Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold362
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: 59669
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4936 original size:79 final size:81
Alignment explanation
Indices: 4823--5005 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
4813 TACTCGTTCA
* *
4823 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
4886 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
4903 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
4966 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
4982 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
5006 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:5005 original size:40 final size:40
Alignment explanation
Indices: 4821--5005 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
4811 GCTACTCGTT
* *
4821 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
4861 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
4901 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
4940 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
4981 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5006 CATCATTCGA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:13114 original size:79 final size:81
Alignment explanation
Indices: 12972--13154 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
12962 TACTTGTTCA
* * *
12972 AATGCCTTCGGGACATAGCCCAG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
13036 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
**
13052 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
13114 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
13131 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
13155 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:13154 original size:40 final size:40
Alignment explanation
Indices: 12970--13154 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
12960 GCTACTTGTT
* * *
12970 CAAATGCCTTCGGGACATAGCCCAGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
13010 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
13050 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
13089 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
13130 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
13155 CATCATTCGA
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 79 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:15223 original size:3 final size:3
Alignment explanation
Indices: 15215--15285 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
15205 CAACCATCCA
15215 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
15263 ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
15286 GTGTCAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25788 original size:24 final size:24
Alignment explanation
Indices: 25758--25806 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
25748 GAAAAAAAGT
25758 AGTGAAAATTTATTTTAAGAATAA
1 AGTGAAAATTTATTTTAAGAATAA
25782 AGTGAAAATTTATTTTAAGAATAA
1 AGTGAAAATTTATTTTAAGAATAA
25806 A
1 A
25807 TTCTATCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (24 bp):
AGTGAAAATTTATTTTAAGAATAA
Found at i:28467 original size:14 final size:14
Alignment explanation
Indices: 28448--28476 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28438 GCACACGCCT
28448 GTGTGTGACATACG
1 GTGTGTGACATACG
28462 GTGTGTGACATACG
1 GTGTGTGACATACG
28476 G
1 G
28477 CCATGTGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.28
Consensus pattern (14 bp):
GTGTGTGACATACG
Found at i:29706 original size:18 final size:18
Alignment explanation
Indices: 29683--29721 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
29673 GCCGTGTAGG
*
29683 CCACATGGGCGTGTGAGC
1 CCACATGGGCATGTGAGC
29701 CCACATGGGCATGTGAGC
1 CCACATGGGCATGTGAGC
29719 CCA
1 CCA
29722 ATTTTCTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.15
Consensus pattern (18 bp):
CCACATGGGCATGTGAGC
Found at i:31626 original size:101 final size:101
Alignment explanation
Indices: 31498--31710 Score: 309
Period size: 101 Copynumber: 2.1 Consensus size: 101
31488 TCATGCCCTG
* * * *
