Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1728
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: 27539
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:156 original size:26 final size:28
Alignment explanation
Indices: 109--164 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 28
99 CGTTTTCAGA
109 TAACGAAATTATATATAAAAGTTCTCCG
1 TAACGAAATTATATATAAAAGTTCTCCG
137 TAACGAAA-T-TATATAAAAGTTCTCCG
1 TAACGAAATTATATATAAAAGTTCTCCG
163 TA
1 TA
165 CTAGGATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 19 0.68
27 1 0.04
28 8 0.29
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (28 bp):
TAACGAAATTATATATAAAAGTTCTCCG
Found at i:2388 original size:2 final size:2
Alignment explanation
Indices: 2381--2405 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2371 ATTGGGAAAG
2381 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2406 AAAAGGCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3552 original size:21 final size:21
Alignment explanation
Indices: 3528--3568 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3518 AAAAAATTAT
3528 TTTAT-ATTAATATCTAAATAG
1 TTTATAATTAA-ATCTAAATAG
*
3549 TTTATAATTAAATTTAAATA
1 TTTATAATTAAATCTAAATA
3569 AAATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTATAATTAAATCTAAATAG
Found at i:5759 original size:15 final size:15
Alignment explanation
Indices: 5739--5769 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5729 TATCCCAGAT
5739 TGTATCGATACAATA
1 TGTATCGATACAATA
5754 TGTATCGATACAATA
1 TGTATCGATACAATA
5769 T
1 T
5770 TAATGTATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (15 bp):
TGTATCGATACAATA
Found at i:9591 original size:13 final size:13
Alignment explanation
Indices: 9573--9597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9563 CAAAGATCAG
9573 TGTATCGATACAA
1 TGTATCGATACAA
9586 TGTATCGATACA
1 TGTATCGATACA
9598 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:9675 original size:33 final size:33
Alignment explanation
Indices: 9638--9704 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
9628 AGTAGCTTAA
9638 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
9671 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
9704 A
1 A
9705 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:9678 original size:13 final size:13
Alignment explanation
Indices: 9660--9684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9650 CAAAAAAATA
9660 TGTATCGATACAT
1 TGTATCGATACAT
9673 TGTATCGATACA
1 TGTATCGATACA
9685 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11828 original size:51 final size:51
Alignment explanation
Indices: 11759--11889 Score: 147
Period size: 51 Copynumber: 2.6 Consensus size: 51
11749 AGTAAATGTG
* * * * * *
11759 TCGATACATGTGTGAATGTATCGATACCTTTTGTTTTTTTA-TGCAGATGCA
1 TCGATACATTTTTCAATGTATCGATACATTCTGTGTTTTTACT-CAGATGCA
* *
11810 TCGATACATTTTTCAATGTATCGATACATTCTGTGTTTTTACTTAGATGTA
1 TCGATACATTTTTCAATGTATCGATACATTCTGTGTTTTTACTCAGATGCA
* * *
11861 TCGACACATTTTTCAATATATCAATACAT
1 TCGATACATTTTTCAATGTATCGATACAT
11890 CTAGTTAATT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
51 67 0.99
52 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (51 bp):
TCGATACATTTTTCAATGTATCGATACATTCTGTGTTTTTACTCAGATGCA
Found at i:12328 original size:28 final size:28
Alignment explanation
Indices: 12295--13142 Score: 798
Period size: 28 Copynumber: 30.0 Consensus size: 28
12285 CAACCACATT
* * *
12295 AGTCAGTGGCACCCTTTCAAAGTCCATA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
*
12323 AGTCAGTGGCA-CCCTTCAAAAGCCCACA
1 AGTCAGTGGCATCCTTTC-AAAGCCCACA
* *
12351 AGTCAGTGGCATCCCTCTCAAAGTCCACA
1 AGTCAGTGGCAT-CCTTTCAAAGCCCACA
*
12380 AGTCGGTGGCA-CCTTTCCAAAGCCCACA
1 AGTCAGTGGCATCCTTT-CAAAGCCCACA
* *
12408 AGTTAGTGGCATCTTTTTCAAAGCCCACA
1 AGTCAGTGGCATC-CTTTCAAAGCCCACA
* * *
12437 AGTCAGTTGCATCCTTTCAAAGCCTATA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * *
12465 AGTCAATAGCA-CCATTTCAAAGCCCATA
1 AGTCAGTGGCATCC-TTTCAAAGCCCACA
12493 AGTCAGTGGCATCCTTTCAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * *
