Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3172.1
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: 155273
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.31
Warning! 3582 characters in sequence are not A, C, G, or T
Found at i:3122 original size:47 final size:48
Alignment explanation
Indices: 3051--3279 Score: 206
Period size: 47 Copynumber: 4.9 Consensus size: 48
3041 AGGGTAATGT
* *
3051 GCCGATGCCATGTCCTAGACATGGTCTTATACTGGCTCAT-ATCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA
* * *
3098 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCCCATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCA-A
* * * * *
3146 GCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTTA-CGTCTTGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATC-TCAA
* * * * *
3192 GCCGTTG-CATGTCCCAAACAT-GTCTTACACTAGC-CCTCGTCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA
* * *
3237 TGTCGATGCCATGTCCTAGACATGGTCTTACACCGGCTC-TCAT
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAT
3280 AATGTGGCCG
Statistics
Matches: 148, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.01
46 59 0.40
47 65 0.44
48 21 0.14
49 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA
Found at i:3233 original size:46 final size:46
Alignment explanation
Indices: 3146--3269 Score: 133
Period size: 46 Copynumber: 2.7 Consensus size: 46
3136 TCATCCCATA
* *
3146 GCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTTGAG
1 GCCGATGCATGTCCCAAACATGTCTTACACTGCCCTACGTCTTGAG
* ** *
3192 GCCGTTGCATGTCCCAAACATGTCTTACACTAGCCCT-CGTCTCAAT
1 GCCGATGCATGTCCCAAACATGTCTTACACT-GCCCTACGTCTTGAG
* * *
3238 GTCGATGCCATGTCCTAGACATGGTCTTACAC
1 GCCGATG-CATGTCCCAAACAT-GTCTTACAC
3270 CGGCTCTCAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 41 0.63
47 15 0.23
48 9 0.14
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTGCCCTACGTCTTGAG
Found at i:11336 original size:24 final size:24
Alignment explanation
Indices: 11298--11346 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
11288 GCACTATAGA
* *
11298 GTAACAGACATAATATGCCACAAG
1 GTAACAGACAAAATACGCCACAAG
* *
11322 GTAACATACAAAATACGTCACAAG
1 GTAACAGACAAAATACGCCACAAG
11346 G
1 G
11347 CGACCTAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.16
Consensus pattern (24 bp):
GTAACAGACAAAATACGCCACAAG
Found at i:13596 original size:27 final size:27
Alignment explanation
Indices: 13566--13841 Score: 213
Period size: 27 Copynumber: 10.3 Consensus size: 27
13556 GGTAAAATAG
* * *
13566 TCATCTTACCATAAAAGGGCAAAACAA
1 TCATTTTACCCTATAAGGGCAAAACAA
* * *
13593 TCATTTTACCCCATAAGGGAAAAACAG
1 TCATTTTACCCTATAAGGGCAAAACAA
* * * *
13620 TTATTTTACCCCATAAGGGAAAAACAG
1 TCATTTTACCCTATAAGGGCAAAACAA
* *
13647 TCATTTTACACC-ATAAAGGCAAAATAA
1 TCATTTTAC-CCTATAAGGGCAAAACAA
* *
13674 TCATTTTA-CCTCATAAGGGCAAAAGAG
1 TCATTTTACCCT-ATAAGGGCAAAACAA
* * * *
13701 TCATTTTATCCTAAAAGGGGAAAAAAA
1 TCATTTTACCCTATAAGGGCAAAACAA
*
13728 GTTATTTTA-CCTCATAAGGGCAAAACAA
1 -TCATTTTACCCT-ATAAGGGCAAAACAA
* * *
13756 TCATGTTACCCCATAAGGGCAAAATAA
1 TCATTTTACCCTATAAGGGCAAAACAA
* *
13783 TCATGTTACCCCATAAGGGCAAAAC-A
1 TCATTTTACCCTATAAGGGCAAAACAA
* * * * *
13809 --GTGTTACCCCATAAGGGTAAAACAT
1 TCATTTTACCCTATAAGGGCAAAACAA
13834 TCATTTTA
1 TCATTTTA
13842 TCGATTAAGG
Statistics
Matches: 206, Mismatches: 33, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
24 21 0.10
25 2 0.01
26 1 0.00
27 156 0.76
28 26 0.13
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (27 bp):
TCATTTTACCCTATAAGGGCAAAACAA
Found at i:13638 original size:54 final size:54
Alignment explanation
Indices: 13580--13841 Score: 255
Period size: 54 Copynumber: 4.9 Consensus size: 54
13570 CTTACCATAA
*
13580 AAGGGCAAAACAATCATTTTACCCCATAAGGGAAAAACAGTTATTTTACCCCAT
1 AAGGGCAAAACAATCATTTTACCCCATAAGGGAAAAACAATTATTTTACCCCAT
* * * * * * * *
13634 AAGGGAAAAACAGTCATTTTACACCATAAAGGCAAAATAATCATTTTACCTCAT
1 AAGGGCAAAACAATCATTTTACCCCATAAGGGAAAAACAATTATTTTACCCCAT
* * * * * *
13688 AAGGGCAAAAGAGTCATTTTATCCTAAAAGGGGAAAAA-AAGTTATTTTACCTCAT
