Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013760.1 Kokia drynarioides strain JFW-HI SEQ_128788, 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: 26726
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:296 original size:29 final size:28
Alignment explanation
Indices: 242--297 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
232 TAAAATTAGG
* **
242 TTTAAATTGGTTTAAATTTATTTTTAAA
1 TTTAAATTGCTTTAAATTTAAATTTAAA
270 TTTAAATTTGCTTTAAATTTAAATTTAA
1 TTTAAA-TTGCTTTAAATTTAAATTTAA
298 TCAAATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTAAATTGCTTTAAATTTAAATTTAAA
Found at i:1096 original size:3 final size:3
Alignment explanation
Indices: 1076--1142 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
1066 TGGCATTTAT
* * * **
1076 TAA TAA TAG TAA TTA TAA TAA TTAA TAA TTAA TAA TAA CT-G TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA -TAA TAA TAA -TAA TAA TAA
1123 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
1143 TTTATTAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 1 0.02
3 44 0.85
4 7 0.13
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2263 original size:29 final size:28
Alignment explanation
Indices: 2230--2423 Score: 156
Period size: 29 Copynumber: 6.6 Consensus size: 28
2220 ATTTTCGACC
*
2230 CCAAAACTTCCATTTTTACCCTAGAACTT
1 CCAAAAATTCCATTTTTACCCTA-AACTT
* *
2259 CCAAAAATTCCATTTTGACCCCAAAACTT
1 CCAAAAATTCCATTTTTA-CCCTAAACTT
** * *
2288 TTAAAAATTTCATTTTTACACCGAAACTT
1 CCAAAAATTCCATTTTTAC-CCTAAACTT
*
2317 CCAAAAAAAATTCCATTTTTACCCTTGAACTT
1 CC---AAAAATTCCATTTTTACCC-TAAACTT
* * *
2349 CCAAAAATTACATTTTTACACTCAAACCT
1 CCAAAAATTCCATTTTTACCCT-AAACTT
* *
2378 CC-AAAATTTCATTTTTGACCCCGAAACTT
1 CCAAAAATTCCATTTTT-A-CCCTAAACTT
*
2407 TCAAAAATTACCATTTT
1 CCAAAAATT-CCATTTT
2424 GCCCTCGGAT
Statistics
Matches: 131, Mismatches: 23, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
28 15 0.11
29 73 0.56
30 12 0.09
31 8 0.06
32 23 0.18
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
CCAAAAATTCCATTTTTACCCTAAACTT
Found at i:2265 original size:50 final size:49
Alignment explanation
Indices: 2190--2287 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 49
2180 CTGAAAATTA
* *
2190 CATTTTTACCATTGAACTTTCAAAAATTCCATTTTCGACCCCAAAACTTC
1 CATTTTTACCATAGAACTTCCAAAAATTCCATTTT-GACCCCAAAACTTC
*
2240 CATTTTTACCCTAGAACTTCCAAAAATTCCATTTTGACCCCAAAACTT
1 CATTTTTACCATAGAACTTCCAAAAATTCCATTTTGACCCCAAAACTT
2288 TTAAAAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 13 0.29
50 32 0.71
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.35
Consensus pattern (49 bp):
CATTTTTACCATAGAACTTCCAAAAATTCCATTTTGACCCCAAAACTTC
Found at i:2334 original size:32 final size:32
Alignment explanation
Indices: 2290--2383 Score: 92
Period size: 32 Copynumber: 3.0 Consensus size: 32
