Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015129.1 Kokia drynarioides strain JFW-HI SEQ_130173, 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: 947447
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1279 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:838251 original size:16 final size:15
Alignment explanation
Indices: 838230--838277 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
838220 TTTAAATAAA
838230 TTTTTTACTTTAAATT
1 TTTTTTA-TTTAAATT
*
838246 TTTTTTAATTAAATT
1 TTTTTTATTTAAATT
* *
838261 CTATTTATTTTAAATT
1 TTTTTTA-TTTAAATT
838277 T
1 T
838278 ATTTATATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTATTTAAATT
Found at i:838291 original size:15 final size:15
Alignment explanation
Indices: 838226--838296 Score: 58
Period size: 15 Copynumber: 4.7 Consensus size: 15
838216 TTATTTTAAA
838226 TAAATTT-TTTACT-T
1 TAAATTTATTTA-TAT
*
838240 TAAATTT-TTTTTAAT
1 TAAATTTATTTAT-AT
*
838255 TAAATTCTATTTATTT
1 TAAATT-TATTTATAT
838271 TAAATTTATTTATAT
1 TAAATTTATTTATAT
* *
838286 TCAATTAATTT
1 TAAATTTATTT
838297 CTTTTTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
13 1 0.02
14 10 0.21
15 24 0.51
16 8 0.17
17 4 0.09
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
TAAATTTATTTATAT
Found at i:838372 original size:21 final size:21
Alignment explanation
Indices: 838348--838398 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
838338 TGAAACTGTA
*
838348 TTTTTAATTAAATTCTATTTC
1 TTTTAAATTAAATTCTATTTC
** *
838369 TTTTAAATTTTATTTTATTTC
1 TTTTAAATTAAATTCTATTTC
838390 TTTTAAATT
1 TTTTAAATT
838399 TTATTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTAAATTAAATTCTATTTC
Found at i:838399 original size:16 final size:15
Alignment explanation
Indices: 838380--838413 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
838370 TTTAAATTTT
*
838380 ATTTTATTTCTTTTAA
1 ATTTTATTT-TTTAAA
838396 ATTTTATTTTTTAAA
1 ATTTTATTTTTTAAA
838411 ATT
1 ATT
838414 AATTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTATTTTTTAAA
Found at i:838399 original size:21 final size:21
Alignment explanation
Indices: 838363--838405 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
838353 AATTAAATTC
838363 TATTTCTTTTAAATTTTATTT
1 TATTTCTTTTAAATTTTATTT
838384 TATTTCTTTTAAATTTTATTT
1 TATTTCTTTTAAATTTTATTT
838405 T
1 T
838406 TTAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTTCTTTTAAATTTTATTT
Found at i:838428 original size:11 final size:11
Alignment explanation
Indices: 838412--838441 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
838402 TTTTTTAAAA
838412 TTAATTAATTT
1 TTAATTAATTT
*
838423 TTAATTTATTT
1 TTAATTAATTT
838434 TTAATTAA
1 TTAATTAA
838442 AAATACAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTAATTAATTT
Found at i:838483 original size:15 final size:16
Alignment explanation
Indices: 838463--838647 Score: 85
Period size: 16 Copynumber: 10.9 Consensus size: 16
838453 AAAGAAATAT
838463 AAATAAAT-TAATTTA
1 AAATAAATATAATTTA
* *
838478 AAATAAATAGAATCTA
1 AAATAAATATAATTTA
838494 ATAA-AAATATAATTTCA
1 A-AATAAATATAATTT-A
838511 ACTTATATAAAT-TAATTTA
1 A---A-ATAAATATAATTTA
*
838530 AAATAAATAGAATTTA
1 AAATAAATATAATTTA
* *
838546 ATAAAAAATCAAAATTAATTGA
1 A-AATAAAT----A-TAATTTA
*
838568 ATATAAATA-AATTTA
1 AAATAAATATAATTTA
*
838583 AAATAAATAGAATTTA
1 AAATAAATATAATTTA
*
838599 ATTAA-AAATAAAATTTTA
1 A--AATAAATATAA-TTTA
* *
838617 AACAAAAAAAT-ATTTA
1 AA-ATAAATATAATTTA
*
838633 AAATAAATACAATTT
1 AAATAAATATAATTT
838648 CAACCTGCTT
Statistics
Matches: 131, Mismatches: 18, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
15 32 0.24
16 41 0.31
17 20 0.15
18 11 0.08
19 4 0.03
20 7 0.05
21 10 0.08
22 6 0.05
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATAAATATAATTTA
Found at i:838527 original size:52 final size:51
Alignment explanation
Indices: 838465--838647 Score: 196
Period size: 53 Copynumber: 3.5 Consensus size: 51
838455 AGAAATATAA
*
838465 ATAAATTAATTTAAAATAAATAGAATCTAATAAAAATATAATTTCAACTT-AT
1 ATAAATTAATTTAAAATAAATAGAATTTAATAAAAATATAATTT-AA-TTAAT
*
838517 ATAAATTAATTTAAAATAAATAGAATTTAATAAAAA-ATCAAAATTAATTGAAT
1 ATAAATTAATTTAAAATAAATAGAATTTAATAAAAATAT--AATTTAATT-AAT
* * **
838570 ATAAATAAATTTAAAATAAATAGAATTTAATTAAAAATAAAATTTTAAACAA-
1 ATAAATTAATTTAAAATAAATAGAATTTAA-TAAAAATATAA-TTTAATTAAT
