Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4882.1
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: 41015
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.29
Warning! 2141 characters in sequence are not A, C, G, or T
Found at i:4997 original size:54 final size:54
Alignment explanation
Indices: 4915--5017 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
4905 TGGATATCTC
*
4915 CCTGGACAGAGCTTCAATACTCATGCCGTTTGTTTCTATAGAAACTAGAATGAG
1 CCTGGAAAGAGCTTCAATACTCATGCCGTTTGTTTCTATAGAAACTAGAATGAG
4969 CCTGGAAAGAGCTTCAATACTCATGCCGTTTGTTTCTATAGAAACTAGA
1 CCTGGAAAGAGCTTCAATACTCATGCCGTTTGTTTCTATAGAAACTAGA
5018 CTCAGAGAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (54 bp):
CCTGGAAAGAGCTTCAATACTCATGCCGTTTGTTTCTATAGAAACTAGAATGAG
Found at i:5762 original size:100 final size:100
Alignment explanation
Indices: 5589--5788 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
5579 CCAAAGTTCA
*
5589 AACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCGACTAAGAAGAAAGTACCAA
1 AACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCGACTAAGAAGAAAGTAACAA
*
5654 TACTTGCTAGCCGGTGTGATGACTCCAATGACGGC
66 AACTTGCTAGCCGGTGTGATGACTCCAATGACGGC
5689 AACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCGACTAAGAAGAAAGTAACAA
1 AACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCGACTAAGAAGAAAGTAACAA
5754 AACTTGCTAGCCGGTGTGATGACTCCAATGACGGC
66 AACTTGCTAGCCGGTGTGATGACTCCAATGACGGC
5789 CCGATCACGC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (100 bp):
AACACAACATAATAGCCTATACATGCCGAAATGTTCTCCTAAGCCGACTAAGAAGAAAGTAACAA
AACTTGCTAGCCGGTGTGATGACTCCAATGACGGC
Found at i:6365 original size:28 final size:28
Alignment explanation
Indices: 6303--7184 Score: 1703
Period size: 28 Copynumber: 31.5 Consensus size: 28
6293 ATATTAAGTC
* *
6303 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
6330 CGCACACTTAGTTCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6358 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6386 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6414 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6442 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6470 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6498 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6526 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6554 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6582 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6610 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6638 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6666 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6694 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6722 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6750 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6778 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6806 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6834 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6862 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6890 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6918 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6946 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
6974 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
7002 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
7030 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
7058 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
7086 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
7114 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
7142 CACACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
7170 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
7185 GTACAATTTA
Statistics
Matches: 846, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
27 21 0.02
28 825 0.98
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:10920 original size:238 final size:238
Alignment explanation
Indices: 10497--10948 Score: 868
Period size: 238 Copynumber: 1.9 Consensus size: 238
10487 GCAAACAATT
10497 ATTTCCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGATAGTCAATGACAAGCTCA
1 ATTTCCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGATAGTCAATGACAAGCTCA
10562 TAATCCTTTAACAACTCGAGCCAACGTCTTTGTCACAGATTTAAGTCTCTTTGAGTCATCAAATA
66 TAATCCTTTAACAACTCGAGCCAACGTCTTTGTCACAGATTTAAGTCTCTTTGAGTCATCAAATA
*
10627 TTTGAGACTTTTGTGATCCGAAAATACATGGCACTTTTCGCCAAACAAATAATGTCGCCATATTT
131 TTTGAGACTTTTGTGATCCGAAAATACATGGCACTTTTCACCAAACAAATAATGTCGCCATATTT
