Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1937
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: 57681
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:67 original size:20 final size:21
Alignment explanation
Indices: 37--76 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
27 CTACATTTTC
37 AAATATGTATCGATACATCAA
1 AAATATGTATCGATACATCAA
58 AAAT-TGTATCGATACATCA
1 AAATATGTATCGATACATCA
77 CACGGGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (21 bp):
AAATATGTATCGATACATCAA
Found at i:497 original size:34 final size:35
Alignment explanation
Indices: 434--500 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
424 CTAAGTGATT
434 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
470 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
501 TGTTGTAAGG
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:2197 original size:83 final size:84
Alignment explanation
Indices: 2026--2184 Score: 191
Period size: 83 Copynumber: 1.9 Consensus size: 84
2016 TCAAAGAAGA
* * * *
2026 AAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAAAAGAGT
1 AAAATAAATCAATAAGTGTAGAGAATCATATTCTTAAAAAGAAAATAAATGAATTAGAAAAGAGA
*
2091 ATGAAAGAGTTACAAAATG
66 AAGAAAGAGTTACAAAATG
* * *
2110 AAAATAAATCAATGAGTTTAGA-AAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAAGAGA
1 AAAATAAATCAATAAGTGTAGAGAATCATATTC--TTAAAAAGAAAATAAATGAATTAGAAAAGA
2172 -AAAGAAATGAGTT
64 GAAAGAAA-GAGTT
2185 GCAAGTCGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
81 4 0.06
82 6 0.09
83 34 0.53
84 20 0.31
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.26
Consensus pattern (84 bp):
AAAATAAATCAATAAGTGTAGAGAATCATATTCTTAAAAAGAAAATAAATGAATTAGAAAAGAGA
AAGAAAGAGTTACAAAATG
Found at i:5497 original size:13 final size:13
Alignment explanation
Indices: 5479--5504 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5469 TACAGCAAGT
5479 ATGTATCGATACA
1 ATGTATCGATACA
5492 ATGTATCGATACA
1 ATGTATCGATACA
5505 CAAAAAATTG
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:6025 original size:34 final size:35
Alignment explanation
Indices: 5962--6028 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
5952 CTAAGTGATT
5962 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
5998 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
6029 TGTTGTAAGG
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:6693 original size:26 final size:26
Alignment explanation
Indices: 6663--6750 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
6653 GTTGGTGGCA
6663 CCTTTCAGTCCTCAAAAAGCAGGACG
1 CCTTTCAGTCCTCAAAAAGCAGGACG
*** * ** * *
6689 CCTTTCAAAGCTCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCA-AAAAG-CAG-GACG
*
6718 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAAAGCAGGACG
6744 CCTTTCA
1 CCTTTCA
6751 AAGCCCACAC
Statistics
Matches: 42, Mismatches: 17, Indels: 6
0.65 0.26 0.09
Matches are distributed among these distances:
26 20 0.48
27 5 0.12
28 4 0.10
29 13 0.31
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAAAGCAGGACG
Found at i:6718 original size:55 final size:55
Alignment explanation
Indices: 6634--7140 Score: 698
Period size: 55 Copynumber: 9.0 Consensus size: 55
6624 GACGCCTTTT
* *
6634 CCTTTAAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAAAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
*
6689 CCTTTCAAAGCTCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
**
6744 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
* *
6799 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACG
* *
6854 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCGAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACG
*
6909 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
* * *
6964 CCTTTTAAAGCCCACATAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
* *
7018 CCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG
1 CCTT-T-C----AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
* *
7079 CTTTCTTTTTGCATAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG
1 C---C--TTT-CAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACG
7140 C
1 C
7141 TCTCTCCTTT
Statistics
Matches: 412, Mismatches: 24, Indels: 26
0.89 0.05 0.06
Matches are distributed among these distances:
54 31 0.08
55 282 0.68
56 4 0.01
60 25 0.06
61 65 0.16
64 1 0.00
65 2 0.00
66 2 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:6731 original size:29 final size:29
Alignment explanation
Indices: 6646--6731 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 29
6636 TTTAAAAGCC
6646 CACACAAGTTGGTGGCACCTTTCAGTCCT
1 CACACAAGTTGGTGGCACCTTTCAGTCCT
* ** * * ***
6675 CA-AAAAG-CAG-GACGCCTTTCAAAGCT
1 CACACAAGTTGGTGGCACCTTTCAGTCCT
6701 CACACAAGTTGGTGGCACCTTTCAGTCCT
1 CACACAAGTTGGTGGCACCTTTCAGTCCT
6730 CA
1 CA
6732 AAGAGCAGGA
Statistics
Matches: 38, Mismatches: 16, Indels: 6
0.63 0.27 0.10
Matches are distributed among these distances:
26 13 0.34
27 5 0.13
28 5 0.13
29 15 0.39
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (29 bp):
CACACAAGTTGGTGGCACCTTTCAGTCCT
Found at i:6831 original size:27 final size:27
Alignment explanation
Indices: 6750--6886 Score: 76
Period size: 27 Copynumber: 5.0 Consensus size: 27
6740 GACGCCTTTC
6750 AAAGCCCACACAAGTTGGTGGCATTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT
** * * * ** ** *
6777 TCAGTCCTCAAAGAGCAGGACGCCTTTT
1 AAAGCCCACACA-AGTTGGTGGCATTTT
6805 AAAGCCCACACAAGTTGGTGGCATTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT
** * * * ** ** *
6832 CCAGTCCTCAAAGAGCAGGACGCCTTTT
1 AAAGCCCACACA-AGTTGGTGGCATTTT
6860 AAAGCCCACACAAGTTGGTGGCATTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT
6887 CGAGTCCTCA
Statistics
Matches: 68, Mismatches: 40, Indels: 4
0.61 0.36 0.04
Matches are distributed among these distances:
27 34 0.50
28 34 0.50
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (27 bp):
AAAGCCCACACAAGTTGGTGGCATTTT
Found at i:7246 original size:57 final size:58
Alignment explanation
Indices: 7157--7268 Score: 165
Period size: 57 Copynumber: 1.9 Consensus size: 58
7147 CTTTTGCCTT
* * *
7157 TTTCTTTTAAAGCCCACATAAGTTGGTGGCACTT-TTCAGTCCTCAAAGAGCAGGATAC
1 TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCT-AGTCCTCAAAAAGCAGGATAC
*
7215 TTTCTTTT-AAGCGCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAAAGCAGGA
1 TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAAAGCAGGA
7269 CGTTCTCTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 40 0.82
58 9 0.18
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (58 bp):
TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAAAGCAGGATAC
Found at i:7291 original size:131 final size:133
Alignment explanation
Indices: 7016--7394 Score: 548
Period size: 131 Copynumber: 2.8 Consensus size: 133
7006 AAGAGCAGGA
* * * *
7016 CGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCT
1 CGCCTTTTTCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATACT
* *
7081 TTCTTTTTGCATAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCT
66 TTCTTTTT--AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAAAGCAGGACGCTCTCT
7146 CCTTT
129 CCTTT
*
7151 TGCCTTTTTCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATACT
1 CGCCTTTTTCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATACT
* *
7216 TTC-TTTT-AAGCGCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAAAGCAGGACGTTCTCTCC
66 TTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAAAGCAGGACGCTCTCTCC
7279 TTT
131 TTT
* * * * * *
7282 CGCCTTTTTCTTTTAAAGTCCATATAAGCTGGCGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCC
1 CGCCTTTTTCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAT-AC
**
7346 TTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAA
65 TT-TCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAA
7395 GAGTAGGATG
Statistics
Matches: 221, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
130 22 0.10
131 91 0.41
132 2 0.01
133 4 0.02
134 39 0.18