2280 CAAAACTTTT
*
2290 AAAAATTTCATTTTTACACCGAAACTTCCAAA
1 AAAAATTACATTTTTACACCGAAACTTCCAAA
*
2322 AAAAATTCCATTTTTAC-CCTTG-AACTTCC---
1 AAAAATTACATTTTTACACC--GAAACTTCCAAA
*
2351 AAAAATTACATTTTTACACTC-AAACCTCCAAA
1 AAAAATTACATTTTTACAC-CGAAACTTCCAAA
2383 A
1 A
2384 TTTCATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
29 22 0.43
30 1 0.02
31 3 0.06
32 24 0.47
33 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.32
Consensus pattern (32 bp):
AAAAATTACATTTTTACACCGAAACTTCCAAA
Found at i:2355 original size:61 final size:61
Alignment explanation
Indices: 2261--2423 Score: 165
Period size: 61 Copynumber: 2.7 Consensus size: 61
2251 TAGAACTTCC
** * *
2261 AAAAATTCCATTTTGACCCCAAAACTTTTAAAAATTTCATTTTTACAC-CGAAACTTCCAAA
1 AAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTACATTTTTACACTC-AAACCTCCAAA
* ***
2322 AAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTACATTTTTACACTCAAACCTCC---
1 AAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTACATTTTTACACTCAAACCTCCAAA
* * *
2380 -AAAATTTCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTT
1 AAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTA-CATTTT
2424 GCCCTCGGAT
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
57 8 0.09
58 22 0.26
59 6 0.07
61 48 0.56
62 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (61 bp):
AAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTACATTTTTACACTCAAACCTCCAAA
Found at i:2402 original size:90 final size:90
Alignment explanation
Indices: 2232--2413 Score: 242
Period size: 90 Copynumber: 2.0 Consensus size: 90
2222 TTTCGACCCC
* * * *
2232 AAAACTTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTGACCCCAAAACTTTTAAAAATT
1 AAAAATTCCATTTTTACCCTAGAACTTCCAAAAATTACATTTTGACCCCAAAACTCTCAAAAATT
2297 TCATTTTTACACCGAAACTTCCAAA
66 TCATTTTTACACCGAAACTTCCAAA
* * * *
2322 AAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTACATTTTTACACTC-AAAC-CTCCAAAAT
1 AAAAATTCCATTTTTACCCTAGAACTTCCAAAAATTACATTTTGAC-CCCAAAACTCTCAAAAAT
* *
2385 TTCATTTTTGACCCCGAAACTTTCAAA
65 TTCATTTTT-ACACCGAAACTTCCAAA
2412 AA
1 AA
2414 TTACCATTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
89 15 0.19
90 63 0.79
91 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (90 bp):
AAAAATTCCATTTTTACCCTAGAACTTCCAAAAATTACATTTTGACCCCAAAACTCTCAAAAATT
TCATTTTTACACCGAAACTTCCAAA
Found at i:2439 original size:58 final size:57
Alignment explanation
Indices: 2377--2560 Score: 172
Period size: 58 Copynumber: 3.2 Consensus size: 57
2367 CACTCAAACC
* * *
2377 TCCAAAATTTCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTGCCCTCGGATG
1 TCCAAAATTTCATTTTTGACCACGAAACTTTC-AAAATTACCATTTTGCCCTCGAATA
** * * * * *
2435 TCCAAAAACTCTATTTTCGACCACGAAACTCTCAAAATTACCCTTTTACCCCCGAATA
