Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014788.1 Kokia drynarioides strain JFW-HI SEQ_129830, 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: 48787
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:256 original size:7 final size:7
Alignment explanation
Indices: 239--318 Score: 65
Period size: 7 Copynumber: 11.7 Consensus size: 7
229 TCGAAACTTA
239 AAACCTT
1 AAACCTT
246 AAACCTT
1 AAACCTT
*
253 AAACCTA
1 AAACCTT
*
260 AAACC-A
1 AAACCTT
*
266 AAACC-C
1 AAACCTT
272 AAACCTT
1 AAACCTT
*
279 AAACCTA
1 AAACCTT
*
286 AAACCCT
1 AAACCTT
**
293 AAACCCA
1 AAACCTT
*
300 AAAACTT
1 AAACCTT
*
307 AAACCTC
1 AAACCTT
314 AAACC
1 AAACC
319 CCAAACTGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
6 11 0.18
7 49 0.82
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCTT
Found at i:256 original size:14 final size:14
Alignment explanation
Indices: 239--318 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
229 TCGAAACTTA
*
239 AAACCTTAAACCTT
1 AAACCTAAAACCTT
*
253 AAACCTAAAACC-A
1 AAACCTAAAACCTT
*
266 AAACC-CAAACCTT
1 AAACCTAAAACCTT
*
279 AAACCTAAAACCCT
1 AAACCTAAAACCTT
* *
293 AAACCCAAAAACTT
1 AAACCTAAAACCTT
*
307 AAACCTCAAACC
1 AAACCTAAAACC
319 CCAAACTGAA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
12 5 0.10
13 10 0.19
14 37 0.71
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCTAAAACCTT
Found at i:261 original size:21 final size:21
Alignment explanation
Indices: 232--318 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 21
222 TCGAAGCTCG
* * *
232 AAACTTAAAACCTTAAACCTT
1 AAACCTAAAACCTAAAACCTC
253 AAACCTAAAACC-AAAACC-C
1 AAACCTAAAACCTAAAACCTC
*
272 AAACCTTAAACCTAAAACC-C
1 AAACCTAAAACCTAAAACCTC
* * *
292 TAAACCCAAAAACTTAAACCTC
1 -AAACCTAAAACCTAAAACCTC
314 AAACC
1 AAACC
319 CCAAACTGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
19 11 0.20
20 12 0.22
21 31 0.56
22 1 0.02
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACCTAAAACCTAAAACCTC
Found at i:281 original size:33 final size:34
Alignment explanation
Indices: 239--302 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
229 TCGAAACTTA
*
239 AAACCTTAAACCTTAAA-CCTAAAACCAAAACCC
1 AAACCTTAAACCTAAAACCCTAAAACCAAAACCC
*
272 AAACCTTAAACCTAAAACCCTAAACCCAAAA
1 AAACCTTAAACCTAAAACCCTAAAACCAAAA
303 ACTTAAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (34 bp):
AAACCTTAAACCTAAAACCCTAAAACCAAAACCC
Found at i:1241 original size:23 final size:23
Alignment explanation
Indices: 1200--1258 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1190 CTAGTTTTTA
* *
1200 TCTACCTCTGT-GCACGCTTTTTC
1 TCTACCT-TGTGGCATGCTTTTCC
* *
1223 TTTACTTTGTGGCATGCTTTTCC
1 TCTACCTTGTGGCATGCTTTTCC
1246 TCTACCTTGTGGC
1 TCTACCTTGTGGC
1259 TCGCTTCTGC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.08, C:0.29, G:0.17, T:0.46
Consensus pattern (23 bp):
TCTACCTTGTGGCATGCTTTTCC
Found at i:2272 original size:20 final size:20
Alignment explanation
Indices: 2247--2313 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
2237 GAATTTATTA
2247 TTAATGCAACCATCATTTTT
1 TTAATGCAACCATCATTTTT
2267 TTAATGCAA-CAGTCATTTTT
1 TTAATGCAACCA-TCATTTTT
* * *
2287 TTAATGTAACGATCATGTTT
1 TTAATGCAACCATCATTTTT
2307 TTAATGC
1 TTAATGC
2314 TACCTCTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.05
20 38 0.93
21 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
TTAATGCAACCATCATTTTT
Found at i:2587 original size:35 final size:35
Alignment explanation
Indices: 2539--2622 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
2529 CCATAAACCT
2539 TAAACCTTGAAACCAAAACCACT-TAC-CCTTACACCC
1 TAAACCTT-AAACC-AAA-CACTCTACACCTTACACCC
**
2575 TACAACC-TAAACCTTACACTCTACACCTTACACCC
