Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014891.1 Kokia drynarioides strain JFW-HI SEQ_129934, 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: 84876
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:338 original size:29 final size:29
Alignment explanation
Indices: 273--504 Score: 183
Period size: 29 Copynumber: 8.1 Consensus size: 29
263 TTTTTTTAAG
* *
273 AATAGTGGAAAAACTGTAAAAT-TTG-AA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
*
300 AATAGTGGCAAAATTGTAAAATCTGGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* * * *
329 AATAGTGGCAGAGCTG-AAAATTTTGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* *
357 AACCAATGGCAAAACTGTAAAATCT-G-AA
1 AA-TAGTGGCAAAACTGTAAAATCTGGAAA
* *
385 AATCAATGGCAGAACTGTAAAATCTGGAAA
1 AAT-AGTGGCAAAACTGTAAAATCTGGAAA
* *
415 ATTAGTGGCAAAACTGTAAAATTTTGGAAA
1 AATAGTGGCAAAACTGTAAAA-TCTGGAAA
* **
445 ACAAAG-GTAAAAACTGTAAAATCT-GAAA
1 A-ATAGTGGCAAAACTGTAAAATCTGGAAA
* * *
473 AACCAATGG-AAATACTGTAAAATCTGAAAA
1 AA-TAGTGGCAAA-ACTGTAAAATCTGGAAA
503 AA
1 AA
505 AAAATACTCG
Statistics
Matches: 164, Mismatches: 28, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
27 21 0.13
28 47 0.29
29 58 0.35
30 36 0.22
31 2 0.01
ACGTcount: A:0.50, C:0.10, G:0.18, T:0.22
Consensus pattern (29 bp):
AATAGTGGCAAAACTGTAAAATCTGGAAA
Found at i:408 original size:86 final size:87
Alignment explanation
Indices: 281--504 Score: 285
Period size: 86 Copynumber: 2.6 Consensus size: 87
271 AGAATAGTGG
* * * * *
281 AAAAACTGTAAAATTTGAAAAT-AGTGGCAAAATTGTAAAATCTGGAAAAATAGTGGCAGAGCTG
1 AAAAACTGTAAAATCTGAAAATCAATGGCAAAACTGTAAAATCTGGAAAAATAGTGGCAAAACTG
*
345 -AAAATTTTGAAAAACCAATGG-
66 TAAAATTTTGAAAAA-CAAAGGT
* * *
366 CAAAACTGTAAAATCTGAAAATCAATGGCAGAACTGTAAAATCTGGAAAATTAGTGGCAAAACTG
1 AAAAACTGTAAAATCTGAAAATCAATGGCAAAACTGTAAAATCTGGAAAAATAGTGGCAAAACTG
*
431 TAAAATTTTGGAAAACAAAGGT
66 TAAAATTTTGAAAAACAAAGGT
* *
453 AAAAACTGTAAAATCTGAAAAACCAATGG-AAATACTGTAAAATCTGAAAAAA
1 AAAAACTGTAAAATCTG-AAAATCAATGGCAAA-ACTGTAAAATCTGGAAAAA
505 AAAATACTCG
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
85 20 0.17
86 41 0.34
87 31 0.26
88 27 0.23
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.22
Consensus pattern (87 bp):
AAAAACTGTAAAATCTGAAAATCAATGGCAAAACTGTAAAATCTGGAAAAATAGTGGCAAAACTG
TAAAATTTTGAAAAACAAAGGT
Found at i:490 original size:59 final size:58
Alignment explanation
Indices: 352--502 Score: 175
Period size: 59 Copynumber: 2.6 Consensus size: 58
342 CTGAAAATTT
* * *
352 TGAAAAACCAATGGCAAAACTGTAAAA-TCTGAAAATCAATGGCAGAACTGTAAAATC
1 TGAAAAACCAATGGCAAAACTGTAAAATTCTGAAAATCAAAGGAAAAACTGTAAAATC
* ** * *
409 TGGAAAATTAGTGGCAAAACTGTAAAATTTTGGAAAA-CAAAGGTAAAAACTGTAAAATC
1 TGAAAAACCAATGGCAAAACTGTAAAATTCT-GAAAATCAAAGG-AAAAACTGTAAAATC
468 TGAAAAACCAATGG-AAATACTGTAAAA-TCTGAAAA
1 TGAAAAACCAATGGCAAA-ACTGTAAAATTCTGAAAA
503 AAAAAATACT
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
57 28 0.36
58 12 0.16
59 37 0.48
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (58 bp):
