Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1275
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: 47612
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1260 original size:49 final size:49
Alignment explanation
Indices: 1204--1317 Score: 201
Period size: 49 Copynumber: 2.3 Consensus size: 49
1194 AAAAATGCCT
* *
1204 GAATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAACCCA
1 GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCA
*
1253 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCA
1 GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCA
1302 GAATGTATCGATACAA
1 GAATGTATCGATACAA
1318 ATTGTGAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (49 bp):
GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAACCA
Found at i:1267 original size:29 final size:28
Alignment explanation
Indices: 1225--1316 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 28
1215 TACATTGAAA
1225 AATGTATCGATACATCTGGGTAAACCCAG
1 AATGTATCGATACATCTGGGTAAA-CCAG
*
1254 AATGTATCGATACA-AT--G--AA-C--
1 AATGTATCGATACATCTGGGTAAACCAG
1274 AATGTATCGATACATCTGGGTAAAACCAG
1 AATGTATCGATACATCTGGGT-AAACCAG
1303 AATGTATCGATACA
1 AATGTATCGATACA
1317 AATTGTGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
20 14 0.27
21 1 0.02
22 1 0.02
23 1 0.02
24 2 0.04
26 3 0.06
27 1 0.02
28 1 0.02
29 28 0.54
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (28 bp):
AATGTATCGATACATCTGGGTAAACCAG
Found at i:4824 original size:153 final size:153
Alignment explanation
Indices: 4446--4830 Score: 387
Period size: 153 Copynumber: 2.5 Consensus size: 153
4436 CAAGTTTAAG
* * * * ** *
4446 AAAAATTACGAAAATGTCTTTAGGGGATACCTTCTACGTGGAAGTACCTGATACCCTTAAAAGAC
1 AAAAATTACGAAAATGTCTCTAAGGGATACCTTCGACATAAAAGTACCTGATACCC-TAAAGGAC
* * * * *
4511 TTAAAAAAGATTATAAATGGGATGAACTTATCCTAAATACCCTCATTTGTCATAAAAGTAGACAC
65 TTAAAAAAGATT-TAAATGGGATGAACCTACCCTAAATACCCACATTTGGCATAAAAGCAGACAC
* * *
4576 GGTGACAATCTAGGACTCGATTTTA
129 AGTGACAACCTAGGACTCGATTCTA
* ** * * ** *
4601 AAAAATTACCAAAATACCCCTAAGGGATACCTTCGACATAAAAATACCCAATACCCCTAAAGGGC
1 AAAAATTACGAAAATGTCTCTAAGGGATACCTTCGACATAAAAGTACCTGATA-CCCTAAAGGAC
* * * *
4666 CTAAAAAAGATTTAAAT-GGATGAACCTACCCTAAATATCCACCTTTGGCATAAAAGCAGACCCA
65 TTAAAAAAGATTTAAATGGGATGAACCTACCCTAAATACCCACATTTGGCATAAAAGCAGACACA
* * * *
4730 GTGATAACCTAGGAGTTGGTTCTA
130 GTGACAACCTAGGACTCGATTCTA
** * * * *
4754 GGAAATTATGAAAATGTCTCTAAGGGATACCTTCGACATAAAAGTATCTGATACTTCTGAAGGAC
1 AAAAATTACGAAAATGTCTCTAAGGGATACCTTCGACATAAAAGTACCTGATAC-CCTAAAGGAC
4819 TT-AAAAAGATTT
65 TTAAAAAAGATTT
4831 TTAAAAAATG
Statistics
Matches: 182, Mismatches: 46, Indels: 7
0.77 0.20 0.03
Matches are distributed among these distances:
152 11 0.06
153 106 0.58
154 5 0.03
155 57 0.31
156 3 0.02
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (153 bp):
AAAAATTACGAAAATGTCTCTAAGGGATACCTTCGACATAAAAGTACCTGATACCCTAAAGGACT
TAAAAAAGATTTAAATGGGATGAACCTACCCTAAATACCCACATTTGGCATAAAAGCAGACACAG
TGACAACCTAGGACTCGATTCTA
Found at i:6436 original size:11 final size:11
Alignment explanation
Indices: 6422--6463 Score: 59
Period size: 10 Copynumber: 3.7 Consensus size: 11
