Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2493
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: 65605
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3312 original size:89 final size:91
Alignment explanation
Indices: 3139--3342 Score: 231
Period size: 89 Copynumber: 2.3 Consensus size: 91
3129 AATTTTGACT
* * * *
3139 TTGGGGAAACTCCAACCCCACTACTTCGGGAGGATACTCCAACCCCGTTCTTTATTCAAAATTAA
1 TTGGGGAAACTCCAACCCCACTACTCCGAGAGGATACTCCAACCCCATTCTTTATTAAAAATTAA
**
3204 AATTTTCATTTCGTGTAATTTTACCC
66 AATTTTCATTTCGCATAATTTTACCC
* * *
3230 TTGGAGAAACTCCAACCCCACT-CTCCGAG-GGATATTCTAACCCCATTCTTTA-TAAAGAATTT
1 TTGGGGAAACTCCAACCCCACTACTCCGAGAGGATACTCCAACCCCATTCTTTATTAAA-AA-TT
* * *
3292 AAATTTTTTC-TTT-GCATAATTTTATCT
64 AAA-ATTTTCATTTCGCATAATTTTACCC
3319 TTGGGGAAACTCCAA-CCCACTACT
1 TTGGGGAAACTCCAACCCCACTACT
3343 TTAAAGGAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
88 9 0.09
89 48 0.50
90 13 0.14
91 26 0.27
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (91 bp):
TTGGGGAAACTCCAACCCCACTACTCCGAGAGGATACTCCAACCCCATTCTTTATTAAAAATTAA
AATTTTCATTTCGCATAATTTTACCC
Found at i:3517 original size:108 final size:107
Alignment explanation
Indices: 3317--3518 Score: 248
Period size: 108 Copynumber: 1.9 Consensus size: 107
3307 ATAATTTTAT
* * * *
3317 CTTTGGGGAAACTCCAACCCACTACTTTAAAGGAATACTTTAACCCCATTTTTCATAAAAAAACT
1 CTTTGAGGAAACTCCAACCCACCACTCTAAAGGAATACTCTAACCCCATTTTTCATAAAAAAACT
* *
3382 CAAATTTTCTCTTTTTTCTTAAGTATTTTAAAAAGTTTTTGA
66 CAAATCTTCTCTTTTTTCTTAAATATTTTAAAAAGTTTTTGA
* * * *
3424 CTTTGAGGAAACTCTAACCTTACCACTCTAAGAGG-ATACTCTAACCTCATTCTTT-ATAAAAAT
1 CTTTGAGGAAACTCCAACC-CACCACTCTAA-AGGAATACTCTAACCCCATT-TTTCATAAAAAA
*
3487 ACTCAAATCTTCTTTTTGTTTC-TAAATATTTT
63 ACTCAAATCTTCTCTTT-TTTCTTAAATATTTT
3519 TATAATTTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
107 17 0.21
108 53 0.66
109 10 0.12
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.40
Consensus pattern (107 bp):
CTTTGAGGAAACTCCAACCCACCACTCTAAAGGAATACTCTAACCCCATTTTTCATAAAAAAACT
CAAATCTTCTCTTTTTTCTTAAATATTTTAAAAAGTTTTTGA
Found at i:13845 original size:1 final size:1
Alignment explanation
Indices: 13839--13897 Score: 82
Period size: 1 Copynumber: 59.0 Consensus size: 1
13829 AAATCTTCAC
* * * *
13839 TTTTTTTTTGTTTTTTTTTTTCTTTTTTTTTTGTTTTGTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13898 CCAATTGCCA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.02, G:0.05, T:0.93
Consensus pattern (1 bp):
T
Found at i:13869 original size:23 final size:22
Alignment explanation
Indices: 13839--13897 Score: 93
Period size: 23 Copynumber: 2.7 Consensus size: 22
13829 AAATCTTCAC
13839 TTTTTTTTTGTTTTTTTTTTTCT
1 TTTTTTTTTGTTTTTTTTTTT-T
*
13862 TTTTTTTTTGTTTTGTTTTTTT