12521 AGTTAATGGCA-CCTTTCCAAAGCCCACC
1 AGTCAGTGGCATCCTTT-CAAAGCCCACA
* **
12549 AGTCAATAACATCCTTTTCAAAGCCCACA
1 AGTCAGTGGCATCC-TTTCAAAGCCCACA
*
12578 AGTTAGTGGCATCCTTTCAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
12606 AGTCAGTGGTC-TCCTTTCAAAGCCCACA
1 AGTCAGTGG-CATCCTTTCAAAGCCCACA
* * *
12634 AGTCAGTGGCATCCTTTCAAAACCTATA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* *
12662 AGTCTGTAGCATCCTTTCAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * * *
12690 AGTTAGTGGTATCCTTTTAAAGCCCATA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
12718 AGGT-AGTGGCATCCTTTCAAAGCCCACA
1 A-GTCAGTGGCATCCTTTCAAAGCCCACA
* * *
12746 AGACAGTGGCATCCTTTTAAAGCTCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * * * *
12774 AATCAATGGTATCCTTCCAAAGCCCATA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * * *
12802 AGTTAGTGGCACCCTTCCAAAGCCTACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
*
12830 AGTTAGTGGCA-CCTTTTTCAAAGCCCACA
1 AGTCAGTGGCATCC--TTTCAAAGCCCACA
*
12859 AGTCAGTGACATCCTTTCAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * * * *
12887 AGTTAGTGGTACCCTTTTAAAGCTCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
** * * *
12915 AGTTGGTGGCATCTTTTTAAAGCCCATA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * * *
12943 AGTCAGTAGTATCCTTCCAAAG-CCAGA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * *
12970 AATCAGTGGCACCCTTTCAAAGCTCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * *
12998 AGTTAGTGGCACCCTTTTCAAAGCCCACG
1 AGTCAGTGGCATCC-TTTCAAAGCCCACA
*
13027 AGTCAGTGGCATCC-TTCTAAAGCCCATA
1 AGTCAGTGGCATCCTTTC-AAAGCCCACA
* * * *
13055 AGTTATTAGCATCCTTTCAAAGCTCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
*
13083 AGTCAGTGGC-GCCTTTTCAAAGCCTACACA
1 AGTCAGTGGCATCC-TTTCAAAGCC--CACA
* * *
13113 AGTCGGTGGCAACCCATTCTAAAGCCCACA
1 AGTCAGTGGC-ATCCTTTC-AAAGCCCACA
13143 CAAGTTAGTG
Statistics
Matches: 670, Mismatches: 122, Indels: 54
0.79 0.14 0.06
Matches are distributed among these distances:
27 46 0.07
28 467 0.70
29 117 0.17
30 29 0.04
31 3 0.00
32 8 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
AGTCAGTGGCATCCTTTCAAAGCCCACA
Found at i:13144 original size:32 final size:31
Alignment explanation
Indices: 13101--13535 Score: 389
Period size: 32 Copynumber: 13.6 Consensus size: 31
13091 GCGCCTTTTC
*
13101 AAAGCCTACACAAGTCGGTGGCAACCCATTCT
1 AAAGCCCACACAAGTCGGTGGCAACCC-TTCT
**
13133 AAAGCCCACACAAGTTAGTGGCAACCCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAA-CCCTTCT
* *
13165 AAAGCCCATACAAGTCGGTGAC-A-CCTTCTTT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC--T
*
13196 AAAGCCCACACAAG-CTGGTGGTAACCCTTCTCT
1 AAAGCCCACACAAGTC-GGTGGCAACCC-T-TCT
*
13229 AAAGCCCACACAAGTCGATGGCAACCTCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACC-CTTCT
* * *
13261 AAAGCCCACACAAGCCGGTGGCTACCTTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACC-CTTCT
* * * * *
13293 AAAACCCATACAAGCCGGTGGCTACCTTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACC-CTTCT
* *
13325 AAAACCCACACAAGCCGGTGGCAACCCTTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCC-T-TCT
*
13358 AAAGCCCACACAAGTGGGTGGCAACCCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAA-CCCTTCT
* *
13390 AAAGCCCACACAAGTCGGTGGCATCCCTTTT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * *
13421 AAAGCCCA-TCAAG-CTGGTGGTAACCTCTTTT
1 AAAGCCCACACAAGTC-GGTGGCAACC-CTTCT
* *
13452 AAAGCCCACACAAGTTGGTGGCAACCCTTTT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
* *
13483 CAAAG-CCACACAAAGT-AGTGGCAACCTTTTTCT
1 -AAAGCCCACAC-AAGTCGGTGGCAACC--CTTCT
* *
13516 AAAGCCCACTCAAGTTGGTG
1 AAAGCCCACACAAGTCGGTG
13536 ATATCTTCTT
Statistics
Matches: 342, Mismatches: 38, Indels: 45
0.80 0.09 0.11
Matches are distributed among these distances:
29 6 0.02
30 13 0.04
31 66 0.19
32 184 0.54
33 65 0.19
34 6 0.02
35 2 0.01
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (31 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCT
Found at i:13381 original size:129 final size:127
