Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2176
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: 59263
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:1153 original size:15 final size:15
Alignment explanation
Indices: 1133--1201 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
1123 GTATCTTGGG
1133 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
1148 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
1163 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
1178 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
1193 TTTCTTTAT
1 TTTCTTTAT
1202 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:1202 original size:30 final size:30
Alignment explanation
Indices: 1124--1211 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
1114 CATAGTATCG
* * * *
1124 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
1154 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
1184 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
1212 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:3648 original size:45 final size:46
Alignment explanation
Indices: 3593--3766 Score: 196
Period size: 45 Copynumber: 3.8 Consensus size: 46
3583 TATTTGGGCA
*
3593 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
3639 TCC-AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
3685 TCCGAACTCGTTGAGTTGAGTCCGAGTT-ACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
3730 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3767 GTGGGTTACA
Statistics
Matches: 106, Mismatches: 13, Indels: 18
0.77 0.09 0.13
Matches are distributed among these distances:
42 6 0.06
44 3 0.03
45 52 0.49
46 13 0.12
47 27 0.25
49 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:3746 original size:92 final size:92
Alignment explanation
Indices: 3589--3758 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 92
3579 GGGATATTTG
* * *
3589 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAACTCGTTGAGT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCAACTCGTTGAGT
3654 TGAGTCCGAGTTCGTGAGATGTAACTA
66 TGAGTCCGAGTTCGTGAGATGTAACTA
* *
3681 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTT-ACTCATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCC-AACTCGTTGAG
3745 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
3759 ACTTATGGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
91 16 0.22
92 56 0.78
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:25048 original size:12 final size:12
Alignment explanation
Indices: 25031--25060 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25021 CCATACACGC
25031 CCGTGTGCTAGG
1 CCGTGTGCTAGG
25043 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
25055 CTGTGT
1 CCGTGT
25061 CAAACCTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:29779 original size:25 final size:26
Alignment explanation
Indices: 29734--29804 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 26
29724 ATTGATTTAA
* *
29734 TTTGTTTTCTCTTTTCTTTTTTA-TGT
1 TTTGTTTTAT-TTTTATTTTTTAGTGT
29760 TTATG-TTTATTTTTA-TTTTTAGTTGT
1 TT-TGTTTTATTTTTATTTTTTAG-TGT
*
29786 TTTGTTTTATTTTCATTTT
1 TTTGTTTTATTTTTATTTT
29805 CTTGTACTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 6 0.16
25 6 0.16
26 20 0.54
27 5 0.14
ACGTcount: A:0.10, C:0.06, G:0.08, T:0.76
Consensus pattern (26 bp):
TTTGTTTTATTTTTATTTTTTAGTGT
Found at i:29786 original size:20 final size:17
Alignment explanation
Indices: 29750--29798 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
29740 TTCTCTTTTC
*
29750 TTTTTTATGTTTATGTT
1 TTTTTTATTTTTATGTT
29767 TATTTTTATTTTTAGTTGTT
1 T-TTTTTATTTTTA--TGTT
29787 TTGTTTTATTTT
1 TT-TTTTATTTT
29799 CATTTTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.04
18 11 0.41
19 1 0.04
20 14 0.52
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTTTATTTTTATGTT
Found at i:32196 original size:20 final size:22
Alignment explanation
Indices: 32166--32213 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
32156 GAATATGCTG
*
32166 TAAATTGAAA-GTTTTTGATAGA
1 TAAA-TGAAAGGTTATTGATAGA
32188 -AAATGAAAGGTTATTGATAGA
1 TAAATGAAAGGTTATTGATAGA
32209 TAAAT
1 TAAAT
32214 CACTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (22 bp):
TAAATGAAAGGTTATTGATAGA
Found at i:32905 original size:29 final size:29
Alignment explanation
Indices: 32873--32935 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
32863 TACCACGTGG
*
32873 AAAGGGATAGCTTTGACTATCGAATGTGA
1 AAAGGGATAGCTTTGACTATCGAATATGA
**
32902 AAAGGGATAGCTTTGGTTATCGAATATGA
1 AAAGGGATAGCTTTGACTATCGAATATGA
32931 AAAGG
1 AAAGG
32936 AAAGGTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.27
Consensus pattern (29 bp):
AAAGGGATAGCTTTGACTATCGAATATGA
Found at i:37487 original size:25 final size:25
Alignment explanation
Indices: 37459--37528 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
37449 CTCTTTTAAT
*
37459 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
37484 AACTGGGGCAAAGTCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