6412 CTTGGATTTT
6422 TCTTTTTTCTC
1 TCTTTTTTCTC
6433 TCTTTTCTTTCTC
1 TC-TTT-TTTCTC
6446 TCTTTTTTCT-
1 TCTTTTTTCTC
6456 TCTTTTTT
1 TCTTTTTT
6464 TCCTTGCTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.28
11 7 0.24
12 6 0.21
13 8 0.28
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTTTTCTC
Found at i:6445 original size:13 final size:13
Alignment explanation
Indices: 6427--6451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6417 ATTTTTCTTT
6427 TTTCTCTCTTTTC
1 TTTCTCTCTTTTC
6440 TTTCTCTCTTTT
1 TTTCTCTCTTTT
6452 TTCTTCTTTT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTCTCTTTTC
Found at i:6453 original size:15 final size:15
Alignment explanation
Indices: 6418--6456 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6408 TTTTCTTGGA
*
6418 TTTTTCTTTTTTCTCT
1 TTTTTC-TTTCTCTCT
*
6434 CTTTTCTTTCTCTCT
1 TTTTTCTTTCTCTCT
6449 TTTTTCTT
1 TTTTTCTT
6457 CTTTTTTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTCTCTCT
Found at i:6453 original size:24 final size:22
Alignment explanation
Indices: 6422--6465 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
6412 CTTGGATTTT
6422 TCTTTTTTCTCTCTTTTCTTTCTC
1 TCTTTTTTCT-TCTTTT-TTTCTC
6446 TCTTTTTTCTTCTTTTTTTC
1 TCTTTTTTCTTCTTTTTTTC
6466 CTTGCTGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TCTTTTTTCTTCTTTTTTTCTC
Found at i:6464 original size:11 final size:11
Alignment explanation
Indices: 6424--6465 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
6414 TGGATTTTTC
6424 TTTTTTCTCTCT
1 TTTTTTCT-TCT
6436 TTTCTTTC-TCT
1 TTT-TTTCTTCT
6447 CTTTTTTCTTCT
1 -TTTTTTCTTCT
6459 TTTTTTC
1 TTTTTTC
6466 CTTGCTGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 14 0.52
12 9 0.33
13 4 0.15
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:6894 original size:20 final size:20
Alignment explanation
Indices: 6871--6908 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6861 TTGCTAGTGT
*
6871 TTGCGGGAGCTGCTGTTTGG
1 TTGCGGGAGCTACTGTTTGG
*
6891 TTGCTGGAGCTACTGTTT
1 TTGCGGGAGCTACTGTTT
6909 CATGCTTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.16, G:0.37, T:0.39
Consensus pattern (20 bp):
TTGCGGGAGCTACTGTTTGG
Found at i:7183 original size:64 final size:63
Alignment explanation
Indices: 7097--7299 Score: 284
Period size: 64 Copynumber: 3.2 Consensus size: 63
7087 GCAACAACCT
*
7097 TTTACTTGTTTTTTTTCTTTTGTTGCTCCTTGCTCTCGTTTCTTCTTAATTGTTTTTGTAGCA
1 TTTACTTGTTTTTTTTCTTTTGTTGCTCCTTGTTCTCGTTTCTTCTTAATTGTTTTTGTAGCA
* *
7160 TTTACTTGCTTTTTTTTCTTTTGTTGCTCCTTGTTGC-CATTCCTTCTTAATTGTTTTTGTAG-A
1 TTTACTTG-TTTTTTTTCTTTTGTTGCTCCTTGTT-CTCGTTTCTTCTTAATTGTTTTTGTAGCA
* * * * *
7223 TTTTACTTGTTTTTTTTTCTTTTGTTGCTCCATGTTGTTGTTTCTTCTTAATTGTTTTTGCAGCT
1 -TTTACTTG-TTTTTTTTCTTTTGTTGCTCCTTGTTCTCGTTTCTTCTTAATTGTTTTTGTAGCA
7288 TTTACTTGTTTT
1 TTTACTTGTTTT
7300 CATTTATTGC
Statistics
Matches: 124, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
63 13 0.10
64 110 0.89
65 1 0.01
ACGTcount: A:0.08, C:0.16, G:0.13, T:0.63
Consensus pattern (63 bp):
TTTACTTGTTTTTTTTCTTTTGTTGCTCCTTGTTCTCGTTTCTTCTTAATTGTTTTTGTAGCA
Found at i:10339 original size:85 final size:85