* *
838622 A-AAAAT-ATTTAAAATAAATACAATTT
1 ATAAATTAATTTAAAATAAATAGAATTT
838648 CAACCTGCTT
Statistics
Matches: 114, Mismatches: 10, Indels: 16
0.81 0.07 0.11
Matches are distributed among these distances:
50 19 0.17
51 7 0.06
52 38 0.33
53 39 0.34
54 10 0.09
55 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (51 bp):
ATAAATTAATTTAAAATAAATAGAATTTAATAAAAATATAATTTAATTAAT
Found at i:838591 original size:21 final size:21
Alignment explanation
Indices: 838567--838610 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
838557 AAATTAATTG
* *
838567 AATATAAATAAATTTAAAATA
1 AATAGAAATAAATTAAAAATA
* *
838588 AATAGAATTTAATTAAAAATA
1 AATAGAAATAAATTAAAAATA
838609 AA
1 AA
838611 ATTTTAAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAGAAATAAATTAAAAATA
Found at i:838613 original size:17 final size:18
Alignment explanation
Indices: 838479--838614 Score: 69
Period size: 17 Copynumber: 7.8 Consensus size: 18
838469 ATTAATTTAA
* *
838479 AATAAATAGAATCTAA-T
1 AATAAATAAAATTTAATT
*
838496 AA-AAATATAATTTCAACTT
1 AATAAATAAAATTT-AA-TT
*
838515 ATATAAAT-TAATTTAA--
1 A-ATAAATAAAATTTAATT
*
838531 AATAAATAGAATTTAA-T
1 AATAAATAAAATTTAATT
*
838548 AAAAAATCAAAA-TTAATT
1 AATAAAT-AAAATTTAATT
838566 GAATATAA-ATAAATTTAA--
1 -AATA-AATA-AAATTTAATT
*
838584 AATAAATAGAATTTAATT
1 AATAAATAAAATTTAATT
838602 AA-AAATAAAATTT
1 AATAAATAAAATTT
838615 TAAACAAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 32
0.70 0.06 0.24
Matches are distributed among these distances:
15 6 0.06
16 26 0.27
17 29 0.31
18 7 0.07
19 10 0.11
20 13 0.14
21 4 0.04
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
AATAAATAAAATTTAATT
Found at i:840680 original size:13 final size:14
Alignment explanation
Indices: 840646--840680 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
840636 TTTCCCCAAA
*
840646 TTCTTTCCTCTTTC
1 TTCTTCCCTCTTTC
840660 TTCTTCCCTCTTTC
1 TTCTTCCCTCTTTC
840674 -TCTTCCC
1 TTCTTCCC
840681 CCCCCCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (14 bp):
TTCTTCCCTCTTTC
Found at i:842158 original size:20 final size:20
Alignment explanation
Indices: 842135--842173 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
842125 TTTAAAAGTC
842135 ATAAAAATATT-AAAAAATAT
1 ATAAAAAT-TTCAAAAAATAT
842155 ATAAAAATTTCAAAAAATA
1 ATAAAAATTTCAAAAAATA
842174 AAAATCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAAAATTTCAAAAAATAT
Found at i:842394 original size:21 final size:20
Alignment explanation
Indices: 842359--842398 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
842349 GTCAATAACT
*
842359 AAATTTATCATTATATCTATA
1 AAATTTATCAGTATA-CTATA
*
842380 AAATTTATGAGTATACTAT
1 AAATTTATCAGTATACTAT
842399 TATCTTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTTATCAGTATACTATA
Found at i:843275 original size:29 final size:29
Alignment explanation
Indices: 843242--843302 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
843232 AGAGCTTATG
843242 TGATAGATTCTAAAGTGAATTAAATATTT
1 TGATAGATTCTAAAGTGAATTAAATATTT
843271 TGATAGATTCTAAAGTGAATTAAATATTT
1 TGATAGATTCTAAAGTGAATTAAATATTT
843300 TGA
1 TGA
843303 ACTAGTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (29 bp):
TGATAGATTCTAAAGTGAATTAAATATTT
Found at i:844659 original size:51 final size:51
Alignment explanation
Indices: 844533--844763 Score: 257
Period size: 51 Copynumber: 4.5 Consensus size: 51
844523 AAGGGATCCA
* * * *
844533 ATGACTAAGTGTCATTGTGAGCAAATGAATCCTTTATGGATTACAAGGGTCTG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTA-AA-GGTCCG
*
844586 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCA
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCG
* * *
844637 ATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCG
* * ** * ** *
844688 ATGACTTAGTGTCATTGTGAGTGTATGAATTCCTATACGGAACAAGAGATCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AGGTCCG
*
844741 ATGACTATA-TGTCATCATGAGTA
1 ATGACTA-AGTGTCATCGTGAGTA
844764 TTAAATGAAA
Statistics
Matches: 151, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
51 76 0.50
52 11 0.07
53 63 0.42
54 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCG
Found at i:844745 original size:104 final size:104
Alignment explanation
Indices: 844527--844763 Score: 291
Period size: 104 Copynumber: 2.3 Consensus size: 104
844517 AAACGAAAGG
