Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3708.1
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: 108704
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.30
Warning! 16728 characters in sequence are not A, C, G, or T
Found at i:118 original size:51 final size:50
Alignment explanation
Indices: 5--416 Score: 253
Period size: 51 Copynumber: 8.6 Consensus size: 50
1 CTAG
* *
5 TCTTATCTCCCTGAAGTTGCAGTGG-G--G--CAAA-CTACAAATAGAAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCAAAGCTACAATTACAA-A
* * * *
50 TCTTATCTCTCTAAAGTTACAGTAGAGTAGATCAAAGCTACAGATTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCAAAGCTACA-ATTACAAA
* * * * * *
101 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGGT---TG--A-AGTTACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCAAAGCTACAATTACAAA
* * * *
145 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAATCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCAAAGCTAC-AATTACAAA
* * * * *
196 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAGTTACAAATACCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATC-AAAGCTACAATTA-CAAA
* * * * * * *
247 CCTTATCTCCCTGAAGTTGCACTGGAGTAGGT---TG--A-ATTTACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCAAAGCTACAATTACAAA
* * * *
291 TCTTATCCCCCTGAAGTTGCAGTGG-G--G--CAGA-CTACAAATAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCAAAGCTACAATTA-CAAA
* * * *
336 TCTTATCTCTCTGAAGTTACAGTAGAGTAAATCAAAGCTACAGATTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCAAAGCTACA-ATTACAAA
*
387 TGTTATCTCCCTGAAGTTGCAGTGGAGTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAG
417 GTTGAAGTCA
Statistics
Matches: 279, Mismatches: 57, Indels: 56
0.71 0.15 0.14
Matches are distributed among these distances:
41 1 0.00
43 2 0.01
44 61 0.22
45 47 0.17
46 4 0.01
47 1 0.00
48 3 0.01
49 1 0.00
50 10 0.04
51 141 0.51
52 8 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (50 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCAAAGCTACAATTACAAA
Found at i:150 original size:44 final size:44
Alignment explanation
Indices: 101--641 Score: 273
Period size: 44 Copynumber: 11.8 Consensus size: 44
91 AGATTACAAA
* * *
101 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGGTTGAAGTTACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAG
* *
145 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAATCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTAC---T----AG
* * *
196 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACAAATACCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTAC---T----AG
* * * * *
247 CCTTATCTCCCTGAAGTTGCACTGGAGTAGGTTGAATTTACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAG
* * * **
291 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGACT-ACAAATAGC-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGTTA-CTAG
* * * * * * * *
335 ATCTTATCTCTCTGAAGTTACAGTAGAGTAAATCAAAGCTACAGATTACAAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT---TG--A-AG-TTACTAG
* * * *
387 TGTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTCACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAG
** * *
431 TCTTATCTCCCTGAAGTTGCAACGGAGCAGA-TCAA-ATACGGCGTA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA---C-TAG
* * * * * *** *
476 TCTTATTTTCCTAAAGTTGCAGCGAAGCAGATTGAAACCACCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAG
* * * *
520 CCTTATCTCCCTGAAGTTGCAATGGAGCAGGTTGAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAG
* * * * * *
564 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA-CTAG
* * **
609 TCTTATCTCTCTAAAGTTGCAGTAAAGCAGATT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
642 AAAGCTATAA
Statistics
Matches: 381, Mismatches: 90, Indels: 51
0.73 0.17 0.10
Matches are distributed among these distances:
42 1 0.00
43 5 0.01
44 165 0.43
45 84 0.22
46 6 0.02
47 2 0.01
48 2 0.01
51 113 0.30
52 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAG
Found at i:201 original size:95 final size:95
Alignment explanation
Indices: 5--466 Score: 350
Period size: 95 Copynumber: 4.8 Consensus size: 95
1 CTAG
* * ** ** * * *
5 TCTTATCTCCCTGAAGTTGCAGTGGGGCAAACT-ACAAATAGAAGATCTTATCTCTCTAAAGTTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA-AGTTACTAG-TCTTATCTCCCTGAAGTTG
*
69 CAGTAGAGTAGATCAAAGCTACAGATTACAAA
64 CAGTGGAGTAGATCAAAGCTACAGATTACAAA
* * **
101 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGGTTGAAGTTACTAGTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACTAGTCTTATCTCCCTGAAGTTGCA
* * * * *
166 GTGGAGCAGATTAAAGTTACAAATCACAAA
66 GTGGAGTAGATCAAAGCTACAGATTACAAA
* **
196 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACAAATACCAAACCTTATCTCCCTGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTAC---T----AGTCTTATCTCCCTGA
* * * * * *
261 AGTTGCACTGGAGTAGGT---TG--A-A-TTTACTAG
59 AGTTGCAGTGGAGTAGATCAAAGCTACAGATTACAAA
* * ** *
291 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGACT-ACAAATAGC-AGATCTTATCTCTCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA-AGTTA-CTAG-TCTTATCTCCCTGAAGTT
* * *
354 ACAGTAGAGTAAATCAAAGCTACAGATTACAAA
63 GCAGTGGAGTAGATCAAAGCTACAGATTACAAA
* * ** *
387 TGTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTCACTAGTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACTAGTCTTATCTCCCTGAAGTTGCA
** *
452 ACGGAGCAGATCAAA
66 GTGGAGTAGATCAAA
467 TACGGCGTAT
Statistics
Matches: 279, Mismatches: 67, Indels: 41
0.72 0.17 0.11
Matches are distributed among these distances:
88 1 0.00
89 25 0.09
92 1 0.00
94 2 0.01
95 146 0.52
96 70 0.25
97 3 0.01
98 1 0.00
99 1 0.00
102 29 0.10
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (95 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACTAGTCTTATCTCCCTGAAGTTGCA
GTGGAGTAGATCAAAGCTACAGATTACAAA
Found at i:414 original size:140 final size:140
Alignment explanation
Indices: 1--648 Score: 630
Period size: 140 Copynumber: 4.6 Consensus size: 140
* * *
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAAACTACAAATAGAAGATCTTATCTCTCTAAAG
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTACAAATAGCAGATCTTATCTCTCTGAAG