TGAAAAACCAATGGCAAAACTGTAAAATTCTGAAAATCAAAGGAAAAACTGTAAAATC
Found at i:2915 original size:13 final size:13
Alignment explanation
Indices: 2897--2936 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2887 TTTTAGTTTA
2897 TGCATGATATATT
1 TGCATGATATATT
*
2910 TGCATGAAATATT
1 TGCATGATATATT
*
2923 TGCTATGTTATATT
1 TGC-ATGATATATT
2937 GGAAAGGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (13 bp):
TGCATGATATATT
Found at i:5210 original size:16 final size:15
Alignment explanation
Indices: 5183--5215 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
5173 ATGAATTTAA
5183 AATTAAATTAATTCT
1 AATTAAATTAATTCT
5198 AATTAAATATAATTCT
1 AATTAAAT-TAATTCT
5214 AA
1 AA
5216 ATGTTCTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAAATTAATTCT
Found at i:8288 original size:17 final size:17
Alignment explanation
Indices: 8268--8300 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
8258 TTTAAGGACT
8268 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
8285 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
8301 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:8574 original size:50 final size:50
Alignment explanation
Indices: 8495--8650 Score: 174
Period size: 50 Copynumber: 3.1 Consensus size: 50
8485 TGACATTCAT
*
8495 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
1 TAACTCTCATG-TTAGTTAAATTTGCATCATAAATAATGACATGCATTAAG
* ** *
8546 TAACT-TACATGTTAGTTAAATATGCATCATAAATCCT-ATCATGCATTATG
1 TAACTCT-CATGTTAGTTAAATTTGCATCATAAATAATGA-CATGCATTAAG
* *
8596 TAACTCTCATGTTAGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCTCATGTTAGTTAAA-TTTGCATCA-TAAAT-AATGACATGCATTAAG
8648 TAA
1 TAA
8651 TCCATTAGTT
Statistics
Matches: 87, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
49 1 0.01
50 51 0.59
51 18 0.21
52 17 0.20
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (50 bp):
TAACTCTCATGTTAGTTAAATTTGCATCATAAATAATGACATGCATTAAG
Found at i:19029 original size:26 final size:26
Alignment explanation
Indices: 18990--19041 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
18980 CTCAATTACC
*
18990 TATGTCCACTACCTTAGCTTTCCTTA
1 TATGTCCACAACCTTAGCTTTCCTTA
19016 TATGTCCACAACCTTAGCTTTCCTTA
1 TATGTCCACAACCTTAGCTTTCCTTA
19042 ACTAAGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.40
Consensus pattern (26 bp):
TATGTCCACAACCTTAGCTTTCCTTA
Found at i:22317 original size:33 final size:33
Alignment explanation
Indices: 22231--22330 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
22221 AGGCGATCAG
* * *
22231 AATGATGAAGCTGCCCCGAGAGATGATCCAATC
1 AATGATGAAGCTGCCCTGATAGATGTTCCAATC
22264 AATGATGAAGCTGCCCTGATAGATGTTCCAATC
1 AATGATGAAGCTGCCCTGATAGATGTTCCAATC
* * * *
22297 ATTGATGAAGTTGCCGTGATAGTTGTTCCAATC
1 AATGATGAAGCTGCCCTGATAGATGTTCCAATC
22330 A
1 A
22331 CTTATGTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (33 bp):
AATGATGAAGCTGCCCTGATAGATGTTCCAATC
Found at i:32921 original size:18 final size:17
Alignment explanation
Indices: 32892--32933 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