1 AAGGGCAAAACAATCATTTTACCCCATAA-GGGAAAAACAA-TTATTTTACCCCAT
* * * * *
13743 AAGGGCAAAACAATCATGTTACCCCATAAGGGCAAAATAATCATGTTACCCCAT
1 AAGGGCAAAACAATCATTTTACCCCATAAGGGAAAAACAATTATTTTACCCCAT
* * *
13797 AAGGGCAAAAC-A--GTGTTACCCCATAAGGGTAAAAC-ATTCATTTTA
1 AAGGGCAAAACAATCATTTTACCCCATAAGGGAAAAACAATT-ATTTTA
13842 TCGATTAAGG
Statistics
Matches: 171, Mismatches: 33, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
50 2 0.01
51 25 0.15
53 1 0.01
54 99 0.58
55 44 0.26
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (54 bp):
AAGGGCAAAACAATCATTTTACCCCATAAGGGAAAAACAATTATTTTACCCCAT
Found at i:13754 original size:109 final size:108
Alignment explanation
Indices: 13580--13808 Score: 323
Period size: 109 Copynumber: 2.1 Consensus size: 108
13570 CTTACCATAA
* *
13580 AAGGGCAAAACAATCATTTTACCCCATAAGGGAAAAACAGTTATTTTACCCCATAAGGGAAAAAC
1 AAGGGCAAAACAATCATTTTACCCCAAAAGGGAAAAAAAGTTATTTTACCCCATAAGGGAAAAAC
* * * *
13645 AGTCATTTTACACCATAAAGGCAAAATAATCATTTTACCTCAT
66 AATCATGTTACACCATAAAGGCAAAATAATCATGTTACCCCAT
* * * * * *
13688 AAGGGCAAAAGAGTCATTTTATCCTAAAAGGGGAAAAAAAGTTATTTTACCTCATAAGGGCAAAA
1 AAGGGCAAAACAATCATTTTACCCCAAAA-GGGAAAAAAAGTTATTTTACCCCATAAGGGAAAAA
* *
13753 CAATCATGTTACCCCATAAGGGCAAAATAATCATGTTACCCCAT
65 CAATCATGTTACACCATAAAGGCAAAATAATCATGTTACCCCAT
13797 AAGGGCAAAACA
1 AAGGGCAAAACA
13809 GTGTTACCCC
Statistics
Matches: 105, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
108 24 0.23
109 81 0.77
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (108 bp):
AAGGGCAAAACAATCATTTTACCCCAAAAGGGAAAAAAAGTTATTTTACCCCATAAGGGAAAAAC
AATCATGTTACACCATAAAGGCAAAATAATCATGTTACCCCAT
Found at i:13758 original size:82 final size:81
Alignment explanation
Indices: 13580--13841 Score: 280
Period size: 82 Copynumber: 3.3 Consensus size: 81
13570 CTTACCATAA
* * * *
13580 AAGGGCAAAACAATCATTTTACCCCATAAGGGAAAAACAGTTATTTTACCCCATAAGGGAAAAAC
1 AAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTACCCCAAAAGGGAAAAAA
13645 AGTCATTTTACACCAT
66 AGTCATTTTACACCAT
* * * * * *
13661 AAAGGCAAAATAATCATTTTACCTCATAAGGGCAAAAGAGTCATTTTATCCTAAAAGGGGAAAAA
1 AAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTACCCCAAAA-GGGAAAAA
*
13726 AAGTTATTTTAC-CTCAT
65 AAGTCATTTTACAC-CAT
* * * * * * *
13743 AAGGGCAAAACAATCATGTTACCCCATAAGGGCAAAATAATCATGTTACCCCATAAGGGCAAAAC
1 AAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTACCCCAAAAGGGAAAAAA
* *
13808 AG---TGTTACCCCAT
66 AGTCATTTTACACCAT
* *
13821 AAGGGTAAAACATTCATTTTA
1 AAGGGCAAAACAATCATTTTA
13842 TCGATTAAGG
Statistics
Matches: 151, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
78 26 0.17
79 1 0.01
81 57 0.38
82 67 0.44
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (81 bp):
AAGGGCAAAACAATCATTTTACCCCATAAGGGCAAAACAGTCATTTTACCCCAAAAGGGAAAAAA
AGTCATTTTACACCAT
Found at i:18124 original size:15 final size:15
Alignment explanation
Indices: 18106--18159 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
18096 GTATCTTGGG
18106 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
18121 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
18136 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
18151 TTTCTTTAT
1 TTTCTTTAT
18160 TCAGTTTTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:18138 original size:30 final size:30
Alignment explanation
Indices: 18102--18161 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
18092 TATCGTATCT
*
18102 TGGGTTTCTTTATCCTGGATTTCTTTATTC
1 TGGGTTTCTCTATCCTGGATTTCTTTATTC
*
18132 TGGGTTTCTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTCTATCCTGGATTTCTTTATTC
18162 AGTTTTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.10, C:0.17, G:0.17, T:0.57
Consensus pattern (30 bp):
TGGGTTTCTCTATCCTGGATTTCTTTATTC
Found at i:25641 original size:21 final size:22
Alignment explanation
Indices: 25616--25656 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
25606 CATGAAATTC
25616 AACACATTAC-ATGCCAACTTA
1 AACACATTACAATGCCAACTTA
*
25637 AACACATTACAATTCCAACT
1 AACACATTACAATGCCAACT