1 TTTTTTTTTGTTTTTTTTTTTT
13884 TTTTTTTTT-TTTTT
1 TTTTTTTTTGTTTTT
13898 CCAATTGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 4 0.12
22 10 0.29
23 20 0.59
ACGTcount: A:0.00, C:0.02, G:0.05, T:0.93
Consensus pattern (22 bp):
TTTTTTTTTGTTTTTTTTTTTT
Found at i:13876 original size:28 final size:26
Alignment explanation
Indices: 13839--13897 Score: 100
Period size: 28 Copynumber: 2.2 Consensus size: 26
13829 AAATCTTCAC
13839 TTTTTTTTTGTTTTTTTTTTTCTTTTT
1 TTTTTTTTTGTTTTTTTTTTT-TTTTT
13866 TTTTTGTTTTGTTTTTTTTTTTTTTTT
1 TTTTT-TTTTGTTTTTTTTTTTTTTTT
13893 TTTTT
1 TTTTT
13898 CCAATTGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.00, C:0.02, G:0.05, T:0.93
Consensus pattern (26 bp):
TTTTTTTTTGTTTTTTTTTTTTTTTT
Found at i:16366 original size:1 final size:1
Alignment explanation
Indices: 16356--16409 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
16346 TGGCAATTGG
* * * ** *
16356 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16410 GTGAAGATTT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:16398 original size:16 final size:15
Alignment explanation
Indices: 16356--16409 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
16346 TGGCAATTGG
*
16356 AAAAAGAAAAAAACA
1 AAAAAAAAAAAAACA
* **
16371 AAACAAAAAAAAGGA
1 AAAAAAAAAAAAACA
16386 AAAAAAAAAAAAACA
1 AAAAAAAAAAAAACA
16401 AAAAAAAAA
1 AAAAAAAAA
16410 GTGAAGATTT
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:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAACA
Found at i:24320 original size:991 final size:991
Alignment explanation
Indices: 22399--24381 Score: 3903
Period size: 991 Copynumber: 2.0 Consensus size: 991
22389 TCCACTACGG
22399 AAAAAGAACTTTTGTCAATTGTTTTTGCTTTGGATAAATTTCGTTCTTATGTGCTTGGCTCTAAA
1 AAAAAGAACTTTTGTCAATTGTTTTTGCTTTGGATAAATTTCGTTCTTATGTGCTTGGCTCTAAA
22464 GTTATTGTGTATTCTGACCATACAGCTTTAAAGTATCTTTTGGCCAAGAAAGAGTCGAAACCAAG
66 GTTATTGTGTATTCTGACCATACAGCTTTAAAGTATCTTTTGGCCAAGAAAGAGTCGAAACCAAG
22529 GCTGATTCGATGGATTTTGCTTCTCCAAGAGTTTGACATGAAGATAAAGGACCGAAAAGGAGTGG
131 GCTGATTCGATGGATTTTGCTTCTCCAAGAGTTTGACATGAAGATAAAGGACCGAAAAGGAGTGG
*
22594 AGAATCCTGTTGCTGACCACTTGAGTCGATTGATAAGTGAAAAGGACGATGCACCCTTCAATGAC
196 AGAATCCTGTTGCTGACCACTTGAGTCGATTGATAAGGGAAAAGGACGATGCACCCTTCAATGAC
22659 AACTTCCCAGATGAGTATTTGTTCCAACTCAAAGGTATGATTCCTTGGTACGCCGATATGGTCAA
261 AACTTCCCAGATGAGTATTTGTTCCAACTCAAAGGTATGATTCCTTGGTACGCCGATATGGTCAA
22724 TTATTTGGTTACGGGAAGTCTACCTAGTAGCCTTAGTAAATCTAGGAAGGCTAAGATTAAGAGTG
326 TTATTTGGTTACGGGAAGTCTACCTAGTAGCCTTAGTAAATCTAGGAAGGCTAAGATTAAGAGTG
*
22789 AGTCTAAGTACTATGTTTGGGATGAACCTTACTTATGGAAATTTTGTTCTGATCAAGTGATTAGG
391 AGTCTAAGTACTATGTTTGGGATGAACCCTACTTATGGAAATTTTGTTCTGATCAAGTGATTAGG
22854 AGATGTGTGCCTGAAAATGAGTTTCAATCTATTTTAGCTTTTTGCCATGATTATGCTTGTGGAGG