37509 AACTAGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
37529 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:37647 original size:27 final size:27
Alignment explanation
Indices: 37617--37788 Score: 191
Period size: 27 Copynumber: 6.0 Consensus size: 27
37607 GGGGCAAAAT
* * * *
37617 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
37644 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
37671 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
37698 GGGTATTTTGGTAATTCTACCTTACAGGGGTATTTC
1 ---------GGTAATTCTACCCTACAGGGGTATTTC
*
37734 GGTAATTCTACCCTACAGCGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
37761 GGTAATTATACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
37788 G
1 G
37789 ATATTTTACA
Statistics
Matches: 125, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
27 100 0.80
36 25 0.20
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:37713 original size:36 final size:36
Alignment explanation
Indices: 37662--37735 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
37652 TACCCTACAG
37662 GGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
1 GGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
* * *
37698 GGGTATTTTGGTAATTCTACCTTACAGGGGTATTTC
1 GGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
37734 GG
1 GG
37736 TAATTCTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (36 bp):
GGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
Found at i:37734 original size:63 final size:63
Alignment explanation
Indices: 37635--37762 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 63
37625 TACCCCACAA
*
37635 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
1 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGCGGTATTTC
* * * *
37698 GGGTATTTTGGTAATTCTACCTTACAGGGGTATTTCGGTAATTCTACCCTACAGCGGTATTTC
1 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGCGGTATTTC
37761 GG
1 GG
37763 TAATTATACC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (63 bp):
GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGCGGTATTTC
Found at i:37773 original size:90 final size:90
Alignment explanation
Indices: 37616--37788 Score: 274
Period size: 90 Copynumber: 1.9 Consensus size: 90
37606 AGGGGCAAAA
* * *
37616 TGGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTA
1 TGGTAATTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGCGGTATTTCGATAATTATA
37681 CCCTACAGGGGTATTTCGGGTATTT
66 CCCTACAGGGGTATTTCGGGTATTT
** * * *
37706 TGGTAATTCTACCTTACAGGGGTATTTCGGTAATTCTACCCTACAGCGGTATTTCGGTAATTATA
1 TGGTAATTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGCGGTATTTCGATAATTATA
37771 CCCTACAGGGGTATTTCG
66 CCCTACAGGGGTATTTCG
37789 ATATTTTACA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (90 bp):
TGGTAATTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGCGGTATTTCGATAATTATA
CCCTACAGGGGTATTTCGGGTATTT
Found at i:37868 original size:28 final size:28
Alignment explanation
Indices: 37777--37931 Score: 149
Period size: 27 Copynumber: 5.7 Consensus size: 28
37767 TATACCCTAC
* * **
37777 AGGGGTATTTCGAT-ATTTTACAAATTG
1 AGGGGTATTTTGGTAATTTTACAAATCA
* *
37804 A-GAGTATTTTGATAATTTTACAAATC-
1 AGGGGTATTTTGGTAATTTTACAAATCA
*
37830 AGGGGTATTTTGGTAATTTTACAAGTCA
1 AGGGGTATTTTGGTAATTTTACAAATCA
*
37858 AGGGGTATTTTGGTAATTTTACAAA-CT
1 AGGGGTATTTTGGTAATTTTACAAATCA
* * ** *
37885 AGGAGTATTTTAGTAATTTTGTAAACCA
1 AGGGGTATTTTGGTAATTTTACAAATCA
*
37913 A-GGGTATTTTAGTAATTTT
1 AGGGGTATTTTGGTAATTTT
37932 GTAAATCGAG
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
26 11 0.10
27 73 0.66
28 26 0.24
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (28 bp):
AGGGGTATTTTGGTAATTTTACAAATCA
Found at i:37875 original size:55 final size:54
Alignment explanation
Indices: 37807--37931 Score: 153
Period size: 55 Copynumber: 2.3 Consensus size: 54
37797 CAAATTGAGA
* * * **
37807 GTATTTTGATAATTTTACAAA-TCAGGGGTATTTTGGTAATTTTACAAGTCAAGGG
1 GTATTTTGGTAATTTTACAAACT-AGGAGTATTTTAGTAATTTTACAAACCAA-GG
**
37862 GTATTTTGGTAATTTTACAAACTAGGAGTATTTTAGTAATTTTGTAAACCAAGG
1 GTATTTTGGTAATTTTACAAACTAGGAGTATTTTAGTAATTTTACAAACCAAGG
*
37916 GTATTTTAGTAATTTT
1 GTATTTTGGTAATTTT
37932 GTAAATCGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
54 17 0.28
55 43 0.70
56 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.43
Consensus pattern (54 bp):
GTATTTTGGTAATTTTACAAACTAGGAGTATTTTAGTAATTTTACAAACCAAGG
Found at i:37895 original size:82 final size:81
Alignment explanation
Indices: 37777--37931 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
37767 TATACCCTAC
* * *
37777 AGGGGTATTTCGATATTTTACAAATTGAGAGTATTTT-GATAATTTTACAAATCAGGGGTATTTT
1 AGGGGTATTTCGATATTTTACAAATAGAGAGTATTTTAG-TAATTTTACAAACCAAGGGTATTTT
*
37841 GGTAATTTTACAAGTCA
65 AGTAATTTTACAAGTCA
* * **
37858 AGGGGTATTTTGGTAATTTTACAAACTAG-GAGTATTTTAGTAATTTTGTAAACCAAGGGTATTT
1 AGGGGTATTTCGAT-ATTTTACAAA-TAGAGAGTATTTTAGTAATTTTACAAACCAAGGGTATTT
37922 TAGTAATTTT
64 TAGTAATTTT
37932 GTAAATCGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
81 12 0.19
82 48 0.76
83 3 0.05
