Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold579
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: 21272
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Found at i:1280 original size:29 final size:29
Alignment explanation
Indices: 1241--1557 Score: 223
Period size: 29 Copynumber: 10.7 Consensus size: 29
1231 TCACCCTTCA
* *
1241 AAAGCTCACAAGTTAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1270 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1299 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1326 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
1356 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1385 AAAGTCCACAACTCTGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
1415 TTTTGTAAGCTCACAACTCCGTAGCA-CTTTTTTCC
1 -----AAAGCCCACAAGTCAGTGGCATC-TTTTT-C
* * * *
1450 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
1482 AAATGCCCACAAGTCAGTGGCAAC-TTTTA
1 AAA-GCCCACAAGTCAGTGGCATCTTTTTC
* *
1511 AAAGCCCACAAGTCAGTAGCAATC--TTTA
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTTC
1539 AAAGCCCACAAGTCAGTGG
1 AAAGCCCACAAGTCAGTGG
1558 AAACCTTCAA
Statistics
Matches: 236, Mismatches: 38, Indels: 29
0.78 0.13 0.10
Matches are distributed among these distances:
27 22 0.09
28 39 0.17
29 83 0.35
30 45 0.19
32 1 0.00
33 23 0.10
34 6 0.03
35 17 0.07
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1336 original size:56 final size:56
Alignment explanation
Indices: 1267--1579 Score: 189
Period size: 56 Copynumber: 5.3 Consensus size: 56
1257 TGGCATCTTT
*
1267 TTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGTCCACAAGTCAGTGGCAACC
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAACC
* * * * * * *
1323 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTTTTCAAAGCCCACAAGTCAGTGGCAAC-C
* * * * * * * *
1381 TTCCAAAGTCCACAACTCTGTGGCACTCTTTTTCTTTTGTAAGCTCACAACTCCGTAGCACTTTT
1 TT-CAAAGCCCACAAGTCAGTGGCA-TCTTTTTC-----AAAGCCCACAAGTCAGTGGCA-----
*
1446 TTCC
54 -ACC
** * * * *
1450 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTCAAATGCCCACAAGTCAGTGGCAACTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAA-GCCCACAAGTCAGTGGCAAC-C
* * * *
1508 TTAAAAGCCCACAAGTCAGTAGCAATC--TTTAAAAGCCCACAAGTCAGTGGAAACC
1 TTCAAAGCCCACAAGTCAGTGGC-ATCTTTTTCAAAGCCCACAAGTCAGTGGCAACC
*
1563 TTCAAAAGCACACAAGT
1 TTC-AAAGCCCACAAGT
1580 TGATGCAAAC
Statistics
Matches: 195, Mismatches: 44, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
55 2 0.01
56 54 0.28
57 32 0.16
58 21 0.11
59 28 0.14
62 2 0.01
63 14 0.07
64 16 0.08
67 6 0.03
68 16 0.08
69 2 0.01
70 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAACC
Found at i:1353 original size:86 final size:86
Alignment explanation
Indices: 1235--1405 Score: 236
Period size: 86 Copynumber: 2.0 Consensus size: 86
1225 CATTCCTCAC
* * * * * *
1235 CCTTCAAAAGCTCACAAGTTAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCA
1 CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
*
1300 AAGTCCACAAGTCAGTGGCAA
66 AAGTCCACAACTCAGTGGCAA
* *
1321 CCTTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCATCTTTTCC
1 CCTTCAAAAGCCCACAAATCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
*
1385 AAAGTCCACAACTCTGTGGCA
65 AAAGTCCACAACTCAGTGGCA
1406 CTCTTTTTCT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 18 0.24
86 56 0.76
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (86 bp):
CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
AAGTCCACAACTCAGTGGCAA
Found at i:1431 original size:35 final size:34
Alignment explanation
Indices: 1390--1480 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 34
1380 TTTCCAAAGT
*
1390 CCACAACTCTGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTGTGGCACTCTTTTTCCTTT-TAAGC
* * *
1425 TCACAACTCCGTAGCACT-TTTTTCCTTTTAAGC
1 CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGC
* *
1458 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCT-GTGGCACTCTTTT
1481 CAAATGCCCA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
33 17 0.38
34 13 0.29
35 15 0.33
