Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1742
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: 88865
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:16057 original size:12 final size:12
Alignment explanation
Indices: 16040--16069 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16030 CCTCACAAGC
16040 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
16052 CCGTGTGCTAGG
1 CCGTGTGCCAGG
16064 CCGTGT
1 CCGTGT
16070 AATAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:19200 original size:42 final size:42
Alignment explanation
Indices: 19141--19227 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
19131 TACGTTTAAG
19141 ATCCACATATGATTTCTGCTAATCTTAAGCTACCTTCAAACT
1 ATCCACATATGATTTCTGCTAATCTTAAGCTACCTTCAAACT
19183 ATCCACATATGATTTCTGCTAATCTTAAGCTACCTTCAAACT
1 ATCCACATATGATTTCTGCTAATCTTAAGCTACCTTCAAACT
19225 ATC
1 ATC
19228 TTGGATCACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (42 bp):
ATCCACATATGATTTCTGCTAATCTTAAGCTACCTTCAAACT
Found at i:22958 original size:40 final size:39
Alignment explanation
Indices: 22914--23046 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 39
22904 AATAGAGTAA
22914 TAGCGGCGTTTTTAAAAAAGCGCCGCTATAGATCGACCAT
1 TAGCGGCGTTTTT-AAAAAGCGCCGCTATAGATCGACCAT
* * * * * *
22954 TAGCGGTGCTTTTTTAAATGCGCCGCTAAAGATCTAACAT
1 TAGCGGCG-TTTTTAAAAAGCGCCGCTATAGATCGACCAT
* * * *
22994 TAGCAGCGTTTTTCAAGAAGCGTCGCTATATATCGACC-T
1 TAGCGGCGTTTTT-AAAAAGCGCCGCTATAGATCGACCAT
*
23033 ATAGCGGCATTTTT
1 -TAGCGGCGTTTTT
23047 TTTTACGTAA
Statistics
Matches: 72, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 6 0.08
40 61 0.85
41 5 0.07
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (39 bp):
TAGCGGCGTTTTTAAAAAGCGCCGCTATAGATCGACCAT
Found at i:23176 original size:40 final size:40
Alignment explanation
Indices: 23121--23215 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
23111 CGTTTTCTAG
* *
23121 AAAACGCCGCTAAAAATCGTCTTACAGCGGCGCTTTTTAA
1 AAAACGCCGCTAAAAATCGACTTACAGCGGCGCTTTTAAA
* *
23161 AAAACACCGCTAAAAATCGACTTATAGCGGCGCTTTTAAA
1 AAAACGCCGCTAAAAATCGACTTACAGCGGCGCTTTTAAA
23201 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
23216 GATTAAATAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGACTTACAGCGGCGCTTTTAAA
Found at i:23474 original size:21 final size:21
Alignment explanation
Indices: 23450--23492 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23440 TCTCTAGTCA
* **
23450 TAAACCTTAAATTGTAAACCT
1 TAAACCCTAAATATTAAACCT
23471 TAAACCCTAAATATTAAACCT
1 TAAACCCTAAATATTAAACCT
23492 T
1 T
23493 GAATTCTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (21 bp):
TAAACCCTAAATATTAAACCT
Found at i:23742 original size:12 final size:12
Alignment explanation
Indices: 23722--23758 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
23712 AATAAATTTC
*
23722 ATATGGATATAT
1 ATATTGATATAT
23734 ATATTGATATAT
1 ATATTGATATAT
23746 ATA-TG-TATAT
1 ATATTGATATAT
23756 ATA
1 ATA
23759 GATATTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 8 0.33
11 2 0.08
12 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (12 bp):
ATATTGATATAT
Found at i:26994 original size:3 final size:3
Alignment explanation
Indices: 26986--27017 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
26976 ATTAATAGGA
26986 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27018 AAGAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27413 original size:187 final size:188
Alignment explanation
Indices: 27119--27457 Score: 476
Period size: 187 Copynumber: 1.8 Consensus size: 188
27109 TTTTGAAGCT
*
27119 TTGTTATTAGTGGCGCTTTCATAAAAATGCCACAAAACATCTATTAAGAGAATGTAAAACGGCAT
1 TTGTTATTAGTGGCGCTTTCATAAAAATGCCACAAAACATCTATAAAGAGAATGTAAAACGGCAT
*
27184 CGTCTACATCCTTGTTATTAGTGGCGCTTCTATAAACGCCACAAAAGGTGAGAATTACCGGCGTT
66 CGTCTACATCCTTGTTATTAGTGGCGCTTCTATAAACGCCACAAAAGGTGAGAAATACCGGCGTT
27249 TGCTCTACAAACGCCACAAAAATCTATTAACAGATTGCAAAACGACGTCGTTATTACC