*
66 TTACAGTAGAGTAGATCAAAGCTACAGATTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGTAG
66 TTACAGTAGAGTAGATCAAAGCTACAGATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAG
131 GTTGAAGTTA
131 GTTGAAGTTA
* * * *
141 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAATCA-CAAACCTTATCTC
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAG-----A-CTACAAAT-AGCAGATCTTATCTC
* * * * * * * *
205 CCTGAAGTTGCAGTGGAGCAGA-CTGAAGTTACA-AATACCAAACCTTATCTCCCTGAAGTTGCA
59 TCTGAAGTTACAGTAGAGTAGATC-AAAGCTACAGATTA-CAAATCTTATCTCCCTGAAGTTGCA
* *
268 CTGGAGTAGGTTGAATTTA
122 GTGGAGTAGGTTGAAGTTA
*
287 CTAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTACAAATAGCAGATCTTATCTCTCTGAAG
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTACAAATAGCAGATCTTATCTCTCTGAAG
* *
352 TTACAGTAGAGTAAATCAAAGCTACAGATTACAAATGTTATCTCCCTGAAGTTGCAGTGGAGTAG
66 TTACAGTAGAGTAGATCAAAGCTACAGATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAG
*
417 GTTGAAGTCA
131 GTTGAAGTTA
** * *
427 CTAGTCTTATCTCCCTGAAGTTGCAACGGAGCAGA-T-CAAATACGGC-GTATCTTAT-TTTCCT
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTACAAATA--GCAG-ATCTTATCTCT-CT
* * * * * * *
488 AAAGTTGCAG-CGAAGCAGATTGAAA-CCACCAG----C----CTTATCTCCCTGAAGTTGCAAT
62 GAAGTTACAGTAG-AGTAGA-TCAAAGCTA-CAGATTACAAATCTTATCTCCCTGAAGTTGCAGT
*
543 GGAGCAGGTTGAAGTTA
124 GGAGTAGGTTGAAGTTA
* * * * *
560 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-CAAGATAGCAAATCTTATCTCTCTAAA
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTACAA-ATAGCAGATCTTATCTCTCTGAA
* * * *
624 GTTGCAGTAAAGCAGATTAAAGCTA
65 GTTACAGTAGAGTAGATCAAAGCTA
649 TAAATCCTAT
Statistics
Matches: 421, Mismatches: 62, Indels: 57
0.78 0.11 0.11
Matches are distributed among these distances:
132 4 0.01
133 95 0.23
134 6 0.01
135 3 0.01
137 1 0.00
138 6 0.01
139 6 0.01
140 169 0.40
141 12 0.03
145 5 0.01
146 113 0.27
147 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (140 bp):
CTAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTACAAATAGCAGATCTTATCTCTCTGAAG
TTACAGTAGAGTAGATCAAAGCTACAGATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAG
GTTGAAGTTA
Found at i:986 original size:41 final size:41
Alignment explanation
Indices: 928--1008 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
918 CTCGACATGT
* *
928 CGCACTTTAGTTTAATAATAGTCTCAACTTACGTAATTTCC
1 CGCACTTTAGTTCAATAATAGTCTCAACTTACATAATTTCC
969 CGCACTTTAGTTCAATAATAGTCTCAACTTACATAATTTC
1 CGCACTTTAGTTCAATAATAGTCTCAACTTACATAATTTC
1009 ATTGTATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (41 bp):
CGCACTTTAGTTCAATAATAGTCTCAACTTACATAATTTCC
Found at i:1470 original size:46 final size:47
Alignment explanation
Indices: 1420--1575 Score: 219
Period size: 46 Copynumber: 3.4 Consensus size: 47
1410 CCATAGTGTT
* *
1420 TTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTTCATGTCACGTTGCCATGGTATC
* *
1466 TTTCAACCATGGTCTTATTC-TTTTCATGTCACGTTGCCATGTTATC
1 TTTCAACCATGGTCTTACTCATTTTCATGTCACGTTGCCATGGTATC
* * * *
1512 TTTCAACCATGGTCTTACACA-TCTCATATCAGGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTTCATGTCACGTTGCCATGGTATC
1558 TTTCAACCATGGTCTTAC
1 TTTCAACCATGGTCTTAC
1576 ACACAGGTTG
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
45 5 0.05
46 93 0.95
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (47 bp):
TTTCAACCATGGTCTTACTCATTTTCATGTCACGTTGCCATGGTATC
Found at i:1607 original size:24 final size:24
Alignment explanation
Indices: 1580--1625 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1570 TCTTACACAC
1580 AGGTTGCCATGGTATCTTTCAATT
1 AGGTTGCCATGGTATCTTTCAATT
1604 AGGTTGCCATGGTATCTTTCAA
1 AGGTTGCCATGGTATCTTTCAA
1626 CCATGGCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (24 bp):
AGGTTGCCATGGTATCTTTCAATT
Found at i:1618 original size:62 final size:62
Alignment explanation
Indices: 1542--1663 Score: 226
Period size: 62 Copynumber: 2.0 Consensus size: 62
1532 ATCTCATATC
*
1542 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAATT
1 AGGTTGCCATGGTATCTTTCAACCATGGCCTTACACACAGGTTGCCATGGTATCTTTCAATT
*
1604 AGGTTGCCATGGTATCTTTCAACCATGGCCTTCCACACAGGTTGCCATGGTATCTTTCAA
1 AGGTTGCCATGGTATCTTTCAACCATGGCCTTACACACAGGTTGCCATGGTATCTTTCAA
1664 CCATGGTCTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (62 bp):
AGGTTGCCATGGTATCTTTCAACCATGGCCTTACACACAGGTTGCCATGGTATCTTTCAATT
Found at i:1647 original size:38 final size:38
Alignment explanation
Indices: 1604--1701 Score: 178
Period size: 38 Copynumber: 2.6 Consensus size: 38
1594 TCTTTCAATT
*
1604 AGGTTGCCATGGTATCTTTCAACCATGGCCTTCCACAC
1 AGGTTGCCATGGTATCTTTCAACCATGGCCTTACACAC
*
1642 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAC
1 AGGTTGCCATGGTATCTTTCAACCATGGCCTTACACAC
1680 AGGTTGCCATGGTATCTTTCAA
1 AGGTTGCCATGGTATCTTTCAA
1702 TTAGGTTGCC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (38 bp):
AGGTTGCCATGGTATCTTTCAACCATGGCCTTACACAC
Found at i:1707 original size:24 final size:24
Alignment explanation
Indices: 1680--1725 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1670 TCTTACACAC
1680 AGGTTGCCATGGTATCTTTCAATT
1 AGGTTGCCATGGTATCTTTCAATT
1704 AGGTTGCCATGGTATCTTTCAA
1 AGGTTGCCATGGTATCTTTCAA
1726 CCATGGCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (24 bp):
AGGTTGCCATGGTATCTTTCAATT
Found at i:1708 original size:62 final size:60
Alignment explanation
Indices: 1642--1797 Score: 189
Period size: 57 Copynumber: 2.6 Consensus size: 60
1632 CCTTCCACAC
* *
1642 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTGCCATGGTA-TC-TTTCA-ATT
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACA--TT---ATCGTACACATTTCATATT
* *
1704 AGGTTGCCATGGTATCTTTCAACCATGGCCTT-C-C-CATTATCTTACACATTTCATATT
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACATTATCGTACACATTTCATATT
1761 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1798 TCTCATATCA
Statistics
Matches: 83, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
54 4 0.05
55 1 0.01
56 5 0.06
57 36 0.43
58 1 0.01
59 3 0.04
60 1 0.01
61 1 0.01
62 31 0.37
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (60 bp):
AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACATTATCGTACACATTTCATATT
Found at i:1714 original size:100 final size:100
Alignment explanation
Indices: 1541--1737 Score: 394
Period size: 100 Copynumber: 2.0 Consensus size: 100
1531 CATCTCATAT
1541 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAATTAG
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAATTAG
1606 GTTGCCATGGTATCTTTCAACCATGGCCTTCCACA
66 GTTGCCATGGTATCTTTCAACCATGGCCTTCCACA
1641 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAATTAG
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAATTAG
1706 GTTGCCATGGTATCTTTCAACCATGGCCTTCC
66 GTTGCCATGGTATCTTTCAACCATGGCCTTCC
1738 CATTATCTTA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (100 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACACAGGTTGCCATGGTATCTTTCAATTAG
GTTGCCATGGTATCTTTCAACCATGGCCTTCCACA
Found at i:1811 original size:46 final size:46
Alignment explanation
Indices: 1743--1854 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
1733 CTTCCCATTA
*
1743 TCTTACACATTTCATATTAGGTTGCCATGGTATCTTTCAACCATGG
1 TCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGG
* *
1789 TCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCCACCATGG
1 TCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGG
1835 TCTTACACATTTCATATCAG
1 TCTTACACATTTCATATCAG
1855 AGAGCACACT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (46 bp):
TCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGG
Found at i:6237 original size:46 final size:47
Alignment explanation
Indices: 6175--6342 Score: 209
Period size: 46 Copynumber: 3.6 Consensus size: 47
6165 TTTGACGTGA
* * * *
6175 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACGT
* * *
6221 TGCCATGGTATTTTTCAACCATGGTCTTATTC-TTTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACGT
* * *
6267 TGCCATGGTATCTTTCAACCATGGTCTTA--CATATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCAT-TTTCATGTCACGT
6313 TGCCATGGTATCTTTCAACCATGGTCTTAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC
6343 ACATCTCATA
Statistics
Matches: 106, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
44 1 0.01
45 6 0.06
46 99 0.93
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACGT
Found at i:6343 original size:46 final size:42
Alignment explanation
Indices: 6175--6739 Score: 520
Period size: 38 Copynumber: 13.7 Consensus size: 42
6165 TTTGACGTGA
* * * * *
6175 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTA--CA--TTCTATCAGGT
* * * * *
6221 TGCCATGGTATTTTTCAACCATGGTCTTATTCTTTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTA--C-ATTC-TATCAGGT
6267 TGCCATGGTATCTTTCAACCATGGTCTTACATATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAC--AT-TC-TATCAGGT
6313 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTT--ACAT-TC-TATCAGGT
6359 TG-C-------CTTTCAACCATGGTCTTACA--C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATTCTATCAGGT
6389 TGCCATGGTATCTTTCAACCATGGTCTTACA--C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATTCTATCAGGT
6427 TGCCATGGTATCTTTCAACCATGGTCTTACA--C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATTCTATCAGGT
6465 TGCCATGGTATCTTTCAACCATGGTCTTACA--C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATTCTATCAGGT
* *
6503 TGCCATGGTATCTTTCAACCAT-G-C--A-TTTCATATTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATTC-TATCAGGT
6541 TGCCATGGTATCTTTCAACCATGGTCTTACA--C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATTCTATCAGGT
* *
6579 TGCCATGGCATCTTTCGACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTT--ACA-TTC-TATCAGGT
6625 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTT--ACA-TTC-TATCAGGT
6671 TGCCATGGTATCTTTCAACCATGGTCTTACA--C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACATTCTATCAGGT
6709 TGCCATGGTATCTTTCAACCATGGTCTTACA
1 TGCCATGGTATCTTTCAACCATGGTCTTACA
6740 CATTTCATAT
Statistics
Matches: 466, Mismatches: 21, Indels: 72
0.83 0.04 0.13
Matches are distributed among these distances:
30 7 0.02
31 2 0.00
33 1 0.00
34 1 0.00
35 1 0.00
36 4 0.01
37 2 0.00
38 234 0.50
39 3 0.01
40 4 0.01
41 2 0.00
42 1 0.00
43 1 0.00
44 4 0.01
45 7 0.02
46 190 0.41
48 2 0.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (42 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACATTCTATCAGGT
Found at i:6404 original size:38 final size:38
Alignment explanation
Indices: 6308--6741 Score: 556
Period size: 38 Copynumber: 11.0 Consensus size: 38
6298 TATCTCATAT
6308 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
***
6346 TCTCATAT--CA-GGT-TGCCTTTCAACCATGGTCTTACACA
1 -CAGGT-TGCCATGGTAT--CTTTCAACCATGGTCTTACACA
6384 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
6422 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
6460 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
* *
6498 CAGGTTGCCATGGTATCTTTCAACCAT-G-CATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTC-TTACACA
*
6535 TTAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
* *
6574 CAGGTTGCCATGGCATCTTTCGACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
6619 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
6665 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
6704 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
6742 TTTCATATCA
Statistics
Matches: 360, Mismatches: 16, Indels: 39
0.87 0.04 0.09
Matches are distributed among these distances:
36 3 0.01
37 11 0.03
38 245 0.68
39 12 0.03
40 6 0.02
41 1 0.00
43 1 0.00
44 3 0.01
45 1 0.00
46 77 0.21
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:8897 original size:11 final size:11
Alignment explanation
Indices: 8881--8928 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
8871 CTTTATATAC
8881 TAATAAAATAA
1 TAATAAAATAA
*
8892 TAATAAAATATCT
1 TAATAAAATA--A
* *
8905 TATTAAAATAT
1 TAATAAAATAA
8916 TAATAAAATAA
1 TAATAAAATAA
8927 TA
1 TA
8929 TTTACCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:9749 original size:44 final size:45
Alignment explanation
Indices: 9701--9825 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
