Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold150
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: 1465027
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 98465 characters in sequence are not A, C, G, or T
File 7 of 9
Found at i:987178 original size:79 final size:79
Alignment explanation
Indices: 987045--987469 Score: 473
Period size: 79 Copynumber: 5.4 Consensus size: 79
987035 TCATTGATGT
** * * * *
987045 TTTTATTTCTAAAATGTCGATTTTTCACCATCAGAGATACTCCAACCCCGTTATTTTCGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTTCATCATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGA
987110 TACTCCAACCCCGA
66 TACTCCAACCCCGA
*
987124 TTTTATTTCTAAAACA-CTGATTTTTCATCATCGGGGATACTCCAACCCCATTA-TTTCTAAGGG
1 TTTTATTTCTAAAACATC-GATTTTTCATCATCGGGGATACTCCAACCCCGTTATTTTC-AAGGG
*
987187 GATGCTCCAACCCC-A
64 GATACTCCAACCCCGA
* * ** * * ** *
987202 GTTTTATTTCTAAAACATTGATTTTCCAAAATCGGGGATACACCAACCCTGTTATTTTTGAGGGA
1 -TTTTATTTCTAAAACATCGATTTTTCATCATCGGGGATACTCCAACCCCGTTATTTTCAAGGGG
987267 ATACTCCAACCCCGA
65 ATACTCCAACCCCGA
* * ** *
987282 TTTTATTTCTAAAACATCGATTTTTAATAATCGGGGATACTCCAACCCCGTTATTTTTTAGGAGA
1 TTTTATTTCTAAAACATCGATTTTTCATCATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGA
*
987347 TACTCCAACCCTGA
66 TACTCCAACCCCGA
* * * * *
987361 TTTTATTTCCAAAACATCGATTTTCCATCATCAGGGATACTCTAACCCCATTA-TTTCTAAGGGG
1 TTTTATTTCTAAAACATCGATTTTTCATCATCGGGGATACTCCAACCCCGTTATTTTC-AAGGGG
987425 ATACTCCAACCCC-A
65 ATACTCCAACCCCGA
* * * *
987439 TTTTTATCTCCAAAATATTGAATTTTTCATC
1 -TTTTATTTCTAAAACATCG-ATTTTTCATC
987470 GGGGGATGTA
Statistics
Matches: 293, Mismatches: 44, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
78 10 0.03
79 270 0.92
80 13 0.04
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCGATTTTTCATCATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGA
TACTCCAACCCCGA
Found at i:991746 original size:13 final size:13
Alignment explanation
Indices: 991728--991786 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 13
991718 CATAAAGTGT
991728 TGTATCGATACAA
1 TGTATCGATACAA
991741 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
991756 GTGTTGTATCGATATAA
1 ----TGTATCGATACAA
991773 TGTATCGATACAA
1 TGTATCGATACAA
991786 T
1 T
991787 ATAAGCTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 24 0.63
15 2 0.05
17 2 0.05
19 10 0.26
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:991763 original size:32 final size:33
Alignment explanation
Indices: 991708--991784 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 33
991698 TTCAACGATT
991708 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
991741 TGTATCGATACAT-AAGTGTTGTATCGATATAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
991773 TGTATCGATACA
1 TGTATCGATACA
991785 ATATAAGCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.70
33 13 0.30
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:991887 original size:52 final size:52
Alignment explanation
Indices: 991805--992111 Score: 542
Period size: 52 Copynumber: 5.9 Consensus size: 52
991795 CTGCAAAAAA
* * * *
991805 ATGTATCGATACATTACTCAAATGTATCGATAGATGTAGGCAAATTTGCCCAG
1 ATGTATCGATACACTA-TAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
991858 ATGTATTGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
* *
991910 ATCTATCGATACACTATAAAATGTATCGATGCATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
991962 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
992014 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
992066 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
992112 TCATATTTCG
Statistics
Matches: 244, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
52 230 0.94
53 14 0.06
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:995868 original size:18 final size:20
Alignment explanation
Indices: 995821--995868 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
995811 GAGAAACAAA
995821 AATGAAAAAAATCAAAAAAG
1 AATGAAAAAAATCAAAAAAG
995841 AA-GAAAAAAA-C-AAAAAG
1 AATGAAAAAAATCAAAAAAG
995858 AATGAATAAAA
1 AATGAA-AAAA
995869 GGGGAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.31
18 4 0.15
19 12 0.46
20 2 0.08
ACGTcount: A:0.77, C:0.04, G:0.10, T:0.08
Consensus pattern (20 bp):
AATGAAAAAAATCAAAAAAG
Found at i:997170 original size:62 final size:62
Alignment explanation
Indices: 997094--997718 Score: 750
Period size: 62 Copynumber: 10.2 Consensus size: 62
997084 TAATGACATC
* * * *
997094 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTTTTGTCCTCAAGGAGCAGGATGCCTTTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
997156 CCTTTTCAAAGCCCACATGA---GGTGGCATCCTTTTGTCCTCAAAGAGCCGGACGCCTTTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
997215 TCTTTTCAAGGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGA-CTAAGACACCTTTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGC-AGGACGCCTTTT
* * *
997277 TCTTTTCAAAGCCTACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACACCTTTTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCC-TTTT
* * **
997340 TCTTTTCAAAGCCTACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACATCTTTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
997402 TCTTTTCAAAGCCCATATGAGTTGGTGGCA-CC--T--T-CTCAAAGAGTAGGACACCATTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
997458 TCTTTTCAAAGCCTAC-TCGAGTTGGTGGCACCCTTTAGTCCTCAAAAAGTAAGATGCCTTTT
1 TCTTTTCAAAGCCCACAT-GAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
997520 TCTTTTCAAAGCCCACAGGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * * *
997582 TCATTTCAAGGCCAACACGAGTTGGTGGCATCCTTTAGTCCTCAAAGAGCAGGATGCCTTTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * * *
997644 TCTTTTCAAGGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGGGTAAGATGCCTTTT
1 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
997706 TCTTTTCAAAGCC
1 TCTTTTCAAAGCC
997719 TTTGATGTAA
Statistics
Matches: 495, Mismatches: 54, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
55 1 0.00
56 45 0.09
57 3 0.01
59 53 0.11
61 4 0.01
62 330 0.67
63 59 0.12
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.31
Consensus pattern (62 bp):
TCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:1005005 original size:20 final size:20
Alignment explanation
Indices: 1004977--1005048 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1004967 AATTAACTAG
*
1004977 ATGTTTCGATACATTGAATA
1 ATGTATCGATACATTGAATA
*
1004997 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAATA
* *
1005017 ATGTATCGATATATT-CATA
1 ATGTATCGATACATTGAATA
1005036 CATGTATCGATAC
1 -ATGTATCGATAC
1005049 TTTAAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 2 0.04
20 43 0.96
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:1006219 original size:28 final size:28
Alignment explanation
Indices: 1006165--1006714 Score: 552
Period size: 28 Copynumber: 19.5 Consensus size: 28
1006155 TCGACTTGTT
* * *
1006165 TGGGCTTT-AAAAGAATGCCATTAACTTG
1 TGGGCTTTGAAAAG-GTGCCACTGACTTG
* * * *
1006193 TGGACCTTGAAAAGATGCCACTGACTTT
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* *
1006221 TGGGCTTTGAAAGGGGTGCCACTGATTTG
1 TGGGCTTTGAAA-AGGTGCCACTGACTTG
* * *
1006250 TGGGCTTTGAGAAGGTGACACTGACTTA
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
*
1006278 TGGGCTTTGAAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAA-GGTGCCACTGACTTG
* * *
1006307 TGAGCTTTGAAAGGGGAGCCACTGACTTG
1 TGGGCTTTGAAA-AGGTGCCACTGACTTG
* * *
1006336 TGAGCTTTGAAAATGTGCCATTGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* *
1006364 TGGGATCTT-AAAAAGTGCCACTGACTTG
1 TGGGCT-TTGAAAAGGTGCCACTGACTTG
*
1006392 TGGG-TTCT-AAGAAGGTGCCACTAACTTG
1 TGGGCTT-TGAA-AAGGTGCCACTGACTTG
*
1006420 TGGGCTTTGAAATGGGTGCCACTGACTTG
1 TGGGCTTTGAAA-AGGTGCCACTGACTTG
* *
1006449 TGGGCTTTGAAAGAGGTGCCTCTGACTTA
1 TGGGCTTTGAAA-AGGTGCCACTGACTTG
* * * *
1006478 TGGGCTTTGAGAAGGTACCACTAACATG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* *
1006506 TGGGCTTTG-AGAGGTGCCACCGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* *
1006533 TGGGCTCTGAAAAGGTGCCACTAACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* *
1006561 TGAGCTTTGAAAAGGTGCCACTAACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* * *
1006589 TGGGTTTTGAAAAGATGCCATTGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* * * *
1006617 TGGGTTTTGAAAAGATGCCACTAACATG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* * *
1006645 TGGGCTTTGAGAAGGTGCCACTAACTTA
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
* *
1006673 TGGGCTTTGAAATGATGCCACTGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTTG
1006701 TGGGCTTTTGAAAA
1 TGGGC-TTTGAAAA
1006715 AAGGGTCATA
Statistics
Matches: 433, Mismatches: 77, Indels: 23
0.81 0.14 0.04
Matches are distributed among these distances:
26 1 0.00
27 24 0.06
28 269 0.62
29 139 0.32
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (28 bp):
TGGGCTTTGAAAAGGTGCCACTGACTTG
Found at i:1006408 original size:142 final size:141
Alignment explanation
Indices: 1006236--1006714 Score: 468
Period size: 142 Copynumber: 3.4 Consensus size: 141
1006226 TTTGAAAGGG
* * * * *
1006236 GTGCCACTGATTTGTGGGCTT-TGAGAAGGTGACACTGACTTATGGGCTTTGAAAAGGGTGCCAC