135 63 0.29
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.31
Consensus pattern (133 bp):
CGCCTTTTTCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATACT
TTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAAAGCAGGACGCTCTCTCC
TTT
Found at i:7379 original size:60 final size:60
Alignment explanation
Indices: 7288--7520 Score: 267
Period size: 61 Copynumber: 3.9 Consensus size: 60
7278 CTTTCGCCTT
* * * * *
7288 TTTC-TTTTAAAGTCCATATAAGCTGGCGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCC
1 TTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTCTTCAGTCCTCAAAGAGCAGGATGCC
* * *
7346 TTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGATG-C
1 TT-TCTTTTTAAAGCCCACACAAGTTGGTGGCACTCTTCAGTCCTCAAAGAGCAGGATGCC
* * *
7406 TTTCTTTTTGCAAAGCCCACACAAGTTGGTGGCA-TCTTCCAGTCCTCAAAGGGTAGGACGCC
1 TTTCTTTTT--AAAGCCCACACAAGTTGGTGGCACTCTT-CAGTCCTCAAAGAGCAGGATGCC
* * *
7468 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGC
1 -TTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTCTTCAGTCCTCAAAGAGC
7521 GGGACACACT
Statistics
Matches: 149, Mismatches: 17, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
58 2 0.01
59 9 0.06
60 29 0.19
61 97 0.65
62 4 0.03
63 8 0.05
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (60 bp):
TTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTCTTCAGTCCTCAAAGAGCAGGATGCC
Found at i:8481 original size:13 final size:13
Alignment explanation
Indices: 8463--8488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8453 TATTATTCCA
8463 TGTATCGATACAT
1 TGTATCGATACAT
8476 TGTATCGATACAT
1 TGTATCGATACAT
8489 GGATCTTTGT
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:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10900 original size:52 final size:52
Alignment explanation
Indices: 10841--11074 Score: 242
Period size: 51 Copynumber: 4.6 Consensus size: 52
10831 TTAAGTTTCT
*
10841 CAATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCTAAAACAC
* * * * *
10893 CAATTTTTCATAATCAGGGATACTCCAAC-CTTGACTTTA-TTCCTAAAATAT
1 CAATTTTTCATAATCGGGGATACTCCAACTC-CGATTTTATTTCCTAAAACAC
** * * * * *
10944 TGATTTCTCATAATCGGAGATACTCGAACCCCGGTTTTATTT-CTAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCTAAAACAC
* * * * *
10995 CAATTCTCCACAATCGGGGATATTCCAACTCTGATTTTATTTCC-AAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCTAAAACAC
* * *
11046 TAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTTTTCATAATCGGGGATACTCCAAC
11075 CTCGTTATTT
Statistics
Matches: 144, Mismatches: 34, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
51 106 0.74
52 38 0.26
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.33
Consensus pattern (52 bp):
CAATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCTAAAACAC
Found at i:11102 original size:79 final size:80
Alignment explanation
Indices: 11007--11212 Score: 197
Period size: 79 Copynumber: 2.6 Consensus size: 80
10997 ATTCTCCACA
* * *
11007 ATCGGGGATATTCCAACTCTGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCC
1 ATCGGGGATACTCCAACTCTGACTTTATTTCCAAAACACTAATTTCTCACAATCGAGGATACTCC
*
11072 AA-CCTCGTTA-TTTC
66 AACCCT-ATTATTTTC
* * * * * * * *
11086 ATCGGGGATACTCCAACCCCCG-CTTTATTTCCAAAATATTGATTTCTCATAATTGGGGATACTC
1 ATCGGGGATACTCCAA-CTCTGACTTTATTTCCAAAACACTAATTTCTCACAATCGAGGATACTC
11150 CAACCCTATTATTTTC
65 CAACCCTATTATTTTC
* * * *
11166 A-CGGGGATACT-CAAATCCTGACTTTATTTTCGAAACATCTATTTTCT
1 ATCGGGGATACTCCAACT-CTGACTTTATTTCCAAAACA-CTAATTTCT
11213 ATAATCGGGA
Statistics
Matches: 100, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
78 5 0.05
79 78 0.78
80 17 0.17
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (80 bp):
ATCGGGGATACTCCAACTCTGACTTTATTTCCAAAACACTAATTTCTCACAATCGAGGATACTCC
AACCCTATTATTTTC
Found at i:22439 original size:20 final size:20
Alignment explanation
Indices: 22414--22465 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
22404 AAATTCCCAG
22414 ATGTATCGATACAAAG-ATCA
1 ATGTATCGATACAAAGAAT-A