32882 ATATTTTTTT
32892 TATTTTTC-TTTTTCTC
1 TATTTTTCTTTTTTCTC
32908 GTATTTTTCTTTTTTTCTC
1 -TATTTTTC-TTTTTTCTC
32927 TATTTTT
1 TATTTTT
32934 TTGATCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 7 0.30
19 8 0.35
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTTTTCTTTTTTCTC
Found at i:37558 original size:24 final size:24
Alignment explanation
Indices: 37526--37576 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
37516 ATGGTTTGGC
37526 GGAAAGAAAGAACTGTACTTTAGT
1 GGAAAGAAAGAACTGTACTTTAGT
37550 GGAAAGAAAGAACTGTACTTTAGT
1 GGAAAGAAAGAACTGTACTTTAGT
37574 GGA
1 GGA
37577 TATGGTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (24 bp):
GGAAAGAAAGAACTGTACTTTAGT
Found at i:41417 original size:15 final size:16
Alignment explanation
Indices: 41378--41430 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
41368 CGAGCTCTGG
41378 TGTTGCGAACACTAGA
1 TGTTGCGAACACTAGA
* *
41394 -GCTGAGAACACT-GA
1 TGTTGCGAACACTAGA
*
41408 TGTTGCGAACACTCG-
1 TGTTGCGAACACTAGA
41423 TGTTGCGA
1 TGTTGCGA
41431 GCATGGATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 2 0.06
15 28 0.90
16 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (16 bp):
TGTTGCGAACACTAGA
Found at i:45760 original size:14 final size:14
Alignment explanation
Indices: 45737--45779 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
45727 AAAATTCTAG
45737 TTTC-TCCTTCTTCT
1 TTTCTTCCTTC-TCT
45751 TTT-TTCCTTCTCT
1 TTTCTTCCTTCTCT
45764 TTTCTTCCTTC-CT
1 TTTCTTCCTTCTCT
45777 TTT
1 TTT
45780 TCGTTTAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTCTTCCTTCTCT
Found at i:45832 original size:17 final size:17
Alignment explanation
Indices: 45812--45845 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45802 CCTTCTTTTG
* *
45812 TTTCTTTTTTTTTTTAT
1 TTTCTTTATTCTTTTAT
45829 TTTCTTTATTCTTTTAT
1 TTTCTTTATTCTTTTAT
45846 ATCTTATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTTATTCTTTTAT
Found at i:54214 original size:17 final size:18
Alignment explanation
Indices: 54180--54215 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54170 TGAATTTCTA
54180 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
54198 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
54215 T
1 T
54216 AACTCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:58753 original size:23 final size:23
Alignment explanation
Indices: 58700--58755 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
58690 TCTCCTTCCA
58700 AAAAAAGAAAAAAAAAAAAGAAG
1 AAAAAAGAAAAAAAAAAAAGAAG
* ** *
58723 AAATAAGAAAAGCAAAGAAGAA-
1 AAAAAAGAAAAAAAAAAAAGAAG
58745 ACAAAAAGAAA
1 A-AAAAAGAAA
58756 GGAAATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAAAAAAAAAAGAAG
Found at i:59327 original size:9 final size:9
Alignment explanation
Indices: 59309--59349 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
59299 TTAAATCAAT
59309 AAAAAA-AG
1 AAAAAAGAG
59317 AAAAAAGAG
1 AAAAAAGAG
*
59326 AAAAAATA-
1 AAAAAAGAG
59334 AAAAAAGAAG
1 AAAAAAG-AG