Alignment explanation
Indices: 10188--10438 Score: 285
Period size: 85 Copynumber: 3.0 Consensus size: 85
10178 ATGAAAGGGG
* *
10188 TTACTCGAGACTAA-ACTGATAAGTAAACAAAGGATACAAAAGTTGACTAAGATTGAACTGATAA
1 TTACTCGAGACTAAGAC-GATAAGTAAACAAAGGATACAAAAGTTGACTAAGATTAAACTGACAA
* *
10252 GTCAATAAAGGATAAAAGAAT
65 GTCAACAAAAGATAAAAGAAT
* * * * * *
10273 TTACCCGAGACTAAGTCGATAGGTAAACAAAGGATA-AAATGGTTGACTAGGATTAAATTGACAA
1 TTACTCGAGACTAAGACGATAAGTAAACAAAGGATACAAA-AGTTGACTAAGATTAAACTGACAA
*
10337 GTCAACAAAAGATAAAAGGAT
65 GTCAACAAAAGATAAAAGAAT
* * ** *
10358 TTACTCG-GTACTAAGCCGACAAGTAAACAAAGGATACAAAAGTTG-CTCGGAATTGAACTGACA
1 TTACTCGAG-ACTAAGACGATAAGTAAACAAAGGATACAAAAGTTGACTAAG-ATTAAACTGACA
*
10421 AGTCAACAATAGATAAAA
64 AGTCAACAAAAGATAAAA
10439 AGCGATACCT
Statistics
Matches: 141, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
84 8 0.06
85 129 0.91
86 4 0.03
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (85 bp):
TTACTCGAGACTAAGACGATAAGTAAACAAAGGATACAAAAGTTGACTAAGATTAAACTGACAAG
TCAACAAAAGATAAAAGAAT
Found at i:10541 original size:44 final size:44
Alignment explanation
Indices: 10467--10891 Score: 194
Period size: 44 Copynumber: 9.8 Consensus size: 44
10457 TAAACGTAAC
* ** *
10467 AAGTTTGACTAGAGCTGGACCATTACGTCAAACAAGGATGAAAA
1 AAGTTTGACTAGGGCTAAACCATCACGTCAAACAAGGATGAAAA
* * *
10511 AATTTTGA-TGAGGGCTAAACCATCATGTCAAACAATGATGAAAA
1 AAGTTTGACT-AGGGCTAAACCATCACGTCAAACAAGGATGAAAA
* * * * *
10555 GAGTTTGACTAGGGCTAAATCATCACGTCAAATAA-TAGTGAAAG
1 AAGTTTGACTAGGGCTAAACCATCACGTCAAACAAGGA-TGAAAA
* * * **
10599 GAGTTTGACTA-AGCAAAACCATCACGTCAAATGA-GAT-AAAA
1 AAGTTTGACTAGGGCTAAACCATCACGTCAAACAAGGATGAAAA
* * * ** * * *
10640 GGAGTTTAACCAACGCTACACCATTACATCAAACGAA--A-GCAAAA
1 -AAGTTTGACTAGGGCTAAACCATCACGTCAAAC-AAGGATG-AAAA
* * * * * * * *
10684 AGGTTTGACCAAGGCAAAACCATCATGTCAAATGAA-AATGAAAG
1 AAGTTTGACTAGGGCTAAACCATCACGTCAAA-CAAGGATGAAAA
* * * * *
10728 GAGTTTGACCAAGG-TAGAACCATCACATCAAATAA-GATGAAAA
1 AAGTTTGACTAGGGCTA-AACCATCACGTCAAACAAGGATGAAAA
* * * *** *
10771 GAGTTTGACTAGGACTTAACCATCACGTCAAATGGGGATGAAAG
1 AAGTTTGACTAGGGCTAAACCATCACGTCAAACAAGGATGAAAA
* * * *
10815 AAGTTTGACTAAGGC-AGAACCATCACGTTAAACGAA-AATGAAAG
1 AAGTTTGACTAGGGCTA-AACCATCACGTCAAAC-AAGGATGAAAA
* * *
10859 GAGTATGACTAGGGC-AGAACCATCACGACAAAC
1 AAGTTTGACTAGGGCTA-AACCATCACGTCAAAC
10892 GAAAATGAGA
Statistics
Matches: 295, Mismatches: 70, Indels: 32
0.74 0.18 0.08
Matches are distributed among these distances:
41 3 0.01
42 10 0.03
43 98 0.33
44 182 0.62
45 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (44 bp):
AAGTTTGACTAGGGCTAAACCATCACGTCAAACAAGGATGAAAA
Found at i:10892 original size:44 final size:44
Alignment explanation
Indices: 10548--11000 Score: 264
Period size: 44 Copynumber: 10.4 Consensus size: 44
10538 TCAAACAATG
* * * * *
10548 ATGAAAAGAGTTTGACTAGGGCTA-AATCATCACGTCAAAT-AATA
1 ATGAAAGGAGTTTGACCAAGGC-AGAACCATCACGACAAATGAA-A
* * * * *
10592 GTGAAAGGAGTTTGACTAA-GCAAAACCATCACGTCAAATG-AG
1 ATGAAAGGAGTTTGACCAAGGCAGAACCATCACGACAAATGAAA
* * * * * *
10634 ATAAAAGGAGTTTAACCAACGCTA-CACCATTAC-ATCAAACGAAA
1 ATGAAAGGAGTTTGACCAAGGC-AGAACCATCACGA-CAAATGAAA
