTTGTATCGGTACAAGTACAGAGTAGGAGAGAGGTTGCTCATTGACTTGGGTTGTATCAATAGTT
*
88416 GCATAGTAGGTATCGGTAGTTTTGTGTATG
66 GCATAGTAGGTATCGGTAGTTCTGTGTATG
*
88446 CTTGTATCGGTACAAGTACAGAGTAGGAGAGAGGTTGCTCATTGACTTGGGTTGTATCGATAGTT
1 CTTGTATCGGTACAAGTACAGAGTAGGAGAGAGGTTGCTCATTGACTTGGGTTGTATCAATAGTT
88511 GCATAGTAGGTATCGGTAGTTCTGTGTATG
66 GCATAGTAGGTATCGGTAGTTCTGTGTATG
*
88541 CTTTTATCGGTA
1 CTTGTATCGGTA
88553 GTTAGGATGC
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 104 1.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.35
Consensus pattern (95 bp):
CTTGTATCGGTACAAGTACAGAGTAGGAGAGAGGTTGCTCATTGACTTGGGTTGTATCAATAGTT
GCATAGTAGGTATCGGTAGTTCTGTGTATG
Found at i:88659 original size:21 final size:21
Alignment explanation
Indices: 88635--88683 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
88625 AAGTAAGACA
88635 TGTATCGGTAGAACTGTCACT
1 TGTATCGGTAGAACTGTCACT
* *
88656 TGTACCAGTAGAACTGTCACT
1 TGTATCGGTAGAACTGTCACT
88677 TGTATCG
1 TGTATCG
88684 ATAGTAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (21 bp):
TGTATCGGTAGAACTGTCACT
Found at i:89205 original size:17 final size:17
Alignment explanation
Indices: 89183--89226 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
89173 TTGACAAAAG
*
89183 AATTGTGCATAATAA-AT
1 AATTGTG-ATAACAAGAT
89200 AATTGTGATAACAAGTAT
1 AATTGTGATAACAAG-AT
89218 AATTGTGAT
1 AATTGTGAT
89227 TGCAACTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 7 0.29
18 11 0.46
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (17 bp):
AATTGTGATAACAAGAT
Found at i:93116 original size:20 final size:17
Alignment explanation
Indices: 93079--93113 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
93069 TATGTAAGCT
93079 TACCTATGAAATTGTTG
1 TACCTATGAAATTGTTG
93096 TACCTATGAAATTGTTG
1 TACCTATGAAATTGTTG
93113 T
1 T
93114 TGTTTTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (17 bp):
TACCTATGAAATTGTTG
Found at i:95518 original size:12 final size:12
Alignment explanation
Indices: 95503--95540 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
95493 ATTATGACTT
95503 AATTTATTTATA
1 AATTTATTTATA
* *
95515 AATTAAATTATA
1 AATTTATTTATA
95527 AATTTATTT-TA
1 AATTTATTTATA
95538 AAT
1 AAT
95541 GATTTCTAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTATTTATA
Found at i:97679 original size:21 final size:21
Alignment explanation
Indices: 97654--97704 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
97644 GGATTATATA
97654 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
97675 CTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
97696 ATTTGGATT
1 ATTTGGATT
97705 ATGCTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Done.