Alignment explanation
Indices: 13101--13535 Score: 526
Period size: 129 Copynumber: 3.4 Consensus size: 127
13091 GCGCCTTTTC
* ** *
13101 AAAGCCTACACAAGTCGGTGGCAACC-CATTCTAAAGCCCACACAAGTTAGTGGCAACCCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTC-TTCTAAAGCCCACACAAGTCGGTGGC-ACCCTTTCT
* * *
13165 AAAGCCCATACAAGTCGGTGAC-ACCTTCTTTAAAGCCCACACAAGCTGGTGGTAACCCTTCTCT
64 AAAGCCCATACAAGCCGGTGGCTACCTT-TTTAAAGCCCACACAAGCTGGTGGCAACCCTTCTCT
* * *
13229 AAAGCCCACACAAGTCGATGGCAACCTCTTCTAAAGCCCACACAAGCCGGTGGCTACCTTTTCTA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTCTAAAGCCCACACAAGTCGGTGGC-ACCCTTTCTA
* * *
13294 AAACCCATACAAGCCGGTGGCTACCTTTTCTAAAACCCACACAAGCCGGTGGCAACCCTTCTCT
65 AAGCCCATACAAGCCGGTGGCTACCTTTT-TAAAGCCCACACAAGCTGGTGGCAACCCTTCTCT
* *
13358 AAAGCCCACACAAGTGGGTGGCAACCCCTTCTAAAGCCCACACAAGTCGGTGGCATCCCTTT-TA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTCTAAAGCCCACACAAGTCGGTGGCA-CCCTTTCTA
* * *
13422 AAGCCCAT-CAAGCTGGTGG-TAACCTCTTTTAAAGCCCACACAAGTTGGTGGCAACCCTTTTC-
65 AAGCCCATACAAGCCGGTGGCT-ACCT-TTTTAAAGCCCACACAAGCTGGTGGCAACCCTTCTCT
* * * *
13484 AAAG-CCACACAAAGT-AGTGGCAACCTTTTTCTAAAGCCCACTCAAGTTGGTG
1 AAAGCCCACAC-AAGTCGGTGGCAACC-TCTTCTAAAGCCCACACAAGTCGGTG
13536 ATATCTTCTT
Statistics
Matches: 269, Mismatches: 30, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
125 15 0.06
126 31 0.12
127 43 0.16
128 88 0.33
129 92 0.34
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (127 bp):
AAAGCCCACACAAGTCGGTGGCAACCTCTTCTAAAGCCCACACAAGTCGGTGGCACCCTTTCTAA
AGCCCATACAAGCCGGTGGCTACCTTTTTAAAGCCCACACAAGCTGGTGGCAACCCTTCTCT
Found at i:14859 original size:21 final size:21
Alignment explanation
Indices: 14830--14869 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
14820 CTATTCATCT
*
14830 TTTGTCTAT-ACATGTTTGTTC
1 TTTGCCTATCACAT-TTTGTTC
14851 TTTGCCTATCACATTTTGT
1 TTTGCCTATCACATTTTGT
14870 CTATGTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTGCCTATCACATTTTGTTC
Found at i:16769 original size:28 final size:28
Alignment explanation
Indices: 16715--16776 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
16705 ATTTTTTCAA
*
16715 AAAGCCCACAAGTCAATGGAATCCTTTT
1 AAAGCCCACAAGTCAATGGAATCCTTTC
16743 AAAGCCCACAAGTCAAT-G-ATACTCTTTC
1 AAAGCCCACAAGTCAATGGAAT-C-CTTTC
16771 AAAGCC
1 AAAGCC
16777 ACCCTTCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 27 0.87
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (28 bp):
AAAGCCCACAAGTCAATGGAATCCTTTC
Found at i:16800 original size:28 final size:29
Alignment explanation
Indices: 16776--18171 Score: 1017
Period size: 28 Copynumber: 49.7 Consensus size: 29
16766 CTTTCAAAGC
*
16776 CACCCTTCT-AAAGCCCACAAGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
** * *
16804 CATCCC-TCTCAAAAACCAAAAGTTAGTGG
1 CA-CCCTTCTCAAAGCCCACAAGTCAGTGG
*
16833 CACCCTTC-AAAAGCCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
** * *
16861 CTTCCTTTTCAAAGCCCACAAGTCAGTGA
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
16890 CA-TCTTTTCAAAGCCCACAAGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
*
16918 CATCCTT-TCAAAGCCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * * *
16946 CACCCTTTTTAAAGCTCACAAGTTAGTAG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
16975 CATCCTT-TCAAAGCCCATAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17003 CACCCTT-TCAAAGCCTATAAATCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17031 CATCCTT-TCAAAACCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17059 CACCCTTC-CAAAGCCCATAAGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * *
17087 TACCTTTTTCAAAGCTCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * * *
17116 CATCCTT-TTAAAGCCTACAAGTCAATGA
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17144 CATCGTT-TCAAAGCCCACAA-T-A-TGA
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
*
17169 CATCCTT-TCAAAGCCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * *
17197 TC-TCCTT-TTAAAGCCCACAAGTTAGTGA