10692 TCAAAGCAAATACGATGGCGGCTAGCTCGAGATCCAAACAGCG
196 TCAAAGCAAATACGATGGCGGCTAGCTCGAGATCCAAACAGCG
10735 ATTTCCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGATAGTCAATGACAAGCTCA
1 ATTTCCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGATAGTCAATGACAAGCTCA
10800 TAATCCTTTAACAACTCGAGCCAACGTCTTTGTCACAGATTTAAGTCTCTTTGAGTCATCAAATA
66 TAATCCTTTAACAACTCGAGCCAACGTCTTTGTCACAGATTTAAGTCTCTTTGAGTCATCAAATA
* *
10865 TTTGAGACTTTTGTGATCCGAAAATACATGGCACTTTTCACCAAATAAGTAATGTCGCCATATTT
131 TTTGAGACTTTTGTGATCCGAAAATACATGGCACTTTTCACCAAACAAATAATGTCGCCATATTT
*
10930 TTAAAGCAAATACGATGGC
196 TCAAAGCAAATACGATGGC
10949 AGCTGCCAAA
Statistics
Matches: 210, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
238 210 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (238 bp):
ATTTCCGGCTTAAGGCGTCCGCAACCACATTAGCCTTTCCCGGGTGATAGTCAATGACAAGCTCA
TAATCCTTTAACAACTCGAGCCAACGTCTTTGTCACAGATTTAAGTCTCTTTGAGTCATCAAATA
TTTGAGACTTTTGTGATCCGAAAATACATGGCACTTTTCACCAAACAAATAATGTCGCCATATTT
TCAAAGCAAATACGATGGCGGCTAGCTCGAGATCCAAACAGCG
Found at i:11560 original size:213 final size:213
Alignment explanation
Indices: 11193--11618 Score: 843
Period size: 213 Copynumber: 2.0 Consensus size: 213
11183 TTTTCAGTTG
11193 ATCGAAGCCTTTCTGACATTTCTCCGTCCATTCGAACTTAGCATCCTTTTGAAGTAGCTTCGTCA
1 ATCGAAGCCTTTCTGACATTTCTCCGTCCATTCGAACTTAGCATCCTTTTGAAGTAGCTTCGTCA
11258 TTGGTGTGGCTATCATCGAGAAACCTTTGACAAATCGTCGGTAATAACCGGCGAGTCCCAAAAAG
66 TTGGTGTGGCTATCATCGAGAAACCTTTGACAAATCGTCGGTAATAACCGGCGAGTCCCAAAAAG
11323 CTCCGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTTAAGTATGGCTGAGATTTTGTTCGGGTC
131 CTCCGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTTAAGTATGGCTGAGATTTTGTTCGGGTC
11388 AACTCGAATACCCGATGC
196 AACTCGAATACCCGATGC
11406 ATCGAAGCCTTTCTGACATTTCTCCGTCCATTCGAACTTAGCATCCTTTTGAAGTAGCTTCGTCA
1 ATCGAAGCCTTTCTGACATTTCTCCGTCCATTCGAACTTAGCATCCTTTTGAAGTAGCTTCGTCA
11471 TTGGTGTGGCTATCATCGAGAAACCTTTGACAAATCGTCGGTAATAACCGGCGAGTCCCAAAAAG
66 TTGGTGTGGCTATCATCGAGAAACCTTTGACAAATCGTCGGTAATAACCGGCGAGTCCCAAAAAG
*
11536 CTCTGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTTAAGTATGGCTGAGATTTTGTTCGGGTC
131 CTCCGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTTAAGTATGGCTGAGATTTTGTTCGGGTC
11601 AACTCGAATACCCGATGC
196 AACTCGAATACCCGATGC
11619 GGATACCACA
Statistics
Matches: 212, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 212 1.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (213 bp):
ATCGAAGCCTTTCTGACATTTCTCCGTCCATTCGAACTTAGCATCCTTTTGAAGTAGCTTCGTCA
TTGGTGTGGCTATCATCGAGAAACCTTTGACAAATCGTCGGTAATAACCGGCGAGTCCCAAAAAG
CTCCGAACCTCAGTAATATTTCTCGGAGGTTTCCAGTTAAGTATGGCTGAGATTTTGTTCGGGTC
AACTCGAATACCCGATGC
Found at i:15847 original size:28 final size:28
Alignment explanation
Indices: 15784--16049 Score: 489
Period size: 28 Copynumber: 9.5 Consensus size: 28
15774 ATATTAAGTC
* *
15784 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
15811 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
15839 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
15867 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
15895 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
15923 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
15951 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
15979 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
16007 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
16035 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16050 GTACAATTTA
Statistics
Matches: 234, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
27 22 0.09
28 212 0.91
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:18727 original size:38 final size:38
Alignment explanation
Indices: 18676--18751 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
18666 ATTGTCTCGA
*
18676 CGCATAGGCCACCAGTCGACCTTCTTGCATCAATACGG
1 CGCATAGGCCACCACTCGACCTTCTTGCATCAATACGG
18714 CGCATAGGCCACCACTCGACCTTCTTGCATCAATACGG
1 CGCATAGGCCACCACTCGACCTTCTTGCATCAATACGG
18752 AACCCAACCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.21
Consensus pattern (38 bp):
CGCATAGGCCACCACTCGACCTTCTTGCATCAATACGG
Found at i:21190 original size:49 final size:49
Alignment explanation
Indices: 21118--21215 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
21108 ACTGCACCAA
21118 TAGTAGGCAGAATCGCGTAGCAAGGAGATAGTACACGTTAGGCATTCAT
1 TAGTAGGCAGAATCGCGTAGCAAGGAGATAGTACACGTTAGGCATTCAT
*
21167 TAGTAGGCAGAATCGCGTAGCAAGGAGATAGTACACTTTAGGCATTCAT
1 TAGTAGGCAGAATCGCGTAGCAAGGAGATAGTACACGTTAGGCATTCAT
21216 CGGGTGTACA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (49 bp):