*** * * * *
10678 GCAAAAAG-GTTTGACCAAGGCAAAACCATCATGTCAAATGAAA
1 ATGAAAGGAGTTTGACCAAGGCAGAACCATCACGACAAATGAAA
* *
10721 ATGAAAGGAGTTTGACCAAGGTAGAACCATCAC-ATCAAAT-AAG
1 ATGAAAGGAGTTTGACCAAGGCAGAACCATCACGA-CAAATGAAA
* * ** * ***
10764 ATGAAAAGAGTTTGA-CTAGGACTTAACCATCACGTCAAATGGGG
1 ATGAAAGGAGTTTGACCAAGG-CAGAACCATCACGACAAATGAAA
* * ** *
10808 ATGAAAGAAGTTTGACTAAGGCAGAACCATCACGTTAAACGAAA
1 ATGAAAGGAGTTTGACCAAGGCAGAACCATCACGACAAATGAAA
* * * *
10852 ATGAAAGGAGTATGACTAGGGCAGAACCATCACGACAAACGAAA
1 ATGAAAGGAGTTTGACCAAGGCAGAACCATCACGACAAATGAAA
* ** * *
10896 ATGAGAGGAGTTTGACCAAGATAGAACCATCA-TATCAATTGAAA
1 ATGAAAGGAGTTTGACCAAGGCAGAACCATCACGA-CAAATGAAA
* * ** * * *
10940 ATGAAAGGAGTTTGACCAGGGTAGAACTGTTATGTCAAATGAAA
1 ATGAAAGGAGTTTGACCAAGGCAGAACCATCACGACAAATGAAA
*
10984 ATGAAAGG-GTTTAACCA
1 ATGAAAGGAGTTTGACCA
11001 GGGCTCATCA
Statistics
Matches: 317, Mismatches: 76, Indels: 33
0.74 0.18 0.08
Matches are distributed among these distances:
42 21 0.07
43 100 0.32
44 193 0.61
45 3 0.01
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (44 bp):
ATGAAAGGAGTTTGACCAAGGCAGAACCATCACGACAAATGAAA
Found at i:10908 original size:88 final size:87
Alignment explanation
Indices: 10548--11000 Score: 351
Period size: 88 Copynumber: 5.2 Consensus size: 87
10538 TCAAACAATG
* * * * * * * *
10548 ATGAAAAGAGTTTGACTAGGGCTA-AATCATCACGTCAAATAATAGTGAAAGGAGTTTGACTA-A
1 ATGAAAGGAGTTTGACCAAGG-TAGAACCATCACATCAAAGAA-AATGAAAGGAGTTTGACTAGG
* *
10611 GCAAAACCATCACGTCAAATG-AG
64 GCAGAACCATCACGTCAAATGAAA
* * * * * *** * * *
10634 ATAAAAGGAGTTTAACCAACGCTA-CACCATTACATCAAACGAAAGCAAAAAG-GTTTGACCAAG
1 ATGAAAGGAGTTTGACCAA-GGTAGAACCATCACATCAAA-GAAAATGAAAGGAGTTTGACTAGG
* *
10697 GCAAAACCATCATGTCAAATGAAA
64 GCAGAACCATCACGTCAAATGAAA
* * * *
10721 ATGAAAGGAGTTTGACCAAGGTAGAACCATCACATCAAATAAGATGAAAAGAGTTTGACTAGGAC
1 ATGAAAGGAGTTTGACCAAGGTAGAACCATCACATCAAAGAAAATGAAAGGAGTTTGACTAGGGC
** ***
10786 TTAACCATCACGTCAAATGGGG
66 AGAACCATCACGTCAAATGAAA
* * * * * *
10808 ATGAAAGAAGTTTGACTAAGGCAGAACCATCACGTTAAACGAAAATGAAAGGAGTATGACTAGGG
1 ATGAAAGGAGTTTGACCAAGGTAGAACCATCACATCAAA-GAAAATGAAAGGAGTTTGACTAGGG
* *
10873 CAGAACCATCACGACAAACGAAA
65 CAGAACCATCACGTCAAATGAAA
* * * * *
10896 ATGAGAGGAGTTTGACCAAGATAGAACCATCATATCAATTGAAAATGAAAGGAGTTTGACCAGGG
1 ATGAAAGGAGTTTGACCAAGGTAGAACCATCACATCAA-AGAAAATGAAAGGAGTTTGACTAGGG
* ** * *
10961 TAGAACTGTTATGTCAAATGAAA
65 CAGAACCATCACGTCAAATGAAA
*
10984 ATGAAAGG-GTTTAACCA
1 ATGAAAGGAGTTTGACCA
11001 GGGCTCATCA
Statistics
Matches: 285, Mismatches: 74, Indels: 15
0.76 0.20 0.04
Matches are distributed among these distances:
85 8 0.03
86 63 0.22
87 102 0.36
88 112 0.39
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (87 bp):
ATGAAAGGAGTTTGACCAAGGTAGAACCATCACATCAAAGAAAATGAAAGGAGTTTGACTAGGGC
AGAACCATCACGTCAAATGAAA
Found at i:24537 original size:141 final size:141
Alignment explanation
Indices: 24374--24883 Score: 614
Period size: 142 Copynumber: 3.6 Consensus size: 141
24364 ACCAAAGGAA
* * * * * *
24374 ACGAAAGGTTTTGAAAATTTCTATACCCCTACGGAAAACCATAAGAATATGAGAAACCCTAAAAA
1 ACGAAAAGTTTT-AAAATTTCTATACCCCTACGAAAAACCATAGGAATATTAGAAATCTTAAAAA