31498 CCATGGTCTTACGTTCATAGTGCCATAACCAAGTTATGGTCTTATCATCAGAATGTCTTAACCGA
1 CCATGGTCTTACGTCCATAGTGCCATAACCAAGTTATGGTCTTATCATCAGAATGCCATAACCCA
* *
31563 GGTATGGTCTTACATATAAACACTTCCATGGTCCAA
66 GGTACGGTCTTACATATAAACACTACCATGGTCCAA
* * * *
31599 CCATGGTCTTACGTCCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCA
1 CCATGGTCTTACGTCCATAGTGCCATAACCAAGTTATGGTCTTATCATCAGAATGCCATAACCCA
* *
31664 GGTACGGTCTTACATATATACACTACCATGTTCCAA
66 GGTACGGTCTTACATATAAACACTACCATGGTCCAA
*
31700 TCATGGTCTTA
1 CCATGGTCTTA
31711 TGTTTGAATA
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (101 bp):
CCATGGTCTTACGTCCATAGTGCCATAACCAAGTTATGGTCTTATCATCAGAATGCCATAACCCA
GGTACGGTCTTACATATAAACACTACCATGGTCCAA
Found at i:33673 original size:5 final size:5
Alignment explanation
Indices: 33645--33686 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
33635 ATGTTTTAAA
33645 TATAT TAT-T TA-AT TATAAAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TAT--AT TATAT TATAT TATAT TATAT TA
33687 GTATGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 6 0.18
5 22 0.67
7 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:33681 original size:15 final size:14
Alignment explanation
Indices: 33640--33686 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
33630 TTTTTATGTT
*
33640 TTAAATATATTAT-
1 TTAATTATATTATA
33653 TTAATTATAAATTATA
1 TTAATTAT--ATTATA
33669 TTATATTATATTATA
1 TTA-ATTATATTATA
33684 TTA
1 TTA
33687 GTATGTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 7 0.24
15 14 0.48
16 3 0.10
17 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATTATATTATA
Found at i:33848 original size:18 final size:19
Alignment explanation
Indices: 33816--33862 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
33806 TAAAACAAAT
33816 GAAACAAATGAAATA-AAAA
1 GAAACAAA-GAAATAGAAAA
*
33835 GAAATAAAGAAATAGAAAA
1 GAAACAAAGAAATAGAAAA
33854 GAAACAAAG
1 GAAACAAAG
33863 TAACAGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.72, C:0.04, G:0.15, T:0.09
Consensus pattern (19 bp):
GAAACAAAGAAATAGAAAA
Found at i:33870 original size:19 final size:19
Alignment explanation
Indices: 33816--33870 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
33806 TAAAACAAAT
*
33816 GAAACAAATGAAATA-AAAA
1 GAAACAAA-GAAACAGAAAA
* *
33835 GAAATAAAGAAATAGAAAA
1 GAAACAAAGAAACAGAAAA
*
33854 GAAACAAAGTAACAGAA
1 GAAACAAAGAAACAGAA
33871 TATGAAACGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.09
Consensus pattern (19 bp):
GAAACAAAGAAACAGAAAA
Found at i:35657 original size:27 final size:27
Alignment explanation
Indices: 35633--35828 Score: 250
Period size: 27 Copynumber: 7.3 Consensus size: 27
35623 CTCAATTTGT
* *
35633 AAAATTACCATTTTACCCTCGATTTAT
1 AAAATTACCGTTTTACCCTCGATTTAC
* * * *
35660 AGAA-TGCCATTTTACCCTCGATTTAT
1 AAAATTACCGTTTTACCCTCGATTTAC
* *
35686 AGAATTACCGTTTTATCCTCGATTTAC
1 AAAATTACCGTTTTACCCTCGATTTAC
*
35713 AAAATTACCGTTTTACCCTCGATTTAT
1 AAAATTACCGTTTTACCCTCGATTTAC
* * *
35740 AGAATTACCATTTTACCCTTGATTTAC
1 AAAATTACCGTTTTACCCTCGATTTAC
*
35767 AAAATTATCGTTTTACCCTCGATTTAC
1 AAAATTACCGTTTTACCCTCGATTTAC
* *
35794 AGAATTACCGTTTTACCCTCAATTTAC
1 AAAATTACCGTTTTACCCTCGATTTAC
35821 AAAATTAC
1 AAAATTAC
35829 TAAAATACCC
Statistics
Matches: 147, Mismatches: 21, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
26 25 0.17
27 122 0.83
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (27 bp):
AAAATTACCGTTTTACCCTCGATTTAC
Found at i:35744 original size:54 final size:54
Alignment explanation
Indices: 35635--35828 Score: 282
Period size: 54 Copynumber: 3.6 Consensus size: 54
35625 CAATTTGTAA
* * * *
35635 AATTACCATTTTACCCTCGATTTATAGAA-TGCCATTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG
* *
35688 AATTACCGTTTTATCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG
* * *
35742 AATTACCATTTTACCCTTGATTTACAAAATTATCGTTTTACCCTCGATTTACAG
1 AATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG
* *
35796 AATTACCGTTTTACCCTCAATTTACAAAATTAC
1 AATTACCATTTTACCCTCGATTTACAAAATTAC
35829 TAAAATACCC
Statistics
Matches: 125, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
53 25 0.20
54 100 0.80
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (54 bp):
AATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG
Found at i:35787 original size:81 final size:81
Alignment explanation
Indices: 35633--35828 Score: 286
Period size: 81 Copynumber: 2.4 Consensus size: 81
35623 CTCAATTTGT
* * * *
35633 AAAATTACCATTTTACCCTCGATTTATAGAA-TGCCATTTTACCCTCGATTTATAGAATTACCGT
1 AAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT
*
35697 TTTATCCTCGATTTAC
66 TTTACCCTCGATTTAC
* *
35713 AAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTTGATTTACAAAATTATCGT
1 AAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT
35778 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* * * *
35794 AGAATTACCGTTTTACCCTCAATTTACAAAATTAC
1 AAAATTACCGTTTTACCCTCGATTTATAGAATTAC
35829 TAAAATACCC
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
80 30 0.29
81 74 0.71
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (81 bp):
AAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT
TTTACCCTCGATTTAC
Found at i:35837 original size:27 final size:27
Alignment explanation
Indices: 35627--35946 Score: 142
Period size: 27 Copynumber: 11.9 Consensus size: 27
35617 AATGTTCTCA
* ***
35627 ATTTGTAAAATTACCATTTTACCCTCG
1 ATTTATAAAATTACCAAAATACCCTCG
* * ***
35654 ATTTATAGAA-TGCCATTTTACCCTCG
1 ATTTATAAAATTACCAAAATACCCTCG
* **** *
35680 ATTTATAGAATTACCGTTTTATCCTCG
1 ATTTATAAAATTACCAAAATACCCTCG
* ****
35707 ATTTACAAAATTACCGTTTTACCCTCG
1 ATTTATAAAATTACCAAAATACCCTCG
* *** *
35734 ATTTATAGAATTACCATTTTACCCTTG
1 ATTTATAAAATTACCAAAATACCCTCG
* * ****
35761 ATTTACAAAATTATCGTTTTACCCTCG
1 ATTTATAAAATTACCAAAATACCCTCG
* * **** *
35788 ATTTACAGAATTACCGTTTTACCCTCA
1 ATTTATAAAATTACCAAAATACCCTCG
* * *
35815 ATTTACAAAATTACTAAAATACCCTTG
1 ATTTATAAAATTACCAAAATACCCTCG
* *
35842 GTTTAGAAAATTACCAAAATACCCTCG
1 ATTTATAAAATTACCAAAATACCCTCG
* *
35869 A-TCAGTAAAATTACCAAAATACCCTTG
1 ATTTA-TAAAATTACCAAAATACCCTCG
* * *
35896 GTTTTTAAAATTACTAAAATA-CCTCTG
1 ATTTATAAAATTACCAAAATACCCTC-G
* * *
35923 GTTTGTAAAATTACCGAAATACCC
1 ATTTATAAAATTACCAAAATACCC
35947 CTGTAGGGTA
Statistics
Matches: 243, Mismatches: 45, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
26 30 0.12
27 210 0.86
28 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (27 bp):
ATTTATAAAATTACCAAAATACCCTCG
Found at i:35838 original size:81 final size:81
Alignment explanation
Indices: 35672--35856 Score: 235
Period size: 81 Copynumber: 2.3 Consensus size: 81
35662 AATGCCATTT
* * * * *
35672 TACCCTCGATTTATAGAATTACCGTTTTATCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
1 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCAATT
* * ***
35737 TATAGAATTACCATTT
66 TACAAAATTACCAAAA
* *
35753 TACCCTTGATTTACAAAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAATT
1 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCAATT
*
35818 TACAAAATTACTAAAA
66 TACAAAATTACCAAAA
* *
35834 TACCCTTGGTTTAGAAAATTACC
1 TACCCTTGATTTACAAAATTACC
35857 AAAATACCCT
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 88 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.38
Consensus pattern (81 bp):
TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCAATT
TACAAAATTACCAAAA
Found at i:35854 original size:54 final size:54
Alignment explanation
Indices: 35627--35909 Score: 210
Period size: 54 Copynumber: 5.3 Consensus size: 54
35617 AATGTTCTCA
* * * * ***
35627 ATTTGTAAAATTACCATTTTACCCTCGATTTATAGAA-TGCCATTTTACCCTCG
1 ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG
* * * ****
35680 ATTTATAGAATTACCGTTTTATCCTCGATTTACAAAATTACCGTTTTACCCTCG
1 ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG
* * * ****
35734 ATTTATAGAATTACCATTTTACCCTTGATTTACAAAATTATCGTTTTACCCTCG
1 ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG
* * * * * *
35788 ATTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACTAAAATACCCTTG
1 ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG
* * *** * * *
35842 GTTTAGAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCAAAATACCCTTG
1 ATTTATAAAATTACCATTTTACCCTCGATTTA-CAAAATTACCAAAATACCCTCG
* *
35896 GTTTTTAAAATTAC
1 ATTTATAAAATTAC
35910 TAAAATACCT
Statistics
