Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015186.1 Kokia drynarioides strain JFW-HI SEQ_130230, 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: 400691
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 303 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:275825 original size:43 final size:43
Alignment explanation
Indices: 275777--275865 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
275767 ACTATATATT
275777 TTAGAAAAAGTCCATTAGATTTAATTTGTCATTAGGAACAATC
1 TTAGAAAAAGTCCATTAGATTTAATTTGTCATTAGGAACAATC
*
275820 TTAGAAAAAGTCCATTAGGTTTAATTTGTCATTAGGAACAATC
1 TTAGAAAAAGTCCATTAGATTTAATTTGTCATTAGGAACAATC
275863 TTA
1 TTA
275866 TTAATCAAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (43 bp):
TTAGAAAAAGTCCATTAGATTTAATTTGTCATTAGGAACAATC
Found at i:286191 original size:13 final size:13
Alignment explanation
Indices: 286159--286192 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
286149 ATTGATCCAT
286159 TATCAACAAAAAAA
1 TATCAA-AAAAAAA
286173 TA-CAAAAAAAAA
1 TATCAAAAAAAAA
286185 TATCAAAA
1 TATCAAAA
286193 TTATTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.47
13 8 0.42
14 2 0.11
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.15
Consensus pattern (13 bp):
TATCAAAAAAAAA
Found at i:309141 original size:70 final size:70
Alignment explanation
Indices: 309058--309201 Score: 270
Period size: 70 Copynumber: 2.1 Consensus size: 70
309048 GAAATGAAGT
*
309058 GCAAATGAGAAGAGATTCGGATGAGATAGACAAAAAATGAAAATAATATAATGTAGGGATAGATT
1 GCAAATGAGAAGAGATTCGGATGAGATAGACAAAAAATGAAAAGAATATAATGTAGGGATAGATT
309123 AGATG
66 AGATG
*
309128 GCAAATGAGAAGAGATTCGGATGAGATAGACAAAAAATGAACAGAATATAATGTAGGGATAGATT
1 GCAAATGAGAAGAGATTCGGATGAGATAGACAAAAAATGAAAAGAATATAATGTAGGGATAGATT
309193 AGATG
66 AGATG
309198 GCAA
1 GCAA
309202 CGGAGGGAGA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.48, C:0.06, G:0.26, T:0.20
Consensus pattern (70 bp):
GCAAATGAGAAGAGATTCGGATGAGATAGACAAAAAATGAAAAGAATATAATGTAGGGATAGATT
AGATG
Found at i:321842 original size:26 final size:26
Alignment explanation
Indices: 321813--321863 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
321803 AACCCTTTTC
321813 ATATAATTTA-ATTTAAAATATTATTT
1 ATATAATTTATATTT-AAATATTATTT
*
321839 ATATATTTTATATTTAAATATTATT
1 ATATAATTTATATTTAAATATTATT
321864 CTTTTGATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATAATTTATATTTAAATATTATTT
Found at i:332070 original size:16 final size:16
Alignment explanation
Indices: 332051--332081 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
332041 TTAAAAATAA
332051 ATTTTATATATACATG
1 ATTTTATATATACATG
*
332067 ATTTTATATTTACAT
1 ATTTTATATATACAT
332082 AAACAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTTATATATACATG
Found at i:350106 original size:7 final size:7
Alignment explanation
Indices: 350094--350123 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
350084 GTCTTGGAGA
350094 TTGAAGC
