Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007769.1 Kokia drynarioides strain JFW-HI SEQ_122402, 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: 47296
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1168 original size:52 final size:50
Alignment explanation
Indices: 1123--1221 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 50
1113 TCATTTTCAC
1123 TTTATTT-ATTTTATTTTAGTTTAGTTTTTTTGTTTAATATTTTCATCACTTTA
1 TTTATTTCATTTTATTTTAGTTT--TTTTTTTGTTTAATATTTTCAT--CTTTA
1176 TTTATTTCATTTTATTTTAGTTTTTTTTTTGTTTAATATTTTCATC
1 TTTATTTCATTTTATTTTAGTTTTTTTTTTGTTTAATATTTTCATC
1222 ACTAAACCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
50 1 0.02
52 22 0.49
53 7 0.16
54 15 0.33
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.70
Consensus pattern (50 bp):
TTTATTTCATTTTATTTTAGTTTTTTTTTTGTTTAATATTTTCATCTTTA
Found at i:1188 original size:49 final size:50
Alignment explanation
Indices: 1119--1224 Score: 169
Period size: 49 Copynumber: 2.1 Consensus size: 50
1109 AACTTCATTT
*
1119 TCACTTTATTTATTTTATTTTAGTTTAG-TTTTTTTGTTTAATATTTTCA
1 TCACTTTATTTATTTCATTTTAGTTTAGTTTTTTTTGTTTAATATTTTCA
*
1168 TCACTTTATTTATTTCATTTTATTTTAGTTTTTTTTTTGTTTAATATTTTCA
1 TCACTTTATTTATTTCATTTTAGTTTAG--TTTTTTTTGTTTAATATTTTCA
1220 TCACT
1 TCACT
1225 AAACCCCCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
49 26 0.50
52 26 0.50
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.67
Consensus pattern (50 bp):
TCACTTTATTTATTTCATTTTAGTTTAGTTTTTTTTGTTTAATATTTTCA
Found at i:1242 original size:52 final size:52
Alignment explanation
Indices: 1126--1245 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 52
1116 TTTTCACTTT
** ***
1126 ATTTATTTTATTTTAGTTTAGTTTTTTTGTTTAATATTTTCATCACTTTATTT
1 ATTTATTTTATTTTAGTTTA-TTTTTTTGTTTAATATTTTCATCACTAAACCC
1179 ATTTCATTTTATTTTAGTTT-TTTTTTTGTTTAATATTTTCATCACTAAACCCC
1 ATTT-ATTTTATTTTAGTTTATTTTTTTGTTTAATATTTTCATCACTAAA-CCC
* *
1232 CTTTAATTTATTTT
1 ATTTATTTTATTTT
1246 CAGGAAGCTC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
52 36 0.62
53 7 0.12
54 15 0.26
ACGTcount: A:0.22, C:0.10, G:0.04, T:0.64
Consensus pattern (52 bp):
ATTTATTTTATTTTAGTTTATTTTTTTGTTTAATATTTTCATCACTAAACCC
Found at i:2929 original size:39 final size:39
Alignment explanation
Indices: 2873--2947 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
2863 GCTGGGGCAA
* *
2873 CTGCTGTTGTTGTTGCAGCTG-GGAGAGTTGCTGCTGCTG
1 CTGCTGCTGTTGCTGCAGCTGAGG-GAGTTGCTGCTGCTG
*
2912 CTGCTGCTGTTGCTGCAGCTGAGGGAGTTGTTGCTG
1 CTGCTGCTGTTGCTGCAGCTGAGGGAGTTGCTGCTG
2948 TTGCAAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.08, C:0.19, G:0.39, T:0.35
Consensus pattern (39 bp):
CTGCTGCTGTTGCTGCAGCTGAGGGAGTTGCTGCTGCTG
Found at i:2984 original size:15 final size:15
Alignment explanation
Indices: 2964--3010 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2954 ATGTGGGAGC
2964 GGCTGTTGCTGCTGT
1 GGCTGTTGCTGCTGT
2979 GGCTGTTGCTGCTGCT
1 GGCTGTTGCTGCTG-T
* *
2995 -GTTGTTGCAGCTGT
1 GGCTGTTGCTGCTGT