59344 AAAAAA
1 AAAAAA
59350 TAGAGGGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 12 0.43
9 10 0.36
10 6 0.21
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:59338 original size:18 final size:18
Alignment explanation
Indices: 59317--59351 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
59307 ATAAAAAAAG
59317 AAAAAAG-AGAAAAAATA
1 AAAAAAGAAGAAAAAATA
59334 AAAAAAGAAGAAAAAATA
1 AAAAAAGAAGAAAAAATA
59352 GAGGGAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAAAAGAAGAAAAAATA
Found at i:59812 original size:42 final size:41
Alignment explanation
Indices: 59753--60174 Score: 488
Period size: 42 Copynumber: 10.0 Consensus size: 41
59743 AAGGAAAGCA
** *
59753 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCTGTTTACAT
1 TTCATTGCATTTAGAGGCCAA-GTGTGGAGGTCCATTTACTT
59795 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCC-AAGTGTGGAGGTCCATTTACTT
* *
59837 TTCATTGCATTTAGAGGTCCAAGTGTAGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGG-CCAAGTGTGGAGGTCCATTTACTT
* * **
59879 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTTTATTTACTT
1 TTCATTGCATTTAGAGG-CCAAGTGTGGAGGTCCATTTACTT
* * *
59921 TTCATCT-CATTTAGAGGCCTAGGTGTGGAGATTCATTTACTT
1 TTCAT-TGCATTTAGAGGCC-AAGTGTGGAGGTCCATTTACTT
*
59963 TTCATTGCATTTAGAGGCCCAAGTGTGGAGATCCATTTACTT
1 TTCATTGCATTTAGAGG-CCAAGTGTGGAGGTCCATTTACTT
* *
60005 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCACTTACTT
1 TTCATTGCATTTAGAGG-CCAAGTGTGGAGGTCCATTTACTT
* * * *
60047 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTAATT
1 TTCATTGCATTTAGAGG-CCAAGTGTGGAGGTCCATTTACTT
* * *
60089 TTAATCT-CATTTAAAGGCCCAAGTGTGAAGGTCCATTTACTT
1 TTCAT-TGCATTTAGAGG-CCAAGTGTGGAGGTCCATTTACTT
* * * *
60131 TTCATTGCATTTAGAGGCCTAGGCGTAGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCC-AAGTGTGGAGGTCCATTTACTT
60173 TT
1 TT
60175 TTATTGTATA
Statistics
Matches: 333, Mismatches: 38, Indels: 18
0.86 0.10 0.05
Matches are distributed among these distances:
41 6 0.02
42 321 0.96
43 6 0.02
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (41 bp):
TTCATTGCATTTAGAGGCCAAGTGTGGAGGTCCATTTACTT
Found at i:59924 original size:126 final size:125
Alignment explanation
Indices: 59753--60174 Score: 551
Period size: 126 Copynumber: 3.4 Consensus size: 125
59743 AAGGAAAGCA
* * * * *
59753 TTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCTGTTTACATTTCATTGCATTTAGAGGCCTAAG
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTTTTCATTGCATTTAGAGGCCTAGG
* *
59818 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGTCCAAGTGTAGAGGCCCATTTACTT
66 TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAGTGT-GAGGTCCATTTACTT
*
59879 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTTTATTTACTTTTCATCT-CATTTAGAGGCCTAG
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTTTTCAT-TGCATTTAGAGGCCTAG
* * *
59943 GTGTGGAGATTCATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGGAGATCCATTTACTT
65 GTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAGTGT-GAGGTCCATTTACTT
