Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011325.1 Kokia drynarioides strain JFW-HI SEQ_126305, 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: 101995
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1913 original size:2 final size:2
Alignment explanation
Indices: 1906--1931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1896 TATTATGAGA
1906 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1932 TGTATAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2478 original size:62 final size:61
Alignment explanation
Indices: 2401--2520 Score: 188
Period size: 62 Copynumber: 1.9 Consensus size: 61
2391 CTGAAAAAAT
2401 AATAAACTGTTTTAAATACTTACCACATGTCTATCAAAGAATA-AAATACATGTCGATTGTCG
1 AATAAACTGTTTTAAATACTTACCACATGTCTATC-AAGAA-ACAAATACATGTCGATTGTCG
* *
2463 AATAAATTGTTTTAAATACTTACCACGTGTCTATCAAGAAACTAAATACATGTCGATT
1 AATAAACTGTTTTAAATACTTACCACATGTCTATCAAGAAAC-AAATACATGTCGATT
2521 ATATATTCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
60 1 0.02
61 5 0.09
62 48 0.89
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (61 bp):
AATAAACTGTTTTAAATACTTACCACATGTCTATCAAGAAACAAATACATGTCGATTGTCG
Found at i:2950 original size:24 final size:25
Alignment explanation
Indices: 2910--2968 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
2900 ACCTGTTTCA
2910 AAAAATTAAAAACAAAATAAATTTTT
1 AAAAA-TAAAAACAAAATAAATTTTT
**
2936 AAAAATAAAAA-AAAATATTTTTTT
1 AAAAATAAAAACAAAATAAATTTTT
*
2960 ACAAATAAA
1 AAAAATAAA
2969 TTTTATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 19 0.63
25 6 0.20
26 5 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAATAAAAACAAAATAAATTTTT
Found at i:3235 original size:21 final size:21
Alignment explanation
Indices: 3211--3290 Score: 57
Period size: 21 Copynumber: 4.1 Consensus size: 21
3201 ACAAAAATAA
3211 ATAATATATAATTAAATTTAT
1 ATAATATATAATTAAATTTAT
* *
3232 ATAATAAAAAATTAAA---AT
1 ATAATATATAATTAAATTTAT
*
3250 A-AATATAT-TTTAAATTTA-
1 ATAATATATAATTAAATTTAT
* *
3268 ATTAA-ATATAAATATATTTAT
1 A-TAATATATAATTAAATTTAT
3289 AT
1 AT
3291 TAAATACAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 15
0.66 0.12 0.22
Matches are distributed among these distances:
16 5 0.11
17 5 0.11
18 4 0.09
19 5 0.11
20 10 0.23
21 15 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATATATAATTAAATTTAT
Found at i:4615 original size:15 final size:15
Alignment explanation
Indices: 4595--4624 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4585 TTTAATATTG
4595 ATATTAAAATTATAA
1 ATATTAAAATTATAA
*
4610 ATATTAATATTATAA
1 ATATTAAAATTATAA
4625 TCACAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTAAAATTATAA
Found at i:7198 original size:87 final size:87
Alignment explanation
Indices: 7052--7432 Score: 349
Period size: 87 Copynumber: 4.4 Consensus size: 87
7042 CTTTCTCTTT
* * *
7052 CCAGTAATCAGGA-TATCAGTTTTCAATACTTTGATCTCCCTCATTGCCGATAAATCCATCTT-T
1 CCAGTAATC-GGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATATATCCATCTTAT
7115 CCAGTGACACAAAGGTTATCAGTG
65 -CAGTGACACAAAGGTTATCAGTG
**
7139 CCAGTAATCGGAGTATCAGTTTCCAATACTTCAATCTCCCTCATTGCTGATATATCCATCTTATC