Matches: 192, Mismatches: 36, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
53 33 0.17
54 159 0.83
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37
Consensus pattern (54 bp):
ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG
Found at i:35915 original size:54 final size:54
Alignment explanation
Indices: 35821--35946 Score: 164
Period size: 54 Copynumber: 2.3 Consensus size: 54
35811 CTCAATTTAC
*
35821 AAAATTACTAAAATACCCTTGGTTTAGAAAATTACCAAAATACC-CTCGATCAGT
1 AAAATTACCAAAATACCCTTGGTTTAGAAAATTACCAAAATACCTCT-GATCAGT
** * * **
35875 AAAATTACCAAAATACCCTTGGTTTTTAAAATTACTAAAATACCTCTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTAGAAAATTACCAAAATACCTCTGATCAGT
*
35929 AAAATTACCGAAATACCC
1 AAAATTACCAAAATACCC
35947 CTGTAGGGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 61 0.97
55 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTTGGTTTAGAAAATTACCAAAATACCTCTGATCAGT
Found at i:35961 original size:27 final size:27
Alignment explanation
Indices: 35931--36072 Score: 169
Period size: 27 Copynumber: 5.3 Consensus size: 27
35921 TGGTTTGTAA
*
35931 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
35958 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
35985 AATTACCAAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
36012 AAATACCGAAATATCCCTT-TAGGGTAG
1 AATTACCGAAATA-CCCTTGTAGGGTAG
* * * * *
36039 AATTATCGAGATACCATTGTGGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAG
36066 AATTACC
1 AATTACC
36073 ATTTTGCCCC
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 4 0.04
27 90 0.91
28 5 0.05
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAG
Found at i:35962 original size:81 final size:81
Alignment explanation
Indices: 35821--35976 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 81
35811 CTCAATTTAC
35821 AAAATTACTAAAATACCCTTGGTTTAGAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAA
1 AAAATTACTAAAATACCCTTGGTTTAGAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAA
35886 AATACCCTTGGTTTTT
66 AATACCCTTGGTTTTT
* *
35902 AAAATTACTAAAATA-CCTCTGGTTT-GTAAAATTACCGAAATACCC-CTG-T-AGGGTAGAATT
1 AAAATTACTAAAATACCCT-TGGTTTAG-AAAATTACCAAAATACCCTC-GATCA--GTAAAATT
35962 ACCAAAATACCCTTG
61 ACCAAAATACCCTTG
35977 TAGGGTAGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
79 1 0.01
80 6 0.09
81 61 0.90
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (81 bp):
AAAATTACTAAAATACCCTTGGTTTAGAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAA
AATACCCTTGGTTTTT
Found at i:35989 original size:81 final size:78
Alignment explanation
Indices: 35821--36071 Score: 213
Period size: 81 Copynumber: 3.1 Consensus size: 78
35811 CTCAATTTAC
* *
35821 AAAATTACTAAAATACCCTTGGTTTAG-AAAATTACCAAAATACCCTCGATCA--GTAAAATTAC
1 AAAATTACTAAAATACCC-TGGTTT-GTAAAATTACCGAAATACCCT-G-T-AGGGTAGAATTAC
***
35883 CAAAATACCCTTGGTTTTT
61 CAAAATACCCTT-GTGGGT
35902 AAAATTACTAAAATACCTCTGGTTTGTAAAATTACCGAAATACCCCTGTAGGGTAGAATTACCAA
1 AAAATTACTAAAATACC-CTGGTTTGTAAAATTACCGAAATA-CCCTGTAGGGTAGAATTACCAA
35967 AATACCCTTGTAGGGT
64 AATACCCTTGT-GGGT
* * ** ** * * *
35983 AGAATTACCAAAATACCCTTATAGGATAGAAA-TACCGAAATATCCCTTTAGGGTAGAATTATCG
1 AAAATTACTAAAATACCCTGGTTTG-TA-AAATTACCGAAATA-CCCTGTAGGGTAGAATTACCA
* *
36047 AGATACCATTGTGGGGT
63 AAATACCCTTGT-GGGT
36064 AAAATTAC
1 AAAATTAC
36072 CATTTTGCCC
Statistics
Matches: 143, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
79 1 0.01
80 8 0.06
81 126 0.88
82 8 0.06
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (78 bp):
AAAATTACTAAAATACCCTGGTTTGTAAAATTACCGAAATACCCTGTAGGGTAGAATTACCAAAA
TACCCTTGTGGGT
Found at i:36314 original size:25 final size:25
Alignment explanation
Indices: 36277--36371 Score: 163
Period size: 25 Copynumber: 3.8 Consensus size: 25
36267 AGGAAGTGCT
*
36277 AAAAGGGCCTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
36302 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
36327 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
36352 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
36372 ATTAAAAGAG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 67 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:36384 original size:24 final size:24