1 TA-AACCTTAAACCAAACACTCTACACCTTACACCC
2610 TAAACCTTAAACC
1 TAAACCTTAAACC
2623 CTAATACCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
33 4 0.10
34 8 0.19
35 23 0.55
36 3 0.07
37 4 0.10
ACGTcount: A:0.38, C:0.39, G:0.01, T:0.21
Consensus pattern (35 bp):
TAAACCTTAAACCAAACACTCTACACCTTACACCC
Found at i:2602 original size:14 final size:14
Alignment explanation
Indices: 2575--2626 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
2565 CCTTACACCC
*
2575 TACAACCTAAACCT
1 TACACCCTAAACCT
* *
2589 TACACTCTACACCT
1 TACACCCTAAACCT
2603 TACACCCTAAACCT
1 TACACCCTAAACCT
*
2617 TAAACCCTAA
1 TACACCCTAA
2627 TACCCAAGCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (14 bp):
TACACCCTAAACCT
Found at i:2606 original size:28 final size:27
Alignment explanation
Indices: 2560--2618 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
2550 ACCAAAACCA
*
2560 CTTACCCTTACACCCTACAACCTAAAC
1 CTTACACTTACACCCTACAACCTAAAC
* *
2587 CTTACACTCTACACCTTACACCCTAAAC
1 CTTACACT-TACACCCTACAACCTAAAC
2615 CTTA
1 CTTA
2619 AACCCTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.25
Consensus pattern (27 bp):
CTTACACTTACACCCTACAACCTAAAC
Found at i:5996 original size:17 final size:17
Alignment explanation
Indices: 5974--6015 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5964 TAAATACAAG
* *
5974 TTATTTTATAAACGTAA
1 TTATTTTAGAAACGCAA
*
5991 TTATTTTAGAAACGCCA
1 TTATTTTAGAAACGCAA
6008 TTATTTTA
1 TTATTTTA
6016 AACAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (17 bp):
TTATTTTAGAAACGCAA
Found at i:6620 original size:28 final size:28
Alignment explanation
Indices: 6589--6647 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
6579 ATATGATCAT
6589 CTTAATCCAGTAAAAGTATTTTAATTAA
1 CTTAATCCAGTAAAAGTATTTTAATTAA
6617 CTTAATCCAGTAAAAGTATTTTAATTAA
1 CTTAATCCAGTAAAAGTATTTTAATTAA
6645 CTT
1 CTT
6648 TTAAGCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (28 bp):
CTTAATCCAGTAAAAGTATTTTAATTAA
Found at i:14617 original size:211 final size:211
Alignment explanation
Indices: 14253--14889 Score: 1053
Period size: 211 Copynumber: 3.0 Consensus size: 211
14243 TAAAGCACAT
* *
14253 GTTGAGGTTTGAGTTCATAAGTAGCTTCAAAAGGTATCTTCTTAATTGTTCTATTCACAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
* *
14318 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTTACCTGATTCCAAA-CAGGACACC
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCA-GACACC
14382 TAAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
130 TAAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTG
* *
14447 CTAGAAAATTTTAATTG
195 CTAGAAAATTTCAATCG
14464 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
* * *
14529 AATGTAAACTCATTTTGAGGACTAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
* * *
14594 AAGCATATTTCCTAAACTTTGGTTAACAACCTCTATTTTCCCATCTATTTGTGGATGAAATGTGC
131 AAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
*
14659 TA-AAATATTTCAGTCG
196 TAGAAA-ATTTCAATCG
* * *
14675 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTATTCTTAATTGATCTATTCATAGAGTTG
1 GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
*
14740 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACAAGACACCT
66 TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
* *
14805 AAGCATATTTCCTAAACTTTGATTGACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
131 AAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
*
14870 TAGGAAATTTCAATCAG
196 TAGAAAATTTCAATC-G
14887 GTT
1 GTT
14890 CCCATTTTCT
Statistics
Matches: 395, Mismatches: 27, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
210 3 0.01
211 384 0.97
