Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003914.1 Kokia drynarioides strain JFW-HI SEQ_116982, 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: 40702
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:513 original size:20 final size:22
Alignment explanation
Indices: 488--527 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
478 TTCATCATTT
488 CTTTTCT-TC-ATTTCTCTAGA
1 CTTTTCTATCAATTTCTCTAGA
508 CTTTTCTATCAATTTCTCTA
1 CTTTTCTATCAATTTCTCTA
528 TAAAAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.17, C:0.25, G:0.03, T:0.55
Consensus pattern (22 bp):
CTTTTCTATCAATTTCTCTAGA
Found at i:10837 original size:18 final size:18
Alignment explanation
Indices: 10814--10849 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10804 AGGTCAAAAG
10814 ATTGATAGTCTTTATGTT
1 ATTGATAGTCTTTATGTT
10832 ATTGATAGTCTTTATGTT
1 ATTGATAGTCTTTATGTT
10850 CTGCAAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (18 bp):
ATTGATAGTCTTTATGTT
Found at i:11522 original size:14 final size:13
Alignment explanation
Indices: 11493--11537 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
11483 TTTATATGTG
*
11493 TTAGGTTTGGGGT
1 TTAGGTTTGAGGT
*
11506 TTAAGGTTTGAGTT
1 TT-AGGTTTGAGGT
*
11520 TTAGGTTTTAGGT
1 TTAGGTTTGAGGT
11533 TTAGG
1 TTAGG
11538 GTATTGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.49
Consensus pattern (13 bp):
TTAGGTTTGAGGT
Found at i:11533 original size:27 final size:28
Alignment explanation
Indices: 11493--11549 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
11483 TTTATATGTG
*
11493 TTAGGTTTGGGGTTTAAGGT-TTGAGTT
1 TTAGGTTTGAGGTTTAAGGTATTGAGTT
* * *
11520 TTAGGTTTTAGGTTTAGGGTATTGATTT
1 TTAGGTTTGAGGTTTAAGGTATTGAGTT
11548 TT
1 TT
11550 TAGTTTCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.53
Consensus pattern (28 bp):
TTAGGTTTGAGGTTTAAGGTATTGAGTT
Found at i:11735 original size:28 final size:29
Alignment explanation
Indices: 11704--11785 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
11694 TAGGTTTCAA
* *
11704 GTTTAT-GATTCAATGTTTTGGATTTATG
1 GTTTATAGTTTCAATGTTTTGGATTTAGG
* **
11732 GTTT-TAGTTTTAATGTTTTTTATTTAGG
1 GTTTATAGTTTCAATGTTTTGGATTTAGG
*
11760 GTTTATAGTTTCAA-GTTTAGGATTTA
1 GTTTATAGTTTCAATGTTTTGGATTTA
11786 AAGTTTTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
27 1 0.02
28 34 0.79
29 8 0.19
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.56
Consensus pattern (29 bp):
GTTTATAGTTTCAATGTTTTGGATTTAGG
Found at i:11778 original size:21 final size:21
Alignment explanation
Indices: 11754--11806 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
11744 ATGTTTTTTA
*
11754 TTTAGGGTTTATAGTTTCAAG
1 TTTAGGGTTTAAAGTTTCAAG
* * *
11775 TTTAGGATTTAAAGTTTTAAT
1 TTTAGGGTTTAAAGTTTCAAG
*
11796 TTTATGGTTTA
1 TTTAGGGTTTA
11807 GGATATAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (21 bp):