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (34 bp):
CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGC
Found at i:1457 original size:33 final size:35
Alignment explanation
Indices: 1390--1463 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
1380 TTTCCAAAGT
* * *
1390 CCACAACTCTGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
*
1425 TCACAACTCCGTAGCACT-TTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
1458 CCACAA
1 CCACAA
1464 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 10 0.29
34 9 0.26
35 15 0.44
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.36
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
Found at i:1525 original size:28 final size:28
Alignment explanation
Indices: 1454--1579 Score: 146
Period size: 28 Copynumber: 4.4 Consensus size: 28
1444 TTTTCCTTTT
* *
1454 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCA-ACTTTT-AA
*
1484 ATGCCCACAAGTCAGTGGCAACTTTTAA
1 AAGCCCACAAGTCAGTGGCAACTTTTAA
*
1512 AAGCCCACAAGTCAGTAGCAA-TCTTTAA
1 AAGCCCACAAGTCAGTGGCAACT-TTTAA
* * *
1540 AAGCCCACAAGTCAGTGGAAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACTTTTAA
*
1568 AAGCACACAAGT
1 AAGCCCACAAGT
1580 TGATGCAAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.01
28 60 0.71
29 5 0.06
30 18 0.21
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACTTTTAA
Found at i:1605 original size:29 final size:29
Alignment explanation
Indices: 1454--1605 Score: 138
Period size: 28 Copynumber: 5.3 Consensus size: 29
1444 TTTTCCTTTT
* *
1454 AAGCCCACAAGTTAGTGGC-ACCCTTTTCAA
1 AAGCCCACAAGTCAGT-GCAAACC-TTTCAA
* *
1484 ATGCCCACAAGTCAGTGGC-AA-CTTTTAA
1 AAGCCCACAAGTCAGT-GCAAACCTTTCAA
*
1512 AAGCCCACAAGTCAGTAGC-AATCTTT-AA
1 AAGCCCACAAGTCAGT-GCAAACCTTTCAA
*
1540 AAGCCCACAAGTCAGTGGAAACC-TTCAA
1 AAGCCCACAAGTCAGTGCAAACCTTTCAA
* *
1568 AAGCACACAAGT-TGATGCAAACCTTTCAA
1 AAGCCCACAAGTCAG-TGCAAACCTTTCAA
1597 AAGCCCACA
1 AAGCCCACA
1606 CAAGTTGGTG
Statistics
Matches: 105, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.04
28 65 0.62
29 18 0.17
30 18 0.17
ACGTcount: A:0.37, C:0.28, G:0.16, T:0.20
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGCAAACCTTTCAA
Found at i:1792 original size:52 final size:51
Alignment explanation
Indices: 1625--1921 Score: 390
Period size: 52 Copynumber: 5.9 Consensus size: 51
1615 GGCATCTTCT
* *
1625 TTTAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACC-TTG--TC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGCATC
* *
1673 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-TT-CATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGCATC
* * *
1721 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTTGGCACC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT-GCATC
*
1773 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTTGCATC
* * * * *
1825 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCATATTGACGCCTTTGGCAGC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT-GCATC
* *
1877 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1922 CATCCTCTTT
Statistics
Matches: 216, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
47 3 0.01
48 76 0.35
49 1 0.00
50 2 0.01
51 3 0.01
52 128 0.59
53 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (51 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGCATC
Found at i:1976 original size:156 final size:153
Alignment explanation
Indices: 1625--1993 Score: 380
Period size: 156 Copynumber: 2.4 Consensus size: 153
1615 GGCATCTTCT
* * * * *
1625 TTTAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACC--TT-G--TCTTTAAGTCCAAT
1 TTTAAACCCAATATAGCTGGCCATGAATCAGCACATTAGCACCTTTTCGCATCTTTAAGTCCAAT
*
1685 GTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATC
66 GTAGCTGGCCTTGAATCAGCACATTGGCACTTCAGCTTTAAGTCCAATATCGCTGGCCTTGAATC
**
1750 AGCATATTGACACCTTTGGCACC
131 AGCATATTGACACCTTCAGCACC
** * * * *
1773 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CATCTTTAAGTTCAAT
1 TTTAAACCCAATATAGCTGGCCATGAATCAGCACATTAGCACCTTTTCGCATCTTTAAGTCCAAT
* *
1837 GTAGCTGGCCTTGAATCAGCATATTGACGC-CTTTGGCAGCTTTAAGTCTAATATCGCTGGCCTT