* * * * *
844527 GATCCAATGACTAAGTGTCATTGTGAGCAAATGAATCCTTTATGGATTACAAGGGTCTGATGACT
1 GATCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTACAAGGGTCCGATGACT
* **
844592 AAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
66 AAGTGTCATCGTGAGTAAATGAATCCTATACGGAACAAA
*
844631 GGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTA-AA-GGTCCGATGACT
1 GATCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTACAAGGGTCCGATGACT
* * **
844694 TAGTGTCATTGTGAGTGTATGAATTCCTATACGGAACAAGA
66 AAGTGTCATCGTGAGTAAATGAA-TCCTATACGGAACAA-A
* *
844735 GATCCGATGACTATA-TGTCATCATGAGTA
1 GATCCAATGACTA-AGTGTCATCGTGAGTA
844764 TTAAATGAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
102 30 0.26
103 14 0.12
104 69 0.61
105 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (104 bp):
GATCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTACAAGGGTCCGATGACT
AAGTGTCATCGTGAGTAAATGAATCCTATACGGAACAAA
Found at i:849551 original size:2 final size:2
Alignment explanation
Indices: 849544--849577 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
849534 ACATACCTTT
*
849544 CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
849578 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:849954 original size:23 final size:23
Alignment explanation
Indices: 849923--850065 Score: 61
Period size: 23 Copynumber: 6.4 Consensus size: 23
849913 GTTTTTGGGC
*
849923 AACAAAGAGCACACACAATGCTA
1 AACAGAGAGCACACACAATGCTA
*
849946 AACAGAGAGTACACA-AA-G-T-
1 AACAGAGAGCACACACAATGCTA
* * *
849965 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAATGCTA
* * * *
849985 ATCATAGAGCACACGA-ATTGCAAA
1 AACAGAGAGCACAC-ACAATGC-TA
** *
850009 TAACAGAGAGCACGAGGC-GTGCTA
1 -AACAGAGAGCAC-ACACAATGCTA
* *
850033 AACGGAGAGCACACACATTGCTA
1 AACAGAGAGCACACACAATGCTA
850056 AACAGAGAGC
1 AACAGAGAGC
850066 GCGCTAAAGT
Statistics
Matches: 87, Mismatches: 20, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
16 8 0.09
17 1 0.01
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 4 0.05
23 50 0.57
24 3 0.03
25 13 0.15
26 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAATGCTA
Found at i:854243 original size:70 final size:68
Alignment explanation
Indices: 854122--854250 Score: 188
Period size: 70 Copynumber: 1.9 Consensus size: 68
854112 TTTAATAGAT
*
854122 TTAATATATAATTTAGTTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTTATT
1 TTAATATATAATTTAGTTTAATACTTATCTTAATAGTATTATATTAATTTAATATTAAAGTTATT
854187 GTC
66 GTC
* * *
854190 TTAATAT-TAAATTTAATTTTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAA
1 TTAATATAT-AATTT-AGTTTAATACTTATCTTAAT-AGTATTATATTAATTTAATATTAAA
854251 ATGATTAAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
67 1 0.02
68 12 0.22
69 17 0.31
70 24 0.44
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (68 bp):
TTAATATATAATTTAGTTTAATACTTATCTTAATAGTATTATATTAATTTAATATTAAAGTTATT
GTC
Found at i:857780 original size:18 final size:18
Alignment explanation
Indices: 857757--857808 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
857747 ACTCAACTTG
857757 ACAATGGAAAATTTTATA
1 ACAATGGAAAATTTTATA
857775 ACAATGGAAAATTTTATA
1 ACAATGGAAAATTTTATA
* *
857793 ACAATTGATAATTTTA
1 ACAATGGAAAATTTTA
857809 CAAATTAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (18 bp):
ACAATGGAAAATTTTATA
Found at i:858123 original size:17 final size:17
Alignment explanation
Indices: 858101--858134 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
858091 TAGGTTTAGT
858101 AGTTTTGGGTAAGTTTA
1 AGTTTTGGGTAAGTTTA
858118 AGTTTTGGGTAAGTTTA
1 AGTTTTGGGTAAGTTTA
858135 CCGGGTTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (17 bp):
AGTTTTGGGTAAGTTTA
Found at i:859882 original size:20 final size:20
Alignment explanation
Indices: 859859--859927 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
859849 GAAACAGAGA
*
859859 CAAAAGTCAAAAAACAAAAG
1 CAAAAGACAAAAAACAAAAG
*
859879 CAAAAGACAAGAAACAAGAAG
1 CAAAAGACAAAAAACAA-AAG
* *
859900 ACAAGAGAAAAAAAAACAAAATG
1 -CAAAAG-ACAAAAAACAAAA-G
859923 CAAAA
1 CAAAA
859928 ACCGATTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 15 0.38
21 3 0.08
22 11 0.28
23 10 0.26
ACGTcount: A:0.71, C:0.13, G:0.13, T:0.03
Consensus pattern (20 bp):
CAAAAGACAAAAAACAAAAG
Found at i:860790 original size:30 final size:30
Alignment explanation