1 GTGCCACTGACTTGTGGG-TTCTAAGAAGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCAC
* * * * * * * *
1006300 TAACTTGTGAGCTTTGAAAGGGGAGCCACTGACTTGTGAGCTTTGAAAATGTGCCATTGACTTGT
65 TAACTTGTGGGCTTTGAAAGAGGAGCCACTGACTTATGAGCTTTGAAAAGGTACCACTAACATGT
1006365 GGGATCTTAAAAA
130 GGGAT-TTAAAAA
*
1006378 GTGCCACTGACTTGTGGGTTCTAAGAAGGTGCCACTAACTTGTGGGCTTTGAAATGGGTGCCACT
1 GTGCCACTGACTTGTGGGTTCTAAGAAGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACT
* * * * *
1006443 GACTTGTGGGCTTTGAAAGAGGTGCCTCTGACTTATGGGCTTTGAGAAGGTACCACTAACATGTG
66 AACTTGTGGGCTTTGAAAGAGGAGCCACTGACTTATGAGCTTTGAAAAGGTACCACTAACATGTG
* * * *
1006508 GGCTTTGAGAG
131 GGATTTAAAAA
* * *
1006519 GTGCCACCGACTTGTGGGCTCTGAA-AAGGTGCCACTAACTTGTGAGCTTTGAAAA-GGTGCCAC
1 GTGCCACTGACTTGTGGGTTCT-AAGAAGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCAC
* * * * * * *
1006582 TAACTTGTGGGTTTTGAAA-A-GATGCCATTGACTTGTGGGTTTTGAAAAGATGCCACTAACATG
65 TAACTTGTGGGCTTTGAAAGAGGA-GCCACTGACTTATGAGCTTTGAAAAGGTACCACTAACATG
* * *
1006645 TGGGCTTTGAGAAG
129 TGGGATTT-AAAAA
* * * * *
1006659 GTGCCACTAACTTATGGGCTT-TGAA-ATGATGCCACTGACTTGTGGGCTTTTGAAAA
1 GTGCCACTGACTTGTGGG-TTCT-AAGAAGGTGCCACTAACTTGTGGGC-TTTGAAAA
1006715 AAGGGTCATA
Statistics
Matches: 283, Mismatches: 48, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
138 1 0.00
139 42 0.15
140 64 0.23
141 63 0.22
142 113 0.40
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (141 bp):
GTGCCACTGACTTGTGGGTTCTAAGAAGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACT
AACTTGTGGGCTTTGAAAGAGGAGCCACTGACTTATGAGCTTTGAAAAGGTACCACTAACATGTG
GGATTTAAAAA
Found at i:1006999 original size:26 final size:26
Alignment explanation
Indices: 1006961--1007017 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
1006951 TTGAAGTGAT
** * *
1006961 ATGATGTTTAATGGTATTATGAATGC
1 ATGATGTGGAATGCTATCATGAATGC
**
1006987 ATGATGTGGAATGCTATCATGGTTGC
1 ATGATGTGGAATGCTATCATGAATGC
1007013 ATGAT
1 ATGAT
1007018 ACAAAGTCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.39
Consensus pattern (26 bp):
ATGATGTGGAATGCTATCATGAATGC
Found at i:1013688 original size:2 final size:2
Alignment explanation
Indices: 1013681--1013715 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1013671 GAGATTTTCA
*
1013681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1013716 AATAAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1023611 original size:14 final size:14
Alignment explanation
Indices: 1023592--1023618 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1023582 AAGGGAAAAT
1023592 AAGATACTATTAGA
1 AAGATACTATTAGA
1023606 AAGATACTATTAG
1 AAGATACTATTAG
1023619 GGTCATGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (14 bp):
AAGATACTATTAGA
Found at i:1024479 original size:51 final size:52
Alignment explanation
Indices: 1024387--1024495 Score: 132
Period size: 51 Copynumber: 2.1 Consensus size: 52
1024377 AATTAACTAG
* * * * *
1024387 ATGTATCGATACATTAAATAATGTATCGATATATCTAGGT-AACAAAACAGA
1 ATGTATCAAAACATTAAATAATATATCGATACATCTAGGTAAAAAAAACAGA
* *
1024438 ATGTATCAAAACATTGAAA-AATATATTGATACATCTTGGTAAAAAAAACAGA
1 ATGTATCAAAACATT-AAATAATATATCGATACATCTAGGTAAAAAAAACAGA
1024490 ATGTAT
1 ATGTAT
1024496 TGATGCATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 30 0.61
52 19 0.39
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (52 bp):
ATGTATCAAAACATTAAATAATATATCGATACATCTAGGTAAAAAAAACAGA
Found at i:1030690 original size:44 final size:44
Alignment explanation
Indices: 1030627--1030714 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
1030617 GGAGAGATAG
1030627 AAGTCCAGTTTGTAACTAAATCCTTAGTGAAAGGGAAATTTTCT
1 AAGTCCAGTTTGTAACTAAATCCTTAGTGAAAGGGAAATTTTCT
1030671 AAGTCCAGTTTGTAACTAAATCCTTAGTGAAAGGGAAATTTTCT
1 AAGTCCAGTTTGTAACTAAATCCTTAGTGAAAGGGAAATTTTCT
1030715 TTCTCCCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (44 bp):
AAGTCCAGTTTGTAACTAAATCCTTAGTGAAAGGGAAATTTTCT
Found at i:1030851 original size:34 final size:34
Alignment explanation
Indices: 1030792--1030892 Score: 118
Period size: 34 Copynumber: 3.0 Consensus size: 34
1030782 CTTTTGTATG
*
1030792 TATTAATTTATTTTTACATAAATATAATTTTAGTA
1 TATTAA-TTATTTTTACATAAATATAATTTTAATA
**
1030827 T-TTAATTATTTTTAACATTGATATAATTTTAATA
1 TATTAATTATTTTT-ACATAAATATAATTTTAATA
* *
1030861 TATT-ATTA-TTTAATATAAATATAATTTTAATA
1 TATTAATTATTTTTACATAAATATAATTTTAATA
1030893 AATTTTAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
32 17 0.30
33 11 0.19
34 26 0.46
35 3 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (34 bp):
TATTAATTATTTTTACATAAATATAATTTTAATA
Found at i:1030891 original size:17 final size:17
Alignment explanation
Indices: 1030809--1030892 Score: 66
Period size: 17 Copynumber: 5.1 Consensus size: 17
1030799 TTATTTTTAC
*
1030809 ATAAATATAATTTTAGT
1 ATAAATATAATTTTAAT
* * *
1030826 ATTTAAT-TATTTTTAAC
1 A-TAAATATAATTTTAAT
**
1030843 ATTGATATAATTTTAAT
1 ATAAATATAATTTTAAT
* *
1030860 AT-ATTATTA-TTTAAT
1 ATAAATATAATTTTAAT
1030875 ATAAATATAATTTTAAT
1 ATAAATATAATTTTAAT
1030892 A
1 A
1030893 AATTTTAATT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
15 8 0.16
16 13 0.25
17 26 0.51
18 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
ATAAATATAATTTTAAT
Found at i:1030893 original size:15 final size:15
Alignment explanation
Indices: 1030847--1030895 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1030837 TTTAACATTG
1030847 ATATAATTTTAATATA
1 ATATAATTTTAATA-A
* * *
1030863 TTATTATTTAATATAA
1 ATATAATTTTA-ATAA
1030879 ATATAATTTTAATAA
1 ATATAATTTTAATAA
1030894 AT
1 AT
1030896 TTTAATTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 6 0.23
16 17 0.65
17 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATAATTTTAATAA
Found at i:1030898 original size:10 final size:11
Alignment explanation
Indices: 1030847--1030918 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
1030837 TTTAACATTG
1030847 ATATAATTTTA
1 ATATAATTTTA
1030858 ATAT-ATTATT-
1 ATATAATT-TTA
* * *
1030868 ATTTAATATAA
1 ATATAATTTTA
1030879 ATATAATTTTA
1 ATATAATTTTA
1030890 ATA-AATTTTA
1 ATATAATTTTA
1030900 ATTATTAATTTTA
1 A-TA-TAATTTTA
1030913 TATATA
1 -ATATA
1030919 TGATAATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
10 15 0.31
11 21 0.44
12 2 0.04
13 9 0.19
14 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATAATTTTA
Found at i:1030933 original size:39 final size:41
Alignment explanation
Indices: 1030851--1030935 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 41
1030841 ACATTGATAT
1030851 AATTTTAATATATTATTATTTAATATAAATATAATTTTAATA
1 AATTTTAATATATTA-TATTTAATATAAATATAATTTTAATA
* *
1030893 AATTTTAAT-TATTA-ATTTTATATATATGATAATTTT-ATA
1 AATTTTAATATATTATATTTAATATAAAT-ATAATTTTAATA
1030932 AATT
1 AATT
1030936 AGAGTTATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
39 18 0.45
40 8 0.20
41 5 0.12
42 9 0.22
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (41 bp):
AATTTTAATATATTATATTTAATATAAATATAATTTTAATA
Found at i:1030944 original size:39 final size:38
Alignment explanation
Indices: 1030862--1030944 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 38
1030852 ATTTTAATAT
**
1030862 ATTATTATTTAATATAAATATAATTTTAATAAATTTTA
1 ATTATTATTTAATATAAATATAATTTTAATAAATTAGA
* *
1030900 ATTATTAATTTTATATATATGATAATTTT-ATAAATTAGA
1 ATTATT-ATTTAATATAAAT-ATAATTTTAATAAATTAGA
*
1030939 GTTATT
1 ATTATT
1030945 CGATCTCATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
38 6 0.16
39 24 0.63
40 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (38 bp):
ATTATTATTTAATATAAATATAATTTTAATAAATTAGA
Found at i:1034123 original size:2 final size:2
Alignment explanation
Indices: 1034116--1034154 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1034106 ACCTACATGC
*
1034116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1034155 ATTCCTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1034408 original size:15 final size:16
Alignment explanation
Indices: 1034390--1034423 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1034380 GTAAATAAAT
1034390 AAAATAACATGAAAAA
1 AAAATAACATGAAAAA
**
1034406 AAAATGTCATGAAAAA
1 AAAATAACATGAAAAA
1034422 AA
1 AA
1034424 GGTATATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.15
Consensus pattern (16 bp):
AAAATAACATGAAAAA
Found at i:1034878 original size:14 final size:14
Alignment explanation
Indices: 1034846--1034896 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1034836 CTTAATTTAT
1034846 GTTTTGTTTGTTTC
1 GTTTTGTTTGTTTC
* *
1034860 ATTTTGTTTGTTTG
1 GTTTTGTTTGTTTC
*
1034874 GTTTTTGTTT-TTTT
1 G-TTTTGTTTGTTTC
1034888 GTTTTGTTT
1 GTTTTGTTT
1034897 TGTTCGAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 8 0.25
14 16 0.50
15 8 0.25
ACGTcount: A:0.02, C:0.02, G:0.20, T:0.76
Consensus pattern (14 bp):
GTTTTGTTTGTTTC
Found at i:1036497 original size:17 final size:17
Alignment explanation
Indices: 1036465--1036496 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1036455 ATAAATATCG
1036465 TTAAAAATAATAAAAAT
1 TTAAAAATAATAAAAAT
1036482 TTAAAAAT-ATAAAAA
1 TTAAAAATAATAAAAA
1036497 AGATATCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TTAAAAATAATAAAAAT
Found at i:1037037 original size:12 final size:13
Alignment explanation