25657 AGAACTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.24
Consensus pattern (22 bp):
AACACATTACAATGCCAACTTA
Found at i:29746 original size:42 final size:42
Alignment explanation
Indices: 29593--29757 Score: 154
Period size: 42 Copynumber: 3.9 Consensus size: 42
29583 AGTAAGATGC
* **
29593 CAATGCCATATCCCAGATATGGTCTTACATGGGATCACATAT
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCACATAT
* * ** * *
29635 CGATGCCGATAGCCCA-ACTATGGTCTTACACGATGTCTCGTAT
1 CAATGCC-ATATCCCAGA-TATGGTCTTACACGAAATCACATAT
** * * *
29678 TGATG-CATGTCCCAGACATGGTCTTACATGAAATCACATAT
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCACATAT
* *
29719 CAATGCCATATCCCAGATATGGCCTTACACGTAATCACA
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCACA
29758 CATAACCCTA
Statistics
Matches: 95, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
41 28 0.29
42 37 0.39
43 30 0.32
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTACACGAAATCACATAT
Found at i:33495 original size:42 final size:42
Alignment explanation
Indices: 33343--33505 Score: 161
Period size: 42 Copynumber: 3.9 Consensus size: 42
33333 TAAGATGCCA
* **
33343 ATGCCATATCCCAGATATGGTCTTACATGGGATCACATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCACATATCG
* ** * * *
33385 ATGCCGATAGCCCA-ACTATGGTCTTACACGATGTCTCGTATTG
1 ATGCC-ATATCCCAGA-TATGGTCTTACACGAAATCACATATCG
* * *
33428 ATG-CATGTCCCAGACATGGTCTTACATGAAATCACATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCACATATCG
*
33469 ATGCCATATCCCAGATATGG-CATTACACGTAATCACA
1 ATGCCATATCCCAGATATGGTC-TTACACGAAATCACA
33506 CATAACCCTA
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
41 30 0.32
42 35 0.37
43 30 0.32
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCACATATCG
Found at i:35850 original size:23 final size:23
Alignment explanation
Indices: 35791--35834 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
35781 TTAATGTTAG
35791 TTGAATGTTGGTTGATGATTTAT
1 TTGAATGTTGGTTGATGATTTAT
35814 TTGAATGTTGGTTGATGATTT
1 TTGAATGTTGGTTGATGATTT
35835 TTGCATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.52
Consensus pattern (23 bp):
TTGAATGTTGGTTGATGATTTAT
Found at i:47468 original size:47 final size:48
Alignment explanation
Indices: 47399--47625 Score: 202
Period size: 47 Copynumber: 4.9 Consensus size: 48
47389 GGTAATGTGC
* *
47399 CGATGCCATGTCCTAGACATGGTCTTATACTGGCTCAT-ATCTCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGT
* * *
47446 CGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCCCATAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCA-AGT
* * * * ** *
47494 CAATG-CATGTCCCAAACAT-GTCTTACACTGGCTTA-CGTCTTGAGG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGT
* * * *
47539 CTGTTG-CATGTCCCAGACGT-GTCTTACACTAGC-CCTCATCTCAATGT
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAA-GT
* *
47586 TGATGCCATGTCCTAGACATGGTCTTACACTGGCTC-TCAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAT
47626 AATGTGGTCG
Statistics
Matches: 142, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
45 3 0.02
46 52 0.37
47 64 0.45
48 22 0.15
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGT
Found at i:69793 original size:45 final size:45
Alignment explanation
Indices: 69741--69827 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
69731 TATGTAATCT
* *
69741 GAACTCATTGAGTTGTAG-TTTGATTTCATGATATATGTGACATTC
1 GAACTCATTGAGTTGT-GCTTTGAGTTCATGATATATATGACATTC
*
69786 GAACTCATTGAGTTGTGCTTTGAGTTCGTGATATATATGACA
1 GAACTCATTGAGTTGTGCTTTGAGTTCATGATATATATGACA
69828 CATGTTTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.40
Consensus pattern (45 bp):
GAACTCATTGAGTTGTGCTTTGAGTTCATGATATATATGACATTC
Found at i:91911 original size:92 final size:92
Alignment explanation
Indices: 91754--91937 Score: 359
Period size: 92 Copynumber: 2.0 Consensus size: 92
91744 CGAAGATTTT
91754 ACTTTCACTAAGTTCGGTCCAAAACAACGGTGTACGGCATTTACGACCATACAAAGCCTCGTAAG
1 ACTTTCACTAAGTTCGGTCCAAAACAACGGTGTACGGCATTTACGACCATACAAAGCCTCGTAAG
91819 GTGCCATCTTAATGCTTGATTGAAAAC