456 AGATGTGTGCCTGAAAATGAGTTTCAATCTATTTTAGCTTTTTGCCATGATTATGCTTGTGGAGG
22919 ACATTTTGGTCCTAGACGAACTGCTAGGAAAGTTTTAGATAGTGGTTTGTATTGGGAATCTTTGT
521 ACATTTTGGTCCTAGACGAACTGCTAGGAAAGTTTTAGATAGTGGTTTGTATTGGGAATCTTTGT
22984 TTAAAGATGCATATCAATTTTGCAAAACTTGTGAGAGGTGCCAAAGAGTAGGAGCATTATCATGC
586 TTAAAGATGCATATCAATTTTGCAAAACTTGTGAGAGGTGCCAAAGAGTAGGAGCATTATCATGC
23049 AAGAATGAAATGCCTCAAGTTCCAATTCTTATTTGTGAAATATTTGATGTTTGGGGCATTGATTT
651 AAGAATGAAATGCCTCAAGTTCCAATTCTTATTTGTGAAATATTTGATGTTTGGGGCATTGATTT
*
23114 TATGGGTCCTTTGCCCTCATCTTGTGGTTTTTCTTACATTCTTTTGGCTGTGGATTATGTTTCGA
716 TATGGGTCCTTTGCCCTCATCTTGTGGTTTTTCTTACATTCATTTGGCTGTGGATTATGTTTCGA
23179 AATGGGTGGAAGCAAAAGCCACCAAAACTGATGATTCTCAAGCTGTTGTAGGTTTTATCAAGGCT
781 AATGGGTGGAAGCAAAAGCCACCAAAACTGATGATTCTCAAGCTGTTGTAGGTTTTATCAAGGCT
23244 AACATATTTGCTAGGTTTGGAATTCCAAGAGCAATTATCAGTGATCAAGGAACGCATTTTTGCAA
846 AACATATTTGCTAGGTTTGGAATTCCAAGAGCAATTATCAGTGATCAAGGAACGCATTTTTGCAA
*
23309 TAGATCGGTTGAAGCTTTGATGAAGAAGTATGGAGTGAATCACCGACTTGCAACCGCATATCATC
911 TAGATCGGTTGAAGCTTTGATGAAGAAGTATGGAGTAAATCACCGACTTGCAACCGCATATCATC
23374 CTCAAACGAACGGACA
976 CTCAAACGAACGGACA
23390 AAAAAGAACTTTTGTCAATTGTTTTTGCTTTGGATAAATTTCGTTCTTATGTGCTTGGCTCTAAA
1 AAAAAGAACTTTTGTCAATTGTTTTTGCTTTGGATAAATTTCGTTCTTATGTGCTTGGCTCTAAA
23455 GTTATTGTGTATTCTGACCATACAGCTTTAAAGTATCTTTTGGCCAAGAAAGAGTCGAAACCAAG
66 GTTATTGTGTATTCTGACCATACAGCTTTAAAGTATCTTTTGGCCAAGAAAGAGTCGAAACCAAG
23520 GCTGATTCGATGGATTTTGCTTCTCCAAGAGTTTGACATGAAGATAAAGGACCGAAAAGGAGTGG
131 GCTGATTCGATGGATTTTGCTTCTCCAAGAGTTTGACATGAAGATAAAGGACCGAAAAGGAGTGG
*
23585 AGAATCCTGTTGCTGACCACTTGAGTCGATTGATAAGGGAAAATGACGATGCACCCTTCAATGAC
196 AGAATCCTGTTGCTGACCACTTGAGTCGATTGATAAGGGAAAAGGACGATGCACCCTTCAATGAC
*
23650 AACTTCCCAGATGAGTATTTGTTCCAACTCAAAGGTATGATTCCTTGGTACGCCGATATGGTTAA
261 AACTTCCCAGATGAGTATTTGTTCCAACTCAAAGGTATGATTCCTTGGTACGCCGATATGGTCAA
23715 TTATTTGGTTACGGGAAGTCTACCTAGTAGCCTTAGTAAATCTAGGAAGGCTAAGATTAAGAGTG
326 TTATTTGGTTACGGGAAGTCTACCTAGTAGCCTTAGTAAATCTAGGAAGGCTAAGATTAAGAGTG
23780 AGTCTAAGTACTATGTTTGGGATGAACCCTACTTATGGAAATTTTGTTCTGATCAAGTGATTAGG
391 AGTCTAAGTACTATGTTTGGGATGAACCCTACTTATGGAAATTTTGTTCTGATCAAGTGATTAGG
23845 AGATGTGTGCCTGAAAATGAGTTTCAATCTATTTTAGCTTTTTGCCATGATTATGCTTGTGGAGG
456 AGATGTGTGCCTGAAAATGAGTTTCAATCTATTTTAGCTTTTTGCCATGATTATGCTTGTGGAGG
23910 ACATTTTGGTCCTAGACGAACTGCTAGGAAAGTTTTAGATAGTGGTTTGTATTGGGAATCTTTGT
521 ACATTTTGGTCCTAGACGAACTGCTAGGAAAGTTTTAGATAGTGGTTTGTATTGGGAATCTTTGT
23975 TTAAAGATGCATATCAATTTTGCAAAACTTGTGAGAGGTGCCAAAGAGTAGGAGCATTATCATGC
586 TTAAAGATGCATATCAATTTTGCAAAACTTGTGAGAGGTGCCAAAGAGTAGGAGCATTATCATGC
24040 AAGAATGAAATGCCTCAAGTTCCAATTCTTATTTGTGAAATATTTGATGTTTGGGGCATTGATTT
