Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1527
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: 16955
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:571 original size:27 final size:29
Alignment explanation
Indices: 527--581 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
517 TCCTGCGATG
* * *
527 TAAATATACCTTTTAAACTTATGGATAAA
1 TAAATATACCTTTCAAACTCATAGATAAA
556 TAAA-ATA-CTTTCAAACTCATAGATAA
1 TAAATATACCTTTCAAACTCATAGATAA
582 CATGACATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.70
28 3 0.13
29 4 0.17
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (29 bp):
TAAATATACCTTTCAAACTCATAGATAAA
Found at i:1491 original size:34 final size:33
Alignment explanation
Indices: 1443--1663 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 33
1433 TGGTAAAAAC
* *
1443 CACCATTTAATCAACAATGGCAATCTACCAAAT
1 CACCATTTAATCAACAATGGTAAGCTACCAAAT
* *
1476 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
1510 CACCTATTTAATCAATAATGGTAAGCTACCAAAT
1 CACC-ATTTAATCAACAATGGTAAGCTACCAAAT
**
1544 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * *
1578 CTCCCATTTAGTCAACAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
1612 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1646 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1664 TCTCCTACTT
Statistics
Matches: 163, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
33 20 0.12
34 141 0.87
35 2 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:1622 original size:102 final size:101
Alignment explanation
Indices: 1443--1663 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
1433 TGGTAAAAAC
* * *
1443 CACCATTTAATCAACAATGGCAATCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
1508 ATCACCTATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
1544 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
1609 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1646 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1664 TCTCCTACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:6117 original size:34 final size:33
Alignment explanation
Indices: 6069--6287 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 33
6059 TGGTAAAAAC
*
6069 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
6102 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
6136 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
6170 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * * *
6204 CTCCCATTTAGTCAACAATGGCAAACC-ACTAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
6238 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
6272 CACCATTTAATCAACA
1 CACCATTTAATCAACA
6288 GACAGTTCAC
Statistics
Matches: 158, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 21 0.13
34 131 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:6185 original size:68 final size:67
Alignment explanation
Indices: 6071--6287 Score: 283
Period size: 68 Copynumber: 3.2 Consensus size: 67
6061 GTAAAAACCA
* * *
6071 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
6136 CAC
65 CAC
* * * *
6139 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
6204 CTC
65 CAC
* * * * *
6207 CCATTTAGTCAACAATGGCAAACCACTAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
6272 CA-
65 CAC
6274 CCATTTAATCAACA
1 CCATTTAATCAACA
6288 GACAGTTCAC
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 15 0.12
68 113 0.88
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:6213 original size:102 final size:101
Alignment explanation
Indices: 6069--6287 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
6059 TGGTAAAAAC
* *
6069 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
6134 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
6170 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACTA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
6235 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
6272 CACCATTTAATCAACA
1 CACCATTTAATCAACA
6288 GACAGTTCAC
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 14 0.13
102 91 0.87
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:7039 original size:223 final size:223
Alignment explanation
Indices: 6614--7237 Score: 1114
Period size: 223 Copynumber: 2.8 Consensus size: 223
6604 AAATGCAAGG
* *
6614 CTTCACCCTCCTTGCAAGTTGCAACTTGAAAAA-AAA-A-AAAAGAAGAAATATGTAAACATTAT
1 CTTCACACTCCTTGCAAGTTGCAACTCGAAAAACAAATATAAAAGAAGAAATATGTAAACATTAT