1 TTGAAGC
350101 TTGAAGC
1 TTGAAGC
350108 TTGAAGC
1 TTGAAGC
350115 TTGAAGC
1 TTGAAGC
350122 TT
1 TT
350124 TGAAACCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (7 bp):
TTGAAGC
Found at i:358042 original size:17 final size:18
Alignment explanation
Indices: 358010--358043 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
358000 AAAGATTACT
358010 AGTTGTTAGCCTTGTTGG
1 AGTTGTTAGCCTTGTTGG
*
358028 AGTTG-TAGGCTTGTTG
1 AGTTGTTAGCCTTGTTG
358044 TAGGCTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.09, G:0.35, T:0.44
Consensus pattern (18 bp):
AGTTGTTAGCCTTGTTGG
Found at i:369624 original size:11 final size:11
Alignment explanation
Indices: 369608--369638 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
369598 AATCCAAGTA
369608 ACAACAATAAC
1 ACAACAATAAC
369619 ACAACAATAAC
1 ACAACAATAAC
369630 ACAACAATA
1 ACAACAATA
369639 TTGTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.26, G:0.00, T:0.10
Consensus pattern (11 bp):
ACAACAATAAC
Found at i:369726 original size:13 final size:14
Alignment explanation
Indices: 369701--369743 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
369691 AAACCATTCC
369701 AAACAAC-AAAACA
1 AAACAACAAAAACA
*
369714 AAA-AATAAAAACA
1 AAACAACAAAAACA
369727 AAACAACAAAAATCA
1 AAACAACAAAAA-CA
369742 AA
1 AA
369744 TAAACGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
14 7 0.28
15 4 0.16
ACGTcount: A:0.79, C:0.16, G:0.00, T:0.05
Consensus pattern (14 bp):
AAACAACAAAAACA
Found at i:375442 original size:18 final size:18
Alignment explanation
Indices: 375419--375458 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
375409 ATTATTTTTT
* *
375419 AAAAATATTTTTGAGATA
1 AAAAATACTTTTGAAATA
375437 AAAAATACTTTTGAAATA
1 AAAAATACTTTTGAAATA
375455 AAAA
1 AAAA
375459 CATTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAAATACTTTTGAAATA
Found at i:376676 original size:25 final size:23
Alignment explanation
Indices: 376648--376693 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
376638 ATTGGATATA
376648 AATTAAATTCTAAAAAAATAATTAG
1 AATTAAA-TCT-AAAAAATAATTAG
*
376673 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
376694 TCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:380787 original size:58 final size:59
Alignment explanation
Indices: 380711--380939 Score: 193
Period size: 58 Copynumber: 3.9 Consensus size: 59
380701 AAAAAATTGC
380711 ATTTTTTGGTGTTGGCCATTGCATGGCCGACACCCCTTTT-TGAGAAAAAAAAATTCAAA
1 ATTTTTT-GTGTTGGCCATTGCATGGCCGACACCCCTTTTCTGAGAAAAAAAAATTCAAA
* ***
380770 ATTTTTTGTGTTAGCCATCAAATGGCCGACACCCCTTTTTCTG-GAAAAAAAAATTGC---
1 ATTTTTTGTGTTGGCCATTGCATGGCCGACACCCC-TTTTCTGAGAAAAAAAAATT-CAAA
* ** * **
380827 ATTTTTGGGTGTTGGCCATTGCATGGCAAACACCACCTTTTCTCA-AGAAAAAATTTTCAAA
1 ATTTTT-TGTGTTGGCCATTGCATGGCCGACACC-CCTTTTCTGAGA-AAAAAAAATTCAAA
* *** * *
380888 ATTTTTTGGTATTGGCCATCAAATAGCCGACACCCCCTTTTCTCA-AAAAAAA
1 ATTTTTT-GTGTTGGCCATTGCATGGCCGACA-CCCCTTTTCTGAGAAAAAAA