Indices: 860754--860846 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 30
860744 ATTTATTGTG
*
860754 TTTTTTAAAATTAAATCCTTTTATATTTAT
1 TTTTTTAAAATTAAACCCTTTTATATTTAT
* *
860784 TTTTTT-AAATTTAACCCTTTTATTTTTAT
1 TTTTTTAAAATTAAACCCTTTTATATTTAT
* *
860813 TTCTTTTAAAATT--ACCCTTTGAT-TCTAT
1 TT-TTTTAAAATTAAACCCTTTTATATTTAT
860841 TTTTTT
1 TTTTTT
860847 TATTTTGTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
27 4 0.07
28 6 0.11
29 31 0.55
30 10 0.18
31 5 0.09
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTTTAAAATTAAACCCTTTTATATTTAT
Found at i:860847 original size:28 final size:30
Alignment explanation
Indices: 860754--860848 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
860744 ATTTATTGTG
* *
860754 TTTTTTAAAATTAAATCCTTTTATATT-TA-T
1 TTTTTTAAAATT-AACCCTTTGAT-TTCTATT
* * *
860784 TTTTTTAAATTTAACCCTTTTATTTTTATT
1 TTTTTTAAAATTAACCCTTTGATTTCTATT
*
860814 TCTTTTAAAATT-ACCCTTTGA-TTCTATT
1 TTTTTTAAAATTAACCCTTTGATTTCTATT
860842 TTTTTTA
1 TTTTTTA
860849 TTTTGTAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 14 0.25
29 20 0.36
30 22 0.39
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTTTAAAATTAACCCTTTGATTTCTATT
Found at i:860896 original size:18 final size:18
Alignment explanation
Indices: 860869--860906 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
860859 CTTTTATATC
860869 TTTTTTAATTAAAT-CTT
1 TTTTTTAATTAAATCCTT
*
860886 TTTTTTAAATTTAATCCTT
1 TTTTTT-AATTAAATCCTT
860905 TT
1 TT
860907 ATCACTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTTAATTAAATCCTT
Found at i:875229 original size:13 final size:15
Alignment explanation
Indices: 875204--875236 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
875194 TTGTTGTGAA
875204 AAAATTGTAAAAAG-
1 AAAATTGTAAAAAGT
875218 AAAATT-TAAAAAGT
1 AAAATTGTAAAAAGT
875232 AAAAT
1 AAAAT
875237 GATAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (15 bp):
AAAATTGTAAAAAGT
Found at i:879585 original size:14 final size:15
Alignment explanation
Indices: 879566--879600 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
879556 ATCCGGGCTT
*
879566 AAAAAATAA-AACCA
1 AAAAAATAATAAACA
879580 AAAAAATAATAAACA
1 AAAAAATAATAAACA
879595 AAAAAA
1 AAAAAA
879601 AGAGATACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAAATAATAAACA
Found at i:881385 original size:59 final size:60
Alignment explanation
Indices: 881292--881756 Score: 520
Period size: 59 Copynumber: 7.8 Consensus size: 60
881282 AAACCTATCT
* ** * * * *
881292 AAAATCACATTTTAACCCCCAAACTTATCTAAAATTACATTTTGA-TCTTAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCC
*
881351 AAAATTACATTTTGAACCCTT-AACTTTTCCAAAA-T-CATTATTTGACCCTTAAACTTTTCC
1 AAAATTACATTTT-AACCCTTAAACTTTTCCAAAATTACA-T-TTTAACCCTTAAACTTTTCC
* * * *
881411 AAAATTACATTTTTACCCTTAAACTTTTCTAAAATTATATTTTAACCCTTAAAC-TTCCC
1 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCC
* * * * *
881470 AAAATTACATTTTGACCCTTTAACTTTTCCAAAATCATATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCC
* * * * *
881530 AAACTTACATTTTGACCCTTAAACTTTTCCAAAATTACATTTTGA-CCTTAAACATTTCT
1 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCC
881589 AAAATTACATTTTAACCCTTAAAC--TTCCTTAAAATTACA-TTTAACCCTTAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC--AAAATTACATTTTAACCCTTAAACTTTTCC
* * * *
881648 AAAGTCACATTTTAACCCTTAAACTTTCCCAAAGTTACATTTTAATGCCC--AAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAA--CCCTTAAACTTTTCC
* * * *
881708 AAAATCACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCT
1 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCT
881757 CGAACTTATT
Statistics
Matches: 349, Mismatches: 40, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
57 6 0.02
58 9 0.03
59 171 0.49
60 154 0.44
61 5 0.01
62 4 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (60 bp):
AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCC
Found at i:881445 original size:119 final size:119
Alignment explanation
Indices: 881292--881756 Score: 557
Period size: 119 Copynumber: 3.9 Consensus size: 119
881282 AAACCTATCT
** * * * *
881292 AAAATCACATTTTAACCCCCAAACTTATCTAAAATTACATTTTGATCTTAAACTTTTCCAAAATT
1 AAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCTTAAACTTTTCCAAAATT
*
881357 ACATTTTGAACCCTT-AACTTTTCCAAAATCAT-TATTTGACCCTTAAACTTTTCC