9691 AACCATTAGC
* * *
9701 CTTATCTCCCTGAAGTTACAATGGAGCAGGTTGAAGATA-CAAGT
1 CTTATCTCCCTGAAGTTACAATAGAGCAGATTGAAGATAGCAAAT
* * * *
9745 CTTATCTCCCTTAAGTTGCAGTAGAGCAGATTGAATATAGCAAAT
1 CTTATCTCCCTGAAGTTACAATAGAGCAGATTGAAGATAGCAAAT
* * * *
9790 CTTATCTCTCTGAAGTTGCAGTAGAACAGATTGAAG
1 CTTATCTCCCTGAAGTTACAATAGAGCAGATTGAAG
9826 CCACAAACCT
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 33 0.48
45 36 0.52
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTACAATAGAGCAGATTGAAGATAGCAAAT
Found at i:9806 original size:45 final size:44
Alignment explanation
Indices: 9701--9855 Score: 166
Period size: 44 Copynumber: 3.5 Consensus size: 44
9691 AACCATTAGC
* * * * *
9701 CTTATCTCCCTGAAGTTACAATGGAGCAGGTTGAAGATACAAGT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAAT
* *
9745 CTTATCTCCCTTAAGTTGCAGTAGAGCAGATTGAATATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATA-CAAAT
* * ** *
9790 CTTATCTCTCTGAAGTTGCAGTAGAACAGATTGAAGCCACAAAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAAT
* * *
9834 CTTGTCCCCCTGAAATTGCAGT
1 CTTATCTCCCTGAAGTTGCAGT
9856 GGGGCAAGTT
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 55 0.60
45 37 0.40
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATACAAAT
Found at i:10120 original size:19 final size:20
Alignment explanation
Indices: 10096--10136 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10086 ATTTTGGCCC
*
10096 AAACAACT-AAATCCCAAAT
1 AAACAACTAAAAGCCCAAAT
*
10115 AAACAATTAAAAGCCCAAAT
1 AAACAACTAAAAGCCCAAAT
10135 AA
1 AA
10137 TAAAAAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.61, C:0.22, G:0.02, T:0.15
Consensus pattern (20 bp):
AAACAACTAAAAGCCCAAAT
Found at i:10909 original size:38 final size:38
Alignment explanation
Indices: 10858--10936 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
10848 GGCGGCAATG
10858 AAGGGTTCTCCTAACCCTAGCAGAGAAAAGAAAATAGA
1 AAGGGTTCTCCTAACCCTAGCAGAGAAAAGAAAATAGA
*
10896 AAGGGTTCTCCTAACCCTAGCAGAGAAAAGAAAATGGA
1 AAGGGTTCTCCTAACCCTAGCAGAGAAAAGAAAATAGA
10934 AAG
1 AAG
10937 AAGGGTATCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (38 bp):
AAGGGTTCTCCTAACCCTAGCAGAGAAAAGAAAATAGA
Found at i:11452 original size:44 final size:45
Alignment explanation
Indices: 11337--11460 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 45
11327 GGTTTGTGGC
* * * * *
11337 TTCAATCTACTCTACTACAACTTCAGAGAGATAAGATTTGCTATA
1 TTCAACCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTATA
** * *
11382 TTCAGTCTATTCCACTGCAACTTCAGGGAGATAAGACTTGC-ATC
1 TTCAACCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTATA
* * *
11426 TTCAACCTGCTCCATTGTAACTTCAGGGAGATAAG
1 TTCAACCTACTCCACTGCAACTTCAGGGAGATAAG
11461 GTTAATGACC
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
44 31 0.47
45 35 0.53
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (45 bp):
TTCAACCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTATA
Found at i:11951 original size:44 final size:43
Alignment explanation
Indices: 11851--12052 Score: 127
Period size: 44 Copynumber: 4.6 Consensus size: 43
11841 CTTGAGTCTA
* ** *
11851 CTCCACTGCAACTTCAGGGAGATAAGACTTA-TAACTTTAACCTG
1 CTCCGCTGCAACTTCAGGGAGATAAGAC-TAGT-GGTTTAATCTG
** * *
11895 CTCCATTTCAACTTTAGGGAGATAAGACTAGTGGTTTCAATCTG
1 CTCCGCTGCAACTTCAGGGAGATAAGACTAGTGGTTT-AATCTG
* * * * * * * * *
11939 CTTCGCTGCAACTTCAAGAAAATAAGATTCGCCGTATTTGATCTG
1 CTCCGCTGCAACTTCAGGGAGATAAGACTAG-TG-GTTTAATCTG
* * * * *
11984 CTCCGTTGTAACTTCAGGGAGATAAGACTAGTGACTTTAACCTA
1 CTCCGCTGCAACTTCAGGGAGATAAGACTAGTG-GTTTAATCTG
* *
12028 CTCCACTGCAACTTTAGGGAGATAA
1 CTCCGCTGCAACTTCAGGGAGATAA
12053 CATTTGTAAT
Statistics
Matches: 117, Mismatches: 37, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
43 5 0.04
44 80 0.68
45 29 0.25
46 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
CTCCGCTGCAACTTCAGGGAGATAAGACTAGTGGTTTAATCTG
Found at i:11968 original size:227 final size:229
Alignment explanation
Indices: 11335--11968 Score: 640
Period size: 227 Copynumber: 2.8 Consensus size: 229
11325 AAGGTTTGTG
* * *
11335 GCTTCAATCTACTCTACTACAACTTCAGAGAGATAAGATTTGCTATATTCAGTCTATTCCACTGC
1 GCTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATATTCAGTCTACTCCACTGC
* *
11400 AACTTCAGGGAGATAAGACTTGCATCTTCAACCTGCTCCATTGT-AACTTCAGGGAGATAAGGTT
66 AACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCATT-TCAACTTCAGGGAGATAAGGTT
* * * * * * * * *
11464 AATGACCT-ACATCTAC-TCCATGAAATTTTAGGGAGATAAAATTCACCATGATAGATTTGATCC
130 AGTGGCTTCA-ATCT-CTTCC-TGCAACTTCAAGAAGATAAGATTCACCATGATAGATTTGATCC
*
11527 GACCCACTGCGACTTCAGAGGTATAGGACTTGTAACTCGTA
192 GACCCACTGCAACTTCAGAGGTATAGGACTTGTAA--C-TA
* * * * *
11568 GCTTTAACCTATTCCACTGCAACTTCAG-GAAAATAAGATTTACTATATTCAGTCTAC-CCTACT
1 GCTTTAATCTACTCTACTGCAACTTCAGAG-AGATAAGATTTGCTATATTCAGTCTACTCC-ACT
* * * * * * * *
11631 GTAATTTCGGGGGGCTAAGACTTGTAACTTCAACCTGCTCTACTGCAACTTCAGGGAGATAAGGT
64 GCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCATTTCAACTTCAGGGAGATAAGGT
* * * * *
11696 TAGTGGCTTCGATCTATTCCACTGCAACTTC-AGAGAGACAAGATTCATCATGGTAGATTTGATC
129 TAGTGGCTTCAATCTCTT-C-CTGCAACTTCAAGA-AGATAAGATTCACCATGATAGATTTGATC
* **
11760 CGATCTGCTGCAACTTCAGAGGTATAGGA-TT-T-A-TA
191 CGACCCACTGCAACTTCAGAGGTATAGGACTTGTAACTA
* * * * *
11795 GCTTTAATCTGCTCTACTGCAACTTCCGAGAGATAAGATTCGCTATCTTGAGTCTACTCCACTGC
1 GCTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATATTCAGTCTACTCCACTGC
* * * **
11860 AACTTCAGGGAGATAAGACTTATAACTTTAACCTGCTCCATTTCAACTTTAGGGAGATAAGACTA
66 AACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCATTTCAACTTCAGGGAGATAAGGTTA
* *
11925 GTGGTTTCAATCTGCTTCGCTGCAACTTCAAGAAAATAAGATTC
131 GTGGCTTCAATCT-CTTC-CTGCAACTTCAAGAAGATAAGATTC
11969 GCCGTATTTG
Statistics
Matches: 324, Mismatches: 65, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
227 135 0.42
228 8 0.02
231 1 0.00
232 4 0.01
233 118 0.36
234 57 0.18
235 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (229 bp):
GCTTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATATTCAGTCTACTCCACTGC
AACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCATTTCAACTTCAGGGAGATAAGGTTA