TTTAGGGTTTAAAGTTTCAAG
Found at i:22254 original size:20 final size:20
Alignment explanation
Indices: 22218--22256 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22208 ACCTTTCCAA
*
22218 TTTTAATTAATGATAATTAT
1 TTTTAATTAATCATAATTAT
*
22238 TTTTAATTAATCTTAATTA
1 TTTTAATTAATCATAATTA
22257 ACGTGATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTAATTAATCATAATTAT
Found at i:25133 original size:16 final size:16
Alignment explanation
Indices: 25083--25133 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
25073 TAAATTACTG
*
25083 ATTACAACTTTATTCC
1 ATTACAACTCTATTCC
*
25099 ATTACAACTCGATTCC
1 ATTACAACTCTATTCC
* *
25115 ATTACAGCTCTATTTC
1 ATTACAACTCTATTCC
25131 ATT
1 ATT
25134 CCCCTCAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.41
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:25315 original size:48 final size:48
Alignment explanation
Indices: 25244--25340 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
25234 TCCATGGTTC
*
25244 GTTTAGAGACTATTTGTAACTTGAGTCGTTTGTCAAATTGGGTGTCCT
1 GTTTAGAGACTATTTGTAACTTGAGTCGTTTGTCAAATTAGGTGTCCT
25292 GTTTAGAGACTATTTGTAACTTGAGTCGTTTGTCAAATTAGGTGTCCT
1 GTTTAGAGACTATTTGTAACTTGAGTCGTTTGTCAAATTAGGTGTCCT
25340 G
1 G
25341 ATGTTATGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (48 bp):
GTTTAGAGACTATTTGTAACTTGAGTCGTTTGTCAAATTAGGTGTCCT
Found at i:26778 original size:29 final size:30
Alignment explanation
Indices: 26746--27114 Score: 206
Period size: 30 Copynumber: 12.2 Consensus size: 30
26736 AATCGAGGTC
* * *
26746 AAAATGCAATTTTAGAGATGTCT-GGAGTT
1 AAAATGTAATTTTAGAGAAGTTTAGGAGTT
* * * *
26775 AAAATGTGATTTTGGATACGTTTAGG-GTT
1 AAAATGTAATTTTAGAGAAGTTTAGGAGTT
26804 AAAATGTAATTTTAGAGAAGTTTA-GAGATT
1 AAAATGTAATTTTAGAGAAGTTTAGGAG-TT
* *
26834 AAAATGTAATTTTAAAGAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAGAAGTTTAGGAGTT
* * * *
26864 AAAATGTAATTTTGGAAAAATTTTGGAAAATTGTAGGGT
1 AAAATGTAATTTTAGAGAAGTTTAGG---A--GT----T
* * *
26903 CAAAATGTAATTTTGGA-AAATTTTGG-GTT
1 -AAAATGTAATTTTAGAGAAGTTTAGGAGTT
* *
26932 AAAATATAATTTTGGAGAAGTTTAAGG-GTT
1 AAAATGTAATTTTAGAGAAGTTT-AGGAGTT
* *
26962 AAAATGTAATTTT-GAAAAGTATATGGA-TT
1 AAAATGTAATTTTAGAGAAGTTTA-GGAGTT
* * * * *
26991 AAAATGAAATTTTGGAAAATTTTAGGGGTT
1 AAAATGTAATTTTAGAGAAGTTTAGGAGTT
* * *
27021 AAAATGTGATTTTTAGA-ATGTTTGAGG-GTC
1 AAAATGT-AATTTTAGAGAAGTTT-AGGAGTT
* *
27051 AAAATGTGATTTTTG-GAAGTTTAAGG-GTT
1 AAAATGTAATTTTAGAGAAGTTT-AGGAGTT
* *
27080 AAAATGTGATTTTTA-AGAAGTTTAGGAGTC
1 AAAATGT-AATTTTAGAGAAGTTTAGGAGTT
27110 AAAAT
1 AAAAT
27115 ATGATTTTTG
Statistics
Matches: 270, Mismatches: 44, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
28 17 0.06
29 97 0.36
30 114 0.42
31 12 0.04
33 2 0.01
35 2 0.01
39 10 0.04
40 16 0.06
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTAGAGAAGTTTAGGAGTT
Found at i:26838 original size:30 final size:30
Alignment explanation
Indices: 26667--27104 Score: 204
Period size: 29 Copynumber: 14.5 Consensus size: 30
26657 AAAAACAGAG
* *
26667 TTTTAGAGAA--TTCGAGGTTAAAATGCAA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
* * * * *
26695 ATTTGGAAAAGTTTAAGCGGTAAAAATGTAA
1 TTTTAGAGAAGTTT-AGAGGTTAAAATGTAA
*** * * *
26726 TTTTAG-GAAAAATCGAGGTCAAAATGCAA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
* * * *
26755 TTTTAGAGATGTCTGGA-GTTAAAATGTGA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
* * *
26784 TTTTGGATACGTTTAG-GGTTAAAATGTAA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
*
26813 TTTTAGAGAAGTTTAGAGATTAAAATGTAA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
* *
26843 TTTTAAAGAAGTTTAGGGGTTAAAATGTAA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
* * * *
26873 TTTTGGAAAAATTTTGGAAAATTGTAGGGTCAAAATGTAA
1 TTTTAG-AGAAGTTT-----A--G-A-GGTTAAAATGTAA
* * * *
26913 TTTTGGA-AAATTTTG-GGTTAAAATATAA
1 TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
*
26941 TTTTGGAGAAGTTTA-AGGGTTAAAATGTAA
1 TTTTAGAGAAGTTTAGA-GGTTAAAATGTAA
* * * *
26971 TTTT-GAAAAGTATATG-GATTAAAATGAAA
1 TTTTAGAGAAGTTTA-GAGGTTAAAATGTAA
* * * * *
27000 TTTTGGAAAATTTTAGGGGTTAAAATGTGAT
1 TTTTAGAGAAGTTTAGAGGTTAAAATGT-AA
* * *
27031 TTTTAGA-ATGTTT-GAGGGTCAAAATGTGA
1 TTTTAGAGAAGTTTAGA-GGTTAAAATGTAA
* *
27060 TTTTTG-GAAGTTTA-AGGGTTAAAATGTGAT
1 TTTTAGAGAAGTTTAGA-GGTTAAAATGT-AA
27090 TTTTA-AGAAGTTTAG
1 TTTTAGAGAAGTTTAG
27105 GAGTCAAAAT
Statistics
Matches: 307, Mismatches: 73, Indels: 57
0.70 0.17 0.13
Matches are distributed among these distances:
28 25 0.08
29 114 0.37
30 112 0.36
31 30 0.10
36 1 0.00
38 6 0.02
39 1 0.00
40 18 0.06
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTTAGAGAAGTTTAGAGGTTAAAATGTAA
Found at i:26857 original size:59 final size:60
Alignment explanation
Indices: 26682--27114 Score: 264
Period size: 59 Copynumber: 7.2 Consensus size: 60
26672 GAGAATTCGA
* * * * * **
26682 GGTTAAAATGCAAATTTGGAAAAGTTTA-AGCGGTAAAAATGTAATTTTAGGAA-AAATCGA-
1 GGTTAAAATGTAATTTTGGAGAAGTTTAGAG-GGTTAAAATGTAATTTT--GAAGAAGTTTAG
* * * * * * * * * *
26742 GGTCAAAATGCAATTTTAGAGATGTCT-G-GAGTTAAAATGTGATTTTGGATACGTTTAG
1 GGTTAAAATGTAATTTTGGAGAAGTTTAGAGGGTTAAAATGTAATTTTGAAGAAGTTTAG
* * *
26800 GGTTAAAATGTAATTTTAGAGAAGTTTAGA-GATTAAAATGTAATTTTAAAGAAGTTTAGG
1 GGTTAAAATGTAATTTTGGAGAAGTTTAGAGGGTTAAAATGTAATTTTGAAGAAGTTTA-G
* * *
26860 GGTTAAAATGTAATTTTGGAAAAATTTTGGAAAATTGTAGGGTCAAAATGTAATTTTGGAA-AA-
1 GGTTAAAATGTAATTTTGG-AGAAGTTT-----A--G-AGGGTTAAAATGTAATTTT-GAAGAAG
*
26923 TTTTG
56 TTTAG
* *
26928 GGTTAAAATATAATTTTGGAGAAGTTTA-AGGGTTAAAATGTAATTTTGAA-AAGTATATG
1 GGTTAAAATGTAATTTTGGAGAAGTTTAGAGGGTTAAAATGTAATTTTGAAGAAGTTTA-G
* * * * * *
26987 GATTAAAATGAAATTTTGGAAAATTTTAG-GGGTTAAAATGTGATTTT-TAGAATGTTTGAG