1 TCCAAAATTTC-ATTTTTGACCACGAAACTTTCAAAATTACCATTTTGCCCTCGAATA
* * * * * *
2493 TCTAAAAATTCCATTTTTAACCTCG-AGCTTTCCCAAAATTACCATTTTGCCCTCGAAAA
1 TC-CAAAATTTCATTTTTGACCACGAAACTTT--CAAAATTACCATTTTGCCCTCGAATA
2552 TCCAAAATT
1 TCCAAAATT
2561 ACCATTTTAC
Statistics
Matches: 98, Mismatches: 24, Indels: 8
0.75 0.18 0.06
Matches are distributed among these distances:
57 4 0.04
58 47 0.48
59 47 0.48
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (57 bp):
TCCAAAATTTCATTTTTGACCACGAAACTTTCAAAATTACCATTTTGCCCTCGAATA
Found at i:2464 original size:59 final size:58
Alignment explanation
Indices: 2387--2558 Score: 175
Period size: 59 Copynumber: 2.9 Consensus size: 58
2377 TCCAAAATTT
* * *
2387 CATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTGCCCTCGGATGTCCAAAAACTC
1 CATTTTTGACCACGAAACTTTC-AAAATTACCATTTTGCCCTCGAATATCCAAAAACTC
* * * * * * * *
2446 TATTTTCGACCACGAAACTCTCAAAATTACCCTTTTACCCCCGAATATCTAAAAATTC
1 CATTTTTGACCACGAAACTTTCAAAATTACCATTTTGCCCTCGAATATCCAAAAACTC
* * * *
2504 CATTTTTAACCTCG-AGCTTTCCCAAAATTACCATTTTGCCCTCGAAAATCCAAAA
1 CATTTTTGACCACGAAACTTT--CAAAATTACCATTTTGCCCTCGAATATCCAAAA
2559 TTACCATTTT
Statistics
Matches: 89, Mismatches: 22, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
57 4 0.04
58 39 0.44
59 46 0.52
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.31
Consensus pattern (58 bp):
CATTTTTGACCACGAAACTTTCAAAATTACCATTTTGCCCTCGAATATCCAAAAACTC
Found at i:2490 original size:29 final size:29
Alignment explanation
Indices: 2458--2574 Score: 89
Period size: 29 Copynumber: 4.0 Consensus size: 29
2448 TTTTCGACCA
*
2458 CGAAACTCTCAAAATTACCCTTTTACCCC
1 CGAAACTCTCAAAATTACCATTTTACCCC
* * *
2487 CGAATA-TCTAAAAATT-CCATTTTTAACCT
1 CGAA-ACTCTCAAAATTACCA-TTTTACCCC
* * * *
2516 CG-AGCTTTCCCAAAATTACCATTTTGCCCT
1 CGAAAC--TCTCAAAATTACCATTTTACCCC
*
2546 CGAAAATC-CAAAATTACCATTTTACCCC
1 CGAAACTCTCAAAATTACCATTTTACCCC
2574 C
1 C
2575 CGGGTATCCG
Statistics
Matches: 68, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
28 22 0.32
29 24 0.35
30 18 0.26
31 4 0.06
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (29 bp):
CGAAACTCTCAAAATTACCATTTTACCCC
Found at i:4429 original size:31 final size:31
Alignment explanation
Indices: 4394--4494 Score: 73
Period size: 31 Copynumber: 3.2 Consensus size: 31
4384 CACCGATATT
4394 TTAAATAGATATGATAGAGATACAGAATTAG
1 TTAAATAGATATGATAGAGATACAGAATTAG
* * * * * *
4425 TTAAA-AAAT-TTACATGCACA-ACAAGTAAAAATAT
1 TTAAATAGATATGATA-G-AGATAC-AG---AATTAG
4459 TTAAATAGATATGATAGAGATACAGAATTAG
1 TTAAATAGATATGATAGAGATACAGAATTAG
4490 TTAAA
1 TTAAA
4495 AAATTTACAT
Statistics
Matches: 49, Mismatches: 12, Indels: 18
0.62 0.15 0.23
Matches are distributed among these distances:
29 3 0.06
30 6 0.12
31 18 0.37
34 13 0.27
35 6 0.12
36 3 0.06
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (31 bp):
