Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold712
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: 72607
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1729 original size:12 final size:11
Alignment explanation
Indices: 1706--1760 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
1696 TCTTTCTATC
*
1706 TTTTTCTTTGT
1 TTTTTTTTTGT
1717 TTTGTTTTTTGT
1 TTT-TTTTTTGT
** *
1729 TTTTTTCCTCT
1 TTTTTTTTTGT
*
1740 TTTTTTTTTGC
1 TTTTTTTTTGT
1751 TTTTTTTTTG
1 TTTTTTTTTG
1761 ACGGACGGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:14261 original size:28 final size:28
Alignment explanation
Indices: 14180--14261 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
14170 TTTTGGAGAT
*
14180 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
14208 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
14236 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
14262 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:14404 original size:51 final size:51
Alignment explanation
Indices: 14244--14414 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
14234 GAAATAACGA
* * * *
14244 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATTGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
14296 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
14349 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
14400 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
14415 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 39 0.41
52 16 0.17
53 31 0.32
54 10 0.10
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:14460 original size:27 final size:28
Alignment explanation
Indices: 14397--14472 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
14387 AAAATAAAGT
*
14397 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
14425 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
14452 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
14473 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:16955 original size:13 final size:13
Alignment explanation
Indices: 16937--16962 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16927 ACAAAGATCC
16937 ATGTATCGATACA
1 ATGTATCGATACA
16950 ATGTATCGATACA
1 ATGTATCGATACA
16963 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:16958 original size:33 final size:33
Alignment explanation
Indices: 16916--16982 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
16906 AAAATTTCCA
***
16916 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
16949 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
16982 A
1 A
16983 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:17026 original size:19 final size:18
Alignment explanation
Indices: 17002--17069 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
16992 CAGTAGCTAA
17002 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
17021 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
17036 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
17053 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
17070 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:17042 original size:13 final size:13
Alignment explanation
Indices: 17024--17048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17014 ACAATACTTA
17024 TGTATCGATACAT
1 TGTATCGATACAT
17037 TGTATCGATACA
1 TGTATCGATACA
17049 AAACTTATGT
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:17046 original size:32 final size:32
Alignment explanation
Indices: 17005--17067 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
16995 TAGCTAATTA
*
17005 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
17037 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
17068 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:17131 original size:21 final size:21
Alignment explanation
Indices: 17105--17181 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
17095 GTTGGGACCC
* *
17105 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
17126 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
17147 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
17168 TGTATCGATACATT
1 TGTATCGATACATT
17182 TATTTATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:17325 original size:16 final size:16
Alignment explanation
Indices: 17304--17337 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17294 TTATCTAGCA