**
22434 ATGTATCGATACATTGAATA
1 ATGTATCGATACAAAGAATA
22454 ATGTATCGATAC
1 ATGTATCGATAC
22466 TGTAGATACC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAAGAATA
Found at i:23280 original size:11 final size:10
Alignment explanation
Indices: 23237--23269 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
23227 CTTCTTTTCT
23237 AAAAAAACAA
1 AAAAAAACAA
23247 AAAAAAACCAA
1 AAAAAAA-CAA
23258 AAAAAAACAA
1 AAAAAAACAA
23268 AA
1 AA
23270 CAAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:24417 original size:55 final size:55
Alignment explanation
Indices: 24348--24833 Score: 437
Period size: 55 Copynumber: 8.5 Consensus size: 55
24338 TCTCTCTTTT
* * *
24348 CACCCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGGCCACACAAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
* * * *
24403 CACCTTTTTGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTCGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
* *
24458 CA-TTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGG
1 CACCTTT-TAGTCCTCAAAGAGCAGGACGCC-TTTC------AAAGCCCACACAAGTTGGTGG
*
24520 CA--TTTTCCAGTCCTCAAAGAGAAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGG
1 CACCTTTT--AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGG
24575 CA--TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTT--AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
* * * * * * *
24630 CACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACGAGTCGATGA
1 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
* *
24685 CA-TTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGG
1 CACCTTT-TAGTCCTCAAAGAGCAGGACGCC-TTTC------AAAGCCCACACAAGTTGGTGG
* * * * * * *
24747 TACCATCTAGTCCTCAAAGAACAAGATGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGC-AG--GAC--GCC-TTTCAAAGCCCACACAAGTTGGTGG
*
24808 CACTTTTTAGTCCTCAAAGAGCAGGA
1 CACCTTTTAGTCCTCAAAGAGCAGGA
24834 TGCACTTTAT
Statistics
Matches: 357, Mismatches: 46, Indels: 53
0.78 0.10 0.12
Matches are distributed among these distances:
54 8 0.02
55 208 0.58
56 6 0.02
57 3 0.01
58 1 0.00
60 3 0.01
61 41 0.11
62 75 0.21
63 3 0.01
65 2 0.01
67 7 0.02
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (55 bp):
CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:24556 original size:117 final size:117
Alignment explanation
Indices: 24382--24833 Score: 557
Period size: 117 Copynumber: 3.9 Consensus size: 117
24372 GATGCCTTTC
* ** * *
24382 AAAGGCCACACAAGTTGGTGGCACCTTTTTGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGAAGGACGCCTCTTAAAGCCCACA
24447 CGAGTCGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTA
66 CGAGTCGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTA
*
24499 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGAAGGACGCCTCTTAAAGCCCAC
1 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGAAGGACGCCTCTTAAAGCCCAC
* * * *
24563 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC-TTTC------
65 ACGAGTCGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTA
* * *
24609 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGAAGGACGCCTCTTAAAGCCCACA
* *
24674 CGAGTCGATGACATTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTA
66 CGAGTCGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTA
* * * *
24726 AAAGCCCACACAAGTTGGTGGTACC-ATCTAGTCCTCAAAGA-ACAAGATGCCTTTCCTTTTCAA
1 AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGA-AGGACGCC--T-C--TT-AA
*
24789 AGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGA
58 AGCCCACACGAGTCGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGA
24834 TGCACTTTAT
Statistics
Matches: 289, Mismatches: 28, Indels: 30
0.83 0.08 0.09
Matches are distributed among these distances:
110 92 0.32
111 7 0.02
116 9 0.03
117 135 0.47
119 1 0.00
122 2 0.01
123 39 0.13
124 4 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (117 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGAAGGACGCCTCTTAAAGCCCACA
CGAGTCGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTA
