Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1890
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: 35605
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:1788 original size:15 final size:15
Alignment explanation
Indices: 1753--1828 Score: 74
Period size: 13 Copynumber: 5.4 Consensus size: 15
1743 GTATCTTGGG
*
1753 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
1768 --TCTTTATTCTGGA
1 TTTCTTTATTCTGGA
1781 TTTCTTTATTC-GG-
1 TTTCTTTATTCTGGA
*
1794 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
1809 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
1823 TTTCTT
1 TTTCTT
1829 GTTATCTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
12 2 0.04
13 19 0.37
14 12 0.24
15 16 0.31
16 2 0.04
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:4314 original size:48 final size:49
Alignment explanation
Indices: 4193--4363 Score: 184
Period size: 44 Copynumber: 3.7 Consensus size: 49
4183 AGGATATTTG
* *
4193 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATAGATGCGAAT
* *
4242 -G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-AGATG-TAACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATAGATGCGAA-T
*
4286 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-ATGGATGCGAA-
1 -GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATAGATGCGAAT
* *
4334 --C-GCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
4364 GCTTATGGGC
Statistics
Matches: 105, Mismatches: 9, Indels: 21
0.78 0.07 0.16
Matches are distributed among these distances:
43 2 0.02
44 32 0.30
45 3 0.03
46 30 0.29
48 31 0.30
49 5 0.05
50 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (49 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATAGATGCGAAT
Found at i:6980 original size:12 final size:12
Alignment explanation
Indices: 6963--7003 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
6953 TAGTTTTAAA
6963 AATAATACTAAT
1 AATAATACTAAT
* *
6975 AATAATAATAAC
1 AATAATACTAAT
*
6987 AATAATACAAAT
1 AATAATACTAAT
6999 AATAA
1 AATAA
7004 ATAATCTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATACTAAT
Found at i:7056 original size:26 final size:26
Alignment explanation
Indices: 7027--7102 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
7017 TGAAATTATT
*
7027 TAAAAGGATATAAATAAAATAAATGA
1 TAAAAAGATATAAATAAAATAAATGA
* *
7053 TAAAATGATAATAACA-AGAAT-AATGA
1 TAAAAAGAT-ATAA-ATAAAATAAATGA
* *
7079 TATAAAAAATAAAAATAAAATAAA
1 TA-AAAAGATATAAATAAAATAAA
7103 AAATAAACGT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
25 1 0.03
26 22 0.56
27 15 0.38
28 1 0.03
ACGTcount: A:0.68, C:0.01, G:0.08, T:0.22
Consensus pattern (26 bp):
TAAAAAGATATAAATAAAATAAATGA
Found at i:7195 original size:3 final size:3
Alignment explanation
Indices: 7187--7359 Score: 125
Period size: 3 Copynumber: 57.7 Consensus size: 3
7177 GAAAGAAAAT
* * * * *
7187 ATA ATA ATA ATA TTA ATA AT- ACA ATA GTA ATA ATA ATA ATA ACA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
7234 ATA GTA ATA ATA GTA GTA ATA AAA ATA ATA GTA ATA GTA ATA ATA ACGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * * * * * *
7283 A-A ATA GTA GTA ATA ATA GTA ATA AAA ATA ATA GTA ATA GTA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
7330 ATG GTA ATA ATAA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT
7360 TGAAATATTA
Statistics
Matches: 130, Mismatches: 36, Indels: 8
0.75 0.21 0.05
Matches are distributed among these distances:
2 3 0.02
3 122 0.94
4 5 0.04
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:7275 original size:51 final size:51
Alignment explanation
Indices: 7182--7330 Score: 212
Period size: 51 Copynumber: 3.0 Consensus size: 51
7172 ATAAAGAAAG
* * * *
7182 AAAATA-TAATAATAATATTAAT-AATACAATAGTAATAATAATAATAACA
1 AAAATAGTAATAATAATAGTAATAAAAATAATAGTAATAGTAATAATAACA
* *
7231 AAAATAGTAATAATAGTAGTAATAAAAATAATAGTAATAGTAATAATAACG
1 AAAATAGTAATAATAATAGTAATAAAAATAATAGTAATAGTAATAATAACA
* *
7282 AAAATAGTAGTAATAATAGTAATAAAAATAATAGTAATAGTAACAATAA
1 AAAATAGTAATAATAATAGTAATAAAAATAATAGTAATAGTAATAATAA
7331 TGGTAATAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
49 6 0.07
50 14 0.16
51 69 0.78
