Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012846.1 Kokia drynarioides strain JFW-HI SEQ_127860, 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: 29551
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Found at i:7263 original size:12 final size:12
Alignment explanation
Indices: 7248--7272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7238 TTCGGGAAGA
7248 CATCATTGAAAT
1 CATCATTGAAAT
7260 CATCATTGAAAT
1 CATCATTGAAAT
7272 C
1 C
7273 CTACAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (12 bp):
CATCATTGAAAT
Found at i:7467 original size:13 final size:13
Alignment explanation
Indices: 7433--7489 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
7423 TATCTCTTTT
*
7433 TCTTCCTTTTCATC
1 TCTTTCTTTTC-TC
*
7447 TTTTTCTTTTCTC
1 TCTTTCTTTTCTC
7460 TCTTTC-TTT-TC
1 TCTTTCTTTTCTC
*
7471 ACTTTCTTTTCTC
1 TCTTTCTTTTCTC
7484 T-TTTCT
1 TCTTTCT
7490 CTCATTTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
11 7 0.19
12 11 0.31
13 9 0.25
14 9 0.25
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTTCTTTTCTC
Found at i:7503 original size:24 final size:25
Alignment explanation
Indices: 7447--7505 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
7437 CCTTTTCATC
*
7447 TTTTTCTTTTCTCTCTTTCTTTTCA
1 TTTTTCTTTTCTCTCTTTCTTCTCA
*
7472 -CTTTCTTTTCTCT-TTTC-TCTCA
1 TTTTTCTTTTCTCTCTTTCTTCTCA
*
7494 TTTTTCCTTTCT
1 TTTTTCTTTTCT
7506 TTTTTTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 4 0.14
23 13 0.45
24 12 0.41
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTCTTTTCTCTCTTTCTTCTCA
Found at i:7508 original size:11 final size:11
Alignment explanation
Indices: 7445--7534 Score: 53
Period size: 11 Copynumber: 8.1 Consensus size: 11
7435 TTCCTTTTCA
7445 TCTTTTTCTTT
1 TCTTTTTCTTT
7456 TCTCTCTTTCTTT
1 TCT-T-TTTCTTT
**
7469 TCACTTTCTTT
1 TCTTTTTCTTT
*
7480 TCTCTTTTC-TC
1 TCT-TTTTCTTT
*
7491 TCATTTTTCCTT
1 TC-TTTTTCTTT
7503 TC--TTT-TTT
1 TCTTTTTCTTT
* *
7511 TCAATTTTATTT
1 TC-TTTTTCTTT
7523 TCTTTTTCTTT
1 TCTTTTTCTTT
7534 T
1 T
7535 TCCCTCGCTT
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
11 31 0.51
12 14 0.23
13 9 0.15
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:7509 original size:29 final size:30
Alignment explanation
Indices: 7445--7509 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
7435 TTCCTTTTCA
*
7445 TCTTTTTCTTTTCTCTCTTTCTTTTCACTT
1 TCTTTTTCTTTTCTCTCTATCTTTTCACTT
7475 TCTTTTCTCTTTTCTCTC-AT-TTTTC-CTT
1 TCTTTT-TCTTTTCTCTCTATCTTTTCACTT
7503 TCTTTTT
1 TCTTTTT
7510 TTCAATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 1 0.03
28 9 0.27
29 5 0.15
30 7 0.21
31 11 0.33
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (30 bp):
TCTTTTTCTTTTCTCTCTATCTTTTCACTT
Found at i:10597 original size:17 final size:17
Alignment explanation
Indices: 10577--10609 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10567 TTTAAGGACT
10577 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
10594 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
10610 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:10888 original size:50 final size:48
Alignment explanation
Indices: 10832--10956 Score: 121
Period size: 50 Copynumber: 2.5 Consensus size: 48