* *
24439 ATTAAGATAATAA-TTTTATTTAATTTTTTAATTTTCAAAAAATTCATTTCGTACCTTAATGGAG
65 ATTAAGACAATAATTTTTATTTAATTTTTTAATTTTCAAAAAATTCATTTTGTACCTTAATGGAG
*
24503 AACTGAAAAGAT
130 AACCGAAAAGAT
* ** *
24515 ACGAAAAGTTTTAAAGATTTCTATACCTCTATAAAAAACCATAGGAATATTAAAAATCTTAAAAA
1 ACGAAAAGTTTTAAA-ATTTCTATACCCCTACGAAAAACCATAGGAATATTAGAAATCTTAAAAA
* * *
24580 ATTAAGGCAATAATTTTTATTTAATTTTTTAATTTCCAAAAAATTCATTTTATACCTTAATGGAG
65 ATTAAGACAATAATTTTTATTTAATTTTTTAATTTTCAAAAAATTCATTTTGTACCTTAATGGAG
24645 AACCGAAAAGAT
130 AACCGAAAAGAT
* * * * * * *
24657 AAGAAAAGTTTTGAATATTTCTATACCTCTATGAAAAACTATAGGAATATTAGAAATATTGAAAA
1 ACGAAAAGTTTT-AAAATTTCTATACCCCTACGAAAAACCATAGGAATATTAGAAATCTTAAAAA
* *
24722 ATTAAGACAATAATTTTTATTTTATTATTTAATTTTC--AAAATTCATTTTGTACCTTAATGGAG
65 ATTAAGACAATAATTTTTATTTAATTTTTTAATTTTCAAAAAATTCATTTTGTACCTTAATGGAG
24785 AACCGAAAAGAT
130 AACCGAAAAGAT
* * * * * * * * ** *
24797 ATGAAAAGTTTTAAAAATTTTTATACCCCCACGGATACCCAT-GAAAATATTAGAAATATCGAGA
1 ACGAAAAGTTTT-AAAATTTCTATACCCCTACGAAAAACCATAG-GAATATTAGAAATCTTAAAA
*
24861 AATTAAGAAAATAATTTTTATTT
64 AATTAAGACAATAATTTTTATTT
24884 GGTGAAAAAA
Statistics
Matches: 322, Mismatches: 43, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
139 1 0.00
140 110 0.34
141 62 0.19
142 147 0.46
143 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (141 bp):
ACGAAAAGTTTTAAAATTTCTATACCCCTACGAAAAACCATAGGAATATTAGAAATCTTAAAAAA
TTAAGACAATAATTTTTATTTAATTTTTTAATTTTCAAAAAATTCATTTTGTACCTTAATGGAGA
ACCGAAAAGAT
Found at i:25096 original size:27 final size:30
Alignment explanation
Indices: 25066--25120 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
25056 TATGACCAAA
25066 AATTTGA-ATTTGAT-A-TTTAGTCCTCCT
1 AATTTGACATTTGATCACTTTAGTCCTCCT
* *
25093 AATTTTACATTTTATCACTTTAGTCCTC
1 AATTTGACATTTGATCACTTTAGTCCTC
25121 ACAAAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 6 0.26
29 1 0.04
30 10 0.43
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (30 bp):
AATTTGACATTTGATCACTTTAGTCCTCCT
Found at i:26734 original size:334 final size:332
Alignment explanation
Indices: 26248--26957 Score: 900
Period size: 334 Copynumber: 2.1 Consensus size: 332
26238 AAAAAAATTC
* ** * *
26248 AAAATTCATGAAATAATTTGAATTTTTCAAAACTAATTT-ATGTGAATTTAATGACAATACTAGA
1 AAAACTCATGAAATAA-AAGAATTTTTCAAAACTAATTTAATATGAATTTAATAACAATACTAGA
* * * *
26312 TGAATTTTAAAAATTTTAAATCAAGAAAAATTCTCTCGAAAACATTTATAGAATAGAAAACTCGA
65 TAAATTTTAAAAATTTTAAATCAAGAAAAATTCTCCCGAAAACATTTACAGAATAGAAAACTAGA
* * * * * *
26377 TTTTTTAAAAATAGGAGAATTTCAAGAAAAAAATGAATAACTCATGAAA-TAATTGAATTTTTCA
130 TTTTTTAAAAATAGGAAAATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATAAAATTTTCA
* * * * *
26441 AAACTAATTT-AT-TG-TGAATTTAATGACAATATTAGATGAATTTTTAAATTTTTAAATCAAGA
195 AAACTAATTTAATATGATGAATTAAATCACAATATTAGATAAATTTTAAAAATTTTAAATCAAGA
* * * *
26503 AAAA-TCCCTTGAAAACATTTATGGAATAGAAAACTTAGTTTCTCGAAAATAAAAAAATTT-CAA
260 AAAATTCCCTCGAAAACATTTATGGAATAGAAAAC-TAGTTTCTCAAAAACAAAAAAATTTAAAA
*
26566 GAAAAAATGA
324 G-AAAAATAA
26576 AAAACTCATGAAAATAAATA-AATTTTTCAAAACTAATTTAATATGAATTTAATTAAATCATAAT
1 AAAACTCATG-AAATAAA-AGAATTTTTCAAAACTAATTTAATATGAATTTAA-T-AA-C--AAT