1 -CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17225 CA-CCTTTTCAAAACCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17253 CA-TCTTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * *
17281 CATCCTT-TTAAAGCTCACAAGTTAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * *
17309 CATCCTT-TTAAAACCCACAAGTTAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
** * * *
17337 CGTCCTT-TTAAAGCCCACAAGTTAGTAG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * * *
17365 TATCCTT-TCAAAGCCCATATGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17393 CA-CCTTTTTAAAGCTCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17421 CATCCTT-TTAAAGCCCACAAGGT-AGTGG
1 CACCCTTCTCAAAGCCCACAA-GTCAGTGG
*
17449 CATCCTT-TCAAAGCCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17477 CACCCTTTTCAAAGCCTACAAGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17506 CATCCTT-TCAAAGCCCATAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17534 CACCCTT-TCAAAGCCTATAAATCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17562 CATCCTT-TCAAAACCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17590 CACCCTTC-CAAAGCCCATAAGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * *
17618 TACCTTTTTCAAAGCTCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * * *
17647 CATCCTT-TTAAAGCCTACAAGTCAATGA
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17675 CATCGTT-TCAAAGCCCACAA-T-A-TGA
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17700 CA-TCTTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * * *
17728 TC-TCCTT-TTAAAGCCCACAAGTTAATGA
1 -CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17756 CA-CCTTTTCAAAACCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
17784 CA-TCTTTTCAAAGCCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * *
17812 CATCCTT-TTAAAGCTCACAAGTTAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17840 CATCCTT-TTAAAACCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
*** * * *
17868 TGTCCTT-TTAAAGCCCACAAGTTAGTAG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * * *
17896 TATCCTT-TCAAAGCCCATATGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17924 CA-CCTTTTTAAAGCTCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * *
17952 CATCCTT-TTAAAGCCCACAAGTTAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
*
17980 CATCCTT-TCAAAGCCCACAAGTCAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* *
18008 CACCCTTTTCAAAGCCCACAAGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * *
18037 CA-TCTTTTCAAAACCCACAAGTTAGTGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* * * *
18065 CA-CCTTTTTAAAGCTCACAAGTCAATGG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
* ** *
18093 CATCCTT-TCAAAGCAGACAAGTCAGTAG
1 CACCCTTCTCAAAGCCCACAAGTCAGTGG
*
18121 CACCCTT-TCAAAGCCCACACAAGTCGGTGG
1 CACCCTTCTCAAAG-CC-CACAAGTCAGTGG
18151 CAATCCCTTCT-AAAGCCCACA
1 C-A-CCCTTCTCAAAGCCCACA
18172 CAAGCTGGTG
Statistics
Matches: 1129, Mismatches: 199, Indels: 78
0.80 0.14 0.06
Matches are distributed among these distances:
24 2 0.00
25 40 0.04
26 4 0.00
27 24 0.02
28 850 0.75
29 181 0.16
30 15 0.01
31 3 0.00
32 9 0.01
33 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (29 bp):
CACCCTTCTCAAAGCCCACAAGTCAGTGG
Found at i:16943 original size:56 final size:56
Alignment explanation
Indices: 16785--18171 Score: 1336
Period size: 56 Copynumber: 24.7 Consensus size: 56
16775 CCACCCTTCT
* * ** * * **
16785 AAAGCCCACAAGTCAATGGCATCCCTCTCAAAAACCAAAAGTTAGTGGCA-CCCTTC
1 AAAGCCCACAAGTCAGTGGCAT-CCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* *
16841 AAAAGCCCACAAGTCAGTGGCTTCCTTTTCAAAGCCCACAAGTCAGTGACATCTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * *
16899 AAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTC
* * * * * *
16956 AAAGCTCACAAGTTAGTAGCATCCTTTCAAAGCCCATAAGTCAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * * * * *
17012 AAAGCCTATAAATCAGTGGCATCCTTTCAAAACCCACAAGTCAGTGGCACCCTTCC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * *
17068 AAAGCCCATAAGTCAATGGTA-CCTTTTTCAAAGCTCACAAGTCAGTGGCATCCTTTT-