1 CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATATATCCATCTTATC
*
7204 AGTGACACAAAGGTTATCTGTG
66 AGTGACACAAAGGTTATCAGTG
** * * * *
7226 CCAGTAATCACAGCATCAGTTTCCCATTCTTTGATCTCCCCCA---CTG-------C-T-TTATC
1 CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATATATCCATCTTATC
* *
7279 AGTGACAAAAAGATTATCAGTG
66 AGTGACACAAAGGTTATCAGTG
* * * *
7301 CCAGTAATTGGGGTATAAGTTTCTAATACTTTGATCTCCCTCATTGCTGATAGATCCAGATCCAT
1 CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGAT--AT----ATCCAT
* * * *
7366 CTTATCAGTGACATAAAGGTCACCAGTT
60 CTTATCAGTGACACAAAGGTTATCAGTG
* * * * *
7394 CCAGCAATCAGAGTATCACTTTCCAAAACTTCGATCTCC
1 CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCC
7433 ATTACTGCTG
Statistics
Matches: 233, Mismatches: 41, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
75 57 0.24
76 1 0.00
77 1 0.00
78 3 0.01
84 3 0.01
86 3 0.01
87 110 0.47
88 1 0.00
91 1 0.00
92 1 0.00
93 52 0.22
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (87 bp):
CCAGTAATCGGAGTATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATATATCCATCTTATC
AGTGACACAAAGGTTATCAGTG
Found at i:7322 original size:75 final size:75
Alignment explanation
Indices: 7199--7340 Score: 176
Period size: 75 Copynumber: 1.9 Consensus size: 75
7189 TATATCCATC
* * * * * *
7199 TTATCAGTGACACAAAGGTTATCTGTGCCAGTAATCACAGCATCAGTTTCCCATTCTTTGATCTC
1 TTATCAGTGACAAAAAGATTATCAGTGCCAGTAATCACAGCATAAGTTTCCAATACTTTGATCTC
7264 CCCCACTGCT
66 CCCCACTGCT
**** * *
7274 TTATCAGTGACAAAAAGATTATCAGTGCCAGTAATTGGGGTATAAGTTTCTAATACTTTGATCTC
1 TTATCAGTGACAAAAAGATTATCAGTGCCAGTAATCACAGCATAAGTTTCCAATACTTTGATCTC
7339 CC
66 CC
7341 TCATTGCTGA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
75 55 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (75 bp):
TTATCAGTGACAAAAAGATTATCAGTGCCAGTAATCACAGCATAAGTTTCCAATACTTTGATCTC
CCCCACTGCT
Found at i:8182 original size:39 final size:39
Alignment explanation
Indices: 8139--8223 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
8129 TTCGCAGCTA
* *
8139 CAAGCTTTGGTTTCTTTT-CCTTGACTTGCATTGGAGTTG
1 CAAGCTTTGGTCTCTTTTCCCTT-ACCTGCATTGGAGTTG
* *
8178 CAAGCCTTGGTCTCTTTTCCCTTACCTGCTTTGGAGTTG
1 CAAGCTTTGGTCTCTTTTCCCTTACCTGCATTGGAGTTG
8217 CAAGCTT
1 CAAGCTT
8224 CAGTGTGGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 36 0.90
40 4 0.10
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (39 bp):
CAAGCTTTGGTCTCTTTTCCCTTACCTGCATTGGAGTTG
Found at i:9655 original size:85 final size:84
Alignment explanation
Indices: 9512--9683 Score: 308
Period size: 85 Copynumber: 2.0 Consensus size: 84
9502 GGGTTTTGTG
*
9512 TTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTCTTTTTTTCAATTGTGGGATCAACATAA
1 TTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTCTTTTTTTCAATTGGGGGATCAACATAA
*
9577 TATCAACTAAATACCTTTTT
66 TATCAACCAAATA-CTTTTT
*
9597 TTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTCTTTTTTTCAATTGGGGGATCAATATAA
1 TTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTCTTTTTTTCAATTGGGGGATCAACATAA
9662 TATCAACCAAATACTTTTT
66 TATCAACCAAATACTTTTT