Found at i:24644 original size:172 final size:166
Alignment explanation
Indices: 24356--24841 Score: 489
Period size: 172 Copynumber: 2.8 Consensus size: 166
24346 TTCACCCTTT
* * * *
24356 AGTCCTCAAAGAGCAGGATGCCT-TTCAAAGGCCACACAAGTTGGTGGCACCTTTT-TGTCCTCA
1 AGTCCTCAAAGAGCAGGACGCCTCTTAAAAGCCCACACAAGTTGGTGGCA--TTTTCAGTCCTCA
* *
24419 AAGAGCAGGACGCCTTTTAAAGCCCACACGAGTCGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGG
64 AAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGG
* * * * *
24483 ACACCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGGCATTTTCC
128 A-A----TGCCTTTT-AAAGCCCACACAAGTCGATGACATTTTCC
*
24528 AGTCCTCAAAGAGAAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTCTTAAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAA
* *
24592 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGG-A
65 AGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAA
* *
24656 TGCCTTTTAAAGCCCACACGAGTCGATGACATTTTCT
130 TGCCTTTTAAAGCCCACACAAGTCGATGACATTTTCC
* * ***
24693 AGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGGTACCATCTAGT
1 AGTCCTCAAAGAGCAGGACGCC---TC---TTAAAAGCCCACACAAGTTGGTGGCATTTTC-AGT
* * * *
24758 CCTCAAAGAACAAGATGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTC
59 CCTCAAAGAGC-AG--GAC--GCC-TTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTC
24823 AAAGAGCAGG-ATGCACTTT
118 AAAGAGCAGGAATGC-CTTT
24842 ATTTTCCTCT
Statistics
Matches: 268, Mismatches: 27, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
165 44 0.16
166 6 0.02
168 2 0.01
170 5 0.02
171 3 0.01
172 141 0.53
173 8 0.03
175 2 0.01
177 2 0.01
178 51 0.19
179 4 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (166 bp):
AGTCCTCAAAGAGCAGGACGCCTCTTAAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAA
GAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAAT
GCCTTTTAAAGCCCACACAAGTCGATGACATTTTCC
Found at i:24761 original size:227 final size:231
Alignment explanation
Indices: 24356--24833 Score: 734
Period size: 227 Copynumber: 2.1 Consensus size: 231
24346 TTCACCCTTT
* * **
24356 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGGCCACACAAGTTGGTGGCACCTTTTTGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
* *
24421 GAGCAGGACGCCTTTTAAAGCCCACACGAGTCGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACA
66 GAGCAGGACGCCTTTTAAAGCCCACACGAGTCGATGACATTTTCTAGTCCTCAAAGAGCAGGACA
*** *
24486 CCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGA-AGGACGCC
131 CCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGGCACCATCCAGTCCTCAAAGA-ACAAGACGCC
24550 -T-C-TT-AAAGCCCACACAAGTTGGTGGCA-TTTTCC
195 TTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-C
24583 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
24648 GAGCAGGATGCCTTTTAAAGCCCACACGAGTCGATGACATTTTCTAGTCCTCAAAGAGCAGGACA
66 GAGCAGGACGCCTTTTAAAGCCCACACGAGTCGATGACATTTTCTAGTCCTCAAAGAGCAGGACA
* * *
24713 CCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGGTACCATCTAGTCCTCAAAGAACAAGATGCCT
131 CCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGGCACCATCCAGTCCTCAAAGAACAAGACGCC-
* *
24778 TTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
195 TTCC-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
24816 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
24834 TGCACTTTAT
Statistics
Matches: 227, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
226 1 0.00
227 178 0.78
229 1 0.00
230 1 0.00
232 2 0.01
233 40 0.18
234 4 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (231 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
GAGCAGGACGCCTTTTAAAGCCCACACGAGTCGATGACATTTTCTAGTCCTCAAAGAGCAGGACA
CCTTTTCTTTTTAAAAGCCCACACAAGTTGGTGGCACCATCCAGTCCTCAAAGAACAAGACGCCT
TCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:28044 original size:51 final size:51
Alignment explanation
Indices: 27964--28132 Score: 173
Period size: 51 Copynumber: 3.3 Consensus size: 51
27954 ATTTTTCATC
* * * *
