Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1336
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: 71416
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1554 original size:47 final size:47
Alignment explanation
Indices: 1476--1885 Score: 597
Period size: 47 Copynumber: 8.6 Consensus size: 47
1466 CCCTTCGGGA
* * * * * *
1476 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1522 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1570 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1617 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1664 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1713 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1760 CTTATCACATATATATATACACTTTCACATTCATCTCATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1811 CTTATCAAATGTATATACACTCTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1860 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
1886 CACAATTATC
Statistics
Matches: 332, Mismatches: 22, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
46 2 0.01
47 193 0.58
48 2 0.01
49 91 0.27
51 44 0.13
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:1710 original size:96 final size:96
Alignment explanation
Indices: 1476--1885 Score: 618
Period size: 96 Copynumber: 4.3 Consensus size: 96
1466 CCCTTCGGGA
* * * * * *
1476 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT-TATCACATATATA
1538 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
* *
1570 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1633 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
1664 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
1729 ACTTTCACATTCATCACATCGGCCATTAGAC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
1760 CTTATCACATATATATATACACTTTCACATTCATCTCATCGGCCATTAGGCCTTATCAAATGTAT
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA--TAT
*
1825 ATACACTCTCACATTCATCACATCGGCCATTAGGC
62 ATACACTTTCACATTCATCACATCGGCCATTAGGC
1860 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
1886 CACAATTATC
Statistics
Matches: 292, Mismatches: 15, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
93 1 0.00
94 87 0.30
95 2 0.01
96 99 0.34
98 59 0.20
100 44 0.15
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:5029 original size:47 final size:47
Alignment explanation
Indices: 4951--5360 Score: 615
Period size: 47 Copynumber: 8.6 Consensus size: 47
4941 CCCTTCGGGA
* * * * * *
4951 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4997 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5045 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5092 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5139 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5188 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5235 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5286 CTTATCACATGTATATACACTCTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5335 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
5361 CACAATTATC
Statistics
Matches: 336, Mismatches: 18, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
46 2 0.01
47 193 0.57
48 2 0.01
49 93 0.28
51 46 0.14
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:5185 original size:96 final size:96
Alignment explanation
Indices: 4951--5360 Score: 636
Period size: 96 Copynumber: 4.3 Consensus size: 96
4941 CCCTTCGGGA
* * * * * *
4951 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT-TATCACATATATA
5013 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
* *
5045 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
5108 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
5139 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
5204 ACTTTCACATTCATCACATCGGCCATTAGAC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
5235 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATGTAT
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA--TAT
*
5300 ATACACTCTCACATTCATCACATCGGCCATTAGGC
62 ATACACTTTCACATTCATCACATCGGCCATTAGGC
5335 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
5361 CACAATTATC
Statistics
Matches: 294, Mismatches: 13, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
93 1 0.00
94 87 0.30
95 2 0.01
96 99 0.34
98 61 0.21
100 44 0.15
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:8503 original size:47 final size:47
Alignment explanation
Indices: 8425--8834 Score: 615
Period size: 47 Copynumber: 8.6 Consensus size: 47
8415 CCCTTCGGGA
* * * * * *
8425 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8471 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8519 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8566 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8613 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8662 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8709 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8760 CTTATCACATGTATATACACTCTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8809 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
8835 CACAATTATC
Statistics
Matches: 336, Mismatches: 18, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
46 2 0.01
47 193 0.57
48 2 0.01
49 93 0.28
51 46 0.14
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:8659 original size:96 final size:96
Alignment explanation
Indices: 8425--8834 Score: 636
Period size: 96 Copynumber: 4.3 Consensus size: 96
8415 CCCTTCGGGA
* * * * * *
8425 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT-TATCACATATATA
8487 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
* *
8519 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
8582 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
8613 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