17304 CATATGTCGGATCCTC
1 CATATGTCGGATCCTC
17320 CATATGTCGGATCCTC
1 CATATGTCGGATCCTC
17336 CA
1 CA
17338 CCTACTAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (16 bp):
CATATGTCGGATCCTC
Found at i:17550 original size:11 final size:10
Alignment explanation
Indices: 17534--17603 Score: 74
Period size: 10 Copynumber: 6.8 Consensus size: 10
17524 CATCCTCCGC
17534 CAAAAAAAAA
1 CAAAAAAAAA
17544 GCAAAAAAAAA
1 -CAAAAAAAAA
17555 -AAAAACAAATA
1 CAAAAA-AAA-A
17566 -AAAGAAAAAA
1 CAAA-AAAAAA
17576 CAAAAAAAAA
1 CAAAAAAAAA
17586 -ACAAAAAAAA
1 CA-AAAAAAAA
17596 CAAAAAAA
1 CAAAAAAA
17604 CGACAAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
9 6 0.11
10 24 0.45
11 21 0.40
12 2 0.04
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:17580 original size:27 final size:26
Alignment explanation
Indices: 17546--17603 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
17536 AAAAAAAAGC
* *
17546 AAAAAAAAAAAAAACAAATAAAAGAA
1 AAAAAAAAAAAAAACAAAAAAAACAA
17572 AAAACAAAAAAAAAACAAAAAAAACAA
1 AAAA-AAAAAAAAAACAAAAAAAACAA
17599 AAAAA
1 AAAAA
17604 CGACAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.90, C:0.07, G:0.02, T:0.02
Consensus pattern (26 bp):
AAAAAAAAAAAAAACAAAAAAAACAA
Found at i:17609 original size:20 final size:19
Alignment explanation
Indices: 17552--17612 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 19
17542 AAGCAAAAAA
17552 AAAAAAAACAAATAAAAGA-
1 AAAAAAAACAAA-AAAAGAC
*
17571 AAAAACAA-AAAAAAA-AC
1 AAAAAAAACAAAAAAAGAC
17588 AAAAAAAACAAAAAAACGAC
1 AAAAAAAACAAAAAAA-GAC
17608 AAAAA
1 AAAAA
17613 GGGTTCGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.03
17 11 0.31
18 10 0.28
19 7 0.19
20 7 0.19
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAGAC
Found at i:17612 original size:1 final size:1
Alignment explanation
Indices: 17535--17603 Score: 66
Period size: 1 Copynumber: 69.0 Consensus size: 1
17525 ATCCTCCGCC
** * * * * * *
17535 AAAAAAAAAGCAAAAAAAAAAAAAACAAATAAAAGAAAAAACAAAAAAAAAACAAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17600 AAAA
1 AAAA
17604 CGACAAAAAG
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.88, C:0.07, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:17612 original size:11 final size:9
Alignment explanation
Indices: 17546--17603 Score: 75
Period size: 9 Copynumber: 6.6 Consensus size: 9
17536 AAAAAAAAGC
17546 AAAAAA-AA
1 AAAAAACAA
17554 AAAAAACAA
1 AAAAAACAA
* *
17563 ATAAAAGAA
1 AAAAAACAA
17572 AAAACAA-AA
1 AAAA-AACAA
17581 AAAAAACAA
1 AAAAAACAA
17590 AAAAAACAA
1 AAAAAACAA
17599 AAAAA
1 AAAAA
17604 CGACAAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
8 8 0.18
9 34 0.77
10 2 0.05
ACGTcount: A:0.90, C:0.07, G:0.02, T:0.02
Consensus pattern (9 bp):
AAAAAACAA
Found at i:19111 original size:57 final size:57
Alignment explanation
Indices: 19048--19206 Score: 187
Period size: 57 Copynumber: 2.8 Consensus size: 57
19038 TCAACCTTCA
* * * ***
19048 AAAGCCCACAAGTCAGTGGCATCTTTTTAAAAACCCACAAGTT-AGTGGCA-CTTTTTC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAACCCACAAGTTGA-TGGCACCCCATTC
* *
19105 AAAGCCCACAAGTCAGTGGCAACCTTCAGAAGCCCACAAGTTGATGGCACCCCATTC
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAACCCACAAGTTGATGGCACCCCATTC
*
19162 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCATACAAGTTG
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAACCC--ACAAGTTG
19207 GTCGCATCTT
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
56 20 0.22
57 61 0.69
59 8 0.09
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCAAAAACCCACAAGTTGATGGCACCCCATTC
Found at i:19112 original size:28 final size:29
Alignment explanation
Indices: 19048--19187 Score: 137
Period size: 28 Copynumber: 4.9 Consensus size: 29
19038 TCAACCTTCA
* *
19048 AAAGCCCACAAGTCAGTGGCATCTTTTTA
1 AAAGCCCACAAGTCAGTGGCACCTTTTTC
* *
19077 AAAACCCACAAGTTAGTGGCA-CTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTC
19105 AAAGCCCACAAGTCAGTGGCAACC---TTC
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTTC
* ***
19132 AGAAGCCCACAAGT-TGATGGCACCCCATTC
1 A-AAGCCCACAAGTCAG-TGGCACCTTTTTC
19162 AAAGCCCACAAGTCAGTGGCAACCTT
1 AAAGCCCACAAGTCAGTGGC-ACCTT
19188 CAAAAGCCCA
Statistics
Matches: 93, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
27 8 0.09
28 40 0.43
29 36 0.39
30 9 0.10
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTTC
Found at i:19382 original size:49 final size:49
Alignment explanation
Indices: 19216--19767 Score: 650
Period size: 49 Copynumber: 11.1 Consensus size: 49
19206 GGTCGCATCT
* * *
19216 TCTTCTAAGTCCAATATCGTTGGCCTTGAATCAGTATATT-G-A----CA
1 TCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * * * *
19260 CCTTGAAGACCAATGTCACTGGCCTAGAATCAGCACATTGGCACCTTAACCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTT---CA
* *
19312 TCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
19361 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * *
19410 ACTTGAA-TCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA
1 TCTTTAAGT-CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
* *
19462 TCTTCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTA
1 TCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
19512 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
19561 ACTTGAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
19610 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * ** * **
19659 ACTTGAAACCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCATTTGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT-G-GCACCT-TCA
* *
19711 TCTTCTAAGTCCAATGTCGATGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
19761 TCTTTAA
1 TCTTTAA
19768 CATTCCTAAG
Statistics
Matches: 432, Mismatches: 57, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
43 27 0.06
44 4 0.01
45 1 0.00
48 1 0.00
49 254 0.59
50 14 0.03
51 10 0.02
52 56 0.13
53 64 0.15
54 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (49 bp):
TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
Found at i:19515 original size:151 final size:149
Alignment explanation
Indices: 19261--19767 Score: 664
Period size: 151 Copynumber: 3.4 Consensus size: 149
19251 ATATTGACAC
* * * * ** *
19261 CTTGAAGACCAATGTCACTGGCCTAGAATCAGCACATTGGCACCTTAACCATCTTTAAGACCAAT
1 CTTGAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT-TTCATCTTTAAGTCCAAT
* *
19326 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAAT
65 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAAT
19391 CAGCACATTGGCACCTTCAA
130 CAGCACATTGGCACCTTCAA
* *
19411 CTTGAA-TCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTCTAAGTCCA
1 CTTGAAGT-CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-TCATCTT-TAAGTCCA
* * *
19475 ATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTCGCTGGCCTTGA
63 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
19540 ATCAGCACATTGGCACCTTCAA
128 ATCAGCACATTGGCACCTTCAA
*
19562 CTTGAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TTCATCTTTAAGTCCAATG
1 CTTGAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTTTAAGTCCAATG
* * ** *
19625 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCAACTTGAAACCCAATATCGCTGGCCTTGAATC
66 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATC
* ** *
19690 AGCATATTGGCGCATTTGTCAT
131 AGCACATT-G-GCACCT-TCAA
* * *
19712 CTTCTAAGTCCAATGTCGATGGCCTTGAATCAGCACATTGGCACC--TTCATCTTTAA
1 CTT-GAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTTTAA
19768 CATTCCTAAG
Statistics
Matches: 320, Mismatches: 29, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
147 75 0.23
148 8 0.03
149 5 0.02
150 51 0.16
151 180 0.56
152 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (149 bp):
CTTGAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTTTAAGTCCAATG
TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATC
AGCACATTGGCACCTTCAA
Found at i:19649 original size:249 final size:248
Alignment explanation
Indices: 19216--19767 Score: 880
Period size: 249 Copynumber: 2.2 Consensus size: 248
19206 GGTCGCATCT
* * * * *
19216 TCTTCTAAGTCCAATATCGTTGGCCTTGAATCAGTATATT-G-AC--ACCTTGAAGACCAATGTC
1 TCTTCTAAGTCCAATGTCGATGGCCTTGAATCAGCATATTGGCACTTATCTTTAAGACCAATGTC
* *
19277 ACTGGCCTAGAATCAGCACATTGGCACCTTAACCATCTTTAAGACCAATATCGCTGGCCTTGAAT
66 ACTGGCCTAGAATCAGCACATTGGCACCTT-A-CAACTTGAAGACCAATATCGCTGGCCTTGAAT
19342 CAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
129 CAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
* *
19407 TCAACTTGAATCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA
194 TCAACTTGAAACCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCATTTGTCA
* *
19462 TCTTCTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATG
1 TCTTCTAAGTCCAATGTCGATGGCCTTGAATCAGCATATTGGCAC--TTATCTTTAAGACCAATG