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (51 bp):
AAAATAGTAATAATAATAGTAATAAAAATAATAGTAATAGTAATAATAACA
Found at i:9128 original size:60 final size:57
Alignment explanation
Indices: 8994--9130 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 57
8984 TTTAATTCAT
* **
8994 ATAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AATATGGTTAAATTATATATTATTTTATTAAATTATATTTA
* *
9052 ATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTT-TTAAATAAAATATATTTA
1 ATAATAATTATATTAAAATATGGTTAAATTATATATTATTTTATTAAAT----TATATTTA
*
9112 ACT-ATAATTTTATTAAAAT
1 A-TAATAATTATATTAAAAT
9131 TTAATTATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
56 6 0.09
57 22 0.33
58 15 0.22
60 23 0.34
61 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGGTTAAATTATATATTATTTTATTAAATTATATTTA
Found at i:9294 original size:16 final size:16
Alignment explanation
Indices: 9268--9329 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
9258 GACTATAGCC
*
9268 CTATTCCATTACAACT
1 CTATTCAATTACAACT
* * *
9284 TTATTCAATTATAGCT
1 CTATTCAATTACAACT
*
9300 CTATTCAATTACAACC
1 CTATTCAATTACAACT
*
9316 CTATTCCATTACAA
1 CTATTCAATTACAA
9330 TGAACCAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.39
Consensus pattern (16 bp):
CTATTCAATTACAACT
Found at i:9321 original size:32 final size:32
Alignment explanation
Indices: 9261--9326 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
9251 AATTACTGAC
* **
9261 TATAGCCCTATTCCATTACAACTTTATTCAAT
1 TATAGCCCTATTCAATTACAACCCTATTCAAT
* *
9293 TATAGCTCTATTCAATTACAACCCTATTCCAT
1 TATAGCCCTATTCAATTACAACCCTATTCAAT
9325 TA
1 TA
9327 CAATGAACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (32 bp):
TATAGCCCTATTCAATTACAACCCTATTCAAT
Found at i:11918 original size:166 final size:167
Alignment explanation
Indices: 11643--11972 Score: 486
Period size: 166 Copynumber: 2.0 Consensus size: 167
11633 TAATATGTGT
* *
11643 ATTGAGAAAGTTAAATTTGGCATTATAGATACTAAAAGAAAGTGATTCGGGTCTTGATAGGGGGA
1 ATTGAGAAAGTTAAATTTGGCATTATAAATACTAAAAGAAAGTGATTCGGGTCTTGATAGGAGGA
* * * * * **
11708 AGAACAAGGTTTACGATGACTAGGCTTGTTTCTATCTTTTTTGTACCAAGGTAAGTTCATTTGCA
66 AAAACAAGGTTTACGAGGACTAGGCTCGTTTCTATCATTTTTGTACCAAGGTAACTTCATTCACA
11773 AATAATACAACATATACCATGCTTTAAATGCTTTGGC
131 AATAATACAACATATACCATGCTTTAAATGCTTTGGC
* *
11810 ATTGAGAAAGTTAAATTTGGCATTATAAAT-C-AAGAA-AAATGTGATTTGGGTCTTGATCGGAG
1 ATTGAGAAAGTTAAATTTGGCATTATAAATACTAA-AAGAAA-GTGATTCGGGTCTTGATAGGAG
* *
11872 GAAAAACAAGGTTTACGAGGATTAGGCTCGTTTCTATCATTTTTGTACCGAGGTAACTTCATTCA
64 GAAAAACAAGGTTTACGAGGACTAGGCTCGTTTCTATCATTTTTGTACCAAGGTAACTTCATTCA
* *
11937 CAAATAATGCAACATATAGCATGCTTTAAATGCTTT
129 CAAATAATACAACATATACCATGCTTTAAATGCTTT
11973 AATATTGCAT
Statistics
Matches: 146, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
165 5 0.03
166 112 0.77
167 29 0.20
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (167 bp):
ATTGAGAAAGTTAAATTTGGCATTATAAATACTAAAAGAAAGTGATTCGGGTCTTGATAGGAGGA
AAAACAAGGTTTACGAGGACTAGGCTCGTTTCTATCATTTTTGTACCAAGGTAACTTCATTCACA
AATAATACAACATATACCATGCTTTAAATGCTTTGGC
Found at i:12296 original size:45 final size:44
Alignment explanation
Indices: 12212--12296 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 44
12202 ATGTAATCTG
*
12212 AACTCATTGAGTTGTGACTGAGTTCATGATATATGTGACATCCA
1 AACTCATTGAGTTGTGACTGAGTTCATGATATATATGACATCCA
* * *
12256 AACTCATTGAGTTGTGGTCTGAGTTCGTGATATGTATGACA
1 AACTCATTGAGTTGT-GACTGAGTTCATGATATATATGACA
12297 CATTTTTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 15 0.42
45 21 0.58
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (44 bp):
AACTCATTGAGTTGTGACTGAGTTCATGATATATATGACATCCA
Found at i:19982 original size:20 final size:20
Alignment explanation
Indices: 19957--20003 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19947 AGCTCGTTTC
19957 CAGCTCACTCAAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * * *
19977 CAGCTCATTCGAGCTTAATT
1 CAGCTCACTCAAGCTCAAGT
19997 CAGCTCA
1 CAGCTCA
20004 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:21526 original size:12 final size:12
Alignment explanation
Indices: 21487--21544 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
21477 TTGGAGTAAC
21487 AAAAAAA-TCAA
1 AAAAAAATTCAA
*