Indices: 1037020--1037067 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 13
1037010 AATTATCCTA
1037020 TTTTATT-TTATC
1 TTTTATTATTATC
1037032 TTTTATTATTAT-
1 TTTTATTATTATC
*
1037044 TATTATTATTAT-
1 TTTTATTATTATC
*
1037056 TATTATTATTAT
1 TTTTATTATTAT
1037068 TAATATCTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 30 0.88
13 4 0.12
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTATTATC
Found at i:1037042 original size:3 final size:3
Alignment explanation
Indices: 1037034--1037069 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1037024 ATTTTATCTT
1037034 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1037070 ATATCTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1040880 original size:10 final size:9
Alignment explanation
Indices: 1040859--1040897 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
1040849 AAAAACCAAT
1040859 AACAACAAAA
1 AACAA-AAAA
1040869 AACAAAACAA
1 AACAAAA-AA
1040879 AACAAAAAA
1 AACAAAAAA
1040888 AA-AAAAAA
1 AACAAAAAA
1040896 AA
1 AA
1040898 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.29
9 6 0.21
10 14 0.50
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (9 bp):
AACAAAAAA
Found at i:1040897 original size:17 final size:17
Alignment explanation
Indices: 1040862--1040897 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1040852 AACCAATAAC
* *
1040862 AACAAAAAACAAAACAA
1 AACAAAAAAAAAAAAAA
1040879 AACAAAAAAAAAAAAAA
1 AACAAAAAAAAAAAAAA
1040896 AA
1 AA
1040898 GAGAGAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AACAAAAAAAAAAAAAA
Found at i:1040902 original size:2 final size:2
Alignment explanation
Indices: 1040897--1040921 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1040887 AAAAAAAAAA
1040897 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1040922 TATTGTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1042155 original size:11 final size:11
Alignment explanation
Indices: 1042139--1042173 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1042129 TATGTAATAT
1042139 TTTTATTTTTA
1 TTTTATTTTTA
1042150 TTTTATTTTTA
1 TTTTATTTTTA
*
1042161 TTCTA-TTTTA
1 TTTTATTTTTA
1042171 TTT
1 TTT
1042174 CAAGGAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1042946 original size:11 final size:12
Alignment explanation
Indices: 1042925--1042962 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1042915 TAAATTAATT
1042925 TTTTAAAATATA
1 TTTTAAAATATA
1042937 TTTT-AAATATA
1 TTTTAAAATATA
*
1042948 TATTTGAAATATA
1 T-TTTAAAATATA
1042961 TT
1 TT
1042963 ATTTAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 8 0.33
13 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
TTTTAAAATATA
Found at i:1045710 original size:34 final size:35
Alignment explanation
Indices: 1045662--1045728 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
1045652 TACTCAAATA
*
1045662 AATTTAAAACATATAT-CTTTTATGTTTTAATAGC
1 AATTTAAAACATATATACTTTTATATTTTAATAGC
*
1045696 AATTCTAAAA-ATATATATTTTTATATTTTAATA
1 AATT-TAAAACATATATACTTTTATATTTTAATA
1045729 AATCAACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (35 bp):
AATTTAAAACATATATACTTTTATATTTTAATAGC
Found at i:1046901 original size:22 final size:23
Alignment explanation
Indices: 1046858--1046905 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1046848 TATTTTTATA
1046858 TTTTTATAATTAAATTTAAATAAT
1 TTTTTATAATTAAA-TTAAATAAT
1046882 TTTTTATTAATTAAA-T-AATAAT
1 TTTTTA-TAATTAAATTAAATAAT
1046904 TT
1 TT
1046906 GAGTCGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
23 1 0.04
24 6 0.26
25 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTATAATTAAATTAAATAAT
Found at i:1047270 original size:31 final size:33
Alignment explanation
Indices: 1047234--1047294 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
1047224 GATTTAAATA
*
1047234 TAAATATGAAATA-TTTAAA-AAAGTAAATTAT
1 TAAATATAAAATATTTTAAATAAAGTAAATTAT
*
1047265 TAAATATAAAATATTTTAAATATAGTAAAT
1 TAAATATAAAATATTTTAAATAAAGTAAAT
1047295 AAATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 12 0.46
32 6 0.23
33 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (33 bp):
TAAATATAAAATATTTTAAATAAAGTAAATTAT
Found at i:1047283 original size:16 final size:16
Alignment explanation
Indices: 1047234--1047288 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
1047224 GATTTAAATA
*
1047234 TAAATATGAAATATTT
1 TAAATATAAAATATTT
* * *
1047250 AAAAAAGT-AAAT-TAT
1 TAAATA-TAAAATATTT
1047265 TAAATATAAAATATTT
1 TAAATATAAAATATTT
1047281 TAAATATA
1 TAAATATA
1047289 GTAAATAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
14 1 0.03
15 10 0.33
16 18 0.60
17 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (16 bp):
TAAATATAAAATATTT
Found at i:1054712 original size:34 final size:34
Alignment explanation
Indices: 1054674--1054809 Score: 263
Period size: 34 Copynumber: 4.0 Consensus size: 34
1054664 CTTTGTTAAG
1054674 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1054708 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1054742 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
1054776 TGTGTTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1054810 GAATGTTAGG
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 101 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:1054808 original size:22 final size:22
Alignment explanation
Indices: 1054776--1054831 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1054766 TGTTAGGTGA
*
1054776 TGTGTTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
1054798 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
1054820 TGTGTTAGGTGA
1 TGTGTTAGGTGA
1054832 TGTATTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:1054843 original size:68 final size:66
Alignment explanation
Indices: 1054677--1054860 Score: 244
Period size: 68 Copynumber: 2.9 Consensus size: 66
1054667 TGTTAAGTGT
1054677 ATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 ATTTGGT-AG-ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
1054742 TGT
64 TGA
*
1054745 ATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA-G-G-
1 ATTTGGT-AG-ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1054807 TG-
64 TGA
1054809 A----G-A-ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 ATTTGGTAGATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1054861 ACATGTATAT
Statistics
Matches: 114, Mismatches: 2, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
56 48 0.42
58 1 0.01
60 1 0.01
64 1 0.01
65 2 0.02
66 1 0.01
67 1 0.01
68 59 0.52
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.41
Consensus pattern (66 bp):
ATTTGGTAGATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATG
A
Found at i:1159288 original size:16 final size:16
Alignment explanation
Indices: 1159239--1159294 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
1159229 GATTTAAATA
*
1159239 TAAATATGAAATATTT
1 TAAATATAAAATATTT
* * *
1159255 AAAAAAGT-AAAT-TAT
1 TAAATA-TAAAATATTT
1159270 TAAATATAAAATATTT
1 TAAATATAAAATATTT
1159286 TAAATATAA
1 TAAATATAA
1159295 TAAATAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
14 1 0.03
15 10 0.32
16 19 0.61
17 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (16 bp):
TAAATATAAAATATTT
Found at i:1167690 original size:52 final size:52
Alignment explanation
Indices: 1167613--1167714 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
1167603 GAATTTAAAT
* *
1167613 AATAAAAAAAATTAGCTTTAACTTTTTATTAGTCTGTG-TTATTGAAATTGA
1 AATAAAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATTGA
** * *
1167664 AATAGAAAAAAATTAGCTTTGGCTTTTTGTTAATCTGAGTTTTTTGAAATT
1 AATA-AAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATT
1167715 TTGGTTAGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 4 0.09
52 29 0.67
53 10 0.23
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (52 bp):
AATAAAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATTGA
Found at i:1167748 original size:25 final size:25
Alignment explanation
Indices: 1167688--1167744 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1167678 AGCTTTGGCT
* *
1167688 TTTTGTTAATCTGAGTTTTTTGAAA
1 TTTTGTTAGTCTGAGTTTTTTAAAA
1167713 TTTTGGTTAGTCTGAG-TTTTTAAAA
1 TTTT-GTTAGTCTGAGTTTTTTAAAA
1167738 TTTTGTT
1 TTTTGTT
1167745 TAGTTCGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 3 0.10
25 16 0.55
26 10 0.34
ACGTcount: A:0.21, C:0.04, G:0.18, T:0.58
Consensus pattern (25 bp):
TTTTGTTAGTCTGAGTTTTTTAAAA
Found at i:1168506 original size:17 final size:16
Alignment explanation
Indices: 1168472--1168517 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
1168462 TAGAGGAAAA
*
1168472 TTATGAAA-CTACTTT
1 TTATGAAATCTACTCT
1168487 TTATGAAATTCTACTCT
1 TTATGAAA-TCTACTCT
1168504 TTATGAAACTCTAC
1 TTATGAAA-TCTAC
1168518 AGTGTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 8 0.30
17 19 0.70
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (16 bp):
TTATGAAATCTACTCT
Found at i:1168719 original size:21 final size:21
Alignment explanation
Indices: 1168678--1168723 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1168668 TCAGAAGTGT
*
1168678 TATTTCTTTTAACCTTGATAA
1 TATTTCTTTTAACCTTAATAA
1168699 TATTTCATTTTAACC-TAATAA
1 TATTTC-TTTTAACCTTAATAA
1168720 -ATTT
1 TATTT