212 8 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (211 bp):
GTTGAGGTTTGAGTCCATAAGTAGCTTCAAAAGGTGTCTTCTTAATTGTTCTATTCACAGAGTTG
TATGTAAACTCATCTTGAGGAATAACCAAATCCTAACTCTTCACATGATTCCAAACCAGACACCT
AAGCATATTTCCTAAACTTTGGTTAACAGCCTCTATTTGCCCATCTATTTGTGGATGAAAAGTGC
TAGAAAATTTCAATCG
Found at i:19462 original size:94 final size:94
Alignment explanation
Indices: 19301--19471 Score: 297
Period size: 94 Copynumber: 1.8 Consensus size: 94
19291 GAAATTGAAT
* *
19301 ATATAATTATAATTATTTAAATGCTCCTAGCTCTTATTACAATTGTAAAAGTTTTACTTGTGTTA
1 ATATAATTATAATTATTTAAATGCTCCTAGATCTTATTACAATTGTAAAAGTTTTACTTGTGCTA
*
19366 TAAAGTTATATATATAATTTTTTTCCAAA
66 TAAACTTATATATATAATTTTTTTCCAAA
* *
19395 ATATAATTATAATTATTTAAATGCTCCTAGATTTTATTACCATTGTAAAAGTTTTACTTGTGCTA
1 ATATAATTATAATTATTTAAATGCTCCTAGATCTTATTACAATTGTAAAAGTTTTACTTGTGCTA
19460 TAAACTTATATA
66 TAAACTTATATA
19472 AAAAAAAATT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 72 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (94 bp):
ATATAATTATAATTATTTAAATGCTCCTAGATCTTATTACAATTGTAAAAGTTTTACTTGTGCTA
TAAACTTATATATATAATTTTTTTCCAAA
Found at i:22854 original size:12 final size:12
Alignment explanation
Indices: 22837--22874 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
22827 TAATTTCAAA
22837 TTCATCTCTAAT
1 TTCATCTCTAAT
*
22849 TTCATCT-TGA-
1 TTCATCTCTAAT
22859 TTCATCTCTAAT
1 TTCATCTCTAAT
22871 TTCA
1 TTCA
22875 ACATGATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 7 0.32
11 4 0.18
12 11 0.50
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.50
Consensus pattern (12 bp):
TTCATCTCTAAT
Found at i:22881 original size:22 final size:22
Alignment explanation
Indices: 22822--22881 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
22812 TAGAGTATTT
22822 ATCTCTAATTTC-A-A--ATTC
1 ATCTCTAATTTCAACATGATTC
* *
22840 ATCTCTAATTTCATCTTGATTC
1 ATCTCTAATTTCAACATGATTC
22862 ATCTCTAATTTCAACATGAT
1 ATCTCTAATTTCAACATGAT
22882 ATCAAAGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 12 0.35
22 22 0.65
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (22 bp):
ATCTCTAATTTCAACATGATTC
Found at i:24173 original size:19 final size:19
Alignment explanation
Indices: 24149--24189 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
24139 ATTTTTAGAG
* *
24149 ATTCTAATTAATATATATT
1 ATTCTAATTAAGAGATATT
24168 ATTCTAATTAAGAGATATT
1 ATTCTAATTAAGAGATATT
24187 ATT
1 ATT
24190 TCCTTAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTCTAATTAAGAGATATT
Found at i:24856 original size:211 final size:210
Alignment explanation
Indices: 24492--25119 Score: 988
Period size: 211 Copynumber: 3.0 Consensus size: 210
24482 ATGGGTACTT
* *
24492 GATTGAAATTTCCTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGATTGTTAATCAAAGT
1 GATTGAAATTT-TTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGATTGTTAACCAAAGT
24557 TTAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTCCTCA
65 TTAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTCCTCA
*
24622 AGATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAATACACCTTTTGAAGCTACTTATG
130 AGATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTATG
*
24687 GACTCAAACCTTAATC
195 GACTCAAACCTTAACC
* * * *
24703 GATTGAAATATTTTAGCACTTTTCATCCACAAATAGATGAGAAAATAGAGGTTGTTAACCGAAGT
1 GATTGAAAT-TTTTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGATTGTTAACCAAAGT
* * * *
24768 TTAGGAAATATGCTTAGGTGT-TTGGCTTGAAATCATGTGAACAGTTAGGATTTGGTTAGTCCTC
65 TTAGGAAATATGCTTAGGTGTCTT-GTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTCCTC
* *
24832 AAAATGAGTTTACATTCAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTAT
129 AAGATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTAT
24897 GGACTCAAACCTTAACC
194 GGACTCAAACCTTAACC
* *
24914 AATTGAAATTTTCTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGACTGTTAACCAAAGT
1 GATTGAAATTTT-TAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGATTGTTAACCAAAGT
* * * *
24979 TTAGGAAATATGCTTAAGTGTCCTGTTTGGAATCAGGTGAAGAGTTAGGATATGGTTATTCCTCA
65 TTAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTCCTCA
* * * *
25044 AGATGAGTTTACATACAACTTTGTGAATATAACAATTAAGAAGATACCTTTTGAAGCTACTTATG
130 AGATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTATG
*
25109 AACTCAAACCT
195 GACTCAAACCT
25120 CAACATGTGC
Statistics
Matches: 378, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
210 5 0.01
211 370 0.98
212 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (210 bp):
GATTGAAATTTTTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGATTGTTAACCAAAGTT
TAGGAAATATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTCCTCAA
GATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTATGG
ACTCAAACCTTAACC
Found at i:32852 original size:27 final size:27
Alignment explanation
Indices: 32820--32876 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
32810 AAATTCAATT
32820 AATAAATTAAT-TTTATGTTAAAATTAA
1 AATAAATTAATATTTAT-TTAAAATTAA
* *
32847 AATAAATTCATATTTATTTAATATTAA
1 AATAAATTAATATTTATTTAAAATTAA
32874 AAT
1 AAT
32877 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
AATAAATTAATATTTATTTAAAATTAA
Found at i:35597 original size:183 final size:184
Alignment explanation
Indices: 35289--35651 Score: 656
Period size: 183 Copynumber: 2.0 Consensus size: 184
35279 CGTTTAGCAC
*
35289 TGCATGATATATAATACAATATTTTCAAATGAAATAGCAGAACCTCTTATGACCTATAGTATATT
1 TGCATGATATATAATACAATATTTTCAAATGAAATAGCAGAACCTCTCATGACCTATAGTATATT
** *
35354 AAAAGAAACTTTGATAAAAGTAGTGTCTTTATGTGAGCTAATACCTATCAAAGAAAAGTTCTTAT
66 AAAAGAAACTTTGATAAAAAAAATGTCTTTATGTGAGCTAATACCTATCAAAGAAAAGTTCTTAT
35419 AGACAACAAAGCATTAGCAATC-TTTTTTTTAAAAATCTTAAATAAAGACAGTT
131 AGACAACAAAGCATTAGCAATCTTTTTTTTTAAAAATCTTAAATAAAGACAGTT
35472 TGCATGATATATAATACAATATTTTCAAATGAAATAGCAGAACCTCTCATGACCTATAGTATATT
1 TGCATGATATATAATACAATATTTTCAAATGAAATAGCAGAACCTCTCATGACCTATAGTATATT
*
35537 AAAAGAAACTTTGATAAAAAAAATTTCTTTATGTGAGCTAATACCTATCAAAGAAAAGTTCTTAT
66 AAAAGAAACTTTGATAAAAAAAATGTCTTTATGTGAGCTAATACCTATCAAAGAAAAGTTCTTAT
* *
35602 AGACAACAAATCATTAGCAATCTTTTTTTTTTAAAATCTTAAATAAAGAC
131 AGACAACAAAGCATTAGCAATCTTTTTTTTTAAAAATCTTAAATAAAGAC
35652 TATTTAGGAA
Statistics
Matches: 172, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
183 146 0.85
184 26 0.15
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (184 bp):
TGCATGATATATAATACAATATTTTCAAATGAAATAGCAGAACCTCTCATGACCTATAGTATATT
AAAAGAAACTTTGATAAAAAAAATGTCTTTATGTGAGCTAATACCTATCAAAGAAAAGTTCTTAT
AGACAACAAAGCATTAGCAATCTTTTTTTTTAAAAATCTTAAATAAAGACAGTT
Found at i:44668 original size:29 final size:29
Alignment explanation
Indices: 44635--44694 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
44625 ATAAATGATT
*
44635 TTAAAATTATTTTTTAAAGTA-TAAAATTA
1 TTAAAATTA-TTTTAAAAGTATTAAAATTA
*
44664 TTAAAATTATTTTAAAATTATTAAAATTA
1 TTAAAATTATTTTAAAAGTATTAAAATTA
44693 TT
1 TT
44695 TTTTTGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TTAAAATTATTTTAAAAGTATTAAAATTA
Found at i:44670 original size:9 final size:9
Alignment explanation
Indices: 44656--44694 Score: 60
Period size: 9 Copynumber: 4.1 Consensus size: 9
44646 TTTTAAAGTA
44656 TAAAATTAT
1 TAAAATTAT
44665 TAAAATTATTT
1 TAAAATTA--T
44676 TAAAATTAT
1 TAAAATTAT
44685 TAAAATTAT
1 TAAAATTAT
44694 T
1 T
44695 TTTTTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 19 0.68
