Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1185
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: 20847
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Found at i:600 original size:54 final size:54
Alignment explanation
Indices: 509--974 Score: 470
Period size: 53 Copynumber: 8.5 Consensus size: 54
499 TTCGCTTTTT
* * *
509 AGTCCTCAAAGAGCAAGAC-CCTTCAAAGCCCACAC-AGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
561 AGTCCTCAGAGAGCAGGACACCTCTTAAAGCCCACAC-AGTTGGTGGCACC-TTC
1 AGTCCTCAAAGAGCAGGACACCT-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
614 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACC-TTC
1 AGTCCTCAAAGAGCAGGAC-AC----C-TTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
673 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C----ACCTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
734 AGTCC-CAAAGAGCAGGAC-CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
787 AGTCC-CCAAGAGCA-GACACCTTTAAAGCCCACACAAGTTGATGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
838 CGTCCTCAAAGAGGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGA-GCAGGACACCT-TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * * *
894 AGTTC-CAAAGAGCAGGACGCCTTTCAAAGCCTACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
948 ACTCCTCAATGAGCAGGATACACTTTA
1 AGTCCTCAAAGAGCAGGACAC-CTTTA
975 TTTTCCTCTT
Statistics
Matches: 355, Mismatches: 33, Indels: 49
0.81 0.08 0.11
Matches are distributed among these distances:
51 8 0.02
52 47 0.13
53 78 0.22
54 71 0.20
55 43 0.12
56 11 0.03
58 14 0.04
59 37 0.10
60 36 0.10
61 9 0.03
64 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (54 bp):
AGTCCTCAAAGAGCAGGACACCTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:772 original size:113 final size:108
Alignment explanation
Indices: 509--965 Score: 461
Period size: 105 Copynumber: 4.2 Consensus size: 108
499 TTCGCTTTTT
* * *
509 AGTCCTCAAAGAGCAAGAC-CC-TTCAAAGCCCACAC-AGTTGGTGGCA-TTTTCCAGTCCTCAG
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC-CAA
*
570 AGAGCAGGACACCTCTTAAAGCCCACAC-AGTTGGTGGCACC-TTC
64 AGAGCAGGACA-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
614 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACC-TTCAGTCC
1 AGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*
678 TCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
61 -CAAAGAGCAGGA--C----ACTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
734 AGTCC-CAAAGAGCAGGAC-CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAG
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCAAAG
* * *
797 AGCA-GACACCTTTAAAGCCCACACAAGTTGATGGCA-TTTTC
66 AGCAGGACACTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
838 CGTCCTCAAAGAGGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTTCCAA
1 AGTCCTCAAAGA-GCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCAA
* * * * * *
902 AGAGCAGGACGCCTTTCAAAGCCTACACGAGTTGGTGGCACTTTTT
64 AGAGCAGGAC-ACTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
948 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
966 TACACTTTAT
Statistics
Matches: 299, Mismatches: 27, Indels: 48
0.80 0.07 0.13
Matches are distributed among these distances:
104 8 0.03
105 45 0.15
106 13 0.04
107 44 0.15
108 8 0.03
109 29 0.10
110 14 0.05
112 30 0.10
113 45 0.15
114 9 0.03
117 8 0.03
118 13 0.04
119 25 0.08
120 8 0.03
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (108 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCAAAG
AGCAGGACACTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:794 original size:29 final size:28
Alignment explanation
Indices: 709--792 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 28
699 CTTTTCAAAG
709 CCCACACAAGTTGGTGGCACCTTTCAGT
1 CCCACACAAGTTGGTGGCACCTTTCAGT
* **
737 -CC-CA-AAG-AGCAGG-ACCCTTTCAAAG-
1 CCCACACAAGTTGGTGGCA-CCTTTC--AGT
762 CCCACACAAGTTGGTGGCACCTTTCAGT
1 CCCACACAAGTTGGTGGCACCTTTCAGT
790 CCC
1 CCC
793 CAAGAGCAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
23 1 0.02
24 9 0.22
25 3 0.07
26 6 0.15
27 6 0.15
28 6 0.15
29 9 0.22
30 1 0.02
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.20
Consensus pattern (28 bp):
CCCACACAAGTTGGTGGCACCTTTCAGT
Found at i:4294 original size:52 final size:51
Alignment explanation
Indices: 4216--4389 Score: 172
Period size: 52 Copynumber: 3.4 Consensus size: 51
4206 CCTGTTAATC
* * * *
4216 ATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACA
1 ATCGAGGATACTCCAACCCTGGTTTTATT-CTAAAACACCAATTTTTCCATA
* * * *
4268 ATCGGGGATACTCCAACCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTA
1 ATCGAGGATACTCCAACCCTGGTTTTATTCT-AAAACACCAATTTTTCC-ATA
** * * *
4320 ATCGAGGATACTCCAACTTTGATTTTATTTCCAAAAATACCAATTTTT-CATA
1 ATCGAGGATACTCCAACCCTGGTTTTA-TT-CTAAAACACCAATTTTTCCATA
4372 ATCGAGGATACTCCAACC
1 ATCGAGGATACTCCAACC
4390 TCGTTATTTC
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
51 7 0.07
52 79 0.78
53 11 0.11
54 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
ATCGAGGATACTCCAACCCTGGTTTTATTCTAAAACACCAATTTTTCCATA
Found at i:4323 original size:131 final size:129
Alignment explanation
Indices: 4085--4336 Score: 287
Period size: 131 Copynumber: 1.9 Consensus size: 129
4075 ATTCTCCACA
* * * * * *
4085 ATCGGGGATATTCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCAGGGATACTCTA
1 ATCGGGGATATCCAACCCCGATTTTATTCTCAAAACACTAATTTTCCACAATCAGGGATACTCCA
*
4150 ACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCTGTTAAT
66 ACTCCGATTTTATTTCC-AAAAACACCAATTTCTT-ACAATCGAGGATACTCCAACCCTGTTAAT
4215 C
129 C
* *
4216 ATCGGGGATACTCCAACCCCGGTTTTATTGCT-AAAACACTAATTTTTCCACAATCGGGGATACT
1 ATCGGGGATA-TCCAACCCCGATTTTATT-CTCAAAACACTAA-TTTTCCACAATCAGGGATACT
* * * *
4280 CCAAC-CCTGGTTTTATTTTC-AAAACGCCAATTTTCCTT-TAATCGAGGATACTCCAAC
63 CCAACTCC-GATTTTATTTCCAAAAACACCAA-TTT-CTTACAATCGAGGATACTCCAAC
4337 TTTGATTTTA
Statistics
Matches: 102, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
131 36 0.35
132 30 0.29
133 36 0.35
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (129 bp):
ATCGGGGATATCCAACCCCGATTTTATTCTCAAAACACTAATTTTCCACAATCAGGGATACTCCA
ACTCCGATTTTATTTCCAAAAACACCAATTTCTTACAATCGAGGATACTCCAACCCTGTTAATC
Found at i:4404 original size:184 final size:183
Alignment explanation
Indices: 4079--4420 Score: 487
Period size: 184 Copynumber: 1.9 Consensus size: 183
4069 TTCTCAATTC
* *
4079 TCCACAATCGGGGATATTCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCAGGGAT
1 TCCACAATCGGGGATATCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGAT
* *
4144 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCT
66 ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCT
4209 GTTAATCATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTT
131 GTTAATCATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTT
* * *
4262 TCCACAATCGGGGATACTCCAAC-CCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC-GA
1 TCCACAATCGGGGATA-TCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCAG-
** * *
4325 GGATACTCCAACTTTGATTTTATTTCC-AAAAATACCAATTT-TTCATAATCGAGGATACTCCAA
62 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
*
4388 -CCTCGTTATTTCATCGGGGATACTCCAACCCCG
127 CCCT-GTTA-ATCATCGGGGATACTCCAACCCCG
4421 TTACTTTCGA
Statistics
Matches: 141, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
182 3 0.02
183 42 0.30
184 65 0.46
185 31 0.22
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (183 bp):
TCCACAATCGGGGATATCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGAT
ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCT
GTTAATCATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTT
Found at i:4408 original size:28 final size:30
Alignment explanation
Indices: 4372--4448 Score: 108
Period size: 28 Copynumber: 2.7 Consensus size: 30
4362 ATTTTTCATA
* *
4372 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
4400 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
4430 A--GGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
4449 GCTTATTCCC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 40 0.89
29 4 0.09
30 1 0.02
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:4546 original size:78 final size:78
Alignment explanation
Indices: 4402--4583 Score: 195
Period size: 78 Copynumber: 2.3 Consensus size: 78
4392 GTTATTTCAT
* * *
4402 CGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGGCTTATTCCCAAAATATT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTATTCCCAAAATATT
* * *
4467 GATTTCTCATAAT
66 GATTTCTAACAAA
* * * * * ** *
4480 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCTCGATTTTTTTTC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTATTCCCAAAAT-AT
4544 TGATTTCTAACAAA
65 TGATTTCTAACAAA
* *
4558 CGGGGACTACTCCAGCCCCATTATTT
1 CGGGGA-TACTCCAACCCCGTTATTT
4584 CAAGGAAACA
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
77 3 0.04
78 65 0.76
79 17 0.20
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTATTCCCAAAATATT
GATTTCTAACAAA
Found at i:5896 original size:79 final size:78
Alignment explanation
Indices: 5796--5997 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 78
5786 AATAACAGGG
* * * * *
5796 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
*
5859 GAAAAAAAAATCGGGA
64 G-AAAAAAAACCGGGA
