Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3793
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: 41554
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:446 original size:36 final size:36
Alignment explanation
Indices: 387--463 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
377 TTATTACGAA
* * * * *
387 GTCTTACCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGACAAAATCCCCACACGAAGTCATCAG
*
423 GTCTTACCCGACAAAATCCCCACACGTAGTCATCAG
1 GTCTTACCCGACAAAATCCCCACACGAAGTCATCAG
459 GTCTT
1 GTCTT
464 TAGAGCTCGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (36 bp):
GTCTTACCCGACAAAATCCCCACACGAAGTCATCAG
Found at i:779 original size:46 final size:47
Alignment explanation
Indices: 578--1042 Score: 669
Period size: 46 Copynumber: 10.1 Consensus size: 47
568 GCCCTTCGGA
* * * * * *
578 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-C
* *
626 CTGCA-CATATATATACACTTTCACATTCATCACATCGGCCATTA--C
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
671 C-T-TCACATATATTACCACTTTCACATTCA-CACATCGGCCA-TAGGC
1 CTTATCACATATA-TA-CACTTTCACATTCATCACATCGGCCATTAGGC
716 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
763 CCTATCACATAT-TACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
808 CTTATCACATATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
854 C-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTA-GC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
901 CTTATCAC--ATATACAC-TTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
944 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
990 CTTATCACATA-ATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1036 CTTATCA
1 CTTATCA
1043 TCATTTCATA
Statistics
Matches: 383, Mismatches: 12, Indels: 46
0.87 0.03 0.10
Matches are distributed among these distances:
42 5 0.01
43 38 0.10
44 21 0.05
45 98 0.26
46 112 0.29
47 61 0.16
48 47 0.12
49 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:934 original size:182 final size:184
Alignment explanation
Indices: 580--1042 Score: 671
Period size: 182 Copynumber: 2.5 Consensus size: 184
570 CCTTCGGACT
* * * * ** * *
580 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGCA-CATATATATACAC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAG-CCT-TATCACATATATACAC
644 TTTCACATTCATCACATCGGCCATTA--CCT-TCACATATATTACCACTTTCACATTCACACATC
63 TTTCACATTCATCACATCGGCCATTAGGCCTATCACATATATTACCACTTTCACATTCACACATC
706 GGCCATAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
128 GGCCATAGGCCTTATCACA-ATATACACTTTCACATTCATCACATCGG-CATTAGGCCC
765 TATCACATAT-TACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATACACTT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTTATCACATATATACACTT
828 TCACATTCATCACATC-GCCATTAGGCCTATCACATATATATA-CACTTTCACATTCATCACATC
65 TCACATTCATCACATCGGCCATTAGGCCTATCACATATAT-TACCACTTTCACATTCA-CACATC
*
891 GGCCATTA-GCCTTATCAC-ATATACAC-TTCACATTCATCACATCGGCATTAGGCCT
128 GGCCA-TAGGCCTTATCACAATATACACTTTCACATTCATCACATCGGCATTAGGCCC
946 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTTATCACATA-ATACACTTT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTTATCACATATATACACTTT
1010 CACATTCATCACATCGGCCATTAGGCCTTATCA
66 CACATTCATCACATCGGCCATTAGGCC-TATCA
1043 TCATTTCATA
Statistics
Matches: 257, Mismatches: 9, Indels: 26
0.88 0.03 0.09
Matches are distributed among these distances:
181 51 0.20
182 102 0.40
183 24 0.09
184 46 0.18
185 32 0.12
186 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (184 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGCCTTATCACATATATACACTTT
CACATTCATCACATCGGCCATTAGGCCTATCACATATATTACCACTTTCACATTCACACATCGGC
CATAGGCCTTATCACAATATACACTTTCACATTCATCACATCGGCATTAGGCCC
Found at i:4522 original size:39 final size:39
Alignment explanation
Indices: 4468--4653 Score: 200
Period size: 39 Copynumber: 4.8 Consensus size: 39
4458 ACACGTCACC
* * *
4468 AGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACC
1 AGCATGA-TGCTCTTCGGGACTTAGCCCGGATACAACACT
* * * *
4508 AGCACGATGCTCTTCGGG-TTTAGCACGGATA-TACACT
1 AGCATGATGCTCTTCGGGACTTAGCCCGGATACAACACT
* * *
4545 AGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACT
1 AGCATG-ATGCTCTTCGGGACTTAGCCCGGATACAACACT
* * *
4585 AGCATAATGCTCTTCGGAACTTAGCCCGGATACATCACT
1 AGCATGATGCTCTTCGGGACTTAGCCCGGATACAACACT
4624 AGCATGAATGCTCTTC-GGAC-TAGCCCGGAT