66 GTAGCTGGCCTTGAATCAGCACATTG--GCAC-TT--CAGCTTTAAGTCCAATATCGCTGGCCTT
* *
1901 GAATCAGCATATTGGCACCTTCATC-CTC
126 GAATCAGCATATTGACACCTTCAGCAC-C
* * * * * *
1929 TTTAAAACCCAATGA-CGCTGGTCATGAATCAGCACATTATCA-TTTTTCGCATCTTCAAGCCCA
1 TTT-AAACCCAAT-ATAGCTGGCCATGAATCAGCACATTAGCACCTTTTCGCATCTTTAAGTCCA
1992 AT
64 AT
1994 ATCGCTAGCC
Statistics
Matches: 185, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
148 41 0.22
150 2 0.01
152 38 0.21
153 1 0.01
154 4 0.02
155 1 0.01
156 56 0.30
157 41 0.22
158 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (153 bp):
TTTAAACCCAATATAGCTGGCCATGAATCAGCACATTAGCACCTTTTCGCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGGCACTTCAGCTTTAAGTCCAATATCGCTGGCCTTGAATC
AGCATATTGACACCTTCAGCACC
Found at i:2744 original size:13 final size:13
Alignment explanation
Indices: 2726--2750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2716 ATTACTCAAA
2726 TGTATCGATACAT
1 TGTATCGATACAT
2739 TGTATCGATACA
1 TGTATCGATACA
2751 CTGATCTTTG
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:2800 original size:52 final size:52
Alignment explanation
Indices: 2762--2887 Score: 243
Period size: 52 Copynumber: 2.4 Consensus size: 52
2752 TGATCTTTGG
*
2762 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAATGT
1 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGT
2814 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGT
1 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGT
2866 ATCGATACATGCAGGCAAATTT
1 ATCGATACATGCAGGCAAATTT
2888 TCATATTTCG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGT
Found at i:6995 original size:62 final size:61
Alignment explanation
Indices: 6577--7710 Score: 1150
Period size: 62 Copynumber: 18.5 Consensus size: 61
6567 TTTTAGCCCT
*
6577 TTTAGTCCTCAAAGAGCAGGA--CACTTTTTCATTTTCAAAGCTCACACA-AGTTGGTGGCACC
1 TTTAGTCCTCAAAGAGCAGGATGC-CTTTTTC-TTTTCAAAGCCCACA-AGAGTTGGTGGCACC
* * *
6638 TTTTAGTCCTCAAAGAGCAGGATAG-ATTTTCCTTTT-AAAGCCTACACA-AGTTGGTGGCACC
1 -TTTAGTCCTCAAAGAGCAGGAT-GCCTTTTTCTTTTCAAAGCCCACA-AGAGTTGGTGGCACC
* * *
6699 TTTCAGTCCTCAAAGAGCAAGATGCC-TTTTCCTTT-AAAGCCCACACA-AGTTGGTGGCACT
1 TTT-AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACA-AGAGTTGGTGGCACC
* * **
6759 TTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTT-AAAGCCCACACA-AGTTGGTGGCATT
1 TTT-AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACA-AGAGTTGGTGGCACC
* * **
6820 TTTCAGTCCTCCAAGAACAGGATG-CTTTTTCCTTTT-AAAGCCCACACA-AGTTGGTAACACC
1 TTT-AGTCCTCAAAGAGCAGGATGCCTTTTT-CTTTTCAAAGCCCACA-AGAGTTGGTGGCACC
* * *
6881 TTCCAGTCCTCAAAGAGCAAGA--CAC--TTTCCTTTCAAAGCCCACACA-AGTTGGTGGCACC
1 TT-TAGTCCTCAAAGAGCAGGATGC-CTTTTTCTTTTCAAAGCCCACA-AGAGTTGGTGGCACC
* * * * *
6940 TTTCTGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTCAAAGCCCGCAAGAGTTGGTGGCACC
1 TTT-AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCACC
* * * * *
7002 TTTTAGTCCTTAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGACACC
1 -TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCACC
* * * * *
7064 TTTTAGTCCTCAAAAAGTAGGATGTCTTTTTCTTTTCAAAGCCCACATGAGTTAGTGGCACCC
1 -TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCA-CC
* * * *
7127 TTCAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCACTC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCAC-C
* * *
7189 TTTTA-TCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCTA-AACGAGTTAGTGGCACCC
1 -TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAA-GAGTTGGTGGCA-CC
* ***
7251 TTTAGTCCTCAAAGAGCAAGACATCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCA-CC
* *
7313 TTTAGTCCTCAAAGAGCAGGATGCCTTTTT-TTTTCAAAGCCCACACGAATTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCA-CC
* * * *** * *
7374 TTTAATCTTCAAAGAGCAAGACATCTTTTTCTTTTCAAAGCCCACACA-AATTGGTGGCACTG
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACA-AGAGTTGGTGGCAC-C
* * * * *
7436 TTTAGTCCTCAAAGAGCAAGACGTCTTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCA-CC
* ** * *