1 GGTTAAAATGTAATTTTGGAGAAGTTTAGAGGGTTAAAATGTAATTTTGAAGAA-GTTT-AG
* * * * *
27047 GGTCAAAATGTGATTTTTG-GAAGTTTA-AGGGTTAAAATGTGATTTTTAAGAAGTTTAG
1 GGTTAAAATGTAATTTTGGAGAAGTTTAGAGGGTTAAAATGTAATTTTGAAGAAGTTTAG
*
27105 GAGTCAAAAT
1 G-GTTAAAAT
27115 ATGATTTTTG
Statistics
Matches: 293, Mismatches: 54, Indels: 53
0.73 0.14 0.13
Matches are distributed among these distances:
56 2 0.01
57 8 0.03
58 61 0.21
59 102 0.35
60 62 0.21
61 7 0.02
62 1 0.00
66 1 0.00
67 6 0.02
68 20 0.07
69 4 0.01
70 17 0.06
71 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.36
Consensus pattern (60 bp):
GGTTAAAATGTAATTTTGGAGAAGTTTAGAGGGTTAAAATGTAATTTTGAAGAAGTTTAG
Found at i:26954 original size:98 final size:99
Alignment explanation
Indices: 26797--26979 Score: 262
Period size: 98 Copynumber: 1.9 Consensus size: 99
26787 TGGATACGTT
* * * *
26797 TAGGGTTAAAATGTAATTTTAGAGAAGTTTAGAGATTAAAATGTAATTTTAAAGAAGTTTAGGGG
1 TAGGGTCAAAATGTAATTTTAGAGAAATTTAGAGATTAAAATATAATTTTAAAGAAGTTTAAGGG
26862 TTAAAATGTAATTTTGGAAAAATTTTGGAAAATTG
66 TTAAAATGTAATTTT-GAAAAATTTTGGAAAATTG
* * * **
26897 TAGGGTCAAAATGTAATTTTGGA-AAATTTTG-GGTTAAAATATAATTTTGGAGAAGTTTAAGGG
1 TAGGGTCAAAATGTAATTTTAGAGAAATTTAGAGATTAAAATATAATTTTAAAGAAGTTTAAGGG
26960 TTAAAATGTAATTTTGAAAA
66 TTAAAATGTAATTTTGAAAA
26980 GTATATGGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
97 5 0.07
98 42 0.57
99 6 0.08
100 21 0.28
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (99 bp):
TAGGGTCAAAATGTAATTTTAGAGAAATTTAGAGATTAAAATATAATTTTAAAGAAGTTTAAGGG
TTAAAATGTAATTTTGAAAAATTTTGGAAAATTG
Found at i:27971 original size:10 final size:10
Alignment explanation
Indices: 27924--27971 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
27914 AATAATAATG
*
27924 TGTATATATA
1 TGTATATATT
27934 TGTATATATT
1 TGTATATATT
* *
27944 TGTATGTATG
1 TGTATATATT
*
27954 TATATATATT
1 TGTATATATT
*
27964 TTTATATA
1 TGTATATA
27972 AGCATGAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (10 bp):
TGTATATATT
Found at i:28899 original size:46 final size:48
Alignment explanation
Indices: 28847--28963 Score: 150
Period size: 46 Copynumber: 2.5 Consensus size: 48
28837 ATCATGGTCT
* * * *
28847 ACTTCTCTGTATCTCATCAGGAAGATGATCA-TTTGTTG--TCTAATCC
1 ACTTCTCTGTATCTCATCAGGAAAATGAACACTTTATTGCTTC-AACCC
*
28893 ACTTCTCTATATCTCATCAGGAAAATGAACACTTTATTGCTTCAACCC
1 ACTTCTCTGTATCTCATCAGGAAAATGAACACTTTATTGCTTCAACCC
*
28941 ACTTCTTTGTATCTCATCAGGAA
1 ACTTCTCTGTATCTCATCAGGAA
28964 TATGGGGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
46 28 0.46
47 6 0.10
48 25 0.41
49 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (48 bp):
ACTTCTCTGTATCTCATCAGGAAAATGAACACTTTATTGCTTCAACCC
Found at i:29078 original size:105 final size:104
Alignment explanation
Indices: 28893--29169 Score: 378
Period size: 105 Copynumber: 2.6 Consensus size: 104