11 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TAAAATTAT
Found at i:44679 original size:20 final size:20
Alignment explanation
Indices: 44656--44696 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
44646 TTTTAAAGTA
44656 TAAAATTATTAAAATTATTT
1 TAAAATTATTAAAATTATTT
44676 TAAAATTATTAAAATTATTT
1 TAAAATTATTAAAATTATTT
44696 T
1 T
44697 TTTGAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAATTATTAAAATTATTT
Found at i:45802 original size:29 final size:29
Alignment explanation
Indices: 45770--45839 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
45760 ATTTCAAAAA
45770 AAATAATTTTAATAAATTT-AAAATAATTT
1 AAATAATTTTAAT-AATTTAAAAATAATTT
*
45799 AAATAATTTT-ATATTTTAAAAAATAATTT
1 AAATAATTTTAATAATTT-AAAAATAATTT
*
45828 TAATAATTTTAA
1 AAATAATTTTAA
45840 AATCATTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 4 0.11
28 2 0.06
29 29 0.81
30 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATAATTTTAATAATTTAAAAATAATTT
Found at i:45822 original size:20 final size:22
Alignment explanation
Indices: 45799--45841 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
45789 AAAATAATTT
45799 AAATAATTTT-AT-ATTTTAAA
1 AAATAATTTTAATAATTTTAAA
45819 AAATAATTTTAATAATTTTAAA
1 AAATAATTTTAATAATTTTAAA
45841 A
1 A
45842 TCATTTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATAATTTTAATAATTTTAAA
Found at i:45834 original size:9 final size:9
Alignment explanation
Indices: 45771--45839 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
45761 TTTCAAAAAA
45771 AATAATTTT
1 AATAATTTT
*
45780 AATAAATTTAA
1 AAT-AATTT-T
*
45791 AATAATTTA
1 AATAATTTT
45800 AATAATTTT
1 AATAATTTT
45809 -AT-ATTTT
1 AATAATTTT
45816 AA-AA----
1 AATAATTTT
45820 AATAATTTT
1 AATAATTTT
45829 AATAATTTT
1 AATAATTTT
45838 AA
1 AA
45840 AATCATTTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 5 0.10
8 4 0.08
9 23 0.47
10 10 0.20
11 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATAATTTT
Found at i:45839 original size:49 final size:51
Alignment explanation
Indices: 45736--45848 Score: 160
Period size: 49 Copynumber: 2.3 Consensus size: 51
45726 AAAATGGAAA
*
45736 TTAAAATTATTT-AATAATTTTATTATTTCAAAAAAAATAATTTTAATAAAT
1 TTAAAATAATTTAAATAATTTTATTATTT-AAAAAAAATAATTTTAATAAAT
* *
45787 TTAAAATAATTTAAATAATTTTA-TATTT-TAAAAAATAATTTTAATAATT
1 TTAAAATAATTTAAATAATTTTATTATTTAAAAAAAATAATTTTAATAAAT
*
45836 TTAAAATCATTTA
1 TTAAAATAATTTA
45849 CTAACGTGAC
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
49 31 0.54
51 16 0.28
52 10 0.18
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (51 bp):
TTAAAATAATTTAAATAATTTTATTATTTAAAAAAAATAATTTTAATAAAT
Found at i:45842 original size:20 final size:20
Alignment explanation
Indices: 45771--45847 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
45761 TTTCAAAAAA
* *
45771 AATAATTTTAATA-AATTTAA
1 AATAATTTTAAAATAATTT-T
45791 AATAA-TTT-AAATAATTTT
1 AATAATTTTAAAATAATTTT
45809 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
45829 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
45848 ACTAACGTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
16 1 0.02
17 5 0.11
18 2 0.04
19 8 0.17
20 24 0.51
21 2 0.04
22 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:47872 original size:23 final size:24
Alignment explanation
Indices: 47842--47896 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
47832 TAATAGAGAT
47842 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
47865 TTTCAA-TTCCAATTCACTTTCAC
1 TTTCAATTTACAATTCACTATCAC
47888 TTTCAATTT
1 TTTCAATTT
47897 TGATCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.32
23 17 0.61
24 2 0.07
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Done.