Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007710.1 Hibiscus syriacus cultivar Beakdansim tig00109925_pilon, whole genome shotgun sequence
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: 668603
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:545722 original size:29 final size:31
Alignment explanation
Indices: 545654--545726 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
545644 TCTTTAAGGT
545654 ATATTTTA-TT-A-TATTTAATATTTTGTTA
1 ATATTTTATTTAATTATTTAATATTTTGTTA
*
545682 GTATTTTATTTAATTATTTAAT-TTTT-TTA
1 ATATTTTATTTAATTATTTAATATTTTGTTA
545711 ATAATTTT-TTTAATTA
1 AT-ATTTTATTTAATTA
545727 ATTTTTTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 7 0.18
29 14 0.36
30 10 0.26
31 8 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (31 bp):
ATATTTTATTTAATTATTTAATATTTTGTTA
Found at i:545734 original size:12 final size:13
Alignment explanation
Indices: 545699--545733 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
545689 ATTTAATTAT
545699 TTAATTTTTTTAA
1 TTAATTTTTTTAA
545712 -TAATTTTTTTAA
1 TTAATTTTTTTAA
545724 TTAATTTTTT
1 TTAATTTTTT
545734 ACAGTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTAATTTTTTTAA
Found at i:548098 original size:24 final size:24
Alignment explanation
Indices: 548066--548215 Score: 291
Period size: 24 Copynumber: 6.2 Consensus size: 24
548056 CCTTACAACG
548066 AAAGATCGAACGAACTTCTGAATC
1 AAAGATCGAACGAACTTCTGAATC
548090 AAAGATCGAACGAACTTCTGAATC
1 AAAGATCGAACGAACTTCTGAATC
548114 AAAGATCGAACGAACTTCTGAATC
1 AAAGATCGAACGAACTTCTGAATC
548138 AAAGATCGAACGAACTTCTGAATC
1 AAAGATCGAACGAACTTCTGAATC
548162 AAAGATCGAACGAACTTCTGAATC
1 AAAGATCGAACGAACTTCTGAATC
*
548186 AAAGATCGAACGAACTTCTGTATC
1 AAAGATCGAACGAACTTCTGAATC
548210 AAAGAT
1 AAAGAT
548216 AAGAGGATTG
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 125 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (24 bp):
AAAGATCGAACGAACTTCTGAATC
Found at i:552032 original size:16 final size:15
Alignment explanation
Indices: 551987--552039 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
551977 ATCGTTAGGA
*
551987 TAAATATATATTTTG
1 TAAAAATATATTTTG
* *
552002 TAAAAAGTATTTTTTT
1 TAAAAA-TATATTTTG
552018 TCAAAAATATATTTTG
1 T-AAAAATATATTTTG
552034 TAAAAA
1 TAAAAA
552040 GAGTCTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 10 0.32
16 16 0.52
17 5 0.16
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (15 bp):
TAAAAATATATTTTG
Found at i:553232 original size:20 final size:20
Alignment explanation
Indices: 553185--553234 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
553175 AAAGATTTTA
* *
553185 TTCTTCATTCATTCTTCATCT
1 TTCTTCATT-TTTCTTCATCC
*
553206 TTC-TCATTTTTCTTCTTCC
1 TTCTTCATTTTTCTTCATCC
553225 TTCTTCATTT
1 TTCTTCATTT
553235 CTCAAGCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 11 0.44
20 11 0.44
21 3 0.12
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (20 bp):
TTCTTCATTTTTCTTCATCC
Found at i:557461 original size:39 final size:42
Alignment explanation
Indices: 557418--557505 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 42
557408 TGTTTTTTTG
557418 TATTAAAAT-A-ATATTA-TTAA-TTAATAATATTTTATTATT
1 TATTAAAATAATATATTAGTTAACTT-ATAATATTTTATTATT
* *
557457 TATTAAAAATAATATATTAGTTAACTTATTATTTTTTATTATT
1 TATT-AAAATAATATATTAGTTAACTTATAATATTTTATTATT
557500 TATTAA
1 TATTAA
557506 TAAATTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 4 0.10
40 5 0.12
41 1 0.02
42 8 0.19
43 22 0.52
44 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (42 bp):
TATTAAAATAATATATTAGTTAACTTATAATATTTTATTATT
Found at i:565525 original size:45 final size:45
Alignment explanation
Indices: 565410--565650 Score: 331
Period size: 45 Copynumber: 5.3 Consensus size: 45
565400 GCTTATAATG
* * * *
565410 CACCATTATGCATTTTCATTTATGGAAAT-CATTCATGTCTTTTTATA
1 CACCATTATACA-TTTCATTTAT-GACATCCTTTCATG-CCTTTTATA
* * * *
565457 TACTATTATACATTTCATTTATGACATCCTTTCATGCATTTTTTA
1 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
565502 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
1 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
*
565547 CACCATTATACATTTCATTTATGATATCCTTTCATGCCTTTTATA
1 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
* * **
565592 CACCATTATACATTTTATTTATGGCATTTTTTCATGCCTTTTATA
1 CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
565637 CACCATTATACATT
1 CACCATTATACATT
565651 GTTATACATC
Statistics
Matches: 176, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
45 150 0.85
46 17 0.10
47 9 0.05
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.47
Consensus pattern (45 bp):
CACCATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATA
Found at i:565590 original size:22 final size:22
Alignment explanation
Indices: 565474--565590 Score: 71
Period size: 22 Copynumber: 5.2 Consensus size: 22
565464 ATACATTTCA
*
565474 TTTATGACATCCTTTCATGCAT
1 TTTATGACATCCTTTCATGCCT
* ** *
565496 TTT-TTACA-CCATTATACATTTCA
1 TTTATGACATCC-TT-T-CATGCCT
565519 TTTATGACATCCTTTCATGCCT
1 TTTATGACATCCTTTCATGCCT
** *
565541 TTTAT-ACA-CCATTATACATTTCA
1 TTTATGACATCC-TT-T-CATGCCT
*
565564 TTTATGATATCCTTTCATGCCT
1 TTTATGACATCCTTTCATGCCT
565586 TTTAT
1 TTTAT
565591 ACACCATTAT
Statistics
Matches: 69, Mismatches: 16, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
20 4 0.06
21 11 0.16
22 23 0.33
23 17 0.25
24 10 0.14
25 4 0.06
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTATGACATCCTTTCATGCCT
Found at i:565787 original size:68 final size:68
Alignment explanation
Indices: 565686--566284 Score: 849
Period size: 68 Copynumber: 8.8 Consensus size: 68
565676 AGGTATTTAA
* * * * * *
565686 CCTTTCATCTAACTGACATGATTGGCACCTTTCTGTCCAATGCACAGCTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
565751 TAG
66 TAG
* * * * * * * *
565754 TCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATTCAGAGTTAGGTCTCAAAGACATT
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
565819 TAG
66 TAG
* *
565822 CCTTTCATTTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGTACT
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
565887 TAG
66 TAG
* * *
565890 CCTTTCATCGAACTGGCATAATTGACATATTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
565955 TAG
66 TAG
* *
565958 TCTTTCATCTAACTGGCATAATTGACACATATCTGTCAAAT-CTACAGTTAGGCCTCAAAGGCAC
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC-ACAGTTAGGCCTCAAAGGCAC
566022 TTAG
65 TTAG
* * * *
566026 CCTTTCATCTAACTGGCATAATTTACACCTATCTGTCAAATGCACAGTTAGGCCTCAAAGACACT
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
566091 TAG
66 TAG
* * * *
566094 CATTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGTACAATTAGGCCTCAAAGGAACT
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
*
566159 TAA
66 TAG
* * ** *
566162 CTTTTCATCTAATTGGCATAATTGACATTTTTCTGTCAAATGCACAATTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
566227 TAG
66 TAG
* *
566230 CCTTTCATCTAACTGGTATAATTGACACATTTCTGTCAAATGCACAATTAGGCCT
1 CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCT
566285 TTAATATTTT
Statistics
Matches: 472, Mismatches: 57, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
67 1 0.00
68 470 1.00
69 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (68 bp):
CCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TAG
Found at i:566913 original size:57 final size:57
Alignment explanation
Indices: 566766--566932 Score: 212
Period size: 58 Copynumber: 2.9 Consensus size: 57
566756 ACTCACATTT
* * * *
566766 CCCAAATGAAAATTCATACATTTATTATGAATCTCTTAACGA-TTTGCACACACAGTG
1 CCCAAATGGAAATTCATACACTTAGTATGAATTTCTTAAC-ATTTTGCACACACAGTG
* *
566823 CCCAATATGGAAATTTATACACTTAGTATGAATTTCTCAACATTTTGCACACGA-AGTG
1 CCCAA-ATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACAC-ACAGTG
* *
566881 CCCAAACGGAAATTCATACACTTAGTATGAATTTTTTTAACATTTTGCACAC
1 CCCAAATGGAAATTCATACACTTAGTATGAA-TTTCTTAACATTTTGCACAC
566933 TTAGTGTCAT
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
57 30 0.31
58 65 0.68
59 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (57 bp):
CCCAAATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACACAGTG
Found at i:571572 original size:17 final size:18
Alignment explanation
Indices: 571542--571579 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
571532 AATTTTAATT
571542 AAATTAAAAATATTA-AA
1 AAATTAAAAATATTATAA
* *
571559 AAATTTAAATTATTATAA
1 AAATTAAAAATATTATAA
571577 AAA
1 AAA
571580 ATAATAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTAAAAATATTATAA
Found at i:574753 original size:28 final size:25
Alignment explanation
Indices: 574720--574784 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
574710 TAAAATTGTG
*
574720 AATATAAAAATATTCAAAAATTTTAAAA
1 AATATAAAAATATT-AAAAA--TAAAAA
574748 AATATAAAAATATTAAAAATAAAAA
1 AATATAAAAATATTAAAAATAAAAA
*
574773 AATAAAAAAATA
1 AATATAAAAATA
574785 AATTACTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 16 0.46
27 5 0.14
28 14 0.40
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (25 bp):
AATATAAAAATATTAAAAATAAAAA
Found at i:574756 original size:8 final size:8
Alignment explanation
Indices: 574720--574801 Score: 62
Period size: 8 Copynumber: 9.9 Consensus size: 8
574710 TAAAATTGTG
574720 AATATAAA