66 GTGCCATCTTAATGCTTGATTGAAAAC
*
91846 ACTTTCACTATGTTCGGTCCAAAACAACGGTGTACGGCATTTACGACCATACAAAGCCTCGTAAG
1 ACTTTCACTAAGTTCGGTCCAAAACAACGGTGTACGGCATTTACGACCATACAAAGCCTCGTAAG
91911 GTGCCATCTTAATGCTTGATTGAAAAC
66 GTGCCATCTTAATGCTTGATTGAAAAC
91938 TATTGTTGTA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (92 bp):
ACTTTCACTAAGTTCGGTCCAAAACAACGGTGTACGGCATTTACGACCATACAAAGCCTCGTAAG
GTGCCATCTTAATGCTTGATTGAAAAC
Found at i:93441 original size:96 final size:96
Alignment explanation
Indices: 93300--93492 Score: 359
Period size: 96 Copynumber: 2.0 Consensus size: 96
93290 AAATTCTACT
*
93300 TCTCGAACGGGTGGTAATCCCAGTAACTCCTCAGGAAAAACATCTGGATACTCACGAACCACTGG
1 TCTCGAACGGGTGGTAATCCCAGTAACTCCTCAGGAAAAACATCTGGATACTCACGAACCACCGG
* *
93365 TACCTTTTCAAGTTTCTTTTCCGACTCTTTG
66 TACCGTTTCAAGTTTCCTTTCCGACTCTTTG
93396 TCTCGAACGGGTGGTAATCCCAGTAACTCCTCAGGAAAAACATCTGGATACTCACGAACCACCGG
1 TCTCGAACGGGTGGTAATCCCAGTAACTCCTCAGGAAAAACATCTGGATACTCACGAACCACCGG
93461 TACCGTTTCAAGTTTCCTTTCCGACTCTTTG
66 TACCGTTTCAAGTTTCCTTTCCGACTCTTTG
93492 T
1 T
93493 GATCAAGTAC
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (96 bp):
TCTCGAACGGGTGGTAATCCCAGTAACTCCTCAGGAAAAACATCTGGATACTCACGAACCACCGG
TACCGTTTCAAGTTTCCTTTCCGACTCTTTG
Found at i:96807 original size:24 final size:24
Alignment explanation
Indices: 96757--96810 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
96747 GATCGAATTT
*
96757 GCACACATAGTGCTAGTCACACTC
1 GCACACATAGTGCTAGTCAAACTC
96781 GCACACATAGTGCCATAGT-AAAC-C
1 GCACACATAGTG-C-TAGTCAAACTC
96805 GCACAC
1 GCACAC
96811 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 4 0.15
26 4 0.15
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCAAACTC
Found at i:101083 original size:40 final size:40
Alignment explanation
Indices: 101039--101302 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
101029 GCTCCTCGTT
* *
101039 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
101079 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
101119 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
101159 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
101199 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
101238 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
101279 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
101303 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:109098 original size:40 final size:40
Alignment explanation
Indices: 109054--109315 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
109044 GCTCCTCGTT
* *
109054 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
109094 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
109134 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
109173 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
109212 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
109251 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
109292 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
109316 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:111987 original size:22 final size:21
Alignment explanation
Indices: 111954--112006 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
111944 TAACATGTGT
111954 CACATATATCATGAGCTCAGAC
1 CACATA-ATCATGAGCTCAGAC
*
111976 CACATAACTCATGAGCTCAGAT
1 CACATAA-TCATGAGCTCAGAC
111998 CACATAATC
1 CACATAATC
112007 CCTAGTGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (21 bp):
CACATAATCATGAGCTCAGAC
Found at i:120422 original size:50 final size:51
Alignment explanation
Indices: 120305--120423 Score: 141
Period size: 52 Copynumber: 2.3 Consensus size: 51
120295 GTTGTGAGAA
* * ** *
120305 CACATGTGTAGTACTATGTGCAGCCTACTATGTGTTTAAAATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGCCTACTACGTGTACAAAAT-GTGTTAGGT
* * * *
120357 CACGTGTGTACTACTAAGTGCAGGCTACTACGTGTACCAAAT-TGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGCCTACTACGTGTACAAAATGTGTTAGGT
120407 CACATGTGTAGTACTAA
1 CACATGTGTAGTACTAA
120424 CTTTAGCTAC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 22 0.39