9681 TTT
1 TTT
9684 ATAGTCACTA
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
84 9 0.11
85 75 0.89
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (84 bp):
TTTTCGCCTTTGGTTTGGGTATTCTATTAGTCATCTTCTTTTTTTCAATTGGGGGATCAACATAA
TATCAACCAAATACTTTTT
Found at i:15824 original size:18 final size:18
Alignment explanation
Indices: 15792--15838 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
15782 TGAAAAGAAA
* *
15792 CCTCATCTGACTCATCTT
1 CCTCATCAGAATCATCTT
*
15810 CGTCATCAGAATCATCTT
1 CCTCATCAGAATCATCTT
15828 CCTCATCAGAA
1 CCTCATCAGAA
15839 CCACTCTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.32
Consensus pattern (18 bp):
CCTCATCAGAATCATCTT
Found at i:19044 original size:6 final size:6
Alignment explanation
Indices: 19033--19068 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
19023 ATATACATAC
19033 GAGTGT GAGTGT GAGTGT GAGTGT GAGTGT GAGTGT
1 GAGTGT GAGTGT GAGTGT GAGTGT GAGTGT GAGTGT
19069 TAAAAATCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
GAGTGT
Found at i:21713 original size:91 final size:91
Alignment explanation
Indices: 21561--21784 Score: 247
Period size: 91 Copynumber: 2.4 Consensus size: 91
21551 TGGAAGTAAT
* * * *
21561 CAATTTTATTAACTTATTTCTAACTATATCTTTTTTATTTATGTAAATTTTTTTATATTTTTCAT
1 CAATTTTATTAATTTATTTTTAACTATATCTTTTGTATTCATGT--A---TTTT-T-TTTTTCAT
21626 GTTCATAT-AT-TAAATTT-GGAATTATCCTTTCTAA
59 -TTCATATCATGT--ATTTAGG-ATTATCCTTTCTAA
**
21660 CAATTTTATTAATTTATTTTTAACTATATCTTTTGTATTCATGTATTTTTTTTTTCATTTTTTAT
1 CAATTTTATTAATTTATTTTTAACTATATCTTTTGTATTCATGTATTTTTTTTTTCATTTCATAT
*
21725 CATGTATTTAGGATTATCCTTTTTAA
66 CATGTATTTAGGATTATCCTTTCTAA
* *
21751 CAATTTTATTAATTTATTTTTAATTATATTTTTT
1 CAATTTTATTAATTTATTTTTAACTATATCTTTT
21785 ATGTAACTTT
Statistics
Matches: 113, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
91 54 0.48
92 12 0.11
93 2 0.02
94 4 0.04
97 1 0.01
99 40 0.35
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.60
Consensus pattern (91 bp):
CAATTTTATTAATTTATTTTTAACTATATCTTTTGTATTCATGTATTTTTTTTTTCATTTCATAT
CATGTATTTAGGATTATCCTTTCTAA
Found at i:26852 original size:2 final size:2
Alignment explanation
Indices: 26845--26883 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
26835 AGTTTTACTA
26845 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
26884 TTTGGTAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27374 original size:5 final size:5
Alignment explanation
Indices: 27364--27389 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27354 TTAATGCGAC
27364 ACATA ACATA ACATA ACATA ACATA A
1 ACATA ACATA ACATA ACATA ACATA A
27390 TTAAACTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
ACATA
Found at i:27612 original size:21 final size:23
Alignment explanation
Indices: 27585--27636 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
27575 TTATTAAAGT
* *
27585 AATAAAATGTGT-ATAAT-TTAA
1 AATAAAATATGTAAAAATATTAA
*
27606 ATTAAAATATGTAAAAATATTAA
1 AATAAAATATGTAAAAATATTAA
27629 AATAAAAT
1 AATAAAAT
27637 TTTAGTTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 10 0.40
22 4 0.16