1 AATATAAA
574728 AATATTCAAA
1 AATA-T-AAA
*
574738 AATTTTAAAA
1 AA-TAT-AAA
574748 AATATAAA
1 AATATAAA
574756 AATATTAAA
1 AATA-TAAA
574765 AATA-AAA
1 AATATAAA
574772 AA-ATAAA
1 AATATAAA
*
574779 AAAAT-AA
1 AATATAAA
*
574786 ATTACTAAA
1 AATA-TAAA
574795 AATATAA
1 AATATAA
574802 CTAAAATACT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
6 1 0.02
7 14 0.23
8 17 0.28
9 16 0.27
10 11 0.18
11 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (8 bp):
AATATAAA
Found at i:574768 original size:9 final size:9
Alignment explanation
Indices: 574720--574768 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
574710 TAAAATTGTG
574720 AATA-TAAA
1 AATATTAAA
574728 AATATTCAAA
1 AATATT-AAA
*
574738 AATTTTAAA
1 AATATTAAA
574747 AA-ATATAAA
1 AATAT-TAAA
574756 AATATTAAA
1 AATATTAAA
574765 AATA
1 AATA
574769 AAAAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 5 0.14
9 20 0.57
10 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (9 bp):
AATATTAAA
Found at i:576474 original size:18 final size:18
Alignment explanation
Indices: 576451--576539 Score: 142
Period size: 18 Copynumber: 4.9 Consensus size: 18
576441 ACTGAATATT
576451 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
576469 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
576487 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
576505 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
576523 TCTCCCGAAGAACCACT
1 TGTCCCGAAGGACCACT
576540 GATAATATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.29, C:0.34, G:0.19, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:578123 original size:24 final size:22
Alignment explanation
Indices: 578073--578128 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 22
578063 AATAAAGGTA
578073 TGCATCGATGCATTCTACAGTG
1 TGCATCGATGCATTCTACAGTG
578095 T--ATCGATGCATTCCTTA-ACGTG
1 TGCATCGATGCATT-C-TACA-GTG
578117 TGCATCGATGCA
1 TGCATCGATGCA
578129 CTACCTGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 7 0.24
24 9 0.31
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (22 bp):
TGCATCGATGCATTCTACAGTG
Found at i:579753 original size:12 final size:13
Alignment explanation
Indices: 579717--579766 Score: 68
Period size: 12 Copynumber: 4.0 Consensus size: 13
579707 GCCCCGATTA
*
579717 CCCGATTACCTGG
1 CCCGATTACCCGG
579730 CCCGATTACCCGG
1 CCCGATTACCCGG
*
579743 CCCGA-TACCCGA
1 CCCGATTACCCGG
579755 CCCGA-TACCCGG
1 CCCGATTACCCGG
579767 GTATTCATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 17 0.50
13 17 0.50
ACGTcount: A:0.18, C:0.46, G:0.22, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGG
Found at i:582449 original size:28 final size:29
Alignment explanation
Indices: 582418--582474 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
582408 TTGTTTAATC
582418 AGTTTCT-ATTTGTATCTTGTATTTATTT
1 AGTTTCTAATTTGTATCTTGTATTTATTT
*
582446 AGTTTCTAATTTGTATGTTGTATTTATTT
1 AGTTTCTAATTTGTATCTTGTATTTATTT
582475 CAGTCTATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.19, C:0.05, G:0.12, T:0.63
Consensus pattern (29 bp):
AGTTTCTAATTTGTATCTTGTATTTATTT
Found at i:583717 original size:20 final size:20
Alignment explanation
Indices: 583692--583729 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
583682 CTATATGAGT
583692 TTGTTTTATTTATCTTTTGA
1 TTGTTTTATTTATCTTTTGA
*
583712 TTGTTTTATTTATGTTTT
1 TTGTTTTATTTATCTTTT
583730 AAATGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.11, T:0.74
Consensus pattern (20 bp):
TTGTTTTATTTATCTTTTGA
Found at i:594095 original size:21 final size:22
Alignment explanation
Indices: 594065--594112 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
594055 TTGATTGTCA
* * *
594065 ATTTAAATTATTAAATTATATT
1 ATTTTAATTATAAAATAATATT
594087 -TTTTAATTATAAAATAATATT
1 ATTTTAATTATAAAATAATATT
594108 ATTTT
1 ATTTT
594113 TCTAAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTAATTATAAAATAATATT
Found at i:594524 original size:3 final size:3
Alignment explanation
Indices: 594516--594563 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
594506 TTTATTTTAA
*
594516 ATT ATT ATT ATT ATT ATT ATT ATTT ACTT -TT ATT ATT ACTA ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT ATT ATT A-TT ATT ATT
594563 A
1 A
594564 CATTTTGTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
2 2 0.05
3 30 0.77
4 7 0.18
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:594564 original size:22 final size:23
Alignment explanation
Indices: 594523--594569 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
594513 TAAATTATTA
*
594523 TTATTATTATTATTATTTAC-TT
1 TTATTATTATAATTATTTACATT