52 34 0.61
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (51 bp):
CACATGTGTAGTACTAAGTGCAGCCTACTACGTGTACAAAATGTGTTAGGT
Found at i:131064 original size:52 final size:51
Alignment explanation
Indices: 130968--131167 Score: 204
Period size: 51 Copynumber: 3.9 Consensus size: 51
130958 CCATTGCGAA
* * ** * *
130968 CACATGTGTAGTACTACGTGCAAGCTACTATGTGTTTAAAATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAG-TTTAGGT
* * *
131020 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAGAT-GGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTTAGGT
* * * ** * * *
131070 CTCATATGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTTAGGT
* * *
131121 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGTTT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTT
131168 TTTTCACAAG
Statistics
Matches: 120, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
50 41 0.34
51 44 0.37
52 35 0.29
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (51 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATAGTTTAGGT
Found at i:131087 original size:50 final size:50
Alignment explanation
Indices: 130968--131162 Score: 201
Period size: 50 Copynumber: 3.8 Consensus size: 50
130958 CCATTGCGAA
* * ** *
130968 CACATGTGTAGTACTACGTGCAAGCTACTATGTGTTTAAAATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATGG--TTAGGT
* *
131020 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATGGTTAGGT
* * * ** * * *
131070 CTCATATGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGAT-GGTTAGGT
* * *
131121 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGAT
131163 AGTTTTTTTC
Statistics
Matches: 117, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
50 41 0.35
51 39 0.33
52 37 0.32
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACAAGATGGTTAGGT
Found at i:142865 original size:39 final size:39
Alignment explanation
Indices: 142811--143106 Score: 495
Period size: 39 Copynumber: 7.5 Consensus size: 39
142801 TAATGGAGAA
142811 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
142850 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
142889 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
142928 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
142967 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
143006 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * * *
143045 TTATATCCGGGCTAAAGTCACGCAGGC-TTTGTTCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
143084 TCATATCCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
143107 CATGCTTTGT
Statistics
Matches: 246, Mismatches: 9, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
39 226 0.92
40 20 0.08
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:145363 original size:13 final size:13
Alignment explanation
Indices: 145342--145376 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
145332 TGAAAAAAAT
*
145342 TGAAATGTTTGAA
1 TGAAGTGTTTGAA
145355 TGAAGTGTTTGAA
1 TGAAGTGTTTGAA
145368 TGAAAGTGT
1 TG-AAGTGT
145377 GTAATACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (13 bp):
TGAAGTGTTTGAA
Found at i:149089 original size:39 final size:39
Alignment explanation
Indices: 149035--149320 Score: 495
Period size: 39 Copynumber: 7.3 Consensus size: 39
149025 TAATGGAGAA
149035 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
149074 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
149113 TTATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
149152 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
149191 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
149230 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
149269 TTATATCCGGGCTAAAGTCCGGCAA-GC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCG-AAGGCATTCGTGCTGGTG
149308 TTATATCCGGGCT
1 TTATATCCGGGCT
149321 TAAAGTCCTA
Statistics
Matches: 238, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
39 227 0.95
40 9 0.04
41 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Done.