* * *
19527 TCGCTGGCCTTGAATCAGCACATTGGCACCTT-CAACTTGAAGTCCAATATCGCTGGCCTTGAAT
64 TCACTGGCCTAGAATCAGCACATTGGCACCTTACAACTTGAAGACCAATATCGCTGGCCTTGAAT
19591 CAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
129 CAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
19656 TCAACTTGAAACCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCATTTGTCA
194 TCAACTTGAAACCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCATTTGTCA
*
19711 TCTTCTAAGTCCAATGTCGATGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
1 TCTTCTAAGTCCAATGTCGATGGCCTTGAATCAGCATATTGGCA-CTT-ATCTTTAA
19768 CATTCCTAAG
Statistics
Matches: 283, Mismatches: 15, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
246 37 0.13
247 1 0.00
248 4 0.01
249 197 0.70
250 1 0.00
252 43 0.15
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (248 bp):
TCTTCTAAGTCCAATGTCGATGGCCTTGAATCAGCATATTGGCACTTATCTTTAAGACCAATGTC
ACTGGCCTAGAATCAGCACATTGGCACCTTACAACTTGAAGACCAATATCGCTGGCCTTGAATCA
GCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTC
AACTTGAAACCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCATTTGTCA
Found at i:20634 original size:19 final size:19
Alignment explanation
Indices: 20610--20707 Score: 85
Period size: 19 Copynumber: 5.8 Consensus size: 19
20600 TGTCAACGAT
20610 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
20629 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
* *
20643 -TGTATCAATACATAAGTG
1 TTGTATCGATACATAAGTA
20661 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
*
20675 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
20693 TTGTATCGATACATA
1 TTGTATCGATACATA
20708 TGAAGCTACT
Statistics
Matches: 62, Mismatches: 5, Indels: 24
0.68 0.05 0.26
Matches are distributed among these distances:
13 21 0.34
14 1 0.02
16 4 0.06
19 36 0.58
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:20647 original size:32 final size:32
Alignment explanation
Indices: 20611--20705 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
20601 GTCAACGATT
*
20611 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
20643 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
20675 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
20706 TATGAAGCTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:20648 original size:13 final size:13
Alignment explanation
Indices: 20630--20686 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
20620 ACATAAGTAT
20630 TGTATCGATACAA
1 TGTATCGATACAA
*
20643 TGTATCAATACATAA
1 TGTATCGATAC--AA
20658 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
20675 TGTATCGATACA
1 TGTATCGATACA
20687 TAAGTGTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:24670 original size:78 final size:79
Alignment explanation
Indices: 24552--24704 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 79
24542 AATAAAATCG
* * * *
24552 AGGTTAGAGTATCTCCTCGAAAATAATAGGGTTGGAGTATCCCC-ATTATGGAAAATTGATGTTT
1 AGGTTAGAGTATCCCCTCGAAAATAATAGGGTTAGAGTATCCCCGATTATGAAAAATCGATGTTT
24616 CAAAAATAAAGCCA
66 CAAAAATAAAGCCA
* * *
24630 AGGTTGGAGTATCCCCTCGAAAATAA-CGGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTT
1 AGGTTAGAGTATCCCCTCGAAAATAATAGGG-TTAGAGTATCCCCGATTATGAAAAATCGATGTT
*
24694 TTAAAAATAAA
65 TCAAAAATAAA
24705 ATCAAGTTTG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
77 3 0.05
78 36 0.55
79 26 0.40
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (79 bp):
AGGTTAGAGTATCCCCTCGAAAATAATAGGGTTAGAGTATCCCCGATTATGAAAAATCGATGTTT
CAAAAATAAAGCCA
Found at i:24910 original size:79 final size:78
Alignment explanation
Indices: 24822--25210 Score: 381
Period size: 78 Copynumber: 4.9 Consensus size: 78
24812 ATAAAAATAG
* * * *
24822 GGTTGGAGTATTCCATTGGAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAATCAATATTTT
1 GGTTGGAGTATTCC-TTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGTTTT
24887 AGAAATAAAATCGA
65 AGAAATAAAATCGA
* * ** * * ** *
24901 GGTTAGAGTATCTCCTCGAAAATAATAGGGTTGGAGTATCCCC-ATTATGGAAAATTGATGTTTC
1 GGTTGGAGTAT-TCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGTTTT
* ** *
24965 AAAAATAAAGCCAA
65 AGAAATAAAATCGA
* * * * *
24979 GGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTTTT
1 GGTTGGAGTAT-TCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGTTTT
*
25044 AAAAATAAAATC-A
65 AGAAATAAAATCGA
* * * * *
