Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002252.1 Kokia drynarioides strain JFW-HI SEQ_114261, 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: 69893
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:302 original size:58 final size:60
Alignment explanation
Indices: 232--371 Score: 142
Period size: 58 Copynumber: 2.4 Consensus size: 60
222 TTTTGGATAC
* * ** * **
232 TCGAGGGCAAAATGATAATTTTGGGAAAATTTTGGG-TTTAAAATGGAA-TTTTAGACAT
1 TCGAGGGTAAAATGATAATTTTGAGAAAAAATCGGGATAAAAAATGGAACTTTTAGACAT
* *
290 TCGAGGGTAAAAT-AGTAATTTTTAGAAAAAATCGGGATAAAAAATGGAACTTTTGGACAT
1 TCGAGGGTAAAATGA-TAATTTTGAGAAAAAATCGGGATAAAAAATGGAACTTTTAGACAT
* * *
350 TTGGGGGTAAAATGGTAATTTT
1 TCGAGGGTAAAATGATAATTTT
372 TAAGTTTCGA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
57 1 0.02
58 28 0.42
59 10 0.15
60 27 0.41
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
TCGAGGGTAAAATGATAATTTTGAGAAAAAATCGGGATAAAAAATGGAACTTTTAGACAT
Found at i:312 original size:29 final size:29
Alignment explanation
Indices: 280--429 Score: 90
Period size: 29 Copynumber: 5.1 Consensus size: 29
270 TAAAATGGAA
280 TTTTAGACATTCGAGGGTAAAATAGTAAT
1 TTTTAGACATTCGAGGGTAAAATAGTAAT
* * * * * *
309 TTTTAGAAAAAATCG-GGATAAAAAATGGAAC
1 TTTTAG--ACATTCGAGGGTAAAATA-GTAAT
* * * *
340 TTTTGGACATTTGGGGGTAAAATGGTAAT
1 TTTTAGACATTCGAGGGTAAAATAGTAAT
**
369 TTTTA-AGTTTCGAGGGTAAAA-ATGTAAT
1 TTTTAGACATTCGAGGGTAAAATA-GTAAT
* ** * *
397 TTTTGGAGGTTCGGGGGTAAAATGGTAAT
1 TTTTAGACATTCGAGGGTAAAATAGTAAT
426 TTTT
1 TTTT
430 GGAAGTTTCA
Statistics
Matches: 89, Mismatches: 25, Indels: 14
0.70 0.20 0.11
Matches are distributed among these distances:
28 21 0.24
29 40 0.45
30 15 0.17
31 13 0.15
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
TTTTAGACATTCGAGGGTAAAATAGTAAT
Found at i:459 original size:30 final size:29
Alignment explanation
Indices: 366--638 Score: 118
Period size: 30 Copynumber: 9.3 Consensus size: 29
356 GTAAAATGGT
366 AATTTTT--AAGTTTCGAGGGTAAAAAT-G
1 AATTTTTGAAAGTTTC-AGGGTAAAAATAG
* * * *
393 TAATTTTTG-GAGGTTCGGGGGT-AAAATGG
1 -AATTTTTGAAAGTTTC-AGGGTAAAAATAG
* *
422 TAATTTTTGGAAGTTTCAAGGTCAAAAATAG
1 -AATTTTTGAAAGTTTCAGGGT-AAAAATAG
* * *
453 AATTTTT-AGAGGTTTGAGGGGGT-AAAATTG
1 AATTTTTGA-AAGTTTCA--GGGTAAAAATAG
* * * *
483 TAATTTTCGAAAGTTTTAGGGTTAAAATGG
1 -AATTTTTGAAAGTTTCAGGGTAAAAATAG
*
513 AATTTTTGAAAG-TTCGAGGGTAAAAAATAT
1 AATTTTTGAAAGTTTC-AGGGT-AAAAATAG
* ** *
543 AATTTTCGAAAGTTTTGGGGTTAAAAATGG
1 AATTTTTGAAAGTTTCAGGG-TAAAAATAG
* * *
573 AATTTTT-AGAAGTTT-GGGGTACAAATAT
1 AATTTTTGA-AAGTTTCAGGGTAAAAATAG
***
601 AATTTCCAAAAGTTTC-GAGGTCAAAAATAG
1 AATTTTTGAAAGTTTCAG-GGT-AAAAATAG
631 AATTTTTG
1 AATTTTTG
639 GACAGTTTAT
Statistics
Matches: 187, Mismatches: 38, Indels: 38
0.71 0.14 0.14
Matches are distributed among these distances:
28 32 0.17
29 52 0.28
30 78 0.42
31 21 0.11
32 4 0.02
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
AATTTTTGAAAGTTTCAGGGTAAAAATAG
Found at i:465 original size:59 final size:57
Alignment explanation
Indices: 352--637 Score: 215
Period size: 59 Copynumber: 4.9 Consensus size: 57