380940 TTGCATTTTT
Statistics
Matches: 136, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
57 6 0.04
58 52 0.38
59 33 0.24
60 9 0.07
61 34 0.25
62 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (59 bp):
ATTTTTTGTGTTGGCCATTGCATGGCCGACACCCCTTTTCTGAGAAAAAAAAATTCAAA
Found at i:380843 original size:116 final size:116
Alignment explanation
Indices: 380673--380965 Score: 373
Period size: 116 Copynumber: 2.5 Consensus size: 116
380663 GGATGTTGGT
* * *
380673 CATCAAATGACTGACACCCCTTTTCTCG--AAAAAATTGCATTTTTTGGTGTTGGCCATTGCATG
1 CATCAAATGGCCGACACCCCTTTTCT-GAAAAAAAATTGCATTTTTGGGTGTTGGCCATTGCATG
** * *
380736 GCCGACACC-CCTTTT-T-GAGAAAAAAAAATTCAAAATTTTTT-GTGTTAGC
65 GCAAACACCACCTTTTCTCAAG-AAAAAAAATTCAAAATTTTTTGGTATTAGC
380785 CATCAAATGGCCGACACCCCTTTTTCTGGAAAAAAAAATTGCATTTTTGGGTGTTGGCCATTGCA
1 CATCAAATGGCCGACACCCC-TTTTCT-G-AAAAAAAATTGCATTTTTGGGTGTTGGCCATTGCA
** *
380850 TGGCAAACACCACCTTTTCTCAAGAAAAAATTTTCAAAATTTTTTGGTATTGGC
63 TGGCAAACACCACCTTTTCTCAAGAAAAAAAATTCAAAATTTTTTGGTATTAGC
* * *
380904 CATCAAATAGCCGACACCCCCTTTTCTCAAAAAAAATTGCATTTTTGGGTGTCGGCCATTGC
1 CATCAAATGGCCGACA-CCCCTTTTCTGAAAAAAAATTGCATTTTTGGGTGTTGGCCATTGC
380966 TCTAGAAAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
112 18 0.11
113 7 0.04
116 41 0.26
117 39 0.25
118 20 0.13
119 29 0.18
120 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (116 bp):
CATCAAATGGCCGACACCCCTTTTCTGAAAAAAAATTGCATTTTTGGGTGTTGGCCATTGCATGG
CAAACACCACCTTTTCTCAAGAAAAAAAATTCAAAATTTTTTGGTATTAGC
Found at i:381363 original size:58 final size:58
Alignment explanation
Indices: 381264--381647 Score: 306
Period size: 58 Copynumber: 6.5 Consensus size: 58
381254 ACGCCATCTT
* *
381264 TCGACTATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTTCGAGAAAAGAGGGTG
1 TCGACCATTGCATGGCCAACA-CAAAAAA-TTTGAATTTTTTTTTCGAGAAAAGAGGGTG
* * *
381324 TCGACCATTGCATGACCAAC-CAAAAAATTTTGAATTTTTTTTTCGAAAAAAGGGGGTG
1 TCGACCATTGCATGGCCAACACAAAAAA-TTTGAATTTTTTTTTCGAGAAAAGAGGGTG
* *
381382 TCGGCCA-TGCAATGGCCAACACCCAAAAA--TGCAA-TTTTTTTTCGAGAAAAG-GGAGTG
1 TCGACCATTGC-ATGGCCAACA-CAAAAAATTTG-AATTTTTTTTTCGAGAAAAGAGG-GTG
* * * *
381439 TCGGCCATTTG-ATGACCAACACAAAAAATTTTTGAAATTTTTTTCTCAAGAAAAGAGGGTG
1 TCGACCA-TTGCATGGCCAACACAAAAAA--TTTG-AATTTTTTTTTCGAGAAAAGAGGGTG
* * * ** *
381500 TCGACTA-TGCAATGGTCAACATCCAAAAA-TACAATTTTTTTTTCGAGAAAAGGGGGTG
1 TCGACCATTGC-ATGGCCAACA-CAAAAAATTTGAATTTTTTTTTCGAGAAAAGAGGGTG
** * * *
381558 TC-AGCCATTTTATGGCCAACACAAAAAAATTG--TTTTTTTTATCTGACAAAAAAGGGGTG
1 TCGA-CCATTGCATGGCCAACACAAAAAATTTGAATTTTTTTT-TC-GAGAAAAGA-GGGTG
* * *
381617 TCGGCCATTGCATGGCCAACACCACAAATTT
1 TCGACCATTGCATGGCCAACACAAAAAATTT
381648 TTTTTCAAAT
Statistics
Matches: 261, Mismatches: 40, Indels: 47
0.75 0.11 0.14
Matches are distributed among these distances:
56 16 0.06
57 49 0.19
58 94 0.36
59 35 0.13
60 28 0.11
61 31 0.12
62 8 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (58 bp):