GTGGCTTCAATCTCTTCCTGCAACTTCAAGAAGATAAGATTCACCATGATAGATTTGATCCGACC
CACTGCAACTTCAGAGGTATAGGACTTGTAACTA
Found at i:12193 original size:44 final size:44
Alignment explanation
Indices: 12130--12288 Score: 183
Period size: 44 Copynumber: 3.5 Consensus size: 44
12120 TCTTCCCCAC
*
12130 TGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTACTCCAG
1 TGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTACTCCAA
* * ** * *
12174 TGCAACTTCAGGGAGATAAGGTTTGGTATTTGTAACTTCAGTCTGCTCCAC
1 TGCAACTTCAGGGAGATAA------G-ACTAGTAACTTCAACCTACTCCAA
12225 TGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTACTCCAA
1 TGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTACTCCAA
*
12269 TGTAACTTCAGGGAGATAAG
1 TGCAACTTCAGGGAGATAAG
12289 GTTTATGGAT
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
44 56 0.59
45 1 0.01
50 1 0.01
51 37 0.39
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTACTCCAA
Found at i:12232 original size:140 final size:136
Alignment explanation
Indices: 11802--12245 Score: 429
Period size: 140 Copynumber: 3.2 Consensus size: 136
11792 ATAGCTTTAA
* *
11802 TCTGCTCTACTGCAACTTCCGAGAGATAAGATTCGCTATCTTGAGTCTACTCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGCTAT-TTGAGTCTACTCCACTGCAACTTCA
* * * ** * *
11867 GGGAGATAAGACTTA-TAACTTTAACCTGCTCCATTTCAACTTTAGGGAGATAAG--ACTAGTGG
65 GGGAGATAAGAC-TAGTAACTTTAACCTACTCCACTGCAACTTTAGGGAGATAAGTTTGTATTTG
*
11929 T--TTCAA
129 TACTTCAG
* * * * ** *
11935 TCTGCTTCGCTGCAACTTCA-AGAAAATAAGATTCGCCGTATTTGA-TCTGCTCCGTTGTAACTT
1 TCTGCTCCACTGCAACTTCAGAG-AGATAAGATTCG-C-TATTTGAGTCTACTCCACTGCAACTT
* *
11998 CAGGGAGATAAGACTAGTGACTTTAACCTACTCCACTGCAACTTTAGGGAGATAACATTTGTAAT
63 CAGGGAGATAAGACTAGTAACTTTAACCTACTCCACTGCAACTTTAGGGAGATAA-GTTTGT-AT
* *
12063 ATGTAGCTT-TG
126 TTGTA-CTTCAG
* * * * *
12074 ATCTACTCTACTGTAACTTCAGAGAGATAAGA-TCTGCTATTTGTAGTCTTCCCCACTGCAACTT
1 -TCTGCTCCACTGCAACTTCAGAGAGATAAGATTC-GCTATTTG-AGTCTACTCCACTGCAACTT
* * *
12138 CAGGGAGATAAGACTAGTAACTTCAACCTACTCCAGTGCAACTTCAGGGAGATAAGGTTTGGTAT
63 CAGGGAGATAAGACTAGTAACTTTAACCTACTCCACTGCAACTTTAGGGAGATAA-GTTT-GTAT
12203 TTGTAACTTCAG
126 TTGT-ACTTCAG
*
12215 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGA
12246 CTAGTAACTT
Statistics
Matches: 248, Mismatches: 44, Indels: 31
0.77 0.14 0.10
Matches are distributed among these distances:
132 4 0.02
133 89 0.36
134 5 0.02
135 3 0.01
136 1 0.00
137 3 0.01
138 6 0.02
139 4 0.02
140 127 0.51
141 6 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (136 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGCTATTTGAGTCTACTCCACTGCAACTTCAG
GGAGATAAGACTAGTAACTTTAACCTACTCCACTGCAACTTTAGGGAGATAAGTTTGTATTTGTA
CTTCAG
Found at i:12487 original size:92 final size:93
Alignment explanation
Indices: 12330--12509 Score: 326
Period size: 92 Copynumber: 1.9 Consensus size: 93
12320 TCTTGCAACA
*
12330 CCATTAATCAAAAAACAGAACAGAAGTTTCGAAAATCTTGATCTTTTCACTATCTATTTTCATTT
1 CCATTAATCAAAAAACAGAACAGAAGTTTCGAAAAACTTGATCTTTTCACTATCTATTTTCATTT
*
12395 TTTT-CTTTTTTTATTTTATTTTTTTAT
66 TTTTGCTTATTTTATTTTATTTTTTTAT
*
12422 CCATTAATCAAAAAACAGAACAGAAGTTTCGAAAAAGTTGATCTTTTCACTATCTATTTTCATTT
1 CCATTAATCAAAAAACAGAACAGAAGTTTCGAAAAACTTGATCTTTTCACTATCTATTTTCATTT
12487 TTTTGCTTATTTTATTTTATTTT
66 TTTTGCTTATTTTATTTTATTTT
12510 ATTTTATTTT
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
92 67 0.80
93 17 0.20
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.49
Consensus pattern (93 bp):
CCATTAATCAAAAAACAGAACAGAAGTTTCGAAAAACTTGATCTTTTCACTATCTATTTTCATTT
TTTTGCTTATTTTATTTTATTTTTTTAT
Found at i:12503 original size:5 final size:5
Alignment explanation
Indices: 12493--12519 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12483 ATTTTTTTGC
12493 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
12520 TATGACACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:13392 original size:21 final size:22
Alignment explanation
Indices: 13355--13395 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13345 ATTTATTTAT
*
13355 TTATTTTAAAATGTTTTATATG
1 TTATTTTAAAATATTTTATATG
13377 TTATTTT-AAATATTTTATA
1 TTATTTTAAAATATTTTATA
13396 GGCTGTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
TTATTTTAAAATATTTTATATG
Found at i:13722 original size:25 final size:26
Alignment explanation
Indices: 13667--13723 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
13657 TTTATTATTT
*
13667 TTAAAATTGACTTATATATTATTTATT
1 TTAAAATTGA-TTATATATTATTTATG
*
13694 TTAAAATTG-TTTTATA-TATCTTATG
1 TTAAAATTGATTATATATTAT-TTATG
13719 TTAAA
1 TTAAA
13724 CTCTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 3 0.11
25 15 0.56
27 9 0.33
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (26 bp):
TTAAAATTGATTATATATTATTTATG
Found at i:13799 original size:25 final size:25
Alignment explanation
Indices: 13748--13805 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
13738 TTAAAAATGG
***
13748 TTTTAT-TATTATTTACTTTAGGTT
1 TTTTATATATTATTTACTTTACACT
*
13772 TTTTATATATTATTTATTTTACACT
1 TTTTATATATTATTTACTTTACACT
13797 TTTGTATAT
1 TTT-TATAT
13806 GTATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 6 0.21
25 17 0.61
26 5 0.18
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (25 bp):
TTTTATATATTATTTACTTTACACT
Found at i:13915 original size:52 final size:49
Alignment explanation
Indices: 13859--13956 Score: 115
Period size: 52 Copynumber: 1.9 Consensus size: 49
13849 TTTTTAATTT
* * *
13859 GCTTTGTGTAATATAGATTTTAAAATTCTTTTACATTATTTATTTTAAACTC
1 GCTTTATGTAATATACATTTT-AAATTCTTTT--ATTATTTACTTTAAACTC
* * *
13911 GCTTTATGTATTATTCATTTTAAATTGTTTTATTATTTACTTTAAA
1 GCTTTATGTAATATACATTTTAAATTCTTTTATTATTTACTTTAAA
13957 ATTTTATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
49 14 0.35
51 9 0.22
52 17 0.43
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (49 bp):
GCTTTATGTAATATACATTTTAAATTCTTTTATTATTTACTTTAAACTC
Found at i:16098 original size:130 final size:130
Alignment explanation
Indices: 15865--16195 Score: 424
Period size: 130 Copynumber: 2.6 Consensus size: 130
15855 TAATTATTCA
* ** * *