342 TTGGACATTT
* * *
352 GGGGGTAAAATGGTAATTTT--TAAGTTTCGAGGGTAAAAAT-GTAATTTTTGGAGGTTC
1 GGGGGTAAAAT-GTAATTTTCGAAAGTTTC-AGGGTAAAAATAG-AATTTTTAGAAGTTC
* * * * *
409 GGGGGTAAAATGGTAATTTTTGGAAGTTTCAAGGTCAAAAATAGAATTTTTAGAGGTTTGA
1 GGGGGTAAAAT-GTAATTTTCGAAAGTTTCAGGGT-AAAAATAGAATTTTTAGAAG-TT-C
* * *
470 GGGGGTAAAATTGTAATTTTCGAAAGTTTTAGGGTTAAAATGGAATTTTT-GAAAGTTC
1 GGGGGTAAAA-TGTAATTTTCGAAAGTTTCAGGGTAAAAATAGAATTTTTAG-AAGTTC
* * ** *
528 GAGGGTAAAAAATATAATTTTCGAAAGTTTTGGGGTTAAAAATGGAATTTTTAGAAGTT-
1 GGGGGT--AAAATGTAATTTTCGAAAGTTTCAGGG-TAAAAATAGAATTTTTAGAAGTTC
* * * *
587 TGGGGTACAAATATAATTTCCAAAAGTTTC-GAGGTCAAAAATAGAATTTTT
1 GGGGGTA-AAATGTAATTTTCGAAAGTTTCAG-GGT-AAAAATAGAATTTTT
638 GGACAGTTTA
Statistics
Matches: 192, Mismatches: 22, Indels: 29
0.79 0.09 0.12
Matches are distributed among these distances:
57 23 0.12
58 44 0.23
59 52 0.27
60 42 0.22
61 30 0.16
62 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (57 bp):
GGGGGTAAAATGTAATTTTCGAAAGTTTCAGGGTAAAAATAGAATTTTTAGAAGTTC
Found at i:586 original size:60 final size:59
Alignment explanation
Indices: 445--646 Score: 212
Period size: 58 Copynumber: 3.4 Consensus size: 59
435 TTTCAAGGTC
* * * *
445 AAAAATAGAATTTTTAGAGGTTTGAGGGGGTAAAATTGTAATTTTCGAAAGTTTTAGGGTT
1 AAAAATAGAATTTTTAGAAGTTTGA--GGGTAAAAATATAATTTTCGAAAGTTTTGGGGTT
* *
506 -AAAATGGAATTTTT-GAAAGTTCGAGGGTAAAAAATATAATTTTCGAAAGTTTTGGGGTT
1 AAAAATAGAATTTTTAG-AAGTTTGAGGGT-AAAAATATAATTTTCGAAAGTTTTGGGGTT
* * * * * * *
565 AAAAATGGAATTTTTAGAAGTTTG-GGGTACAAATATAATTTCCAAAAGTTTCGAGGTC
1 AAAAATAGAATTTTTAGAAGTTTGAGGGTAAAAATATAATTTTCGAAAGTTTTGGGGTT
*
623 AAAAATAGAATTTTTGGACAGTTT
1 AAAAATAGAATTTTTAGA-AGTTT
647 ATGGACCTCC
Statistics
Matches: 121, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
58 44 0.36
59 37 0.31
60 39 0.32
61 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (59 bp):
AAAAATAGAATTTTTAGAAGTTTGAGGGTAAAAATATAATTTTCGAAAGTTTTGGGGTT
Found at i:589 original size:29 final size:29
Alignment explanation
Indices: 329--592 Score: 146
Period size: 29 Copynumber: 9.0 Consensus size: 29
319 AATCGGGATA
* *
329 AAAAATGGAACTTTTGGACA-TTTGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTGGGGTT
358 -AAAATGGTAATTTTT--AAGTTTCGAGGG-T
1 AAAAATGG-AATTTTTGGAAGTTT-G-GGGTT
* * * *
386 AAAAATGTAATTTTTGGAGGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGTT
** *
415 -AAAATGGTAATTTTTGGAAGTTTCAAGGTC
1 AAAAATGG-AATTTTTGGAAGTTT-GGGGTT
* * * *
445 AAAAATAGAATTTTTAGAGGTTTGAGGGGGT
1 AAAAATGGAATTTTTGGAAGTTT--GGGGTT
* * * * *
476 AAAATTGTAATTTTCGAAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAAG-TTTGGGGTT
* * *
506 -AAAATGGAATTTTTGAAAGTTCGAGGGTA
1 AAAAATGGAATTTTTGGAAGTTTG-GGGTT
** * *
535 AAAAATATAATTTTCGAAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAG-TTTGGGGTT
*
565 AAAAATGGAATTTTTAGAAGTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGT
593 ACAAATATAA
Statistics
Matches: 175, Mismatches: 44, Indels: 32
0.70 0.18 0.13
Matches are distributed among these distances:
26 1 0.01
27 4 0.02
28 27 0.15
29 58 0.33