TCGACCATTGCATGGCCAACACAAAAAATTTGAATTTTTTTTTCGAGAAAAGAGGGTG
Found at i:381510 original size:118 final size:115
Alignment explanation
Indices: 381264--381644 Score: 391
Period size: 118 Copynumber: 3.2 Consensus size: 115
381254 ACGCCATCTT
* * *
381264 TCGACTATTGC-ATGGCCAACACCAAAAAATTTTGAAATTTTTTTTCGAGAAAAGAGGGTGTCGA
1 TCGACTA-TGCAATGGCCAACACCCAAAAA---TGCAATTTTTTTTCGAGAAAAG-GGGTGTCGG
* *
381328 CCA-TTGCATGACCAAC-CAAAAAATTTTGAATTTTTTTTTCGAAAAAAGGGGGTG
61 CCATTTG-ATGACCAACACAAAAAATTTTGAATTTTTTTCTCGAAAAAAGAGGGTG
* *
381382 TCGGCCATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTCGAGAAAAGGGAGTGTCGGCCAT
1 TCGACTATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTCGAGAAAAGGG-GTGTCGGCCAT
381447 TTGATGACCAACACAAAAAATTTTTGAAATTTTTTTCTC-AAGAAAAGAGGGTG
65 TTGATGACCAACACAAAAAA-TTTTG-AATTTTTTTCTCGAA-AAAAGAGGGTG
* * * *
381500 TCGACTATGCAATGGTCAACATCCAAAAATACAATTTTTTTTTCGAGAAAAGGGGGTGTCAGCCA
1 TCGACTATGCAATGGCCAACACCCAAAAATGCAA-TTTTTTTTCGAGAAAA-GGGGTGTCGGCCA
* * * * *
381565 TTTTATGGCCAACACAAAAAA-ATTG-TTTTTTTTATCTGACAAAAA-AGGGGTG
64 TTTGATGACCAACACAAAAAATTTTGAATTTTTTTCTC-GA-AAAAAGA-GGGTG
* *
381617 TCGGCCATTGC-ATGGCCAACACCACAAA
1 TCGACTA-TGCAATGGCCAACACC-CAAA
381645 TTTTTTTTCA
Statistics
Matches: 226, Mismatches: 22, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
114 2 0.01
115 48 0.21
116 11 0.05
117 38 0.17
118 80 0.35
119 44 0.19
120 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (115 bp):
TCGACTATGCAATGGCCAACACCCAAAAATGCAATTTTTTTTCGAGAAAAGGGGTGTCGGCCATT
TGATGACCAACACAAAAAATTTTGAATTTTTTTCTCGAAAAAAGAGGGTG
Found at i:383467 original size:6 final size:6
Alignment explanation
Indices: 383458--383516 Score: 73
Period size: 6 Copynumber: 9.5 Consensus size: 6
383448 TTCTCCACGG
* * *
383458 AAAAGC AAAAGC AAAAGC AAAGGAGC AAGAGC AAGAGC AAGAGC AAAAGC
1 AAAAGC AAAAGC AAAAGC AAA--AGC AAAAGC AAAAGC AAAAGC AAAAGC
383508 AAAAGC AAA
1 AAAAGC AAA
383517 CAGAGATGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
6 44 0.90
8 5 0.10
ACGTcount: A:0.61, C:0.15, G:0.24, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:387174 original size:60 final size:59
Alignment explanation
Indices: 387110--387272 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 59
387100 ATTGGCCGTA
**
387110 CAATGACCGACACCCCTATTTATCTGATAAAAACAATCAAATTTTTGGGTATTGGTCATG
1 CAATGACCGACACCCCTATTTATCTGATAAAAA-AATCAAATTTTTGGGTATTGCCCATG
** * * ** * *
387170 CAATGGTCGACACCCCTTTTTTTATCAGATAAAAAAAT-TTATTTTTTGGTGTTGCCCATG
1 CAATGACCGACACCCC--TATTTATCTGATAAAAAAATCAAATTTTTGGGTATTGCCCATG
* * *
387230 CAATGACTGACACCCTTATTTATCTAATAAAAAAAATCAAATT
1 CAATGACCGACACCCCTATTTATCTGAT-AAAAAAATCAAATT
387273 GTTGAAAAGA
Statistics
Matches: 80, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
58 9 0.11
59 8 0.10
60 45 0.56
61 3 0.04
62 15 0.19
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (59 bp):
CAATGACCGACACCCCTATTTATCTGATAAAAAAATCAAATTTTTGGGTATTGCCCATG