651 AAGAATGAAATGCCTCAAGTTCCAATTCTTATTTGTGAAATATTTGATGTTTGGGGCATTGATTT
24105 TATGGGTCCTTTGCCCTCATCTTGTGGTTTTTCTTACATTCATTTGGCTGTGGATTATGTTTCGA
716 TATGGGTCCTTTGCCCTCATCTTGTGGTTTTTCTTACATTCATTTGGCTGTGGATTATGTTTCGA
24170 AATGGGTGGAAGCAAAAGCCACCAAAACTGATGATTCTCAAGCTGTTGTAGGTTTTATCAAGGCT
781 AATGGGTGGAAGCAAAAGCCACCAAAACTGATGATTCTCAAGCTGTTGTAGGTTTTATCAAGGCT
24235 AACATATTTGCTAGGTTTGGAATTCCAAGAGCAATTATCAGTGATCAAGGAACGCATTTTTGCAA
846 AACATATTTGCTAGGTTTGGAATTCCAAGAGCAATTATCAGTGATCAAGGAACGCATTTTTGCAA
*
24300 TAGATCGGTTGAAGCTTTGATGAAGAAGTATGGAGTAAATCACCGAGTTGCAACCGCATATCATC
911 TAGATCGGTTGAAGCTTTGATGAAGAAGTATGGAGTAAATCACCGACTTGCAACCGCATATCATC
24365 CTCAAACGAACGGACA
976 CTCAAACGAACGGACA
24381 A
1 A
24382 GCCGAGGTTT
Statistics
Matches: 985, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
991 985 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (991 bp):
AAAAAGAACTTTTGTCAATTGTTTTTGCTTTGGATAAATTTCGTTCTTATGTGCTTGGCTCTAAA
GTTATTGTGTATTCTGACCATACAGCTTTAAAGTATCTTTTGGCCAAGAAAGAGTCGAAACCAAG
GCTGATTCGATGGATTTTGCTTCTCCAAGAGTTTGACATGAAGATAAAGGACCGAAAAGGAGTGG
AGAATCCTGTTGCTGACCACTTGAGTCGATTGATAAGGGAAAAGGACGATGCACCCTTCAATGAC
AACTTCCCAGATGAGTATTTGTTCCAACTCAAAGGTATGATTCCTTGGTACGCCGATATGGTCAA
TTATTTGGTTACGGGAAGTCTACCTAGTAGCCTTAGTAAATCTAGGAAGGCTAAGATTAAGAGTG
AGTCTAAGTACTATGTTTGGGATGAACCCTACTTATGGAAATTTTGTTCTGATCAAGTGATTAGG
AGATGTGTGCCTGAAAATGAGTTTCAATCTATTTTAGCTTTTTGCCATGATTATGCTTGTGGAGG
ACATTTTGGTCCTAGACGAACTGCTAGGAAAGTTTTAGATAGTGGTTTGTATTGGGAATCTTTGT
TTAAAGATGCATATCAATTTTGCAAAACTTGTGAGAGGTGCCAAAGAGTAGGAGCATTATCATGC
AAGAATGAAATGCCTCAAGTTCCAATTCTTATTTGTGAAATATTTGATGTTTGGGGCATTGATTT
TATGGGTCCTTTGCCCTCATCTTGTGGTTTTTCTTACATTCATTTGGCTGTGGATTATGTTTCGA
AATGGGTGGAAGCAAAAGCCACCAAAACTGATGATTCTCAAGCTGTTGTAGGTTTTATCAAGGCT
AACATATTTGCTAGGTTTGGAATTCCAAGAGCAATTATCAGTGATCAAGGAACGCATTTTTGCAA
TAGATCGGTTGAAGCTTTGATGAAGAAGTATGGAGTAAATCACCGACTTGCAACCGCATATCATC
CTCAAACGAACGGACA
Found at i:25921 original size:1 final size:1
Alignment explanation
Indices: 25911--25987 Score: 73
Period size: 1 Copynumber: 77.0 Consensus size: 1
25901 TGGCAATTGG
* * * * * ** *
25911 AAAAACAAAAAAAAAGAAAAAAGAAAAAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
25976 ACAAAAAAAAAA
1 AAAAAAAAAAAA
25988 GTGAAGATTT
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.88, C:0.05, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:25941 original size:27 final size:27
Alignment explanation
Indices: 25912--25986 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
25902 GGCAATTGGA
* *
25912 AAAACAAAAAAA-AAGAAAAAAGAAAA
1 AAAAAAAAAAAACAAAAAAAAAGAAAA
* *
25938 AAAAAAACAAAACAAAAAAAAGGAAAA
1 AAAAAAAAAAAACAAAAAAAAAGAAAA
*
25965 AGAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAAA
25987 AGTGAAGATT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 10 0.24
27 31 0.76
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAAACAAAAAAAAAGAAAA
Found at i:25951 original size:34 final size:33
Alignment explanation
Indices: 25912--25987 Score: 120
Period size: 32 Copynumber: 2.3 Consensus size: 33
25902 GGCAATTGGA
25912 AAAACAAAAAAAAAGAAAAAAGAAAAAAAAAAAC
1 AAAACAAAAAAAAAGAAAAAAG-AAAAAAAAAAC
*
25946 AAAAC-AAAAAAAAGGAAAAAGAAAAAAAAAAC
1 AAAACAAAAAAAAAGAAAAAAGAAAAAAAAAAC
25978 AAAA-AAAAAA
1 AAAACAAAAAA
25988 GTGAAGATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 20 0.50
33 15 0.38
34 5 0.12
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (33 bp):
AAAACAAAAAAAAAGAAAAAAGAAAAAAAAAAC
Found at i:28155 original size:1 final size:1
Alignment explanation
Indices: 28149--28225 Score: 109
Period size: 1 Copynumber: 77.0 Consensus size: 1
28139 GAAAGAGTTT
* ** *
28149 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAGGAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
28214 ACAAAAAAAAAA
1 AAAAAAAAAAAA
28226 GTGAAGATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.94, C:0.03, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:28192 original size:33 final size:33
Alignment explanation
Indices: 28150--28225 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
28140 AAAGAGTTTA
28150 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC
** *
28183 AAAAAAAAAAAAAAGGAAAAAGAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC
28216 AAAAAAAAAA
1 AAAAAAAAAA
28226 GTGAAGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.93, C:0.03, G:0.04, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC
Found at i:30313 original size:1 final size:1
Alignment explanation
Indices: 30307--30363 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
30297 AAATCTTCAC
* * ** * * *
30307 TTTTTTTTTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30364 CCAATTGCCA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:30340 original size:28 final size:29
Alignment explanation
Indices: 30309--30365 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
30299 ATCTTCACTT
30309 TTTTTTTTGTTTT-TTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
30337 TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
30366 AATTGCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (29 bp):
TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
Found at i:30343 original size:22 final size:22
Alignment explanation
Indices: 30310--30363 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
30300 TCTTCACTTT
30310 TTTTT-TTGTTTTTT-TTTT-TCT
1 TTTTTCTT-TTTTTTGTTTTGT-T
*
30331 TTTTCCTTTTTTTTGTTTTGTT
1 TTTTTCTTTTTTTTGTTTTGTT
30353 TTTTTCTTTTT
1 TTTTTCTTTTT
