Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005752.1 Kokia drynarioides strain JFW-HI SEQ_120003, 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: 56390
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:57 original size:2 final size:2
Alignment explanation
Indices: 1--42 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42 T
1 T
43 TTCGACATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123 original size:17 final size:17
Alignment explanation
Indices: 103--139 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
93 CTCATTTAAA
*
103 TGTCATTGCATTTTAGT
1 TGTCATTGCATTTTACT
*
120 TGTCGTTGCATTTTACT
1 TGTCATTGCATTTTACT
137 TGT
1 TGT
140 TAGTTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.54
Consensus pattern (17 bp):
TGTCATTGCATTTTACT
Found at i:2437 original size:148 final size:147
Alignment explanation
Indices: 2270--2888 Score: 636
Period size: 148 Copynumber: 4.2 Consensus size: 147
2260 AAGTTTTGAA
* * * *
2270 TAGTGTTTTTCTTTTAAAAAAA-AAATTAGA-TTTTAAAAATAAAAATATATTTTTTAGCCATTT
1 TAGTGATTTTCATTAAAAAAAATAAATTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTT
* * * * *
2333 CAAGGAAAAAGTTTAAAATTTTAAACAAACTTTTGATTTTTTTTTTTAACTTTTTTGAAATAAAA
66 TAAAGAAAAAGTTTAAAATTTTAAACAAAGTTTTGA---TTTTTTTTAACTATTTCGAAATAAAA
2398 GTTTGGATTTTTAAGTAAAG
128 GTTTGGATTTTTAAGTAAAG
* * *
2418 TAGTGATTTTCATTAAAAAATAAATAAAGTTTAGATTTTTAAAACTAAAAATATGTTTTTTTGTC
1 TAGTGATTTTCATT-AAAAA-AAATAAA--TTAGATTTTTAAAAATAAAAATATATTTTTTAGTC
*
2483 ATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGA--TTTTTTAACTATTTCGAAATAAA
62 ATTTTAAAGAAAAAGTTTAAAATTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAAT-AA
*
2546 AAATTTGGATTTTTAAGTAAAG
126 AAGTTTGGATTTTTAAGTAAAG
* * * *
2568 TAGTGATTTTCATTAAAAAAAGA-AACTTTAGATTTTTAAAAAATAAAAATTTGTTTTTTGGTCA
1 TAGTGATTTTCATTAAAAAAA-ATAA-ATTAGATTTTT-AAAAATAAAAATATATTTTTTAGTCA
* *
2632 TTTTAAAGAAAAA-TTTAAATTTTTTAAACAAAGTTTCGATTTTTTTTAACTATTTCGAAATAAA
63 TTTTAAAGAAAAAGTTTAAA-ATTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAA
2696 AGTTTGGATTTTTAAGTAAAG
127 AGTTTGGATTTTTAAGTAAAG
** *** * *
2717 TAGTGATTCTT--TTAAAAAAAATTATTTTA-A-AAAT-AAAATAAAAAAAGCTATTTTTTAGGC
1 TAGTGATT-TTCATTAAAAAAAA-TAAATTAGATTTTTAAAAATAAAAATA--TATTTTTTAGTC
* * *
2777 ATTTTAAAAGAAAAAGTTT--AATTTTCAAACAAAG-TTTGATATTTTTTAAGTATTTTGAAATA
62 ATTTT-AAAGAAAAAGTTTAAAATTTT-AAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATA
* * * *
2839 AAATTTTTGATTTTTAAGAAAAA
125 AAAGTTTGGATTTTTAAGTAAAG
* **
2862 TAGTAATTTTGTTTAAAAAAAGATAAA
1 TAGTGATTTTCATTAAAAAAA-ATAAA
2889 CCTTTTGATT
Statistics
Matches: 406, Mismatches: 41, Indels: 50
0.82 0.08 0.10
Matches are distributed among these distances:
144 12 0.03
145 54 0.13
146 35 0.09
147 28 0.07
148 86 0.21
149 60 0.15
150 62 0.15
151 3 0.01
153 5 0.01
154 61 0.15
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (147 bp):
TAGTGATTTTCATTAAAAAAAATAAATTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTT
TAAAGAAAAAGTTTAAAATTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTT
TGGATTTTTAAGTAAAG
Found at i:2800 original size:147 final size:146
Alignment explanation
Indices: 2283--2887 Score: 619
Period size: 150 Copynumber: 4.1 Consensus size: 146
2273 TGTTTTTCTT
* * * * *
2283 TTAAAAAAAA-AA--TTAGATTTTAAAAATAAAAATA-TATTTTTTAGCCATTTCAAGGAAAAAG
1 TTAAAAAAAATAACTTTAGATTTTTAAAATAAAAAAAGTATTTTTT-GGCATTTTAAAGAAAAAG
* * * *