* * * * *
60005 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCACTTACTTTTCATCGCATTTAGAGGCCCAGG
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTTTTCATTGCATTTAGAGGCCTAGG
* * * *
60070 TGTGGAGGCCCATTTAATTTTAATCT-CATTTAAAGGCCCAAGTGTGAAGGTCCATTTACTT
66 TGTGGAGGTCCATTTACTTTTCAT-TGCATTTAGAGGCCCAAGTGTG-AGGTCCATTTACTT
* * * * * *
60131 TTCATTGCATTTAGAGGCCTAGGCGTAGAGGTCCATTTATTTTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTTTT
60175 TTATTGTATA
Statistics
Matches: 260, Mismatches: 32, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
125 1 0.00
126 257 0.99
127 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (125 bp):
TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTTTTCATTGCATTTAGAGGCCTAGG
TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGAGGTCCATTTACTT
Found at i:60622 original size:3 final size:3
Alignment explanation
Indices: 60614--60644 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
60604 AAGGGCCAAA
60614 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
60645 GGGTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:61055 original size:51 final size:49
Alignment explanation
Indices: 61000--61161 Score: 132
Period size: 51 Copynumber: 3.2 Consensus size: 49
60990 GAAAGTTCGG
* *
61000 ATTTTTAAAAATAAAAATCTATTTTTAGGCATTTTAAAAGAAAAAGTTTAA
1 ATTTTTAAAAATAAAAAT-TATTTTTAGACATTTTGAAA-AAAAAGTTTAA
** * **
61051 ATTTTTAAACAA-AATTTGATTATTTTTA-ACTATTTTGAAATAAAAGTTTTG
1 ATTTTTAAA-AATAA--AAATTATTTTTAGAC-ATTTTGAAAAAAAAGTTTAA
** *
61102 ATTTTTAAAAATAAAAA-TAGTTTTTTAGTTATTTTGGAATAAAAAGTTTAA
1 ATTTTTAAAAATAAAAATTA--TTTTTAGACATTTT-GAAAAAAAAGTTTAA
61153 ATTTTTAAA
1 ATTTTTAAA
61162 CAAAGTTTGA
Statistics
Matches: 87, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
48 2 0.02
49 1 0.01
50 13 0.15
51 51 0.59
52 18 0.21
53 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.45
Consensus pattern (49 bp):
ATTTTTAAAAATAAAAATTATTTTTAGACATTTTGAAAAAAAAGTTTAA
Found at i:61113 original size:102 final size:102
Alignment explanation
Indices: 60999--61211 Score: 311
Period size: 102 Copynumber: 2.1 Consensus size: 102
60989 GGAAAGTTCG
60999 GATTTTTAAAAATAAAAAT-CTATTTTTAGGCATTTTAAAAGAAAAAGTTTAAATTTTTAAACAA
1 GATTTTTAAAAATAAAAATACT-TTTTTAGGCATTTTAAAAGAAAAAGTTTAAATTTTTAAACAA
** *
61063 AATTTGATTATTTTTAACTATTTTGAAATAAAAGTTTT
65 AATTTGATTATTTTTAACTATTTCAAAATAAAAATTTT
* ** ** *
61101 GATTTTTAAAAATAAAAATAGTTTTTTAGTTATTTTGGAATAAAAAGTTTAAATTTTTAAACAAA
1 GATTTTTAAAAATAAAAATACTTTTTTAGGCATTTTAAAAGAAAAAGTTTAAATTTTTAAACAAA
* *
61166 GTTTGATTTTTTTTAACTATTTCAAAATAAAAATTTT
66 ATTTGATTATTTTTAACTATTTCAAAATAAAAATTTT
61203 GATTTTTAA
1 GATTTTTAA
61212 GTAAAGTAGT
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 98 0.99
103 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (102 bp):
GATTTTTAAAAATAAAAATACTTTTTTAGGCATTTTAAAAGAAAAAGTTTAAATTTTTAAACAAA
ATTTGATTATTTTTAACTATTTCAAAATAAAAATTTT
Found at i:61177 original size:51 final size:51
Alignment explanation