1168724 AGGTGGGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 8 0.35
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTTCTTTTAACCTTAATAA
Found at i:1169223 original size:46 final size:46
Alignment explanation
Indices: 1169167--1169258 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
1169157 CTTCCAATGT
* *
1169167 ATTTGAGCTTGGCATCAATCAAATGAATCTCG-AGTAAATTTGTTA
1 ATTTGAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
**
1169212 ATTTCGAGCTTGACATCAATAAAATGAATCTCGTAGTAGTTTTGTTA
1 ATTT-GAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
1169259 TTTAGGTGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 4 0.10
46 26 0.63
47 11 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (46 bp):
ATTTGAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
Found at i:1181739 original size:23 final size:21
Alignment explanation
Indices: 1181703--1181751 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
1181693 AATATTTTAA
1181703 TTAAAAATTAATAATGAAAATAT
1 TTAAAAATTAATAA--AAAATAT
*
1181726 TTAAAAA-TATATAAATAATAT
1 TTAAAAATTA-ATAAAAAATAT
1181747 TTAAA
1 TTAAA
1181752 TAAATCAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.46
22 2 0.08
23 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAAAAATTAATAAAAAATAT
Found at i:1181751 original size:11 final size:11
Alignment explanation
Indices: 1181721--1181754 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1181711 TAATAATGAA
1181721 AATATTTAAA-
1 AATATTTAAAT
*
1181731 AATATATAAAT
1 AATATTTAAAT
1181742 AATATTTAAAT
1 AATATTTAAAT
1181753 AA
1 AA
1181755 ATCAACTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATTTAAAT
Found at i:1187236 original size:16 final size:16
Alignment explanation
Indices: 1187217--1187250 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1187207 TCGAGTTTTC
1187217 TCGGGTTCAGGTTCTT
1 TCGGGTTCAGGTTCTT
*
1187233 TCGGGTTCTGGTTCTT
1 TCGGGTTCAGGTTCTT
1187249 TC
1 TC
1187251 AAGTTCAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.21, G:0.29, T:0.47
Consensus pattern (16 bp):
TCGGGTTCAGGTTCTT
Found at i:1187298 original size:16 final size:16
Alignment explanation
Indices: 1187267--1187320 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
1187257 AAGCTTTTTC
* *
1187267 GGGTTTGGGCTTTCTT
1 GGGTTTAGGCTATCTT
*
1187283 GGGTTTAGGTTATCTT
1 GGGTTTAGGCTATCTT
* *
1187299 GGGTTTATGCTATTTT
1 GGGTTTAGGCTATCTT
1187315 GGGTTT
1 GGGTTT
1187321 GGGTAATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.07, C:0.07, G:0.33, T:0.52
Consensus pattern (16 bp):
GGGTTTAGGCTATCTT
Found at i:1192386 original size:52 final size:51
Alignment explanation
Indices: 1192297--1192425 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 51
1192287 CGAAATATGA
* *
1192297 AAATTTGCCTACATGTATCGATACATTAAATAGTGTATCGATACATCTAGG
1 AAATTTGCCTGCATGTATCGATACATTAAATAATGTATCGATACATCTAGG
* ** *
1192348 AAACTTTGCCTGCAGGTATCGATACATTTTATAATGTATCGATACATCTGGG
1 AAA-TTTGCCTGCATGTATCGATACATTAAATAATGTATCGATACATCTAGG
1192400 CAAATTTGCCTGCATGTATCGATACA
1 -AAATTTGCCTGCATGTATCGATACA
1192426 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 3 0.04
52 63 0.91
53 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAAATAATGTATCGATACATCTAGG
Found at i:1192438 original size:52 final size:50
Alignment explanation
Indices: 1192297--1192445 Score: 183
Period size: 52 Copynumber: 2.9 Consensus size: 50
1192287 CGAAATATGA
*
1192297 AAATTTGCCTACATGTATCGATACATTAAATAGTGTATCGATACATCTAGG
1 AAATTTGCCTGCATGTATCGATACA-TAAATAGTGTATCGATACATCTAGG
* ** * *
1192348 AAACTTTGCCTGCAGGTATCGATACATTTTATAATGTATCGATACATCTGGG
1 AAA-TTTGCCTGCATGTATCGATACA-TAAATAGTGTATCGATACATCTAGG
1192400 CAAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 -AAATTTGCCTGCATGTATCGATACATAA-AT-AGTGTATCGATACA
1192446 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
51 5 0.06
52 76 0.90
53 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACATAAATAGTGTATCGATACATCTAGG
Found at i:1192452 original size:13 final size:13
Alignment explanation
Indices: 1192434--1192458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192424 CAAAGATCAG
1192434 TGTATCGATACAA
1 TGTATCGATACAA
1192447 TGTATCGATACA
1 TGTATCGATACA
1192459 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1192540 original size:13 final size:13
Alignment explanation
Indices: 1192522--1192546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192512 AAAAAAAATA
1192522 TGTATCGATACAT
1 TGTATCGATACAT
1192535 TGTATCGATACA
1 TGTATCGATACA
1192547 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1194740 original size:21 final size:21
Alignment explanation
Indices: 1194693--1194750 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1194683 AAAAATTATC
*
1194693 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
1194714 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
*
1194735 CAAATGTATCAATACA
1 CAAATGTATCGATACA
1194751 GGGTCCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:1194808 original size:18 final size:18
Alignment explanation
Indices: 1194785--1194836 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
1194775 AATTTCAGCG
1194785 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
1194803 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
1194821 GTATTGTATCGATACA
1 AT-TTGTATCGATACA
1194837 GTATCAATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:1194829 original size:19 final size:19
Alignment explanation
Indices: 1194787--1194869 Score: 85
Period size: 19 Copynumber: 4.8 Consensus size: 19
1194777 TTTCAGCGAT
*
1194787 TTGTATCGATACATAAAT-
1 TTGTATCGATACATAAGTA
1194805 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
1194824 TTGTATCGATAC------A
1 TTGTATCGATACATAAGTA
*
1194837 --GTATCAATACATAAGTA
1 TTGTATCGATACATAAGTA
1194854 TTGTATCGATACATAA
1 TTGTATCGATACATAA
1194870 TTAGCTACTG
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
11 9 0.17
13 1 0.02
17 1 0.02
18 17 0.32
19 25 0.47
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:1194841 original size:30 final size:30
Alignment explanation
Indices: 1194807--1194866 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1194797 ACATAAATTT
*
1194807 GTATCGATACATAAGTATTGTATCGATACA
1 GTATCAATACATAAGTATTGTATCGATACA
1194837 GTATCAATACATAAGTATTGTATCGATACA
1 GTATCAATACATAAGTATTGTATCGATACA
1194867 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (30 bp):
GTATCAATACATAAGTATTGTATCGATACA
Found at i:1194927 original size:13 final size:13
Alignment explanation
Indices: 1194909--1194934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1194899 CATTTTTCTG
1194909 TGTATCGATACAT
1 TGTATCGATACAT
1194922 TGTATCGATACAT
1 TGTATCGATACAT
1194935 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1194952 original size:34 final size:33
Alignment explanation
Indices: 1194891--1194955 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
1194881 CAAGGGAATA
*
1194891 TATCGATACATTTTTCTGTGTATCGATACATTG
1 TATCGATACATTATTCTGTGTATCGATACATTG
*
1194924 TATCGATACATCTATTCTTTGTATCGATACAT
1 TATCGATACAT-TATTCTGTGTATCGATACAT
1194956 CTAGGAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (33 bp):
TATCGATACATTATTCTGTGTATCGATACATTG
Found at i:1197358 original size:51 final size:52
Alignment explanation
Indices: 1197291--1197423 Score: 153
Period size: 51 Copynumber: 2.6 Consensus size: 52
1197281 TTGAGTTTCT
* * * * * * *
1197291 CAATTCTTCGCAATCGGGGATATTCCATCTCTGATTTTATTTTC-AAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACTCCGATTTCATTTCCAAAAACAC
* *
1197342 TAA-TTTTCTATAATCGGGGATACTCCAACTCCGATTTCATTTCCAAAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAACTCCGATTTCATTTCC-AAAAACAC
1197395 CAATTTTTCACAATCGGGGATACTCCAAC
1 CAATTTTTCACAATCGGGGATACTCCAAC
1197424 CCCGTTACCT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
50 4 0.06
51 30 0.45
53 28 0.42
54 5 0.07
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (52 bp):
CAATTTTTCACAATCGGGGATACTCCAACTCCGATTTCATTTCCAAAAACAC
Found at i:1197558 original size:79 final size:79
Alignment explanation
Indices: 1197357--1197613 Score: 230
Period size: 79 Copynumber: 3.2 Consensus size: 79
1197347 TTCTATAATC
* * * * * * * *
1197357 GGGGATACTCCAACTCCGA-TTTCATTTCCAAAAAACACCAATTTTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTT-A-TTCC-CAAAATATCGATTTCTCACAACCGGGGATACTCA
**
1197421 AACCCCGTTACCTCCGA
63 AACCCCGTTATTTCCGA
* * * ** *
1197438 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGACTTTATTCCCAAAATATCGATTTCTCACAACCGGGGATACTCAAAC
1197503 CCCGTTATTTCCGA
66 CCCGTTATTTCCGA
* * * ** *
1197517 GGGGATACTCCAATCCCGATTTTTTTTTC-TAATCATCGATTTCTCACAACCGGGGATACTCAAA
1 GGGGATACTCCAACCCCGACTTTATTCCCAAAAT-ATCGATTTCTCACAACCGGGGATACTCAAA
* * *
1197581 CCCCGTCATTTTCAA
65 CCCCGTTATTTCCGA
*
1197596 GGGGACACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1197614 TTATTATCTC
Statistics
Matches: 144, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
78 3 0.02
79 116 0.81
80 4 0.03
81 18 0.12
82 3 0.02
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGACTTTATTCCCAAAATATCGATTTCTCACAACCGGGGATACTCAAAC
CCCGTTATTTCCGA
Found at i:1204620 original size:28 final size:28
Alignment explanation