1 AAAGCCCACAAGTCAGTGGCATCC--TTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTC
* * * * * *
17125 AAAGCCTACAAGTCAATGACATCGTTTCAAAGCCCACAA-T-A-TGACATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * *
17178 AAAGCCCACAAGTCAGTGGTC-TCCTTTTAAAGCCCACAAGTTAGTGACACCTTTTC
1 AAAGCCCACAAGTCAGTGG-CATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* *
17234 AAAACCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTT-
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTC
* * * * * *
17290 AAAGCTCACAAGTTAGTGGCATCCTTTTAAAACCCACAAGTTAGTGGCGTCCTTTT-
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTC
* * * * * * * *
17346 AAAGCCCACAAGTTAGTAGTATCCTTTCAAAGCCCATATGTCAATGGCACCTTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * *
17402 AAAGCTCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGGT-AGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAA-GTCAGTGGCATCTTTTC
* * * *
17458 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCTACAAGTCAATGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * * * *
17515 AAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCTATAAATCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * * * * *
17571 AAAACCCACAAGTCAGTGGCACCCTTCCAAAGCCCATAAGTCAATGGTACCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC-TTTTC
* * * * * *
17628 AAAGCTCACAAGTCAGTGGCATCCTTTTAAAGCCTACAAGTCAATGACATCGTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* *
17684 AAAGCCCACAA-T-A-TGACATCTTTTCAAAGCCCACAAGTCAGTGGTC-TCCTTTT-
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG-CAT-CTTTTC
* * * *
17737 AAAGCCCACAAGTTAATGACA-CCTTTTCAAAACCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * *
17793 AAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCTCACAAGTTAGTGGCATCCTTTT-
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTC
* ** * * * * *
17849 AAAACCCACAAGTCAGTGGTGTCCTTTTAAAGCCCACAAGTTAGTAGTATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * * * *
17905 AAAGCCCATATGTCAATGGCA-CCTTTTTAAAGCTCACAAGTCAGTGGCATCCTTTT-
1 AAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTC
* *
17961 AAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTC
* * * * * *
18018 AAAGCCCACAAGTCAATGGCATCTTTTCAAAACCCACAAGTTAGTGGCACCTTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* * ** * * *
18074 AAAGCTCACAAGTCAATGGCATCCTTTCAAAGCAGACAAGTCAGTAGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
* *
18130 AAAGCCCACACAAGTCGGTGGCAATCCCTTCTAAAGCCCACA
1 AAAG-CC-CACAAGTCAGTGGC-ATCCTTTC-AAAGCCCACA
18172 CAAGCTGGTG
Statistics
Matches: 1108, Mismatches: 183, Indels: 75
0.81 0.13 0.05
Matches are distributed among these distances:
52 4 0.00
53 74 0.07
54 10 0.01
55 25 0.02
56 651 0.59
57 309 0.28
58 20 0.02
59 7 0.01
60 8 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (56 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTC
Found at i:17880 original size:531 final size:531
Alignment explanation
Indices: 16864--18137 Score: 2232
Period size: 531 Copynumber: 2.4 Consensus size: 531
16854 TCAGTGGCTT
* * * *
16864 CCTTTTCAAAGCCCACAAGTCAGTGACAT-CTTTTCAAAGCCCACAA-GTCAATGGCATCCTTTC
1 CCTTTTTAAAGCTCACAAGTCAGTGGCATCCTTTT-AAAGCCCACAAGGT-AGTGGCATCCTTTC
* * * *
16927 AAAGCCCACAAGTCAGTGGCACCCTTTTTAAAG-CTCACAAGTTAGTAGCATCCTTTCAAAGCCC
64 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCT-ACAAGTCAATGGCATCCTTTCAAAGCCC
16991 ATAAGTCAGTGGCACCCTTTCAAAGCCTATAAATCAGTGGCATCCTTTCAAAACCCACAAGTCAG
128 ATAAGTCAGTGGCACCCTTTCAAAGCCTATAAATCAGTGGCATCCTTTCAAAACCCACAAGTCAG
17056 TGGCACCCTTCCAAAGCCCATAAGTCAATGGTACCTTTTTCAAAGCTCACAAGTCAGTGGCATCC
193 TGGCACCCTTCCAAAGCCCATAAGTCAATGGTACCTTTTTCAAAGCTCACAAGTCAGTGGCATCC
17121 TTTTAAAGCCTACAAGTCAATGACATCGTTTCAAAGCCCACAATATGACATCCTTTCAAAGCCCA
258 TTTTAAAGCCTACAAGTCAATGACATCGTTTCAAAGCCCACAATATGACATCCTTTCAAAGCCCA
*
17186 CAAGTCAGTGGTCTCCTTTTAAAGCCCACAAGTTAGTGACACCTTTTCAAAACCCACAAGTCAGT
323 CAAGTCAGTGGTCTCCTTTTAAAGCCCACAAGTTAATGACACCTTTTCAAAACCCACAAGTCAGT
17251 GGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCTCACAAGTTAGTGGCATCCTT
388 GGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCTCACAAGTTAGTGGCATCCTT
*
17316 TTAAAACCCACAAGTTAGTGGCGTCCTTTTAAAGCCCACAAGTTAGTAGTATCCTTTCAAAGCCC
453 TTAAAACCCACAAGTCAGTGGCGTCCTTTTAAAGCCCACAAGTTAGTAGTATCCTTTCAAAGCCC
17381 ATATGTCAATGGCA
518 ATATGTCAATGGCA
17395 CCTTTTTAAAGCTCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGGTAGTGGCATCCTTTCAA
1 CCTTTTTAAAGCTCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGGTAGTGGCATCCTTTCAA
17460 AGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCTACAAGTCAATGGCATCCTTTCAAAGCCCATA
66 AGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCTACAAGTCAATGGCATCCTTTCAAAGCCCATA
17525 AGTCAGTGGCACCCTTTCAAAGCCTATAAATCAGTGGCATCCTTTCAAAACCCACAAGTCAGTGG
131 AGTCAGTGGCACCCTTTCAAAGCCTATAAATCAGTGGCATCCTTTCAAAACCCACAAGTCAGTGG
17590 CACCCTTCCAAAGCCCATAAGTCAATGGTACCTTTTTCAAAGCTCACAAGTCAGTGGCATCCTTT
196 CACCCTTCCAAAGCCCATAAGTCAATGGTACCTTTTTCAAAGCTCACAAGTCAGTGGCATCCTTT
*
17655 TAAAGCCTACAAGTCAATGACATCGTTTCAAAGCCCACAATATGACATCTTTTCAAAGCCCACAA
261 TAAAGCCTACAAGTCAATGACATCGTTTCAAAGCCCACAATATGACATCCTTTCAAAGCCCACAA
17720 GTCAGTGGTCTCCTTTTAAAGCCCACAAGTTAATGACACCTTTTCAAAACCCACAAGTCAGTGGC
326 GTCAGTGGTCTCCTTTTAAAGCCCACAAGTTAATGACACCTTTTCAAAACCCACAAGTCAGTGGC
17785 ATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCTCACAAGTTAGTGGCATCCTTTTA
391 ATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCTCACAAGTTAGTGGCATCCTTTTA
*
17850 AAACCCACAAGTCAGTGGTGTCCTTTTAAAGCCCACAAGTTAGTAGTATCCTTTCAAAGCCCATA
456 AAACCCACAAGTCAGTGGCGTCCTTTTAAAGCCCACAAGTTAGTAGTATCCTTTCAAAGCCCATA
17915 TGTCAATGGCA
521 TGTCAATGGCA
*
17926 CCTTTTTAAAGCTCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTTAGTGGCATCCTTTCAA
1 CCTTTTTAAAGCTCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGGTAGTGGCATCCTTTCAA
* * * *
17991 AGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAATGGCATCTTTTCAAAACCCACA
66 AGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCTACAAGTCAATGGCATCCTTTCAAAGCCCATA
* * * * * * * ** *
18056 AGTTAGTGGCACCTTTTTAAAG-CTCACAAGTCAATGGCATCCTTTCAAAGCAGACAAGTCAGTA
131 AGTCAGTGGCACCCTTTCAAAGCCT-ATAAATCAGTGGCATCCTTTCAAAACCCACAAGTCAGTG
*
18120 GCACCCTTTCAAAGCCCA
195 GCACCCTTCCAAAGCCCA
18138 CACAAGTCGG
Statistics
Matches: 711, Mismatches: 28, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
530 2 0.00
531 700 0.98
532 9 0.01
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (531 bp):
CCTTTTTAAAGCTCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGGTAGTGGCATCCTTTCAA
AGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCTACAAGTCAATGGCATCCTTTCAAAGCCCATA
AGTCAGTGGCACCCTTTCAAAGCCTATAAATCAGTGGCATCCTTTCAAAACCCACAAGTCAGTGG
CACCCTTCCAAAGCCCATAAGTCAATGGTACCTTTTTCAAAGCTCACAAGTCAGTGGCATCCTTT
TAAAGCCTACAAGTCAATGACATCGTTTCAAAGCCCACAATATGACATCCTTTCAAAGCCCACAA
GTCAGTGGTCTCCTTTTAAAGCCCACAAGTTAATGACACCTTTTCAAAACCCACAAGTCAGTGGC
ATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCTCACAAGTTAGTGGCATCCTTTTA
AAACCCACAAGTCAGTGGCGTCCTTTTAAAGCCCACAAGTTAGTAGTATCCTTTCAAAGCCCATA
TGTCAATGGCA
Found at i:18166 original size:32 final size:31
Alignment explanation
Indices: 18109--18580 Score: 354
Period size: 32 Copynumber: 14.8 Consensus size: 31
18099 TTCAAAGCAG
* *
18109 ACAAGTCAGTAGC-ACCCTT-TCAAAGCCCAC
1 ACAAGTCGGTGGCAACCCTTCT-AAAGCCCAC
18139 ACAAGTCGGTGGCAATCCCTTCTAAAGCCCAC
1 ACAAGTCGGTGGCAA-CCCTTCTAAAGCCCAC
*
18171 ACAAG-CTGGTGGTAACCCCTTCTAAAGCCCAC
1 ACAAGTC-GGTGGCAA-CCCTTCTAAAGCCCAC
* ** *
18203 ATAAGTCGGTGGC-ACATTCTCTAAAACCCAC
1 ACAAGTCGGTGGCAACCCT-TCTAAAGCCCAC
*
18234 ACAAG-CTGGTGGCAACCCTTCTCTAAAGCCTAC
1 ACAAGTC-GGTGGCAACCC-T-TCTAAAGCCCAC
* *
18267 ACAAGTCGGTGGCAACCCTTTCTAAAACCCAT
1 ACAAGTCGGTGGCAACCC-TTCTAAAGCCCAC
* * * * * **
18299 ATAAGTTGGTGACAACCTTTTATAAAGTGCAC
1 ACAAGTCGGTGGCAACC-CTTCTAAAGCCCAC
** * *
18331 ACAAGTTAGTGGCAACCCTTTTTTAAAGCCCAT
1 ACAAGTCGGTGGCAACCC--TTCTAAAGCCCAC
*
18364 ACAAGTCGGTGGCAACCTCTTCTAAAGCCCAT
1 ACAAGTCGGTGGCAACC-CTTCTAAAGCCCAC
*
18396 ACAAG-CTGGTGGCAACCTCTTCTAAAGCCCTC
1 ACAAGTC-GGTGGCAACC-CTTCTAAAGCCCAC
* * *