3009 GG
1 GG
3011 GAGCTGCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.02, C:0.19, G:0.40, T:0.38
Consensus pattern (15 bp):
GGCTGTTGCTGCTGT
Found at i:3027 original size:33 final size:33
Alignment explanation
Indices: 2980--3055 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
2970 TGCTGCTGTG
*
2980 GCTGTTGCTGCTGCTGTTGTTGCAGCTGTGGGA
1 GCTGCTGCTGCTGCTGTTGTTGCAGCTGTGGGA
3013 GCTGCTGCTGCTGCTGTTGTTGCAGCTGTGGGA
1 GCTGCTGCTGCTGCTGTTGTTGCAGCTGTGGGA
*
3046 CCTGCTGCTG
1 GCTGCTGCTG
3056 TGGCATCTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.05, C:0.22, G:0.38, T:0.34
Consensus pattern (33 bp):
GCTGCTGCTGCTGCTGTTGTTGCAGCTGTGGGA
Found at i:3068 original size:33 final size:33
Alignment explanation
Indices: 2965--3055 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
2955 TGTGGGAGCG
* *
2965 GCTGTTGCTGCTGT-GG--CTGTTGCTGCTGCT
1 GCTGTTGCAGCTGTGGGACCTGCTGCTGCTGCT
* *
2995 GTTGTTGCAGCTGTGGGAGCTGCTGCTGCTGCT
1 GCTGTTGCAGCTGTGGGACCTGCTGCTGCTGCT
*
3028 GTTGTTGCAGCTGTGGGACCTGCTGCTG
1 GCTGTTGCAGCTGTGGGACCTGCTGCTG
3056 TGGCATCTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
30 12 0.22
31 2 0.04
33 40 0.74
ACGTcount: A:0.04, C:0.22, G:0.38, T:0.35
Consensus pattern (33 bp):
GCTGTTGCAGCTGTGGGACCTGCTGCTGCTGCT
Found at i:12520 original size:20 final size:20
Alignment explanation
Indices: 12497--12535 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12487 AATATCTCTT
12497 AATTAGAAAATCTAAAAATC
1 AATTAGAAAATCTAAAAATC
* **
12517 AATTATAATCTCTAAAAAT
1 AATTAGAAAATCTAAAAAT
12536 ACTATTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (20 bp):
AATTAGAAAATCTAAAAATC
Found at i:16911 original size:125 final size:126
Alignment explanation
Indices: 16682--16920 Score: 345
Period size: 125 Copynumber: 1.9 Consensus size: 126
16672 AATTCAGTAT
* *
16682 TACTTAAATTATAGATTTTGTCTCATTTTATCCAAATAAAAACTGTATGAATTCCAATAAAAACA
1 TACTTAAATTATAAACTTTGTCTCATTTTATCCAAATAAAAACTGTATGAATTCCAATAAAAACA
* * *
16747 TGTCACATATCACAGTTTTATTAGTTAGCATTGTATATCGAGGTAAGATTGAATTTAGTGA
66 TCTCACATATCACACTTTTATTAGTCAGCATTGTATATCGAGGTAAGATTGAATTTAGTGA
** * *
16808 TACTTAAATTATAAACTTTGTCTCATTTTATCCAAA-AAAAGGTGTATGAATTCCAATAAGAACG
1 TACTTAAATTATAAACTTTGTCTCATTTTATCCAAATAAAAACTGTATGAATTCCAATAAAAACA
* * * * *
16872 TCTTACATGTCACACTTTTATTAGTCAGTATTGTGTATCGGGGTAAGAT
66 TCTCACATATCACACTTTTATTAGTCAGCATTGTATATCGAGGTAAGAT
16921 GAGACAAAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
125 65 0.66
126 34 0.34
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (126 bp):
TACTTAAATTATAAACTTTGTCTCATTTTATCCAAATAAAAACTGTATGAATTCCAATAAAAACA
TCTCACATATCACACTTTTATTAGTCAGCATTGTATATCGAGGTAAGATTGAATTTAGTGA
Found at i:19831 original size:20 final size:20
Alignment explanation
Indices: 19798--19835 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19788 TCTTACATAA
19798 TTAACTTAATTTAATCCATT
1 TTAACTTAATTTAATCCATT
19818 TTAACCTTAA-TTAATCCA
1 TTAA-CTTAATTTAATCCA
