Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008365.1 Hibiscus syriacus cultivar Beakdansim tig00111106_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: 68636
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2741 original size:22 final size:22
Alignment explanation
Indices: 2714--2771 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
2704 AAACCATTCA
2714 GGGGGAATCGGTTCCCTCCTTG
1 GGGGGAATCGGTTCCCTCCTTG
2736 GGGGGAATCGGTTCCCTCCTTG
1 GGGGGAATCGGTTCCCTCCTTG
2758 GGGGGAATCGGTTC
1 GGGGGAATCGGTTC
2772 TCTCTGGGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.10, C:0.24, G:0.40, T:0.26
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTCCTTG
Found at i:3278 original size:13 final size:13
Alignment explanation
Indices: 3260--3304 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
3250 CCATGTATAG
3260 TATATATAAACTCTA
1 TATATATAAA--CTA
*
3275 TATATATAACCTA
1 TATATATAAACTA
3288 TATATATAAACTA
1 TATATATAAACTA
3301 TATA
1 TATA
3305 AAGTAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 19 0.68
15 9 0.32
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:3280 original size:15 final size:15
Alignment explanation
Indices: 3260--3304 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
3250 CCATGTATAG
3260 TATATATAAACTCTA
1 TATATATAAACTCTA
3275 TATATAT-AAC-CTA
1 TATATATAAACTCTA
*
3288 TATATATAAACTATA
1 TATATATAAACTCTA
3303 TA
1 TA
3305 AAGTAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 10 0.37
14 6 0.22
15 11 0.41
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATATAAACTCTA
Found at i:3828 original size:15 final size:15
Alignment explanation
Indices: 3803--3839 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
3793 TAAAACCATG
3803 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
3819 TATATATATATAAAG
1 TATATATATATAAAC
3834 TATATA
1 TATATA
3840 AAGTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:3925 original size:7 final size:7
Alignment explanation
Indices: 3915--3993 Score: 77
Period size: 7 Copynumber: 11.3 Consensus size: 7
3905 TAGTTTATAA
3915 AAACCCT
1 AAACCCT
3922 AAACCCT
1 AAACCCT
3929 AAACCCT
1 AAACCCT
3936 AAACCCT
1 AAACCCT
*
3943 AAACCAT
1 AAACCCT
**
3950 AAACTTT
1 AAACCCT
*
3957 AAACCAT
1 AAACCCT
*
3964 AAACACT
1 AAACCCT
**
3971 AAACATT
1 AAACCCT
* *
3978 AAATCAT
1 AAACCCT
3985 AAACCCT
1 AAACCCT
3992 AA
1 AA
3994 TGTAAATGGA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:3940 original size:21 final size:21
Alignment explanation
Indices: 3915--3993 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 21
3905 TAGTTTATAA
* **
3915 AAACCCTAAACCCTAAACCCT
1 AAACCATAAACCCTAAACATT
* * *
3936 AAACCCTAAACCATAAACTTT
1 AAACCATAAACCCTAAACATT
*
3957 AAACCATAAACACTAAACATT
1 AAACCATAAACCCTAAACATT
*
3978 AAATCATAAACCCTAA
1 AAACCATAAACCCTAA
3994 TGTAAATGGA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (21 bp):
AAACCATAAACCCTAAACATT
Found at i:4267 original size:545 final size:533
Alignment explanation
Indices: 3042--4492 Score: 2007
Period size: 545 Copynumber: 2.7 Consensus size: 533
3032 GTTTTCAACA
* * *
3042 GCTATTAATGTGAATTAACCTAACACGCAACTAAAATATTAATTATGCAAATAAAATTAATATGG
1 GCTATTAATGTGAATTAACCTAACATGCAACTAAAATATTAATTATGCAAATGAAATTAATATGA
* * *
3107 CATGTACTACTATTTATGAATCATGTAATATGCAATGTGACATACTAATTATTTAACACTTAATT
66 CATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACATAATT
*
3172 AATCATGTTTTATATAATATACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAAT
131 AATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAAT
3237 ATGTATGTATAAACCATGTATAGTATATATAAACTCTATATATATAACCTATATATATAAACTAT
196 ATGTATGTATAAACCATGTATAGTATATATAAA--C--------T-A--TATATATATAAACTAT
*
3302 ATAAAGTAAATTACTTATATAGTTTATAGAAAATCTATGCATAAACTATATAAAGTAATAAAGTA
248 ATAAAGTAAATTACTTATATAGTTTATAGAAAAACTATGCATAAACTATATAAAGTAATAAAGTA
* * *
3367 TATATTTTATAGAAACCCTAAACCCTAAA--TAA--T-AACCCTAAACTCTAAACTTTAAACCAT
313 TATAGTTTATAAAAACCCTAAACCCTAAACCTAACCTAAACCCTAAACTCTAAACATTAAACCAT
* * * *