15865 TTTAAAAATTCTTTAAAACGAAGGCAATACTCGATGTTTGGTAATT-TGGGAATCGTGCCCTATC
1 TTTAAAAATTC-TTAAAACGAAGGTAATGTTCGATG-TTGGAAATTCGGGGAATCGTGCCCTATC
* * * *
15929 GTGTTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCGAATATTCCTTTGGAATTTCGCTCATG-
64 GTGCTGGGTTGCGATTTCCTATTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCACTCATGT
15993 TC
129 TC
* *
15995 TTTAAAAATCCTTCAAAACGAAGGTAATGTTCGATGTTGGCAATTCGGGGAATCGTGCCCTATCG
1 TTTAAAAATTCTT-AAAACGAAGGTAATGTTCGATGTTGGAAATTCGGGGAATCGTGCCCTATCG
*
16060 TGCTGGGTTGCGATTTCCTATTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGTT
65 TGCTGGGTTGCGATTTCCTATTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCACTCATGTT
16125 C
130 C
* * * *
16126 TTT--AAATTC-TAAAA-TAAGGTAATGTCCGATGTCTAGAAATTCGAGGAATCGTGCCCTA-CT
1 TTTAAAAATTCTTAAAACGAAGGTAATGTTCGATGT-TGGAAATTCGGGGAATCGTGCCCTATC-
16186 GTGCTGGGTT
64 GTGCTGGGTT
16196 TTGATTGTAA
Statistics
Matches: 179, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
126 17 0.09
127 36 0.20
128 1 0.01
129 15 0.08
130 105 0.59
131 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (130 bp):
TTTAAAAATTCTTAAAACGAAGGTAATGTTCGATGTTGGAAATTCGGGGAATCGTGCCCTATCGT
GCTGGGTTGCGATTTCCTATTTGTTCAAAACAATCGAATATTCCTTTAGAATTTCACTCATGTTC
Found at i:16553 original size:26 final size:26
Alignment explanation
Indices: 16524--16633 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
16514 TGGTACAAAT
16524 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
16550 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
16576 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
16602 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
16628 TGATAA
1 TGATAA
16634 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:18117 original size:28 final size:26
Alignment explanation
Indices: 18075--18149 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
18065 AAAAGTAGCT
* * *
18075 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
*
18103 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
18129 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
18150 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.55
27 1 0.02
28 18 0.43
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:18294 original size:27 final size:27
Alignment explanation
Indices: 18253--18379 Score: 182
Period size: 27 Copynumber: 4.7 Consensus size: 27
18243 GAGGAAGCGT
*
18253 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
18280 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
18307 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
18334 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* *
18362 TCTGGTGACTCTGTCACA
1 TCTGGTGGCTCTGCCACA
18380 TTATCTGTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 74 0.83
28 15 0.17
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:19927 original size:52 final size:49
Alignment explanation
Indices: 19871--19968 Score: 115
Period size: 52 Copynumber: 1.9 Consensus size: 49
19861 TTTTTAATTT
* * *
19871 GCTTTGTGTAATATAGATTTTAAAATTCTTTTACATTATTTATTTTAAACTC
1 GCTTTATGTAATATACATTTT-AAATTCTTTT--ATTATTTACTTTAAACTC
* * *
19923 GCTTTATGTATTATTCATTTTAAATTGTTTTATTATTTACTTTAAA
1 GCTTTATGTAATATACATTTTAAATTCTTTTATTATTTACTTTAAA
19969 ATTTTATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
49 14 0.35
51 9 0.22
52 17 0.43
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (49 bp):
GCTTTATGTAATATACATTTTAAATTCTTTTATTATTTACTTTAAACTC
Found at i:32127 original size:12 final size:12
Alignment explanation
Indices: 32106--32135 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
32096 CTACACTGGT
32106 GTGTGCCTGGCC
1 GTGTGCCTGGCC
*
32118 GTGTGGCTGGCC
1 GTGTGCCTGGCC
32130 GTGTGC
1 GTGTGC
32136 GAGACACGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.47, T:0.27
Consensus pattern (12 bp):
GTGTGCCTGGCC
Found at i:34985 original size:6 final size:6
Alignment explanation
Indices: 34974--35015 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
34964 ATAGATAAAT
34974 AAAAAG AAAAAG AAAAATAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG --AAA-AAG AAAAAG AAAAAG AAAAAG AAA
35016 GAAAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 24 0.73
7 3 0.09
8 3 0.09
9 3 0.09
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:34997 original size:15 final size:15
Alignment explanation
Indices: 34977--35020 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
34967 GATAAATAAA
*
34977 AAGAAAAAGAAAAAT
1 AAGAAAAAGAAAAAG
34992 AAGAAAAAGAAAAAG
1 AAGAAAAAGAAAAAG
*
35007 AAAAAGAAAGAAAA
1 AAGAA-AAAGAAAA
35021 TTTTTTACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
AAGAAAAAGAAAAAG
Found at i:35000 original size:21 final size:22
Alignment explanation
Indices: 34974--35020 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
34964 ATAGATAAAT
*
34974 AAAAAGAAAAAGAAAAA-TAAG
1 AAAAAGAAAAAGAAAAAGAAAG
34995 AAAAAGAAAAAGAAAAAGAAAG
1 AAAAAGAAAAAGAAAAAGAAAG
35017 AAAA
1 AAAA
35021 TTTTTTACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAAGAAAAAGAAAG
Found at i:35812 original size:17 final size:18
Alignment explanation
Indices: 35790--35823 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
35780 ATTATTAATA
35790 ATTATTTTTTAA-ACATT
1 ATTATTTTTTAATACATT
35807 ATTATTTTTTAATACAT
1 ATTATTTTTTAATACAT
35824 GCATATGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATTTTTTAATACATT
Found at i:36443 original size:3 final size:3
Alignment explanation
Indices: 36396--36428 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
36386 TACATACATC
*
36396 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36429 GTATATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:36460 original size:21 final size:21
Alignment explanation
Indices: 36417--36478 Score: 56
Period size: 25 Copynumber: 2.8 Consensus size: 21
36407 ATTATAATTA
*
36417 TTATTAT-TAT-TAGTATATGT
1 TTATTATATATGTA-TATATCT
36437 TTATTATATATGTATATATCT
1 TTATTATATATGTATATATCT
36458 TTAACATATATATATGTATAT
1 TT---AT-TATATATGTATAT
36479 GTTTATGCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 7 0.20