25057 GAGTTGGAGTATCCCCTCAAAATAACGGGGTTGGAGTATCTCCGA-TGATGAAAAATCAGTGTTT
1 G-GTTGGAGTATTCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTG-TGAAAAATCAATGTTT
25121 TAGAAATAAAATCGA
64 TAGAAATAAAATCGA
* * * * * *
25136 GGTTGAAGTA-TCCTCTCAAAAATATCGGGGTTGGAGCATCCTCGATTGTGAAAAATCGATGTTT
1 GGTTGGAGTATTCCT-T-GAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGTTT
25200 TAGAAATAAAA
64 TAGAAATAAAA
25211 AATCAAAGAA
Statistics
Matches: 256, Mismatches: 46, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
77 4 0.02
78 126 0.49
79 121 0.47
80 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (78 bp):
GGTTGGAGTATTCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGTTTTA
GAAATAAAATCGA
Found at i:25006 original size:157 final size:157
Alignment explanation
Indices: 24822--25210 Score: 460
Period size: 157 Copynumber: 2.5 Consensus size: 157
24812 ATAAAAATAG
* * * * * * * *
24822 GGTTGGAGTATTCCATTGGAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAATCAATATTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTT
* * *
24887 AGAAATAAAATC-GAGGTTAGAGTATCTCCTCGAAAATAATAGGGTTGGAGTATC-CCCATTATG
66 AGAAATAAAATCAGA-GTTAGAGTATCCCCTC-AAAATAACAGGGTTGGAGTATCTCCCATGATG
* * *
24950 GAAAAT-TGATGTTTCAAAAATAAAGCCAA
129 AAAAATCAG-TGTTTCAAAAATAAAACCAA
* *
24979 GGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTT
* * * *
25044 AAAAATAAAATCAGAGTTGGAGTATCCCCTCAAAATAACGGGGTTGGAGTATCTCCGATGATGAA
66 AGAAATAAAATCAGAGTTAGAGTATCCCCTCAAAATAACAGGGTTGGAGTATCTCCCATGATGAA
* * * *
25109 AAATCAGTGTTTTAGAAATAAAATCGA
131 AAATCAGTGTTTCAAAAATAAAACCAA
* * * * * *
25136 GGTTGAAGTATCCTCTCAAAAATATCGGGGTTGGAGCATCCTCGATTGTGAAAAATCGATGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTT
25201 AGAAATAAAA
66 AGAAATAAAA
25211 AATCAAAGAA
Statistics
Matches: 196, Mismatches: 33, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
156 20 0.10
157 173 0.88
158 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (157 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTT
AGAAATAAAATCAGAGTTAGAGTATCCCCTCAAAATAACAGGGTTGGAGTATCTCCCATGATGAA
AAATCAGTGTTTCAAAAATAAAACCAA
Found at i:28809 original size:32 final size:32
Alignment explanation
Indices: 28754--28822 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
28744 GGTACTATTT
*
28754 TCAAAACCCATAAAAATTGGTGGCAACCTTTC
1 TCAAAACCCACAAAAATTGGTGGCAACCTTTC
* *
28786 TCAAAAGCCCACACAAATT-GTGGCATCCTTTC
1 TCAAAA-CCCACAAAAATTGGTGGCAACCTTTC
28818 TCAAA
1 TCAAA
28823 GTCTGCACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 23 0.70
33 10 0.30
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.25
Consensus pattern (32 bp):
TCAAAACCCACAAAAATTGGTGGCAACCTTTC
Found at i:29137 original size:52 final size:52
Alignment explanation
Indices: 29065--29246 Score: 199
Period size: 52 Copynumber: 3.5 Consensus size: 52
29055 TGTTAGCCTT
* * *
29065 CAGCATATTGGCA-TTCTTGTCATCTTTAAATCCAATATCGCTGGCCTTGAAC
1 CAGCATATTGGCACCT-TTGTCATCTTTAAGTCCAATATCGCTAGCCTTGAAC
* *
29117 C-GACATATTGGCACCTTTGTCATCTTTAAGTCCAATATTGCTAGCCTTGAAT
1 CAG-CATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTAGCCTTGAAC
* * ** *
29169 CAGCATATTGGCACCTTTATCAT-TTTCAAGTCCAATGTCATTAGCCTTGAAT
1 CAGCATATTGGCACCTTTGTCATCTTT-AAGTCCAATATCGCTAGCCTTGAAC
* * *
29221 CAGCACATTGGCACTTTTCTCATCTT
1 CAGCATATTGGCACCTTTGTCATCTT
29247 CATGTCTAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
51 4 0.04
52 104 0.93
53 4 0.04
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (52 bp):
CAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTAGCCTTGAAC
Found at i:29258 original size:52 final size:52
Alignment explanation
Indices: 29123--29409 Score: 193
Period size: 52 Copynumber: 5.4 Consensus size: 52
29113 GAACCGACAT
* * * ** *
29123 ATTGGCACCTTTGTCATCTTTAAGTCCAATATTGCTAGCCTTGAATCAGCAT
1 ATTGGCACCTTTATCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAGCAC
* *
29175 ATTGGCACCTTTATCATTTTCAAGTCCAATGTCATTAGCCTTGAATCAGCAC
1 ATTGGCACCTTTATCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAGCAC
* * * * * * * *
29227 ATTGGCACTTTTCTCATCTTCATGTCTAATGTCGCTGGCCTTAAATCAGAAC
1 ATTGGCACCTTTATCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAGCAC
* * * * * * *
29279 ATTGACA-TTTGTCAAATCCATCTTTCTAAAGCCCAATGTCGCTGGCCTTGAATCAACAT
1 ATTGGCACCTT-T---AT-CATC-TTC--AAGTCCAATGTCACTAGCCTTGAATCAGCAC
* * * * *
29338 ATTGGCTA-CTTCATCATATTTAA-TCCCAATGTCACTGGCCTTGAATCAGCAT