Indices: 1204539--1204620 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1204529 TTTTGGAGAT
*
1204539 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
1204567 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
1204595 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
1204621 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:1204763 original size:51 final size:51
Alignment explanation
Indices: 1204603--1204773 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1204593 GAAATAACGA
* * *
1204603 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
1204655 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
1204708 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
1204759 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1204774 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:1204819 original size:27 final size:28
Alignment explanation
Indices: 1204756--1204831 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
1204746 AAAATAAAGT
*
1204756 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1204784 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1204811 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1204832 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1207311 original size:13 final size:13
Alignment explanation
Indices: 1207293--1207318 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1207283 ACAAAGATCC
1207293 ATGTATCGATACA
1 ATGTATCGATACA
1207306 ATGTATCGATACA
1 ATGTATCGATACA
1207319 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1207314 original size:33 final size:33
Alignment explanation
Indices: 1207272--1207338 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1207262 AAAATTTCCA
***
1207272 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1207305 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1207338 A
1 A
1207339 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1207382 original size:19 final size:18
Alignment explanation
Indices: 1207358--1207425 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1207348 CAGTAGCTAA
1207358 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1207377 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1207392 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1207409 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1207426 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1207398 original size:13 final size:13
Alignment explanation
Indices: 1207380--1207404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1207370 ACAATACTTA
1207380 TGTATCGATACAT
1 TGTATCGATACAT
1207393 TGTATCGATACA
1 TGTATCGATACA
1207405 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1207402 original size:32 final size:32
Alignment explanation
Indices: 1207361--1207423 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1207351 TAGCTAATTA
*
1207361 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1207393 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1207424 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1207490 original size:5 final size:5
Alignment explanation
Indices: 1207479--1207519 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
1207469 TACATTTGGA
* * *
1207479 ATTTT TTTTT TTTTT ATTTT ATTTT ATTTT ATTTT TTTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
1207520 AAAAAAACAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
ATTTT
Found at i:1207503 original size:15 final size:15
Alignment explanation
Indices: 1207479--1207519 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1207469 TACATTTGGA
*
1207479 ATTTTTTTTTTTTTT
1 ATTTTTTTTTATTTT
*
1207494 ATTTTATTTTATTTT
1 ATTTTTTTTTATTTT
1207509 ATTTTTTTTTA
1 ATTTTTTTTTA
1207520 AAAAAAACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
ATTTTTTTTTATTTT
Found at i:1214160 original size:1 final size:1
Alignment explanation
Indices: 1214149--1214206 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
1214139 CCTTCTCTTC
* * * * * * *
1214149 AAAAAACAAAAAAAAAACAAAAAAACAAAAAAACAAAACAAAGAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1214207 TCTGCTTAAG
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1214178 original size:16 final size:17
Alignment explanation
Indices: 1214151--1214198 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
1214141 TTCTCTTCAA
1214151 AAAACAAA-AAAAAAAC
1 AAAACAAACAAAAAAAC
1214167 AAAA-AAACAAAAAAAC
1 AAAACAAACAAAAAAAC
*
1214183 AAAACAAAGAAAAAAA
1 AAAACAAACAAAAAAA
1214199 AAGAAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 3 0.10
16 16 0.55
17 10 0.34
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAACAAACAAAAAAAC
Found at i:1214185 original size:27 final size:27
Alignment explanation
Indices: 1214149--1214206 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
1214139 CCTTCTCTTC
1214149 AAAAAACAAAA-AAAAAACAAAAAAACA
1 AAAAAACAAAACAAAAAA-AAAAAAACA
* *
1214176 AAAAAACAAAACAAAGAAAAAAAAAGA
1 AAAAAACAAAACAAAAAAAAAAAAACA
1214203 AAAA
1 AAAA
1214207 TCTGCTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (27 bp):
AAAAAACAAAACAAAAAAAAAAAAACA
Found at i:1214205 original size:8 final size:8
Alignment explanation
Indices: 1214159--1214198 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
1214149 AAAAAACAAA
1214159 AAAAAAAC
1 AAAAAAAC
1214167 AAAAAAAC
1 AAAAAAAC
1214175 AAAAAAAC
1 AAAAAAAC
*
1214183 AAAACAAAG
1 AAAA-AAAC
1214192 AAAAAAA
1 AAAAAAA
1214199 AAGAAAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.88, C:0.10, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1215486 original size:175 final size:173
Alignment explanation
Indices: 1215166--1216032 Score: 902
Period size: 175 Copynumber: 5.1 Consensus size: 173
1215156 TCTCCTTCCG
* * * *
1215166 CTTTTTAGCCCTCAAA-AGCAGGATGCCTTTGCCTTTTAAAGCCCACACAAGTTGGTGGCA----
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTT--CTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
1215226 -CC-T--TC-AAGAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCA
64 TCCGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTT--CAGTCCTCA
*
1215286 AAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
127 AAGAGCAGGACGCCTTCACCTTTTAAAGCCCACACAAGTTGGTGGCA
1215333 -TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTT-CAGTCCTCAAAGAGCAGGACGCC-TTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * *
1215397 TCCGTCCCCAAAGAGCAGGACCCCTTTTGAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAA
64 TCCGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTT-CAGTCCTCAA
*
1215462 AGAGCAGGACGCCTTCAACTTTTAAAGCCCACACAAGTTGGTGGCA
128 AGAGCAGGACGCCTTCACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1215508 -TTTTCCAATCCTCAAAGAGCGGGACGCCTTTTCTCTT-AAAACCCACACAAGTTGGTGGCACC-
1 CTTTT-CAGTCCTCAAAGAGCAGGACGCC-TTTCT-TTCAAAGCCCACACAAGTTGGTGGCACCT
* * * *
1215570 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGT
63 TTCCGTCCTCAAAGAGCAGGAC-AC----CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCAGT
* ***
1215635 CCTCAAAGAGCAGGATG-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
122 CCTCAAAGAGCAGGACGCCTTCACCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * * *
1215687 CCTTTCAGTCCCCAAAGAGCAGGAC-CC---CTTTCGAAGCCCACACAAGTTGGTGGCA-TTTTC
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
1215747 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG-----CA-TCCTCAAAG
66 C-GTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCAGTCCTCAAAG
*
1215806 AGCAGGA------CACCTCTTAAAGCCCACACAAGTTGGTGGCA
130 AGCAGGACGCCTTCACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1215844 CCTTTCAGTCCCCAAAGAGCAGGAC-AC---CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
1215904 CAGTCCTCAAAGAGTAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAA
66 C-GTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAC--TTCAGTCCTCAA
* * *
1215969 AGAGCAGGA------CACCTTTCAAAGCCTACACGAGTTGGTGGCA
128 AGAGCAGGACGCCTTCACCTTTTAAAGCCCACACAAGTTGGTGGCA
*
1216009 CTTTTTAGTCCTCAAAGAGCAGGA
1 CTTTTCAGTCCTCAAAGAGCAGGA
1216033 TACACTTTAT
Statistics
Matches: 617, Mismatches: 51, Indels: 66
0.84 0.07 0.09
Matches are distributed among these distances:
157 126 0.20
158 4 0.01
163 16 0.03
164 3 0.00
165 64 0.10
166 4 0.01
167 36 0.06
168 10 0.02
169 3 0.00
170 24 0.04
172 2 0.00
173 3 0.00
174 46 0.07
175 131 0.21
176 43 0.07
178 10 0.02
179 86 0.14
180 6 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (173 bp):
CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
CGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCAGTCCTCAAAGA
GCAGGACGCCTTCACCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1215751 original size:55 final size:55
Alignment explanation
Indices: 1215231--1216032 Score: 799
Period size: 55 Copynumber: 14.2 Consensus size: 55
1215221 TGGCACCTTC
* * * *
1215231 AAGAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCA
1 AAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* *
1215286 AAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
1 AAGAGCAGGA---C--C-CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
*
1215347 AAGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC-GTCCCCA