* * *
6676 TTATATACAAAGGATCAAGTTCTACGAGTGTGAAAATAAGTTTGTTTTAATTATAATTTAATGTA
66 TTATATACATAGGATCAAGTTCTACGAGTGTCAAAATAAATTTGTTTTAATTATAATTTAATGTA
6741 TAATTAATATTTTCACAAACAATTTGTTATATTAAAATTTTCATATATATTTTATTTTTATTTTA
131 TAATTAATATTTTCACAAACAATTTGTTATATTAAAATTTTCATATATATTTTATTTTTATTTTA
6806 TTTATTATAAGGTTTAGGGTTTGTAAGA
196 TTTATTATAAGGTTTAGGGTTTGTAAGA
*
6834 CTTCACACTCCTTGCAAGTTGCAACTCGAAAAACAAATATAAAAGAAGAAATATGTAAAAATTAT
1 CTTCACACTCCTTGCAAGTTGCAACTCGAAAAACAAATATAAAAGAAGAAATATGTAAACATTAT
6899 TTATATACATAGGATCAAGTTCTACGAGTGTCAAAATAAATTTGTTTTAATTATAATTTAATGTA
66 TTATATACATAGGATCAAGTTCTACGAGTGTCAAAATAAATTTGTTTTAATTATAATTTAATGTA
*
6964 TAATTAATATTTTCACAAACAATTTGTTATATTAAAATTTTCGTATATATTTTATTTTTATTTTA
131 TAATTAATATTTTCACAAACAATTTGTTATATTAAAATTTTCATATATATTTTATTTTTATTTTA
7029 TTTATTATAAGGTTTAGGGTTTGTAAGA
196 TTTATTATAAGGTTTAGGGTTTGTAAGA
7057 CTTCACACTCCTTGCAAGTTGCAACTCGAAAAACAAATATAAAAGAAGAAATATGTAAACATTAT
1 CTTCACACTCCTTGCAAGTTGCAACTCGAAAAACAAATATAAAAGAAGAAATATGTAAACATTAT
* *
7122 TTATATACATAGGATCAGGTTCTATGAGTGTCAAAATAAATTTGTTTTAATTATAATTTAATGTA
66 TTATATACATAGGATCAAGTTCTACGAGTGTCAAAATAAATTTGTTTTAATTATAATTTAATGTA
* *
7187 TAATTAATATTTTCACAAACAATTTGTTATATT-ACATTTTTATAT-TATTTT
131 TAATTAATATTTTCACAAACAATTTGTTATATTAAAATTTTCATATATATTTT
7238 TATAATAATA
Statistics
Matches: 388, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
220 31 0.08
221 9 0.02
222 10 0.03
223 338 0.87
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (223 bp):
CTTCACACTCCTTGCAAGTTGCAACTCGAAAAACAAATATAAAAGAAGAAATATGTAAACATTAT
TTATATACATAGGATCAAGTTCTACGAGTGTCAAAATAAATTTGTTTTAATTATAATTTAATGTA
TAATTAATATTTTCACAAACAATTTGTTATATTAAAATTTTCATATATATTTTATTTTTATTTTA
TTTATTATAAGGTTTAGGGTTTGTAAGA
Found at i:7690 original size:26 final size:26
Alignment explanation
Indices: 7652--7716 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
7642 ATAGTTTAAT
*
7652 ATAAAAAGTTTTA-TTCATTTAAAAA-
1 ATAAAAAATTTTATTTCA-TTAAAAAG
7677 ATAAAAAATATTTATTTTCATTAAAAAG
1 ATAAAAAAT-TTTA-TTTCATTAAAAAG
*
7705 ATAAATAATTTT
1 ATAAAAAATTTT
7717 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 8 0.24
26 4 0.12
27 10 0.29
28 12 0.35
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (26 bp):
ATAAAAAATTTTATTTCATTAAAAAG
Found at i:7734 original size:18 final size:19
Alignment explanation
Indices: 7697--7744 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 19
7687 TTTATTTTCA
*
7697 TTAAAAAGATAAATAATTTT
1 TTAAAAAAATAAATAA-TTT
7717 TTAAAAAAAT-AA-AATTT
1 TTAAAAAAATAAATAATTT
7734 TTAAAAGAAAT
1 TTAAAA-AAAT
7745 GAAGAGTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 9 0.35
18 6 0.23
19 2 0.08
20 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
TTAAAAAAATAAATAATTT
Found at i:8858 original size:80 final size:79
Alignment explanation
Indices: 8723--8927 Score: 223
Period size: 80 Copynumber: 2.6 Consensus size: 79
8713 GAGATAATAA
* * * *** * *
8723 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAACTATGAGAAATCAAT-A
*
8788 -TTAGAAAAAAAAAAT
65 TTTAG-AAAAAAAAAC
*
8803 CGGGATTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAACTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAACTATGAGAAATCAATAT
* ** * *
8868 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* * *
8882 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCC
8928 GATGAAATAA
Statistics
Matches: 105, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
79 48 0.46
80 57 0.54
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAACTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:8938 original size:28 final size:28
Alignment explanation
Indices: 8882--8953 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
8872 GGAATAAAGC
** *
8882 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
8910 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
8938 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
8954 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:8945 original size:107 final size:108
Alignment explanation
Indices: 8803--9007 Score: 252
Period size: 107 Copynumber: 1.9 Consensus size: 108
8793 AAAAAAAAAT
* ** *
8803 CGGGATTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAACTATGAGAAATCAATA-
1 CGGGATTGGAGTATCCCCATGAAAATAACAAGGTTGGAGTATCCCCAACTATGAAAAATCAATAT
* * *
8867 TTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAA
66 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