* *
26640 ATTAGATAAATTTTAAAAATTTTAAATCAAGAAAAATT-TCCCCGAAAATATTTACAGAATAGAA
59 ACTAGATAAATTTTAAAAATTTTAAATCAAGAAAAATTCT-CCCGAAAACATTTACAGAATAGAA
* *
26704 AACTA-AGTTTTTTGAAAATATGAAAATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATAA
123 AACTAGA-TTTTTTAAAAATAGGAAAATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATAA
** *
26768 AATTTTCAAAACTGTTTTAATATGAATTTAATTAAATCACAATATTAGATAAATTTTAAAAATTT
187 AATTTTCAAAACTAATTTAATATG-A-TGAATTAAATCACAATATTAGATAAATTTTAAAAATTT
* *
26833 TAAATCAAGAAAAATTCTCTCGAAAACATTTATGGAATAGAAAACTAGTTTTTCAAAAACAAAAA
250 TAAATCAAGAAAAATTCCCTCGAAAACATTTATGGAATAGAAAACTAGTTTCTCAAAAACAAAAA
26898 AATTTAAAAGAAAAATAA
315 AATTTAAAAGAAAAATAA
*
26916 AAAATTCATGAAATAAAAGGAATTTTTCAAAACTAATTTAAT
1 AAAACTCATGAAATAAAA-GAATTTTTCAAAACTAATTTAAT
26958 GCCAATTAAA
Statistics
Matches: 327, Mismatches: 35, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
328 28 0.09
329 17 0.05
330 1 0.00
331 1 0.00
332 1 0.00
333 2 0.01
334 108 0.33
335 20 0.06
336 2 0.01
337 2 0.01
338 1 0.00
339 7 0.02
340 106 0.32
341 31 0.09
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (332 bp):
AAAACTCATGAAATAAAAGAATTTTTCAAAACTAATTTAATATGAATTTAATAACAATACTAGAT
AAATTTTAAAAATTTTAAATCAAGAAAAATTCTCCCGAAAACATTTACAGAATAGAAAACTAGAT
TTTTTAAAAATAGGAAAATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATAAAATTTTCAA
AACTAATTTAATATGATGAATTAAATCACAATATTAGATAAATTTTAAAAATTTTAAATCAAGAA
AAATTCCCTCGAAAACATTTATGGAATAGAAAACTAGTTTCTCAAAAACAAAAAAATTTAAAAGA
AAAATAA
Found at i:26789 original size:171 final size:169
Alignment explanation
Indices: 26268--26957 Score: 818
Period size: 171 Copynumber: 4.1 Consensus size: 169
26258 AAATAATTTG
* * * *
26268 AATTTTTCAAAACTAATTT-ATGTGAATTTAA-T-GA-C-AATACTAGATGAATTTTAAAAATTT
1 AATTTTTCAAAACTAATTTAATATGAATTTAATTAAATCAAATATTAGATAAATTTTAAAAATTT
* * * **
26328 TAAATCAAGAAAAATTCTCTCGAAAACATTTATAGAATAGAAAACTCGATTTTTTAAAAATAGGA
66 TAAATCAAGAAAAATTCTCCCGAAAACATTTATAGAATAGAAAACTAG-TTTTTCAAAAATAAAA
* * * * *
26393 GAATTTCAAGAAAAAAATGAATAACTCATGAAA-TAATTG
130 AAATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATA
* * * * * *
26432 AATTTTTCAAAACTAATTTATTGTGAATTTAA-T-GA-C-AATATTAGATGAATTTTTAAATTTT
1 AATTTTTCAAAACTAATTTAATATGAATTTAATTAAATCAAATATTAGATAAATTTTAAAAATTT
* * * *
26493 TAAATCAAGAAAAA-TC-CCTTGAAAACATTTATGGAATAGAAAACTTAGTTTCTCGAAAATAAA
66 TAAATCAAGAAAAATTCTCC-CGAAAACATTTATAGAATAGAAAAC-TAGTTTTTCAAAAATAAA
* *
26556 AAAATTTCAAG-AAAAAATGAAAAACTCATGAAAATAAATA
129 AAAATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATA
26596 AATTTTTCAAAACTAATTTAATATGAATTTAATTAAATCATAATATTAGATAAATTTTAAAAATT
1 AATTTTTCAAAACTAATTTAATATGAATTTAATTAAATCA-AATATTAGATAAATTTTAAAAATT
* * ** *
26661 TTAAATCAAGAAAAATT-TCCCCGAAAATATTTACAGAATAGAAAACTAAGTTTTTTGAAAATAT
65 TTAAATCAAGAAAAATTCT-CCCGAAAACATTTATAGAATAGAAAACT-AGTTTTTCAAAAATAA
*
26725 GAAAATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATA
128 AAAAATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATA
* **
26767 AAATTTTCAAAACTGTTTTAATATGAATTTAATTAAATCACAATATTAGATAAATTTTAAAAATT