2344 TTTAAAATTTTAAACAAACTTTTGATTTTTTTTTTTAACTTTTTTGAAATAAAAGTTTGGATTTT
65 TTTAAATTTTTAAACAAAGTTTTGA---TTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTT
2409 TAAGTAAAGTAGTGATTTTCA
127 TAAGTAAAGTAGTGATTTT-A
* * *
2430 TTAAAAAATAAATAAAGTTTAGATTTTTAAAACTAAAAATATGT-TTTTTTGTCATTTTAAAGAA
1 TT-AAAAA-AAAT-AACTTTAGATTTTTAAAA-TAAAAA-AAGTATTTTTTGGCATTTTAAAGAA
*
2494 AAAGTTTAAATTTTTAAACAAAGTTTTGA--TTTTTTAACTATTTCGAAATAAAAAATTTGGATT
61 AAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAAT-AAAAGTTTGGATT
2557 TTTAAGTAAAGTAGTGATTTTCA
125 TTTAAGTAAAGTAGTGATTTT-A
* *
2580 TTAAAAAAAGA-AACTTTAGATTTTTAAAA-AATAAAAATTTGTTTTTTGGTCATTTTAAAGAAA
1 TTAAAAAAA-ATAACTTTAGATTTTTAAAATAA-AAAAA-GTATTTTTTGG-CATTTTAAAGAAA
*
2643 AA-TTTAAATTTTTTAAACAAAGTTTCGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTT
62 AAGTTTAAA-TTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTT
2707 TTAAGTAAAGTAGTGATTCTT-
126 TTAAGTAAAGTAGTGATT-TTA
* * ***
2728 TTAAAAAAAATTATTTTA-A-AAATAAAATAAAAAAAGCTATTTTTTAGGCATTTTAAAAGAAAA
1 TTAAAAAAAATAACTTTAGATTTTTAAAATAAAAAAAG-TATTTTTT-GGCATTTT-AAAGAAAA
* * * * * *
2791 AGTTT-AATTTTCAAACAAAG-TTTGATATTTTTTAAGTATTTTGAAATAAAATTTTTGATTTTT
63 AGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTT
* * * *
2854 AAGAAAAATAGTAATTTTGT
128 AAGTAAAGTAGTGATTTT-A
2874 TTAAAAAAAGATAA
1 TTAAAAAAA-ATAA
2888 ACCTTTTGAT
Statistics
Matches: 395, Mismatches: 35, Indels: 56
0.81 0.07 0.12
Matches are distributed among these distances:
144 2 0.01
145 53 0.13
146 48 0.12
147 52 0.13
148 57 0.14
149 58 0.15
150 59 0.15
151 2 0.01
153 13 0.03
154 44 0.11
155 6 0.02
156 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (146 bp):
TTAAAAAAAATAACTTTAGATTTTTAAAATAAAAAAAGTATTTTTTGGCATTTTAAAGAAAAAGT
TTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAG
TAAAGTAGTGATTTTA
Found at i:3466 original size:16 final size:17
Alignment explanation
Indices: 3437--3482 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
3427 ATAATTTTTA
*
3437 TTTATTTTTATTTCATC
1 TTTATTTATATTTCATC
*
3454 TTTATTTAT-TTTCATG
1 TTTATTTATATTTCATC
*
3470 TCTATTTATATTT
1 TTTATTTATATTT
3483 ATGCTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATTTATATTTCATC
Found at i:11734 original size:5 final size:5
Alignment explanation
Indices: 11697--11730 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
11687 CGTTAAACTA
* *
11697 AAAAC AAAAC AAAAC AAAAC AAAAT AAAAT AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
11731 TAAATCTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (5 bp):
AAAAC
Found at i:22057 original size:2 final size:2
Alignment explanation
Indices: 22050--22106 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
22040 CTATGTAGCA
*
22050 AT AT AT AT AT AT AT AT AT AT AT AT AT TT 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 AT AT AT AT
*
22092 AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT A
22107 CTTTTACTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:22512 original size:32 final size:33
Alignment explanation
Indices: 22469--22534 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
22459 TGTACTTATA
* *
22469 TTTAATTAATGTA-TTAGAGTAGATATATCTAG
1 TTTAATGAATGTATTTAGAGAAGATATATCTAG
*
22501 TTTAATGAATGTATTTAGAGAAGATGTATCTAG
1 TTTAATGAATGTATTTAGAGAAGATATATCTAG
22534 T
1 T
22535 AGTCATGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.42
Consensus pattern (33 bp):
TTTAATGAATGTATTTAGAGAAGATATATCTAG