23 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (23 bp):
AATAAAATATGTAAAAATATTAA
Found at i:36238 original size:13 final size:13
Alignment explanation
Indices: 36220--36244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36210 GTTTTTTTAA
36220 TTAATATTGTTAT
1 TTAATATTGTTAT
36233 TTAATATTGTTA
1 TTAATATTGTTA
36245 AAGTATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TTAATATTGTTAT
Found at i:36485 original size:276 final size:274
Alignment explanation
Indices: 35977--36692 Score: 864
Period size: 276 Copynumber: 2.6 Consensus size: 274
35967 TATTAGTAAG
* * * *
35977 TTATATTTTGTTATTAATTAAAAAGTTAGTATTTAATTAATTTATTATTTCC-AGAAATTAAATA
1 TTATATTTTTTTGTTAATTAAGAAGTTAGTATTTAATTAAATTATTATTTCCGA-AAATTAAATA
* * * *
36041 AAAAATATGGTTAA-TTTTTAATATAATTAATTATATTAATAGATTTTTGTACTAATTAATTTGT
65 AAAAATATGGTTAATTTTTTAGTATAATTAGTTATATTAATAGGTTTTTGTACTAATTAATTTAT
* * * * *
36105 ATATTTAATTTTTTTTATATCACAAACATTTAGAATTTTGTGAAAACAATTTTCAACTCTTTTGC
130 ATATTTAA-TTTTTTTATATTACAACCATTTAGAATTGTGTTAAAACAACTTTCAACTCTTTTGC
*
36170 TCTCTCATACAGATAAGTTCTTTTCTTCTCTTCTTACTTTG-TTTTTTTAATTAATATTGTTATT
194 TCCCTCATACAGATAAGTTCTTTTCTTCTCTTCTTACTTTGTTTTTTTTAATTAATATTGTTATT
36234 TAATATTGTTAAAGTATA
259 TAATATTGTTAAAG--TA
*
36252 TTATATTTTTTTTGTTAATTAAGAAGTTAGTATTTAATTAACTTATTATTTCCGAAAATTAAATA
1 TTATA-TTTTTTTGTTAATTAAGAAGTTAGTATTTAATTAAATTATTATTTCCGAAAATTAAATA
* * *
36317 AAAAATATGGTTAATTTTTTAGTATAATTAGTTATATTAGTAGGTTTATGTATTAATTAAATTT-
65 AAAAATATGGTTAATTTTTTAGTATAATTAGTTATATTAATAGGTTTTTGTACTAATT-AATTTA
* * *
36381 TGTATTCAATTTTTTTATATTTCAACCATTTAGAATTGTGTTAAAACAACTTTCGAACTCTTTT-
129 TATATTTAATTTTTTTATATTACAACCATTTAGAATTGTGTTAAAACAACTTTC-AACTCTTTTG
* *
36445 TTCCCTCATCCATG-TAAGTTCTTTTCTTCTCCTT-TTACTTTGTTTTTTTTTTTTTAATTAATA
193 CTCCCTCATACA-GATAAGTTCTTTTCTTCT-CTTCTTACTTTG-----TTTTTTTTAATTAATA
* *
36508 TTGTTATTTAGTGTTGTTAAAGTA
251 TTGTTATTTAATATTGTTAAAGTA
** * *
36532 -GGTATTTTTTTGTTAATTAAGAAATTACTATTTAATTAAATTATTATTTCCG------------
1 TTATATTTTTTTGTTAATTAAGAAGTTAGTATTTAATTAAATTATTATTTCCGAAAATTAAATAA
*
36584 AAAATATGGTTAATTTTTTTAGTATAATTAGTTATATTAATGGGTTTTTGTACTAATTAATTTAT
66 AAAATATGGTTAA-TTTTTTAGTATAATTAGTTATATTAATAGGTTTTTGTACTAATTAATTTAT
36649 ATATTTAA-TTTTTTATATTACAAACC-TTTAGAATTGTGTTAAAA
130 ATATTTAATTTTTTTATATTAC-AACCATTTAGAATTGTGTTAAAA
36693 GTTTAATTTC
Statistics
Matches: 390, Mismatches: 35, Indels: 41
0.84 0.08 0.09
Matches are distributed among these distances:
266 48 0.12
267 51 0.13
275 5 0.01
276 139 0.36
277 58 0.15
278 50 0.13
279 2 0.01
280 2 0.01
282 35 0.09
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (274 bp):
TTATATTTTTTTGTTAATTAAGAAGTTAGTATTTAATTAAATTATTATTTCCGAAAATTAAATAA
AAAATATGGTTAATTTTTTAGTATAATTAGTTATATTAATAGGTTTTTGTACTAATTAATTTATA
TATTTAATTTTTTTATATTACAACCATTTAGAATTGTGTTAAAACAACTTTCAACTCTTTTGCTC
CCTCATACAGATAAGTTCTTTTCTTCTCTTCTTACTTTGTTTTTTTTAATTAATATTGTTATTTA
ATATTGTTAAAGTA
Found at i:37203 original size:10 final size:11
Alignment explanation
Indices: 37178--37207 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
37168 CTTTTCAGCT
37178 TAAAAAATTAA