28883 TGTCTAATCC
*
28893 ACTTCTCTA-TATCTCATCAGGAAA-ATGAACACTTTATTGCTTCAACCCACTTCTTTGTATCTC
1 ACTTCTC-AGTATCTCATCA-GAAAGATGAACACTTTATTACTTCAA-CCACTTCTTTGTATCTC
* * *
28956 ATCAGGAATATGGGGTTTAAAGTTTCACTCACATTGAGGTCT
63 ATCAGAAAGATGAGGTTTAAAGTTTCACTCACATTGAGGTCT
*
28998 ACTTCTCAGTATCTCATCAAAAAGATGAACACTTTATTACTTCAACCTACTTCTTTGTATCTCAT
1 ACTTCTCAGTATCTCATCAGAAAGATGAACACTTTATTACTTCAACC-ACTTCTTTGTATCTCAT
*
29063 CAGAAAGATTAGGTTTAAAGTTTCACTCACATTGAGGTCT
65 CAGAAAGATGAGGTTTAAAGTTTCACTCACATTGAGGTCT
* * * * * * *
29103 ACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATCTCAT
1 ACTTCTCAGTATCTCATCAGAAAGATGAACACTTTATTACTTCAA-CCACTTCTTTGTATCTCAT
29168 CA
65 CA
29170 AGAAGACAGA
Statistics
Matches: 154, Mismatches: 14, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
104 6 0.04
105 146 0.95
106 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (104 bp):
ACTTCTCAGTATCTCATCAGAAAGATGAACACTTTATTACTTCAACCACTTCTTTGTATCTCATC
AGAAAGATGAGGTTTAAAGTTTCACTCACATTGAGGTCT
Found at i:29198 original size:37 final size:37
Alignment explanation
Indices: 29143--29213 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
29133 GCTTCATTAT
29143 TTTAATCCACTTCTCTGTATCTCATCAAGAAGACAGA
1 TTTAATCCACTTCTCTGTATCTCATCAAGAAGACAGA
* *
29180 TTTAGTCCACTTCTCTGTATCTCATCAGGAAGAC
1 TTTAATCCACTTCTCTGTATCTCATCAAGAAGAC
29214 GACCGCTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (37 bp):
TTTAATCCACTTCTCTGTATCTCATCAAGAAGACAGA
Found at i:29501 original size:39 final size:39
Alignment explanation
Indices: 29355--29746 Score: 170
Period size: 39 Copynumber: 10.1 Consensus size: 39
29345 TTTTTTTTTT
* * * * *** *
29355 GTAAGATATTGGATGGTTGCAATCTGCCCTTGGCTCGAG
1 GTAAGAGATTGGATGATGGTAATCTGCCCCAAGCTCGGG
* *
29394 GTAAGAGATTGGTTGATGGTAATCTGCCCCAAGCTCGAG
1 GTAAGAGATTGGATGATGGTAATCTGCCCCAAGCTCGGG
* *
29433 GTAAGAGA-TCGA--ATGGCTACAATCCGCCCCAAGCTCGGG
1 GTAAGAGATTGGATGATGG-T--AATCTGCCCCAAGCTCGGG
* * * * *
29472 GTAAGAGATTGGTTGATGGTGATCTGCCCCAGGTTTGGG
1 GTAAGAGATTGGATGATGGTAATCTGCCCCAAGCTCGGG
* *** * * * *
29511 GTAAAAGATCAAACGACT-GCAATCTACCCCAAGCTC-CG
1 GTAAGAGATTGGATGA-TGGTAATCTGCCCCAAGCTCGGG
* * * *
29549 GTAAGAGA-TCGACTGATGGTGATCTGCCCCAGGCTCGAG
1 GTAAGAGATTGGA-TGATGGTAATCTGCCCCAAGCTCGGG
* ** * * * *
29588 GTAAAAGATCAGATGATTGTAATCT-ACCCAGGCTCGAG
1 GTAAGAGATTGGATGATGGTAATCTGCCCCAAGCTCGGG
* * * * * * *
29626 GTAAGAAATTGGTTGATGGTGATTTGCCCTAGGCTCAGG
1 GTAAGAGATTGGATGATGGTAATCTGCCCCAAGCTCGGG
* * * ** * *
29665 GTAAAAGATTGGACGGTTATAATCTACCTC-AGACTCGGG
1 GTAAGAGATTGGATGATGGTAATCTGCCCCAAG-CTCGGG
* * * * * *
29704 GTAAGAGATTGGCTAATGGTGATATGCCTCATGCTCGGG
1 GTAAGAGATTGGATGATGGTAATCTGCCCCAAGCTCGGG
29743 GTAA
1 GTAA
29747 AAGTTCAAAC
Statistics
Matches: 254, Mismatches: 85, Indels: 28
0.69 0.23 0.08
Matches are distributed among these distances:
36 4 0.02