66 ACATTTT-AACCCTTAAACTTTTCCAAAATCATAT-TTTAACCCTTAAACTTTTCC
* * * * *
881411 AAAATTACATTTTTACCCTTAAACTTTTCTAAAATTATATTTTAACCCTTAAAC-TTCCCAAAAT
1 AAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAA-CCTTAAACTTTTCCAAAAT
* * *
881475 TACATTTTGACCCTTTAACTTTTCCAAAATCATATTTTAACCCCTAAACTTTTCC
65 TACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTAACCCTTAAACTTTTCC
* * * * * *
881530 AAACTTACATTTTGACCCTTAAACTTTTCCAAAATTACATTTTGACCTTAAACATTTCTAAAATT
1 AAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCTTAAACTTTTCCAAAATT
* *
881595 ACATTTTAACCCTTAAAC--TTCCTTAAAATTACA-TTTAACCCTTAAACTTTTCC
66 ACATTTTAACCCTTAAACTTTTCC--AAAATCATATTTTAACCCTTAAACTTTTCC
* * * *
881648 AAAGTCACATTTTAACCCTTAAACTTTCCCAAAGTTACATTTTAATGCC-CAAACTTTTCCAAAA
1 AAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAA--CCTTAAACTTTTCCAAAA
* *
881712 TCACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCT
64 TTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTAACCCT
881757 CGAACTTATT
Statistics
Matches: 298, Mismatches: 37, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
117 4 0.01
118 72 0.24
119 200 0.67
120 18 0.06
121 4 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (119 bp):
AAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCTTAAACTTTTCCAAAATT
ACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTAACCCTTAAACTTTTCC
Found at i:881763 original size:30 final size:30
Alignment explanation
Indices: 881292--881756 Score: 520
Period size: 30 Copynumber: 15.6 Consensus size: 30
881282 AAACCTATCT
* ** * *
881292 AAAATCACATTTTAACCCCCAAACTTATCT
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* *
881322 AAAATTACATTTTGA-TCTTAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
881351 AAAATTACATTTTGAACCCTT-AACTTTTCC
1 AAAATTACATTTT-AACCCTTAAACTTTTCC
*
881381 AAAA-T-CATTATTTGACCCTTAAACTTTTCC
1 AAAATTACA-T-TTTAACCCTTAAACTTTTCC
* *
881411 AAAATTACATTTTTACCCTTAAACTTTTCT
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* *
881441 AAAATTATATTTTAACCCTTAAAC-TTCCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* *
881470 AAAATTACATTTTGACCCTTTAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* * *
881500 AAAATCATATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* *
881530 AAACTTACATTTTGACCCTTAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* * *
881560 AAAATTACATTTTGA-CCTTAAACATTTCT
1 AAAATTACATTTTAACCCTTAAACTTTTCC
881589 AAAATTACATTTTAACCCTTAAAC--TTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
881617 TTAAAATTACA-TTTAACCCTTAAACTTTTCC
1 --AAAATTACATTTTAACCCTTAAACTTTTCC
* * *
881648 AAAGTCACATTTTAACCCTTAAACTTTCCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
*
881678 AAAGTTACATTTTAATGCCC--AAACTTTTCC
1 AAAATTACATTTTAA--CCCTTAAACTTTTCC
*
881708 AAAATCACATTTTAACCCTTAAACTTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTCC
* * *
881738 AAAATCATATTTTGACCCT
1 AAAATTACATTTTAACCCT
881757 CGAACTTATT
Statistics
Matches: 373, Mismatches: 44, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
28 8 0.02
29 101 0.27
30 250 0.67
31 9 0.02
32 5 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTTTCC
Found at i:882707 original size:28 final size:29
Alignment explanation
Indices: 882675--882734 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
882665 TGTTTCAATT
*
882675 AATA-TATGATCTTTTGCATTTTCTATGA
1 AATATTATGATCCTTTGCATTTTCTATGA
882703 AATATTATGATCCTTTGCATTTTCTATGA
1 AATATTATGATCCTTTGCATTTTCTATGA
882732 AAT
1 AAT
882735 GACATGACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (29 bp):
AATATTATGATCCTTTGCATTTTCTATGA
Found at i:883739 original size:37 final size:37
Alignment explanation
Indices: 883689--883764 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
883679 TACATTCTTG
883689 TTTCTTTGCTTTTAATTGCAATTTATTTCAAGTTTTA
1 TTTCTTTGCTTTTAATTGCAATTTATTTCAAGTTTTA
883726 TTTCTTTGCTTTTAATTGCAATTTATTTCAAGTTTTA
1 TTTCTTTGCTTTTAATTGCAATTTATTTCAAGTTTTA
883763 TT
1 TT
883765 CCTGTATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (37 bp):
TTTCTTTGCTTTTAATTGCAATTTATTTCAAGTTTTA
Found at i:891400 original size:4 final size:4
Alignment explanation
Indices: 891391--891418 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
891381 CAAGTAAGAT
891391 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