131 TGCTCTACAAACGCCACAAAAATCTATTAACAGATTGCAAAACGACGTCGTTATTACC
* *
27307 TTGTTATTAGTGGCGCTTTTTATAAAAATGCCACAAAACAT-T-TAAAGAG-ATTTCAAAACGTG
1 TTGTTATTAGTGGCGC-TTTCATAAAAATGCCACAAAACATCTATAAAGAGAATGT-AAAACG-G
* * * **
27369 -GTCGTTTTATAGT-CTT-TTATTAGTGGCGCCTT-TATAAACGCCACAAAAGGTTTGAAATACC
63 CATCG-TCTACA-TCCTTGTTATTAGTGGCG-CTTCTATAAACGCCACAAAAGGTGAGAAATACC
* *
27430 GGCGTTTTCTCTAGAAACGCCACAAAAA
125 GGCGTTTGCTCTACAAACGCCACAAAAA
27458 ACCCCAATTT
Statistics
Matches: 134, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
186 3 0.02
187 79 0.59
188 28 0.21
189 24 0.18
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (188 bp):
TTGTTATTAGTGGCGCTTTCATAAAAATGCCACAAAACATCTATAAAGAGAATGTAAAACGGCAT
CGTCTACATCCTTGTTATTAGTGGCGCTTCTATAAACGCCACAAAAGGTGAGAAATACCGGCGTT
TGCTCTACAAACGCCACAAAAATCTATTAACAGATTGCAAAACGACGTCGTTATTACC
Found at i:30271 original size:23 final size:23
Alignment explanation
Indices: 30241--30290 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
30231 AACATTAATC
30241 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
30264 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
30287 AAAT
1 AAAT
30291 AAACTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:31128 original size:9 final size:9
Alignment explanation
Indices: 31105--31232 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
31095 ATTGATCATT
*
31105 ACTTAAATA
1 ACTTACATA
*
31114 AATTACATA
1 ACTTACATA
31123 ACTTACATA
1 ACTTACATA
*
31132 ACTTATATA
1 ACTTACATA
31141 ACTTACATA
1 ACTTACATA
*
31150 ATTTACATAACA
1 ACTTACAT---A
31162 ACTTACATA
1 ACTTACATA
*
31171 ACTCACATA
1 ACTTACATA
31180 ACTTACATA
1 ACTTACATA
*
31189 ATTTACATA
1 ACTTACATA
*
31198 ACTCACATA
1 ACTTACATA
* *
31207 ACGTACAGAACA
1 ACTTAC---ATA
31219 ACTTACATA
1 ACTTACATA
31228 ACTTA
1 ACTTA
31233 ACTAATACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 81 0.84
12 15 0.16
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:31181 original size:39 final size:39
Alignment explanation
Indices: 31122--31199 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
31112 TAAATTACAT
* *
31122 AACTTACATAACTTATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
31161 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
31200 TCACATAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:31195 original size:48 final size:48
Alignment explanation
Indices: 31116--31208 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
31106 CTTAAATAAA
* * * *
31116 TTACATAACTTACATAACTTATATAACTTACATAATTTACATAACAAC
1 TTACATAACTCACATAACTTACATAACTTACATAACTCACATAACAAC
*
31164 TTACATAACTCACATAACTTACATAATTTACATAACTCACATAAC
1 TTACATAACTCACATAACTTACATAACTTACATAACTCACATAAC
31209 GTACAGAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (48 bp):
TTACATAACTCACATAACTTACATAACTTACATAACTCACATAACAAC
Found at i:31199 original size:57 final size:57
Alignment explanation
Indices: 31118--31230 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
31108 TAAATAAATT
* * ** *
31118 ACATAACTTACATAACTTATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTTACATAACTCACATAACGTACAGAACAACTTACATAACTC
*
31175 ACATAACTTACATAATTTACATAACTCACATAACGTACAGAACAACTTACATAACT
1 ACATAACTTACATAACTTACATAACTCACATAACGTACAGAACAACTTACATAACT
31231 TAACTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTTACATAACTCACATAACGTACAGAACAACTTACATAACTC
Found at i:31222 original size:39 final size:37
Alignment explanation
Indices: 31105--31228 Score: 108
Period size: 39 Copynumber: 3.3 Consensus size: 37
31095 ATTGATCATT
* * * * * *
31105 ACTTAAATAAATTACAT-AACTTACATAACTTATATA
1 ACTTACATAATTTACATAAACTCACATAACTCAAACA
* * *
31141 ACTTACATAATTTACATAACAACTTACATAACTCACATA
1 ACTTACATAATTTACAT-A-AACTCACATAACTCAAACA
31180 ACTTACATAATTTACAT-AACTCACATAACGTACAGAACA
1 ACTTACATAATTTACATAAACTCACATAAC-T-CA-AACA
31219 ACTTACATAA
1 ACTTACATAA
31229 CTTAACTAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