8678 ACTTTCACATTCATCACATCGGCCATTAGAC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
8709 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATGTAT
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA--TAT
*
8774 ATACACTCTCACATTCATCACATCGGCCATTAGGC
62 ATACACTTTCACATTCATCACATCGGCCATTAGGC
8809 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
8835 CACAATTATC
Statistics
Matches: 294, Mismatches: 13, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
93 1 0.00
94 87 0.30
95 2 0.01
96 99 0.34
98 61 0.21
100 44 0.15
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11977 original size:47 final size:47
Alignment explanation
Indices: 11899--12306 Score: 606
Period size: 47 Copynumber: 8.6 Consensus size: 47
11889 CCCTTCGGGA
* * * * * *
11899 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
11945 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
11993 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12040 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12087 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12136 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12183 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12234 CTTATCACATGTATATACAC--TCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12281 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
12307 CACAATTATC
Statistics
Matches: 335, Mismatches: 15, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
45 8 0.02
46 2 0.01
47 221 0.66
48 2 0.01
49 56 0.17
51 46 0.14
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12225 original size:98 final size:96
Alignment explanation
Indices: 11899--12306 Score: 627
Period size: 96 Copynumber: 4.3 Consensus size: 96
11889 CCCTTCGGGA
* * * * * *
11899 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT-TATCACATATATA
11961 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
* *
11993 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
12056 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
12087 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
12152 ACTTTCACATTCATCACATCGGCCATTAGAC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
12183 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATGTAT
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA--TAT
12248 ATACAC--TCACATTCATCACATCGGCCATTAGGC
62 ATACACTTTCACATTCATCACATCGGCCATTAGGC
12281 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
12307 CACAATTATC
Statistics
Matches: 293, Mismatches: 12, Indels: 18
0.91 0.04 0.06
Matches are distributed among these distances:
93 1 0.00
94 94 0.32
95 2 0.01
96 103 0.35
98 84 0.29
100 9 0.03
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12342 original size:194 final size:188
Alignment explanation
Indices: 11899--12306 Score: 583
Period size: 194 Copynumber: 2.1 Consensus size: 188
11889 CCCTTCGGGA
* * ** * * *
11899 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCTC-TGTCACATATATA
1 CTTATCACATATATATACAC-TTCACATTCATCACATCAGCCATTAGGC-CATATCACATATATA
*
11961 CACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCAC
64 CACTTTCACATTCATCACATCGGCCATTAGACCTCATCACATATATACACTTTCACATTCATCAC
*
12026 ATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 ATCGGCCATTAGGCCTTATCACATATATACAC-TTCACATTCATCACATCGGCCATTAGGC
* *
12087 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACAC-TTCACATTCATCACATCAGCCATTAGGCCATATCACATATATAC
*
12152 ACTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATATATACACTTTCACATTCAT
65 ACTTTCACATTCATCACATCGGCCATTAGACCTCATCAC----ATATATACACTTTCACATTCAT
12217 CACATCGGCCATTAGGCCTTATCACATGTATATACAC-TCACATTCATCACATCGGCCATTAGGC
126 CACATCGGCCATTAGGCCTTATCACA--TATATACACTTCACATTCATCACATCGGCCATTAGGC
12281 CTTATCACATATATATACA-TTCACAT
1 CTTATCACATATATATACACTTCACAT
12307 CACAATTATC
Statistics
Matches: 202, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
188 10 0.05
189 2 0.01
190 81 0.40
192 7 0.03
194 93 0.46
196 9 0.04
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (188 bp):
CTTATCACATATATATACACTTCACATTCATCACATCAGCCATTAGGCCATATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGACCTCATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATACACTTCACATTCATCACATCGGCCATTAGGC
Found at i:15046 original size:24 final size:24
Alignment explanation
Indices: 15019--15066 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
15009 CCAAATAGAA
15019 AGTGAAGAAGTCATGGTTCTGGTG
1 AGTGAAGAAGTCATGGTTCTGGTG
15043 AGTGAAGAAGTCATGGTTCTGGTG
1 AGTGAAGAAGTCATGGTTCTGGTG
15067 GAAGCCGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.38, T:0.29
Consensus pattern (24 bp):
AGTGAAGAAGTCATGGTTCTGGTG
Found at i:19884 original size:43 final size:43
Alignment explanation
Indices: 19836--19990 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 43
19826 GTTGTTCTCA
* *
19836 TGTAAGACCATGTCTAGGACGTTGGCATCGATAAATGATTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATATATGATTACG
* * *
19879 TGTAAGACCATGTCTGGGACATCGGCATCG-TATTTGATT-CG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATATATGATTACG
* * * *
19920 TGCAAGACCCTGTCTGGGTTA-G-TGGCATCGATATGTGATTACA
1 TGTAAGACCATGTCTGGG--ACGTTGGCATCGATATATGATTACG
* *
19963 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
19991 TGTACGATAT
Statistics
Matches: 92, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
41 26 0.28
42 16 0.17
43 50 0.54
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATATATGATTACG
Found at i:26031 original size:46 final size:47
Alignment explanation
Indices: 25925--26040 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 47
25915 TGTCTTCGAC
** * *
25925 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTATT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTATT
*
25975 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGA-T
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCT-ATT