21 11 0.31
22 2 0.06
24 2 0.06
25 13 0.37
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (21 bp):
TTATTATATATGTATATATCT
Found at i:36580 original size:23 final size:22
Alignment explanation
Indices: 36530--36637 Score: 67
Period size: 25 Copynumber: 4.6 Consensus size: 22
36520 TTATTTCTAA
36530 TATGTATATATATATTAACAACTATAT
1 TATGTATATAT-T-TTAAC-AC--TAT
*
36557 TATGTATGTATTCTTAACACTATTT
1 TATGTATATATT-TTAACACTA--T
* *
36582 TATGTATATACTTTTAATATTAT
1 TATGTATATA-TTTTAACACTAT
* *
36605 TATGTATTTATTTTAATA-TA-
1 TATGTATATATTTTAACACTAT
*
36625 TATGTACATATTT
1 TATGTATATATTT
36638 ATGTAGCATT
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
20 11 0.16
21 2 0.03
22 8 0.11
23 12 0.17
25 19 0.27
26 8 0.11
27 10 0.14
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (22 bp):
TATGTATATATTTTAACACTAT
Found at i:36584 original size:25 final size:27
Alignment explanation
Indices: 36530--36591 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 27
36520 TTATTTCTAA
36530 TATGTATATATATATTAACAACTATAT
1 TATGTATATATATATTAACAACTATAT
* * *
36557 TATGTATGTAT-TCTTAAC-ACTATTT
1 TATGTATATATATATTAACAACTATAT
36582 TATGTATATA
1 TATGTATATA
36592 CTTTTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 15 0.48
26 6 0.19
27 10 0.32
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.48
Consensus pattern (27 bp):
TATGTATATATATATTAACAACTATAT
Found at i:36636 original size:20 final size:22
Alignment explanation
Indices: 36554--36637 Score: 75
Period size: 22 Copynumber: 3.7 Consensus size: 22
36544 TTAACAACTA
*
36554 TATTATGTATGTATTCTTAACACTAT
1 TATTATGTATATATT-TT-A-A-TAT
36580 T-TTATGTATATACTTTTAATAT
1 TATTATGTATATA-TTTTAATAT
*
36602 TATTATGTATTTATTTTAATA-
1 TATTATGTATATATTTTAATAT
*
36623 TA-TATGTACATATTT
1 TATTATGTATATATTT
36638 ATGTAGCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 11 0.21
21 2 0.04
22 12 0.23
23 11 0.21
24 1 0.02
25 12 0.23
26 3 0.06
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (22 bp):
TATTATGTATATATTTTAATAT
Found at i:36743 original size:15 final size:15
Alignment explanation
Indices: 36698--36737 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
36688 ATGTTCATTT
*
36698 TATATATATTATGTG
1 TATATATATTATGTA
*
36713 TACATATATTATGTA
1 TATATATATTATGTA
36728 TATATATATT
1 TATATATATT
36738 TAGTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
TATATATATTATGTA
Found at i:40145 original size:42 final size:46
Alignment explanation
Indices: 40084--40204 Score: 144
Period size: 49 Copynumber: 2.7 Consensus size: 46
40074 CTTCGTTTTC
**
40084 TCGATGCCATAGTTCAACTATGGTCTTACAC-AT-C-T-TCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACAATACATATCACAT-A
40127 T-GATGCCATAGCCCAACTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC--AAT-ACATATCACATA
*
40175 TCGATGCCATAGCCCAGCTATGGTCTTACA
1 TCGATGCCATAGCCCAACTATGGTCTTACA
40205 TGAATCGCAT
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
42 27 0.40
43 1 0.01
45 2 0.03
47 1 0.01
48 3 0.04
49 33 0.49
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (46 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACAATACATATCACATA
Found at i:40185 original size:49 final size:47
Alignment explanation
Indices: 40119--40248 Score: 156
Period size: 49 Copynumber: 2.7 Consensus size: 47
40109 TTACACATCT
40119 TCACATAATGATGCCATAGCCCAACTATGGTCTTACACGTAATCACATA
1 TCACAT-ATGATGCCATAGCCCAACTATGGTCTTACACG-AATCACATA
* * *
40168 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACATGAATCGCATA
1 TCACATAT-GATGCCATAGCCCAACTATGGTCTTACACGAATCACATA
* * *
40216 TCTCA-CTGATGCCATATCCCAGA-TATGGTCTTA
1 TCACATATGATGCCATAGCCCA-ACTATGGTCTTA
40249 TACAGTAGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
46 23 0.32
47 1 0.01
48 14 0.19
49 34 0.47
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (47 bp):
TCACATATGATGCCATAGCCCAACTATGGTCTTACACGAATCACATA
Found at i:40359 original size:31 final size:31
Alignment explanation
Indices: 40324--40564 Score: 367
Period size: 31 Copynumber: 7.8 Consensus size: 31
40314 CTTGTCACTT
* *
40324 GTAGCCGGAGCTGCCACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
40355 GTAGCCGGAGCTACCACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
40386 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* * *
40417 GTAACC-AAGATACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
40447 GTAGCAGCAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
40478 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
40509 GTAGCAGGAGCTACCGCTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
40540 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
40565 TTTCATTTGT
Statistics
Matches: 191, Mismatches: 18, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
30 25 0.13
31 166 0.87
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:43958 original size:22 final size:22
Alignment explanation
Indices: 43933--43988 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
43923 ATTCATGACT
*
43933 AACATTCATTCGTCATTTATTC
1 AACATTCATTCGTCATTCATTC
*
43955 AACATTCATTTGTCATTCATTC
1 AACATTCATTCGTCATTCATTC
*
43977 ATTCATTCATTC
1 A-ACATTCATTC
43989 ATTGTATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (22 bp):
AACATTCATTCGTCATTCATTC
Found at i:43974 original size:4 final size:4
Alignment explanation
Indices: 43967--43991 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
43957 CATTCATTTG
43967 TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT T
43992 GTATGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:50976 original size:31 final size:30
Alignment explanation
Indices: 50931--50998 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
50921 ATCTAATTTT
*
50931 TTTTGTCCAATTTGGAACCCAAACTTGACAA
1 TTTT-TCCAATTTGGAACACAAACTTGACAA
* * *
50962 TTTTTCCTAATTTGGTACATAAACTTGACAC
1 TTTTTCC-AATTTGGAACACAAACTTGACAA
50993 TTTTTC
1 TTTTTC
50999 TTAAGTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (30 bp):
TTTTTCCAATTTGGAACACAAACTTGACAA
Found at i:51016 original size:31 final size:31
Alignment explanation