36 26 0.35
37 1 0.01
38 2 0.03
39 46 0.61
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.31
Consensus pattern (37 bp):
ACTTACATAATTTACATAAACTCACATAACTCAAACA
Found at i:33082 original size:12 final size:12
Alignment explanation
Indices: 33065--33090 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33055 ACGATCCAGG
33065 GATGAATCTGAT
1 GATGAATCTGAT
33077 GATGAATCTGAT
1 GATGAATCTGAT
33089 GA
1 GA
33091 GGAGGATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:37238 original size:43 final size:44
Alignment explanation
Indices: 37118--37238 Score: 144
Period size: 43 Copynumber: 2.8 Consensus size: 44
37108 CGTTTGTTTG
* *
37118 AAAAAAAG-GCCGCTAAAGATCATGACTTTTAGCGATGCTTTTT
1 AAAAAAAGCGCCACTAAAGATCATGACTTTTAGCGGTGCTTTTT
* * *
37161 ATAAAAA-CGCCACTAAAGACCAAGACTTTTAGCGGTG-TTTTT
1 AAAAAAAGCGCCACTAAAGATCATGACTTTTAGCGGTGCTTTTT
37203 AAAAAAAGCGCCACTAAA-AGTCATGA-TCTTTAGCGG
1 AAAAAAAGCGCCACTAAAGA-TCATGACT-TTTAGCGG
37239 CACTTTTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
42 13 0.20
43 53 0.80
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (44 bp):
AAAAAAAGCGCCACTAAAGATCATGACTTTTAGCGGTGCTTTTT
Found at i:42438 original size:47 final size:47
Alignment explanation
Indices: 42386--42791 Score: 614
Period size: 47 Copynumber: 8.6 Consensus size: 47
42376 GATAATTGTG
* * *
42386 ATGTGAATGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42433 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
42480 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTAATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
42527 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42576 ATGTGAAAGTGTATATATATGTGATAAAGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42625 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42672 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
42719 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42766 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
42792 TCCCGAAGGG
Statistics
Matches: 332, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
47 240 0.72
49 92 0.28
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:42677 original size:192 final size:190
Alignment explanation
Indices: 42386--42790 Score: 647
Period size: 192 Copynumber: 2.1 Consensus size: 190
42376 GATAATTGTG
*
42386 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAAGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
42449 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
66 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
* * * *
42514 GCCAATGTAATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
131 GCCAATGTAATGAATGTGAAAGTG--TATATATGTGACAAGGCCGAATGGCCAACGTGATGA
*
42576 ATGTGAAAGTGTATATATATGTGATAAAGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAAGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
* *
42641 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATG
66 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
* * * * *
42706 GCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
131 GCCAATGTAATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGA
42766 ATGTGAAAGTGTATA-A-ATGTGATAA
1 ATGTGAAAGTGTATATATATGTGATAA
42791 GTCCCGAAGG
Statistics
Matches: 200, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
188 9 0.05
189 1 0.00
190 49 0.25
191 2 0.01
192 139 0.69
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (190 bp):
ATGTGAAAGTGTATATATATGTGATAAAGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
GCCAATGTAATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGA
Found at i:50642 original size:21 final size:21
Alignment explanation
Indices: 50605--50645 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
50595 CTTGTTCGAC
*
50605 AATGATTCGACAGTGATTTGT
1 AATGATTCCACAGTGATTTGT
50626 AATGATTCCACTA-TGATTTG
1 AATGATTCCAC-AGTGATTTG
50646 GTATTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (21 bp):