19836 CCTAATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAACTTAATTTAATCCATT
Found at i:21560 original size:19 final size:19
Alignment explanation
Indices: 21538--21585 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 19
21528 AGTTTTAGGG
21538 TTTAAGGGAAGTAAATTTT
1 TTTAAGGGAAGTAAATTTT
21557 TTTAAGGGGGAAGTAAATTTT
1 TTTAA--GGGAAGTAAATTTT
21578 TTTAAGGG
1 TTTAAGGG
21586 GGAAGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.30
21 19 0.70
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTAAGGGAAGTAAATTTT
Found at i:21569 original size:21 final size:21
Alignment explanation
Indices: 21543--21594 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
21533 TAGGGTTTAA
21543 GGGAAGTAAATTTTTTTAAGG
1 GGGAAGTAAATTTTTTTAAGG
21564 GGGAAGTAAATTTTTTTAAGG
1 GGGAAGTAAATTTTTTTAAGG
21585 GGGAAGTAAA
1 GGGAAGTAAA
21595 AGTATCTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.33
Consensus pattern (21 bp):
GGGAAGTAAATTTTTTTAAGG
Found at i:24441 original size:14 final size:14
Alignment explanation
Indices: 24419--24465 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
24409 GAATTATTAC
*
24419 TTAATTAATTGAAA
1 TTAAATAATTGAAA
*
24433 TTAAATAATTGAAG
1 TTAAATAATTGAAA
* *
24447 TTCAATGA-TGAAA
1 TTAAATAATTGAAA
24460 TTAAAT
1 TTAAAT
24466 TAGTTAAGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (14 bp):
TTAAATAATTGAAA
Found at i:24618 original size:14 final size:14
Alignment explanation
Indices: 24599--24638 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
24589 AGAAATTAAT
*
24599 TTAATTAACTAAAA
1 TTAATTAAATAAAA
*
24613 TTAATTAAATTAAA
1 TTAATTAAATAAAA
24627 TT-ATTAAATAAA
1 TTAATTAAATAAA
24639 TAATATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:28731 original size:21 final size:21
Alignment explanation
Indices: 28703--28755 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
28693 CAGATTTGTG
28703 CCGATACAAGTGACAATTCTA
1 CCGATACAAGTGACAATTCTA
* * **
28724 CTGTTACAAGTGACTCTTCTA
1 CCGATACAAGTGACAATTCTA
28745 CCGATACAAGT
1 CCGATACAAGT
28756 CTTACCTCTA
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:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (21 bp):
CCGATACAAGTGACAATTCTA
Found at i:30630 original size:20 final size:20
Alignment explanation
Indices: 30594--30638 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
30584 TCATTAAGCT
*
30594 TTAATTAATCTCTTTTAATC
1 TTAATTAAGCTCTTTTAATC
*
30614 TTAATTAAGC-CTATTTACTC
1 TTAATTAAGCTCT-TTTAATC
30634 TTAAT
1 TTAAT
30639 AAAAATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAATTAAGCTCTTTTAATC
Found at i:31914 original size:195 final size:196
Alignment explanation
Indices: 31662--32052 Score: 651
Period size: 195 Copynumber: 2.0 Consensus size: 196
31652 ACAGAGTTCT
*
31662 CATTTCCAACACTCCACATTATTCTATCACGAAAAAAGTGCCAAACTTTCGCAAGAGAACACCAA
1 CATTCCCAACACTCCACATTATTCTATCACGAAAAAAGTGCCAAACTTTCGCAAGAGAACACCAA
* * *
31727 ACAA-ACGAGCAAACATGTTGATCAATAAACATTGGACAAATCTCCAAAATTTTATACTTAGAGC
66 ACAATA-GAGCAAACAGGTTGATCAATAAACATTGGAAAAATCTCCAAAATTTTATACTTAGAGA