Found at i:387750 original size:44 final size:43
Alignment explanation
Indices: 387702--387810 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 43
387692 ACATCTAAAT
* * *
387702 AACAAAAATAATAATAAAAACAGCAGCAAAACAACAACAAAAAC
1 AACAAAAATAATAAAAAAAACAACACCAAAACAACAA-AAAAAC
** **
387746 AACAAAAATAATAGCAAAAACAACACCAAAACAGTAAAAAAAC
1 AACAAAAATAATAAAAAAAACAACACCAAAACAACAAAAAAAC
*
387789 AACACCAAAATAACAAAAAAAA
1 AACA--AAAATAATAAAAAAAA
387811 ACAATCAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
43 10 0.19
44 31 0.57
45 13 0.24
ACGTcount: A:0.72, C:0.18, G:0.04, T:0.06
Consensus pattern (43 bp):
AACAAAAATAATAAAAAAAACAACACCAAAACAACAAAAAAAC
Found at i:387786 original size:22 final size:22
Alignment explanation
Indices: 387761--387831 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
387751 AAATAATAGC
387761 AAAAACAACACCAAAACAGTAA
1 AAAAACAACACCAAAACAGTAA
* **
387783 AAAAACAACACCAAAATAACAA
1 AAAAACAACACCAAAACAGTAA
*
387805 AAAAA-AACAATCAAAACAGTAA
1 AAAAACAAC-ACCAAAACAGTAA
387827 AAAAA
1 AAAAA
387832 TAGCATCAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 3 0.07
22 38 0.93
ACGTcount: A:0.73, C:0.18, G:0.03, T:0.06
Consensus pattern (22 bp):
AAAAACAACACCAAAACAGTAA
Found at i:387839 original size:22 final size:21
Alignment explanation
Indices: 387761--387842 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
387751 AAATAATAGC
* *
387761 AAAAACAACACCAAAACAGTA
1 AAAAAAAACATCAAAACAGTA
* * **
387782 AAAAAACAACACCAAAATAACA
1 AAAAAA-AACATCAAAACAGTA
387804 AAAAAAAACAATCAAAACAGTA
1 AAAAAAAAC-ATCAAAACAGTA
*
387826 AAAAAATAGCATCAAAA
1 AAAAAA-AACATCAAAA
387843 TAACAATATA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 8 0.16
22 39 0.80
23 2 0.04
ACGTcount: A:0.71, C:0.18, G:0.04, T:0.07
Consensus pattern (21 bp):
AAAAAAAACATCAAAACAGTA
Found at i:388493 original size:23 final size:23
Alignment explanation
Indices: 388466--388509 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
388456 AAATTAAAAA
388466 TATAATGTAAAATATATATTTTT
1 TATAATGTAAAATATATATTTTT
* * *
388489 TATAATTTGAAATCTATATTT
1 TATAATGTAAAATATATATTT
388510 GTCTCTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
TATAATGTAAAATATATATTTTT
Found at i:390045 original size:287 final size:282
Alignment explanation
Indices: 389481--390051 Score: 1016
Period size: 287 Copynumber: 2.0 Consensus size: 282
389471 AAGAAGATAC
389481 CAGTGGAGAACACAATCAAGGCAGTACCAATGACATCAATGAAGAAGACACTGAAGGTAGTCTCT
1 CAGTGGAGAACACAATCAAGGCAGTACCAATGACATCAATGAAGAAGACACTGAAGGTAGTCTCT
*
389546 GTGTGTGTGTTTTAATTTCAATAATATTTTGTTGTTCTTATGGCTTTTGTAGAGAACCTTTTTCT
66 GTGTGTGTGTTTTAATTTCAATAATATTTTGCTGTTCTTATGGCTTTTGTAGAGAACCTTTTTCT
389611 GGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTTTAAA
131 GGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTTTAAA
* *
389676 ACCTATAATTAGAATGAAATGAAGTAGTAAATCTGTGTCATATTAACCAGGTAATTATATAACCA
196 ACCTATAATTAGAATGAAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTAAATAACCA
*
389741 GTGAAGAACACAATGTAGGTAA
261 GTAAAGAACACAATGTAGGTAA
* *
389763 CAGTGGAGAACACAATCAAGGCAGTAGCAATGGCATCAATGAAGAAGACACTGAAGGTAGTGTCT
1 CAGTGGAGAACACAATCAAGGCAGTACCAATGACATCAATGAAGAAGACACTGAAGGTA--GTCT
*
389828 CTGTGTGTGTGTTTTAATTTCAATAATATTTTGCTGTTGTTATGGCTTTTGTAGAGAACCTTTTT
64 CTGTGTGTGTGTTTTAATTTCAATAATATTTTGCTGTTCTTATGGCTTTTGTAGAGAACC--TTT
389893 TTCTGGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTT
127 TTCTGGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTT
*
389958 TAAAAACCTATAATTAGAATGGAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTAAAT
192 T-AAAACCTATAATTAGAATGAAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTAAAT
*
390023 AACCAGTAAAGAACCCAATGTAGGTAA
256 AACCAGTAAAGAACACAATGTAGGTAA
390050 CA
1 CA
390052 CCCACGAAGA
Statistics
Matches: 275, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
282 57 0.21
284 62 0.23
286 69 0.25
287 87 0.32
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (282 bp):
CAGTGGAGAACACAATCAAGGCAGTACCAATGACATCAATGAAGAAGACACTGAAGGTAGTCTCT
GTGTGTGTGTTTTAATTTCAATAATATTTTGCTGTTCTTATGGCTTTTGTAGAGAACCTTTTTCT
GGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTTTAAA
ACCTATAATTAGAATGAAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTAAATAACCA
GTAAAGAACACAATGTAGGTAA
Found at i:390594 original size:338 final size:337
Alignment explanation
Indices: 389763--390697 Score: 1600
Period size: 338 Copynumber: 2.8 Consensus size: 337
389753 ATGTAGGTAA
*
389763 CAGTGGAGAACACAATCAAGGCAGTAGCAATGGCATCAATGAAGAAGACACTGAAGGTAGTGTCT
1 CAGTGGAGAACACAATCAAGGCAGTACCAATGGCATCAATGAAGAAGACACTGAAGGTAGTGTCT
* *
389828 CTGTGTGTGTGTTTTAATTTCAATAATATTTTGCTGTTGTTATGGCTTTTGTAGAGAACCTTTTT
66 CTGTGTGTGTGTTTTAATTTCAATAATATTTTGTTGTTCTTATGGCTTTTGTAGAGAACCTTTTT
389893 TTCTGGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTT
131 TTCTGGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTT
*
389958 TAAAAACCTATAATTAGAATGGAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTAAAT
196 TAAAAACCTATAATTAGAAT-GAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTATAT
* *
390023 AACCAGTAAAGAACCCAATGTAGGTAACACCCACGAAGACGGTGAAGGATCCAATGGAGGGAATA
260 AACCAATAAAGAACCCAATGTAGGTAACACCCACGAAGACGATGAAGGATCCAATGGAGGGAATA
390088 ACCAAGAAGATAC
325 ACCAAGAAGATAC
* * *
390101 CAGTGGAGAACACAATAAAGGCAGTACCAATGGCATCAATGAAGAGGACACTAAAGGTAGTGTCT
1 CAGTGGAGAACACAATCAAGGCAGTACCAATGGCATCAATGAAGAAGACACTGAAGGTAGTGTCT
* *
390166 CTCTGTGTGTGTTTTAATTTCAATAATATTTTGTTGTTCTTATGCCTTTTGTAGAGAACCTTTTT
66 CTGTGTGTGTGTTTTAATTTCAATAATATTTTGTTGTTCTTATGGCTTTTGTAGAGAACCTTTTT
* *
390231 TTCTGGAGATCTAGAAAGTAAAAACCCAACTTTAGATTTCAAAGTCAATGCAGGAAAACAAGTTT
131 TTCTGGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTT
*
390296 TAAAAACCTATAATTAGAATGAATGTAGTAGTAAATCTGTGCCATATTAACCAGGTAATTATATA
196 TAAAAACCTATAATTAGAATGAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTATATA
* * *
390361 ACCAATGAAGAACCCTATGTAGGTAACACCCATGAAGACGATGAAGGATCCAATGGAGGGAATAA
261 ACCAATAAAGAACCCAATGTAGGTAACACCCACGAAGACGATGAAGGATCCAATGGAGGGAATAA
390426 CCAAGAAGATAC
326 CCAAGAAGATAC
* * * * **
390438 CAGTGAAGAATACAATCAAGGCAGTACCACTGACATCAATGAAGAAGACACTGAAGGTAGACTCT
1 CAGTGGAGAACACAATCAAGGCAGTACCAATGGCATCAATGAAGAAGACACTGAAGGTAGTGTCT
* * *
390503 GTGTGTGTGTGTTTTAATTTCAATAATACTTTGTTGTTCTTATGGCTTTGGTAGAGAACCTTTTT
66 CTGTGTGTGTGTTTTAATTTCAATAATATTTTGTTGTTCTTATGGCTTTTGTAGAGAACCTTTTT
*
390568 TTCTGGAGATCTAGAAAGTAAAAAACCCAACTTCAGATTTCAGAGTTAATGCAGGAAAACAAGTT
131 TTCTGGAGATCTAGAAAGT-AAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTT
390633 TTAAAAACCTATAATTAGAATGAAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTATA
195 TTAAAAACCTATAATTAGAATG-AATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTATA
390698 CAATGTAGCT
Statistics
Matches: 560, Mismatches: 35, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
337 250 0.45
338 269 0.48
339 41 0.07
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (337 bp):
CAGTGGAGAACACAATCAAGGCAGTACCAATGGCATCAATGAAGAAGACACTGAAGGTAGTGTCT
CTGTGTGTGTGTTTTAATTTCAATAATATTTTGTTGTTCTTATGGCTTTTGTAGAGAACCTTTTT
TTCTGGAGATCTAGAAAGTAAAAACCCAACTTCAGATTTCAGAGTCAATGCAGGAAAACAAGTTT
TAAAAACCTATAATTAGAATGAATGAAGTAGTAAATCTGTGCCATATTAACCAGGTAATTATATA
ACCAATAAAGAACCCAATGTAGGTAACACCCACGAAGACGATGAAGGATCCAATGGAGGGAATAA
CCAAGAAGATAC
Found at i:391714 original size:30 final size:30
Alignment explanation
Indices: 391678--391740 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
391668 ACATTGCAAA
391678 GGATAAATCTAGGGAGTTAAAAGCTGCTTT
1 GGATAAATCTAGGGAGTTAAAAGCTGCTTT
391708 GGATAAATCTAGGGAGTTAAAAGCTGCTTT
1 GGATAAATCTAGGGAGTTAAAAGCTGCTTT
391738 GGA
1 GGA
391741 GGCAGCTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (30 bp):
GGATAAATCTAGGGAGTTAAAAGCTGCTTT
Found at i:393718 original size:26 final size:26
Alignment explanation
Indices: 393682--393734 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
393672 AAAACTGAAT
393682 TGGTGTTTGAGGATTTTATCGTAAAC
1 TGGTGTTTGAGGATTTTATCGTAAAC
393708 TGGTGTTTGAGGATTTTATCGTAAAC
1 TGGTGTTTGAGGATTTTATCGTAAAC
393734 T
1 T
393735 CAACTACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.43
Consensus pattern (26 bp):
TGGTGTTTGAGGATTTTATCGTAAAC
Found at i:396595 original size:46 final size:47
Alignment explanation
Indices: 396521--396615 Score: 111
Period size: 46 Copynumber: 2.0 Consensus size: 47
396511 TGCAGTACAG
* ** *
396521 ATATGCAATACCTTCAATGTACAAAAGC-TGTTATGATCATATATAT
1 ATATGCAATAACTTCAAACTACAAAAGCATGCTATGATCATATATAT
* * *
396567 ATATGCAGTAACTTCAAACTACACAAGCTATGCTATGATCCTATATAT
1 ATATGCAATAACTTCAAACTACAAAAGC-ATGCTATGATCATATATAT
396615 A
1 A
396616 GAGAGAGGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 23 0.57
48 17 0.43
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (47 bp):
ATATGCAATAACTTCAAACTACAAAAGCATGCTATGATCATATATAT
Done.