1 ATTGGC-ACCTTTATCATCTTCAAGT-CCAATGTCACTAGCCTTGAATCAGCAC
* *
29390 ATTGGCACCCTTATTATCTT
1 ATTGGCACCTTTATCATCTT
29410 TAAGCAGTGT
Statistics
Matches: 185, Mismatches: 39, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
51 4 0.02
52 134 0.72
54 2 0.01
55 4 0.02
56 6 0.03
57 3 0.02
59 29 0.16
60 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (52 bp):
ATTGGCACCTTTATCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAGCAC
Found at i:30096 original size:21 final size:21
Alignment explanation
Indices: 30048--30098 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
30038 ATACAACAAA
30048 TGAAA-GTATCGATACATAAG
1 TGAAATGTATCGATACATAAG
***
30068 TG-AATGTATCGATACATGTT
1 TGAAATGTATCGATACATAAG
30088 TGAAATGTATC
1 TGAAATGTATC
30099 AATGTAAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 8 0.31
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (21 bp):
TGAAATGTATCGATACATAAG
Found at i:30205 original size:50 final size:52
Alignment explanation
Indices: 30141--30259 Score: 188
Period size: 51 Copynumber: 2.3 Consensus size: 52
30131 TTTGGAAAGA
*
30141 AAATGTATCAATACATTTTT-ATTGTATCGATACATTCTGGGTTTTGA-TCC
1 AAATGTATCAATACATTTTTCATTGTATCGATACATTCTGGGTTTTGAGCCC
* *
30191 AAATGTATCTATACATTTTTCATTGTATCGATACATTCTGGGTTTTTAGCCC
1 AAATGTATCAATACATTTTTCATTGTATCGATACATTCTGGGTTTTGAGCCC
*
30243 AAATGTATCGATACATT
1 AAATGTATCAATACATT
30260 CTGGGTTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 19 0.30
51 26 0.41
52 18 0.29
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (52 bp):
AAATGTATCAATACATTTTTCATTGTATCGATACATTCTGGGTTTTGAGCCC
Found at i:30250 original size:32 final size:32
Alignment explanation
Indices: 30214--30293 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
30204 CATTTTTCAT
30214 TGTATCGATACATTCTGGGTTTTT-AGCCCAAA
1 TGTATCGATACATTCTGGGTTTTTGA-CCCAAA
*
30246 TGTATCGATACATTCTGGGTTTTTGACCTAAA
1 TGTATCGATACATTCTGGGTTTTTGACCCAAA
*
30278 TGTATCGATGCATTCT
1 TGTATCGATACATTCT
30294 ATAATGTATC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 44 0.98
33 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATTCTGGGTTTTTGACCCAAA
Found at i:32810 original size:96 final size:97
Alignment explanation
Indices: 32648--32846 Score: 260
Period size: 96 Copynumber: 2.1 Consensus size: 97
32638 TTATCCATGA
* *
32648 GGGATATTCCAACCTTGCTTTTAAACTTCTCAAGATTAAAATCTTATTTTTGCTCAAATTACCAT
1 GGGATACTCCAACCTCGCTTTTAAACTTCTCAAGATTAAAATCTTATTTTTGCTCAAATTACCAT
* * *
32713 CATCGAGGATATTTCAA-TCGTATTCTTCCGAG
66 CATCGAGGATACTCCAACTC-TATTCCTCCGAG
* * * * *
32745 GGGATACTCCAACC-CGCTTTTGAACTTGTTAAGATTTAAATCTTATTTTTGC-CTAAATTATCA
1 GGGATACTCCAACCTCGCTTTTAAACTTCTCAAGATTAAAATCTTATTTTTGCTC-AAATTACCA
*
32808 TCATCGAGGATACTCCAACTCTATTCCTCTGAG
65 TCATCGAGGATACTCCAACTCTATTCCTCCGAG
32841 GGGATA
1 GGGATA
32847 TTCTAATCCC
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
95 1 0.01
96 73 0.82
97 15 0.17
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (97 bp):
GGGATACTCCAACCTCGCTTTTAAACTTCTCAAGATTAAAATCTTATTTTTGCTCAAATTACCAT
CATCGAGGATACTCCAACTCTATTCCTCCGAG
Found at i:33330 original size:21 final size:21
Alignment explanation
Indices: 33297--33337 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33287 CTAAGTAAAA
33297 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
33318 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
33338 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:33402 original size:20 final size:19
Alignment explanation
Indices: 33377--33447 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
33367 ACCCTGAAAA
33377 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
33397 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
33416 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
33437 GTATCGATACA
1 GTATCGATACA
33448 GGTCATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:33543 original size:10 final size:10
Alignment explanation
Indices: 33524--33554 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
33514 AATCTCATTT
33524 TCACTGTTCA
1 TCACTGTTCA
*
33534 TCACTATTCA
1 TCACTGTTCA
33544 TCACTGTTCA
1 TCACTGTTCA
33554 T
1 T
33555 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:33570 original size:22 final size:22
Alignment explanation
Indices: 33542--33662 Score: 228
Period size: 22 Copynumber: 5.6 Consensus size: 22
33532 CATCACTATT