1 AATTTTTCAAAACTAATTTAATATGAATTTAATTAAATCA-AATATTAGATAAATTTTAAAAATT
* * *
26832 TTAAATCAAGAAAAATTCTCTCGAAAACATTTATGGAATAGAAAACTAGTTTTTCAAAAACAAAA
65 TTAAATCAAGAAAAATTCTCCCGAAAACATTTATAGAATAGAAAACTAGTTTTTCAAAAATAAAA
* * **
26897 AAATTT-AA-AAGAAAAATAAAAAATTCATGAAATAAAAGG
130 AAATTTCAAGAA-AAAAATAAAAAACTCATGAAATTAAATA
26936 AATTTTTCAAAACTAATTTAAT
1 AATTTTTCAAAACTAATTTAAT
26958 GCCAATTAAA
Statistics
Matches: 457, Mismatches: 53, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
163 22 0.05
164 98 0.21
165 54 0.12
166 1 0.00
167 1 0.00
168 2 0.00
169 82 0.18
170 65 0.14
171 131 0.29
172 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (169 bp):
AATTTTTCAAAACTAATTTAATATGAATTTAATTAAATCAAATATTAGATAAATTTTAAAAATTT
TAAATCAAGAAAAATTCTCCCGAAAACATTTATAGAATAGAAAACTAGTTTTTCAAAAATAAAAA
AATTTCAAGAAAAAAATAAAAAACTCATGAAATTAAATA
Found at i:32179 original size:11 final size:11
Alignment explanation
Indices: 32151--32188 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
32141 ATCAGCTGCA
*
32151 AAAAGAGAGAAT
1 AAAAGAGA-AAG
32163 AAAAGAGAAAG
1 AAAAGAGAAAG
32174 AAAAGAGAAAG
1 AAAAGAGAAAG
32185 AAAA
1 AAAA
32189 AAATAGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:34128 original size:21 final size:22
Alignment explanation
Indices: 34105--34145 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34095 TTTGGATTAT
34105 TTTTA-CTTG-AAAACATTTGA
1 TTTTAGCTTGAAAAACATTTGA
34125 TTTTAGCTTGAAAAACATTTG
1 TTTTAGCTTGAAAAACATTTG
34146 TACTTAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (22 bp):
TTTTAGCTTGAAAAACATTTGA
Found at i:34686 original size:129 final size:126
Alignment explanation
Indices: 34349--34714 Score: 489
Period size: 129 Copynumber: 2.8 Consensus size: 126
34339 AATTTAAACG
* *
34349 AATATTAATCATTTTTAATCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAAGATTTTAAA
1 AATATTAATCATTTTAAATCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAAGA-TTTCAA
* ** *
34414 AACTTTTCGTATCTTTTCAAGTATCCATTAAGGTAAAAAATGATTTTTTTCAAACATAAATA
65 AACTTTTCATATCTTTTCGGGTATCCATTAAGGTAAGAAATGATTTTTTTCAAACATAAATA
* * *
34476 AATATTAATTATTTTTAAGTCTTTTATATTCCTATGGGTATCCGTAGGGGTACAAAAGATTTCAA
1 AATATTAATCA-TTTTAAATCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAAGATTTC--
* *
34541 AAAACTTTTCATATCTTTTTGGGTATCCATTAAGGTATGAAATGATTTTTTTTTCAAACATAAAT
63 AAAACTTTTCATATCTTTTCGGGTATCCATTAAGGTAAGAAATGA--TTTTTTTCAAACATAAAT
34606 A
126 A
* *
34607 AATATTAATCGTTTTAAATCTTTTATATTCCTATGGGTATCCATAGGGGTATTAAAAGATTTCAA
1 AATATTAATCATTTTAAATCTTTTATATTCCTATGGGTATCCGTAGGGGTA-TAAAAGATTTCAA
* * ** * * *
34672 AATTTTTCACATCTTGGCGGGTTTCCATCAAGGTACGAAATGA
65 AACTTTTCATATCTTTTCGGGTATCCATTAAGGTAAGAAATGA
34715 CACTTTTTAA
Statistics
Matches: 209, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
127 13 0.06
128 44 0.21
129 76 0.36
130 38 0.18
131 38 0.18
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (126 bp):
AATATTAATCATTTTAAATCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAAGATTTCAAA
ACTTTTCATATCTTTTCGGGTATCCATTAAGGTAAGAAATGATTTTTTTCAAACATAAATA
Found at i:35519 original size:20 final size:19
Alignment explanation
