Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1397
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: 60165
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:6779 original size:27 final size:27
Alignment explanation
Indices: 6749--6926 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
6739 ATATTGAGTC
* * * *
6749 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
6776 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
6803 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
6831 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
6858 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
6885 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
6912 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
6927 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:6888 original size:82 final size:81
Alignment explanation
Indices: 6770--6925 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
6760 TGCTATATAA
* *
6770 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
6835 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
6852 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
6916 CACTTAGTGC
65 CACTTAGTGC
6926 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:8909 original size:30 final size:30
Alignment explanation
Indices: 8799--8909 Score: 81
Period size: 30 Copynumber: 3.8 Consensus size: 30
8789 GGGGGAAAAG
* * *
8799 AAGAAAAGAAAGTAGATGAAGAGAA-TAGAA
1 AAGAAAAGAAAATAGAAGAAGA-AAGAAGAA
8829 AAGAAAAG-AAA-AGAAG--GTAAAGAAGAA
1 AAGAAAAGAAAATAGAAGAAG-AAAGAAGAA
* * * * *
8856 GAAG-GAAGGAAGTAGATGAAGAAAGGAGAA
1 -AAGAAAAGAAAATAGAAGAAGAAAGAAGAA
8886 AAGAAAAGAAAATAGAAGAAGAAA
1 AAGAAAAGAAAATAGAAGAAGAAA
8910 AAACTGAATC
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
26 3 0.05
27 8 0.13
28 9 0.15
29 9 0.15
30 32 0.52
31 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (30 bp):
AAGAAAAGAAAATAGAAGAAGAAAGAAGAA
Found at i:18154 original size:29 final size:31
Alignment explanation
Indices: 18105--18163 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
18095 AATGTGTATC
* *
18105 TATTTATTTGATGGATGAAAT-T-GAGATAG
1 TATTTATTTAATAGATGAAATATGGAGATAG
18134 TATTTATTATAATAGAT-AAATATGGAGATA
1 TATTTATT-TAATAGATGAAATATGGAGATA
18164 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 12 0.48
30 7 0.28
31 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (31 bp):
TATTTATTTAATAGATGAAATATGGAGATAG
Found at i:27912 original size:51 final size:49
Alignment explanation
Indices: 27791--27985 Score: 228
Period size: 49 Copynumber: 3.9 Consensus size: 49
27781 TAAAAAAGGC
* * * * * **
27791 TATCTGGTACGCATAGTATCCTGCACTTAATACTACACATGCAACCAAT
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
** *
27840 TATCAGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGT
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-T
* * * *
27891 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
27940 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
27986 TCACAATAGA
Statistics
Matches: 122, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 77 0.63
50 6 0.05
51 39 0.32
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:27931 original size:100 final size:100
Alignment explanation
Indices: 27791--27983 Score: 332
Period size: 100 Copynumber: 1.9 Consensus size: 100
27781 TAAAAAAGGC
* * *
27791 TATCTGGTACGCATAGTATCCTGCACTTAATACTACACATGCAACCAATTATCAGGTACATGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAATACTACACATGCAACCAATTATCAGGTACACGTAG
27856 TAGCCTGCACTTAGTACTACACACGTGATCAAAGT
66 TAGCCTGCACTTAGTACTACACACGTGATCAAAGT