* *
5875 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTTG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAG
* * * *
5940 GAATAAAGCCGGGG
65 AAAAAAAACCGGGA
* * *
5954 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
5998 GAAATAACGA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
78 7 0.07
79 94 0.90
80 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (78 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAACCGGGA
Found at i:5989 original size:28 final size:28
Alignment explanation
Indices: 5949--6020 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
5939 GGAATAAAGC
** *
5949 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
5977 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
6005 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
6021 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:6078 original size:52 final size:50
Alignment explanation
Indices: 6013--6140 Score: 132
Period size: 51 Copynumber: 2.5 Consensus size: 50
6003 AACGAGGTTG
* * *
6013 GAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATC-GGAGTTA
1 GAGTATCCCCGATTGTGAAAAATTGG-AGTTTT-GAAATAAAACCAGGA-TTA
** * * *
6065 GAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAATAAAACCAGGATTG
1 GAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAATAAAACCAGGATTA
6116 GAGTATCCCCGATTGTGGAAAAATT
1 GAGTATCCCCGATTGT-GAAAAATT
6141 AGTGTTTTAG
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
51 33 0.53
52 20 0.32
53 9 0.15
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (50 bp):
GAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAATAAAACCAGGATTA
Found at i:6139 original size:51 final size:52
Alignment explanation
Indices: 6009--6177 Score: 166
Period size: 52 Copynumber: 3.3 Consensus size: 52
5999 AAATAACGAG
* * * *
6009 GTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGG-AGTTTTAGAAATAAAACCGGA
* ** *
6061 GTTAGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTT-GAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTAGAAATAAAACC-GGA
* * ** *
6113 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGATAAAACCCGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTAGAAATAAAACCGGA
6164 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
6178 TCGAAAATAA
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
50 2 0.02
51 40 0.42
52 45 0.47
53 8 0.08
54 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTAGAAATAAAACCGGA
Found at i:6215 original size:27 final size:28
Alignment explanation
Indices: 6168--6239 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
6158 ACCCGAGTTG
* * *
6168 GAGTATCCCCTCGA-AAATAACGGGGTTA
1 GAGTATCCCC-CGATTATTAACAGGGTTA
*
6196 GAGTA-CCCCCGATTATTAACAGGGTTG
1 GAGTATCCCCCGATTATTAACAGGGTTA
6223 GAGTATCCCCCGATTAT
1 GAGTATCCCCCGATTAT
6240 AGAAAATTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 19 0.50
28 16 0.42
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (28 bp):
GAGTATCCCCCGATTATTAACAGGGTTA
Found at i:8670 original size:13 final size:13
Alignment explanation
Indices: 8652--8678 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8642 AGAAAGATCC
8652 ATGTATCGATACA
1 ATGTATCGATACA
8665 ATGTATCGATACA
1 ATGTATCGATACA
8678 A
1 A
8679 AGAAAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:8673 original size:33 final size:33
Alignment explanation
Indices: 8631--8697 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8621 AAAATTTCCA
* ***
8631 AATGTATCGATAGAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
8664 AATGTATCGATACAAAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
8697 A
1 A
8698 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:8741 original size:19 final size:19
Alignment explanation
Indices: 8717--8771 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
8707 CAGTAGCTAA
*
8717 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
8736 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
8755 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
8772 TTGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:9697 original size:55 final size:55
Alignment explanation
Indices: 9560--10664 Score: 1717
Period size: 54 Copynumber: 20.3 Consensus size: 55
9550 ATAAACTGTA
* * * * * *
9560 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-A-GCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
9614 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
9669 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
9724 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