594545 TTATTATTACTAATTA-TTACATT
1 TTATTATTA-TAATTATTTACATT
594568 TT
1 TT
594570 GTAGGCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTATTATAATTATTTACATT
Found at i:603852 original size:32 final size:32
Alignment explanation
Indices: 603807--603883 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
603797 AAAAATATTG
603807 AATT-AAAAAATTATTTTTTTATTTAAGTTTT
1 AATTAAAAAAATTATTTTTTTATTTAAGTTTT
603838 AATTAAAAAAATTATTTTTTTATTTAAGTTTT
1 AATTAAAAAAATTATTTTTTTATTTAAGTTTT
603870 AATTAAAAAAATTA
1 AATTAAAAAAATTA
603884 AAATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (32 bp):
AATTAAAAAAATTATTTTTTTATTTAAGTTTT
Found at i:607674 original size:3 final size:3
Alignment explanation
Indices: 607659--607755 Score: 88
Period size: 3 Copynumber: 31.7 Consensus size: 3
607649 TTCATTTAAA
* *
607659 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
607704 TAT AAT TAC TAA TAT TAT TATT TAT TAC TAA TAT TAT TAT TAAA TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT
607751 TAT TA
1 TAT TA
607756 CAAACCCAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
2 1 0.01
3 69 0.91
4 6 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:608242 original size:15 final size:15
Alignment explanation
Indices: 608222--608263 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
608212 TCTCAGCAGC
608222 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
608237 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
608252 AAAGAAGAGAAA
1 AAAGAAAAGAAA
608264 CTTACCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:608247 original size:20 final size:20
Alignment explanation
Indices: 608222--608263 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
608212 TCTCAGCAGC
*
608222 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
608242 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
608262 AA
1 AA
608264 CTTACCGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:608454 original size:13 final size:13
Alignment explanation
Indices: 608436--608466 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
608426 GGCCACCGAA
608436 GGCGGTGGCCGGC
1 GGCGGTGGCCGGC
*
608449 GGCGGTGGCTGGC
1 GGCGGTGGCCGGC
608462 GGCGG
1 GGCGG
608467 ACGAACACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.65, T:0.10
Consensus pattern (13 bp):
GGCGGTGGCCGGC
Found at i:609075 original size:21 final size:21
Alignment explanation
Indices: 609051--609093 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
609041 TATATCGTTC
*
609051 TAATTGTA-TTTTTTATTATTT
1 TAATTGTACTTGTTTA-TATTT
*
609072 TAATTTTACTTGTTTATATTT
1 TAATTGTACTTGTTTATATTT
609093 T
1 T
609094 TAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
TAATTGTACTTGTTTATATTT
Found at i:609148 original size:15 final size:14
Alignment explanation
Indices: 609129--609175 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
609119 ATATCATAAA
609129 TAATAATTTATTTT
1 TAATAATTTATTTT
*
609143 TAAATAAATTA-TTT
1 T-AATAATTTATTTT
609157 TAAT-ATTTATTTT
1 TAATAATTTATTTT
609170 TCAATA
1 T-AATA
609176 TCGAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 4 0.15
13 7 0.26
14 8 0.30
15 8 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATAATTTATTTT
Found at i:609868 original size:21 final size:20
Alignment explanation
Indices: 609835--609877 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
609825 TTTAAATTTT
609835 TTTTATATATATACATATTA
1 TTTTATATATATACATATTA
* *
609855 TTTTAGTATTTATATATATTA
1 TTTTA-TATATATACATATTA
609876 TT
1 TT
609878 AATATTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTATATATATACATATTA
Found at i:620564 original size:8 final size:8
Alignment explanation
Indices: 620543--620584 Score: 66
Period size: 8 Copynumber: 5.0 Consensus size: 8
620533 TATGCTTGAA
620543 AAAAAAAG
1 AAAAAAAG
620551 AGAAAAAAG
1 A-AAAAAAG
620560 AAAAAAAG
1 AAAAAAAG
620568 AGAAAAAAG
1 A-AAAAAAG
620577 AAAAAAAG
1 AAAAAAAG
620585 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 16 0.50
9 16 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:620565 original size:17 final size:17
Alignment explanation
Indices: 620543--620584 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
620533 TATGCTTGAA
620543 AAAAAAAGAGAAAAAAG
1 AAAAAAAGAGAAAAAAG
620560 AAAAAAAGAGAAAAAAG
1 AAAAAAAGAGAAAAAAG
620577 AAAAAAAG
1 AAAAAAAG
620585 GGGGGTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAGAAAAAAG
Found at i:621859 original size:83 final size:83
Alignment explanation
Indices: 621719--622357 Score: 1063
Period size: 83 Copynumber: 7.7 Consensus size: 83
621709 ACATTAACTG
*