* * *
27891 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAATACTACACATGCAACCAATTATCAGGTACACGTAG
27956 TAGCCTGCACTTAGTACTACACACGTGA
66 TAGCCTGCACTTAGTACTACACACGTGA
27984 CCTCACAATA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (100 bp):
TATCGGGTACGCATAGTAGCCTGCACTTAATACTACACATGCAACCAATTATCAGGTACACGTAG
TAGCCTGCACTTAGTACTACACACGTGATCAAAGT
Found at i:28252 original size:27 final size:27
Alignment explanation
Indices: 28212--28265 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
28202 AGGTACAACC
*
28212 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
**
28239 CATGTAATAATAATTTGCCATTCAATT
1 CATGTAATAATAATTTAACATTCAATT
28266 TCACATGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (27 bp):
CATGTAATAATAATTTAACATTCAATT
Found at i:30587 original size:28 final size:28
Alignment explanation
Indices: 30554--30753 Score: 267
Period size: 28 Copynumber: 7.2 Consensus size: 28
30544 CAAAAGCTAA
* *
30554 TCTTTCATAGTTCGCCACAAAGGATTAT
1 TCTTTCATAATTCGCCACAAAGGCTTAT
* ** *
30582 TCTTTCGTAATTTTCCACAAAGGATTAT
1 TCTTTCATAATTCGCCACAAAGGCTTAT
* * *
30610 TATTTTATAATTCGCCACAAATGCTTAT
1 TCTTTCATAATTCGCCACAAAGGCTTAT
30638 TCTTTCATAATTCGCCACAAAGGCTTAT
1 TCTTTCATAATTCGCCACAAAGGCTTAT
*
30666 TCTTTAATAATTCGCCACAAAGGCTTAT
1 TCTTTCATAATTCGCCACAAAGGCTTAT
* * * *
30694 TCTTTCATAGTTCACCA-TAAGGCTTAC
1 TCTTTCATAATTCGCCACAAAGGCTTAT
30721 TCTTTCATAATTCGCCACAAAGGCTTAT
1 TCTTTCATAATTCGCCACAAAGGCTTAT
30749 TCTTT
1 TCTTT
30754 ATTATCATGT
Statistics
Matches: 147, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 23 0.16
28 124 0.84
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.39
Consensus pattern (28 bp):
TCTTTCATAATTCGCCACAAAGGCTTAT
Found at i:34138 original size:27 final size:27
Alignment explanation
Indices: 34108--34199 Score: 132
Period size: 27 Copynumber: 3.4 Consensus size: 27
34098 ATTACCAAAG
*
34108 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
34135 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
34162 TACCCTTGATTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
34189 TACCCTCGATT
1 TACCCTCGATT
34200 GTGAAATTAC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 1 0.02
27 59 0.98
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:34340 original size:26 final size:26
Alignment explanation
Indices: 34232--34354 Score: 115
Period size: 27 Copynumber: 4.6 Consensus size: 26
34222 ATAGGGTAGG
34232 ATTACCAAAATACCCCT-AGTTTGTAAA
1 ATTACCAAAATA-CCCTGA-TTTGTAAA
* *
34259 ATTACCAAAATACCACTGGTTTGTGAA
1 ATTACCAAAATACC-CTGATTTGTAAA
* * * *
34286 ATTATCGAAGTACCCTCAATTTGTAAA
1 ATTACCAAAATACCCT-GATTTGTAAA
**
34313 ATTACCAAAATACCCTGATTTACAAA
1 ATTACCAAAATACCCTGATTTGTAAA
34339 ATTA-CAGAAATACCCT
1 ATTACCA-AAATACCCT
34355 TGACTTTCTA
Statistics
Matches: 78, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.03
26 24 0.31
27 52 0.67
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (26 bp):
ATTACCAAAATACCCTGATTTGTAAA
Found at i:34404 original size:27 final size:27
Alignment explanation
Indices: 34310--34413 Score: 97
Period size: 27 Copynumber: 3.8 Consensus size: 27
34300 CTCAATTTGT
** *
34310 AAAATTACCAAAATACCCT-GATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
34336 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
*
34363 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
34392 AAAATTACTGAAATACCCTTGG
1 AAAATTACTGAAATACCCTTGG
34414 CTTGTAGATT
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
26 17 0.27
27 21 0.33
28 7 0.11
29 19 0.30
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:35400 original size:24 final size:24