* * *
31791 GTAGAATGCGCACCCATAACACATCTACCTTAGTCATCATTTGGAAAGCTAGTTTCAT-AAATAT
130 GTAGAATGCGCACCCATAACACATCTACCTTAGTCACCATTTGGAAACCAAGTTTCATCAAATAT
31855 GA
195 GA
* * *
31857 CATTCCCAACACTCCACATTATTCTATCACGAAAAAAGTGCTAGACTTTCTCAAGAGAACACCAA
1 CATTCCCAACACTCCACATTATTCTATCACGAAAAAAGTGCCAAACTTTCGCAAGAGAACACCAA
*
31922 ACAATAGAGCAAACAGGTTGATCAATAGACATTGGAAAAATCTCCAAAATTTTATACTTAGAGAG
66 ACAATAGAGCAAACAGGTTGATCAATAAACATTGGAAAAATCTCCAAAATTTTATACTTAGAGAG
*
31987 TAGAATGCGCACCCATAACACATCTACTTTAGTCACCATTTGGAAACCAAGTTTCATCAAATATG
131 TAGAATGCGCACCCATAACACATCTACCTTAGTCACCATTTGGAAACCAAGTTTCATCAAATATG
32052 A
196 A
32053 TCTATTTTGC
Statistics
Matches: 182, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
195 173 0.95
196 9 0.05
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (196 bp):
CATTCCCAACACTCCACATTATTCTATCACGAAAAAAGTGCCAAACTTTCGCAAGAGAACACCAA
ACAATAGAGCAAACAGGTTGATCAATAAACATTGGAAAAATCTCCAAAATTTTATACTTAGAGAG
TAGAATGCGCACCCATAACACATCTACCTTAGTCACCATTTGGAAACCAAGTTTCATCAAATATG
A
Found at i:35649 original size:17 final size:17
Alignment explanation
Indices: 35627--35660 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35617 TTAAGTATAA
35627 CTAATCAGCCAAATATG
1 CTAATCAGCCAAATATG
35644 CTAATCAGCCAAATATG
1 CTAATCAGCCAAATATG
35661 GGAACTTAAC
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:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
CTAATCAGCCAAATATG
Found at i:40764 original size:37 final size:38
Alignment explanation
Indices: 40723--40808 Score: 113
Period size: 36 Copynumber: 2.3 Consensus size: 38
40713 GAAAATATTA
*
40723 AAAAATATATTTTATAATTTTTTGAATTTTT-AA-TTTT
1 AAAAATA-ATTTCATAATTTTTTGAATTTTTAAATTTTT
* *
40760 AAAAAGAGTTTCATAATTTTTTGAATTTTTAAATTTTT
1 AAAAATAATTTCATAATTTTTTGAATTTTTAAATTTTT
40798 AAAAATTAATT
1 AAAAA-TAATT
40809 AATTGTTGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 21 0.51
37 8 0.20
38 9 0.22
39 3 0.07
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (38 bp):
AAAAATAATTTCATAATTTTTTGAATTTTTAAATTTTT
Found at i:44652 original size:30 final size:30
Alignment explanation
Indices: 44587--44812 Score: 219
Period size: 30 Copynumber: 7.6 Consensus size: 30
44577 GGTCAAAACA
* * *
44587 TAATTTTGGAAAAGTATAGTGG-TAATATTG
1 TAATTTTGGAAAAGTTTAGGGGTTAA-AATG
*
44617 TAATTTTGGAAAAGTTTAGGGGTCAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
* * * * * *
44647 AAATTTTAGAAAAGTTTAGAGATCAAAATT
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
* * *
44677 TGATTTTGGAAAATTTTAGGGTTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
* * *
44707 TGATTCTGGAAAGGTTTAGGGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
*
44737 TAATTTT-AAGAAAGTTTTA--GGTTAAAATG
1 TAATTTTGGA-AAAG-TTTAGGGGTTAAAATG
* *
44766 TAATTTTAGAAAAGTTTA-AGGTTAAAATG
1 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
44795 TAATTTTGGAAAAGTTTA
1 TAATTTTGGAAAAGTTTA
44813 AAGGACTACC
Statistics