30364 CCAATTGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 10 0.36
22 17 0.61
23 1 0.04
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (22 bp):
TTTTTCTTTTTTTTGTTTTGTT
Found at i:33046 original size:1 final size:1
Alignment explanation
Indices: 33040--33100 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
33030 AAATCTTCAC
* * ** * * *
33040 TTTTTTTTTTGTTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33101 CCAATTGCCA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.89
Consensus pattern (1 bp):
T
Found at i:33078 original size:31 final size:31
Alignment explanation
Indices: 33042--33102 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
33032 ATCTTCACTT
33042 TTTTTTTTGTTTT-TTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
33072 TTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
33103 AATTGCCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (31 bp):
TTTTTTTTGTTTTGTTTTTTTTTCTTTTTCC
Found at i:35787 original size:1 final size:1
Alignment explanation
Indices: 35781--35869 Score: 79
Period size: 1 Copynumber: 89.0 Consensus size: 1
35771 AAATCTTCAC
* ** * * * **
35781 TTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTCCTTTGTTTTTTTTTCTTTTTCTTTTTCCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
35846 TTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
35870 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (1 bp):
T
Found at i:35800 original size:14 final size:14
Alignment explanation
Indices: 35781--35863 Score: 89
Period size: 15 Copynumber: 5.6 Consensus size: 14
35771 AAATCTTCAC
35781 TTTTTTTTTTGTTT
1 TTTTTTTTTTGTTT
35795 TTTTTTTTTT-TTT
1 TTTTTTTTTTGTTT
35808 TTTTTTTCCTTTGTTT
1 TTTTTTT--TTTGTTT
35824 TTTTTTCTTTT-TCTT
1 TTTTTT-TTTTGT-TT
35839 TTTCCTTTTTTTGTTT
1 TTT--TTTTTTTGTTT
35855 TGTTTTTTT
1 T-TTTTTTT
35864 CTTTTTCCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 17
0.78 0.00 0.22
Matches are distributed among these distances:
13 10 0.17
14 11 0.18
15 16 0.27
16 16 0.27
17 7 0.12
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:35807 original size:21 final size:20
Alignment explanation
Indices: 35780--35869 Score: 92
Period size: 20 Copynumber: 4.3 Consensus size: 20
35770 CAAATCTTCA
35780 CTTTTTTTTTTGTTTTTTTTT
1 CTTTTTTTTTT-TTTTTTTTT
**
35801 -TTTTTTTTTTTTTTCCTTT
1 CTTTTTTTTTTTTTTTTTTT
*
35820 GTTTTTTTTTCTTTTTCTTTTT
1 CTTTTTTTTT-TTTTT-TTTTT
*
35842 CCTTTTTTTGTTTTGTTTTTTT
1 -CTTTTTTT-TTTTTTTTTTTT
35864 CTTTTT
1 CTTTTT
35870 CCAATTGCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.12
20 19 0.33
21 11 0.19
22 8 0.14
23 11 0.19
24 2 0.03
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (20 bp):
CTTTTTTTTTTTTTTTTTTT
Found at i:35824 original size:28 final size:27