27964 TCGAGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAA-TTTCTCTTAA
1 TCGAGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTC-CATAA
* * *
28015 TCGAGGATACTCTAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGAGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
* * ** *
28066 TCGGGGATACTCCAACTCTGATTTTATTTCCAAAACACCGGCTTTT-CACAA
1 TCGAGGATACTCCAACTCCGATTTTATTTCCAAAACACC-AATTTTCCATAA
*
28117 TCGGGGATACTCCAAC
1 TCGAGGATACTCCAAC
28133 CCCGTTATTT
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
51 92 0.91
52 9 0.09
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
TCGAGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
Found at i:28230 original size:76 final size:75
Alignment explanation
Indices: 28116--28338 Score: 297
Period size: 76 Copynumber: 2.9 Consensus size: 75
28106 GCTTTTCACA
* *
28116 ATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGACACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAA-CCCGTTATTTTTTAGGGGACACTCCAACCCCGGTTTTATTTCTAAAAC
28181 ATCAATTTTTC
65 ATCAATTTTTC
* * *
28192 ATTGGGGATACTCCAACCCTGTTATTTTTTAGGGGACACTCCAACCCCGATTTTGTTTCTAAAAC
1 ATCGGGGATACTCCAACCC-GTTATTTTTTAGGGGACACTCCAACCCCGGTTTTATTTCTAAAAC
*
28257 ATCAACTTTTC
65 ATCAATTTTTC
* * * *
28268 ATCGGGGATACTCCAA-CC-TCATTATTTTCGGGGAAAACTCCAACTCCGGTTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCGTTATT-TTTTAGGGG-ACACTCCAACCCCGGTTTTATTTCTAAAA
*
28331 CACCAATT
64 CATCAATT
28339 CTCCACAATC
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
73 4 0.03
74 8 0.06
75 36 0.28
76 81 0.63
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (75 bp):
ATCGGGGATACTCCAACCCGTTATTTTTTAGGGGACACTCCAACCCCGGTTTTATTTCTAAAACA
TCAATTTTTC
Found at i:28372 original size:51 final size:50
Alignment explanation
Indices: 28295--28464 Score: 196
Period size: 51 Copynumber: 3.3 Consensus size: 50
28285 CTCATTATTT
* * *
28295 TCGGGGAAAACTCCAACTCCGGTTTTATTTCTAAAACACCAATTCTCCACAA
1 TCGGGG-ATACTCCAACTCCGATTTTATTTCCAAAACACCAATT-TCCACAA
* * *
28347 TCGGGGATATTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA-TTTCCACAA
** * * * *
28398 TTAGGGATACTCCAACTCCGATTGTATTTCCAAAGCATCAATTTCTTACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTC-CACAA
28449 TCGGGGATACTCCAAC
1 TCGGGGATACTCCAAC
28465 CTCGTTATTT
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 3 0.03
51 88 0.89
52 8 0.08
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (50 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCCACAA
Found at i:30903 original size:7 final size:7
Alignment explanation
Indices: 30873--30925 Score: 72
Period size: 7 Copynumber: 7.6 Consensus size: 7
30863 TTTTTTCCAA
*
30873 AAAAAAT
1 AAAAAAG
30880 AACAAAA-
1 AA-AAAAG
*
30887 AAAAAGG
1 AAAAAAG
30894 AAAAAAG
1 AAAAAAG
30901 AAAAAAG
1 AAAAAAG
30908 AAAAAAG
1 AAAAAAG
30915 AAAAAAG
1 AAAAAAG
30922 AAAA
1 AAAA
30926 GAACCTGCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 3 0.07
7 35 0.83
8 4 0.10
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:31975 original size:61 final size:61
Alignment explanation
Indices: 31880--32207 Score: 396
Period size: 61 Copynumber: 5.4 Consensus size: 61
31870 ACCTTTTATA
* * ** * **
31880 CTTTTAGTCCTCAAAGAGCAGAATACCTTTTCCTTTTAAAGCTTACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * *
31941 CTTTTAGTCCTCAAAAAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGTAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * *
32002 CTTTCAGTCCTCAAAGAGCAAGATGTCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* *
32063 CTTTCAGTCCTTAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCATACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * ** *
32124 CTTCCACTCCTTAAAGAGCAAAAC-CCTT-TCC-TTTCAAGTCCCACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAG-CCCACACAAGTTGGTGGCAC
*
32183 C-TTCTAGTCCTC-AAGAACAGGACGC
1 CTTTC-AGTCCTCAAAGAGCAGGACGC
32208 ACGTTATTTC
Statistics
Matches: 231, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