891419 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:892966 original size:18 final size:19
Alignment explanation
Indices: 892934--892969 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
892924 TGGGTTTTGA
*
892934 TATTATTTTTGTATTTATT
1 TATTATTTTTATATTTATT
892953 TATT-TTTTTATATTTAT
1 TATTATTTTTATATTTAT
892970 AAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TATTATTTTTATATTTATT
Found at i:898712 original size:17 final size:17
Alignment explanation
Indices: 898690--898723 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
898680 AGTTTAATTT
898690 GCTTACTTCTTATCATC
1 GCTTACTTCTTATCATC
898707 GCTTACTTCTTATCATC
1 GCTTACTTCTTATCATC
898724 AAGACTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.06, T:0.47
Consensus pattern (17 bp):
GCTTACTTCTTATCATC
Found at i:902576 original size:28 final size:28
Alignment explanation
Indices: 902543--902600 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
902533 CTAGGTGACA
902543 TTCCATGCACATGTATAAATCATACTTG
1 TTCCATGCACATGTATAAATCATACTTG
902571 TTCCATGCACATGTATAAATCATACTTG
1 TTCCATGCACATGTATAAATCATACTTG
902599 TT
1 TT
902601 ATATTTTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (28 bp):
TTCCATGCACATGTATAAATCATACTTG
Found at i:902878 original size:69 final size:69
Alignment explanation
Indices: 902742--902891 Score: 268
Period size: 69 Copynumber: 2.2 Consensus size: 69
902732 TTTTAAAGGA
* *
902742 TTAAATTAAAATTTTTTATCATTTTTAGGGAGGGCCAAAGTGCAATTTTACCTTTATTAATTTAA
1 TTAAATTAAATTTTTTTATCATTTTTAGGGAGGGCCAAAGTACAATTTTACCTTTATTAATTTAA
902807 AATT
66 AATT
902811 TTAAATTAAATTTTTTTATCATTTTTAGGGAGGGCCAAAGTACAATTTTACCTTTATTAATTTAA
1 TTAAATTAAATTTTTTTATCATTTTTAGGGAGGGCCAAAGTACAATTTTACCTTTATTAATTTAA
902876 AATT
66 AATT
902880 TTAAA--AAATTTT
1 TTAAATTAAATTTT
902892 AAGAGCCTAA
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
67 7 0.09
69 72 0.91
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (69 bp):
TTAAATTAAATTTTTTTATCATTTTTAGGGAGGGCCAAAGTACAATTTTACCTTTATTAATTTAA
AATT
Found at i:903246 original size:2 final size:2
Alignment explanation
Indices: 903241--903273 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
903231 AAAATTAAAC
*
903241 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
903274 CTATGAACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:905429 original size:24 final size:24
Alignment explanation
Indices: 905397--905453 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
905387 AATCTTCCAG
*
905397 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
*
905421 TTAAACTCTATTTATTTGTTTCAG
1 TTAAACTCTATTTATTTGTTTCAA
*
905445 TCAAACTCT
1 TTAAACTCT
905454 TATTAGTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (24 bp):
TTAAACTCTATTTATTTGTTTCAA
Found at i:907117 original size:37 final size:38
Alignment explanation
Indices: 907076--907163 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
907066 AGATATGTTC
* * *
907076 ATGCAGCGACATTTCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAGCGACAGTTCTAGATGCAATTTGAAGAATACTT
* *
907113 ATGCAGCGATAGTTCTAGATGCAATTTGAAGAATATTT
1 ATGCAGCGACAGTTCTAGATGCAATTTGAAGAATACTT
* *
907151 ATACAACGACAGT
1 ATGCAGCGACAGT
907164 CTTGGGTGCA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 20 0.48
38 22 0.52
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.30
Consensus pattern (38 bp):
ATGCAGCGACAGTTCTAGATGCAATTTGAAGAATACTT
Found at i:908805 original size:24 final size:23
Alignment explanation
Indices: 908773--908853 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 23
908763 AATCTTCCAG
908773 TTAAACTCTATTTATTTGTTTAAA
1 TTAAACTCTATTTATTT-TTTAAA
* *
908797 TTAAACTCTGTTTATTTATTACAA
1 TTAAACTCTATTTATTTTTTA-AA
* *
908821 CTAAACTCTATTTATTTATTTCAA
1 TTAAACTCTATTTATTT-TTTAAA
*
908845 TCAAACTCT
1 TTAAACTCT
908854 TATTAGTCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
23 3 0.06
24 42 0.89
25 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAAACTCTATTTATTTTTTAAA
Found at i:915904 original size:21 final size:21
Alignment explanation
Indices: 915880--915934 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
915870 GAAATTTAAA
915880 ACAAACATAATGAGGAAAGTT
1 ACAAACATAATGAGGAAAGTT
* *
915901 ACAAAACATTATGAGGAGAGTT
1 AC-AAACATAATGAGGAAAGTT
915923 ACAAACATAATG
1 ACAAACATAATG