* * * * ***
8910 CGGGGTTGGAGTATCCCCGATG-AAATAACAAGGTTGGAGTATCCTCGACTGTGAAAAATTGGTA
1 CGGGATTGGAGTATCCCC-ATGAAAATAACAAGGTTGGAGTATCCCCAACTATGAAAAATCAATA
*
8974 TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
65 TTTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
9008 GATTAAAGGA
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
107 50 0.62
108 31 0.38
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (108 bp):
CGGGATTGGAGTATCCCCATGAAAATAACAAGGTTGGAGTATCCCCAACTATGAAAAATCAATAT
TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
Found at i:9099 original size:51 final size:49
Alignment explanation
Indices: 8941--9107 Score: 154
Period size: 52 Copynumber: 3.2 Consensus size: 49
8931 GAAATAACAA
* * * *
8941 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTAGAAAT-AAATCG
* * * * *
8992 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTAGCAATAAAACTGG
1 G-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTAGAAAT-AAA-TCG
* **
9045 GGTTGGAATATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAGTCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAA-TC-G
9096 GGTTGGAGTATC
1 GGTTGGAGTATC
9108 TCCTCGGAAA
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
50 4 0.04
51 31 0.33
52 45 0.48
53 13 0.14
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (49 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAATCG
Found at i:9129 original size:28 final size:27
Alignment explanation
Indices: 9095--9168 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
9085 AATAAAGTCA
9095 GGGTTGGAGTATCTCCTCGGA-AAT-AACG
1 GGGTTGGAGTATC-CC-C-GATAATCAACG
*
9123 GGGTTGGAGTATCCCCGATGATCAACG
1 GGGTTGGAGTATCCCCGATAATCAACG
9150 GGGTTGGAGTATCCCCGAT
1 GGGTTGGAGTATCCCCGAT
9169 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.05
26 3 0.07
27 25 0.58
28 13 0.30
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGATAATCAACG
Found at i:9233 original size:211 final size:210
Alignment explanation
Indices: 8831--9274 Score: 617
Period size: 211 Copynumber: 2.1 Consensus size: 210
8821 TTGAAAATAA
* * * * * * *
8831 CGGGGTTGGAGTATCCCCAACTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAATATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTAT
* *
8896 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGACTG
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AATAACAAGGTTGGAGTATCCCCGACTG
*
8961 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
130 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
*
9026 GTTTT-AGCAATAAAA-
195 GTTTTGA-AAATAAAAT
* *
9041 CTGGGGTTGGAATATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAGTCAGGGTTGGAGTA
1 C-GGGGTTGGAATATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTA
* ** *
9106 TCTCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATT
65 TCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAT-AACAAGGTTGGAGTATCCCCGACT
* *
9170 GTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAATT
129 GTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATT
9234 AGTGTTTTGAAAATAAAAT
192 AGTGTTTTGAAAATAAAAT
* *
9253 CGGAGCTGGAATATCCCCGATT
1 CGGGGTTGGAATATCCCCGATT
9275 GTGGAGAATT
Statistics
Matches: 207, Mismatches: 21, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
209 2 0.01
210 26 0.13
211 137 0.66
212 42 0.20
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (210 bp):
CGGGGTTGGAATATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAATAACAAGGTTGGAGTATCCCCGACTGT
GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
TTTTGAAAATAAAAT
Found at i:9256 original size:51 final size:53
Alignment explanation
Indices: 9152--9274 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 53
9142 GATCAACGGG
* * *
9152 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGA
9206 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGA
* *
9257 GCTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
9275 GTGGAGAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.54
52 2 0.03
53 8 0.13
54 19 0.30
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:11652 original size:13 final size:13
Alignment explanation
Indices: 11634--11659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11624 ACAAAGATCC
11634 ATGTATCGATACA
1 ATGTATCGATACA
11647 ATGTATCGATACA
1 ATGTATCGATACA
11660 TAGAAAAATG
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:11655 original size:33 final size:33