30 58 0.33
31 24 0.14
32 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGTT
Found at i:1775 original size:12 final size:12
Alignment explanation
Indices: 1722--1833 Score: 59
Period size: 12 Copynumber: 9.1 Consensus size: 12
1712 TATTAAAATT
*
1722 TATTAATATTAA
1 TATTATTATTAA
*
1734 TATTA--ATTAT
1 TATTATTATTAA
1744 TATTATTATTGAAA
1 TATTATTATT--AA
*
1758 CAATTATTATTAA
1 -TATTATTATTAA
*
1771 TATTATTAATGTCA
1 TATTATT-AT-TAA
* *
1785 T-TTATTACTAC
1 TATTATTATTAA
*
1796 TGTTTATTATTAA
1 T-ATTATTATTAA
* **
1809 TGTTATTAGAAA
1 TATTATTATTAA
1821 TATTATTATTAA
1 TATTATTATTAA
1833 T
1 T
1834 GCAATTATTA
Statistics
Matches: 75, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
10 9 0.12
11 2 0.03
12 33 0.44
13 18 0.24
14 4 0.05
15 9 0.12
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:2560 original size:17 final size:17
Alignment explanation
Indices: 2528--2606 Score: 81
Period size: 17 Copynumber: 4.5 Consensus size: 17
2518 AATAAGTTTT
2528 AAATTTAAATTTTAAAAC
1 AAATTTAAA-TTTAAAAC
*
2546 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAC
*
2563 AAATTTAAATTCAAAATC
1 AAATTTAAATTTAAAA-C
*
2581 -AATTT-AATCTTAAAAT
1 AAATTTAAAT-TTAAAAC
2597 AAATCTTAAA
1 AAAT-TTAAA
2607 ATGGGTTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.06
17 35 0.69
18 11 0.22
19 2 0.04
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAAAC
Found at i:2566 original size:35 final size:34
Alignment explanation
Indices: 2527--2606 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 34
2517 TAATAAGTTT
*
2527 TAAATTTAAATTTTAAAA-CAAATTTAAAT-TTAAAA
1 TAAATTTAAA-TTCAAAATC-AATTT-AATCTTAAAA
2562 TAAATTTAAATTCAAAATCAATTTAATCTTAAAA
1 TAAATTTAAATTCAAAATCAATTTAATCTTAAAA
2596 TAAATCTTAAA
1 TAAAT-TTAAA
2607 ATGGGTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
33 3 0.07
34 22 0.54
35 16 0.39
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (34 bp):
TAAATTTAAATTCAAAATCAATTTAATCTTAAAA
Found at i:6336 original size:14 final size:14
Alignment explanation
Indices: 6317--6343 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6307 AACATTTAGC
6317 AAAAAGAAAGAAAG
1 AAAAAGAAAGAAAG
6331 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
6344 AATATGGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAG
Found at i:10905 original size:64 final size:64
Alignment explanation
Indices: 10871--11132 Score: 357
Period size: 64 Copynumber: 4.1 Consensus size: 64
10861 GCCATTTGGG
* * * **
10871 TTTCAAA-CCCATCAGTCTCTATTCATCTCGTTTAGAATAATGATTAAAGTTTTTGTGATTTGG
1 TTTCAAATCCCATCAGTCTCTATTCATCTCTTTTAGAATAATGATTAAAGTTTTTGCGATATAA
* * *
10934 TTTCAAATCTCATCATTCTCTATTCATCTCTTTTAGAATAATGATTAAAATTTTTGCGATATAA
1 TTTCAAATCCCATCAGTCTCTATTCATCTCTTTTAGAATAATGATTAAAGTTTTTGCGATATAA
* * * *
10998 TTCCAAA-CCTCATCAGTCTCTATTTATCTCTTTTAAAATAATGGTTAAAGTTTTTGCGATATAA
1 TTTCAAATCC-CATCAGTCTCTATTCATCTCTTTTAGAATAATGATTAAAGTTTTTGCGATATAA
* ** *
11062 TTTCAAATCCCATCATTCTCTATTCATCTCTTTTAGAATAACAATTAAAGTTTTTGCGATATAG
1 TTTCAAATCCCATCAGTCTCTATTCATCTCTTTTAGAATAATGATTAAAGTTTTTGCGATATAA
11126 TTTCAAA
1 TTTCAAA