10822 AAGTTTGTAG
10832 CATAAATAATGACATGCATTAAGTAACTTAC-ATGTTAGTTAAATATGCAT
1 CATAAATAATGACATGCATTAAGTAAC-TACAATGTTAGTT-AA-ATGCAT
** * *
10882 CATAAATCCT-ATCATGCATTATGTAACTCCAATGTTAGTTAAATGCAT
1 CATAAATAATGA-CATGCATTAAGTAACTACAATGTTAGTTAAATGCAT
* *
10930 CATTAAATCAA-GTCATGCATTTAGTAA
1 CA-TAAAT-AATGACATGCATTAAGTAA
10957 TCCATTAGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
48 8 0.13
49 22 0.36
50 31 0.51
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (48 bp):
CATAAATAATGACATGCATTAAGTAACTACAATGTTAGTTAAATGCAT
Found at i:12679 original size:16 final size:16
Alignment explanation
Indices: 12658--12693 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
12648 ATCCTTTGCT
12658 GAAAATC-ATGTCTGAA
1 GAAAATCTA-GTCTGAA
12674 GAAAATCTAGTCTGAA
1 GAAAATCTAGTCTGAA
12690 GAAA
1 GAAA
12694 GGCTACAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (16 bp):
GAAAATCTAGTCTGAA
Found at i:13245 original size:34 final size:34
Alignment explanation
Indices: 13141--13251 Score: 86
Period size: 34 Copynumber: 3.2 Consensus size: 34
13131 AGGAAATTGA
* *
13141 AAAGGAAAGAAAAGGAGAATGTGTAAAAAAAGAA--
1 AAAGGAAAGAAAAAGA-AAT-TGAAAAAAAAGAATG
* * ***
13175 AAA-GAAGATAAAATAGATATT-AAAAAAAATTGTG
1 AAAGGAA-AGAAAA-AGAAATTGAAAAAAAAGAATG
13209 AAAGGAAAGAAAAAGAAATTGAAAAAAAAGAATG
1 AAAGGAAAGAAAAAGAAATTGAAAAAAAAGAATG
13243 AAAGTGAAA
1 AAAG-GAAA
13252 TTCCAAAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
32 7 0.12
33 10 0.17
34 32 0.55
35 9 0.16
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (34 bp):
AAAGGAAAGAAAAAGAAATTGAAAAAAAAGAATG
Found at i:15006 original size:50 final size:50
Alignment explanation
Indices: 14922--15055 Score: 139
Period size: 50 Copynumber: 2.7 Consensus size: 50
14912 TGACATCCAT
* * * *
14922 TAACTCTCATGATTAGTTAAGTTTGCAGCATAAATAATGA-CATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCATAAATAAT-ATCATGCATTAAG
* ** *
14973 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAG
*
15023 TAACTCCCATGTTAGTT-AA-ATGCATCATTAAAT
1 TAACTCACATGTTAGTTAAATATGCATCA-TAAAT
15056 TAATCCATTA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 8 0.11
49 8 0.11
50 46 0.65
51 9 0.13
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATCATAAATAATATCATGCATTAAG
Found at i:16396 original size:32 final size:32
Alignment explanation
Indices: 16360--16422 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
16350 GCCATCCATA
* * *
16360 CATGTACCTGAAATATATTAATCATCTAATTG
1 CATGTACCTGAAACACATTAATCAGCTAATTG
16392 CATGTACCTGAAACACATTAATCAGCTAATT
1 CATGTACCTGAAACACATTAATCAGCTAATT
16423 AATTTCAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (32 bp):
CATGTACCTGAAACACATTAATCAGCTAATTG
Found at i:17955 original size:216 final size:215
Alignment explanation
Indices: 16885--18196 Score: 1467
Period size: 216 Copynumber: 6.1 Consensus size: 215
16875 CCGTGGCCGT
* * *
16885 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AGGTTTTGCTGTTTGAATTAAAAACTTATT
1 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
* * * *
16949 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTAGTCAAACTTTTACGAGT
66 TACGTGAGAATT-TTTTTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGT
** * * * * *
17014 TCTTTCGTATCTTTGGTTCCTTAAAGTATTCAAGATGATCAATTCCTTCGAGCAATTCTCTAAAC
130 TCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGAAC
* * * * *
17079 ATTCGATTCTTGAGAAATAGC
195 ATTCCATGCTCGGGAAATCGC
* * * * * * *
17100 AGCATTTGGTCTAAAGAGTTTGTCATTTTGAAAACAAGTTCTGGCCATTGAATCAAAAACTTATT
1 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
* * * *
17165 TATGTGAGAA-TTGTTTCTCTTGGTTCTTGGACAAACTTCCGAACTTGTCAAACTTTTACGAGCT
66 TACGTGAGAATTTTTTTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTT
* * * * *
17229 CTTTTATAACTTCGATTCCTTACAGTATTCAAGACGAT-ACATTCCTTTGAGCAACTTTCTTAAC
131 CTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCA-ATTCCTTCGAGCAATTTTCTGAAC
* **
17293 ATTCTATGCTCGAAAAATCGC
195 ATTCCATGCTCGGGAAATCGC
* * * * *
17314 ATAATTT-TTCTAAATTGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAAACTTATT
1 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
* * * * *
17378 TACGTGAGGATTGTTTCTCTCTCTTTGTTCTTGGATGAACTTCCAAACTTTTCAAACTTTTACGA
66 TACGTGAGAATT-TTT-T-TCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGA
* * * *
17443 GTACTTTTATAACTTCGGTACCTTAAAGTATTCAAGAAC-ATCCATTCCTATC-AGTAATTTT-T
128 GTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAG-ACGATCAATTCCT-TCGAGCAATTTTCT
* *
17505 GAACATTCCATTCTCGGGTAATCGC
191 GAACATTCCATGCTCGGGAAATCGC
* * * * * **
17530 ATCATTTAGTCTAAATAGTTTTTCTTTTTGTAAACAAGTATTGGTCTTTAAAGCAAAAACTTATT
1 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
* * * * * * *
17595 TACGTGAGAA-TTGTTTCTCTTGGCTGTTGGATGAACTTCCGAACTTTTTAAACTTTTATGAGTT
66 TACGTGAGAATTTTTTTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTT
* * * * *
17659 CTTTTATAACTT-GGTTCCTTACAA-TATTCAAGATGACCCATTCCTTCGAGCTATTTTCTAAAC
131 CTTTTATAACTTCGGTTCCTTA-AAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGAAC
**
17722 ATTCCATGCTCGGGAAATCAT
195 ATTCCATGCTCGGGAAATCGC
* * * * *
17743 ATCATTTTGTCTAAATAGTTTGTCATTTTATGAACAACTTTTGGTCTTTGAATTAAATACTTATT
1 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
* * * *
17808 TACGCGAGAATTATTTTTCTTTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTATGAGT
66 TACGTGAGAATT-TTTTTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGT
* * ** *
17873 TCTTTTATAATTTCAGTTCCAAAAAGTATTCAAGACGATCAATTCCTTCGACCAATTTTCTGAAC
130 TCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGAAC
17938 ATTCCATGCTCGGGAAATCGC
195 ATTCCATGCTCGGGAAATCGC
* *
17959 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGGTTTTGTTGTTTGAATTAAAAACTTAT
1 ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAA-GTTTTGGTCTTTGAATTAAAAACTTAT
* * * * *
18023 TTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCAAACTAGTCAAACTTTTATGAG
65 TTACGTGAGAATT-TTTTTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAG
* * * * * *
18088 TTCTTTCATATCTTCAGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTTTGAA
129 TTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGAA
* * * * *
18153 CATTCGATTCTTGAGAAATAGC
194 CATTCCATGCTCGGGAAATCGC
* *
18175 AGCATTTGGTCTAAAGAGTTTG
1 ATCATTTGGTCTAAATAGTTTG
18197 ATATGAGCTC
Statistics
Matches: 920, Mismatches: 158, Indels: 37
0.83 0.14 0.03
Matches are distributed among these distances:
211 3 0.00
212 32 0.03
213 196 0.21