18428 ACAAGTTGGTGACACCCCTGT-TAAAGCCCAC
1 ACAAGTCGGTGGCAACCCT-TCTAAAGCCCAC
*
18459 -CAAG-CTGGTGGTAACCTCTTCTAAAGCCCAC
1 ACAAGTC-GGTGGCAACC-CTTCTAAAGCCCAC
* *
18490 ACAAGCCGATGGCAACCCATT-TCAAAGGCCCAC
1 ACAAGTCGGTGGCAACCC-TTCT-AAA-GCCCAC
*
18523 ACAAAGT-GGTGGCAACCTTTTTCTAAAGCCCAC
1 AC-AAGTCGGTGGCAACC--CTTCTAAAGCCCAC
* *
18556 ACAAGTTGGTGGCATCTCCTTCTAA
1 ACAAGTCGGTGGCAAC-CCTTCTAA
18581 GCCTAATGTC
Statistics
Matches: 357, Mismatches: 54, Indels: 60
0.76 0.11 0.13
Matches are distributed among these distances:
30 26 0.07
31 50 0.14
32 179 0.50
33 90 0.25
34 11 0.03
35 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (31 bp):
ACAAGTCGGTGGCAACCCTTCTAAAGCCCAC
Found at i:18368 original size:97 final size:97
Alignment explanation
Indices: 18126--18569 Score: 410
Period size: 97 Copynumber: 4.6 Consensus size: 97
18116 AGTAGCACCC
* *
18126 TTTC-AAAGCCCACACAAGTCGGTGGCAATCCC--TTCTAAAGCCCACACAAG-CTGGTGGTAAC
1 TTTCTAAAGCCCACACAAGTTGGTGGCAA-CCCTTTTCTAAAGCCCACACAAGTC-GGTGGCAAC
* * * *
18187 CCCTTCTAAAGCCCACATAAGTCGGTGGC-ACAT
64 CCTTTCTAAAGCCCATATAAGTTGGTGGCAACCT
* * * * *
18220 TCTCTAAAACCCACACAAGCTGGTGGCAACCCTTCTCTAAAGCCTACACAAGTCGGTGGCAACCC
1 TTTCTAAAGCCCACACAAGTTGGTGGCAACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCC
* *
18285 TTTCTAAAACCCATATAAGTTGGTGACAACCT
66 TTTCTAAAGCCCATATAAGTTGGTGGCAACCT
* ** * * *
18317 TTTATAAAGTGCACACAAGTTAGTGGCAACCCTTTTTTAAAGCCCATACAAGTCGGTGGCAA-CC
1 TTTCTAAAGCCCACACAAGTTGGTGGCAACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCC
* *
18381 TCTTCTAAAGCCCATACAAGCTGGTGGCAACCT
66 T-TTCTAAAGCCCATATAAGTTGGTGGCAACCT
* * * * * *
18414 CTTCTAAAGCCCTCACAAGTTGGTGAC-ACCCCTGT-TAAAGCCCAC-CAAG-CTGGTGGTAA-C
1 TTTCTAAAGCCCACACAAGTTGGTGGCAACCCTTTTCTAAAGCCCACACAAGTC-GGTGGCAACC
* * ** * *
18474 CTCTTCTAAAGCCCACACAAGCCGATGGCAACCCA
65 CT-TTCTAAAGCCCATATAAGTTGGTGGCAA-CCT
* *
18509 TTTC-AAAGGCCCACACAAAG-TGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGCA
1 TTTCTAAA-GCCCACAC-AAGTTGGTGGCAACCCTTTTCTAAAGCCCACACAAGTCGGTGGCA
18570 TCTCCTTCTA
Statistics
Matches: 285, Mismatches: 51, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
93 1 0.00
94 49 0.17
95 48 0.17
96 65 0.23
97 112 0.39
98 10 0.04
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (97 bp):
TTTCTAAAGCCCACACAAGTTGGTGGCAACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCC
TTTCTAAAGCCCATATAAGTTGGTGGCAACCT
Found at i:18559 original size:225 final size:225
Alignment explanation
Indices: 18130--18569 Score: 552
Period size: 225 Copynumber: 2.0 Consensus size: 225
18120 GCACCCTTTC
*
18130 AAAGCCCACACAAGTCGGTGGCAATCCCTTCTAAAGCCCACACAAGCTGGTGGTAACCCCTTCTA
1 AAAGCCCACACAAGTCGGTGGCAATCCCTTCTAAAGCCCACACAAGCTGGTGGCAACCCCTTCTA
* * **
18195 AAGCCCACATAAGTCGGTGGCACATTCTCTAAAACCCACACAAGCTGGTGGCAACCCTTCTCTAA
66 AAGCCCACACAAGTCGGTGACACACCCTCTAAAACCCACACAAGCTGGTGGCAACCCTTCTCTAA
* * * * *
18260 AGCCTACACAAGTCGGTGGCAACCCTTTCTAAAACCCATATAAGTTGGTGACAACCTTTTATAAA
131 AGCCCACACAAGCCGATGGCAACCCTTTCTAAAACCCACAAAAGTTGGTGACAACCTTTTATAAA
**
18325 GTGCACACAAGTTAGTGGCAACCCTTTTTT
196 GCCCACACAAGTTAGTGGCAACCCTTTTTT
* * *
18355 AAAGCCCATACAAGTCGGTGGCAA-CCTCTTCTAAAGCCCATACAAGCTGGTGGCAACCTCTTCT
1 AAAGCCCACACAAGTCGGTGGCAATCC-CTTCTAAAGCCCACACAAGCTGGTGGCAACCCCTTCT
* * * * *
18419 AAAGCCCTCACAAGTTGGTGACAC-CCCTGTTAAAGCCCAC-CAAGCTGGTGGTAA-CC-TCTTC
65 AAAGCCCACACAAGTCGGTGACACACCCT-CTAAAACCCACACAAGCTGGTGGCAACCCTTC-TC
* *
18480 TAAAGCCCACACAAGCCGATGGCAACCCATTTC-AAAGGCCCACACAAAG-TGGTGGCAACCTTT
128 TAAAGCCCACACAAGCCGATGGCAACCC-TTTCTAAA-ACCCACA-AAAGTTGGTGACAACC-TT
* *
18543 TTCTAAAGCCCACACAAGTTGGTGGCA
189 TTATAAAGCCCACACAAGTTAGTGGCA
18570 TCTCCTTCTA
Statistics
Matches: 184, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
222 2 0.01
223 32 0.17
224 36 0.20
225 114 0.62
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (225 bp):
AAAGCCCACACAAGTCGGTGGCAATCCCTTCTAAAGCCCACACAAGCTGGTGGCAACCCCTTCTA
AAGCCCACACAAGTCGGTGACACACCCTCTAAAACCCACACAAGCTGGTGGCAACCCTTCTCTAA
AGCCCACACAAGCCGATGGCAACCCTTTCTAAAACCCACAAAAGTTGGTGACAACCTTTTATAAA
GCCCACACAAGTTAGTGGCAACCCTTTTTT