33542 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
33564 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
33585 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
33607 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
33629 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
33650 CATCACTGTTCAT
1 CATCACTGTTCAT
33663 AGGTCACTGT
Statistics
Matches: 97, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
21 42 0.43
22 55 0.57
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:33589 original size:43 final size:44
Alignment explanation
Indices: 33542--33662 Score: 228
Period size: 43 Copynumber: 2.8 Consensus size: 44
33532 CATCACTATT
33542 CATCACTGTTCATGTATCGATACATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATACATCACTGTTCATGTATCGATA
33585 CATCACTGTTCATGTATCGATACATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATACATCACTGTTCATGTATCGATA
33629 CATCACT-TTCATGTATCGATACATCACTGTTCAT
1 CATCACTGTTCATGTATCGATACATCACTGTTCAT
33663 AGGTCACTGT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
43 56 0.73
44 21 0.27
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (44 bp):
CATCACTGTTCATGTATCGATACATCACTGTTCATGTATCGATA
Found at i:33763 original size:13 final size:13
Alignment explanation
Indices: 33745--33770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33735 ACATATTTGT
33745 GTGTATCGATACA
1 GTGTATCGATACA
33758 GTGTATCGATACA
1 GTGTATCGATACA
33771 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:34312 original size:34 final size:35
Alignment explanation
Indices: 34249--34315 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
34239 CTAAGTGATT
34249 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
34285 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
34316 TCTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:42401 original size:12 final size:12
Alignment explanation
Indices: 42384--42409 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42374 CCCGAGTGAC
42384 GATTAGTCATAG
1 GATTAGTCATAG
42396 GATTAGTCATAG
1 GATTAGTCATAG
42408 GA
1 GA
42410 GTTGTCGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATTAGTCATAG
Found at i:43530 original size:13 final size:13
Alignment explanation
Indices: 43512--43536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43502 ATATTACTTA
43512 GTATCGATACATT
1 GTATCGATACATT
43525 GTATCGATACAT
1 GTATCGATACAT
43537 GTTCATAGTA
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):
GTATCGATACATT
Found at i:44498 original size:21 final size:21
Alignment explanation
Indices: 44474--44515 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
44464 TTGATTATCT
44474 TGAGATA-ATCGATAGTTATTA
1 TGAGATACATCG-TAGTTATTA
* *
44495 TGAGGTACATCGTGGTTATTA
1 TGAGATACATCGTAGTTATTA
44516 AAATTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (21 bp):
TGAGATACATCGTAGTTATTA
Found at i:46248 original size:31 final size:31
Alignment explanation
Indices: 46213--46277 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
46203 ATCCCCTCAT
46213 AAATAACGAGGTT-AGAGTATCCCCGATTGTG
1 AAATAACGAGGTTGA-AGTATCCCCGATTGTG
* *
46244 AAATAACGGGGTTGAAGTATCCCTGATTGTG
1 AAATAACGAGGTTGAAGTATCCCCGATTGTG
46275 AAA
1 AAA
46278 AATTGGTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (31 bp):
AAATAACGAGGTTGAAGTATCCCCGATTGTG
Found at i:46380 original size:109 final size:108
Alignment explanation
Indices: 46134--46496 Score: 476
Period size: 110 Copynumber: 3.3 Consensus size: 108
46124 ATCCTCTTAA
* * * * * * *
46134 AAATAACGGGGTTGGAGTATCCTCGATTGTAAAAAATCAATGTTTTGGAAATAAAATCAGGGTTA
1 AAATAACGGGGTTGAAGTATCCTTGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTA
*
46199 GAGTATCCCCTCATAAATAACGAGGTTAGAGTATCCCCGATTGTG
66 GAGTATCCCCTGA-AAATAACG-GGTTAGAGTATCCCCGATTGTG
* * * * *
46244 AAATAACGGGGTTGAAGTATCCCTGATTGTGAAAAATTGGTGTTTTAGAAACAAAATTGGGGTTG
1 AAATAACGGGGTTGAAGTATCCTTGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTA
* * *
46309 GAGTATCCCCTGGAAATAACGGGATTTGAGTATCCCCAATTGTG
66 GAGTATCCCCTGAAAATAACGGG-TTAGAGTATCCCCGATTGTG
*
46353 AAATAACGGGGTTAAAGTATCCTTGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTA
1 AAATAACGGGGTTGAAGTATCCTTGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTA
* *
46418 GAGTATCCCCTTGAAAATAACAGGGTTGGAGTATCCTCGATTGTG
66 GAGTATCCCC-TGAAAATAAC-GGGTTAGAGTATCCCCGATTGTG
* *
46463 AAATAACAGGGTTGGAGTAT-CTTCGATTGTGAAA