214 121 0.13
215 96 0.10
216 324 0.35
217 145 0.16
218 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (215 bp):
ATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
TACGTGAGAATTTTTTTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTTACGAGTT
CTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGAACA
TTCCATGCTCGGGAAATCGC
Found at i:18026 original size:429 final size:428
Alignment explanation
Indices: 16884--18157 Score: 1560
Period size: 430 Copynumber: 3.0 Consensus size: 428
16874 GCCGTGGCCG
* * *
16884 TATCATTTGGTCTAAATAGTTTGTCATTTTGTAA-AAGGTTTTGCTGTTTGAATTAAAAACTTAT
1 TATCATTTTGTCTAAATAGTTTGTCATTTTGTAACAA-GTTTTGGTCTTTGAATTAAAAACTTAT
* * *
16948 TTACGTGAGAATTATTTCTCTCTTGGTTCTTGGATGAACTTTCGAACTAGTCAAACTTTTACGAG
65 TTACGTGAGAATTATTTTTCTTTTGGTTCTTGGATGAACTTTCGAACTTGTCAAACTTTTACGAG
* * * *
17013 TTCTTTCGTAT-CTTT-GGTTCCTTAAAGTATTCAAGATGATCAATTCCTTCGAGCAATTCTCTA
130 TTCTTT--TATAATTTCGGTTCCTTAAAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTG
* * * * * * * *
17076 AACATTCGATTCTTGAGAAATAGCAGCATTTGGTCTAAAGAGTTTGTCATTTTGAAAACAAGTTC
193 AACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAGTTT
* * * *
17141 TGGCCATTGAATCAAAAACTTATTTATGTGAGAATTGTTTCTCTTGGTTCTTGGACAAACTTCCG
257 TGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTCTTGGACGAACTTCCG
* * * * * *
17206 AACTTGTCAAACTTTTACGAGCTCTTTTATAACTTCGATTCCTTACAGTATTCAAGACGATACAT
322 AACTTGTCAAACTTTTATGAGTTCTTTTATAACTTCGGTTCCTTACAATATTCAAGATGATCCAT
* * * * *
17271 TCCTTTGAGCAACTTTCTTAACATTCTATGCTCGAAAAATCG
387 TCCTTCGAGCAATTTTCTAAACATTCCATGCTCGAAAAATCA
* * * * *
17313 CATAATTTT-TCTAAATTGTTTGTTATTTTGTAAACAAGTTTTGGTCTTTAAATTAAAAACTTAT
1 TATCATTTTGTCTAAATAGTTTGTCATTTTGT-AACAAGTTTTGGTCTTTGAATTAAAAACTTAT
* * * * *
17377 TTACGTGAGGATTGTTTCTCTCTCTTT-GTTCTTGGATGAACTTCCAAACTTTTCAAACTTTTAC
65 TTACGTGAGAATTATTT-T-TCT-TTTGGTTCTTGGATGAACTTTCGAACTTGTCAAACTTTTAC
* * * * *
17441 GAGTACTTTTATAACTTCGGTACCTTAAAGTATTCAAGAAC-ATCCATTCCTATC-AGTAATTTT
127 GAGTTCTTTTATAATTTCGGTTCCTTAAAGTATTCAAG-ACGATCAATTCCT-TCGAGCAATTTT
* * * *
17504 -TGAACATTCCATTCTCGGGTAATCGCATCATTTAGTCTAAATAGTTTTTCTTTTTGTAAACAAG
190 CTGAACATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAA-AAG
* * * * * *
17568 TATTGGTCTTTAAAGCAAAAACTTATTTACGTGAGAATTGTTTCTCTTGGCTGTTGGATGAACTT
254 TTTTGGTCTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTCTTGGACGAACTT
* * *
17633 CCGAACTTTTTAAACTTTTATGAGTTCTTTTATAACTT-GGTTCCTTACAATATTCAAGATGACC
319 CCGAACTTGTCAAACTTTTATGAGTTCTTTTATAACTTCGGTTCCTTACAATATTCAAGATGATC
* **
17697 CATTCCTTCGAGCTATTTTCTAAACATTCCATGCTCGGGAAATCA
384 CATTCCTTCGAGCAATTTTCTAAACATTCCATGCTCGAAAAATCA
* * *
17742 TATCATTTTGTCTAAATAGTTTGTCATTTTATGAACAACTTTTGGTCTTTGAATTAAATACTTAT
1 TATCATTTTGTCTAAATAGTTTGTCATTTTGT-AACAAGTTTTGGTCTTTGAATTAAAAACTTAT
* * *
17807 TTACGCGAGAATTATTTTTCTTTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTATGAG
65 TTACGTGAGAATTATTTTTCTTTTGGTTCTTGGATGAACTTTCGAACTTGTCAAACTTTTACGAG
* ** *
17872 TTCTTTTATAATTTCAGTTCCAAAAAGTATTCAAGACGATCAATTCCTTCGACCAATTTTCTGAA
130 TTCTTTTATAATTTCGGTTCCTTAAAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGAA
*
17937 CATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAGGTTTTG
195 CATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAA-GTTTTG
* * * * *
18002 TTGTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTTCA
259 GTCTTTGAATCAAAAACTTATTTACGTGAGAATTG-TT-TCTCTTGGTTCTTGGACGAACTTCCG
* * * *
18067 AACTAGTCAAACTTTTATGAGTTCTTTCATATCTTCAGTTCCTTA-AAGTATTCAAGATGATCCA
322 AACTTGTCAAACTTTTATGAGTTCTTTTATAACTTCGGTTCCTTACAA-TATTCAAGATGATCCA
* *
18131 TTCCTTCGAGCAATTTTTTGAACATTC
386 TTCCTTCGAGCAATTTTCTAAACATTC
18158 GATTCTTGAG
Statistics
Matches: 710, Mismatches: 116, Indels: 35
0.82 0.13 0.04
Matches are distributed among these distances:
427 7 0.01
428 105 0.15
429 206 0.29
430 208 0.29
431 132 0.19
432 52 0.07
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (428 bp):
TATCATTTTGTCTAAATAGTTTGTCATTTTGTAACAAGTTTTGGTCTTTGAATTAAAAACTTATT
TACGTGAGAATTATTTTTCTTTTGGTTCTTGGATGAACTTTCGAACTTGTCAAACTTTTACGAGT
TCTTTTATAATTTCGGTTCCTTAAAGTATTCAAGACGATCAATTCCTTCGAGCAATTTTCTGAAC
ATTCCATTCTCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAAAAGTTTTGGT
CTTTGAATCAAAAACTTATTTACGTGAGAATTGTTTCTCTTGGTTCTTGGACGAACTTCCGAACT
TGTCAAACTTTTATGAGTTCTTTTATAACTTCGGTTCCTTACAATATTCAAGATGATCCATTCCT
TCGAGCAATTTTCTAAACATTCCATGCTCGAAAAATCA
Found at i:18789 original size:80 final size:79
Alignment explanation
Indices: 18656--18812 Score: 260
Period size: 80 Copynumber: 2.0 Consensus size: 79
18646 ACTAATTTCA
* * *
18656 TTTTAACTCTTGTAGGAAAGCTAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGTTAAAAAG
1 TTTTAACTCTTGTAGGAAAGCCAATGAGTCATGTCTCTTCAATAGGATCTGATGTAGCTAAAAAG
*
18721 GCATGGCAATTTCGT
66 GCATAGC-ATTTCGT
*
18736 TTTTAACTCTTGTAGGAAAGCCAATGAGTCATGTCTCTTCAATAGGATCTGATGTAGCTGAAAAG
1 TTTTAACTCTTGTAGGAAAGCCAATGAGTCATGTCTCTTCAATAGGATCTGATGTAGCTAAAAAG
18801 GCATAGCATTTC
66 GCATAGCATTTC
18813 TCCTTAATGA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
79 5 0.07
80 67 0.93
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (79 bp):
TTTTAACTCTTGTAGGAAAGCCAATGAGTCATGTCTCTTCAATAGGATCTGATGTAGCTAAAAAG
GCATAGCATTTCGT
Found at i:25034 original size:78 final size:79
Alignment explanation
Indices: 24918--25074 Score: 237
Period size: 78 Copynumber: 2.0 Consensus size: 79
24908 TACAAACTCT
* *
24918 AATTTCATTTTAACTCTTATAGGGAAGCTAATGAGTCATGTCTCTTCATTAGGATCTGATGTAG-
1 AATTTCATTTTAACTCTTATAGGAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGC
*
24982 T-TAAAGGCATGGC
66 TGAAAAGGCATGGC
* * *
24995 AATTTCATTTTTAACTTTTGTAGGAAAGCCAATGTGTCATGTCTCTTCATTAGGATCTGATGTAG
1 AATTTCA-TTTTAACTCTTATAGGAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAG
25060 CTGAAAAGGCATGGC
65 CTGAAAAGGCATGGC
25075 GTTTCTCCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
77 7 0.10
78 52 0.73
79 1 0.01
80 11 0.15
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (79 bp):
AATTTCATTTTAACTCTTATAGGAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGC
TGAAAAGGCATGGC
Found at i:25585 original size:48 final size:48
Alignment explanation
Indices: 25515--25627 Score: 181
Period size: 48 Copynumber: 2.4 Consensus size: 48
25505 TTAATGCAAG
* *
25515 GCATTTAACAAACAAAATAGTTAATAATGCATATTACTAAACAAAGAT
1 GCATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGAT
* *
25563 GCATTTAACAAACATAACAGTTAATAATGTAGATTACTAAACAAAGAT