1 AGCATG-ATGCTCTTCGGGACTTAGCCCGGAT
4654 TTAGTAACTC
Statistics
Matches: 127, Mismatches: 15, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
37 10 0.08
38 31 0.24
39 63 0.50
40 23 0.18
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
AGCATGATGCTCTTCGGGACTTAGCCCGGATACAACACT
Found at i:4571 original size:77 final size:77
Alignment explanation
Indices: 4476--4653 Score: 216
Period size: 77 Copynumber: 2.3 Consensus size: 77
4466 CCAGCATGAT
* * ** *
4476 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGATGCTCTTCGG-GTTTAGCACGGATAT
1 TGCTCTTC-GGA-CTAGCCCGGATACAACACCAGCACAATGCTCTTCGGAACTTAGCACGGATAC
4540 A-CACTAGCACGAA
64 ATCACTAGCACGAA
* * * *
4553 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATAATGCTCTTCGGAACTTAGCCCGGATAC
1 TGCTCTTCGG-AC-TAGCCCGGATACAACACCAGCACAATGCTCTTCGGAACTTAGCACGGATAC
*
4618 ATCACTAGCATGAA
64 ATCACTAGCACGAA
4632 TGCTCTTCGGACTAGCCCGGAT
1 TGCTCTTCGGACTAGCCCGGAT
4654 TTAGTAACTC
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
76 3 0.03
77 49 0.56
78 14 0.16
79 21 0.24
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (77 bp):
TGCTCTTCGGACTAGCCCGGATACAACACCAGCACAATGCTCTTCGGAACTTAGCACGGATACAT
CACTAGCACGAA
Found at i:4685 original size:37 final size:38
Alignment explanation
Indices: 4546--4762 Score: 128
Period size: 39 Copynumber: 5.6 Consensus size: 38
4536 ATATACACTA
* ** *
4546 GCACGAATGCTCTTCGGAACTTAGCCCGGATACA-TCACTA
1 GCACAAATGC-CTTCGG-ACTTAGCCCGGATTTAGT-ACTC
* ** *
4586 GCA-TAATGCTCTTCGGAACTTAGCCCGGATACA-TCACTA
1 GCACAAATGC-CTTCGG-ACTTAGCCCGGATTTAGT-ACTC
**
4625 GCATGAATGCTCTTCGGAC-TAGCCCGGATTTAGTAACTC
1 GCACAAATGC-CTTCGGACTTAGCCCGGATTTAGT-ACTC
*
4664 GCACCAATG-CTTCGG-CTTAGCCC-GA-TTAGTACTC
1 GCACAAATGCCTTCGGACTTAGCCCGGATTTAGTACTC
* * * *
4698 GCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTA
1 GCACAAATGCCTTCGGA-CTTAGCCCGGATTTAGT-AC-TC
4739 GCACAAA-GCCTTCGGGACTTAGCC
1 GCACAAATGCCTTC-GGACTTAGCC
4763 GGACATCATT
Statistics
Matches: 152, Mismatches: 14, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
34 12 0.08
35 11 0.07
36 3 0.02
37 19 0.12
38 13 0.09
39 54 0.36
40 29 0.19
41 11 0.07
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (38 bp):
GCACAAATGCCTTCGGACTTAGCCCGGATTTAGTACTC
Found at i:4712 original size:35 final size:38
Alignment explanation
Indices: 4630--4714 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 38
4620 CACTAGCATG
*
4630 AATGCTCTTCGGACTAGCCCGGATTTAGTAACTCGCACC
1 AATGC-CTTCGGACTAGCCCGGATTTAGTAACTCGCACA
4669 AATG-CTTCGG-CTTAGCCC-GA-TTAGT-ACTCGCACA
1 AATGCCTTCGGAC-TAGCCCGGATTTAGTAACTCGCACA
4703 AATGCCTTCGGA
1 AATGCCTTCGGA
4715 TCTTAGTCCG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
34 12 0.29
35 11 0.26
36 3 0.07
37 12 0.29
39 4 0.10
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (38 bp):
AATGCCTTCGGACTAGCCCGGATTTAGTAACTCGCACA
Found at i:5141 original size:30 final size:29
Alignment explanation
Indices: 5071--5150 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
5061 CTTAATAATC
*
5071 AACCACGCACACTTAGTGCCATGTACTTTA
1 AACC-CGCACACTTAGTGCCATGCACTTTA
*
5101 AACTCGCACACTTAGTGCCTATGCA-TTTCA
1 AACCCGCACACTTAGTGCC-ATGCACTTT-A
*
5131 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
5151 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 19 0.43
30 25 0.57
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCACTTTA
Found at i:5180 original size:14 final size:15
Alignment explanation
Indices: 5155--5183 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5145 GTGCCAATCT
5155 CACAACCGTGAACAC
1 CACAACCGTGAACAC
5170 CACAA-CGTGAACAC
1 CACAACCGTGAACAC
5184 TTATTGCCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.38, G:0.14, T:0.07
Consensus pattern (15 bp):
CACAACCGTGAACAC
Found at i:7094 original size:37 final size:36
Alignment explanation
Indices: 7044--7121 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 36
7034 TTATTACGAA
* * *
7044 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATC-G
*
7081 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
7117 GTCTT
1 GTCTT
7122 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 6 0.16
37 31 0.84
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (36 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCG
Found at i:7368 original size:47 final size:47