58 16 0.07
59 29 0.13
60 4 0.02
61 182 0.79
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (61 bp):
CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
Found at i:32281 original size:43 final size:42
Alignment explanation
Indices: 32189--32367 Score: 195
Period size: 43 Copynumber: 4.2 Consensus size: 42
32179 GCACCTTCTA
*
32189 GTCCTC-AAGAACAGGACGCACGTT-ATTTCTT-TTTCTCCTTT
1 GTCCTCAAAGAACAGGACACAC-TTAATTTCTTCTTT-TCCTTT
* *
32230 GTCTTCAAAGAGCAGGACACACTTAATTTCCTTCTTTTCCTTT
1 GTCCTCAAAGAACAGGACACACTTAATTT-CTTCTTTTCCTTT
* * * * * *
32273 GTTCTCAAAGAGCAGGACGCATTTTATTTCTTTTTTTCCTTT
1 GTCCTCAAAGAACAGGACACACTTAATTTCTTCTTTTCCTTT
*
32315 GTCCTCAAAGAAC-GAGACACATTTAATTTTCTTCTTTTCCTTT
1 GTCCTCAAAGAACAG-GACACACTTAA-TTTCTTCTTTTCCTTT
32358 GTCCTCAAAG
1 GTCCTCAAAG
32368 GGCAAGATGT
Statistics
Matches: 118, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
41 8 0.07
42 49 0.42
43 58 0.49
44 3 0.03
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (42 bp):
GTCCTCAAAGAACAGGACACACTTAATTTCTTCTTTTCCTTT
Found at i:32343 original size:85 final size:85
Alignment explanation
Indices: 32189--32367 Score: 254
Period size: 85 Copynumber: 2.1 Consensus size: 85
32179 GCACCTTCTA
* *
32189 GTCCTC-AAGAACAGGACGCACGTTATTTCTTTTTCTCCTTTGTCTTCAAAGAGCAGGACACACT
1 GTCCTCAAAGAACAGGACGCACGTTATTTCTTTTTCTCCTTTGTCCTCAAAGAACAGGACACACT
32253 TAATTTCCTTCTTTTCCTTT
66 TAATTTCCTTCTTTTCCTTT
* * ** * *
32273 GTTCTCAAAGAGCAGGACGCATTTTATTTCTTTTTTTCCTTTGTCCTCAAAGAAC-GAGACACAT
1 GTCCTCAAAGAACAGGACGCACGTTATTTCTTTTTCTCCTTTGTCCTCAAAGAACAG-GACACAC
*
32337 TTAATTTTCTTCTTTTCCTTT
65 TTAATTTCCTTCTTTTCCTTT
32358 GTCCTCAAAG
1 GTCCTCAAAG
32368 GGCAAGATGT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
84 6 0.07
85 77 0.93
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (85 bp):
GTCCTCAAAGAACAGGACGCACGTTATTTCTTTTTCTCCTTTGTCCTCAAAGAACAGGACACACT
TAATTTCCTTCTTTTCCTTT
Found at i:35651 original size:51 final size:49
Alignment explanation
Indices: 35550--35658 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 49
35540 TATTTTCGAG
* * * *
35550 GGGATACTCTAACCTCGGTTTTATTTTCAAACATCGATTTTTTACCATCA
1 GGGATACTCCAACCCCGATTTTATTTCCAAACATCGATTTTTTA-CATCA
35600 GGGATACTCCAACCCCGATTTTATTTCCAGAACATCGATTTTCTGTA-ATCA
1 GGGATACTCCAACCCCGATTTTATTTCCA-AACATCGATTTT-T-TACATCA
*
35651 GGAATACT
1 GGGATACT
35659 TTCACCCCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 25 0.49
51 23 0.45
52 1 0.02
53 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (49 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAACATCGATTTTTTACATCA
Found at i:35666 original size:51 final size:49
Alignment explanation
Indices: 35553--35658 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 49
35543 TTTCGAGGGG
* * * * *
35553 ATACTCTAACCTCGGTTTTATTTTCAAACATCGATTTTTTACCATCAGGG
1 ATACTCCAACCCCGATTTTATTTCCAAACATCGATTTTTTA-CATCAGGA
35603 ATACTCCAACCCCGATTTTATTTCCAGAACATCGATTTTCTGTA-ATCAGGA
1 ATACTCCAACCCCGATTTTATTTCCA-AACATCGATTTT-T-TACATCAGGA
35654 ATACT
1 ATACT
35659 TTCACCCCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
50 22 0.46
51 23 0.48
52 1 0.02
53 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (49 bp):
ATACTCCAACCCCGATTTTATTTCCAAACATCGATTTTTTACATCAGGA
Found at i:36571 original size:19 final size:20
Alignment explanation
Indices: 36524--36575 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
36514 TTACAAGCCA
*
36524 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
* *
36544 ATCTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
36564 -TGTATCGATACA
1 ATGTATCGATACA
36576 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:37354 original size:41 final size:41
Alignment explanation
Indices: 37257--37356 Score: 173
Period size: 41 Copynumber: 2.4 Consensus size: 41
37247 AATCAAAAAA
*
37257 TTTCTCCCCCTTAATAAAGCAATTTAACAATTACAAGTTTC
1 TTTCTCCCCCTTAATCAAGCAATTTAACAATTACAAGTTTC
* *
37298 TTTCTCCCCTTTAATCAAGCAATTTAACAATTAGAAGTTTC