3427 AAACCCTACTATAAATGGAATAGCACTAATGCGTATATATTTTTAATAAAAGAGTGGGCTTATGT
378 AAACCCTAATATAAATGGAATAACACTAATGCATATATATTTGTAATAAAAGAGTGGGC-T-TGT
* *
3492 ATTGGGCCTATGTAAACTAATGTAAATGTACTGCACTATTGCAAATGGACTTATTTTTGGGTTTT
441 ATT-GGCC----TAAACTAATGTAAATGAACTGCACTATTGCAAATGGACTTATTTTTGAGTTTT
*
3557 ATTATTACTTATTTATAACAACAAAATAAATAG
501 ATTATTACTTATTCATAACAACAAAATAAATAG
3590 GCTATTAATGTGAATTAACCTAACATGCAACTAAAAATATTAATTATGCAAATGAAATTAATATG
1 GCTATTAATGTGAATTAACCTAACATGCAACT-AAAATATTAATTATGCAAATGAAATTAATATG
*
3655 ACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCTAAT
65 ACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACATAAT
3720 TAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAA
130 TAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAA
* *
3785 TATGTA-GT-TAAAACCATGTATAGTATATATAAACTATATATATATAAAGTATATAAAGTATAT
195 TATGTATGTAT-AAACCATGTATAGTATATATAAACTATATATATATAAACTATATAAAGTAAAT
* * *
3848 TACTTATATAGTTTATGGAAAAACTCTGCATAAACTATATAAAAGTAATAAACTATATAGTTTAT
259 TACTTATATAGTTTATAGAAAAACTATGCATAAACTATAT-AAAGTAATAAAGTATATAGTTTAT
3913 AAAAACCCTAAACCCTAAACCCTAAACCCTAAACCATAAACTTTAAACCATAAACACTAAACATT
323 AAAAACCCTAAACCCTAAA-CCT-AA-CCTAAACC-----C--TAAA-C-T-----CTAAACATT
* * *
3978 AAATCATAAACCCTAATGTAAATGGACTAACACTAATGCATATATATTTGTAATAAAAGAGTGGG
371 AAACCATAAACCCTAATATAAATGGAATAACACTAATGCATATATATTTGTAATAAAAGAGTGGG
* *
4043 C-T-TA-T-G-C-AAGCTAATGTAAATGAACTAGCACTATTGCAAATGGACTTATTTTTTAGTTT
436 CTTGTATTGGCCTAAACTAATGTAAATGAACT-GCACTATTGCAAATGGACTTATTTTTGAGTTT
*
4102 TATTATTACTTATTCATAACAACAAAATAAATTG
500 TATTATTACTTATTCATAACAACAAAATAAATAG
*
4136 GCTATTAATGTGAATTAACGTAACATGCAACTAAAATATTAATTATGCAAATGAAATTAATATGA
1 GCTATTAATGTGAATTAACCTAACATGCAACTAAAATATTAATTATGCAAATGAAATTAATATGA
** *
4201 CACATACTACTATTTATGAACCATATAATATGCAACGTGACATACTAATTATTTAACACATAATT
66 CATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACATAATT
* * *
4266 AATCATGTTTTATATAATTGACATTTTAATAATTTTAATAATTTTATTAAATAATTTTATATAAT
131 AATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAAT
* * * *
4331 ATATATGTATAAACCATGCAT-G-ATATATATA-TATATATATATAAACTATATATAGTAAATTA
196 ATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATAAACTATATAAAGTAAATTA
* *
4393 CTTATATAGTTTATAGAAATACTATGCATAAACTATATAAATTAATAAAGTATATAGTTTATAAA
261 CTTATATAGTTTATAGAAAAACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAAA
*
4458 AACCCTAAACCTTAAACCATAACCATAAACCCTAA
326 AACCCTAAACCCTAAACC-TAACC-TAAACCCTAA
4493 TATAAATGGA
Statistics
Matches: 824, Mismatches: 49, Indels: 74
0.87 0.05 0.08
Matches are distributed among these distances:
534 3 0.00
535 62 0.08
536 41 0.05
537 1 0.00
538 1 0.00
539 1 0.00
540 4 0.00
541 10 0.01
542 41 0.05
543 64 0.08
544 12 0.01
545 178 0.22
546 106 0.13
547 2 0.00
548 56 0.07
549 163 0.20
550 1 0.00
551 5 0.01
552 1 0.00
553 2 0.00
554 2 0.00
555 1 0.00
558 67 0.08
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (533 bp):
GCTATTAATGTGAATTAACCTAACATGCAACTAAAATATTAATTATGCAAATGAAATTAATATGA
CATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACATAATT
AATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAAT
ATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATAAACTATATAAAGTAAATTA
CTTATATAGTTTATAGAAAAACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAAA
AACCCTAAACCCTAAACCTAACCTAAACCCTAAACTCTAAACATTAAACCATAAACCCTAATATA
AATGGAATAACACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTGTATTGGCCTAAACTAA
TGTAAATGAACTGCACTATTGCAAATGGACTTATTTTTGAGTTTTATTATTACTTATTCATAACA
ACAAAATAAATAG
Found at i:4683 original size:23 final size:24
Alignment explanation
Indices: 4656--4705 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
4646 TTATTTTTTC
*
4656 TTTATATAAATTAAACTATA-TAA
1 TTTATAAAAATTAAACTATATTAA
4679 TTTATAAAAATTAAACTATATTAA
1 TTTATAAAAATTAAACTATATTAA
4703 TTT
1 TTT
4706 TCCTTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTATAAAAATTAAACTATATTAA
Found at i:5267 original size:18 final size:18
Alignment explanation