Alignment explanation
Indices: 35792--35871 Score: 117
Period size: 28 Copynumber: 3.0 Consensus size: 27
35782 TTTTTTTTTG
35792 TTTTTTTTTTTTTTTTTT-TTTTTCCT
1 TTTTTTTTTTTTTTTTTTCTTTTTCCT
* *
35818 TTGTTTTTTTTTCTTTTTCTTTTTCCT
1 TTTTTTTTTTTTTTTTTTCTTTTTCCT
*
35845 TTTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTTT-TTTTTTTTTTTTCTTTTTCC
35872 AATTGCCATG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 16 0.34
27 13 0.28
28 18 0.38
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (27 bp):
TTTTTTTTTTTTTTTTTTCTTTTTCCT
Found at i:35835 original size:36 final size:35
Alignment explanation
Indices: 35780--35869 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 35
35770 CAAATCTTCA
* * **
35780 CTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTC
1 CTTTGTTTTTT-TTTTTTTTCTTTTTCCTTTTTTTC
*
35816 CTTTGTTTTTTTTTCTTTTTCTTTTTCCTTTTTTTG
1 CTTTGTTTTTTTTT-TTTTTCTTTTTCCTTTTTTTC
* *
35852 TTTTGTTTTTTTCTTTTT
1 CTTTGTTTTTTTTTTTTT
35870 CCAATTGCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
35 7 0.15
36 39 0.85
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (35 bp):
CTTTGTTTTTTTTTTTTTTCTTTTTCCTTTTTTTC
Found at i:43630 original size:349 final size:349
Alignment explanation
Indices: 42991--43690 Score: 1373
Period size: 349 Copynumber: 2.0 Consensus size: 349
42981 TAAACAAATT
*
42991 AAGTCCTAAATAATATAGGATATAGTTTTCTATGATTAATACTCTTGGAATATAAGAAATATAAT
1 AAGTCCTAAATAATATAGGATATAGTTTTCTATGATTAATACTCTTGGAATATAAAAAATATAAT
43056 AATAAAAGAGTTTTCCATGAATTTAACTCCAAAAATCCAACTTTCTTCTTGTCAGTTTCCAGAAG
66 AATAAAAGAGTTTTCCATGAATTTAACTCCAAAAATCCAACTTTCTTCTTGTCAGTTTCCAGAAG
*
43121 CTTGTCAATCACAAGGCGTGGTCGCGTCTTATTGAAAACGATCTTCTGCCCATTTTATGCACTTT
131 CTTGTCAATCACAAGGCGTGGTCGCGCCTTATTGAAAACGATCTTCTGCCCATTTTATGCACTTT
43186 CTTTCCAAATGACTTGATTTTTACATGAGAAGCCAAAATCATGCTTTTAAGCCAGATTCCATCCA
196 CTTTCCAAATGACTTGATTTTTACATGAGAAGCCAAAATCATGCTTTTAAGCCAGATTCCATCCA
43251 TTCTTTGACAATTCACCACCTAAATTAAAACAAACATAATACCCACAATTAAGCACAAAATATAA
261 TTCTTTGACAATTCACCACCTAAATTAAAACAAACATAATACCCACAATTAAGCACAAAATATAA
43316 CTAAAAAATGAAAGAATTAAACAC
326 CTAAAAAATGAAAGAATTAAACAC
43340 AAGTCCTAAATAATATAGGATATAGTTTTCTATGATTAATACTCTTGGAATATAAAAAATATAAT
1 AAGTCCTAAATAATATAGGATATAGTTTTCTATGATTAATACTCTTGGAATATAAAAAATATAAT
43405 AATAAAAGAGTTTTCCATGAATTTAACTCCAAAAATCCAACTTTCTTCTTGTCAGTTTCCAGAAG
66 AATAAAAGAGTTTTCCATGAATTTAACTCCAAAAATCCAACTTTCTTCTTGTCAGTTTCCAGAAG
*
43470 CTTGTCTATCACAAGGCGTGGTCGCGCCTTATTGAAAACGATCTTCTGCCCATTTTATGCACTTT
131 CTTGTCAATCACAAGGCGTGGTCGCGCCTTATTGAAAACGATCTTCTGCCCATTTTATGCACTTT
43535 CTTTCCAAATGACTTGATTTTTACATGAGAAGCCAAAATCATGCTTTTAAGCCAGATTCCATCCA
196 CTTTCCAAATGACTTGATTTTTACATGAGAAGCCAAAATCATGCTTTTAAGCCAGATTCCATCCA