Alignment explanation
Indices: 35369--35414 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
35359 AATTTATCAG
**
35369 AAAGGGCTTTGCC-CCAGTTATTA
1 AAAGGGCTAGGCCTCCAGTTATTA
35392 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTAGGCCTCCAGTTAT
35415 ATGATAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAGGGCTAGGCCTCCAGTTATTA
Found at i:35594 original size:42 final size:42
Alignment explanation
Indices: 35535--35626 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
35525 TAGTCTCCCC
* ** ** *
35535 AAATGGGCTTGCATACATTTATTGGTATTTCATGTGATACTA
1 AAATGGGCGTGCATACATCCATTGACATTACATGTGATACTA
* *
35577 AAATGGGCGTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCGTGCATACATCCATTGACATTACATGTGATACTA
35619 AAATGGGC
1 AAATGGGC
35627 CTAAAGGCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (42 bp):
AAATGGGCGTGCATACATCCATTGACATTACATGTGATACTA
Found at i:43750 original size:27 final size:27
Alignment explanation
Indices: 43685--43753 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
43675 GTAGACTAGT
* *
43685 ATTACTGAAATACCCCTGTAGGGTAGA
1 ATTACTGAAATGCCCCTATAGGGTAGA
*
43712 ATTACTGAAATGCTCCTATAGGGTAGA
1 ATTACTGAAATGCCCCTATAGGGTAGA
43739 ATTACTGAAATGCCC
1 ATTACTGAAATGCCC
43754 TTGGTTTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (27 bp):
ATTACTGAAATGCCCCTATAGGGTAGA
Found at i:43839 original size:27 final size:27
Alignment explanation
Indices: 43746--44052 Score: 162
Period size: 27 Copynumber: 11.4 Consensus size: 27
43736 AGAATTACTG
* * **
43746 AAATGCCCTTGGTTTACAAAATTACTG
1 AAATACCCTTGATTTACAAAATTACCA
* * *
43773 AAATGCCCTTGGTTTACAAAATTA-CT
1 AAATACCCTTGATTTACAAAATTACCA
*
43799 GAATACCCTTGATTTACAAAATTACCA
1 AAATACCCTTGATTTACAAAATTACCA
* *
43826 AAATACCCTCGA-TTAGCAAAACTACCA
1 AAATACCCTTGATTTA-CAAAATTACCA
* * **
43853 AAACACCCTAG-TTTGTAAAATTACCA
1 AAATACCCTTGATTTACAAAATTACCA
* ***
43879 AAATACCCCT-AGTTTTTTAAATTACCA
1 AAATACCCTTGA-TTTACAAAATTACCA
* ** *
43906 AAAGATCCC-TGATTTGGAAAATTACCG
1 AAATA-CCCTTGATTTACAAAATTACCA
** * *
43933 AAATACCCTTGATTTGGAAAAATA-TA
1 AAATACCCTTGATTTACAAAATTACCA
43959 GAAATACCCTTGACTTTTA-AAAATTA-CA
1 -AAATACCCTTGA--TTTACAAAATTACCA
* * ** *
43987 GAAATACCATTGGTTTGTAAAATTACCG
1 -AAATACCCTTGATTTACAAAATTACCA
* ** * *
44015 AAATACCCTTGGTTTGTATATTTACCA
1 AAATACCCTTGATTTACAAAATTACCA
*
44042 AAACACCCTTG
1 AAATACCCTTG
44053 TAGGGTGAAA
Statistics
Matches: 227, Mismatches: 40, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
26 46 0.20
27 155 0.68
28 23 0.10
29 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
AAATACCCTTGATTTACAAAATTACCA
Found at i:43846 original size:53 final size:52
Alignment explanation
Indices: 43738--43886 Score: 129
Period size: 53 Copynumber: 2.8 Consensus size: 52
43728 TATAGGGTAG
* ** * * *
43738 AATTACTGAAATGCCCTTGGTTTACAAAATTACTGAAATGCCCTTGGTTTACAA
1 AATTACTG-AATACCCTT-GTTTACAAAATTACCAAAATACCCTTCGATTACAA
43792 AATTACTGAATACCCTTGATTTACAAAATTACCAAAATACCC-TCGATTAGCAA
1 AATTACTGAATACCCTTG-TTTACAAAATTACCAAAATACCCTTCGATTA-CAA
* ** * * **
43845 AACTACCAAAACACCCTAGTTTGTAAAATTACCAAAATACCC
1 AATTA-CTGAATACCCTTGTTTACAAAATTACCAAAATACCC
43887 CTAGTTTTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
52 6 0.08
53 56 0.71
54 17 0.22
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (52 bp):
AATTACTGAATACCCTTGTTTACAAAATTACCAAAATACCCTTCGATTACAA
Found at i:44333 original size:41 final size:41
Alignment explanation
Indices: 44288--44409 Score: 181
Period size: 41 Copynumber: 3.0 Consensus size: 41
44278 AGAGGAAGAA