TTAAATAGATATGATAGAGATACAGAATTAG
Found at i:4474 original size:65 final size:65
Alignment explanation
Indices: 4393--4528 Score: 263
Period size: 65 Copynumber: 2.1 Consensus size: 65
4383 TCACCGATAT
4393 TTTAAATAGATATGATAGAGATACAGAATTAGTTAAAAAATTTACATGCACAACAAGTAAAAATA
1 TTTAAATAGATATGATAGAGATACAGAATTAGTTAAAAAATTTACATGCACAACAAGTAAAAATA
4458 TTTAAATAGATATGATAGAGATACAGAATTAGTTAAAAAATTTACATGCACAACAAGTAAAAATA
1 TTTAAATAGATATGATAGAGATACAGAATTAGTTAAAAAATTTACATGCACAACAAGTAAAAATA
4523 TCTTAA
1 T-TTAA
4529 TAAATTCAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 66 0.94
66 4 0.06
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (65 bp):
TTTAAATAGATATGATAGAGATACAGAATTAGTTAAAAAATTTACATGCACAACAAGTAAAAATA
Found at i:10400 original size:147 final size:147
Alignment explanation
Indices: 10140--10405 Score: 361
Period size: 147 Copynumber: 1.8 Consensus size: 147
10130 ATTGCCTCAC
* ** * * * * *
10140 TGATTTATTGATGACCAAGGTGTGATGTTACGATGTCATATGTAGGAAGTCGCAATGTTGGCCAT
1 TGATTTATTGATGACCAAGGTGTGATGTCACGATGTCATACATAAGAAGCCACAACGTTGGCCAC
* * * *
10205 TGTTTTATTGATCTAATAGGTGATCAAGGTGTGACATCGTGACGTCATGTGTAGAACGTTGCGAC
66 TATTTCATTGATCTAATAGGTGATCAAGGTGTGACATCATGACATCATGTGTAGAACGTTGCGAC
10270 CTTGACTATTCTTTCAT
131 CTTGACTATTCTTTCAT
* * *
10287 TGATTTATTGGTGACCAAGGTGTGATGTCATGATGTCGTACATAAGAAGCCACAACGTTGGCCAC
1 TGATTTATTGATGACCAAGGTGTGATGTCACGATGTCATACATAAGAAGCCACAACGTTGGCCAC
* * **
10352 TATTTCATTGATTTAATTGGTGATTTAGGTGTGACATCATGACATCATGTGTAG
66 TATTTCATTGATCTAATAGGTGATCAAGGTGTGACATCATGACATCATGTGTAG
10406 GATATTGCGG
Statistics
Matches: 100, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
147 100 1.00
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (147 bp):
TGATTTATTGATGACCAAGGTGTGATGTCACGATGTCATACATAAGAAGCCACAACGTTGGCCAC
TATTTCATTGATCTAATAGGTGATCAAGGTGTGACATCATGACATCATGTGTAGAACGTTGCGAC
CTTGACTATTCTTTCAT
Found at i:14818 original size:31 final size:30
Alignment explanation
Indices: 14763--14820 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
14753 TAAGAAAATT
*
14763 AACAATAAAACAAAAGTTATACAATATTCA
1 AACAATAAAACAAAAGATATACAATATTCA
14793 AACAATAACAACAAAATGATA-ACAATAT
1 AACAATAA-AACAAAA-GATATACAATAT
14821 AATAGTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 14 0.56
32 3 0.12
ACGTcount: A:0.62, C:0.14, G:0.03, T:0.21
Consensus pattern (30 bp):
AACAATAAAACAAAAGATATACAATATTCA
Found at i:16168 original size:23 final size:23
Alignment explanation
Indices: 16142--16197 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
16132 ATTATAAAAA
16142 TATAAATTAATAC-C-TAATAAATT
1 TATAAATTAAT-CTCTTAA-AAATT
**
16165 TATATTTTAATCTCTTAAAAATT
1 TATAAATTAATCTCTTAAAAATT
16188 TAT-AATTAAT
1 TATAAATTAAT
16198 TCTAACCCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 6 0.22