11133 CTCCACATTT
Statistics
Matches: 173, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
63 8 0.05
64 163 0.94
65 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (64 bp):
TTTCAAATCCCATCAGTCTCTATTCATCTCTTTTAGAATAATGATTAAAGTTTTTGCGATATAA
Found at i:11527 original size:16 final size:16
Alignment explanation
Indices: 11506--11539 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
11496 ATATTTTAAT
11506 GTAAAATTAAAATAGG
1 GTAAAATTAAAATAGG
11522 GTAAAATTAAAATAGG
1 GTAAAATTAAAATAGG
11538 GT
1 GT
11540 GTGTTATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (16 bp):
GTAAAATTAAAATAGG
Found at i:28978 original size:118 final size:118
Alignment explanation
Indices: 28807--29043 Score: 289
Period size: 118 Copynumber: 2.0 Consensus size: 118
28797 CTACGGAACC
* * * * *
28807 TTTGACGATGCTCAAGATGATTACTTGCAGGTTCAGCTCCCAGAAAATGACGCCTGAGGAAAGGC
1 TTTGACGATGCTCAAGATGATTACTTACAGATTCAGCTCCCAGAAAATAACGCCCGAGGAAAGAC
** ***
28872 CGGCCTAAAGATTCT-TGAATTTCATTTCCATTGGAACCATGGCTTCTACGCCT
66 CAACCTAAAGATTCTCT-AATTTCATTTCCATCAAAACCATGGCTTCTACGCCT
* * * *
28925 TTTGACGATGCTCAAGATGGTTTCTTATAGATTCTGCTCCCA-ATAAATAACGCCCGAGGAAAGA
1 TTTGACGATGCTCAAGATGATTACTTACAGATTCAGCTCCCAGA-AAATAACGCCCGAGGAAAGA
* * *
28989 CCAACCTAAAGGTTCTCTAATTTCATTTCCATCAAAACTATGGGTTCTACGCCT
65 CCAACCTAAAGATTCTCTAATTTCATTTCCATCAAAACCATGGCTTCTACGCCT
29043 T
1 T
29044 CGAAGAGACT
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
117 1 0.01
118 98 0.98
119 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (118 bp):
TTTGACGATGCTCAAGATGATTACTTACAGATTCAGCTCCCAGAAAATAACGCCCGAGGAAAGAC
CAACCTAAAGATTCTCTAATTTCATTTCCATCAAAACCATGGCTTCTACGCCT
Found at i:31870 original size:3 final size:3
Alignment explanation
Indices: 31862--31904 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
31852 AGATCTCATT
31862 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
31905 AACTTTCCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33911 original size:28 final size:29
Alignment explanation
Indices: 33880--33947 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
33870 AAAAAATTAA
33880 AATATTTTTTTATATTTTTAT-A-CTTTTT
1 AATATTTTTTTA-ATTTTTATAATCTTTTT
* *
33908 AATA-ATATTTAATTTTTATAATCTTTTT
1 AATATTTTTTTAATTTTTATAATCTTTTT
*
33936 GA-ATTTTTTTAA
1 AATATTTTTTTAA
33948 ATTAACTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
26 8 0.25
27 7 0.22
28 17 0.53
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (29 bp):
AATATTTTTTTAATTTTTATAATCTTTTT
Found at i:37123 original size:20 final size:20
Alignment explanation
Indices: 37098--37135 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37088 GGTTTTTCGA
* *
37098 AAAAAGTCTATGGTCAACCC
1 AAAAAGTCAACGGTCAACCC
37118 AAAAAGTCAACGGTCAAC
1 AAAAAGTCAACGGTCAAC
37136 TGTCAATGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAAAGTCAACGGTCAACCC
Found at i:39769 original size:15 final size:16
Alignment explanation
Indices: 39744--39776 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39734 AATTTATTTT
39744 TATATAAAAATAATAA
1 TATATAAAAATAATAA
*