1 TAAAAAATTAA
37189 TAAAAAATTAA
1 TAAAAAATTAA
37200 -AAAAAATT
1 TAAAAAATT
37208 GGGTGTCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAAATTAA
Found at i:42038 original size:6 final size:6
Alignment explanation
Indices: 42024--42062 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
42014 GGGTGGGTAC
42024 GGGGAAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GG
1 GGGG-AA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GG
42063 AGCAGTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:53509 original size:54 final size:55
Alignment explanation
Indices: 53445--53555 Score: 179
Period size: 54 Copynumber: 2.0 Consensus size: 55
53435 GTATATCCCA
*
53445 TGGTGTTTCTTGATTTTCATTGAGTGCAATTAAAGTTTGTATATC-GTCACTATT
1 TGGTGTTTCTTGATTTTCATCGAGTGCAATTAAAGTTTGTATATCTGTCACTATT
* * *
53499 TGGTGTTTCTTGATTTTCATCGAGTGCAATTAAGGTTTGTATGTCTTTCACTATT
1 TGGTGTTTCTTGATTTTCATCGAGTGCAATTAAAGTTTGTATATCTGTCACTATT
53554 TG
1 TG
53556 TAATACTTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 42 0.81
55 10 0.19
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (55 bp):
TGGTGTTTCTTGATTTTCATCGAGTGCAATTAAAGTTTGTATATCTGTCACTATT
Found at i:54812 original size:3 final size:3
Alignment explanation
Indices: 54804--54829 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54794 CATGTTGTAT
54804 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
54830 TCCTTTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:60691 original size:21 final size:21
Alignment explanation
Indices: 60667--60738 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
60657 TATAACCAAT
60667 TTTTATAGATTTATAATAAAC
1 TTTTATAGATTTATAATAAAC
*
60688 TTTTATTTGATTT-TAATTTAACCAAC
1 TTTTA-TAGATTTATAA--T-A--AAC
* *
60714 TTTTATAGAATTATAATAGAC
1 TTTTATAGATTTATAATAAAC
60735 TTTT
1 TTTT
60739 TATTTGATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
21 14 0.35
22 6 0.15
23 2 0.05
24 2 0.05
25 5 0.12
26 11 0.28
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTTATAGATTTATAATAAAC
Found at i:60728 original size:47 final size:49
Alignment explanation
Indices: 60654--60751 Score: 155
Period size: 47 Copynumber: 2.0 Consensus size: 49
60644 CAAATAAATC
* *
60654 AATTATAACCAATTTTTATAGATTTATAATAAAC-TTTTATTTGATTTT
1 AATTATAACCAACTTTTATAGAATTATAATAAACTTTTTATTTGATTTT
*
60702 AATT-TAACCAACTTTTATAGAATTATAATAGACTTTTTATTTGATTTT
1 AATTATAACCAACTTTTATAGAATTATAATAAACTTTTTATTTGATTTT
60750 AA
1 AA
60752 CCTTTTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 26 0.57
48 20 0.43
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (49 bp):
AATTATAACCAACTTTTATAGAATTATAATAAACTTTTTATTTGATTTT
Found at i:80260 original size:19 final size:18
Alignment explanation
Indices: 80223--80260 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
80213 ATAATTTTTT
*
80223 TAAAAAAAATATAATACA
1 TAAAAAAAATATAAAACA
80241 TAAAAAAAATACTAAAACA
1 TAAAAAAAATA-TAAAACA
80260 T
1 T
80261 TAACATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAAAAAAATATAAAACA
Found at i:80469 original size:33 final size:33
Alignment explanation