9779 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGT-GGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
9833 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
9888 TCCTGCTCTTTG-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
**
9942 TCCTGCTCTTTGAGGACTGACTGGAAATGCCACCAACTTGTGTGGGCTTT-A-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGG---TGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
9998 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
10052 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
10107 TCCTGCTCTTTG-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
10161 TCCTGCTCTTTGAGGACTGGAAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
10215 TCCTGCTCTTTGAGGACTGGAAA--TGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
10269 TCCTGCTCTTTG-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
10323 TCCTGCTCTTTGAGGACTGAAA--TGCCACCAACTTGTGTGGGCTTTAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
10375 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
10429 TCCTGCTCTTTGAGGACTGAAA--TGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
10482 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
10537 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
10592 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
10647 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
10665 AAAAAGCGGA
Statistics
Matches: 996, Mismatches: 26, Indels: 57
0.92 0.02 0.05
Matches are distributed among these distances:
52 56 0.06
53 85 0.09
54 452 0.45
55 337 0.34
56 42 0.04
57 1 0.00
58 23 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:9723 original size:29 final size:28
Alignment explanation
Indices: 9633--10646 Score: 195
Period size: 28 Copynumber: 37.2 Consensus size: 28
9623 TTGAGGACTG
9633 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * ** *
9661 GAAAGGTGTCCTGC-TCTT-TG-GGGAATG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
9688 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
9716 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
9744 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
9771 GAAAGGTGTCCTGC-TCTT-TGAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
*
9799 AAA-ATGCCACCAACTTGTGT-GGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
9825 GAAAGGTGTCCTGC-TCTT-TGAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
*
9853 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * *
9880 AAGAGGTGTCCTGC-TCTT-TG-GGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
9906 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * **
9934 AAGAGGTGTCCTGC-TCTT-TGAGGACTGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGG---G-CTTT
9966 AAA--TGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
9992 -AAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AAAGGTG-CCACCAACTTGTGTGGG-CTTT
10017 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
10045 AAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AAAGGTG-CCACCAACTTGTGTGGGCTTT
10071 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * *
10099 AAGAGGTGTCCTGC-TCTT-TG-GGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
10125 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
10153 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
10181 AAA--TGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
10207 GAAAGGTGTCCTGC-TCTT-TGAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
10235 AAA--TGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * *
10261 AAGAGGTGTCCTGC-TCTT-TG-GGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
10287 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
10315 AAGAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
10342 AAA--TGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
10368 AAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AAAGGTG-CCACCAACTTGTGTGGGCTTT
10394 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
10422 AAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AAAGGTG-CCACCAACTTGTGTGGGCTTT
10448 AAA--TGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
10474 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
10501 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
10529 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
10557 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
10584 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
10611 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
10639 AAGAGGTG
1 AA-AGGTG
10647 TCCTGCTCTT
Statistics
Matches: 657, Mismatches: 220, Indels: 216
0.60 0.20 0.20