TAGTAGGCAGAATCGCGTAGCAAGGAGATAGTACACGTTAGGCATTCAT
Found at i:23163 original size:40 final size:40
Alignment explanation
Indices: 23126--23349 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
23116 GCTACTCGTT
* *
23126 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
23166 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
23206 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
23246 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * *
23285 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
23326 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
23350 CATCATTCAA
Statistics
Matches: 167, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 49 0.29
40 107 0.64
41 9 0.05
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:23310 original size:79 final size:80
Alignment explanation
Indices: 23126--23349 Score: 298
Period size: 79 Copynumber: 2.8 Consensus size: 80
23116 GCTACTCGTT
* *
23126 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
23190 GATTTAGTAACTCGCA
65 GAATTAGTAACTCGCA
*
23206 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
23270 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
* * *
23285 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCC
23346 CGGA
63 CGGA
23350 CATCATTCAA
Statistics
Matches: 130, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
78 12 0.09
79 60 0.46
80 56 0.43
81 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:24349 original size:52 final size:52
Alignment explanation
Indices: 24285--24388 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
24275 CATGGGCTAA
24285 TTAGAACTCAAGCTAGCAACTAAAAACATGATGAATCTCATGGCACAACCTC
1 TTAGAACTCAAGCTAGCAACTAAAAACATGATGAATCTCATGGCACAACCTC
24337 TTAGAACTCAAGCTAGCAACTAAAAACATGATGAATCTCATGGCACAACCTC
1 TTAGAACTCAAGCTAGCAACTAAAAACATGATGAATCTCATGGCACAACCTC
24389 AAACATACCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.21
Consensus pattern (52 bp):
TTAGAACTCAAGCTAGCAACTAAAAACATGATGAATCTCATGGCACAACCTC
Found at i:26425 original size:43 final size:42
Alignment explanation
Indices: 26364--26511 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 42
26354 ATCGAGTAGG
* *
26364 GATTACATATAAGACCATGTTTGGGACATTGGCATTGTATTGT
1 GATTACATGTAAGACCATGTTTGGGACATTGGCATCGTATT-T
* * *
26407 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTAATC
1 GATTACATGTAAGACCATGTTTGGGACATTGGCATCG-TATTT
* * * * *
26450 GATTTCATGTAAGACCCTATCTTGGGACAGTGGCATCGATATAT
1 GATTACATGTAAGACCATGT-TTGGGACATTGGCATCG-TATTT
* *
26494 GATAACATGTAAGCCCAT
1 GATTACATGTAAGACCAT
26512 ATCTGGGATA
Statistics
Matches: 85, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
43 51 0.60
44 34 0.40
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTTTGGGACATTGGCATCGTATTT
Found at i:28479 original size:43 final size:43
Alignment explanation
Indices: 28347--28485 Score: 113
Period size: 43 Copynumber: 3.2 Consensus size: 43
28337 GTGATTACAC
* * * * * *
28347 GTAAGACCATGTCTGGGTCATTGGCTTTGTATAGA--GATAACAC
1 GTAAGACCATGTCTGGGACAGTGGCATCG-ATA-ATTGATAGCAT
** * ** *
28390 GTAAGACCATGTCTGGGACTTTGGCATCGTTAATTGATTTCGT
1 GTAAGACCATGTCTGGGACAGTGGCATCGATAATTGATAGCAT
*
28433 GTAAGACCCTGTCTGGGACAGTGGCATCGAT-ATATGATAGCAT
1 GTAAGACCATGTCTGGGACAGTGGCATCGATAAT-TGATAGCAT
28476 GTAAGACCAT
1 GTAAGACCAT
28486 ATATGGGATA
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
41 1 0.01
42 4 0.05
43 71 0.93
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
GTAAGACCATGTCTGGGACAGTGGCATCGATAATTGATAGCAT
Found at i:29308 original size:21 final size:20
Alignment explanation
Indices: 29284--29324 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29274 GACCTATGTT
*
29284 TTCATAAAATTTTTCTAAGTG
1 TTCA-AAAATTTTTATAAGTG
*
29305 TTCAGAAATTTTTATAAGTG
1 TTCAAAAATTTTTATAAGTG
29325 ATCGGTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (20 bp):
TTCAAAAATTTTTATAAGTG
Found at i:30254 original size:44 final size:48
Alignment explanation
Indices: 30164--30276 Score: 157
Period size: 44 Copynumber: 2.5 Consensus size: 48
30154 CAAAACTGTA
30164 TCAA-TCTCGCACACTAAGTGCATATATATATATATAGCCGAAGCTATC
1 TCAATTCTCGCACACTAAGTGCATATATATATATATA-CCGAAGCTATC
* *
30212 TC-ATTCTCACACACTAAGTGGA-A-ATATATATAT-CCGAAGCTATC
1 TCAATTCTCGCACACTAAGTGCATATATATATATATACCGAAGCTATC
30256 TCAATT-TCGCACACTAAGTGC
1 TCAATTCTCGCACACTAAGTGC
30277 CCATAATTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
44 26 0.44
45 3 0.05
46 10 0.17
47 2 0.03
48 18 0.31
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (48 bp):
TCAATTCTCGCACACTAAGTGCATATATATATATATACCGAAGCTATC
Done.