Found at i:26199 original size:17 final size:17
Alignment explanation
Indices: 26175--26240 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
26165 ATATATATGG
**
26175 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
26192 AGATGCAATGATAATAA
1 AAATGCAATGACAATAA
*
26209 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
* *
26226 TAATGCAGTGACAAT
1 AAATGCAATGACAAT
26241 TATACTACAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:30446 original size:66 final size:66
Alignment explanation
Indices: 30340--30473 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 66
30330 ATTTTGAAGC
* * * *
30340 TGTAGCTGTAATTCGTCATACTTTCTTTGAGACTCTGCTTCCCTCGTTGCTGCCTTGGCTTCAAG
1 TGTAGCTGGAATTCATCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTGCCTTCGCTTCAAG
30405 T
66 T
* * * * * *
30406 TGTAGCTGGAGTTCATCATATTTTCTTTGAGCCTCTGCTTCTCTCGCTGCTTCCTTCGCTTTAAG
1 TGTAGCTGGAATTCATCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTGCCTTCGCTTCAAG
30471 T
66 T
30472 TG
1 TG
30474 AGCAAATTGC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (66 bp):
TGTAGCTGGAATTCATCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTGCCTTCGCTTCAAG
T
Found at i:32597 original size:5 final size:5
Alignment explanation
Indices: 32587--32613 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
32577 TGAGCATTCG
32587 ATCGA ATCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA ATCGA AT
32614 GAAAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
ATCGA
Found at i:33347 original size:34 final size:34
Alignment explanation
Indices: 33304--33388 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
33294 CCTAGCTGCT
*
33304 AGTTCAAATACTAAAATTCAACTTTGGGTATTGC
1 AGTTCAAATACTAAAATTCAACTTTGGGTATTAC
*
33338 AGTTCAAATACTAAAATTCAACTTTGTGTATTAC
1 AGTTCAAATACTAAAATTCAACTTTGGGTATTAC
* *
33372 AGTACAAA-ACAAAAATT
1 AGTTCAAATACTAAAATT
33389 GCAGTTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 8 0.17
34 39 0.83
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (34 bp):
AGTTCAAATACTAAAATTCAACTTTGGGTATTAC
Found at i:34058 original size:43 final size:43
Alignment explanation
Indices: 34004--34089 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
33994 ATAAGATAAA
*
34004 ATGTTTCGGCTTTGGGGGAAAATGAGTATTGAAATTGGACTTG
1 ATGTTTCGGCTTTGGGAGAAAATGAGTATTGAAATTGGACTTG
*
34047 ATGTTTGGGCTTTGGGAGAAAATGAGTATTGAAATTGGACTTG
1 ATGTTTCGGCTTTGGGAGAAAATGAGTATTGAAATTGGACTTG
34090 GATAAATTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.35
Consensus pattern (43 bp):
ATGTTTCGGCTTTGGGAGAAAATGAGTATTGAAATTGGACTTG
Found at i:42153 original size:19 final size:19
Alignment explanation
Indices: 42129--42165 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42119 TTTTTATATC
42129 AAATTTTAAAATAAATTTA
1 AAATTTTAAAATAAATTTA
* *
42148 AAATTTTGAAATATATTT
1 AAATTTTAAAATAAATTT
42166 TAAGTAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAATTTTAAAATAAATTTA
Found at i:44283 original size:37 final size:37
Alignment explanation
Indices: 44227--44341 Score: 104
Period size: 37 Copynumber: 3.0 Consensus size: 37
44217 GTTTTTCTCA
*
44227 TAAACGTCGCTAATGCTCTTACCATTTGCGGCGTTTT
1 TAAACGCCGCTAATGCTCTTACCATTTGCGGCGTTTT
* * * *
44264 TAAACGCCGTTAATTCTCTTACCTTTTGCGGTGTTTTCT
1 TAAACGCCGCTAATGCTCTTACCATTTGCGGCG-TTT-T
* * * * *
44303 CATAAACACCACTAATGTTCTTACCTTTTGCAGCGTTTT
1 --TAAACGCCGCTAATGCTCTTACCATTTGCGGCGTTTT
44342 ATCATAAACG