Matches are distributed among these distances:
23 6 0.01
24 25 0.04
25 80 0.12
26 128 0.19
27 120 0.18
28 139 0.21
29 110 0.17
30 43 0.07
31 2 0.00
32 4 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:9998 original size:219 final size:219
Alignment explanation
Indices: 9560--10669 Score: 1730
Period size: 219 Copynumber: 5.1 Consensus size: 219
9550 ATAAACTGTA
* * * * *
9560 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA-GCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTT
*
9624 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGAATG
64 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTT-GGGACTG
*
9688 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTG---GAAAATG
127 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGAAATG
9750 CCACCAACTTGTGTGGGCTTTGAAAGGTG
192 CCACCAACTTGTGTGGGCTTT-AAAGGTG
9779 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGT-GGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTT
*
9843 TGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGACTGA
64 TGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGACTGA
**
9907 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGACTGGAAATGC
128 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGAAATGC
9972 CACCAACTTGTGTGGGCTTT-AAGGTG
193 CACCAACTTGTGTGGGCTTTAAAGGTG
* *
9998 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
10063 GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGACTGAAA
65 GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGACTGAAA
10128 GGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT----GGAAATGCCA
130 GGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGAAATGCCA
10189 CCAACTTGTGTGGGCTTTGAAAGGTG
195 CCAACTTGTGTGGGCTTT-AAAGGTG
*
10215 TCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTT
10280 G-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAA
65 GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTG-GGACTGAA
10344 A--TGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGG---TGCC
129 AGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGAAATGCC
10403 ACCAACTTGTGTGGGCTTTAAAGGTG
194 ACCAACTTGTGTGGGCTTTAAAGGTG
10429 TCCTGCTCTTTGAGGACTG-AAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTT
*
10493 GGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGA
65 GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTG-GGACT-GA
* * *
10558 AA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGACTGAAAGG---TG
128 AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGAAATG
10618 CCACCAACTTGTGTGGGCTTTAAGAGGTG
192 CCACCAACTTGTGTGGGCTTTAA-AGGTG
*
10647 TCCTGCTCTTTGAGGACTAAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
10670 GCGGAAGGAG
Statistics
Matches: 850, Mismatches: 17, Indels: 48
0.93 0.02 0.05
Matches are distributed among these distances:
213 46 0.05
214 109 0.13
215 80 0.09
216 101 0.12
217 107 0.13
218 106 0.12
219 260 0.31
220 14 0.02
221 27 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (219 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTG
AGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGACTGAAAG
GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGAAATGCCAC
CAACTTGTGTGGGCTTTAAAGGTG
Found at i:11686 original size:36 final size:38
Alignment explanation
Indices: 11632--11705 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
11622 TTAAGTAGGT
*
11632 TTTTTCTTTTCTCTC-TTTTTCTTTGTTTTGTTTTTTTG
1 TTTTTCTTTTCTCTCTTTTTTCTTTGCTTT-TTTTTTTG
*
11670 TTTTT-TTTTC-CTCTTTTTTTTTTGCTTTTTTTTTTG
1 TTTTTCTTTTCTCTCTTTTTTCTTTGCTTTTTTTTTTG
11706 AAGAGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 11 0.33
37 17 0.52
38 5 0.15
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (38 bp):
TTTTTCTTTTCTCTCTTTTTTCTTTGCTTTTTTTTTTG
Found at i:11687 original size:14 final size:13
Alignment explanation
Indices: 11670--11704 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
11660 TGTTTTTTTG
11670 TTTTTTTTTCCTCT
1 TTTTTTTTTCCT-T
*
11684 TTTTTTTTTGCTT
1 TTTTTTTTTCCTT
11697 TTTTTTTT
1 TTTTTTTT
11705 GAAGAGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTCCTT
Found at i:11697 original size:12 final size:12
Alignment explanation
Indices: 11647--11705 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
11637 CTTTTCTCTC
* *
11647 TTTTTCTTTGTT
1 TTTTTTTTTGCT
11659 TTGTTTTTTTG-T
1 TT-TTTTTTTGCT
11671 TTTTTTTTCCT-CT
1 TTTTTTTT--TGCT
11684 TTTTTTTTTGCT
1 TTTTTTTTTGCT
11696 TTTTTTTTTG
1 TTTTTTTTTG
11706 AAGAGAAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
11 7 0.17
12 17 0.41
13 17 0.41
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTGCT
Done.