621719 GAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
1 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
621783 GAACCAATCATTGAATTTA
65 GAACCAATCATTGAATTTA
*
621802 AAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
*
621867 AACAAATCATTGAATTTA
66 AACCAATCATTGAATTTA
* *
621885 AAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAA
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
621950 AACCAATCATTGAATTTA
66 AACCAATCATTGAATTTA
*
621968 AAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
622033 AACCAATCATTGAATTTA
66 AACCAATCATTGAATTTA
*
622051 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-TA
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
622115 -AACCAATCATTGAATTTA
65 GAACCAATCATTGAATTTA
* *
622133 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGAACAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
*
622198 AACCAATCATTGAATTTG
66 AACCAATCATTGAATTTA
* * *
622216 GAAGATGAATGTGCTC-ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATA
1 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
*
622280 GAACCAATCATTGAATTTG
65 GAACCAATCATTGAATTTA
* *
622299 GAAGATGAATGTGCTC-ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
622358 TGGTAGGAAC
Statistics
Matches: 534, Mismatches: 17, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
81 3 0.01
82 76 0.14
83 450 0.84
84 5 0.01
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
AACCAATCATTGAATTTA
Found at i:622259 original size:248 final size:249
Alignment explanation
Indices: 621717--622363 Score: 1104
Period size: 248 Copynumber: 2.6 Consensus size: 249
621707 AAACATTAAC
621717 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
*
621782 AGAACCAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
621847 TATCTGATCTGG-TTGGACAGAACAAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTT
131 TATCTGATCTGGTTTGG-TAGAACAAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTT
* *
621911 CTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAAACCAATCATTGAATT
195 CTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGAACAAAACCAATCATTGAATT
** *
621966 TAAAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
1 TGGAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
622030 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
65 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
* *
622095 TTATCTGATCTGGTTTGGTA-AACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTT
130 TTATCTGATCTGGTTTGGTAGAACAAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTT
*
622159 CTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGAACAGAACCAATCATTGAATT
195 CTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGAACAAAACCAATCATTGAATT
* *
622214 TGGAAGATGAATGTGCTCATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAT
1 TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
* * *
622279 AGAACCAATCATTGAATTTGGAAGATGAATGTGCTC-ATAGCATCTTATGGAAGTGTTCTTTGAG
66 AGAACCAATCATTGAATTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAG
622343 TTATCTGATCTGGTTTGGTAG
130 TTATCTGATCTGGTTTGGTAG
622364 GAACTACAGA
Statistics
Matches: 375, Mismatches: 18, Indels: 10
0.93 0.04 0.02
Matches are distributed among these distances:
248 232 0.62
249 139 0.37
250 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (249 bp):
TGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
AGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGGTTTGGTAGAACAAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTTC
TGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGAACAAAACCAATCATTGAATT
Found at i:622322 original size:331 final size:332
Alignment explanation
Indices: 621719--622357 Score: 1063
Period size: 331 Copynumber: 1.9 Consensus size: 332
621709 ACATTAACTG
621719 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
621784 AACCAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
66 AACCAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* * * *
621849 TCTGATCTGGTTGGACAGAACAAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTTCTG
131 TCCGATCTGGTTGAACAGAACAAATCATTGAATTTAAAAGATGAATGTGCCAATAGCATCTTATG
*
621914 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAAACCAATCATTGAATTTAAAAGATGAATT
196 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAAACCAATCATTGAATTTAAAAGATGAATG
*
621979 TGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATT
261 TGCCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATT
622044 GAATTTA
326 GAATTTA
* *
622051 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-T
1 GAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGAC
*
622114 A-AACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
64 AGAACCAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
* **
622178 TATCCGATCTGGTTGAACAGAACCAATCATTGAATTTGGAAGATGAATGTGCTC-ATAGCATCTT
129 TATCCGATCTGGTTGAACAGAACAAATCATTGAATTTAAAAGATGAATGTGC-CAATAGCATCTT
* * **
622242 ATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATAGAACCAATCATTGAATTTGGAAGATGA
193 ATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAAACCAATCATTGAATTTAAAAGATGA
622307 ATGTGCTC-ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
258 ATGTGC-CAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
622358 TGGTAGGAAC
Statistics
Matches: 287, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
331 226 0.79
332 57 0.20
333 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (332 bp):
GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
AACCAATCATTGAATTTAAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TCCGATCTGGTTGAACAGAACAAATCATTGAATTTAAAAGATGAATGTGCCAATAGCATCTTATG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAAACCAATCATTGAATTTAAAAGATGAATG
TGCCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATT
GAATTTA
Found at i:623304 original size:113 final size:114
Alignment explanation
Indices: 623100--623858 Score: 1081
Period size: 113 Copynumber: 6.7 Consensus size: 114
623090 GAATCCATAA
623100 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* * * *
623165 GTTCATAATGAAAAGAACTTGTTCAACCTTTTGCCT-GAATTCATCACT
66 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCCATCACT
* *
623213 TGACGAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* *
623278 ATTCATAATGAGAAGAATTTGTTCAACCTTTT-ACTCAAATCCATCACT
66 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCCATCACT
*
623326 TGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* *
623391 GTTCATAATGAGAAGAATTTGTTCAACTTTTTG-CTTAAATCCATCACT
66 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCCATCACT
* * * **** * *
623439 TGATAGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAATAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
*
623504 GTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTCAAATCCATCATT
66 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCCATCACT
* *
623552 TGATGGATCAGCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* ** * *
623617 GTTCATAATGAGAAGAACTTGTTCAACCTTTTG-CTTGAATTCATCATT
66 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCCATCACT
* * * * * *
623665 TGATGGATCAACATTGCCAG-GTAGAGTTCCTAATGAGAAGAACTCGTCATCTGAAGAAAGAAGA
1 TGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGA
*
623729 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-TTCAAATCCATCACT
62 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCCATCACT
*
623781 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCA--T-ATGAA-GAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
623842 GTTCATAATGAGAAGAA
66 GTTCATAATGAGAAGAA
623859 CTAATCTGAA
Statistics
Matches: 580, Mismatches: 59, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
109 26 0.04
110 4 0.01
111 1 0.00
112 3 0.01
113 445 0.77
114 1 0.00
115 1 0.00
116 98 0.17
117 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (114 bp):
TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCCATCACT
Found at i:623851 original size:36 final size:36
Alignment explanation
Indices: 623804--623882 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
623794 TTTCCAGAGA
* *
623804 AAGTTCATAATGAGAAGAACTCATATGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTAATATGAAAAAGAAG
*
623840 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
1 AAGTTCATAATGAGAAGAACTAATATGAAAAAGAAG
623876 AAGTTCA
1 AAGTTCA
623883 CCATGAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (36 bp):
AAGTTCATAATGAGAAGAACTAATATGAAAAAGAAG
Found at i:623855 original size:20 final size:20
Alignment explanation
Indices: 623804--623858 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
623794 TTTCCAGAGA
623804 AAGTTCATAAT--G-AGAAG
1 AAGTTCATAATGAGAAGAAG
*
623821 AA-CTCAT-ATGAAGAAGAAG
1 AAGTTCATAATG-AGAAGAAG
623840 AAGTTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
623859 CTAATCTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 2 0.07
16 4 0.13
17 2 0.07
18 1 0.03
19 7 0.23
20 11 0.37
21 3 0.10
ACGTcount: A:0.51, C:0.07, G:0.22, T:0.20
Consensus pattern (20 bp):
AAGTTCATAATGAGAAGAAG
Found at i:624149 original size:3 final size:3
Alignment explanation
Indices: 624134--624214 Score: 83
Period size: 3 Copynumber: 26.7 Consensus size: 3
624124 TTCATTTAAA
*