Indices: 35493--35566 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
35483 AAAACCCTTG
* *
35493 AATGTATTGATACATAGCC
1 AATGTATCGATACATAGAC
*
35512 AGATGTATCGATACAT-GTTC
1 A-ATGTATCGATACATAG-AC
* *
35532 ATTGTATTGATACATAGAC
1 AATGTATCGATACATAGAC
35551 AATTGTATCGATACAT
1 AA-TGTATCGATACAT
35567 GAAACTGGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 16 0.36
20 28 0.64
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATAGAC
Found at i:38414 original size:13 final size:13
Alignment explanation
Indices: 38396--38421 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38386 TACACCAAGT
38396 ATGTATCGATACA
1 ATGTATCGATACA
38409 ATGTATCGATACA
1 ATGTATCGATACA
38422 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:38419 original size:32 final size:33
Alignment explanation
Indices: 38378--38441 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
38368 TAGCCAAACT
* **
38378 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
38410 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
38442 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:40085 original size:21 final size:21
Alignment explanation
Indices: 40052--40096 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
40042 TTGCAAGATG
*
40052 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
40074 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
40094 AAA
1 AAA
40097 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:41917 original size:15 final size:15
Alignment explanation
Indices: 41897--41927 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41887 TAAAAATGTC
*
41897 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
41912 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
41927 C
1 C
41928 CACAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:44033 original size:13 final size:13
Alignment explanation
Indices: 44015--44040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44005 ACATTTTTCC
44015 TTGTATCGATACA
1 TTGTATCGATACA
44028 TTGTATCGATACA
1 TTGTATCGATACA
44041 GGGTGATTAT
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):
TTGTATCGATACA
Found at i:44202 original size:20 final size:20
Alignment explanation
Indices: 44159--44205 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
44149 AAATCTTTTG
44159 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
44180 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
44200 CAAAAT
1 CAAAAT
44206 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:46590 original size:13 final size:13
Alignment explanation
Indices: 46572--46597 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46562 TACACCAAGT
46572 ATGTATCGATACA
1 ATGTATCGATACA
46585 ATGTATCGATACA
1 ATGTATCGATACA
46598 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:46595 original size:32 final size:33
Alignment explanation
Indices: 46554--46617 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
46544 TAGCCAAACT
* **
46554 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
46586 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
46618 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Done.