Indices: 5234--5279 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5224 AGCCGATTTC
*
5234 AGTCAGTTTTATAGGTCG
1 AGTCAGTTTTACAGGTCG
*
5252 AGTCAGTTTTGCAGGTCG
1 AGTCAGTTTTACAGGTCG
* *
5270 GGTTAGTTTT
1 AGTCAGTTTT
5280 TTACACCCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.11, G:0.30, T:0.41
Consensus pattern (18 bp):
AGTCAGTTTTACAGGTCG
Found at i:13809 original size:12 final size:12
Alignment explanation
Indices: 13785--13826 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
13775 AACAGTGCCG
13785 TGAACAGT-A-A
1 TGAACAGTAACA
13795 TGAACAGTAACA
1 TGAACAGTAACA
* *
13807 TGAACAATATCA
1 TGAACAGTAACA
13819 TGAACAGT
1 TGAACAGT
13827 TCGTTACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 8 0.30
11 1 0.04
12 18 0.67
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (12 bp):
TGAACAGTAACA
Found at i:14600 original size:30 final size:29
Alignment explanation
Indices: 14564--14653 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
14554 CCCGAAGGAC
*
14564 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAAAGGTCACAA-GAACCTCGGTAA
* * *
14594 CTATCCAAAGGTTATAAAGAACCTCGGCAA
1 CTATCCAAAGGTCA-CAAGAACCTCGGTAA
* * * *
14624 CTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAAAGGTCAC-AAGAACCTCGGTAA
14654 ACTGTCCATA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
30 45 0.96
31 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (29 bp):
CTATCCAAAGGTCACAAGAACCTCGGTAA
Found at i:14729 original size:32 final size:32
Alignment explanation
Indices: 14674--14747 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
14664 TGTTCTTTAG
14674 AACATAGGT-ATATTATCCATATGTCCCGA-AA
1 AACATAGGTAATATTATCCATATGTCCC-ATAA
* * * *
14705 GACATAGGTAATTTTGTCCATATGTTCCATAA
1 AACATAGGTAATATTATCCATATGTCCCATAA
14737 AACATAGGTAA
1 AACATAGGTAA
14748 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (32 bp):
AACATAGGTAATATTATCCATATGTCCCATAA
Found at i:15283 original size:16 final size:16
Alignment explanation
Indices: 15262--15292 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
15252 CTCTTATGTC
15262 TTCTCATATACATATA
1 TTCTCATATACATATA
15278 TTCTCATATACATAT
1 TTCTCATATACATAT
15293 CAATAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCTCATATACATATA
Found at i:20720 original size:2 final size:2
Alignment explanation
Indices: 20713--20745 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20703 ACTTCCCAGT
20713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20746 CTTCACAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26563 original size:21 final size:21
Alignment explanation
Indices: 26539--26599 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
26529 GGCAACCAAC
26539 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
26560 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
26575 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
26596 TTTG
1 TTTG
26600 GTAAAGTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
17 4 0.13
19 4 0.13
21 13 0.43
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:26585 original size:36 final size:35
Alignment explanation
Indices: 26538--26608 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
26528 TGGCAACCAA
26538 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
26574 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
26609 GGTAGATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
Found at i:26814 original size:30 final size:30
Alignment explanation
Indices: 26743--26802 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
26733 ACAATTTAAG
26743 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
26773 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
26803 ATTCAAAGTT
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:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:26888 original size:8 final size:8
Alignment explanation
Indices: 26875--27057 Score: 57
Period size: 8 Copynumber: 24.9 Consensus size: 8
26865 GGGTGTCAAA
26875 ATGCATCC
1 ATGCATCC
26883 ATGCATCC
1 ATGCATCC
*