44288 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
* * *
44329 ATTGAGGATCGAATGGTTGCTTGATGACCGTGGATCCTCCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
* * * *
44370 ATTAAGGATTGCATGGTTTCTTGACGACCTTGGATCCACC
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACC
44410 AATGGCTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:44604 original size:22 final size:22
Alignment explanation
Indices: 44552--44616 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
44542 GCCAATTATT
*
44552 CTGATTATGGCTTTGTGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
* *
44574 CT-ACATATGGCTCTGTGGCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
44596 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
44617 ATGTTTTTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:44647 original size:27 final size:27
Alignment explanation
Indices: 44609--44670 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
44599 ATTATGGTTG
*
44609 TGTGCCAAATGTTTTTTCCTAAGGCTA
1 TGTGCCAAATGTATTTTCCTAAGGCTA
*
44636 TGTGCCAAATGTATTTTCCTAAGGTTA
1 TGTGCCAAATGTATTTTCCTAAGGCTA
*
44663 TGTACCAA
1 TGTGCCAA
44671 TATATGATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (27 bp):
TGTGCCAAATGTATTTTCCTAAGGCTA
Found at i:44873 original size:22 final size:22
Alignment explanation
Indices: 44848--44892 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
44838 TGCTGCGATG
*
44848 TTTACGACTATGTGCTGTCCTA
1 TTTACGACTATGTGCTATCCTA
*
44870 TTTACGGCTATGTGCTATCCTA
1 TTTACGACTATGTGCTATCCTA
44892 T
1 T
44893 CTATGGCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (22 bp):
TTTACGACTATGTGCTATCCTA
Found at i:47136 original size:79 final size:79
Alignment explanation
Indices: 47025--47248 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
47015 GCTACTCGTT
* * *
47025 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
47090 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
*
47105 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
47168 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * *
47183 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
47247 GA
64 GA
47249 CATCATTCAA
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 36 0.28
79 57 0.45
80 34 0.27
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:47142 original size:39 final size:40
Alignment explanation
Indices: 47025--47248 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
47015 GCTACTCGTT
* *
47025 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
47065 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
47105 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
47144 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
47183 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
47224 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
47249 CATCATTCAA
Statistics
Matches: 166, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 77 0.46
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:55160 original size:40 final size:37
Alignment explanation
Indices: 55115--55210 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 37
55105 GTTTATAACT
55115 TCGGCACAAATTGCCTTCGGCTTACCCGGAAT-TAGTATC
1 TCGGCACAAA-TGCCTTCGG-TTA-CCGGAATATAGTATC
*
55154 ATCGGCACAAAGTGCCTTCAGGTTAGCGGAATATAGTATC
1 -TCGGCACAAA-TGCCTTC-GGTTACCGGAATATAGTATC
55194 TC--CACAAATGCCTTCGG
1 TCGGCACAAATGCCTTCGG
55211 GATCTTAGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
35 2 0.04
36 7 0.13
37 6 0.12
39 8 0.15
40 27 0.52
41 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (37 bp):
TCGGCACAAATGCCTTCGGTTACCGGAATATAGTATC
Done.