Indices: 80432--80499 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
80422 ATAGCAGAAT
* * *
80432 AATAATGAAATT-GTAGCAAAATAGTGAGAAAAC
1 AATAA-GAAATTAATAGCAAAATAGTAAAAAAAC
80465 AATAAGAAATTAATAGCAAAATAGTAAAAAAAC
1 AATAAGAAATTAATAGCAAAATAGTAAAAAAAC
80498 AA
1 AA
80500 GAAAAAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.19
Consensus pattern (33 bp):
AATAAGAAATTAATAGCAAAATAGTAAAAAAAC
Found at i:81293 original size:2 final size:2
Alignment explanation
Indices: 81275--81307 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
81265 CTGGAAAGTA
*
81275 AT AT AT A- AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81308 CCATTAGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:90869 original size:16 final size:16
Alignment explanation
Indices: 90837--90874 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
90827 TATTAAGTGT
90837 ATTGAAGTGCTTTGAGAA
1 ATTGAAGTGC-TTGAG-A
90855 ATTGAAGTG-TTGAGA
1 ATTGAAGTGCTTGAGA
90870 ATTGA
1 ATTGA
90875 TTTGGGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 5 0.25
18 9 0.45
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (16 bp):
ATTGAAGTGCTTGAGA
Found at i:96898 original size:24 final size:26
Alignment explanation
Indices: 96871--96918 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
96861 AGAGAAATGT
96871 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
96895 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
96919 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:97071 original size:25 final size:22
Alignment explanation
Indices: 96983--97127 Score: 200
Period size: 22 Copynumber: 6.3 Consensus size: 22
96973 GCTAGCGCGT
96983 TTCTGTTCAGCACTGTGTGTGC
1 TTCTGTTCAGCACTGTGTGTGC
*
97005 TTCTGTTTAGCACTGTGTGTGC
1 TTCTGTTCAGCACTGTGTGTGC
*
97027 TTCTGTTCAACACTGTGTGTGC
1 TTCTGTTCAGCACTGTGTGTGC
97049 TTCTGTTACCCAGCACTGTGTGTGC
1 TTCTGTT---CAGCACTGTGTGTGC
*
97074 TTCTGTTCAGCATTGTGTGTGC
1 TTCTGTTCAGCACTGTGTGTGC
*
97096 TTCTGTTACCCAGCACTGTATGTGC
1 TTCTGTT---CAGCACTGTGTGTGC
97121 TTCTGTT
1 TTCTGTT
97128 TCCCAGCATT
Statistics
Matches: 110, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
22 69 0.63
25 41 0.37
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (22 bp):
TTCTGTTCAGCACTGTGTGTGC
Found at i:97079 original size:47 final size:47
Alignment explanation
Indices: 96983--97127 Score: 233
Period size: 47 Copynumber: 3.1 Consensus size: 47
96973 GCTAGCGCGT
*
96983 TTCTGTTCAGCACTGTGTGTGCTTCTGTT---TAGCACTGTGTGTGC
1 TTCTGTTCAGCACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGC
*
97027 TTCTGTTCAACACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGC
1 TTCTGTTCAGCACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGC
* *
97074 TTCTGTTCAGCATTGTGTGTGCTTCTGTTACCCAGCACTGTATGTGC
1 TTCTGTTCAGCACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGC
97121 TTCTGTT
1 TTCTGTT
97128 TCCCAGCATT
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
44 28 0.30
47 65 0.70
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (47 bp):
TTCTGTTCAGCACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGTGC
Done.