21498 AAAAAATTGATTGAA
1 AAAAAA---ATTCAA
21513 AAAAAAATTCAA
1 AAAAAAATTCAA
* *
21525 AAAAAAAGTGAA
1 AAAAAAATTCAA
21537 AAAAAAAT
1 AAAAAAAT
21545 CGAGCAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 6 0.16
12 22 0.58
14 1 0.03
15 9 0.24
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:21536 original size:24 final size:25
Alignment explanation
Indices: 21487--21544 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 25
21477 TTGGAGTAAC
*
21487 AAAAAAA-TCAAAAAAAATTGATTGAA
1 AAAAAAATTCAAAAAAAA-T-AGTGAA
21513 AAAAAAATTCAAAAAAAA-AGTGAA
1 AAAAAAATTCAAAAAAAATAGTGAA
21537 AAAAAAAT
1 AAAAAAAT
21545 CGAGCAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 13 0.43
26 7 0.23
27 10 0.33
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (25 bp):
AAAAAAATTCAAAAAAAATAGTGAA
Found at i:21555 original size:17 final size:17
Alignment explanation
Indices: 21535--21573 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
21525 AAAAAAAGTG
21535 AAAAAAAA-ATCGAGCAA
1 AAAAAAAAGAT-GAGCAA
*
21552 AAAAAAAAGGTGAGCAA
1 AAAAAAAAGATGAGCAA
21569 AAAAA
1 AAAAA
21574 TCAAGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.72, C:0.08, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAAAAGATGAGCAA
Found at i:21555 original size:29 final size:28
Alignment explanation
Indices: 21523--21596 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
21513 AAAAAAATTC
*
21523 AAAAAAAAAGTGAAAAAAAAATCGAGCAA
1 AAAAAAAAAGTGAAAAAAAAATCAAG-AA
* * **
21552 AAAAAAAAGGTGAGCAAAAAAATCAAGTT
1 AAAAAAAAAGTGA-AAAAAAAATCAAGAA
21581 AAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
21597 GTCTTGCGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 2 0.05
29 24 0.65
30 11 0.30
ACGTcount: A:0.70, C:0.05, G:0.15, T:0.09
Consensus pattern (28 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGAA
Found at i:21571 original size:30 final size:29
Alignment explanation
Indices: 21523--21596 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
21513 AAAAAAATTC
*
21523 AAAAAAAAA-GTGAAAAAAAAATCGAGCA
1 AAAAAAAAAGGTGAAAAAAAAATCAAGCA
* **
21551 AAAAAAAAAGGTGAGCAAAAAAATCAAGTT
1 AAAAAAAAAGGTGA-AAAAAAAATCAAGCA
21581 AAAAAAAAA-GTGAAAA
1 AAAAAAAAAGGTGAAAA
21597 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 11 0.28
29 8 0.21
30 20 0.51
ACGTcount: A:0.70, C:0.05, G:0.15, T:0.09
Consensus pattern (29 bp):
AAAAAAAAAGGTGAAAAAAAAATCAAGCA
Found at i:24093 original size:10 final size:10
Alignment explanation
Indices: 24080--24117 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
24070 AGCTCACTCA
*
24080 AGCTCAAGTC
1 AGCTCAATTC
24090 AGCTC-ATTC
1 AGCTCAATTC
24099 GAGCTCAATTC
1 -AGCTCAATTC
24110 AGCTCAAT
1 AGCTCAAT
24118 CTTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:24094 original size:20 final size:20
Alignment explanation
Indices: 24069--24115 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
24059 AGCTCGTTTC
24069 CAGCTCACTCAAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
24089 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
24109 CAGCTCA
1 CAGCTCA
24116 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:26614 original size:78 final size:77
Alignment explanation
Indices: 26475--26697 Score: 234
Period size: 78 Copynumber: 2.8 Consensus size: 77
26465 TTGAATGCTG
* * * *
26475 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGC-GAGT--ATAAATCCGGGCTAAG-TCCCGAAGGCATT
*
26539 TGTGCGAGATA-CAAGT
62 TGTGCGAGATATCAA-A
* * *
26555 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTATAAATCCGGGTTAAGTCCCGAAGGCATTCGT
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGTATAAATCCGGGCTAAGTCCCGAAGGCATTTGT
* *
26620 GCGAGTTATTAAA
65 GCGAGATATCAAA
* * * *
26633 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAG-TA-TAAATCCGGGCTAAGTCCCGAAGGCATTTG
26698 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
77 10 0.08
78 54 0.45
79 28 0.23
80 21 0.17
81 8 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (77 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGTATAAATCCGGGCTAAGTCCCGAAGGCATTTGTG
CGAGATATCAAA
Found at i:26677 original size:39 final size:38
Alignment explanation
Indices: 26475--26695 Score: 203