37 3 0.01
38 56 0.22
39 180 0.71
40 6 0.02
41 1 0.00
42 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (39 bp):
GTAAGAGATTGGATGATGGTAATCTGCCCCAAGCTCGGG
Found at i:29580 original size:77 final size:78
Alignment explanation
Indices: 29387--29928 Score: 308
Period size: 78 Copynumber: 7.0 Consensus size: 78
29377 TCTGCCCTTG
* * ** * * * * * * *
29387 GCTCGAGGTAAGAGATTGGTTGATGGTAATCTGCCCCAAGCTCGAGGTAAGAGATCGAATGGCTA
1 GCTCGCGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAAACGACTG
**
29452 CAATCCGCCCCAA
66 CAATCTACCCCAA
* * ** * * *
29465 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGTTTGGGGTAAAAGATCAAACGACTG
1 GCTCGCGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAAACGACTG
29530 CAATCTACCCCAA
66 CAATCTACCCCAA
* * *
29543 GCTC-CGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGATTG
1 GCTCGCGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAAACGACTG
* *
29607 TAATCTA-CCCAG
66 CAATCTACCCCAA
* * * ** * * *** **
29619 GCTCGAGGTAAGAAATTGGTTGATGGTGATTTGCCCTAGGCTC-AGGGTAAAAGATTGGACGGTT
1 GCTCGCGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGA-GGTAAAAGATCAAACGACT
** *
29683 ATAATCTACCTC-A
65 GCAATCTACCCCAA
* * * * * * * * * * *
29696 GACTCGGGGTAAGAGATTGGCTAATGGTGATATGCCTCATGCTCGGGGTAAAAGTTCAAACAATT
1 G-CTCGCGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAAACGACT
* * *
29761 GTAATTTACCTCAA
65 GCAATCTACCCCAA
* * * * * * ** * *
29775 GTTTGGGGTAAGACATTGACTGATGGTGATCTACTTCAGGTTCGAGGT-AAA-ATCGAATA-G-T
1 GCTCGCGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATC-AA-ACGAC
*
29836 TGCAATCTACCCCAG
64 TGCAATCTACCCCAA
* * * ** * * * *
29851 GCTCGGGGGTAAGAGATTGACTGATGGTGATCTACCTTAAGCTCGGGGTAAAAGATCAGATGACT
1 GCTC-GCGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAAACGACT
*
29916 GCAATCTGCCCCA
65 GCAATCTACCCCA
29929 GGTTTGGGAA
Statistics
Matches: 367, Mismatches: 84, Indels: 25
0.77 0.18 0.05
Matches are distributed among these distances:
76 25 0.07
77 154 0.42
78 170 0.46
79 18 0.05
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (78 bp):
GCTCGCGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAAACGACTG
CAATCTACCCCAA
Found at i:29623 original size:38 final size:38
Alignment explanation
Indices: 29510--29629 Score: 109
Period size: 38 Copynumber: 3.1 Consensus size: 38
29500 CCAGGTTTGG
* * * * * *
29510 GGTAAAAGATCAAACGACTGCAATCTACCCCAAGCTC-C
1 GGTAAAAGATCAGATGATTGTAATCTA-CCCAGGCTCGA
* * * *
29548 GGTAAGAGATC-GACTGATGGTGATCTGCCCCAGGCTCGA
1 GGTAAAAGATCAGA-TGATTGTAATCT-ACCCAGGCTCGA
29587 GGTAAAAGATCAGATGATTGTAATCTACCCAGGCTCGA
1 GGTAAAAGATCAGATGATTGTAATCTACCCAGGCTCGA
29625 GGTAA
1 GGTAA
29630 GAAATTGGTT
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
37 1 0.02
38 41 0.64
39 20 0.31
40 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (38 bp):