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
37 28 0.45
38 3 0.05
39 2 0.03
40 3 0.05
41 26 0.42
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (37 bp):
TAAACGCCGCTAATGCTCTTACCATTTGCGGCGTTTT
Found at i:44389 original size:82 final size:81
Alignment explanation
Indices: 44236--44472 Score: 293
Period size: 82 Copynumber: 2.9 Consensus size: 81
44226 ATAAACGTCG
* * ** ** *
44236 CTAATGCTCTTACCATTTGCGGCG-TTTT--TAAACGCCGTTAATTCTCTTACCTTTTGCGGTGT
1 CTAATGCTCTTACCTTTTGCAGCGTTTTTCATAAACGCTATTAATTCTCTTACCTTTTATGGCGT
*
44298 TTTCTCATAAACACCA
66 TTTCCCATAAACACCA
*
44314 CTAATGTTCTTACCTTTTGCAGCGTTTTATCATAAACGCTATTAATTCTCTTACCTTTTATGGCG
1 CTAATGCTCTTACCTTTTGCAGCGTTTT-TCATAAACGCTATTAATTCTCTTACCTTTTATGGCG
** **
44379 TTTTCCCATAAATGCTG
65 TTTTCCCATAAACACCA
*
44396 CTATTGCT-TTACCTTTTGCAGCGTTTTCTCATAAACGCTATTAATTCTCTTACCTTTTATGGCG
1 CTAATGCTCTTACCTTTTGCAGCGTTTT-TCATAAACGCTATTAATTCTCTTACCTTTTATGGCG
44460 TTTTTCCCATAAA
65 -TTTTCCCATAAA
44473 TGCTGCTATT
Statistics
Matches: 138, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
78 21 0.15
79 3 0.02
80 1 0.01
81 55 0.40
82 58 0.42
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (81 bp):
CTAATGCTCTTACCTTTTGCAGCGTTTTTCATAAACGCTATTAATTCTCTTACCTTTTATGGCGT
TTTCCCATAAACACCA
Found at i:44461 original size:41 final size:41
Alignment explanation
Indices: 44196--44472 Score: 219
Period size: 41 Copynumber: 6.8 Consensus size: 41
44186 TAGCGGCGTT
* * **
44196 TTCTACTTAACCTTTAGCGTCGTTTTTCTCATAAACG-TCGCTAA
1 TTCT-CTT-ACCTTTTGCGGCG-TTTTCTCATAAACGCT-ATTAA
* * **
44240 TGCTCTTACCATTTGCGGCG-TTT-T--TAAACGCCGTTAA
1 TTCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCTATTAA
* * * *
44277 TTCTCTTACCTTTTGCGGTGTTTTCTCATAAACACCACTAA
1 TTCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCTATTAA
* *
44318 TGT-TCTTACCTTTTGCAGCGTTTTATCATAAACGCTATTAA
1 T-TCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCTATTAA
** * * **
44359 TTCTCTTACCTTTTATGGCGTTTTCCCATAAATGCTGCT-A
1 TTCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCTATTAA
*
44399 TTGCT-TTACCTTTTGCAGCGTTTTCTCATAAACGCTATTAA
1 TT-CTCTTACCTTTTGCGGCGTTTTCTCATAAACGCTATTAA
** *
44440 TTCTCTTACCTTTTATGGCGTTTTTCCCATAAA
1 TTCTCTTACCTTTTGCGGCG-TTTTCTCATAAA
44473 TGCTGCTATT
Statistics
Matches: 185, Mismatches: 37, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
37 27 0.15
38 3 0.02
39 2 0.01
40 36 0.19
41 89 0.48
42 22 0.12
43 3 0.02
44 3 0.02
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (41 bp):
TTCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCTATTAA
Found at i:44494 original size:41 final size:40
Alignment explanation
Indices: 44364--44503 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
44354 ATTAATTCTC
44364 TTACCTTTTATGGCGTTTTCCCATAAATGCTGCTATTGCT
1 TTACCTTTTATGGCGTTTTCCCATAAATGCTGCTATTGCT
*** * * **
44404 TTACCTTTTGCAGCGTTTTCTCATAAACGCTATTAATT-CT
1 TTACCTTTTATGGCGTTTTCCCATAAATGCTGCT-ATTGCT
44444 CTTACCTTTTATGGCGTTTTTCCCATAAATGCTGCTATTGCT
1 -TTACCTTTTATGGCG-TTTTCCCATAAATGCTGCTATTGCT
* *
44486 TTATCTTTTGTGGCGTTT
1 TTACCTTTTATGGCGTTT
44504 ATGAAAAAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
40 32 0.40
41 31 0.39
42 17 0.21
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.47
Consensus pattern (40 bp):
TTACCTTTTATGGCGTTTTCCCATAAATGCTGCTATTGCT
Found at i:44503 original size:82 final size:81
Alignment explanation
Indices: 44264--44495 Score: 320