1 GCATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGAT
*
25611 GCATTTAACAAAAAAAA
1 GCATTTAACAAACAAAA
25628 AACACTTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (48 bp):
GCATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGAT
Found at i:26317 original size:214 final size:214
Alignment explanation
Indices: 25943--29551 Score: 3968
Period size: 216 Copynumber: 16.9 Consensus size: 214
25933 CTCACATTAG
* * *
25943 AGTTTGTCATTTTGTAAATAGGTTTTGTTAC-TTGAATTAAAAACTTATTTACGTGAGAATTGTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGT-CTTTGAATTAAAAACTTATTTACGTGAGAATTG-T
* *
26007 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTAGTCAAACTTTTACGAGTT-TTTTCATATCTTC
64 T-TCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTT-ATAACTTC
* * * *
26071 GGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTCTGAACATTCGATTCTTGAG
127 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAG
* * *
26136 AAATAGCAGCATTTGGTCTAAAG
192 AAATCGCATCATTTGGTCTAAAT
* * *
26159 AGTTTTTCATTTTG-AGAACAAGTTTTGGTCTTTGAATCAAAAACTTATTTATGTGAGAATTGTT
1 AGTTTGTCATTTTGTA-AACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * *
26223 TCGCTTGGTTCTTGGACAAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGT
65 TCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGT
* * * * * * *
26288 TCCTTACAGTATTCAAGACGATACATTCCTTCGAGCAACTTTCTTAACATTCTATGCTCAAAAAA
130 TCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAA
* *
26353 TCGCATTATTT-TTCTAAAT
195 TCGCATCATTTGGTCTAAAT
* *
26372 TGTTTGTCATTTTGTAAACAAGTTTT-GTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TT
* * * * *
26436 CTCTCCCTTTGTTCTTGGACGAACTTCCAAACGTT-TCAAACCTTTACGAGTTCTTTTATAACTC
65 -TCT--CTTGGTTCTTGGACGAACTTTCGAAC-TTGTCAAACTTTTACGAGTTCTTTTATAACTT
* *
26500 CGGTTCCTTGAAGTATTCAAGAAC-ATCCATTCCTTTC-AGCAA-TTT-TGAACATTCCATTCTC
126 CGGTTCCTTAAAGTATTCAAG-ACGATCCATTCC-TTCGAGCAATTTTCTGAACATTCCATGCTC
* * * *
26561 GGGCAATTGCATCATTTAGTCTAAAT
189 GAGAAATCGCATCATTTGGTCTAAAT
* * * * *
26587 AGTTT-TTAGTCTTGTAAACAAGTTTTGGTCTTTAAAGTGAAAACTTATTTACGTGAGAATTGTT
1 AGTTTGTCA-TTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * * * * *
26651 TCTCTTGGCTGTTGGATGAACTTCCGAACTTTTTAAACTTTTACGAGTTCTTTTATAACTT-GGT
65 TCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGT
* * * * *
26715 TCCTTACAGTTTTCAAGATGATCCATTCCTTCGAGCTATTTTCTGAACATT-CATGCTCGGGAAA
130 TCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAA
* * *
26779 TCACATAATTTTGTCTAAAT
195 TCGCATCATTTGGTCTAAAT
* * ** * * **
26799 AGTTTATCATTTTGTGAACAACCTTTGCTCTTTGAATTAAATACTTATTTACACGAGAATTGATT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TT
* * * *
26864 CTCTTTTAGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAATTTCAG
65 -TCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
* * * *
26929 TTCCATAAAGCATTCAAGACGATCCATTCCTTTGAGCAATTTTTTGAACATTCCATGCTCG-GAA
129 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAG-A
26993 AATCGCATCATTTGG-CTAAAT
193 AATCGCATCATTTGGTCTAAAT
* *
27014 AGTTTGTCATTTTGTAAA-AAGGTTTTGTTGC-TTGAATTATAAACTTATTTACGTGAGAATTGT
1 AGTTTGTCATTTTGTAAACAA-GTTTTGGT-CTTTGAATTAAAAACTTATTTACGTGAGAATTG-
* * * * *
27077 TTCTCTCTTGGTTATTGGACGAACTTTCGAACTAGACAAACTTTTACGAGTTCTTTCATATCTTC