23 18 0.67
24 3 0.11
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (23 bp):
TATAAATTAATCTCTTAAAAATT
Found at i:17257 original size:22 final size:19
Alignment explanation
Indices: 17231--17287 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 19
17221 TTTAAATTAA
*
17231 ATAAATTTGAATATATAAATAC
1 ATAAATTT-AATAT-GAAAT-C
17253 ATAAATATTAATATGAAATC
1 ATAAAT-TTAATATGAAATC
17273 ATATAATTTCAATAT
1 ATA-AATTT-AATAT
17288 TATATTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 6 0.19
21 12 0.39
22 11 0.35
23 2 0.06
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (19 bp):
ATAAATTTAATATGAAATC
Found at i:19489 original size:200 final size:202
Alignment explanation
Indices: 19123--19611 Score: 610
Period size: 200 Copynumber: 2.4 Consensus size: 202
19113 GTTAGTTCTA
* * * * ***
19123 TTTCTCCTTCTAGATCTCGCTGTTCGTTTCAAAGTTCATCGATATTTCCGGTTTTTTTTTTAGC-
1 TTTCTCCTTCTAGACCTCG-TATTCATTTCAAAGTTCATCAATATTTCC-GCCATTTTTTTA-CT
*
19187 TTGATTTGTATTAGTGTTTCTTTTCTGATTAATTTGTTCAATCTTTCGTTCTAGATCTCGCTATT
63 TTGATTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAA---TTCGTTCTAGATCTCGCTATT
* *
19252 CGTTTATATTTCCTTGTTTTTTAAACGATTTATAATAGTATTTCTTTGCTGATTAGTTTGAATTC
125 CATTTATATTTCCTTGTTTGTTAAACGATTTATAATAGTATTTCTTTGCTGATTAGTTTGAATTC
*
19317 ATTTTTAGCACAC
190 ATTTTGAGCACAC
* * *
19330 TTTCTCCTTCCAGACCTCGTTTTTCATTTCAAAGTTCATCCATATTTCC-CCATTTTTTTACTTT
1 TTTCTCCTTCTAGACCTCG-TATTCATTTCAAAGTTCATCAATATTTCCGCCATTTTTTTACTTT
* *
19394 CATTTGAATTAGTGTTTCTTTGCTGATTAATTTGTTCAA-TC-TTCTAGATCTCGCTATTCATTT
65 GATTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAATTCGTTCTAGATCTCGCTATTCATTT
** * *
19457 ATATTTCCTT-TTTGTTAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTGATTT
130 ATATTTCCTTGTTTGTTAA-ACGATTTATAATAGTATTTCTTTGCTGATTAGTTTGAATTCATTT
* *
19521 TGAGCTCAT
194 TGAGCACAC
* * * * * *
19530 TTTCTCCTTCTAGACCTCGTATTGATTTCGAAGTTCATCAACATTTCCTCTCCTTTTTTTAGTTT
1 TTTCTCCTTCTAGACCTCGTATTCATTTCAAAGTTCATCAATATTTCCGC-CATTTTTTTACTTT
19595 GATTTGTATTAGTGTTT
65 GATTTGTATTAGTGTTT
19612 GCTGGTTAAT
Statistics
Matches: 247, Mismatches: 31, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
199 31 0.13
200 97 0.39
201 29 0.12
204 1 0.00
205 46 0.19
207 43 0.17
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (202 bp):
TTTCTCCTTCTAGACCTCGTATTCATTTCAAAGTTCATCAATATTTCCGCCATTTTTTTACTTTG
ATTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAATTCGTTCTAGATCTCGCTATTCATTTA
TATTTCCTTGTTTGTTAAACGATTTATAATAGTATTTCTTTGCTGATTAGTTTGAATTCATTTTG
AGCACAC
Found at i:19873 original size:232 final size:224
Alignment explanation
Indices: 19583--20092 Score: 590
Period size: 232 Copynumber: 2.2 Consensus size: 224
19573 TTTCCTCTCC
* * * *
19583 TTTTTTTAGTTTGATTTGTATTAG---TGTTTGCTGGTTAATTTGAATTGATTTTTAGTTCAATT