Indices: 50951--51018 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
50941 TTTGGAACCC
* *
50951 AAACTTGACAATTTTTCCTAATTTGGTACAT
1 AAACTTGACAATTTTTCCTAAGTTGATACAT
* * *
50982 AAACTTGACACTTTTTCTTAAGTTGATACTT
1 AAACTTGACAATTTTTCCTAAGTTGATACAT
51013 AAACTT
1 AAACTT
51019 TTTCGGGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (31 bp):
AAACTTGACAATTTTTCCTAAGTTGATACAT
Found at i:63888 original size:64 final size:65
Alignment explanation
Indices: 63808--63934 Score: 220
Period size: 65 Copynumber: 2.0 Consensus size: 65
63798 ATAAAATCCT
63808 GAAAACCGATTGTAAAGGGG-TACCATTTTTGAAAAACATAGAAGAAAATATACAAAAAAAAAAA
1 GAAAACCGATTGTAAAGGGGTTACCATTTTTGAAAAACATAGAAGAAAATATACAAAAAAAAAAA
* * *
63872 GAAAATCGATTGTAAAGGGGTTCCCCTTTTTGAAAAACATAGAAGAAAATATACAAAAAAAAA
1 GAAAACCGATTGTAAAGGGGTTACCATTTTTGAAAAACATAGAAGAAAATATACAAAAAAAAA
63935 GATTGAATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 19 0.32
65 40 0.68
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.20
Consensus pattern (65 bp):
GAAAACCGATTGTAAAGGGGTTACCATTTTTGAAAAACATAGAAGAAAATATACAAAAAAAAAAA
Found at i:64805 original size:4 final size:4
Alignment explanation
Indices: 64796--64833 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
64786 AATTGAGTCT
* *
64796 TTTA TTTA TTTA TTTA TTTA CTTA TTTA CTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
64834 AGTTTTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:64915 original size:17 final size:17
Alignment explanation
Indices: 64895--64927 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
64885 TATTGTTCCT
64895 TTTTTACTTTT-TTTTTA
1 TTTTTA-TTTTCTTTTTA
64912 TTTTTATTTTCTTTTT
1 TTTTTATTTTCTTTTT
64928 GTGCCTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTATTTTCTTTTTA
Found at i:64956 original size:39 final size:40
Alignment explanation
Indices: 64869--64959 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 40
64859 AAAACTGTTT
* * ** **
64869 TTATTTTATTTTCCTTTATTGTTCCTTTTTTACTTTTTTT
1 TTATTTTATTTTCCTTTATTGTGCCTTTGTTACTTGATCA
64909 TTATTTTTATTTT-CTTT-TTGTGCCTTTGTTATCTTGATCA
1 TTA-TTTTATTTTCCTTTATTGTGCCTTTGTTA-CTTGATCA
64949 TTATTTTATTT
1 TTATTTTATTT
64960 ATTATTATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
39 20 0.47
40 14 0.33
41 9 0.21
ACGTcount: A:0.12, C:0.11, G:0.05, T:0.71
Consensus pattern (40 bp):
TTATTTTATTTTCCTTTATTGTGCCTTTGTTACTTGATCA
Found at i:80478 original size:19 final size:19
Alignment explanation
Indices: 80438--80481 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
80428 CTAAATTGAT
* **
80438 CTATTTAATAATAAAATTA
1 CTATTTAAGAATAAAAGGA
80457 CTATTTAAGAATAAAAGGA
1 CTATTTAAGAATAAAAGGA
80476 CTATTT
1 CTATTT
80482 TATATCAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (19 bp):
CTATTTAAGAATAAAAGGA
Found at i:86128 original size:29 final size:31
Alignment explanation
Indices: 86072--86130 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
86062 TCATAGGGTG
86072 ATAGCAATATGTATATATTAGCCTCTTTTTT
1 ATAGCAATATGTATATATTAGCCTCTTTTTT
*
86103 ATAGCAATATGTATATGTTAGCCT-TTTT
1 ATAGCAATATGTATATATTAGCCTCTTTT
86131 GAGCTCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (31 bp):
ATAGCAATATGTATATATTAGCCTCTTTTTT
Found at i:95313 original size:23 final size:23
Alignment explanation
Indices: 95274--95321 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
95264 CTGTAAATCT
95274 TATAAAAATAGTAAAAAATTATA
1 TATAAAAATAGTAAAAAATTATA
* *
95297 TATAAATATA-TATAAAAATTTTA
1 TATAAAAATAGTA-AAAAATTATA
95320 TA
1 TA
95322 AGGTAGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TATAAAAATAGTAAAAAATTATA
Found at i:95564 original size:10 final size:10
Alignment explanation
Indices: 95544--95633 Score: 62
Period size: 10 Copynumber: 9.4 Consensus size: 10
95534 TTTGATATAC
*
95544 TTTATAGTTT
1 TTTATAATTT
*
95554 TTTATGA-TT
1 TTTATAATTT
**
95563 TTTATAAAAT
1 TTTATAATTT
*
95573 TTTAAAATTT
1 TTTATAATTT
*
95583 TTTATAATAT
1 TTTATAATTT
**
95593 TTTACGA-TT
1 TTTATAATTT
95602 TTTATAA-TT
1 TTTATAATTT
95611 TTT-TAATTT
1 TTTATAATTT
* *
95620 TTAATAAATT
1 TTTATAATTT
95630 TTTA
1 TTTA
95634 ATATTTTTAT
Statistics
Matches: 60, Mismatches: 17, Indels: 6
0.72 0.20 0.07
Matches are distributed among these distances:
8 3 0.05
9 23 0.38
10 34 0.57
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTATAATTT
Found at i:95566 original size:19 final size:19
Alignment explanation
Indices: 95553--95643 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 19
95543 CTTTATAGTT
* *
95553 TTTTATGATTTTTATAAAA
1 TTTTAAGATTTTTATAATA
*
95572 TTTTAAAATTTTTTATAATA
1 TTTTAAGA-TTTTTATAATA
*
95592 TTTTACGATTTTTATAAT-
1 TTTTAAGATTTTTATAATA
*
95610 TTTTTA-ATTTTTAATAA-A
1 TTTTAAGATTTTT-ATAATA
*
95628 TTTTTAATATTTTTAT
1 -TTTTAAGATTTTTAT
95644 TAAAATTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
17 6 0.10
18 8 0.14
19 23 0.39
20 22 0.37
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTAAGATTTTTATAATA
Found at i:95659 original size:20 final size:21
Alignment explanation
Indices: 95614--95659 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
95604 TATAATTTTT
*
95614 TAATTTTTAATAAATTTTTAA
1 TAATTTTTAATAAATATTTAA
*
95635 T-ATTTTTATTAAA-ATTTAA
1 TAATTTTTAATAAATATTTAA
95654 TAATTT
1 TAATTT
95660 AATATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 6 0.27
20 15 0.68
21 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTTAATAAATATTTAA
Found at i:101939 original size:8 final size:8
Alignment explanation
Indices: 101926--101950 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
101916 GATAAAAAAG
101926 AAATAATT
1 AAATAATT
101934 AAATAATT
1 AAATAATT
101942 AAATAATT
1 AAATAATT
101950 A
1 A
101951 TTTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATAATT
Found at i:105252 original size:19 final size:19
Alignment explanation
Indices: 105228--105265 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
105218 CAATACATAA
105228 TCATTTTCGGGTTTTATAT
1 TCATTTTCGGGTTTTATAT
105247 TCATTTTCGGGTTTTATAT
1 TCATTTTCGGGTTTTATAT
105266 GAGCTTACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (19 bp):
TCATTTTCGGGTTTTATAT
Done.