63 TT-TCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* * ** * *
27142 GGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGTAATTTTCTGAACATTCGGTTCTTGAG
127 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAG
* * *
27207 AAATAGCAGCATTTGGTCTAAAG
192 AAATCGCATCATTTGGTCTAAAT
* * * * *
27230 AGTTTGTCATTTTGAAAAGAAGTTTTGGTCTTTGAATCAGAAACTTATTTACGAGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * *
27295 CTCTTGGTTCTTGGACAAACTTCCAAACTTGTCACACTTTTACGAGTTCTTTTATAACTTCGGTT
66 CTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTT
* * * * * * * * * *
27360 CCTTACAGTATTCAAGACGATGCATTCCTTCTAACAACTTTCTTAACATTCTATGCTAGAAAAAA
131 CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAAT
*
27425 CGCATCATTT-TTCTAAAT
196 CGCATCATTTGGTCTAAAT
* * *
27443 TGTTTGTCATTTTGTAAACAAGTTATGGTATTT---TT-AAAACTTATTTACGTGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG--T
* * * * * *
27504 CTCTCTCTTTGTTCTTGGATGAACTTCCAAACTTTTCAAACTTTTACGAGTTCATTTATAAC-TC
64 -T-TCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* * * * * *
27568 TGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTT-TGAAAATTTCATTCTCGG
127 -GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGA
*
27632 GAAATCGCATCATTTAGTCTAAAT
191 GAAATCGCATCATTTGGTCTAAAT
* * * * * ** * * * * *
27656 AGTTCT-TAATTTTGTAAACGAGTTTTGATCATTAAAACAAGAACATATTTTCCTGAGGATT-TT
1 AGTT-TGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * * * *
27719 T-TCTTGGCTGTTTGACGAAC-TTCAGAACATCTCAAACTTTTACGAGTTCTTTTATAACTT-GG
65 TCTCTTGGTTCTTGGACGAACTTTC-GAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
** * *
27781 TTCCTTGCAGTATTCAAGACGATCCATTCCATCAAGCAATTTTCTGAACATTCCATGCTCG-GAA
129 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAA
27845 ATCGCATCATTTGGTCTAAAT
194 ATCGCATCATTTGGTCTAAAT
* * * * *
27866 AATTTGTCATTTTGTAAAAAACTTTTGGTCTTTGAATTAAATACTTATTTACGCGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * * * * *
27931 CTCTTTTAGCTCTTGGACGAACTTCCGAACTTGTTAAACTTTTACAAGTTCTTTTATAATTTCAG
66 CTC--TTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
* * * *
27996 TTCCATAAAGCATTCAAGATGATCCATTCCTTCGAGCAATTTT-TCGAACATTCCATGCTCGAAA
129 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCTCGAGA
*
28060 AATTGCATCATTTGGTCTAAAT
193 AATCGCATCATTTGGTCTAAAT
* * *
28082 AGTTTGTCATTTTGTAAA-AAGTTTTGTTGC-TTAAATTAAAAACTTATTTAAGTGAGAATTGTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGT-CTTTGAATTAAAAACTTATTTACGTGAGAATTG-T
* * * *
28145 TCTCTCTTGGTTCTTGGACGAACTTTCGAACTAGTCAAACTTTTACGAGTTCTTTCATATCGTCG
64 T-TCTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCG
* * * *
28210 GTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTCTGAACATTCGATTCTTGAGA
128 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGA
* * * *
28275 AATAGCAGCATTTGGCCTAAAG
193 AATCGCATCATTTGGTCTAAAT
* * *
28297 AGTTTGTCATTTTGAAAACAAGTTTTGGTCTTTGAATCAGAAACTTATTTACGTGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * * *
28362 CTCTTAGTTCTTGGACGAACTTTCGAACTTGTAAAACTTTTACTAATTCTTTTATAACTCCGGTT
66 CTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTT
* * * * * * * * *
28427 CCTTACAGAATTCAAGATGATACATTCCTTCTAGCAACTTTCTTAACATTCTATGCTCGAAAAAT