7498 TTTAGTCCTCAAAGAGCAGGACGTTTTTTTCTTTTCAAAGCCCACACGAGTTGGTAGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCA-CC
* * * *
7560 TTTTA-TCCTCAAAAAGCAGGATGTCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCACC
1 -TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCACC
* * *
7621 ATTTAGTCCTCAAAGAGCAGGAAGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGT-GTACC
1 -TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCACC
7682 TTTTAGTCCTCAAAGAGCAGGATG-CTTTT
1 -TTTAGTCCTCAAAGAGCAGGATGCCTTTT
7711 GCCTTTTATC
Statistics
Matches: 934, Mismatches: 106, Indels: 66
0.84 0.10 0.06
Matches are distributed among these distances:
58 4 0.00
59 43 0.05
60 71 0.08
61 231 0.25
62 564 0.60
63 21 0.02
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (61 bp):
TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCACC
Found at i:7077 original size:124 final size:124
Alignment explanation
Indices: 6574--7717 Score: 1272
Period size: 124 Copynumber: 9.3 Consensus size: 124
6564 CTCTTTTAGC
** * * *
6574 CCTTTTAGTCCTCAAAGAGCAGGACACTTTTTCATTTTCAAAGCTCACACA-AGTTGGTGGCACC
1 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACA-AGAGTTGGTGGCACC
* * * * * *
6638 TTTTAGTCCTCAAAGAGCAGGATAG-ATTTTCCTTTT-AAAGCCTACACAAGTTGGTGGCA
65 CTTTAGTCCTCAAAGAGCAGGA-CGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* *
6697 CCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCC-TTT-AAAGCCCACACA-AGTTGGTGGCA-C
1 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACA-AGAGTTGGTGGCACC
* * * * * *
6758 TTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
65 CTTT-AGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * * * **
6818 -TTTTTCAGTCCTCCAAGAACAGGATGCTTTTTCCTTTT-AAAGCCCACACA-AGTTGGTAACA-
1 CCTTTT-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACA-AGAGTTGGTGGCAC
* * * * *
6879 CCTTCCAGTCCTCAAAGAGCAAGAC-AC--TTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
64 CCTT-TAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * *
6938 CCTTTCT-GTCCTCAAAGAGTAGGACGCCTTTTCCTTTTCAAAGCCCGCAAGAGTTGGTGGCACC
1 CCTTT-TAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACC
* * *
7002 TTTTAGTCCTTAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGACA
65 CTTTAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * * * * *
7062 CCTTTTAGTCCTCAAAAAGTAGGATGTCTTTTTCTTTTCAAAGCCCACATGAGTTAGTGGCACCC
1 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACCC
* * * * *
7127 TTCAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCA
66 TTTAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * * *
7186 CTCTTTTA-TCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCTA-AACGAGTTAGTGGCAC
1 C-CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAA-GAGTTGGTGGCAC
* * *
7249 CCTTTAGTCCTCAAAGAGCAAGACATCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCA
64 CCTTTAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * * *
7310 CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTT-TTTTTCAAAGCCCACACGAATTGGTGGCACCC
1 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACCC
* * * * * *
7374 TTTAATCTTCAAAGAGCAAGACATCTTTTTCTTTTCAAAGCCCACACAAATTGGTGGCA
66 TTTAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * * * * *
7433 -CTGTTTAGTCCTCAAAGAGCAAGACGTCTTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCACC
1 CCT-TTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACC
* *
7497 CTTTAGTCCTCAAAGAGCAGGACGTTTTTTTCTTTTCAAAGCCCACACGAGTTGGTAGCA
65 CTTTAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * * * *
7557 CCCTTTTA-TCCTCAAAAAGCAGGATGTCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCACC
1 -CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACC
* * * * *
7621 ATTTAGTCCTCAAAGAGCAGGAAGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGT-GTA
65 CTTTAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
7680 CCTTTTAGTCCTCAAAGAGCAGGATG-CTTTTGCCTTTT
1 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTT-CCTTTT
7718 ATCCTTTGTC
Statistics
Matches: 885, Mismatches: 111, Indels: 50
0.85 0.11 0.05
Matches are distributed among these distances:
119 6 0.01
120 59 0.07
121 134 0.15
122 66 0.07
123 164 0.19
124 444 0.50
125 10 0.01
126 2 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (124 bp):
CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACCC
TTTAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
Found at i:7155 original size:186 final size:186
Alignment explanation
Indices: 6580--7717 Score: 1292
Period size: 186 Copynumber: 6.2 Consensus size: 186
6570 TAGCCCTTTT
** * * *
6580 AGTCCTCAAAGAGCAGGACACTTTTTCATTTTCAAAGCTCACACA-AGTTGGTGGCACCTTTTAG
1 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACA-AGAGTTGGTGGCACCTTTTAG
* * * *
6644 TCCTCAAAGAGCAGGATAG-ATTTTCCTTTT-AAAGCCTACACAAGTTGGTGGCACCTTTCAGTC
65 TCCTCAAAGAGCAGGAT-GTCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTC
* * * * **
6707 CTCAAAGAGCAAGATG-CCTTTTCCTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
129 CTCAAAGAGCAAGAAGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTC
* *
6763 AGTCCTCAAAGAGCAAGATGCCTTTTCCTTTT-AAAGCCCACACA-AGTTGGTGGCA-TTTTTCA
1 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACA-AGAGTTGGTGGCACCTTTT-A
* * ** **
6825 GTCCTCCAAGAACAGGATG-CTTTTTCCTTTT-AAAGCCCACACAAGTTGGTAACACCTTCCAGT
64 GTCCTCAAAGAGCAGGATGTCTTTTT-CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGT
* * *
6888 CCTCAAAGAGCAAGACA--C--TTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
128 CCTCAAAGAGCAAGA-AGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTC
* * * *
6944 TGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTCAAAGCCCGCAAGAGTTGGTGGCACCTTTTAGT
1 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACCTTTTAGT
* * * *
7009 CCTTAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGACACCTTTTAGTCCT
66 CCTCAAAGAGCAGGATGTCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCT
* * * * * *
7074 CAAAAAGTAGGATGTCTTTTTCTTTTCAAAGCCCACATGAGTTAGTGGCACCCTTC
131 CAAAGAGCAAGAAGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTC
* * * *
7130 AGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCACTCTTTTA-
1 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCAC-CTTTTAG
* * * * * * *
7194 TCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCTAAACGAGTTAGTGGCACCCTTTAGTCC
65 TCCTCAAAGAGCAGGATGTCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCC
* *
7259 TCAAAGAGCAAGACA-TCTTTTTCTTTTCAAAGCCCACAAGAGTTGGTGGCACCCTTT
130 TCAAAGAGCAAGA-AGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTC
* * * * *
7316 AGTCCTCAAAGAGCAGGATGCCTTTT-TTTTTCAAAGCCCACACGAATTGGTGGCACCCTTTAAT
1 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACCTTTTAGT
* * ** *
7380 CTTCAAAGAGCAAGACATCTTTTTCTTTTCAAAGCCCACACAAATTGGTGGCA-CTGTTTAGTCC
66 CCTCAAAGAGCAGGATGTCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCT-TTTAGTCC
* * *
7444 TCAAAGAGCAAGACGTCTTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCACCCTTT
130 TCAAAGAGCAAGAAGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTC
* ** * * *
7501 AGTCCTCAAAGAGCAGGACGTTTTTTTCTTTTCAAAGCCCACACGAGTTGGTAGCACCCTTTTA-
1 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCA-CCTTTTAG
* * * *
7565 TCCTCAAAAAGCAGGATGTCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCACCATTTAGTCC
65 TCCTCAAAGAGCAGGATGTCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCC
* * * * * *
7630 TCAAAGAGCAGGAAGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGT-GTACCTTTT
130 TCAAAGAGCAAGAAGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTC
7686 AGTCCTCAAAGAGCAGGATG-CTTTTGCCTTTT
1 AGTCCTCAAAGAGCAGGATGCCTTTT-CCTTTT
7718 ATCCTTTGTC
Statistics
Matches: 827, Mismatches: 106, Indels: 42
0.85 0.11 0.04
Matches are distributed among these distances:
180 8 0.01
181 66 0.08
182 129 0.16
183 77 0.09
184 11 0.01
185 187 0.23
186 336 0.41
187 13 0.02
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (186 bp):
AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTCAAAGCCCACAAGAGTTGGTGGCACCTTTTAGT
CCTCAAAGAGCAGGATGTCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCT
CAAAGAGCAAGAAGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTC
Found at i:7780 original size:41 final size:41
Alignment explanation
Indices: 7720--8037 Score: 323
Period size: 41 Copynumber: 7.6 Consensus size: 41
7710 TGCCTTTTAT
7720 CCTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTC
1 CCTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTC
* * ** * *
7761 CCTTTGTCCTTAAAAAGCAGGATGCATTTTTTTTCCTTATTTTC
1 CCTTTGTCCTCAAAGAGCAGGACACACTTTATTTCC---TTTTC
* **
7805 CCTTTTTTCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTC
1 CC-TTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTC
* ** * *
7847 CTTTTTGTCCTCAAAGAGCAAAACACACTCTATTTCCTTCTC
1 C-CTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTC
* * * * *
7889 TCTTTGTCTTCAAAGAGCAGAACACACTCTATTTCCGTTTC
1 CCTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTC
*
7930 CCTTTGTCCTCAAAGAGTAGGACACACTTTATTT-CTCTTTC
1 CCTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCT-TTTC
* * *
7971 CTTTTGTCCTCAAAGAGCAGGACACACTTAATTTCCTTCTTTT
1 CCTTTGTCCTCAAAGAGCAGGACACACTTTATTTCC-T-TTTC
* * *
8014 CCTTTGTCCCCAAGGAGTAGGACA
1 CCTTTGTCCTCAAAGAGCAGGACA
8038 TACTCCTTTT
Statistics
Matches: 230, Mismatches: 39, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
40 1 0.00
41 129 0.56
42 39 0.17
43 25 0.11
44 7 0.03
45 29 0.13
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (41 bp):
CCTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTC
Found at i:8763 original size:63 final size:63
Alignment explanation
Indices: 8664--8793 Score: 208
Period size: 63 Copynumber: 2.1 Consensus size: 63
8654 ATACATTGTT
* *
8664 CATTATATCGATACATTCTGGGTTTTACCTAGATGTATCGATATATTATTC-ATTGTATTGATA
1 CATTATATCGATACATTCTGGGTTTTACCTAGATGTATCGATACATTATTCGA-TGTATCGATA
* *
8727 CATTATATCGATACATTTTGGGTTTTACCTAGATGTATCGATACATTTTTCGATGTATCGATA
1 CATTATATCGATACATTCTGGGTTTTACCTAGATGTATCGATACATTATTCGATGTATCGATA
8790 CATT
1 CATT
8794 CAGGCATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 61 0.98
64 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (63 bp):
CATTATATCGATACATTCTGGGTTTTACCTAGATGTATCGATACATTATTCGATGTATCGATA
Found at i:8774 original size:30 final size:30
Alignment explanation
Indices: 8669--8775 Score: 92
Period size: 30 Copynumber: 3.5 Consensus size: 30
8659 TTGTTCATTA
*
8669 TATCGATACATTCTGGGTTTTACCTAGATG
1 TATCGATACATTTTGGGTTTTACCTAGATG
* ** * * *
8699 TATCGATATATTATTCATTGTATTGA--TACATTA
1 TATCGATACATT-TT--GGGT-TTTACCTAGA-TG
8732 TATCGATACATTTTGGGTTTTACCTAGATG
1 TATCGATACATTTTGGGTTTTACCTAGATG
8762 TATCGATACATTTT
1 TATCGATACATTTT
8776 TCGATGTATC
Statistics
Matches: 57, Mismatches: 13, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
29 3 0.05
30 28 0.49
31 4 0.07
32 5 0.09
33 14 0.25
34 3 0.05
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (30 bp):
TATCGATACATTTTGGGTTTTACCTAGATG
Found at i:9819 original size:79 final size:78
Alignment explanation
Indices: 9685--9900 Score: 240
Period size: 79 Copynumber: 2.8 Consensus size: 78
9675 ATAACAGCCT
* * * *
9685 CTATTTTATTTCTAAAACACCGA-TTTTCACAATTGGGGATACTTCAACCCCGTTATTTTTGAAG
1 CTATTTTATTTCTAAAACACTGATTTTTCACAATCGAGGATACTTCAACCCCGTTATTTTCGAAG
9749 GGATACTCCAACC
66 GGATACTCCAACC
**
9762 CTGATTTTATTTCTAAAACACTGATTTTTCACAATCGAGGATAC-TCTAATGCCGTTATTTTCGA
1 CT-ATTTTATTTCTAAAACACTGATTTTTCACAATCGAGGATACTTC-AACCCCGTTATTTTCGA
*
9826 AGGGATACTCTAACC
64 AGGGATACTCCAACC
* * * * * ** *
9841 CTAGTTTTATTTCCAAAACA-TCGATTTTCCACCATTGGGGATACCCCAACCCTGTTATTT
1 CTA-TTTTATTTCTAAAACACT-GATTTTTCACAATCGAGGATACTTCAACCCCGTTATTT
9901 CTGAGGGGGT
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
77 2 0.02
78 24 0.21
79 90 0.77
80 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (78 bp):
CTATTTTATTTCTAAAACACTGATTTTTCACAATCGAGGATACTTCAACCCCGTTATTTTCGAAG
GGATACTCCAACC
Found at i:12130 original size:25 final size:26
Alignment explanation
Indices: 12094--12145 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
12084 ATTATCGTCA
12094 AGAAATTCTGTCAAG-AATGTTTGTC
1 AGAAATTCTGTCAAGAAATGTTTGTC
*
12119 AGAAACTT-TGTCAAGAAATTTTTGTC
1 AGAAA-TTCTGTCAAGAAATGTTTGTC