Found at i:18838 original size:52 final size:51
Alignment explanation
Indices: 18688--18905 Score: 175
Period size: 52 Copynumber: 4.2 Consensus size: 51
18678 TTCTTTTTAT
* *
18688 CTTTATCATCTTTAAGTTCAATGTCGTTAGCCTTGAATCAGCACATTGGCAC
1 CTTTATCATC-TTAAGTCCAATGTCGTTAGCCTTGAATCAGCATATTGGCAC
* ** * * * * * **
18740 CTTTTTTTTTTCTTAAGTCTAATATCATTGGCTTTGAATCAGCATATTGGTGC
1 C--TTTATCATCTTAAGTCCAATGTCGTTAGCCTTGAATCAGCATATTGGCAC
* * *
18793 CTTTGTCATCTTGAAGTCCAATGTCGTTAGCCTTGAATCAACATATTAGCAC
1 CTTTATCATCTT-AAGTCCAATGTCGTTAGCCTTGAATCAGCATATTGGCAC
* * * * * * * * *
18845 CTTTTTCATCGTTAAGCCCAATATCGCTAGCCTTAAATTAGTATATTGGTAG
1 CTTTATCATC-TTAAGTCCAATGTCGTTAGCCTTGAATCAGCATATTGGCAC
18897 CTTTATCAT
1 CTTTATCAT
18906 TCTTCTCATC
Statistics
Matches: 126, Mismatches: 36, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
51 8 0.06
52 77 0.61
53 35 0.28
54 6 0.05
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (51 bp):
CTTTATCATCTTAAGTCCAATGTCGTTAGCCTTGAATCAGCATATTGGCAC
Found at i:19619 original size:23 final size:21
Alignment explanation
Indices: 19570--19626 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
19560 ATTTTTATCT
19570 AAATATATCGATACATTTCTC
1 AAATATATCGATACATTTCTC
*
19591 AAATATATCGATATATTTCTC
1 AAATATATCGATACATTTCTC
*
19612 AAATATATCAATACA
1 AAATATATCGATACA
19627 AGGTCCCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.37
Consensus pattern (21 bp):
AAATATATCGATACATTTCTC
Found at i:20719 original size:20 final size:21
Alignment explanation
Indices: 20694--20732 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20684 CATCTAAACC
20694 GCTATGT-CCATGCATTTTGA
1 GCTATGTACCATGCATTTTGA
20714 GCTATGTACCATGCATTTT
1 GCTATGTACCATGCATTTT
20733 AACATGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (21 bp):
GCTATGTACCATGCATTTTGA
Found at i:23327 original size:20 final size:21
Alignment explanation
Indices: 23302--23352 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
23292 CCCTCAATTC
23302 TATCGATACA-CATGGT-AATG
1 TATCGATACATCAT-GTAAATG
*
23322 TATCGATACATTATGTAAATG
1 TATCGATACATCATGTAAATG
23343 TATCGATACA
1 TATCGATACA
23353 AGTCATTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
TATCGATACATCATGTAAATG
Found at i:24767 original size:19 final size:19
Alignment explanation
Indices: 24744--24806 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 19
24734 TGAAAATAAC
24744 ATAAATATGACATAAAAAA
1 ATAAATATGACATAAAAAA
* *
24763 TTAAA-A-CACAATAAAAAA
1 ATAAATATGAC-ATAAAAAA
* *
24781 ATAAATATGACATGAATAA
1 ATAAATATGACATAAAAAA
24800 A-AAATAT
1 ATAAATAT
24807 AAAAAATACA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.06
18 19 0.54
19 12 0.34
20 2 0.06
ACGTcount: A:0.67, C:0.06, G:0.05, T:0.22
Consensus pattern (19 bp):
ATAAATATGACATAAAAAA
Found at i:24980 original size:15 final size:15
Alignment explanation
Indices: 24962--24992 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24952 TTTTCTTCCC
24962 TTTTTTTATCTTTCT
1 TTTTTTTATCTTTCT
*
24977 TTTTTTTCTCTTTCT
1 TTTTTTTATCTTTCT
24992 T
1 T
24993 CCCATCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTATCTTTCT
Found at i:26338 original size:13 final size:14
Alignment explanation
Indices: 26320--26350 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
26310 AACTCGATAT
26320 TTAT-AAAAAATAA
1 TTATAAAAAAATAA
26333 TTATAAAAAAATAA
1 TTATAAAAAAATAA
26347 TTAT
1 TTAT
26351 CAACAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTATAAAAAAATAA
Found at i:26823 original size:35 final size:34
Alignment explanation
Indices: 26784--26864 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
26774 TAATCTTTAA
* * *
26784 TTATTATTTAATATGAATATAGTTTTAATATACT-T
1 TTATTATTTAATAT-AAAATAATTTCAATATA-TGT
26819 TTATTATTTAATATAAAATAATTTCAATATATGT
1 TTATTATTTAATATAAAATAATTTCAATATATGT
26853 TTAATTATTTAA
1 TT-ATTATTTAA
26865 AACAAATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 1 0.02
34 17 0.41
35 23 0.56
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (34 bp):
TTATTATTTAATATAAAATAATTTCAATATATGT
Done.