131 CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAAT
*
28492 CGCATCATTT-TTCTAAAT
196 CGCATCATTTGGTCTAAAT
* *
28510 TGTTTGTCATTTTGTAAACAAGTTTT-GTCTTTAAATTAAAAACTTATTTACGTGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TT
* * * * * *
28574 CTCTCACTTTGTTCTTGGACGAACTTCCAAACTTTTCAAACCTTTACGAGTTCTTTTATAACTCC
65 -TCT--CTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* * * *
28639 GGTTCCTTGAAGTATTCAAGAAC-ATCTATTTCTTTC-AGCAA-TTT-TGAACATTCCATTCTCG
127 GGTTCCTTAAAGTATTCAAG-ACGATCCA-TTCCTTCGAGCAATTTTCTGAACATTCCATGCTCG
* * *
28700 GGTAATCGCATCATTTAGTCTAAAT
190 AGAAATCGCATCATTTGGTCTAAAT
* * * * * *
28725 AGTTTTTCATCTTGTAAAGAAGTTTTGGTCTTTAAAGTGAAAACTTATTTACGTGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * * * **
28790 CTCTTGGCTGTTGGATGAACTTTTGAACTT-TTTAA---TTACGAGTTCTTTTATAACTT-GGTT
66 CTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTT
* ** *
28850 CCTTACAA-TACTCAAGATTATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGGGAAA
131 CCTTA-AAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAA
*
28914 TTGCATCATTTGGTCTAAAT
195 TCGCATCATTTGGTCTAAAT
* * * * * *
28934 AGTTTGTCACTTTGCAAAAAACTTTTGGTCTTTGAATTAAATACTTATTTATGTGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* * **
28999 CTCTTTCGGTTCTTGGACGAACTTTCGAACTTATCAAACTTTTACGAGTTCTTTTATAATTTTAG
66 CTC-TT-GGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
* * * *
29064 TTCCATAATGTATTCAAGACGATCCATTCCTTCGAGCTATTTT-TCGAGCATTCCATGCTCG-GA
129 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCT-GAACATTCCATGCTCGAG-
* *
29127 AAATCGCATCATTTGGTCCACAT
192 AAATCGCATCATTTGGTCTAAAT
* *
29150 AGTTTGTCATTTTGTAAA-AAGGTTTTGTTGC-TTGAATTAAAAACTTATTTACGTGAGAATTAT
1 AGTTTGTCATTTTGTAAACAA-GTTTTGGT-CTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * * * *
29213 TTCGCTCTTGGTTCTTGGACGAACTTTTGAACTAGTCAAGCTTTTACGAGTTCTTTCATATCTTC
64 TT--CTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTC
* * * *
29278 GGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTCTGAACATTCGATTCTTGAG
127 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAG
* * *
29343 AAATAGCAGCATTTGGTCTAAAG
192 AAATCGCATCATTTGGTCTAAAT
* * * * * **
29366 AGTTTGTCATTTTGAAAATAAGTTTTGGTCTTTGAATCAGAAACATATTTACAAGAGAATTGTTT
1 AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
* *
29431 CTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAAATTTTACGAGTTCTTTTATAACTTCGGTT
66 CTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTT
* * * * * *
29496 CCTTACAGTATTCAAGACGATACATTCCTTCTAGCAACTTTCTTAACATTCTATGC
131 CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGC
Statistics
Matches: 2837, Mismatches: 465, Indels: 184
0.81 0.13 0.05
Matches are distributed among these distances:
206 7 0.00
207 24 0.01
208 25 0.01
209 117 0.04
210 113 0.04
211 118 0.04
212 243 0.09
213 230 0.08
214 627 0.22
215 559 0.20
216 727 0.26
217 44 0.02
218 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (214 bp):
AGTTTGTCATTTTGTAAACAAGTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTT
CTCTTGGTTCTTGGACGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGGTT
CCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGAGAAAT
CGCATCATTTGGTCTAAAT
Done.