1 AAGAGCAGGAC-CC----CTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCA
**
1215407 AAGAGCAGGACCCCTTTTGAAGCCCACACAAGTTGGTGGCAC-TTCCAGTCCTCA
1 AAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* * *
1215461 AAGAGCAGGACGCCTTCAACTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCA
1 AAGAGCAGGA--CC--C--CTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* * * *
1215522 AAGAGCGGGACGCCTTTTCTCTTAAAACCCACACAAGTTGGTGGCACCTT-CAGTCCTCA
1 AAGAGCAGGAC-CC-CTT-TC--AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* * * *
1215581 AAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTT-CAGTCCTCA
1 AAGAGCAGGAC-CC----CTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* * *
1215640 AAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCA
1 AAGAGCAGGA--C----CCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCA
* *
1215701 AAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
1 AAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
*
1215756 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG-------CA-TCCTCA
1 AAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* *
1215803 AAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCA
1 AAGAGCAGGACCCCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCA
* *
1215858 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
1 AAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* * **
1215913 AAGAGTAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCA
1 AAGAGCAGGACCCCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
* * * **
1215968 AAGAGCAGGACACCTTTCAAAGCCTACACGAGTTGGTGGCACTTTTTAGTCCTCA
1 AAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
1216023 AAGAGCAGGA
1 AAGAGCAGGA
1216033 TACACTTTAT
Statistics
Matches: 650, Mismatches: 51, Indels: 92
0.82 0.06 0.12
Matches are distributed among these distances:
47 42 0.06
48 4 0.01
53 4 0.01
54 29 0.04
55 265 0.41
56 5 0.01
57 3 0.00
58 5 0.01
59 69 0.11
60 121 0.19
61 99 0.15
62 3 0.00
64 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (55 bp):
AAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCA
Found at i:1216734 original size:21 final size:21
Alignment explanation
Indices: 1216708--1216747 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1216698 AAATTATCCA
1216708 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1216729 AATGTATCGATACATTTGT
1 AATGTATCGATACATTTGT
1216748 GATACATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1216835 original size:19 final size:18
Alignment explanation
Indices: 1216809--1216877 Score: 67
Period size: 19 Copynumber: 4.0 Consensus size: 18
1216799 AATTTCAGCG
1216809 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
1216827 ATGTTGTATCCATAC---A
1 AT-TTGTATCGATACATAA
1216843 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
1216859 GTATTGTATCGATACATAA
1 AT-TTGTATCGATACATAA
1216878 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
13 10 0.24
16 3 0.07
18 2 0.05
19 26 0.63
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:1216853 original size:32 final size:32
Alignment explanation
Indices: 1216812--1216874 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1216802 TTCAGCGATT
*
1216812 TGTATCGATACATAAATGTTGTATCCATACAA
1 TGTATCGATACATAAATATTGTATCCATACAA
* *
1216844 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAATATTGTATCCATACA
1216875 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCCATACAA
Found at i:1216935 original size:13 final size:13
Alignment explanation
Indices: 1216917--1216942 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1216907 CATTTTTTTG
1216917 TGTATCGATACAT
1 TGTATCGATACAT
1216930 TGTATCGATACAT
1 TGTATCGATACAT
1216943 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1219367 original size:51 final size:52
Alignment explanation
Indices: 1219306--1219428 Score: 160
Period size: 51 Copynumber: 2.4 Consensus size: 52
1219296 CAATTCTCCG
* * * * *
1219306 CAATTGGGGATATTCCATCTCCGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
*
1219357 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTTTCA
1219410 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
1219429 CCCGTTATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 29 0.47
53 28 0.45
54 5 0.08
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:1219419 original size:53 final size:51
Alignment explanation
Indices: 1219306--1219428 Score: 158
Period size: 53 Copynumber: 2.4 Consensus size: 51
1219296 CAATTCTCCG
* * * * *
1219306 CAATTGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
*
1219357 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAATTTTCT-A
1219410 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
1219429 CCCGTTATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 29 0.47
52 1 0.02
53 32 0.52
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
Found at i:1219444 original size:28 final size:28
Alignment explanation
Indices: 1219412--1219487 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
1219402 ATTTTTCACA
**
1219412 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
*
1219440 ATCGGGGATACTCTAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
***
1219468 CGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
1219488 AGCTTTATTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACCTC
Found at i:1224192 original size:2 final size:2
Alignment explanation
Indices: 1224185--1224225 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1224175 TAAGAACAAC
1224185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1224226 GGTTAAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1226041 original size:40 final size:39
Alignment explanation
Indices: 1225923--1226042 Score: 98
Period size: 40 Copynumber: 2.9 Consensus size: 39
1225913 TTCTATATGC
* * *
1225923 AACCAAAAGAACTTGTTAGC-AGTTACCATTGTAATAACCT
1 AACCAAAATAAATTGTTA-CAAGTTACC-TTGTAATAATCT
* * * ***
1225963 AACCAAAATAACTTTTGCTAGAAGTTACCCTCACAATAATCT
1 AACCAAAATAA--ATTGTTACAAGTTA-CCTTGTAATAATCT
1226005 AACCAAAATAAATTGTTACAAGTTACACTTGTAATAAT
1 AACCAAAATAAATTGTTACAAGTTAC-CTTGTAATAAT
1226043 AATCTAACAA
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
39 1 0.02
40 29 0.48
42 29 0.48
43 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.29
Consensus pattern (39 bp):
AACCAAAATAAATTGTTACAAGTTACCTTGTAATAATCT
Found at i:1226260 original size:117 final size:117
Alignment explanation
Indices: 1226051--1226283 Score: 360
Period size: 117 Copynumber: 2.0 Consensus size: 117
1226041 ATAATCTAAC
** * * *
1226051 AAATGATGGCTTTCTGTCATCTCAAAAATATATCGAGCAAAAGAAATGAGCATAAAAAGAAACAT
1 AAATGATAACTTTCTGTCATCTCAAAAATATATCGACCAAAAGAAATAAGCATAAAAAGAAACAC
* *
1226116 AGCATGTTTTGTTTGCTTTTTCAAGTTTCCTACACATC-AATCAAAATATATT
66 AACATGTTTTGTTTGCTTTTTCAAGTTTCCTACACATCGAA-CAAAAGATATT
* *
1226168 AAATGATAACTTTTTGTCATCTCAAAAATATATCGACCAAAAGAAATAAGCATAAAAAGAAAGAC
1 AAATGATAACTTTCTGTCATCTCAAAAATATATCGACCAAAAGAAATAAGCATAAAAAGAAACAC
*
1226233 AACATGTTTTGTTTGCTTTTTCCAGTTTCCTACACATCGAACAAAAGATAT
66 AACATGTTTTGTTTGCTTTTTCAAGTTTCCTACACATCGAACAAAAGATAT
1226284 AAAACAAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
117 103 0.98
118 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (117 bp):
AAATGATAACTTTCTGTCATCTCAAAAATATATCGACCAAAAGAAATAAGCATAAAAAGAAACAC
AACATGTTTTGTTTGCTTTTTCAAGTTTCCTACACATCGAACAAAAGATATT
Found at i:1226911 original size:21 final size:21
Alignment explanation
Indices: 1226885--1226927 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1226875 ACAATTTTCT
* *
1226885 TTATCTATTTATAATCTTAAA
1 TTATCTATTCAGAATCTTAAA
1226906 TTATCTATTCAGAATCTTAAA
1 TTATCTATTCAGAATCTTAAA
1226927 T
1 T
1226928 CAATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATCTATTCAGAATCTTAAA
Found at i:1227739 original size:16 final size:15
Alignment explanation
Indices: 1227711--1227748 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1227701 TTTGGTTTTC
*
1227711 TTTTTAATTAAAAAT
1 TTTTTAAATAAAAAT
1227726 TTTTTAAATAAAAAT
1 TTTTTAAATAAAAAT
1227741 TTTTTAAA
1 TTTTTAAA
1227749 AAATGTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTAAATAAAAAT
Found at i:1228521 original size:17 final size:18
Alignment explanation
Indices: 1228499--1228551 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
1228489 GGACAATCTA
*
1228499 AAATATAAT-TTTAAATT
1 AAATATAATATATAAATT
*
1228516 AAATAT-ATATATATATT
1 AAATATAATATATAAATT
*
1228533 AAATATAATA-AAAAATT
1 AAATATAATATATAAATT
1228550 AA
1 AA
1228552 TAGAAACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 25 0.83
18 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATAATATATAAATT
Found at i:1229093 original size:13 final size:13
Alignment explanation
Indices: 1229075--1229099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1229065 ATAATGCACA
1229075 GTATCGATACATT
1 GTATCGATACATT
1229088 GTATCGATACAT
1 GTATCGATACAT
1229100 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1229112 original size:20 final size:21
Alignment explanation
Indices: 1229087--1229139 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1229077 ATCGATACAT
*
1229087 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