Alignment explanation
Indices: 11613--11679 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11603 AAAATTTTCA
***
11613 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
11646 AATGTATCGATACATAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
11679 A
1 A
11680 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:11723 original size:19 final size:18
Alignment explanation
Indices: 11699--11766 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
11689 CAGTAGCTAA
11699 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
11718 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
11733 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
11750 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
11767 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:11739 original size:13 final size:13
Alignment explanation
Indices: 11721--11745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11711 ACAATACTTA
11721 TGTATCGATACAT
1 TGTATCGATACAT
11734 TGTATCGATACA
1 TGTATCGATACA
11746 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11743 original size:32 final size:32
Alignment explanation
Indices: 11702--11764 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
11692 TAGCTAATTA
*
11702 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
11734 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
11765 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:12512 original size:55 final size:55
Alignment explanation
Indices: 12448--14040 Score: 2432
Period size: 55 Copynumber: 29.0 Consensus size: 55
12438 TGAGGAGGAA
* ** *
12448 AAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGACGTCCTGTTCTTTGAGGACT-G
1 AAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
* *
12502 AAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGAAT-G
1 AAA-GTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
*
12557 AAAGGTGCCACCAACTTGTGTAGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* *
12613 AAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGTTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
* *
12668 AAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGCGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* * *
12723 AAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACT-G
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
12777 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* * *
12833 AAAATGCCACCAACTTGGGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGACT-G
1 AAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
*
12887 AAAGGTGCCACCATCTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
*
12943 AAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* *
12998 AAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGTTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
* *
13053 AAAATGCCACCAACTTGTGTGGGATTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* * *
13108 AAAATGCCACCAACTTGGGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGACT-G
1 AAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
13162 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* **
13218 AAAATGCCACCAACTTGTGTGGAATTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* *
13273 AAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGTTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
* *
13328 AAAATGTCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* * *
13383 AAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
*
13438 AAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* * *
13493 AAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACT-G
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
13547 AAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGG
1 AAA-GTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
*
13603 AAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* * *
13658 AAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACT-G
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
13712 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* *
13768 AAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACT-G
1 AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
13822 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
* * *
13878 AAAATGCCACCAACTTGGGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGACT-G