1 TTTTTTTAGTTTGATTTGTATTAGTTTTCTTTGCTGATAAATTTGAATTGATTTGTAGTTCAATT
* * *
19645 TCTCGCTCTAGATCTCGCTATTCATTTCAAAGTTCGTCAATATTTCCTTCTTTTTTTAAAAAATA
66 TCTCACTCTAGATCTCGCTATTCATTTCAAAGTTCATC-A-ATTT--TTCCTTTTTT--AAAAT-
* *
19710 AAAATTGATTTGTGTTAATATTTCTTTGCTGAT-TATTTAAATTCATTTTAAGTTCAATT-TTTC
124 ----TTGATTTGTGTTAATATTTCTTTGCTGATGAATTTAAATTCATTTTAAGTTC-ATTGTGTC
19773 CTTCTAGA-CATCG-TTATTCATTTCAAAGTTCA-C-CTG-TG
184 CTTCTAGATC-TCGCTT-TTCATTTCAAAGTTCATCACTGATG
19811 TTTTTTTAGTTTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATTGATTTGTAGTTCAAT
1 TTTTTTTAGTTTGATTTGTATTAGT-TTTCTTTGCTGATAAATTTGAATTGATTTGTAGTTCAAT
* * * *
19876 TTCTCACTCTAGATCTCTCTATTCATTTCAAATTTCATCAGTTTTTCCTTTTTTAAAGTTTGATT
65 TTCTCACTCTAGATCTCGCTATTCATTTCAAAGTTCATCAATTTTTCCTTTTTTAAAATTTGATT
* * * * * *
19941 TGTGTTAGTATTTCTTTGGTGATGAATTTGAATTGATTTTTAGTTCATTGTGTCCTTCTTGATCT
130 TGTGTTAATATTTCTTTGCTGATGAATTTAAATTCATTTTAAGTTCATTGTGTCCTTCTAGATCT
* * *
20006 TGCTTTTCATTTCAAAGTTCATCAGTGTCATT
195 CGCTTTTCATTTCAAAGTTCATCACTG--ATG
20038 TTTTTTTAGTTTGATTTGTATTAGTGTTTCTTTGCTGATAAATTTGAATTGATTT
1 TTTTTTTAGTTTGATTTGTATTAGT-TTTCTTTGCTGATAAATTTGAATTGATTT
20093 CAAAGCAAAT
Statistics
Matches: 246, Mismatches: 23, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
221 30 0.12
222 46 0.19
223 4 0.02
224 2 0.01
226 4 0.02
227 55 0.22
228 33 0.13
230 3 0.01
231 1 0.00
232 68 0.28
ACGTcount: A:0.22, C:0.12, G:0.13, T:0.53
Consensus pattern (224 bp):
TTTTTTTAGTTTGATTTGTATTAGTTTTCTTTGCTGATAAATTTGAATTGATTTGTAGTTCAATT
TCTCACTCTAGATCTCGCTATTCATTTCAAAGTTCATCAATTTTTCCTTTTTTAAAATTTGATTT
GTGTTAATATTTCTTTGCTGATGAATTTAAATTCATTTTAAGTTCATTGTGTCCTTCTAGATCTC
GCTTTTCATTTCAAAGTTCATCACTGATG
Found at i:19956 original size:114 final size:112
Alignment explanation
Indices: 19460--20092 Score: 473
Period size: 114 Copynumber: 5.5 Consensus size: 112
19450 TTCATTTATA
* * * * *
19460 TTTCCTTTTTGTTAA-TTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTGATTTTGA
1 TTTCC-TTTT-TTAAGTTTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATTGATTTT-A
* * * *
19524 GCTCATTTTCTCCTTCTAGA-C-CTCGTATTGATTTCGAAGTTCATCAACATT
63 GTTCAATTTCTCCTTCTAGATCTCTC-TATTCATTTCAAAGTTCATC-A-ATT
* * * *
19575 TCCTCTCCTTTTTTTAGTTTGATTTGTATTAG----TGTTTGCTGGTTAATTTGAATTGATTTTT
1 T--T-TCCTTTTTTAAGTTTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATTGA-TTTT
* *
19636 AGTTCAATTTCTCGC-TCTAGATCTCGCTATTCATTTCAAAGTTCGTCAATATT
62 AGTTCAATTTCTC-CTTCTAGATCTCTCTATTCATTTCAAAGTTCATC-A-ATT
* * * * * *
19689 TCCTTCTTTTTTTAAAAAATAAAAATTGATTTGTGTTAATATTTCTTTGCTGAT-TATTTAAATT
1 T--TTCCTTTTTT---AAGT-----TTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATT
* * * *
19753 CATTTTAAGTTCAATTTTTCCTTCTAGA-CATCGT-TATTCATTTCAAAGTTCA-C-CTG
56 GATTTT-AGTTCAATTTCTCCTTCTAGATC-TC-TCTATTCATTTCAAAGTTCATCAATT