1 AAATAACGGGGTTGAAGTATCCTT-GATTGTGAAA
46497 TAACAGGGTT
Statistics
Matches: 220, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
108 2 0.01
109 98 0.45
110 117 0.53
111 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (108 bp):
AAATAACGGGGTTGAAGTATCCTTGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTA
GAGTATCCCCTGAAAATAACGGGTTAGAGTATCCCCGATTGTG
Found at i:46467 original size:31 final size:31
Alignment explanation
Indices: 46432--46515 Score: 159
Period size: 31 Copynumber: 2.7 Consensus size: 31
46422 ATCCCCTTGA
46432 AAATAACAGGGTTGGAGTATCCTCGATTGTG
1 AAATAACAGGGTTGGAGTATCCTCGATTGTG
*
46463 AAATAACAGGGTTGGAGTATCTTCGATTGTG
1 AAATAACAGGGTTGGAGTATCCTCGATTGTG
46494 AAATAACAGGGTTGGAGTATCC
1 AAATAACAGGGTTGGAGTATCC
46516 CTGAGATGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (31 bp):
AAATAACAGGGTTGGAGTATCCTCGATTGTG
Found at i:48833 original size:20 final size:20
Alignment explanation
Indices: 48808--48859 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
48798 AAAATACCTG
*
48808 AATGTATCGATACATTGAAA
1 AATGTATCGATACAATGAAA
* *
48828 AATGTATTGATACAATGAAC
1 AATGTATCGATACAATGAAA
*
48848 AATGTACCGATA
1 AATGTATCGATA
48860 TAACTTGTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:48925 original size:21 final size:21
Alignment explanation
Indices: 48899--48954 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
48889 GTTGGGACCT
48899 TGTATCGATACATTAAGGGCA
1 TGTATCGATACATTAAGGGCA
*
48920 TGTATCGATACATTAAGGGCT
1 TGTATCGATACATTAAGGGCA
48941 TGTATCGATACATT
1 TGTATCGATACATT
48955 TTGGCAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTAAGGGCA
Found at i:52274 original size:17 final size:17
Alignment explanation
Indices: 52254--52311 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
52244 AAATAAATAT
52254 TCTTAATGGGAAAGAAG
1 TCTTAATGGGAAAGAAG
52271 TCTTAATGGGTAAA-AAG
1 TCTTAATGGG-AAAGAAG
* * *
52288 TCTTAATGAGTAAGAAT
1 TCTTAATGGGAAAGAAG
52305 TCTTAAT
1 TCTTAAT
52312 TATCAAGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 2 0.06
17 31 0.86
18 3 0.08
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (17 bp):
TCTTAATGGGAAAGAAG
Found at i:61640 original size:13 final size:14
Alignment explanation
Indices: 61604--61640 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
61594 ATAATCCCCC
*
61604 TGTATCGATA-TAG
1 TGTATCGATACGAG
61617 TGTATCGATACGA-
1 TGTATCGATACGAG
61630 TGTATCGATAC
1 TGTATCGATAC
61641 AAAGAATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (14 bp):
TGTATCGATACGAG
Found at i:67832 original size:13 final size:13
Alignment explanation
Indices: 67814--67838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67804 CATTTTATGG
67814 TGTATCGATACAA
1 TGTATCGATACAA
67827 TGTATCGATACA
1 TGTATCGATACA
67839 CACTGTGTGT
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:68978 original size:13 final size:13
Alignment explanation
Indices: 68960--68985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68950 ACAAAGATCC
68960 ATGTATCGATACA
1 ATGTATCGATACA
68973 ATGTATCGATACA
1 ATGTATCGATACA
68986 TTGAGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:69061 original size:19 final size:19
Alignment explanation
Indices: 69037--69105 Score: 138
Period size: 19 Copynumber: 3.6 Consensus size: 19
69027 AGCGATACAT
69037 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
69056 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
69075 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
69094 TGTATCGATACA
1 TGTATCGATACA
69106 GTTACTGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:69314 original size:18 final size:18
Alignment explanation
Indices: 69293--69328 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
69283 AACAAAAAGT
69293 TATGAAAATCTAAAAAAC
1 TATGAAAATCTAAAAAAC
69311 TATGAAAATCTAAAAAAC
1 TATGAAAATCTAAAAAAC
69329 CATACGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (18 bp):
TATGAAAATCTAAAAAAC
Found at i:72262 original size:21 final size:21
Alignment explanation
Indices: 72238--72293 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
72228 TTTTTACCTA
* *
72238 CATGTATCGATATATGCCTTC
1 CATGTATCGATACATACCTTC
*
72259 CATGTATCGATACATACCTTT
1 CATGTATCGATACATACCTTC
72280 CATGTATCGATACA
1 CATGTATCGATACA
72294 AGGTCCTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (21 bp):
CATGTATCGATACATACCTTC
Done.