Alignment explanation
Indices: 36277--36407 Score: 129
Period size: 25 Copynumber: 5.2 Consensus size: 24
36267 AGGAAGTGCT
* *
36277 AAAAGGGCCTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTA-TG
*
36302 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTA-TG
*
36327 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTAT-G
*
36352 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATG
**
36375 AAAAGAGGCTAGGCCTCCAGTTATATG
1 AAAAG-GGCTTTGCC-CCAGTT-TATG
36402 ATAAAG
1 A-AAAG
36408 CAGCTATGCT
Statistics
Matches: 93, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
23 5 0.05
24 11 0.12
25 68 0.73
26 1 0.01
27 4 0.04
28 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATG
Found at i:41290 original size:27 final size:27
Alignment explanation
Indices: 41252--41381 Score: 183
Period size: 27 Copynumber: 4.8 Consensus size: 27
41242 AAGACCTCAG
41252 TTTGTAAAATTACCAAAATACCCCTGA
1 TTTGTAAAATTACCAAAATACCCCTGA
* *
41279 TTTGTAATATTA-CAGAAATACCCTTGA
1 TTTGTAAAATTACCA-AAATACCCCTGA
41306 TTTGTAAAATTACCAAAATACCCCATG-
1 TTTGTAAAATTACCAAAATACCCC-TGA
* *
41333 TTTGTAAAATTACCGAAATACCCTTGA
1 TTTGTAAAATTACCAAAATACCCCTGA
*
41360 TTTGTAAAATTACCGAAATACC
1 TTTGTAAAATTACCAAAATACC
41382 TTGTAGTGTA
Statistics
Matches: 93, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
26 4 0.04
27 85 0.91
28 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
TTTGTAAAATTACCAAAATACCCCTGA
Found at i:41337 original size:54 final size:54
Alignment explanation
Indices: 41252--41381 Score: 217
Period size: 54 Copynumber: 2.4 Consensus size: 54
41242 AAGACCTCAG
*
41252 TTTGTAAAATTACCAAAATACCCCTGATTTGTAATATTACAGAAATACCCTTGA
1 TTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCTTGA
*
41306 TTTGTAAAATTACCAAAATACCCCATG-TTTGTAAAATTACCGAAATACCCTTGA
1 TTTGTAAAATTACCAAAATACCCC-TGATTTGTAAAATTACAGAAATACCCTTGA
*
41360 TTTGTAAAATTACCGAAATACC
1 TTTGTAAAATTACCAAAATACC
41382 TTGTAGTGTA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
54 70 0.97
55 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCTTGA
Found at i:41421 original size:27 final size:26
Alignment explanation
Indices: 41255--41420 Score: 127
Period size: 27 Copynumber: 6.2 Consensus size: 26
41245 ACCTCAGTTT
* * **
41255 GTAAAATTACCAAAATACCCCTGATTT
1 GTAAAATTACCGAAATACCCATG-TAG
* * * **
41282 GTAATATTACAGAAATACCCTTGATTT
1 GTAAAATTACCGAAATACCCATG-TAG
* **
41309 GTAAAATTACCAAAATACCCCATGTTT
1 GTAAAATTACCGAAATA-CCCATGTAG
* **
41336 GTAAAATTACCGAAATACCCTTGATTT
1 GTAAAATTACCGAAATACCCATG-TAG
*
41363 GTAAAATTACCGAAATA-CCTTGTAG
1 GTAAAATTACCGAAATACCCATGTAG
*
41388 TGTAAAATTATCGAAATACCCATGTAG
1 -GTAAAATTACCGAAATACCCATGTAG
41415 GTAAAA
1 GTAAAA
41421 AGACTATTTT
Statistics
Matches: 121, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.01
26 32 0.26
27 83 0.69
28 5 0.04
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (26 bp):
GTAAAATTACCGAAATACCCATGTAG
Found at i:42116 original size:22 final size:21
Alignment explanation
Indices: 42086--42126 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
42076 TATTCCCCAC
42086 AGGTAGTGCAGGGTTGGATAG
1 AGGTAGTGCAGGGTTGGATAG
42107 AGGTAAGTGCAGGGTTGGAT
1 AGGT-AGTGCAGGGTTGGAT
42127 TGGATAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.24, C:0.05, G:0.46, T:0.24
Consensus pattern (21 bp):
AGGTAGTGCAGGGTTGGATAG
Found at i:45905 original size:29 final size:27
Alignment explanation
Indices: 45887--45956 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
45877 ATATTAAGTC
45887 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
45914 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
45942 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
45957 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:45950 original size:28 final size:28
Alignment explanation
Indices: 45887--45984 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
45877 ATATTAAGTC
*
45887 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
45914 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
45942 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