GGTAAAAGATCAGATGATTGTAATCTACCCAGGCTCGA
Found at i:29771 original size:78 final size:78
Alignment explanation
Indices: 29466--29908 Score: 355
Period size: 77 Copynumber: 5.7 Consensus size: 78
29456 CCGCCCCAAG
** * * * * *
29466 CTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGTTTGGGGTAAAAGATCAAACGACTGC
1 CTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCAAACGATTGT
29531 AATCTACCCCA-A
66 AATCTACCCCAGA
* * * * * *
29543 GCTC-CGGTAAGAGATCGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGATTG
1 -CTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCAAACGATTG
*
29607 TAATCTA-CCCAGG
65 TAATCTACCCCAGA
* * ** * * *** * *
29620 CTCGAGGTAAGAAATTGGTTGATGGTGATTTGCC-CTAGGCTCAGGGTAAAAGATTGGACGGTTA
1 CTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTC-AGGCTCGGGGTAAAAGATCAAACGATTG
*
29684 TAATCTACCTCAGA
65 TAATCTACCCCAGA
* * * * * *
29698 CTCGGGGTAAGAGATTGGCTAATGGTGATATGCCTCATGCTCGGGGTAAAAGTTCAAACAATTGT
1 CTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCAAACGATTGT
* *
29763 AATTTACCTCA-A
66 AATCTACCCCAGA
* * * * * * *
29775 GTTTGGGGTAAGACATTGACTGATGGTGATCTACTTCAGGTTCGAGGT-AAA-ATCGAATA-G-T
1 -CTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATC-AA-ACGAT
* *
29836 TGCAATCTACCCCAGG
63 TGTAATCTACCCCAGA
* * *
29852 CTCGGGGGTAAGAGATTGACTGATGGTGATCTACCTTAAGCTCGGGGTAAAAGATCA
1 CTC-GGGGTAAGAGATTGACTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCA
29909 GATGACTGCA
Statistics
Matches: 286, Mismatches: 67, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
76 23 0.08
77 152 0.53
78 107 0.37
79 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (78 bp):
CTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCAAACGATTGT
AATCTACCCCAGA
Found at i:32284 original size:63 final size:64
Alignment explanation
Indices: 32146--32289 Score: 166
Period size: 63 Copynumber: 2.3 Consensus size: 64
32136 TGTCAGTTTT
* * ** * *
32146 ATTGCAATATTGAGTGGCT-TGTCCACAACGTTATTAAGTGGTTTGACCACAATGATGCAGCTTG
1 ATTGCGATATTGAGTGGCTCTG-GCACAACGTTATTAAGTGGACTGACCACAAAGATGCAGATTG
* * * *
32210 ATTGTGATATTGTGTGGCTCTGGCACAACGTTATTGAGT-GACTGACCACAAAGATGCATATTG
1 ATTGCGATATTGAGTGGCTCTGGCACAACGTTATTAAGTGGACTGACCACAAAGATGCAGATTG
*
32273 ATTGCGGTATTGAGTGG
1 ATTGCGATATTGAGTGG
32290 TTTGACCACA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
63 33 0.50
64 31 0.47
65 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (64 bp):
ATTGCGATATTGAGTGGCTCTGGCACAACGTTATTAAGTGGACTGACCACAAAGATGCAGATTG
Found at i:34946 original size:15 final size:16
Alignment explanation
Indices: 34926--34957 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
34916 GACTATATAA
34926 AAAAAATTTA-AAAAT
1 AAAAAATTTATAAAAT
34941 AAAAAATTTATAAAAT
1 AAAAAATTTATAAAAT
34957 A
1 A
34958 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAATTTATAAAAT
Done.