Period size: 40 Copynumber: 5.6 Consensus size: 38
26465 TTGAATGCTG
* * * * *
26475 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGT-TATAAA
** * * *
26515 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACAAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTATAA-A
* *
26555 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAG-TATAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTATAAA
26593 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTA-TAAA
*
26633 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTA-TAAA
* * *
26672 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
26696 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
37 3 0.02
38 26 0.17
39 42 0.28
40 73 0.48
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (38 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTATAAA
Found at i:26715 original size:79 final size:78
Alignment explanation
Indices: 26555--26730 Score: 187
Period size: 78 Copynumber: 2.3 Consensus size: 78
26545 AGATACAAGT
* * * * *
26555 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTATAAATCCGGGTTAAGTCCCGAAGGCATTCGT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTATAAAACCGGGCTAAGTCCCGAAGGCATTCGA
* * *
26620 GCGAGTTATTAAA
66 ACGAGTGACTAAA
* * *
26633 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAG-TA-TAAAACCGGGCTAAGTCCCGAAGGCATTC
*
26697 GAACGAG-GAGCTATA
64 GAACGAGTGA-CTAAA
*
26712 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
26731 TACGTGATTT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
77 9 0.11
78 37 0.45
79 36 0.44
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTATAAAACCGGGCTAAGTCCCGAAGGCATTCGA
ACGAGTGACTAAA
Found at i:34126 original size:38 final size:39
Alignment explanation
Indices: 34081--34248 Score: 198
Period size: 38 Copynumber: 4.3 Consensus size: 39
34071 GGACTAAGAT
*
34081 CCGAAGGCATTTGTGCGAGATACAATTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
* *
34119 CCGAAGGCCTTTGTGCGAGAT-TAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
* * *
34157 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
34197 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
34236 CCGAAGGCATTTG
1 CCGAAGGCATTTG
34249 AACGAGGAGC
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
37 13 0.12
38 39 0.35
39 32 0.28
40 29 0.26
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:34193 original size:40 final size:40
Alignment explanation
Indices: 34028--34248 Score: 222
Period size: 40 Copynumber: 5.7 Consensus size: 40
34018 TTGAATGCTG
* * * *
34028 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAA
* * * *
34068 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
34107 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAG--ATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
34144 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
34184 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
34223 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
34249 AACGAGGAGC
Statistics
Matches: 153, Mismatches: 20, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
36 1 0.01
37 13 0.08
38 36 0.24
39 43 0.28
40 52 0.34
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
Found at i:34243 original size:79 final size:77
Alignment explanation
Indices: 34028--34246 Score: 228
Period size: 79 Copynumber: 2.8 Consensus size: 77
34018 TTGAATGCTG
* * * *
34028 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTG-TGAGT-AATAAATCCGGGCTAAG-TCCCGAAGGCATT
* *
34092 TGTGCGAGATACAAT
63 CGTGCGAGATACAAA
* * *
34107 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAG-ATTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGTGAGTAATAAATCCGGGCTAAGTCCCGAAGGCATTCG
* *
34170 TGCGAGTTATTAAA
65 TGCGAGATA-CAAA
* * * *
34184 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGTGAG-TAATAAATCCGGGCTAAGTCCCGAAGGCATT
34247 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
75 1 0.01
76 33 0.28
77 22 0.19
78 18 0.15
79 43 0.37
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (77 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGTGAGTAATAAATCCGGGCTAAGTCCCGAAGGCATTCGT
GCGAGATACAAA
Done.