Indices: 61030--61211 Score: 172
Period size: 51 Copynumber: 3.6 Consensus size: 51
61020 ATTTTTAGGC
* *
61030 ATTTTAAAAGAAAAAGTTTAAATTTTTAAACAAAATTTGATTATTTTTAACT
1 ATTTTGAAATAAAAAGTTTAAATTTTTAAACAAAATTTGATT-TTTTTAACT
** * ** * **
61082 ATTTTGAAAT-AAAAGTTTTGATTTTTAAAAATAAAAAT-AGTTTTTTAGTT
1 ATTTTGAAATAAAAAGTTTAAATTTTTAAACA-AAATTTGATTTTTTTAACT
* *
61132 ATTTTGGAATAAAAAGTTTAAATTTTTAAACAAAGTTTGATTTTTTTTAACT
1 ATTTTGAAATAAAAAGTTTAAATTTTTAAACAAAATTTGA-TTTTTTTAACT
** **
61184 ATTTCAAAATAAAAA-TTTTGATTTTTAA
1 ATTTTGAAATAAAAAGTTTAAATTTTTAA
61212 GTAAAGTAGT
Statistics
Matches: 101, Mismatches: 25, Indels: 9
0.75 0.19 0.07
Matches are distributed among these distances:
50 19 0.19
51 50 0.50
52 32 0.32
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (51 bp):
ATTTTGAAATAAAAAGTTTAAATTTTTAAACAAAATTTGATTTTTTTAACT
Found at i:61267 original size:19 final size:20
Alignment explanation
Indices: 61228--61268 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
61218 TAGTGATTTT
61228 TTTTAGAATAAAAAAAGAAA
1 TTTTAGAATAAAAAAAGAAA
* *
61248 TTTTAGATTTAAAAAA-AAA
1 TTTTAGAATAAAAAAAGAAA
61267 TT
1 TT
61269 ATTTTTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (20 bp):
TTTTAGAATAAAAAAAGAAA
Found at i:61328 original size:28 final size:30
Alignment explanation
Indices: 61295--61354 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 30
61285 AAGGAGAAAA
*
61295 TTTTAAATT-TTT-AAATAAAA-TTTGATT
1 TTTTTAATTATTTAAAATAAAAGTTTGATT
61322 TTTTTAATTATTTCAAAATAAAAGTTTTGATT
1 TTTTTAATTATTT-AAAATAAAAG-TTTGATT
61354 T
1 T
61355 CTAAGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.30
28 3 0.11
30 8 0.30
32 8 0.30
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (30 bp):
TTTTTAATTATTTAAAATAAAAGTTTGATT
Found at i:61372 original size:147 final size:145
Alignment explanation
Indices: 61143--61407 Score: 390
Period size: 147 Copynumber: 1.8 Consensus size: 145
61133 TTTTGGAATA
*
61143 AAAAGTTTAAATTTTTAAACAAAGTTTGATTTTTTTTAACTATTTCAAAATAAAAATTTTGATTT
1 AAAAGTTTAAATTTTTAAACAAAATTTGATTTTTTTTAACTATTTCAAAATAAAAATTTTGATTT
* *
61208 TTAAGTAAAGTAGTGATTTTTTTTAGAATAAAAAAAG-AAATTTTAGATTTAAAAAAAAATTATT
66 CTAAGAAAAGTAGTGATTTTTTTT----TAAAAAAAGAAAATTTTAGATTTAAAAAAAAATTATT
61272 TTTTAGTCATTTTAAGGAG
127 TTTTAGTCATTTTAAGGAG
* * * *
61291 AAAATTTTAAATTTTTAAATAAAATTTGA-TTTTTTTAATTATTTCAAAATAAAAGTTTTGATTT
1 AAAAGTTTAAATTTTTAAACAAAATTTGATTTTTTTTAACTATTTCAAAATAAAAATTTTGATTT
* * *
61355 CTAAGAAAATTAGTGATTTTTTTTTAAAAAGAGAAAATTTTGGATTTAAAAAA
66 CTAAGAAAAGTAGTGATTTTTTTTTAAAAAAAGAAAATTTTAGATTTAAAAAA
61408 TAAAATAAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
143 8 0.08
144 18 0.17
147 54 0.51
148 26 0.25
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (145 bp):
AAAAGTTTAAATTTTTAAACAAAATTTGATTTTTTTTAACTATTTCAAAATAAAAATTTTGATTT
CTAAGAAAAGTAGTGATTTTTTTTTAAAAAAAGAAAATTTTAGATTTAAAAAAAAATTATTTTTT
AGTCATTTTAAGGAG
Found at i:62208 original size:18 final size:18
Alignment explanation
Indices: 62168--62213 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