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (81 bp):
AGGGGTATTTCGATATTTTACAAATAGAGAGTATTTTAGTAATTTTACAAACCAAGGGTATTTTA
GTAATTTTACAAGTCA
Found at i:37910 original size:27 final size:27
Alignment explanation
Indices: 37832--37945 Score: 104
Period size: 27 Copynumber: 4.2 Consensus size: 27
37822 TACAAATCAG
* ** **
37832 GGGTATTTTGGTAATTTTACAAGTCAA
1 GGGTATTTTAGTAATTTTGTAAACCAA
* ** *
37859 GGGGTATTTTGGTAATTTTACAAA-CTA
1 -GGGTATTTTAGTAATTTTGTAAACCAA
37886 GGAGTATTTTAGTAATTTTGTAAACCAA
1 GG-GTATTTTAGTAATTTTGTAAACCAA
* *
37914 GGGTATTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTAGTAATTTTGTAAACCAA
37941 GGGTA
1 GGGTA
37946 AAACGGTAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.03
27 48 0.63
28 26 0.34
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTGTAAACCAA
Found at i:38115 original size:81 final size:81
Alignment explanation
Indices: 37924--38132 Score: 328
Period size: 81 Copynumber: 2.6 Consensus size: 81
37914 GGGTATTTTA
* * *
37924 GTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
37989 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAATG
*
38005 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
*
38070 AATTGAGGGTAAAATG
66 AATCGAGGGTAAAATG
*** * *
38086 GTAATTCTGTAAATCGAGGGTACTTTGGTAATTTTATAAATTGAGGG
1 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGG
38133 CATTTTAGTA
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 117 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
AATCGAGGGTAAAATG
Found at i:38118 original size:27 final size:27
Alignment explanation
Indices: 37924--38107 Score: 305
Period size: 27 Copynumber: 6.8 Consensus size: 27
37914 GGGTATTTTA
* *
37924 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
37951 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
37978 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
38005 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
38032 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
38059 GTAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
38086 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
38108 CTTTGGTAAT
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 149 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:38125 original size:27 final size:27
Alignment explanation
Indices: 37924--38132 Score: 247
Period size: 27 Copynumber: 7.7 Consensus size: 27
37914 GGGTATTTTA
* *
37924 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTTTATAAATCGAGGGTAAAATG
* * *
37951 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTTTATAAATCGAGGGTAAAATG
* *
37978 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTTTATAAATCGAGGGTAAAATG
*
38005 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTTTATAAATCGAGGGTAAAATG
* *
38032 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTTTATAAATCGAGGGTAAAATG
* * *
38059 GTAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTTTATAAATCGAGGGTAAAATG
* * ***
38086 GTAATTCTGTAAATCGAGGGTACTTTG
1 GTAATTTTATAAATCGAGGGTAAAATG
*
38113 GTAATTTTATAAATTGAGGG
1 GTAATTTTATAAATCGAGGG
38133 CATTTTAGTA
Statistics
Matches: 168, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 168 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (27 bp):
GTAATTTTATAAATCGAGGGTAAAATG
Found at i:42543 original size:50 final size:50
Alignment explanation
Indices: 42468--42568 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
42458 TTCCTCGAAG
42468 TGTTTACACATTTCCGACGCAGTTTTGACCCATTTAGTTGCATACTAACT
1 TGTTTACACATTTCCGACGCAGTTTTGACCCATTTAGTTGCATACTAACT
42518 TGTTTACACATTTCCGACGCAGTTTTGACCCATTTAGTTGCATACTAACT
1 TGTTTACACATTTCCGACGCAGTTTTGACCCATTTAGTTGCATACTAACT
42568 T
1 T
42569 AGCCTCACGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.39
Consensus pattern (50 bp):
TGTTTACACATTTCCGACGCAGTTTTGACCCATTTAGTTGCATACTAACT
Found at i:45672 original size:40 final size:40
Alignment explanation
Indices: 45596--45819 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
45586 CAAACTCAAG
* * *
45596 TGCCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAGA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAA
*
45635 TGCCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
* *
45675 AGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
* *
45715 TTCCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
* * *
45755 TGCCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
* *
45795 TGCCCTCGGGACTTAACCCGGATAT
1 TGCCTTCGGGACTTAGCCCGGATAT
45820 CATTCGAATA
Statistics
Matches: 167, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
39 14 0.08
40 150 0.90
41 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAA
Found at i:50935 original size:15 final size:15
Alignment explanation
Indices: 50915--50948 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
50905 AGACAGTAGA
50915 CTCAACTCGGATTAT
1 CTCAACTCGGATTAT
50930 CTCAACTCGGATTAT
1 CTCAACTCGGATTAT
50945 CTCA
1 CTCA
50949 TTATTTGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (15 bp):
CTCAACTCGGATTAT
Done.