1229107 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
1229128 TGTATCGATACA
1 TGTATCGATACA
1229140 GATGATTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:1229194 original size:19 final size:20
Alignment explanation
Indices: 1229170--1229221 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1229160 CTTAACTGTT
1229170 TGTATCGATACAT-A-CAAGA
1 TGTATCGATACATGACCAA-A
1229189 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
1229209 TGTATCGATACAT
1 TGTATCGATACAT
1229222 TGGCTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.42
20 15 0.48
21 3 0.10
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:1235139 original size:8 final size:8
Alignment explanation
Indices: 1235126--1235156 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1235116 ACTTGATTAA
1235126 ATTTTGTG
1 ATTTTGTG
1235134 ATTTTGTG
1 ATTTTGTG
1235142 ATTTTGTG
1 ATTTTGTG
1235150 ATGTTTG
1 AT-TTTG
1235157 ATGTTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (8 bp):
ATTTTGTG
Found at i:1235372 original size:13 final size:13
Alignment explanation
Indices: 1235354--1235391 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1235344 TAGCATTCTC
*
1235354 TGTATCGATACAT
1 TGTATCGATACAG
1235367 TGTATCGATACAG
1 TGTATCGATACAG
1235380 TGTATCGATACA
1 TGTATCGATACA
1235392 AAGGGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1235423 original size:31 final size:31
Alignment explanation
Indices: 1235388--1235450 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1235378 AGTGTATCGA
1235388 TACAAAGGGTTTTTATGAACAGTTCGAACCC
1 TACAAAGGGTTTTTATGAACAGTTCGAACCC
1235419 TACAAAGGGTTTTTATGAACAGTTCGAACCC
1 TACAAAGGGTTTTTATGAACAGTTCGAACCC
1235450 T
1 T
1235451 TTCTTCTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (31 bp):
TACAAAGGGTTTTTATGAACAGTTCGAACCC
Found at i:1236921 original size:13 final size:13
Alignment explanation
Indices: 1236903--1236927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1236893 CATAAAGTGT
1236903 TGTATCGATACAA
1 TGTATCGATACAA
1236916 TGTATCGATACA
1 TGTATCGATACA
1236928 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1236925 original size:33 final size:33
Alignment explanation
Indices: 1236883--1236949 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1236873 TTCAATGATT
1236883 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1236916 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1236949 T
1 T
1236950 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1237008 original size:13 final size:13
Alignment explanation
Indices: 1236990--1237014 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1236980 ATTACTCAAA
1236990 TGTATCGATACAT
1 TGTATCGATACAT
1237003 TGTATCGATACA
1 TGTATCGATACA
1237015 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1237079 original size:52 final size:52
Alignment explanation
Indices: 1237023--1237151 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1237013 CACTGATCTT
* *
1237023 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1237075 TGTATCGATACATGCACGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1237127 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1237152 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1241532 original size:20 final size:20
Alignment explanation
Indices: 1241487--1241560 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
1241477 ACACCTTCAG
* * *
1241487 ATGTATCGATACATAATGCAC
1 ATGTATCGATACATGA-CCAA
1241508 A-GTATCGATACATGACCAA
1 ATGTATCGATACATGACCAA
* *
1241527 ATGTATCGATACTTG-CAAAGA
1 ATGTATCGATACATGAC-CA-A
1241548 ATGTATCGATACA
1 ATGTATCGATACA
1241561 GGTGATTGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.09
20 26 0.59
21 14 0.32
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACATGACCAA
Found at i:1241628 original size:13 final size:13
Alignment explanation
Indices: 1241610--1241635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1241600 ACATACAAGA
1241610 TGTATCGATACAT
1 TGTATCGATACAT
1241623 TGTATCGATACAT
1 TGTATCGATACAT
1241636 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1241651 original size:33 final size:32
Alignment explanation
Indices: 1241590--1241656 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1241580 CCTTAACTGT
1241590 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1241622 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1241655 TT
1 TT
1241657 AGCTTGTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1245466 original size:21 final size:21
Alignment explanation
Indices: 1245440--1245482 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1245430 ACAATTTTCT
*
1245440 TTATCTATTCATAATCTTAAA
1 TTATCTATTCAAAATCTTAAA
1245461 TTATCTATTCAAAATCTTAAA
1 TTATCTATTCAAAATCTTAAA
1245482 T
1 T
1245483 CAATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATCTATTCAAAATCTTAAA
Found at i:1246228 original size:48 final size:48
Alignment explanation
Indices: 1246157--1246252 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1246147 CATGCGACTA
1246157 TACTTTTAGTTTTGATTTTTGTTTATATAAACTGTGAGAAAATAACCT
1 TACTTTTAGTTTTGATTTTTGTTTATATAAACTGTGAGAAAATAACCT
1246205 TACTTTTAGTTTTGATTTTTGTTTATATAAACTGTGAGAAAATAACCT
1 TACTTTTAGTTTTGATTTTTGTTTATATAAACTGTGAGAAAATAACCT
1246253 GGTAAGAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (48 bp):
TACTTTTAGTTTTGATTTTTGTTTATATAAACTGTGAGAAAATAACCT
Found at i:1246883 original size:15 final size:16
Alignment explanation
Indices: 1246863--1246893 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1246853 AAATAAAGGA
1246863 ATTAAAAAAA-AGAAT
1 ATTAAAAAAATAGAAT
1246878 ATTAAAAAAATAGAAT
1 ATTAAAAAAATAGAAT
1246894 GAGAAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
ATTAAAAAAATAGAAT
Found at i:1247312 original size:16 final size:15
Alignment explanation
Indices: 1247284--1247317 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1247274 TTTAGTTTTT
* *
1247284 TTTTTAATTAAAAAG
1 TTTTTAAATAAAAAA
1247299 TTTTTAAATAAAAAA
1 TTTTTAAATAAAAAA
1247314 TTTT
1 TTTT
1247318 AGAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTTTTAAATAAAAAA
Found at i:1247692 original size:34 final size:35
Alignment explanation
Indices: 1247621--1247693 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 35
1247611 AAGTATATTC
* **
1247621 AAAATATATATCTTTTATATTTAATAACAATCCTT
1 AAAATATATATCTTTTATATTTAATAAAAATAATT
1247656 AAAATATATA--TTTTATATTTTAATAAAAATAATT
1 AAAATATATATCTTTTATA-TTTAATAAAAATAATT
1247690 AAAA
1 AAAA
1247694 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 17 0.50
35 10 0.29
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (35 bp):
AAAATATATATCTTTTATATTTAATAAAAATAATT
Found at i:1247801 original size:16 final size:16
Alignment explanation
Indices: 1247761--1247793 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1247751 AAACAAAGTC
1247761 AAACAAAAG--AATTA
1 AAACAAAAGAAAATTA
1247775 AAACAAAAGAAAATTA
1 AAACAAAAGAAAATTA
1247791 AAA
1 AAA
1247794 AAATAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAACAAAAGAAAATTA
Found at i:1248476 original size:913 final size:908
Alignment explanation
Indices: 1246825--1248599 Score: 2669
Period size: 913 Copynumber: 1.9 Consensus size: 908
1246815 ACAAAATAAT
* * * * *
1246825 TCAAGAAAAGAAAATTAGAAAAGAAGTCAAATAAAGGAATTAAAAAAAAGAATATTAAAAAAATA
1 TCAAGAAAAGAAAATTAAAAAAAAAGTCAAACAAAAGAATTAAAAAAAAGAAAATTAAAAAAATA
* * *
1246890 GAATGAGAAAGTAAAATCCTTGGAAAAATCAATTTTCTGCAAGTTTTTGACGACAAAGACAACTC
66 GAATGAGAAAGTAAAAACCTTGGAAAAATCAATTTTCTGCAAGTTTTTGAAGACAAAGACAACTA
* * * * * *
1246955 GATCAATTACCTCCAATATGTCAAGGAATAAACTCTTAATCCCGTCGAACAAAGGGTGACCTATG
131 GATCAATTACCTCCAATATATCAAAGAATAAACCCTTAATCCCATCGAACAAAAGGCGACCTATG
* ** * *
1247020 GTGTTGAAGGTTAGAGTGAAGAGTTTATTAAGGTTATGAAACAGAGGCGATGCTTTCACCTTCAG
196 GTGTTAAAGGTTAGAGCAAAGAGTTGATTAAGGTTATAAAACAGAGGCGATGCTTTCACCTTCAG
*
1247085 GTGTTTTAGTAAAGCTCCTTTCATCATTGCCATTTCAATAGGTAACCCTTCTTTTCTCTTCCCTT
261 GTGTTTTAGTAAAGCTCCTTTCATCATTGCCATTTCAATAGGTAACCCTTCCTTTCTCTTCCCTT
*
1247150 TTTTGGTGTTGTAGCATGTGAGTATATTTTTAGTTTTGGCTTTTGCTTCTTATATAAACTATGAG
326 TTTTGGTGTTGTAGCATGCGAGTATATTTTTAGTTTTGGCTTTTGCTTCTTATATAAACTATGAG
*
1247215 AATAATAACCTAATATGAAGTGGCTAAAAGTATCAAAGAATACGGCGTTGCAATTCTATTTTAGT
391 AATAATAACCTAATAAGAAGTGGCTAAAAGTATCAAAGAATACGGCGTTGCAATTCTATTTTAGT
* * *
1247280 TTTTTTTTTAATTAAAAAGTTTTTAAATAAAAAATTTTAGAAAAATATAATTTTAGAATAAATCC
456 GTTTTTTTTAATTAAAAAGTTTTTAAATAAAAAAATTGAGAAAAATATAATTTTAGAATAAATCC
*
1247345 TAAATTTACTACCTAAAATAAATTTACTTTTTATAATTAATTCAGTTATAATTTTTTCATTATAT
521 TAAATTTACTACCTAAAATAAATGTACTTTTTATAATTAATTCAGTTATAATTTTTTCATTATAT
* *
1247410 TTTGTTAATTTAACTAAAAATAATAAAAATGAATGTAATTTCTTCATTATATTTTTTAATTTAGC
586 TTTGTTAATTTAACTAAAAATAATAAAAATGAATGTAATTTCCTCATAATATTTTTTAATTTAGC
* * *
1247475 CAAAAATAATAAAATAAAGTAATCCATAATCAAGTCAAGTTTGTTAAACTCAATCGGAGCATTGG
651 CAAAAATAATAAAATAAAGTAATCCACAATCAAGTCAAGTTTATTAAACTCAATCGGAGCATTAG
1247540 ATATTTTAAGTTTAAAATTATTAAAAATATTTTATATTAATATAATACATTTTAATCAAATTTAA
716 ATATTTTAAGTTTAAAATTATTAAAAATATTTTATATTAATATAATACATTTTAATCAAATTTAA
* * *
1247605 ATATTCAAGTATATTCAAAATATATATCTTTTATATTTAATAACAATCCTTAAAATATATATTTT
781 ACATTCAAGCATATTCAAAATATATATCTTTTATATTTAATAACAATCCTAAAAATATATATTTT