Alignment explanation
Indices: 7240--7623 Score: 630
Period size: 47 Copynumber: 8.1 Consensus size: 47
7230 CCCTTCGGGA
* * * * * *
7240 CTTATCACATTTAT-CACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7286 CCTGTCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7334 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7381 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7428 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7475 C-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7523 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7570 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7617 CTTATCA
1 CTTATCA
7624 TCATTTCATA
Statistics
Matches: 319, Mismatches: 12, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
46 22 0.07
47 214 0.67
48 74 0.23
49 9 0.03
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:7495 original size:142 final size:141
Alignment explanation
Indices: 7240--7623 Score: 630
Period size: 142 Copynumber: 2.7 Consensus size: 141
7230 CCCTTCGGGA
* * * * * * * *
7240 CTTATCACATTTAT-CACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
7304 AC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
7368 TCGGCCATTAGGC
129 TCGGCCATTAGGC
7381 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
7446 TTTCACATTCATCACATCGGCCATTAGGCC-TATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
7510 TCGGCCATTAGGC
129 TCGGCCATTAGGC
*
7523 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTTGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
7588 TTTCACATTCATCACATCGGCCATTAGGCCTTATCA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCA
7624 TCATTTCATA
Statistics
Matches: 229, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
140 16 0.07
141 42 0.18
142 166 0.72
143 5 0.02
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:7559 original size:189 final size:188
Alignment explanation
Indices: 7240--7623 Score: 671
Period size: 189 Copynumber: 2.0 Consensus size: 188
7230 CCCTTCGGGA
* * * * *
7240 CTTATCACATTTATCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATATACA
1 CTTATCACATATATCACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATATACA
7305 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
7370 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7428 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CCTATCACATATATATAC
1 CTTATCACATATAT-CACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATATAC
7492 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
65 AC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
7557 TCGGCCATTTGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7617 CTTATCA
1 CTTATCA
7624 TCATTTCATA
Statistics
Matches: 186, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
188 32 0.17
189 154 0.83
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACATATATCACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATATACA
CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11471 original size:27 final size:27
Alignment explanation
Indices: 11441--11665 Score: 213
Period size: 27 Copynumber: 8.3 Consensus size: 27
11431 TTAGTTTACC
*
11441 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* * * *
11468 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
11495 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
11522 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* *
11549 AAATTACCAAAATACCTCTGATTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
*** **
11576 AAATTATTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
** *
11603 AAATTACTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
* * *
11630 AAATTACCAAAGTACCCTTGATTTATA
1 AAATTACCAAAATACCCCTGATTTGTA
*
11657 GAATTACCA
1 AAATTACCA
11666 TTTTACCCTC
Statistics
Matches: 167, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.02
27 160 0.96
28 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:11672 original size:27 final size:27
Alignment explanation
Indices: 11642--11969 Score: 406
Period size: 27 Copynumber: 12.2 Consensus size: 27
11632 ATTACCAAAG
* *
11642 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
11669 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* ***
11696 TACCCTTGATTTACAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* * * *
11723 TACCCTCAATTTACAAAATGACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
11750 TACCCTCGATTTACAGAATAACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
11777 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
11804 TACCCTTGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
11831 TACCCTCAATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
11858 TACCCTCGATTTATA-AATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
11884 TACCCTCAATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
11911 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
11938 TACCCTCGATTTATAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
11965 TACCC
1 TACCC
11970 CTAGGGTGTT
Statistics
Matches: 261, Mismatches: 39, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 22 0.08
27 239 0.92
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:11689 original size:81 final size:79
Alignment explanation
Indices: 11604--11969 Score: 369
Period size: 81 Copynumber: 4.5 Consensus size: 79
11594 CGACCTGTAA
** *** ** *
11604 AATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTTGATTTATAGAATTACCATTT
1 AATTACTGATTTACCCTCGA-TT-TAAAATTACCATTTTACCCTCAATTTACAGAATTACCATTT
11669 TACCCTCGATTTACAG
64 TACCCTCGATTTACAG
* * *** * * *
11685 AATTA-TCGTTTTACCCTTGATTTACAGAATTATTGTTTTACCCTCAATTTACAAAATGACTATT
1 AATTACT-GATTTACCCTCGATTTA-A-AATTACCATTTTACCCTCAATTTACAGAATTACCATT
11749 TTACCCTCGATTTACAG
63 TTACCCTCGATTTACAG
* ** *
11766 AATAACT-ATTTTACCCTCGATTTACAAAATTACCATTTTACCCTTGATTTACAGAATTACCGTT
1 AATTACTGA-TTTACCCTCGATTT--AAAATTACCATTTTACCCTCAATTTACAGAATTACCATT
*
11830 TTACCCTCAATTTACAG
63 TTACCCTCGATTTACAG
* *
11847 AATTACT-ATTTTACCCTCGATTTATAAATTACCGTTTTACCCTCAATTTACAGAATTACTATTT
1 AATTACTGA-TTTACCCTCGATTTA-AAATTACCATTTTACCCTCAATTTACAGAATTACCATTT
*
11911 TACCCTCGATTTATAG
64 TACCCTCGATTTACAG
* *
11927 AATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCC
1 AATTACTGATTTACCCTCGA-TT-TAAAATTACCATTTTACCC
11970 CTAGGGTGTT
Statistics
Matches: 234, Mismatches: 40, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
79 3 0.01
80 69 0.29
81 157 0.67
82 4 0.02
83 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (79 bp):
AATTACTGATTTACCCTCGATTTAAAATTACCATTTTACCCTCAATTTACAGAATTACCATTTTA
CCCTCGATTTACAG
Found at i:12250 original size:27 final size:26
Alignment explanation
Indices: 12206--12257 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
12196 CTCGCTGCAA
*
12206 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
12233 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
12258 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:12541 original size:6 final size:6
Alignment explanation
Indices: 12530--12612 Score: 130
Period size: 6 Copynumber: 13.8 Consensus size: 6
12520 TTGTCACCTA
*
12530 ATTCTG ATTCTG ATTTTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
12578 ATTCTG ATTCTG ATTCTA ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
12613 AGTTTTGATA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (6 bp):
ATTCTG
Found at i:17136 original size:46 final size:44
Alignment explanation
Indices: 17047--17166 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 44
17037 TATCTGTGCT
* * *
17047 AGTGTAAGACATGTCTGGGACGTGCAGCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTACGAGAGCC
*
17093 AGTGTAAGACATGTCTGGGACATGCATCGG-CATTGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATT---ACGAGAGCC
* *
17139 AGTGTAAGACATGTCTAGAACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
17167 AGCCTCGAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 4 0.06
46 61 0.94
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCATTACGAGAGCC
Found at i:17293 original size:49 final size:49
Alignment explanation
Indices: 17228--17360 Score: 155
Period size: 49 Copynumber: 2.7 Consensus size: 49
17218 CTTCTTGAGT
* *
17228 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGA
1 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCAATAGATGAAA
* * *
17277 G-CTAGTGTAAGACCTGTCTGGGACACGACATC-AGCCTCAATATATGAAA
1 GTC-AGTGTAAGACCTGTCTGGGACATGGCATCGA-CCTCAATAGATGAAA
* *
17326 GTCAGTGTAAGACCTGTCTAGTACATGGCATCGAC
1 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGAC
17361 TTTGATGTGC
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