AATGATTCCACAGTGATTTGT
Found at i:50869 original size:47 final size:48
Alignment explanation
Indices: 50757--50887 Score: 192
Period size: 47 Copynumber: 2.8 Consensus size: 48
50747 GTGCGAGTTA
* * * * * *
50757 TACCTTGATTCGGCTACGGGCCATGGTATAGGTATTTTGGAGAGGAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGAGAGAAAT
*
50805 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGG-GATAAAT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGAGAGAAAT
50852 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACT
50888 TATCGATTGA
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
47 40 0.53
48 36 0.47
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (48 bp):
TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGAGAGAAAT
Found at i:78277 original size:46 final size:46
Alignment explanation
Indices: 78129--78301 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
78119 TGTAACTCGC
* **
78129 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-TGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
78174 CCAT-AGTGAACTCAGACTC-ACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
78222 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
78265 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
78302 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 12, Indels: 23
0.75 0.09 0.17
Matches are distributed among these distances:
42 2 0.02
43 18 0.17
44 15 0.14
45 6 0.06
46 41 0.39
47 17 0.16
48 3 0.03
49 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:78320 original size:46 final size:45
Alignment explanation
Indices: 78134--78320 Score: 138
Period size: 46 Copynumber: 4.1 Consensus size: 45
78124 CTCGCCCATA
* * *
78134 AGTGAACTCGGACTCAACTCAACGAGCTCGG-TGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-C-T
* *
78178 AGTGAACTCAGACTC-ACTCAACGAGTTCGGATGC-CTAGTTA-CATTT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * * *
78224 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCT
78270 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
78316 AGTGA
1 AGTGA
78321 CATGTCACTT
Statistics
Matches: 113, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
43 15 0.13
44 25 0.22
45 1 0.01
46 45 0.40
47 19 0.17
48 3 0.03
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:80734 original size:15 final size:15
Alignment explanation
Indices: 80686--80765 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
80676 CAAAGATAAC
*
80686 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
80700 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
80715 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
*
80730 AAGAAATCTAGAATA
1 AAGAAATCCAGAATA
* * *
80745 AAGAGATCGAGGATA
1 AAGAAATCCAGAATA
80760 AAGAAA
1 AAGAAA
80766 CCCATGATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.17
15 43 0.81
16 1 0.02
ACGTcount: A:0.59, C:0.11, G:0.19, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:83793 original size:93 final size:93
Alignment explanation
Indices: 83681--83851 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
83671 GCCCATAAGT
* *
83681 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
83746 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
83774 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
83839 CGAGTTCGGATGC
66 CGAGCTCGGATGC
83852 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:83848 original size:46 final size:46
Alignment explanation
Indices: 83673--83848 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
83663 TGTAACCCGC
* *
83673 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
83719 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * *
83769 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
83812 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
83849 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 65 0.58
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Done.