26891 CTGCATCC
1 ATGCATCC
* *
26899 CTGCAGTGC
1 ATGCA-TCC
26908 --GCATCC
1 ATGCATCC
26914 ATGCAT-C
1 ATGCATCC
*
26921 -TGCA-CTA
1 ATGCATC-C
*
26928 ATGCATCG
1 ATGCATCC
26936 ATGCAT-C
1 ATGCATCC
26943 ATGCA---
1 ATGCATCC
26948 ATGCATCC
1 ATGCATCC
26956 ATGCATCC
1 ATGCATCC
** *
26964 AAACATCGA
1 ATGCATC-C
*
26973 ATGCAAT-T
1 ATGC-ATCC
*
26981 AGTGCATCG
1 A-TGCATCC
26990 ATGCATCC
1 ATGCATCC
*
26998 TTGC-T--
1 ATGCATCC
*
27003 ATGCATCA
1 ATGCATCC
27011 ATGCATCC
1 ATGCATCC
27019 -TGC-T--
1 ATGCATCC
*
27023 ATGCATCG
1 ATGCATCC
27031 ATGCATCC
1 ATGCATCC
27039 -TG---CC
1 ATGCATCC
27043 ATGCATCC
1 ATGCATCC
27051 ATGCATC
1 ATGCATC
27058 AAGGATGCAA
Statistics
Matches: 132, Mismatches: 18, Indels: 50
0.66 0.09 0.25
Matches are distributed among these distances:
4 2 0.02
5 13 0.10
6 9 0.07
7 15 0.11
8 82 0.62
9 9 0.07
10 2 0.02
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (8 bp):
ATGCATCC
Found at i:26952 original size:20 final size:20
Alignment explanation
Indices: 26927--27058 Score: 89
Period size: 20 Copynumber: 6.8 Consensus size: 20
26917 CATCTGCACT
26927 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATCATGC
*
26947 AATGCATCCATGCATC---C
1 AATGCATCGATGCATCATGC
* *
26964 AA-ACATCGAATGCA--AT-T
1 AATGCATCG-ATGCATCATGC
* *
26981 AGTGCATCGATGCATCCTTGC
1 AATGCATCGATGCAT-CATGC
* * *
27002 TATGCATCAATGCATCCTGC
1 AATGCATCGATGCATCATGC
* *
27022 TATGCATCGATGCATCCTGC
1 AATGCATCGATGCATCATGC
* *
27042 CATGCATCCATGCATCA
1 AATGCATCGATGCATCA
27059 AGGATGCAAC
Statistics
Matches: 88, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
16 4 0.05
17 14 0.16
18 5 0.06
20 53 0.60
21 12 0.14
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (20 bp):
AATGCATCGATGCATCATGC
Found at i:32583 original size:3 final size:3
Alignment explanation
Indices: 32575--32616 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
32565 TTTTATTAAC
*
32575 TTA TTA TTA TTA TTA TTA TTA TTTA CTAA TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TT
32617 TTACAGGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
3 27 0.79
4 5 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40043 original size:15 final size:15
Alignment explanation
Indices: 40023--40053 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40013 TAACAAATAG
40023 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
40038 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
40053 A
1 A
40054 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:40270 original size:20 final size:20
Alignment explanation
Indices: 40214--40264 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
40204 ATCTTATTAT
40214 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
*
40234 CTGGTAATCTTTTATTCTCA
1 CTGGTAATCTTTTATTCCCA
40254 CTGGTAATCTT
1 CTGGTAATCTT
40265 ACATTCCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:45668 original size:21 final size:21
Alignment explanation
Indices: 45577--45695 Score: 87
Period size: 21 Copynumber: 5.7 Consensus size: 21
45567 GACTCATCTG
*
45577 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
45599 T-ATCATTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
45619 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
45640 ACACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
45661 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
45682 CCACCATTCAAGAG
1 TCATCGTTCAAGAG
45696 CCCGCTTCAC
Statistics
Matches: 72, Mismatches: 24, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
20 3 0.04
21 68 0.94
22 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:45674 original size:42 final size:42
Alignment explanation
Indices: 45602--45695 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
45592 CCTCCCCTAT
*
45602 CATTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCACAC
1 CATTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCACAC
* * ** * *
45644 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCACAC
45686 CATTCAAGAG
1 CATTCAAGAG