12145 A
1 A
12146 ATACAACCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (26 bp):
AGAAATTCTGTCAAGAAATGTTTGTC
Found at i:12142 original size:26 final size:25
Alignment explanation
Indices: 12072--12145 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
12062 TAAATTTACC
* * *
12072 ATTTGCCAAGAAATTATCGTCAAGAA
1 ATTTGTCAAGAAATTTTTGTC-AGAA
*
12098 ATTCTGTCAAG-AATGTTTGTCAGAA
1 ATT-TGTCAAGAAATTTTTGTCAGAA
12123 ACTTTGTCAAGAAATTTTTGTCA
1 A-TTTGTCAAGAAATTTTTGTCA
12146 ATACAACCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 12 0.30
26 22 0.55
27 6 0.15
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (25 bp):
ATTTGTCAAGAAATTTTTGTCAGAA
Found at i:12144 original size:14 final size:14
Alignment explanation
Indices: 12073--12146 Score: 66
Period size: 13 Copynumber: 5.6 Consensus size: 14
12063 AAATTTACCA
*
12073 TTTGCCAAGAAATT
1 TTTGTCAAGAAATT
* *
12087 ATCGTCAAGAAA-T
1 TTTGTCAAGAAATT
* *
12100 TCTGTCAAG-AATG
1 TTTGTCAAGAAATT
*
12113 TTTGTC-AGAAA-C
1 TTTGTCAAGAAATT
12125 TTTGTCAAGAAATT
1 TTTGTCAAGAAATT
12139 TTTGTCAA
1 TTTGTCAA
12147 TACAACCCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
12 10 0.22
13 19 0.41
14 17 0.37
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (14 bp):
TTTGTCAAGAAATT
Found at i:12194 original size:28 final size:28
Alignment explanation
Indices: 12156--12753 Score: 669
Period size: 28 Copynumber: 21.1 Consensus size: 28
12146 ATACAACCCT
*
12156 TTTCAAAGCCCACAAGTTAGTAGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* **
12184 TTTTAAAGCCCACAAGACAGTGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* * *
12212 TTTCAAAGCCCACAGGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* * * *
12240 TTTCAAAGCCCGCAAGTCAGTGGCAACA
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* * * *
12268 TTTCGAAGCCCACAAGTCAGTGGCAACA
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12296 TTTCGAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12324 TTTTAAAGCCCACAAGTTAATGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12352 TTCCAAAGCCCACAAGTTAATGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12380 TTCCAAAGCCCACAAGTTAATGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
*
12408 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12436 TTTTAAAGCCCACAAGTTAATGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12464 TTCCAAAGCCCACAAGTTAATGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12492 TTCCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12520 TTTTAAAGCCCACAAGTTAGTGGCATCA
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12548 TTTCAAAGCCCAAAAGTAAGTGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* *
12576 TTTCAAAGCCCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
*
12604 TTTCAAAGCCAACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
* * *
12632 TTTCAAAGCCAACAAGTTAGTGGTA-CTA
1 TTTCAAAGCCCACAAGTTAGTGGCATC-C
** * *
12660 TTTCAAAATCCACAAGTCAATGGCATACCC
1 TTTCAAAGCCCACAAGTTAGTGGCAT--CC
** * *
12690 TTTCAAAGCCCATACAAGTCGGTAGCAACTCT
1 TTTCAAAGCCC--ACAAGTTAGTGGC-A-TCC
12722 TTTCAAAGCCCACACAAGTTAGTGGCA-CC
1 TTTCAAAG-CC-CACAAGTTAGTGGCATCC
12751 TTT
1 TTT
12754 TTTAAAGCCC
Statistics
Matches: 496, Mismatches: 64, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
27 1 0.00
28 446 0.90
29 4 0.01
30 9 0.02
31 2 0.00
32 29 0.06
33 3 0.01
34 2 0.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTTAGTGGCATCC
Found at i:12764 original size:31 final size:32
Alignment explanation
Indices: 12690--12791 Score: 98
Period size: 32 Copynumber: 3.2 Consensus size: 32
12680 TGGCATACCC
* *
12690 TTTCAAAGCCCATACAAGTCGGTAGCAACTCT
1 TTTCAAAGCCCACACAAGTCAGTAGCAACTCT
* * *
12722 TTTCAAAGCCCACACAAGTTAGTGGCACCT-T
1 TTTCAAAGCCCACACAAGTCAGTAGCAACTCT
* ** * * *
12753 TTTTAAAGCCCACGTAAGTCGGTGGCAAATCT
1 TTTCAAAGCCCACACAAGTCAGTAGCAACTCT
12785 TTTCAAA
1 TTTCAAA
12792 TCACCATTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
31 24 0.43
32 32 0.57
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCAGTAGCAACTCT
Found at i:13658 original size:21 final size:20
Alignment explanation
Indices: 13631--13707 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
13621 AAAAAATTCC
*
13631 AAATGTATCGATACATTTGT
1 AAATGTATCGATACATTTAT
* *
13651 AGAATGTATCGATACATTCAC
1 A-AATGTATCGATACATTTAT
* *
13672 AAATATATCGATACATTCTAC
1 AAATGTATCGATACATT-TAT
13693 AAATGTATCGATACA
1 AAATGTATCGATACA
13708 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
20 16 0.33
21 33 0.67
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (20 bp):
AAATGTATCGATACATTTAT
Found at i:13687 original size:41 final size:40
Alignment explanation
Indices: 13626--13707 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 40
13616 AAAAAAAAAA
* * *
13626 ATTCCAAATGTATCGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATATATCGATACA-TTCTACAAATGTATCGATAC
13666 ATTCACAAATATATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATATATCGATACATTCTACAAATGTATCGATAC
13707 A
1 A
13708 GGGTCCCAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 8 0.22
41 29 0.78
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (40 bp):
ATTCCAAATATATCGATACATTCTACAAATGTATCGATAC
Found at i:13767 original size:19 final size:19
Alignment explanation
Indices: 13743--13810 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
13733 AATTCAACGA
13743 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
13762 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
13777 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
13794 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
13811 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:13781 original size:32 final size:32
Alignment explanation
Indices: 13745--13807 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
13735 TTCAACGATT
*
13745 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
13777 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
13808 TAATTAGCTA
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:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:13782 original size:13 final size:13
Alignment explanation
Indices: 13764--13788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13754 ACATAAGTTT
13764 TGTATCGATACAA
1 TGTATCGATACAA
13777 TGTATCGATACA
1 TGTATCGATACA
13789 TAAGTATTGT
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:15210 original size:21 final size:21
Alignment explanation
Indices: 15184--15225 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
15174 GCTACCTCCC
15184 ATACATGGAGAATAACATGAA
1 ATACATGGAGAATAACATGAA
15205 ATACATGGAGAATAACATGAA
1 ATACATGGAGAATAACATGAA
15226 CTTATGGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (21 bp):
ATACATGGAGAATAACATGAA
Found at i:16432 original size:28 final size:27
Alignment explanation
Indices: 16365--16437 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
16355 CTTCACAATC
* *
16365 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
16392 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
16420 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
16438 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:16482 original size:51 final size:51
Alignment explanation
Indices: 16420--16590 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
16410 TTATTTCTGA
* * *
16420 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
16471 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
16524 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
16576 GAGGATACTCCAACC
1 GGGGATACTCCAACC
16591 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:16609 original size:28 final size:28
Alignment explanation
Indices: 16573--16654 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
16563 ATTTTTCACA
*
16573 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
16601 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
16629 --CGAGGGAACACTCCAACCTTGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
16655 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 40 0.89
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Done.