1 AAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
*
13932 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGAC-CG
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
13987 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
1 AAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
14041 AAAAAGCGGA
Statistics
Matches: 1426, Mismatches: 81, Indels: 62
0.91 0.05 0.04
Matches are distributed among these distances:
54 44 0.03
55 1340 0.94
56 42 0.03
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
AAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG
Found at i:12881 original size:26 final size:26
Alignment explanation
Indices: 12852--12934 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
12842 CCAACTTGGG
12852 TGGGCTTTGAAAGGTGTCCTGCTCTT
1 TGGGCTTTGAAAGGTGTCCTGCTCTT
*** **
12878 TGGGGACTGAAAGGTG-CCACCATCTTGT
1 TGGGCTTTGAAAGGTGTCCTGC-TC-T-T
12906 GTGGGCTTT-AAGAGGTGTCCTGCTCTT
1 -TGGGCTTTGAA-AGGTGTCCTGCTCTT
12933 TG
1 TG
12935 AGGACTGGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
25 3 0.07
26 17 0.41
27 2 0.05
28 4 0.10
29 12 0.29
30 3 0.07
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.34
Consensus pattern (26 bp):
TGGGCTTTGAAAGGTGTCCTGCTCTT
Found at i:15037 original size:10 final size:9
Alignment explanation
Indices: 15024--15072 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
15014 CTTTTCTCTC
15024 TTTTTGTTT
1 TTTTTGTTT
15033 TTTTTGTTT
1 TTTTTGTTT
*
15042 TTTTT-TTC
1 TTTTTGTTT
*
15050 CTTTT-TTT
1 TTTTTGTTT
15058 TTTTTGCTTT
1 TTTTTG-TTT
15068 TTTTT
1 TTTTT
15073 TTGAAGAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 12 0.35
9 14 0.41
10 8 0.24
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:15042 original size:14 final size:13
Alignment explanation
Indices: 15025--15074 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
15015 TTTTCTCTCT
15025 TTTTGTTTTTTTTG
1 TTTT-TTTTTTTTG
**
15039 -TTTTTTTTTTCC
1 TTTTTTTTTTTTG
15051 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
15064 CTTTTTTTTTT
1 -TTTTTTTTTT
15075 GAAGAGAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 7 0.23
13 13 0.43
14 10 0.33
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:15044 original size:26 final size:26
Alignment explanation
Indices: 15015--15070 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
15005 GTTCTTTTTC
*
15015 TTTTCTCTCTTTTTGTTTTTTTTG-TT
1 TTTTCTCTCCTTTT-TTTTTTTTGCTT
* *
15041 TTTTTTTTCCTTTTTTTTTTTTGCTT
1 TTTTCTCTCCTTTTTTTTTTTTGCTT
15067 TTTT
1 TTTT
15071 TTTTGAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (26 bp):
TTTTCTCTCCTTTTTTTTTTTTGCTT
Found at i:15047 original size:12 final size:12
Alignment explanation
Indices: 15030--15075 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
15020 TCTCTTTTTG
15030 TTTTTTTTGTTT
1 TTTTTTTTGTTT
15042 TTTTTTTCCT-TTT
1 TTTTTTT--TGTTT
*
15055 TTTTTTTTGCTT
1 TTTTTTTTGTTT
15067 TTTTTTTTG
1 TTTTTTTTG
15076 AAGAGAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 1 0.03
12 18 0.60
13 10 0.33
14 1 0.03
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:15057 original size:15 final size:15
Alignment explanation
Indices: 15009--15074 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 15
14999 AAGCAGGTTC
*
15009 TTTTTCTTTTCTCTCTT
1 TTTTTTTTTTC-CT-TT
* *
15026 TTTGTTTTTT--TTG
1 TTTTTTTTTTCCTTT
15039 TTTTTTTTTTCC-TT
1 TTTTTTTTTTCCTTT
*
15053 TTTTTTTTTTGCTTT
1 TTTTTTTTTTCCTTT
15068 TTTTTTT
1 TTTTTTT
15075 GAAGAGAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
13 10 0.25
14 13 0.32
15 9 0.22
17 8 0.20
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTCCTTT
Found at i:15070 original size:25 final size:26
Alignment explanation
Indices: 15025--15073 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
15015 TTTTCTCTCT
*
15025 TTTTGTTTTTTTTGTTTTTTTTTTCC
1 TTTTGTTTTTTTTGCTTTTTTTTTCC
15051 TTTT-TTTTTTTTGCTTTTTTTTT
1 TTTTGTTTTTTTTGCTTTTTTTTT
15074 TGAAGAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (26 bp):
TTTTGTTTTTTTTGCTTTTTTTTTCC
Found at i:15071 original size:26 final size:26
Alignment explanation
Indices: 15025--15074 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
15015 TTTTCTCTCT
15025 TTTTGTTTTTTTTGTTTTTTTTTTCC
1 TTTTGTTTTTTTTGTTTTTTTTTTCC
15051 TTTT-TTTTTTTTGCTTTTTTTTTT
1 TTTTGTTTTTTTTG-TTTTTTTTTT
15075 GAAGAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (26 bp):
TTTTGTTTTTTTTGTTTTTTTTTTCC
Done.