Matches: 164, Mismatches: 27, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
28 4 0.02
29 49 0.30
30 105 0.64
31 6 0.04
ACGTcount: A:0.39, C:0.01, G:0.22, T:0.38
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTAGGGGTTAAAATG
Found at i:45696 original size:20 final size:20
Alignment explanation
Indices: 45668--45711 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
45658 ATGTGTATAC
*
45668 ATATGTATATATACATATGT
1 ATATATATATATACATATGT
45688 ATATATATATATACATATGT
1 ATATATATATATACATATGT
45708 ATAT
1 ATAT
45712 GAATATACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATATATATATACATATGT
Found at i:45711 original size:14 final size:14
Alignment explanation
Indices: 45663--45699 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
45653 AAATAATGTG
45663 TATACATATGTATA
1 TATACATATGTATA
45677 TATACATATGTATA
1 TATACATATGTATA
*
45691 TATATATAT
1 TATACATAT
45700 ACATATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (14 bp):
TATACATATGTATA
Found at i:45717 original size:20 final size:20
Alignment explanation
Indices: 45668--45718 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
45658 ATGTGTATAC
*
45668 ATATGTATATATACATATGT
1 ATATGAATATATACATATGT
45688 ATAT-ATATATATACATATGT
1 ATATGA-ATATATACATATGT
45708 ATATGAATATA
1 ATATGAATATA
45719 CCTTGCGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATGAATATATACATATGT
Found at i:45816 original size:124 final size:125
Alignment explanation
Indices: 45687--45926 Score: 446
Period size: 124 Copynumber: 1.9 Consensus size: 125
45677 TATACATATG
45687 TATATATATATATACATATGTATATGAATATACCTTGCGAAAATGACAGGATGAATTTCTTTGTG
1 TATATATATATATACATATGTATATGAATATACCTTGCGAAAATGACAGGATGAATTTCTTTGTG
*
45752 CTTAATCTATTTTTGCTCTTGTTATTTCATTTCAT-TTTTTTTTTCGAAGGGGAGGTATA
66 CTTAATCTATTTTTGCTCTTGTTATTTCATTTCATGTTTTTTTTTCAAAGGGGAGGTATA
*
45811 TATATATATATATACATATGTATATGAATATACCTTGTGAAAATGACAGGATGAATTTCTTTGTG
1 TATATATATATATACATATGTATATGAATATACCTTGCGAAAATGACAGGATGAATTTCTTTGTG
*
45876 CTTAATCTATTTTTGCTCTTTTTATTTCATTTCATGTTTTTTTTTCAAAGG
66 CTTAATCTATTTTTGCTCTTGTTATTTCATTTCATGTTTTTTTTTCAAAGG
45927 TGAGCCCTTT
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
124 98 0.88
125 14 0.12
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.47
Consensus pattern (125 bp):
TATATATATATATACATATGTATATGAATATACCTTGCGAAAATGACAGGATGAATTTCTTTGTG
CTTAATCTATTTTTGCTCTTGTTATTTCATTTCATGTTTTTTTTTCAAAGGGGAGGTATA
Found at i:46103 original size:13 final size:13
Alignment explanation
Indices: 46066--46096 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
46056 GGTGTCAGAT
46066 AGTGGCAGAGGCA
1 AGTGGCAGAGGCA
*
46079 AGTGGCAAAGGCA
1 AGTGGCAGAGGCA
46092 AGTGG
1 AGTGG
46097 GTGAGGCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.45, T:0.10
Consensus pattern (13 bp):
AGTGGCAGAGGCA
Found at i:47060 original size:39 final size:38
Alignment explanation
Indices: 47017--47135 Score: 105
Period size: 42 Copynumber: 3.0 Consensus size: 38
47007 CATTGCTTTG
47017 GATGACTACAATCTGCCCGATGATCGGGGTAAGAGATTA