39760 TATA-AAAAATTATAA
1 TATATAAAAATAATAA
39775 TA
1 TA
39777 CGAAAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATATAAAAATAATAA
Found at i:51225 original size:49 final size:49
Alignment explanation
Indices: 51168--51275 Score: 198
Period size: 49 Copynumber: 2.2 Consensus size: 49
51158 TACATCATAG
*
51168 GAAATTGAATCATCTTTAAACTAAGTTTCTTCAAGCTACATTCTGCTCA
1 GAAATTGAATCATCTTTAAACTAAGTTTCTCCAAGCTACATTCTGCTCA
51217 GAAATTGAATCATCTTTAAACTAAGTTTCTCCAAGCTACATTCTGCTCA
1 GAAATTGAATCATCTTTAAACTAAGTTTCTCCAAGCTACATTCTGCTCA
51266 GAAATGTGAA
1 GAAAT-TGAA
51276 CATGACTCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
49 53 0.93
50 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (49 bp):
GAAATTGAATCATCTTTAAACTAAGTTTCTCCAAGCTACATTCTGCTCA
Found at i:53221 original size:42 final size:42
Alignment explanation
Indices: 53162--53245 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
53152 GCCAGGACTG
53162 CTTATTTAGGCCAATCTTACTTTTGGCTTGAACATCCATCTA
1 CTTATTTAGGCCAATCTTACTTTTGGCTTGAACATCCATCTA
53204 CTTATTTAGGCCAATCTTACTTTTGGCTTGAACATCCATCTA
1 CTTATTTAGGCCAATCTTACTTTTGGCTTGAACATCCATCTA
53246 ATTGAAACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (42 bp):
CTTATTTAGGCCAATCTTACTTTTGGCTTGAACATCCATCTA
Found at i:58532 original size:26 final size:28
Alignment explanation
Indices: 58503--58559 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
58493 GTAGGGAGGA
58503 TATTAG-AGTTAGTGAGTTA-CAGCAGT
1 TATTAGTAGTTAGTGAGTTATCAGCAGT
* *
58529 TATTAGTTAGTTTGTTAGTTATCAGCAGT
1 TATTAG-TAGTTAGTGAGTTATCAGCAGT
58558 TA
1 TA
58560 ACATACTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
28 11 0.42
29 9 0.35
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (28 bp):
TATTAGTAGTTAGTGAGTTATCAGCAGT
Found at i:65202 original size:16 final size:18
Alignment explanation
Indices: 65171--65203 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
65161 ATATATTTAA
65171 ATGATGTATGTTAATGTT
1 ATGATGTATGTTAATGTT
65189 ATGATGT-T-TTAATGT
1 ATGATGTATGTTAATGT
65204 AAATAGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (18 bp):
ATGATGTATGTTAATGTT
Found at i:65364 original size:21 final size:21
Alignment explanation
Indices: 65316--65369 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
65306 TAATTTGAAT
*
65316 ATATAAAT-TATATTTTACAT
1 ATATAAATATATATTTTACAA
65336 AT-TAAA-ATATAATTATTACAA
1 ATATAAATATAT-ATT-TTACAA
65357 ATATAAATATATA
1 ATATAAATATATA
65370 ATGATGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 7 0.25
20 5 0.18
21 7 0.25
22 5 0.18
23 4 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAAATATATATTTTACAA
Found at i:65777 original size:30 final size:31
Alignment explanation
Indices: 65717--65778 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
65707 TACGAAGTTA
* * *
65717 TTTATGTTTTTTTAATAAAATTAGTAAAAAT
1 TTTATGTTTGTTTAATAAAAATAATAAAAAT
65748 TTTA-GTTTGTTT-ATAAAAATAATATAAAAT
1 TTTATGTTTGTTTAATAAAAATAATA-AAAAT
65778 T
1 T
65779 AATTAATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (31 bp):
TTTATGTTTGTTTAATAAAAATAATAAAAAT
Done.