*
19809 TGT--TTTTTT-AGTTTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATTGATTTGTAGT
1 TTTCCTTTTTTAAGTTTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATTGATTT-TAGT
* *
19871 TCAATTTCTCAC-TCTAGATCTCTCTATTCATTTCAAATTTCATCAGTT
65 TCAATTTCTC-CTTCTAGATCTCTCTATTCATTTCAAAGTTCATCAATT
* * *
19919 TTTCCTTTTTTAAAGTTTGATTTGTGTTAGTATTTCTTTGGTGATGAATTTGAATTGATTTTTAG
1 TTTCCTTTTTT-AAGTTTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATTGA-TTTTAG
* * * *
19984 TTC-ATTGTGTCCTTCTTGATCT-TGCTTTTCATTTCAAAGTTCATCAGTGT
64 TTCAATT-TCTCCTTCTAGATCTCT-CTATTCATTTCAAAGTTCATCAAT-T
*
20034 CATTT--TTTTTT-AGTTTGATTTGTATTAGTGTTTCTTTGCTGATAAATTTGAATTGATTT
1 --TTTCCTTTTTTAAGTTTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATTGATTT
20093 CAAAGCAAAT
Statistics
Matches: 425, Mismatches: 51, Indels: 87
0.75 0.09 0.15
Matches are distributed among these distances:
107 28 0.07
108 49 0.12
109 4 0.01
110 3 0.01
112 11 0.03
113 92 0.22
114 113 0.27
115 13 0.03
116 11 0.03
117 21 0.05
118 4 0.01
120 2 0.00
121 12 0.03
123 7 0.02
124 46 0.11
125 9 0.02
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.52
Consensus pattern (112 bp):
TTTCCTTTTTTAAGTTTGATTTGTATTAGTATTTCTTTGCTGATAAATTTGAATTGATTTTAGTT
CAATTTCTCCTTCTAGATCTCTCTATTCATTTCAAAGTTCATCAATT
Found at i:20522 original size:188 final size:189
Alignment explanation
Indices: 20175--20532 Score: 476
Period size: 188 Copynumber: 1.9 Consensus size: 189
20165 TTGCTTTAAC
* * *
20175 TACTCTTAGTTTTATGAAAAAGAAAATTCTTTCCAGATCAGGAAGTTTTTTAAATTTGAATATGA
1 TACTCTTAGTTTTATGAAAAAGAAAA-T-TTTACAGATCAAGAAGTTTTTAAAATTTGAATATGA
* * *
20240 ATTTAAGATATTGATCTTCCTTGATTCATTCATTTGTGATTATTGTATGAAACTGAACATTGACT
64 ATTTAAGATATTGACCTTCCTTGATTCATTCATTTATGATTATTCTATGAAACTGAACATTGACT
* *
20305 GATTTGTTTGGTTGTGTCACTGATTTTAGATCATGGAATCGATTCTATCAGCTTTTAGAGT
129 AATTTGTTTGGTTGTGTCACTGATTTTAGATCACGGAATCGATTCTATCAGCTTTTAGAGT
20366 TACTCTTAGTTTTATG-AAAAGAAAA-TTTACAGATCAAGAA-TTTTTGAAAATTT-AATATGAA
1 TACTCTTAGTTTTATGAAAAAGAAAATTTTACAGATCAAGAAGTTTTT-AAAATTTGAATATGAA
* * *
20427 TTTAAGATATTGACCTTCCTATTGATTCATTGATTTATGATTATTCTAT-AGAATTGAACTTTGA
65 TTTAAGATATTGACCTTCC--TTGATTCATTCATTTATGATTATTCTATGA-AACTGAACATTGA
* * * *
20491 GTAATTTGTTTGGTTGTG-CTGCTGGTTTTAGATTACGGAATC
127 CTAATTTGTTTGGTTGTGTC-ACTGATTTTAGATCACGGAATC
20533 AACTGATTTC
Statistics
Matches: 147, Mismatches: 15, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
186 31 0.21
187 21 0.14
188 70 0.48
190 9 0.06
191 16 0.11
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.43
Consensus pattern (189 bp):
TACTCTTAGTTTTATGAAAAAGAAAATTTTACAGATCAAGAAGTTTTTAAAATTTGAATATGAAT
TTAAGATATTGACCTTCCTTGATTCATTCATTTATGATTATTCTATGAAACTGAACATTGACTAA
TTTGTTTGGTTGTGTCACTGATTTTAGATCACGGAATCGATTCTATCAGCTTTTAGAGT
Done.