624134 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
624179 AAT TAT AAT TAC TAA TAT TAT TAT TAAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
624215 CAAACCCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 60 0.94
4 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:624686 original size:15 final size:15
Alignment explanation
Indices: 624666--624707 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
624656 TCTCAGCAGC
624666 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
624681 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
624696 AAAGAAGAGAAA
1 AAAGAAAAGAAA
624708 CTTACCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:624691 original size:20 final size:20
Alignment explanation
Indices: 624666--624707 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
624656 TCTCAGCAGC
*
624666 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
624686 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
624706 AA
1 AA
624708 CTTACCGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:624897 original size:13 final size:13
Alignment explanation
Indices: 624879--624909 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
624869 GGCCACCGAA
624879 GGCGGTGGCCGGC
1 GGCGGTGGCCGGC
*
624892 GGCGGTGGCTGGC
1 GGCGGTGGCCGGC
624905 GGCGG
1 GGCGG
624910 ACGAACACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.65, T:0.10
Consensus pattern (13 bp):
GGCGGTGGCCGGC
Found at i:625526 original size:21 final size:21
Alignment explanation
Indices: 625502--625544 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
625492 TATATCGTTC
*
625502 TAATTGTA-TTTTTTATTATTT
1 TAATTGTACTTGTTTA-TATTT
*
625523 TAATTTTACTTGTTTATATTT
1 TAATTGTACTTGTTTATATTT
625544 T
1 T
625545 TAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
TAATTGTACTTGTTTATATTT
Found at i:625611 original size:14 final size:15
Alignment explanation
Indices: 625580--625609 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
625570 ATATCATAAA
625580 TAAATAAATTATTTT
1 TAAATAAATTATTTT
625595 TAAATAAATTATTTT
1 TAAATAAATTATTTT
625610 AATATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATAAATTATTTT
Found at i:636375 original size:20 final size:20
Alignment explanation
Indices: 636350--636401 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
636340 AAATTGTCCT
*
636350 GAATGACCTATGTATATCTC
1 GAATGACCTATGTATATCCC
* *
636370 GAATGACCTCTGTATTTCCC
1 GAATGACCTATGTATATCCC
636390 GAATGACCTATG
1 GAATGACCTATG
636402 AACCCTCGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (20 bp):
GAATGACCTATGTATATCCC
Found at i:644846 original size:17 final size:15
Alignment explanation
Indices: 644821--644871 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
644811 ATAACATATA
*
644821 AATATTTTAATGTTATT
1 AATAATTTAAT-TT-TT
644838 AATAATTTAATTTTT
1 AATAATTTAATTTTT
*
644853 AA-AATTTAAAATTTT
1 AATAATTT-AATTTTT
644868 AATA
1 AATA
644872 TACTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 5 0.17
15 12 0.40
16 3 0.10
17 10 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
AATAATTTAATTTTT
Found at i:645343 original size:31 final size:31
Alignment explanation
Indices: 645298--645359 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
645288 ACTATTGAGA
645298 GACTAAACATGAACGGATCGATAAAGTTAGG
1 GACTAAACATGAACGGATCGATAAAGTTAGG
* *
645329 GACTAAA-ATCGAACGGATTGATAACGTTAGG
1 GACTAAACAT-GAACGGATCGATAAAGTTAGG
645360 AACCATTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (31 bp):
GACTAAACATGAACGGATCGATAAAGTTAGG
Found at i:646791 original size:5 final size:5
Alignment explanation
Indices: 646781--646989 Score: 404
Period size: 5 Copynumber: 42.2 Consensus size: 5
646771 CATCGACAAC
646781 ATATA ATATA ATATA ATATA ATAT- A-ATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
646829 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
646879 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
646929 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
646979 ATATA ATATA A
1 ATATA ATATA A
646990 ATTTAGACAA
Statistics
Matches: 202, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
3 2 0.01
4 2 0.01
5 198 0.98
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:649203 original size:19 final size:19
Alignment explanation
Indices: 649175--649225 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
649165 TAATTAAATC
*
649175 AGAGTCCATCGATGCATGA
1 AGAGTGCATCGATGCATGA
*
649194 AGAGTGCATCGGTGCATGA
1 AGAGTGCATCGATGCATGA
649213 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
649226 TTTCAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Found at i:651906 original size:24 final size:22