915935 TTTTGTAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (21 bp):
ACAAACATAATGAGGAAAGTT
Found at i:924314 original size:36 final size:37
Alignment explanation
Indices: 924268--924356 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 37
924258 TCCATACCCA
924268 AGATC-ACATCAAATTTAG-TGAATGGCAATAACATT
1 AGATCAACATCAAATTTAGTTGAATGGCAATAACATT
* *
924303 AGATCAACATCAAA-TTCGTTGAATGGCAATAGCATT
1 AGATCAACATCAAATTTAGTTGAATGGCAATAACATT
* **
924339 AGATTAACAGAAAATTTA
1 AGATCAACATCAAATTTA
924357 CAGCCCTGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 8 0.18
36 35 0.78
37 2 0.04
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (37 bp):
AGATCAACATCAAATTTAGTTGAATGGCAATAACATT
Found at i:932824 original size:25 final size:25
Alignment explanation
Indices: 932747--932896 Score: 128
Period size: 25 Copynumber: 6.1 Consensus size: 25
932737 CAACTTGGTG
932747 GAGCGATATTCTGTCTGGCTCGTAA
1 GAGCGATATTCTGTCTGGCTCGTAA
* * * * * * *
932772 GAACAATATTTTGTATGGTTCATTA
1 GAGCGATATTCTGTCTGGCTCGTAA
*
932797 GAGCGATATTCTGTCTTGCTCGTAA
1 GAGCGATATTCTGTCTGGCTCGTAA
* *
932822 GAGTGATA-T-T-T-TGGCTCATAA
1 GAGCGATATTCTGTCTGGCTCGTAA
* * *
932843 GAGCGATATTCTATCTGACTCGTTA
1 GAGCGATATTCTGTCTGGCTCGTAA
* *
932868 GAGCGATGTTCTATCTAGGCTCGTAA
1 GAGCGATATTCTGTCT-GGCTCGTAA
932894 GAG
1 GAG
932897 TTAAACTCTA
Statistics
Matches: 95, Mismatches: 25, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
21 15 0.16
22 2 0.02
23 2 0.02
24 2 0.02
25 64 0.67
26 10 0.11
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (25 bp):
GAGCGATATTCTGTCTGGCTCGTAA
Found at i:932906 original size:26 final size:26
Alignment explanation
Indices: 932877--932927 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
932867 AGAGCGATGT
*
932877 TCTATCTAGGCTCGTAAGAGTTAAAC
1 TCTATCTAGGCTCGTAAGAGCTAAAC
*
932903 TCTATCTAGGCTCGTATGAGCTAAA
1 TCTATCTAGGCTCGTAAGAGCTAAA
932928 TTTTTAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (26 bp):
TCTATCTAGGCTCGTAAGAGCTAAAC
Found at i:935144 original size:20 final size:19
Alignment explanation
Indices: 935085--935167 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 19
935075 ATGCAAGACA
* **
935085 AGGGCACCAAAGTGTAAAC
1 AGGGCACCAAAGTGCATTC
* * *
935104 AGGGGAACTAAAGTACATTC
1 A-GGGCACCAAAGTGCATTC
*
935124 AGCGGCACCAAATTGCATTC
1 AG-GGCACCAAAGTGCATTC
*
935144 AAGGGCATCAAAGTGCATTC
1 -AGGGCACCAAAGTGCATTC
935164 AGGG
1 AGGG
935168 GCACTGAAGT
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
19 6 0.12
20 41 0.84
21 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (19 bp):
AGGGCACCAAAGTGCATTC
Found at i:935157 original size:40 final size:40
Alignment explanation
Indices: 935086--935211 Score: 119
Period size: 40 Copynumber: 3.1 Consensus size: 40
935076 TGCAAGACAA
* * * *
935086 GGGCACCAAAGTGTAAAC-AGGGGAACTAAAGTACATTCAG
1 GGGCACCAAAGTGCAAACAACGGCATC-AAAGTACATTCAG
* * ** * *
935126 CGGCACCAAATTGCATTCAAGGGCATCAAAGTGCATTCAG
1 GGGCACCAAAGTGCAAACAACGGCATCAAAGTACATTCAG
** *
935166 GGGCACTGAAGTGCAAACTACGGCATCAAAGTACATTCAG
1 GGGCACCAAAGTGCAAACAACGGCATCAAAGTACATTCAG
935206 GGGCAC
1 GGGCAC
935212 GGATGTGCGT
Statistics
Matches: 68, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 62 0.91
41 6 0.09
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (40 bp):
GGGCACCAAAGTGCAAACAACGGCATCAAAGTACATTCAG
Found at i:935169 original size:20 final size:20
Alignment explanation
Indices: 935113--935210 Score: 74
Period size: 20 Copynumber: 4.9 Consensus size: 20
935103 CAGGGGAACT
* * *
935113 AAAGTACATTCAGCGGCACC
1 AAAGTGCATTCAGGGGCATC
* *
935133 AAATTGCATTCAAGGGCATC
1 AAAGTGCATTCAGGGGCATC
935153 AAAGTGCATTCAGGGGCA-C
1 AAAGTGCATTCAGGGGCATC
* ** *
935172 TGAAGTGCAAACTA-CGGCATC
1 -AAAGTGCATTC-AGGGGCATC
*
935193 AAAGTACATTCAGGGGCA
1 AAAGTGCATTCAGGGGCA
935211 CGGATGTGCG
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
19 2 0.03
20 54 0.93
21 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (20 bp):
AAAGTGCATTCAGGGGCATC
Found at i:938239 original size:7 final size:7
Alignment explanation
Indices: 938211--938266 Score: 71
Period size: 7 Copynumber: 8.0 Consensus size: 7
938201 CAAAAAATTG
938211 TTATTTT
1 TTATTTT
938218 CTTATTTT
1 -TTATTTT
*
938226 CGT-TTTT
1 -TTATTTT
938233 TTA-TTT
1 TTATTTT
938239 TTATTTT
1 TTATTTT
938246 TTATTTT