1 GATGACTACAATCTGCCC-ATGATCGGGGTAAGAGATTA
* *
47056 GATGATGTCTTCAATCTGTCCCATGATCGAGGTAAGAGA-TA
1 GATGA---CTACAATCTG-CCCATGATCGGGGTAAGAGATTA
** * * *
47097 GAATGGTTGCAATCTGCCCCTGGCTCGGGGTAAGAGATT
1 G-ATGACTACAATCTGCCCAT-GATCGGGGTAAGAGATT
47136 GACTGATGGT
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
38 4 0.06
39 26 0.40
40 1 0.02
41 3 0.05
42 28 0.43
43 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (38 bp):
GATGACTACAATCTGCCCATGATCGGGGTAAGAGATTA
Found at i:47082 original size:42 final size:40
Alignment explanation
Indices: 47025--47143 Score: 120
Period size: 39 Copynumber: 2.9 Consensus size: 40
47015 TGGATGACTA
*
47025 CAATCTGCCCGATGATCGGGGTAAGAGATTAGATGATGTCTT
1 CAATCTGCCC-ATGATCGGGGTAAGAGATTAGATGATGT-TG
*
47067 CAATCTGTCCCATGATCGAGGTAAGAGA-TAGA--ATGGTTG
1 CAATCTG-CCCATGATCGGGGTAAGAGATTAGATGAT-GTTG
* *
47106 CAATCTGCCCCTGGCTCGGGGTAAGAGATT-GACTGATG
1 CAATCTGCCCAT-GATCGGGGTAAGAGATTAGA-TGATG
47144 GTGATCTGCT
Statistics
Matches: 65, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
38 4 0.06
39 25 0.38
40 3 0.05
41 5 0.08
42 25 0.38
43 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (40 bp):
CAATCTGCCCATGATCGGGGTAAGAGATTAGATGATGTTG
Found at i:47151 original size:39 final size:40
Alignment explanation
Indices: 47108--47251 Score: 124
Period size: 39 Copynumber: 3.7 Consensus size: 40
47098 AATGGTTGCA
*
47108 ATCTGCCCCT-GGCTCGGGGTAAGAGATTGACTGATGGTG
1 ATCTGCCCCTAGGCTCGGGGTAAAAGATTGACTGATGGTG
* * *
47147 ATCTG-CTCTAGGCTCGAGGTAAAAGA-T--CGGATGGCT-
1 ATCTGCCCCTAGGCTCGGGGTAAAAGATTGACTGATGG-TG
* * *
47183 ATAACAT-ACCCTAGGCTCAGGGTAAGAGATTGACTGATGGTG
1 AT--C-TGCCCCTAGGCTCGGGGTAAAAGATTGACTGATGGTG
*
47225 ATCTGCCCC-AGGCTAGGGGTAAAAGAT
1 ATCTGCCCCTAGGCTCGGGGTAAAAGAT
47252 CGGATGGCTG
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
36 8 0.10
37 1 0.01
38 5 0.06
39 53 0.65
40 5 0.06
41 1 0.01
42 8 0.10
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (40 bp):
ATCTGCCCCTAGGCTCGGGGTAAAAGATTGACTGATGGTG
Found at i:47277 original size:78 final size:77
Alignment explanation
Indices: 47084--47292 Score: 249
Period size: 78 Copynumber: 2.7 Consensus size: 77
47074 TCCCATGATC
* * * * *
47084 GAGGTAAGAGATAGAATGGTTGCAATCTGCCCCTGGCTCGGGGTAAGAGATTGACTGATGGTGAT
1 GAGGTAAAAGATCGGATGGCTGCAATCTG-CCCAGGCTCGGGGTAAGAGATTGACTGATGGTGAT
* * *
47149 CTGCTCTAGGCTC
65 CTGCCCCAGGCTA
** * *
47162 GAGGTAAAAGATCGGATGGCTATAA-CATACCCTAGGCTCAGGGTAAGAGATTGACTGATGGTGA
1 GAGGTAAAAGATCGGATGGCTGCAATC-TGCCC-AGGCTCGGGGTAAGAGATTGACTGATGGTGA
47226 TCTGCCCCAGGCTA
64 TCTGCCCCAGGCTA
* *
47240 GGGGTAAAAGATCGGATGGCTGCAATCTGCCTCAGGCTCGGGGTAGGAGATTG
1 GAGGTAAAAGATCGGATGGCTGCAATCTGCC-CAGGCTCGGGGTAAGAGATTG
47293 GCTG
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
77 4 0.04
78 103 0.94
79 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.23
Consensus pattern (77 bp):
GAGGTAAAAGATCGGATGGCTGCAATCTGCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATC
TGCCCCAGGCTA
Done.