Alignment explanation
Indices: 651835--651938 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 22
651825 CATGATCTTG
651835 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
*
651858 TGCATCGGTGCATCATGT---GGA
1 TGCATCGATGCA-CAT-TCAAGGA
651879 TGCATCGATGCACATTCAAAGGAA
1 TGCATCGATGCACATTC-AAGG-A
651903 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AA-GGA
*
651927 TACATCGATGCA
1 TGCATCGATGCA
651939 TTGTTAAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 12 0.17
22 2 0.03
23 13 0.19
24 36 0.51
25 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:657868 original size:64 final size:64
Alignment explanation
Indices: 657800--657960 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
657790 TAGCCTGGTG
* * *
657800 CATCGATGCATGGCTTGTGCATCTATGCATCAAATACATTCGATGTTTTAATTAAATCA-GAGTA
1 CATCGATGCATGGATTGTGCATCGATGCATCAAATACATTCGATGTTTCAATTAAATCATGA-TA
* ** * * * * * *
657864 CATCGATGCATGAAGAGTGCATCGGTGCATGAAATGCATTCGATGTTTCAATTTATTCATTGATG
1 CATCGATGCATGGATTGTGCATCGATGCATCAAATACATTCGATGTTTCAATTAAATCA-TGATA
657929 CATCGATGCATGGTATTGATGCATCGATGCAT
1 CATCGATGCATGG-ATTG-TGCATCGATGCAT
657961 GCCTTTGAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
64 48 0.62
65 13 0.17
66 4 0.05
67 12 0.16
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (64 bp):
CATCGATGCATGGATTGTGCATCGATGCATCAAATACATTCGATGTTTCAATTAAATCATGATA
Found at i:657886 original size:19 final size:19
Alignment explanation
Indices: 657858--657908 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
657848 TAATTAAATC
*
657858 AGAGTACATCGATGCATGA
1 AGAGTGCATCGATGCATGA
*
657877 AGAGTGCATCGGTGCATGA
1 AGAGTGCATCGATGCATGA
657896 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
657909 TTTCAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Found at i:657946 original size:21 final size:21
Alignment explanation
Indices: 657922--657961 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
657912 CAATTTATTC
657922 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
657943 ATTGATGCATCGATGCATG
1 ATTGATGCATCGATGCATG
657962 CCTTTGAAAA
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:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:660940 original size:26 final size:26
Alignment explanation
Indices: 660885--660967 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 26
660875 ATTTAACTCA
*
660885 AATTTAAAAAATTTCAAATCAAATTG
1 AATTTAAAAAATTACAAATCAAATTG
* * *
660911 AATTTAAAAAATTACGAGTCGAATAT-
1 AATTTAAAAAATTACAAATCAAAT-TG
* *
660937 AATTT-AAAATTTA-AAATAAAATT-
1 AATTTAAAAAATTACAAATCAAATTG
660960 AATTTAAA
1 AATTTAAA
660968 TTAAAATTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 6 0.13
24 7 0.15
25 7 0.15
26 25 0.54
27 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (26 bp):
AATTTAAAAAATTACAAATCAAATTG
Found at i:660965 original size:16 final size:16
Alignment explanation
Indices: 660944--660975 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
660934 TATAATTTAA
660944 AATTTAAAATAAAATT
1 AATTTAAAATAAAATT
*
660960 AATTTAAATTAAAATT
1 AATTTAAAATAAAATT
660976 TTCAAATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAATAAAATT
Found at i:661189 original size:20 final size:20
Alignment explanation
Indices: 661164--661209 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
661154 CAGTTAAGTA
661164 AATATTTTATTAAAAATATT
1 AATATTTTATTAAAAATATT
*
661184 AATATTTTATTGAAAATATT
1 AATATTTTATTAAAAATATT
661204 AATATT
1 AATATT
661210 CTTTTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATATTTTATTAAAAATATT
Found at i:661243 original size:12 final size:12
Alignment explanation
Indices: 661226--661250 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
661216 ATATTTTTAG
661226 TAAAATATTATT
1 TAAAATATTATT
661238 TAAAATATTATT
1 TAAAATATTATT
661250 T
1 T
661251 TTTTTACTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:662684 original size:2 final size:2
Alignment explanation
Indices: 662677--662726 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
662667 AGAAACATGC
662677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
662718 AT AT AT AT A
1 AT AT AT AT A
662727 CTTTAAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:664954 original size:17 final size:18
Alignment explanation
Indices: 664934--664967 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
664924 TAGTTATTGT
664934 AATTA-TTGTCCTATTAA
1 AATTACTTGTCCTATTAA
*
664951 AATTACTTGTCTTATTA
1 AATTACTTGTCCTATTA
664968 GTTCTGTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (18 bp):
AATTACTTGTCCTATTAA
Done.