Period size: 82 Copynumber: 2.8 Consensus size: 81
44254 GCGGCGTTTT
** ** * * ** ** * *
44264 TAAACGCCGTTAATTCTCTTACCTTTTGCGGTGTTTTCTCATAAACACCACTAATGTTCTTACCT
1 TAAACGCTATTAATTCTCTTACCTTTTATGGCGTTTTCCCATAAATGCTGCTATTGCT-TTACCT
44329 TTTGCAGCGTTTTATCA
65 TTTGCAGCGTTTTATCA
44346 TAAACGCTATTAATTCTCTTACCTTTTATGGCGTTTTCCCATAAATGCTGCTATTGCTTTACCTT
1 TAAACGCTATTAATTCTCTTACCTTTTATGGCGTTTTCCCATAAATGCTGCTATTGCTTTACCTT
*
44411 TTGCAGCGTTTTCTCA
66 TTGCAGCGTTTTATCA
*
44427 TAAACGCTATTAATTCTCTTACCTTTTATGGCGTTTTTCCCATAAATGCTGCTATTGCTTTATCT
1 TAAACGCTATTAATTCTCTTACCTTTTATGGCG-TTTTCCCATAAATGCTGCTATTGCTTTACCT
44492 TTTG
65 TTTG
44496 TGGCGTTTAT
Statistics
Matches: 135, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
81 55 0.41
82 80 0.59
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (81 bp):
TAAACGCTATTAATTCTCTTACCTTTTATGGCGTTTTCCCATAAATGCTGCTATTGCTTTACCTT
TTGCAGCGTTTTATCA
Found at i:45044 original size:23 final size:23
Alignment explanation
Indices: 44969--45044 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
44959 AGGATAGTGG
44969 TGAAAAGGGTTATGAAATTCACT
1 TGAAAAGGGTTATGAAATTCACT
* *
44992 TG-AAA-GATTATTTGGGACAACTC-CT
1 TGAAAAGGGTTA--T--GA-AATTCACT
45017 TGAAAAGGGTTATGAAATTCACT
1 TGAAAAGGGTTATGAAATTCACT
45040 TGAAA
1 TGAAA
45045 TTCATTATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
21 4 0.10
22 7 0.17
23 12 0.29
25 7 0.17
26 7 0.17
27 4 0.10
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (23 bp):
TGAAAAGGGTTATGAAATTCACT
Found at i:48998 original size:32 final size:33
Alignment explanation
Indices: 48962--49025 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
48952 TGTAGTTATA
*
48962 TTTAATGAATGTA-TTAGAGTAGATGTATCTAC
1 TTTAATGAATGTATTTAGAGAAGATGTATCTAC
*
48994 TTTAATTAATGTATTTAGAGAAGATGTATCTA
1 TTTAATGAATGTATTTAGAGAAGATGTATCTA
49026 GTAGTCATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (33 bp):
TTTAATGAATGTATTTAGAGAAGATGTATCTAC
Found at i:51791 original size:30 final size:31
Alignment explanation
Indices: 51733--51806 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
51723 TAGATTCGTC
* *
51733 TATATTG-TTT-TTTTAATTCTTTTAAA-TT
1 TATATTGTTTTATTTTAATTATTTAAAATTT
51761 TATATTGTTTTATTTTAA-TATTTAATAATTT
1 TATATTGTTTTATTTTAATTATTTAA-AATTT
51792 TATCATT-TTTTATTT
1 TAT-ATTGTTTTATTT
51807 GTTGAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 7 0.18
29 8 0.21
30 8 0.21
31 13 0.33
32 3 0.08
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (31 bp):
TATATTGTTTTATTTTAATTATTTAAAATTT
Found at i:54108 original size:29 final size:29
Alignment explanation
Indices: 54049--54107 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
54039 TTTGGTTTAA
*
54049 TGTGCAATTGTATAAATGAATTTTAATTT
1 TGTGCAATTGTATAAATAAATTTTAATTT
* * *
54078 TGTGCAATTTTATACATCAAATTTTGATTT
1 TGTGCAATTGTATAAAT-AAATTTTAATTT
54108 GATCTAACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (29 bp):
TGTGCAATTGTATAAATAAATTTTAATTT
Found at i:54895 original size:15 final size:14
Alignment explanation
Indices: 54875--54918 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
54865 CCTGGCCACC
54875 AATATTAATTTCTTT
1 AATATTAATTT-TTT
54890 AATATT-ATTTTTT
1 AATATTAATTTTTT
54903 -ATATATAATTTTTT
1 AATAT-TAATTTTTT
54917 AA
1 AA
54919 AAAATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 11 0.42
15 7 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
AATATTAATTTTTT
Done.