43600 TTCTTTGACAATTCACCACCTAAATTAAAACAAACATAATACCCACAATTAAGCACAAAATATAA
261 TTCTTTGACAATTCACCACCTAAATTAAAACAAACATAATACCCACAATTAAGCACAAAATATAA
43665 CTAAAAAATGAAAGAATTAAACAC
326 CTAAAAAATGAAAGAATTAAACAC
43689 AA
1 AA
43691 TAACACATAA
Statistics
Matches: 348, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
349 348 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.31
Consensus pattern (349 bp):
AAGTCCTAAATAATATAGGATATAGTTTTCTATGATTAATACTCTTGGAATATAAAAAATATAAT
AATAAAAGAGTTTTCCATGAATTTAACTCCAAAAATCCAACTTTCTTCTTGTCAGTTTCCAGAAG
CTTGTCAATCACAAGGCGTGGTCGCGCCTTATTGAAAACGATCTTCTGCCCATTTTATGCACTTT
CTTTCCAAATGACTTGATTTTTACATGAGAAGCCAAAATCATGCTTTTAAGCCAGATTCCATCCA
TTCTTTGACAATTCACCACCTAAATTAAAACAAACATAATACCCACAATTAAGCACAAAATATAA
CTAAAAAATGAAAGAATTAAACAC
Found at i:44372 original size:1 final size:1
Alignment explanation
Indices: 44366--44435 Score: 86
Period size: 1 Copynumber: 70.0 Consensus size: 1
44356 AAATCTTCAC
* * ** * *
44366 TTTTTTTTTTGTTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44431 TTTTT
1 TTTTT
44436 CCAATTGCCA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.00, C:0.04, G:0.04, T:0.91
Consensus pattern (1 bp):
T
Found at i:44403 original size:30 final size:30
Alignment explanation
Indices: 44368--44435 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
44358 ATCTTCACTT
44368 TTTTTTTTGTTTT-TTTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTTGTTTTTTTTT-TTTTTCC
**
44398 TTTTTTTTGTTTTGTTTTTTTTTTTTTTTT
1 TTTTTTTTGTTTTGTTTTTTTTTTTTTTCC
44428 TTTTTTTT
1 TTTTTTTT
44436 CCAATTGCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.00, C:0.04, G:0.04, T:0.91
Consensus pattern (30 bp):
TTTTTTTTGTTTTGTTTTTTTTTTTTTTCC
Found at i:62665 original size:1 final size:1
Alignment explanation
Indices: 62659--62740 Score: 56
Period size: 1 Copynumber: 82.0 Consensus size: 1
62649 AAATCTTCAC
* * ** * * * ** *
62659 TTTTTTTTGTTTTTTTTTTCTTTTCCTTTTTTTGTTTTGTTTTTTTTTCTTTTTCCTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
62724 TTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTT
62741 CCAATTGCCA
Statistics
Matches: 61, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (1 bp):
T
Found at i:62698 original size:30 final size:31
Alignment explanation
Indices: 62659--62734 Score: 131
Period size: 30 Copynumber: 2.5 Consensus size: 31
62649 AAATCTTCAC
62659 TTTT-TTTTGTTTTTTTTTTC-TTTTCCTTT
1 TTTTGTTTTGTTTTTTTTTTCTTTTTCCTTT
62688 TTTTGTTTTG-TTTTTTTTTCTTTTTCCTTT
1 TTTTGTTTTGTTTTTTTTTTCTTTTTCCTTT
62718 TTTTGTTTTGTTTTTTT
1 TTTTGTTTTGTTTTTTT
62735 CTTTTTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
29 14 0.32
30 24 0.55
31 6 0.14
ACGTcount: A:0.00, C:0.08, G:0.07, T:0.86
Consensus pattern (31 bp):
TTTTGTTTTGTTTTTTTTTTCTTTTTCCTTT
Done.