45971 CGCACACTTAGTGC
1 CGCACACTTAGTGC
45985 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53944 original size:29 final size:27
Alignment explanation
Indices: 53926--53995 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
53916 ATATTAAGTC
53926 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
53953 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
53981 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
53996 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:53989 original size:28 final size:28
Alignment explanation
Indices: 53926--54023 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
53916 ATATTAAGTC
*
53926 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
53953 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
53981 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
54010 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54024 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:57923 original size:12 final size:12
Alignment explanation
Indices: 57878--57920 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
57868 TATGTTTACT
*
57878 TATTATATAAGTA
1 TATTAT-TAAATA
57891 T-TTATTAAATA
1 TATTATTAAATA
57902 TATTATTAAATA
1 TATTATTAAATA
57914 TTATTAT
1 -TATTAT
57921 AAAACAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 6 0.22
12 14 0.52
13 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
TATTATTAAATA
Found at i:57954 original size:19 final size:19
Alignment explanation
Indices: 57930--57976 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
57920 TAAAACAAAT
57930 GAAATAAATGAAATA-AAAA
1 GAAATAAA-GAAATAGAAAA
57949 GAAATAAAGAAATAGAAAA
1 GAAATAAAGAAATAGAAAA
*
57968 GAAACAAAG
1 GAAATAAAG
57977 TAACAGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (19 bp):
GAAATAAAGAAATAGAAAA
Found at i:57984 original size:19 final size:19
Alignment explanation
Indices: 57945--57984 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
57935 AAATGAAATA
* *
57945 AAAAGAAATAAAGAAATAG
1 AAAAGAAACAAAGAAACAG
*
57964 AAAAGAAACAAAGTAACAG
1 AAAAGAAACAAAGAAACAG
57983 AA
1 AA
57985 TATGAAACGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.07
Consensus pattern (19 bp):
AAAAGAAACAAAGAAACAG
Found at i:58023 original size:17 final size:17
Alignment explanation
Indices: 58003--58039 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
57993 GAAAATAGAG
*
58003 AAGAAAAGAAGGAAAAA
1 AAGAAAAGAAAGAAAAA
*
58020 AAGAAAAGAAAGAAAGA
1 AAGAAAAGAAAGAAAAA
58037 AAG
1 AAG
58040 GGAAATTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAGAAAAA
Found at i:58025 original size:8 final size:9
Alignment explanation
Indices: 58003--58039 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
57993 GAAAATAGAG
58003 AAGAAAAGA
1 AAGAAAAGA
*
58012 AGGAAAA-A
1 AAGAAAAGA
58020 AAGAAAAGA
1 AAGAAAAGA
58029 AAG-AAAGA
1 AAGAAAAGA
58037 AAG
1 AAG
58040 GGAAATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 15 0.60
9 10 0.40
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:59282 original size:18 final size:18
Alignment explanation
Indices: 59246--59359 Score: 95
Period size: 18 Copynumber: 6.2 Consensus size: 18
59236 TAAATAAAAG
* *
59246 TACTGAATGACTGACTGT
1 TACTGAATAACTGATTGT
* *
59264 TATTGAATAATTGATTGT
1 TACTGAATAACTGATTGT
*
59282 TACTGAATAACTGATTGC
1 TACTGAATAACTGATTGT
*
59300 TACTGTGAGA-AAATGATTGT
1 TAC--TGA-ATAACTGATTGT
* *
59320 TACTAAATAACTAATTGT
1 TACTGAATAACTGATTGT
* * *
59338 TACTGAATGATTGAATGT
1 TACTGAATAACTGATTGT
59356 TACT
1 TACT
59360 AAATGAAACT
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
17 1 0.01
18 59 0.79
20 14 0.19
21 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (18 bp):
TACTGAATAACTGATTGT
Found at i:59364 original size:18 final size:18
Alignment explanation
Indices: 59315--59365 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
59305 TGAGAAAATG
*
59315 ATTGTTACTAAATAACTA
1 ATTGTTACTAAATGACTA
* *
59333 ATTGTTACTGAATGATTGA
1 ATTGTTACTAAATGACT-A
59352 A-TGTTACTAAATGA
1 ATTGTTACTAAATGA
59366 AACTGATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (18 bp):
ATTGTTACTAAATGACTA
Done.