1 TTATTTT
938253 TTATTTT
1 TTATTTT
938260 TTATTTT
1 TTATTTT
938267 ATAGGTTGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 7 0.16
7 28 0.64
8 9 0.20
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (7 bp):
TTATTTT
Found at i:938244 original size:20 final size:21
Alignment explanation
Indices: 938211--938266 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
938201 CAAAAAATTG
938211 TTATTTTCTTATTTTCGT-TTTT
1 TTATTTT-TTATTTT-GTATTTT
*
938233 TTA-TTTTTATTTTTTATTTT
1 TTATTTTTTATTTTGTATTTT
938253 TTATTTTTTATTTT
1 TTATTTTTTATTTT
938267 ATAGGTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.45
21 13 0.42
22 3 0.10
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (21 bp):
TTATTTTTTATTTTGTATTTT
Found at i:938252 original size:27 final size:28
Alignment explanation
Indices: 938211--938266 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
938201 CAAAAAATTG
938211 TTATTTTCTTATTTTCGT-TTTTTTATTT
1 TTATTTTCTTATTTT-GTATTTTTTATTT
*
938239 TTATTTT-TTATTTTTTATTTTTTATTT
1 TTATTTTCTTATTTTGTATTTTTTATTT
938266 T
1 T
938267 ATAGGTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 1 0.04
27 18 0.69
28 7 0.27
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (28 bp):
TTATTTTCTTATTTTGTATTTTTTATTT
Found at i:940839 original size:63 final size:63
Alignment explanation
Indices: 940750--940875 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
940740 ACTGAAAAAT
940750 TTCAAGAAAAAACTAACATGCATTTTCAAGAGTTAGACAAGCAGATGAGCAAGCTAGCACTCA
1 TTCAAGAAAAAACTAACATGCATTTTCAAGAGTTAGACAAGCAGATGAGCAAGCTAGCACTCA
*
940813 TTCAAGAAAAAACTAACATGCATTTTCAGGAGTTAGACAAGCAGATGAGCAAGCTAGCACTCA
1 TTCAAGAAAAAACTAACATGCATTTTCAAGAGTTAGACAAGCAGATGAGCAAGCTAGCACTCA
940876 CGGTTAGCCG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (63 bp):
TTCAAGAAAAAACTAACATGCATTTTCAAGAGTTAGACAAGCAGATGAGCAAGCTAGCACTCA
Found at i:947325 original size:334 final size:334
Alignment explanation
Indices: 946716--947447 Score: 1250
Period size: 334 Copynumber: 2.2 Consensus size: 334
946706 NNNNNNNNNN
* * * *
946716 ACCCAAATAATGCTAGGGAAGACGTATTTTCGAGGATAAAAATAAAATAAAAATACGCTAATAAT
1 ACCCAAATAATGCTCGGGGAGTCGTTTTTTCGAGGATAAAAATAAAATAAAAATACGCTAATAAT
* *
946781 ATCCATATATCCCACGAAGCTTTTCTATTTCGCAAAACTGCAAATTTACGATAAATAAAATAATA
66 ATCCATATATCCCACGAAGCTTTACTATTTCGCAAAACTACAAATTTACGATAAATAAAATAATA
* *
946846 CAAAAAAAAGTGGGGTGCAACCCGAGGACTTCTCAGGAGGTCACCAATCCTAGTACTACTCTCGC
131 CAAAAAAAAGGGGGGTGCAACACGAGGACTTCTCAGGAGGTCACCAATCCTAGTACTACTCTCGC
* * *
946911 ACAAGCACGCTTAACTGTGGAGTTCTGATGGATCCGATGCTTTAGCGCTCGTATGATCGCACCCA
196 ACAAGCACGCTTAACTGCGGAGTTCTGATGGATCCGATGCTTTAGCGCTCATATGATCGCACCAA
*
946976 CAAAGCTCTGCGCAATCTACGTACATAAAGGCTACGTCTCATCCCATTCGTGCCTT-GAATTTTA
261 CAAAGCTCTGCGCAATCTACGTACATAAAGGCTACGTCTCATCCCAGTCGTG-CTTCGAATTTTA
947040 ATGTAAATAT
325 ATGTAAATAT
*
947050 ACCCAAATAATGCTCGGGGAGTCGTTTTTTCGAGGATAAAAATAAATTAAAAATACGCTAATAAT
1 ACCCAAATAATGCTCGGGGAGTCGTTTTTTCGAGGATAAAAATAAAATAAAAATACGCTAATAAT
* * *
947115 ATCCATATATCCGATGAAGCTTTACTATTTCGTAAAACTACAAATTTACGATAAATAAAATAATA
66 ATCCATATATCCCACGAAGCTTTACTATTTCGCAAAACTACAAATTTACGATAAATAAAATAATA
* * *
947180 CAAAAAAAAGGGGGGTGCAACACGTGGACTTCTCAGGAGGTCACCCATCCTAGTGCTACTCTCGC
131 CAAAAAAAAGGGGGGTGCAACACGAGGACTTCTCAGGAGGTCACCAATCCTAGTACTACTCTCGC
*
947245 ACAAGCACGCTTAACTGCGGAGTTCTGATGGATCCGATGCTTTAGTGCTCATATGATCGCACCAA
196 ACAAGCACGCTTAACTGCGGAGTTCTGATGGATCCGATGCTTTAGCGCTCATATGATCGCACCAA
**
947310 CAAAGCTCTGCGCAATCTATTTACATAAAGGCTACGTCTCATCCCAGTCGTGCTTCGAATTTTAA
261 CAAAGCTCTGCGCAATCTACGTACATAAAGGCTACGTCTCATCCCAGTCGTGCTTCGAATTTTAA
947375 TGTAAATAT
326 TGTAAATAT
947384 ACCCAAATAATGCTCGGGGAGTCGTTTTTTCGAGGATAAAAATAAAATAAAAATACGCTAATAA
1 ACCCAAATAATGCTCGGGGAGTCGTTTTTTCGAGGATAAAAATAAAATAAAAATACGCTAATAA
Statistics
Matches: 374, Mismatches: 23, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
333 3 0.01
334 371 0.99
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (334 bp):
ACCCAAATAATGCTCGGGGAGTCGTTTTTTCGAGGATAAAAATAAAATAAAAATACGCTAATAAT
ATCCATATATCCCACGAAGCTTTACTATTTCGCAAAACTACAAATTTACGATAAATAAAATAATA
CAAAAAAAAGGGGGGTGCAACACGAGGACTTCTCAGGAGGTCACCAATCCTAGTACTACTCTCGC
ACAAGCACGCTTAACTGCGGAGTTCTGATGGATCCGATGCTTTAGCGCTCATATGATCGCACCAA
CAAAGCTCTGCGCAATCTACGTACATAAAGGCTACGTCTCATCCCAGTCGTGCTTCGAATTTTAA
TGTAAATAT
Done.