1 TTTCTCCCCCTTAATCAAGCAATTTAACAATTACAAGTTTC
37339 TTTCTCCCCCTTAATCAA
1 TTTCTCCCCCTTAATCAA
37357 AAAATTTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (41 bp):
TTTCTCCCCCTTAATCAAGCAATTTAACAATTACAAGTTTC
Found at i:46975 original size:6 final size:7
Alignment explanation
Indices: 46954--46979 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
46944 TTTGAAAGAT
46954 AATTAAA
1 AATTAAA
46961 AATTAAA
1 AATTAAA
46968 AATTAAA
1 AATTAAA
46975 AATTA
1 AATTA
46980 TTAATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATTAAA
Found at i:46985 original size:14 final size:14
Alignment explanation
Indices: 46952--46986 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
46942 ATTTTGAAAG
46952 ATAATTAAAAATTA
1 ATAATTAAAAATTA
*
46966 AAAATTAAAAATTA
1 ATAATTAAAAATTA
*
46980 TTAATTA
1 ATAATTA
46987 TTAATAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATTAAAAATTA
Found at i:47166 original size:22 final size:22
Alignment explanation
Indices: 47110--47167 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
47100 TATCAAAATT
47110 ATAATTTTAAATTTTAAAATTAA
1 ATAATTTTAAA-TTTAAAATTAA
** *
47133 ATTGTTTCAAATTT-AAATTAA
1 ATAATTTTAAATTTAAAATTAA
47154 ATAAATTTTAAATT
1 AT-AATTTTAAATT
47168 ATTTACTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 9 0.32
22 11 0.39
23 8 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAATTTTAAATTTAAAATTAA
Found at i:47390 original size:29 final size:29
Alignment explanation
Indices: 47343--47421 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
47333 TTATTTTATT
*
47343 TAAATAAATTTATATATTTTTA-TCATACA
1 TAAATAAATTT-TAAATTTTTATTCATACA
* **
47372 TAAATAAATTCTTAAA-TTTTATTTATATT
1 TAAATAAATT-TTAAATTTTTATTCATACA
*
47401 TAAATAAATTTTTAATTTTTA
1 TAAATAAATTTTAAATTTTTA
47422 ATTTTTAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 9 0.21
29 32 0.76
30 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (29 bp):
TAAATAAATTTTAAATTTTTATTCATACA
Found at i:47419 original size:7 final size:7
Alignment explanation
Indices: 47407--47432 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
47397 TATTTAAATA
47407 AATTTTT
1 AATTTTT
47414 AATTTTT
1 AATTTTT
47421 AATTTTT
1 AATTTTT
47428 AATTT
1 AATTT
47433 ATATACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:47435 original size:37 final size:36
Alignment explanation
Indices: 47378--47452 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
47368 TACATAAATA
** *
47378 AATTCTTAAATTTTATTTATATTTAAATAAATTTTT
1 AATTCTTAAATTTTATTTATATACAAATAAATTATT
* *
47414 AATTTTTAATTTTTAATTTATATACAAATAAATTATT
1 AATTCTTAAATTTT-ATTTATATACAAATAAATTATT
47451 AA
1 AA
47453 ATAATTTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
36 12 0.36
37 21 0.64
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (36 bp):
AATTCTTAAATTTTATTTATATACAAATAAATTATT
Found at i:51218 original size:2 final size:2
Alignment explanation
Indices: 51213--51238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51203 ATATATATAT
51213 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
51239 GATGGATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:51876 original size:32 final size:32
Alignment explanation
Indices: 51840--51901 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
51830 TTTGAATCAA
* *
51840 AAATGATCCAAACTCGAAATGACACGAACACT
1 AAATGATCCAAACTCAAAATAACACGAACACT
* *
51872 AAATGATTCAAACTCAAAATAACTCGAACA
1 AAATGATCCAAACTCAAAATAACACGAACA
51902 ATTAACCCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.18
Consensus pattern (32 bp):
AAATGATCCAAACTCAAAATAACACGAACACT
Found at i:52622 original size:15 final size:15
Alignment explanation
Indices: 52602--52632 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52592 ACTCTATAAG
52602 CTAAACCATGTCCGA
1 CTAAACCATGTCCGA
52617 CTAAACCATGTCCGA
1 CTAAACCATGTCCGA
52632 C
1 C
52633 CATACTAGAA
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:0.32, C:0.35, G:0.13, T:0.19
Consensus pattern (15 bp):
CTAAACCATGTCCGA
Done.