1247670 -ATATTTTAATAAAAATAATTAAAAATTTAAAAAATGGAATGAAAAAGTGAAAAATTAAAAGA
846 CATATTTTAATAAAAATAATTAAAAATTTAAAAAATGGAATGAAAAAGTGAAAAATTAAAAGA
1247732 TCAAGAAAAGAAAATTAAAAAACAAAGTCAAACAAAAGAATTAAAACAAAAGAAAATTAAAAAAA
1 TCAAGAAAAGAAAATTAAAAAA-AAAGTCAAACAAAAGAATTAAAA-AAAAGAAAATTAAAAAAA
**
1247797 TAGAATGAGAAAGTAAAAACCTT-GAAAACATCAATTTTCTGCAAGTTTTTGAAGACGGAGACAA
64 TAGAATGAGAAAGTAAAAACCTTGGAAAA-ATCAATTTTCTGCAAGTTTTTGAAGACAAAGACAA
** * * * * ** *
1247861 CTAGATCGGTTACGTCCCATGTATCAAAGAATGAACCCTTAATGTCATCGGACAAAAGGCGACCT
128 CTAGATCAATTACCTCCAATATATCAAAGAATAAACCCTTAATCCCATCGAACAAAAGGCGACCT
* * *
1247926 ATGGTTTTAAAGGTTAGAGCAAAGAGTTGATTAGGGTTATAAAACAGAGGTGATGCTTTCACCTT
193 ATGGTGTTAAAGGTTAGAGCAAAGAGTTGATTAAGGTTATAAAACAGAGGCGATGCTTTCACCTT
* * ** * *
1247991 TAGGTGTTTTAGTAAAG-TTCTTTTTTCCATTTCCATTTCAATAGGTAGCCC-TCCTTTCTCTTC
258 CAGGTGTTTTAGTAAAGCTCCTTTCAT-CATTGCCATTTCAATAGGTAACCCTTCCTTTCTCTTC
* *
1248054 TCTTTTTTGGTTGTT-TAGCATGCGAGTATATTTTTAGTTTTGCTTTTTGGCTTTTGCTTTTTAT
322 CCTTTTTTGG-TGTTGTAGCATGCGAGTATATTTTTA-----G--TTTTGGCTTTTGCTTCTTAT
* * * *
1248118 TTAAACTGTGAGAATAATAACC-AAGTAAGAAGTGGCTAAAAGTATTAAAGAATA-GGAGGTTGC
379 ATAAACTATGAGAATAATAACCTAA-TAAGAAGTGGCTAAAAGTATCAAAGAATACGG-CGTTGC
*
1248181 AATTCTATTTT-G-GTTTTTTTTAATTAAAAAGTTTTTAAATAAAAAAATTGAGAAAAATGTAAT
442 AATTCTATTTTAGTGTTTTTTTTAATTAAAAAGTTTTTAAATAAAAAAATTGAGAAAAATATAAT
1248244 TTTAGAATAAATCCTAAATTTACTACCTAAAATAAATGTACTTTTTAT-ATTAATTCAGTTATAA
507 TTTAGAATAAATCCTAAATTTACTACCTAAAATAAATGTACTTTTTATAATTAATTCAGTTATAA
* * *
1248308 TTTTTT-ATTATATTTTTTTACTTTATCTAAAAAT-ATAAAAATGAATGTAATTTCCTCATAATA
572 TTTTTTCATTATATTTTGTTAATTTAACTAAAAATAATAAAAATGAATGTAATTTCCTCATAATA
*
1248371 TTTTTTTAATTTAGCCAAAAATAATAAAAATAAAATTAATTCC-CAATCAAGTCAAGTTTATTAA
637 -TTTTTTAATTTAGCCAAAAATAAT-AAAAT-AAAGTAA-TCCACAATCAAGTCAAGTTTATTAA
* *
1248435 ACTCAATTCGGA-CTTTAGATATTTTAAGTTTAAAGTTATTAAAAATATTTTATATTAATATAAT
698 ACTCAA-TCGGAGCATTAGATATTTTAAGTTTAAAATTATTAAAAATATTTTATATTAATATAAT
*
1248499 ACATTTTAATCAAATTTAAACATTCAAGCATATTTAAAATATATATCTTTTATATTTAATAACAA
762 ACATTTTAATCAAATTTAAACATTCAAGCATATTCAAAATATATATCTTTTATATTTAATAACAA
1248564 TCCTAAAAATATATATTTTCATATTTTAATAAAAAT
827 TCCTAAAAATATATATTTTCATATTTTAATAAAAAT
1248600 CCAAGCCAAA
Statistics
Matches: 780, Mismatches: 68, Indels: 33
0.89 0.08 0.04
Matches are distributed among these distances:
907 21 0.03
908 71 0.09
909 219 0.28
910 27 0.03
911 49 0.06
912 27 0.03
913 255 0.33
914 29 0.04
915 82 0.11
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (908 bp):
TCAAGAAAAGAAAATTAAAAAAAAAGTCAAACAAAAGAATTAAAAAAAAGAAAATTAAAAAAATA
GAATGAGAAAGTAAAAACCTTGGAAAAATCAATTTTCTGCAAGTTTTTGAAGACAAAGACAACTA
GATCAATTACCTCCAATATATCAAAGAATAAACCCTTAATCCCATCGAACAAAAGGCGACCTATG
GTGTTAAAGGTTAGAGCAAAGAGTTGATTAAGGTTATAAAACAGAGGCGATGCTTTCACCTTCAG
GTGTTTTAGTAAAGCTCCTTTCATCATTGCCATTTCAATAGGTAACCCTTCCTTTCTCTTCCCTT
TTTTGGTGTTGTAGCATGCGAGTATATTTTTAGTTTTGGCTTTTGCTTCTTATATAAACTATGAG
AATAATAACCTAATAAGAAGTGGCTAAAAGTATCAAAGAATACGGCGTTGCAATTCTATTTTAGT
GTTTTTTTTAATTAAAAAGTTTTTAAATAAAAAAATTGAGAAAAATATAATTTTAGAATAAATCC
TAAATTTACTACCTAAAATAAATGTACTTTTTATAATTAATTCAGTTATAATTTTTTCATTATAT
TTTGTTAATTTAACTAAAAATAATAAAAATGAATGTAATTTCCTCATAATATTTTTTAATTTAGC
CAAAAATAATAAAATAAAGTAATCCACAATCAAGTCAAGTTTATTAAACTCAATCGGAGCATTAG
ATATTTTAAGTTTAAAATTATTAAAAATATTTTATATTAATATAATACATTTTAATCAAATTTAA
ACATTCAAGCATATTCAAAATATATATCTTTTATATTTAATAACAATCCTAAAAATATATATTTT
CATATTTTAATAAAAATAATTAAAAATTTAAAAAATGGAATGAAAAAGTGAAAAATTAAAAGA
Found at i:1248578 original size:35 final size:35
Alignment explanation
Indices: 1248534--1248601 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
1248524 AAGCATATTT
* *
1248534 AAAATATATATCTTTTATA-TTTAATAACAATCCTA
1 AAAATATATAT-TTTCATATTTTAATAAAAATCCTA
1248569 AAAATATATATTTTCATATTTTAATAAAAATCC
1 AAAATATATATTTTCATATTTTAATAAAAATCC
1248602 AAGCCAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 6 0.20
35 24 0.80
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (35 bp):
AAAATATATATTTTCATATTTTAATAAAAATCCTA
Found at i:1249287 original size:16 final size:16
Alignment explanation
Indices: 1249249--1249288 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1249239 TTGAAAATTG
*
1249249 ATCGATTTTTTATTGA
1 ATCGATTTTTTATTCA
* *
1249265 ATAGATTTTTTTTTCA
1 ATCGATTTTTTATTCA
1249281 ATCGATTT
1 ATCGATTT
1249289 GATTGTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.57
Consensus pattern (16 bp):
ATCGATTTTTTATTCA
Found at i:1256864 original size:51 final size:51
Alignment explanation
Indices: 1256805--1256950 Score: 249
Period size: 50 Copynumber: 2.9 Consensus size: 51
1256795 TTTTAACTAG
*
1256805 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
* *
1256856 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGT-AAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
*
1256906 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1256951 TATGACTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 47 0.53
51 42 0.47
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.27
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:1256949 original size:24 final size:24
Alignment explanation
Indices: 1256879--1256953 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 24
1256869 TTGAAGAATG
1256879 TATCGATACATCTGGGTAAAAGATAGAA
1 TATCGATACATCTGGGTAAAA-AT---A
1256907 TGTATCGATACAT-T--G-AAAAATA
1 --TATCGATACATCTGGGTAAAAATA
1256929 TATCGATACATCTGGGTAAAAATA
1 TATCGATACATCTGGGTAAAAATA
1256953 T
1 T
1256954 GACTTTTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
20 11 0.27
21 1 0.02
22 1 0.02
23 1 0.02
24 8 0.20
25 2 0.05
26 4 0.10
27 1 0.02
29 1 0.02
30 11 0.27
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (24 bp):
TATCGATACATCTGGGTAAAAATA
Found at i:1258106 original size:19 final size:17
Alignment explanation
Indices: 1258082--1258144 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 17
1258072 ATTCAGTAAA
1258082 TGTATCGATACATAACTGT
1 TGTATCGATACATAA-T-T
1258101 TGTATCGATAC--AA--
1 TGTATCGATACATAATT
1258114 TGTATCGATACATAAGTTT
1 TGTATCGATACATAA--TT
1258133 TGTATCGATACA
1 TGTATCGATACA
1258145 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (17 bp):
TGTATCGATACATAATT
Found at i:1258119 original size:13 final size:13
Alignment explanation
Indices: 1258101--1258125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1258091 ACATAACTGT
1258101 TGTATCGATACAA
1 TGTATCGATACAA
1258114 TGTATCGATACA
1 TGTATCGATACA
1258126 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1258121 original size:32 final size:32
Alignment explanation
Indices: 1258080--1258152 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
1258070 ACATTCAGTA
1258080 AATGTATCGATACATAACTGTTGTATCGATAC
1 AATGTATCGATACATAACTGTTGTATCGATAC
* *
1258112 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAACTGTTGTATCGATAC
1258144 AATGTATCG
1 AATGTATCG
1258153 CTAGGAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAACTGTTGTATCGATAC
Found at i:1258214 original size:13 final size:13
Alignment explanation
Indices: 1258196--1258221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1258186 CATTTTTCTG
1258196 TGTATCGATACAT
1 TGTATCGATACAT
1258209 TGTATCGATACAT
1 TGTATCGATACAT
1258222 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1258242 original size:34 final size:33
Alignment explanation
Indices: 1258176--1258242 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
1258166 GCCAAGGAAA
* *
1258176 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGCATCGATACAT
*
1258209 TGTATCGATACATCTATTCTTTGCATCGATACAT
1 TGTATCGATACAT-TATTCTGTGCATCGATACAT
1258243 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGCATCGATACAT
Found at i:1258285 original size:20 final size:20
Alignment explanation
Indices: 1258260--1258315 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1258250 GTTTACCCAG
*
1258260 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTCTACA
1258280 ATGTATCGATACATTCTACA
1 ATGTATCGATACATTCTACA
1258300 ATGTATCGATACATTC
1 ATGTATCGATACATTC
1258316 AGGCATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCTACA
Found at i:1260668 original size:52 final size:52
Alignment explanation
Indices: 1260611--1260885 Score: 166
Period size: 52 Copynumber: 5.2 Consensus size: 52
1260601 CAATTGTTCA
*
1260611 TAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTT
* * * * *
1260663 TAATCGGGGGTACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTCCTT
* * * ** ***** * * *
1260715 CAATCGAGGATACTCCAACCTCATTATTTCATCGGGGATACTCCAA---CCCTGT
1 TAATCGGGGATACTCCAACCCCGGT-TTT-ATTTCCAAAACACCAATTTTCCT-T
* * * * *** *
1260767 TACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAATATTGA-TTTCC-A
1 TA-AT-C--GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTT
* * *
1260821 CAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTT
1260873 TAATCGGGGATAC
1 TAATCGGGGATAC
1260886 CCGATTTTAT
Statistics
Matches: 158, Mismatches: 52, Indels: 26
0.67 0.22 0.11
Matches are distributed among these distances:
50 34 0.22
51 5 0.03
52 62 0.39
53 27 0.17
54 9 0.06
55 3 0.02
56 18 0.11
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (52 bp):
TAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTT
Done.