48 3 0.04
49 65 0.93
50 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (49 bp):
GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCAATAGATGAAA
Found at i:17296 original size:93 final size:96
Alignment explanation
Indices: 17185--17360 Score: 232
Period size: 98 Copynumber: 1.8 Consensus size: 96
17175 GATATAAAAA
* * * * **
17185 CTAGTGTAAGACCAGTCTGGGACATGGCGTCAG-CT-TCT-TGAGTGTCAGTGTAAGACCTGTCT
1 CTAGTGTAAGACCAGTCTGGGACACGACATCAGCCTATATATGAAAGTCAGTGTAAGACCTGTCT
*
17247 GGGACATGGCATCGACACCGATAGATGAGAG
66 AGGACATGGCATCGACACCGATAGATGAGAG
*
17278 CTAGTGTAAGACCTGTCTGGGACACGACATCAGCCTCAATATATGAAAGTCAGTGTAAGACCTGT
1 CTAGTGTAAGACCAGTCTGGGACACGACATCAGCCT--ATATATGAAAGTCAGTGTAAGACCTGT
*
17343 CTAGTACATGGCATCGAC
64 CTAGGACATGGCATCGAC
17361 TTTGATGTGC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
93 29 0.42
94 2 0.03
97 2 0.03
98 36 0.52
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (96 bp):
CTAGTGTAAGACCAGTCTGGGACACGACATCAGCCTATATATGAAAGTCAGTGTAAGACCTGTCT
AGGACATGGCATCGACACCGATAGATGAGAG
Found at i:17352 original size:142 final size:138
Alignment explanation
Indices: 17092--17354 Score: 332
Period size: 141 Copynumber: 1.9 Consensus size: 138
17082 TTATGAGAGC
* **
17092 CAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAG
1 CAGTGTAAGACATGTCTGGGACATGCATCGACACCGAGACGAGAGCTAGTGTAAGACATGTCTAG
* *
17157 AACATGCATCAGCCTCGAGATATAAAAACTAGTGTAAGACCAGTCTGGGACATGGCGTCAGCTTC
66 AACACGCATCAGCCTCGAGATATAAAAACTAGTGTAAGACCAGTCTAGGACATGGCGTCAGCTTC
17222 TTGAGTGT
131 TTGAGTGT
* * *
17230 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGCTAGTGTAAGACCTGTC
1 CAGTGTAAGACATGTCTGGGACAT-GCATCGACACCG--AGACGAGAGCTAGTGTAAGACATGTC
* * * * * *
17295 TGGGACACGACATCAGCCTC-A-ATATATGAAAGTCAGTGTAAGACCTGTCTAGTACATGGC
63 TAGAACACG-CATCAGCCTCGAGATATA-AAAACT-AGTGTAAGACCAGTCTAGGACATGGC
17355 ATCGACTTTG
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
138 23 0.22
139 9 0.09
140 5 0.05
141 35 0.33
142 33 0.31
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (138 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGACACCGAGACGAGAGCTAGTGTAAGACATGTCTAG
AACACGCATCAGCCTCGAGATATAAAAACTAGTGTAAGACCAGTCTAGGACATGGCGTCAGCTTC
TTGAGTGT
Found at i:27380 original size:22 final size:22
Alignment explanation
Indices: 27352--27427 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
27342 AAGTGTATAT
27352 ATGTGATAAGGCCGAGTGGCCA
1 ATGTGATAAGGCCGAGTGGCCA
** ***
27374 ATGTGATGAATGTG-AAAGTGTATA
1 ATGTGAT-AA-G-GCCGAGTGGCCA
27398 TATGTGATAAGGCCGAGTGGCCA
1 -ATGTGATAAGGCCGAGTGGCCA
27421 ATGTGAT
1 ATGTGAT
27428 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAGTGGCCA
Found at i:27602 original size:47 final size:47
Alignment explanation
Indices: 27067--27595 Score: 855
Period size: 47 Copynumber: 11.3 Consensus size: 47
27057 ACAAGATATG
* *
27067 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
27114 TATATGTGATAATGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
27161 TATATGTGATAAGGCC-AATTGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAA-TGGCCAATGTGATGAATGTGAAAGTGTA
27208 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
27255 TATATGTGATAAGGTCGACTGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
27302 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
27349 TATATGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
27396 TATATGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * *
27443 TAAATGTGATAAGGCCGAGTGGCCAACGTGATGAAAGTGAAAGTGTG
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * * *
27490 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
27537 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
27584 TAAATGTG-TAAG
1 TATATGTGATAAG
27596 TCCCGAAGGG
Statistics
Matches: 450, Mismatches: 30, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
46 6 0.01
47 442 0.98
48 2 0.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:30160 original size:25 final size:25
Alignment explanation
Indices: 30132--30184 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
30122 ATTTTCATAG
*
30132 CTCGTGTGAGCATTCTGATTCACAA
1 CTCGTGTGAGCATTCAGATTCACAA
*
30157 CTCGTGTGAGCATTCAGATTTACAA
1 CTCGTGTGAGCATTCAGATTCACAA
30182 CTC
1 CTC
30185 ATGTTAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (25 bp):
CTCGTGTGAGCATTCAGATTCACAA
Done.