26021 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
26041 TCTTTCCTGT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
46 28 0.47
47 1 0.02
50 30 0.51
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTATT
Found at i:37427 original size:49 final size:49
Alignment explanation
Indices: 37355--37548 Score: 185
Period size: 50 Copynumber: 3.9 Consensus size: 49
37345 GCCGAAGCTA
* *
37355 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG
* * *
37404 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAACAG
** * * * * *
37454 TCTTATACACGTAGTAGCCTACACTTAGTACTACCCACGTGATC-ACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG
* * * *
37502 TTTTCGGGTGCGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
37549 TCACAATAGA
Statistics
Matches: 117, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 38 0.32
50 39 0.33
51 37 0.32
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (49 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG
Found at i:50493 original size:39 final size:39
Alignment explanation
Indices: 50432--50572 Score: 176
Period size: 39 Copynumber: 3.6 Consensus size: 39
50422 CAGTGATGTT
*
50432 TATCTGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
1 TATCTGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
* *
50471 TATCTGGACTTAAGGTCTGCAGGCTATGTGCTAGAATTA
1 TATCTGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
* * * *
50510 TAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATA
1 TATCTGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
* * * *
50549 TTTCCGGGC-TAAAGTCCGCAGGCT
1 TATCTGGACTTAAGGTCCGCAGGCT
50573 TCGAGCTGGT
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 14 0.16
39 75 0.84
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
TATCTGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:52621 original size:44 final size:42
Alignment explanation
Indices: 52525--52632 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 42
52515 TCGATGTCTC
* *
52525 TGTCCCAGACAGGGTCTTACACAAAACCAGATACGATGCTGA
1 TGTCCCAGACACGGTCTTACACAAAACCAGATACGAGGCTGA
*
52567 TGTCCCAGACATGGTCTTACACATAAATCTCA-AGT-CGAGGCCTG-
1 TGTCCCAGACACGGTCTTACACA-AAA-C-CAGA-TACGAGG-CTGA
*
52611 TGTCCCAGACACGGTCCTACAC
1 TGTCCCAGACACGGTCTTACAC
52633 GATATCTCAG
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
42 22 0.39
43 3 0.05
44 26 0.46
45 6 0.11
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (42 bp):
TGTCCCAGACACGGTCTTACACAAAACCAGATACGAGGCTGA
Found at i:57807 original size:93 final size:93
Alignment explanation
Indices: 57695--57866 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
57685 CGCCCATAAG
*
57695 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
57759 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
57788 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
57853 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
57867 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:57861 original size:46 final size:46
Alignment explanation
Indices: 57688--57863 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
57678 TGTAACCCGC
* *
57688 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
57734 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
57784 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
57827 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
57864 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:61643 original size:27 final size:28
Alignment explanation
Indices: 61559--61656 Score: 144
Period size: 27 Copynumber: 3.5 Consensus size: 28
61549 CATGAGATTG
* * *
61559 GCACTAAGTGTGCGGGTTTAAATTGTATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
61588 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
61616 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
61643 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
61657 GACTTAATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
27 24 0.37
28 23 0.35
29 18 0.28
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:61667 original size:27 final size:27
Alignment explanation
Indices: 61584--61669 Score: 111
Period size: 27 Copynumber: 3.1 Consensus size: 27
61574 GTTTAAATTG
*
61584 TATAGCACTAAGTGTGCGAGTTTGATTA
1 TATAGCACTAAGTGTGCGA-CTTGATTA
*
61612 TATAGCACTAAGTGTGCGAGTTGATTA
1 TATAGCACTAAGTGTGCGACTTGATTA
* *
61639 TATAGCACTGAGTGTGCGGACTT-AATA
1 TATAGCACTAAGTGTGC-GACTTGATTA
61666 TATA
1 TATA
61670 CTTTTGAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.57
28 23 0.43
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (27 bp):
TATAGCACTAAGTGTGCGACTTGATTA
Found at i:69341 original size:12 final size:12
Alignment explanation
Indices: 69324--69350 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
69314 CCCATTCCGA
69324 ATATATATATAC
1 ATATATATATAC
69336 ATATATATATAC
1 ATATATATATAC
69348 ATA
1 ATA
69351 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:69879 original size:27 final size:28
Alignment explanation
Indices: 69795--69892 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
69785 CATGAGATTG
* * * *
69795 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
69824 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
69852 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
69879 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
69893 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:69903 original size:27 final size:27
Alignment explanation
Indices: 69823--69905 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
69813 TAAATTGTAC
* *
69823 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
69851 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
69878 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
69905 A
1 A
69906 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Done.