62158 AGAGTTTTAG
62168 ATTTTCATTAAATTTACCC
1 ATTTTCATT-AATTTACCC
* *
62187 ATTTTCATTAATTTTCCT
1 ATTTTCATTAATTTACCC
62205 ATTTT-ATTA
1 ATTTTCATTA
62214 CTATTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 12 0.48
19 9 0.36
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTCATTAATTTACCC
Found at i:63430 original size:16 final size:15
Alignment explanation
Indices: 63403--63435 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
63393 ATGAATTTAA
63403 AATTAAATTAATTCT
1 AATTAAATTAATTCT
63418 AATTAAATATAATTCT
1 AATTAAAT-TAATTCT
63434 AA
1 AA
63436 ATGTTCTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAAATTAATTCT
Found at i:64578 original size:18 final size:20
Alignment explanation
Indices: 64524--64579 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
64514 TTTTACGATC
* *
64524 TTTAAA-ATTTTTAATAAAA
1 TTTAAATATTTTTATTATAA
64543 TTTAAATATTTTTATTATAA
1 TTTAAATATTTTTATTATAA
*
64563 TTT-AAT-TTTTTTTTATA
1 TTTAAATATTTTTATTATA
64580 GTTTTTGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.30
19 9 0.27
20 14 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAAATATTTTTATTATAA
Found at i:69376 original size:36 final size:36
Alignment explanation
Indices: 69329--69432 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
69319 TGGTAACAAG
* *
69329 CATGACTTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
* *
69365 CATGACCTTTGGGTCAATAGGGAGAAAAATAAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
**
69401 CATGACCTTTGGGTCAATAAAGAGTAAAATGA
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGA
69433 CGAAGAATAG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
Found at i:69844 original size:12 final size:12
Alignment explanation
Indices: 69827--69853 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
69817 ACTTGAGGAC
69827 TTGTGTAATTAA
1 TTGTGTAATTAA
69839 TTGTGTAATTAA
1 TTGTGTAATTAA
69851 TTG
1 TTG
69854 AATTCTGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (12 bp):
TTGTGTAATTAA
Found at i:73345 original size:22 final size:22
Alignment explanation
Indices: 73317--73375 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
73307 ATTAGAGTAA
**
73317 TCATCTCTAATTTCATCATGGT
1 TCATCTCTAATTTCATCATAAT
73339 TCATCTCTAATTTCATCATAAT
1 TCATCTCTAATTTCATCATAAT
73361 TCATCTCTAATTTCA
1 TCATCTCTAATTTCA
73376 ACAGATTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (22 bp):
TCATCTCTAATTTCATCATAAT
Found at i:73355 original size:12 final size:12
Alignment explanation
Indices: 73317--73375 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
73307 ATTAGAGTAA
73317 TCATCTCTAATT
1 TCATCTCTAATT
* **
73329 TCATC-AT-GGT
1 TCATCTCTAATT
73339 TCATCTCTAATT
1 TCATCTCTAATT
*
73351 TCATC-ATAA-T
1 TCATCTCTAATT
73361 TCATCTCTAATT
1 TCATCTCTAATT
73373 TCA
1 TCA
73376 ACAGATTCCT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
10 12 0.34
11 8 0.23
12 15 0.43
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (12 bp):
TCATCTCTAATT
Done.