45696 CCCGCTTCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.20
Consensus pattern (42 bp):
CATTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCACAC
Found at i:47078 original size:14 final size:14
Alignment explanation
Indices: 47059--47094 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
47049 ATTGTTTAAT
47059 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
47073 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
47087 TGATTTGT
1 TGATTTGT
47095 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:47221 original size:20 final size:21
Alignment explanation
Indices: 47190--47228 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
47180 TGTTAAATGC
47190 AAAATAGACTATCGCAACGCG
1 AAAATAGACTATCGCAACGCG
47211 AAAAT-GACTATCGCAACG
1 AAAATAGACTATCGCAACG
47229 AGAGAATCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (21 bp):
AAAATAGACTATCGCAACGCG
Found at i:47239 original size:14 final size:14
Alignment explanation
Indices: 47220--47273 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
47210 GAAAATGACT
47220 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
47234 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
47253 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
47267 ATCGCAA
1 ATCGCAA
47274 TGCGAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:47257 original size:19 final size:19
Alignment explanation
Indices: 47233--47298 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
47223 GCAACGAGAG
47233 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
47252 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
47266 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
47285 AATCGCAACGCGAA
1 AATCGCAATGCGAA
47299 GCTAAATTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:47257 original size:33 final size:33
Alignment explanation
Indices: 47200--47294 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
47190 AAAATAGACT
* **
47200 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
47234 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
47267 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
47295 CGAAGCTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:47367 original size:33 final size:33
Alignment explanation
Indices: 47311--47417 Score: 169
Period size: 33 Copynumber: 3.2 Consensus size: 33
47301 TAAATTCGCT
*
47311 TTGCGATTTTCATTTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCA-ATTCGCATTGCGATTCTCTCG
*
47345 TTGCGATTTTCAATTCGCATTGCGATTATCTCG
1 TTGCGATTTTCAATTCGCATTGCGATTCTCTCG
* *
47378 TTGCGATTTTCAATTCACATTGCAATTCTCTCG
1 TTGCGATTTTCAATTCGCATTGCGATTCTCTCG
47411 TTGCGAT
1 TTGCGAT
47418 AGTTATTTCC
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 56 0.82
34 12 0.18
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCAATTCGCATTGCGATTCTCTCG
Found at i:47434 original size:20 final size:20
Alignment explanation
Indices: 47409--47497 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
47399 GCAATTCTCT
*
47409 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
47429 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
47449 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
47469 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
47489 CGTTGCGAT
1 CGTTGCGAT
47498 TTCCGCGTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 63 0.97
21 2 0.03
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:51350 original size:45 final size:47
Alignment explanation
Indices: 51298--51386 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
51288 TCGAATAAAT
51298 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
*
51343 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
51387 TAACAAAGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:60999 original size:17 final size:16
Alignment explanation
Indices: 60979--61093 Score: 74
Period size: 17 Copynumber: 6.8 Consensus size: 16
60969 GGAAAAAACG
60979 AAAAATGAAAAAATAAT
1 AAAAATGAAAAAA-AAT
60996 AAAAATGAGAAAAAGAA-
1 AAAAATGA-AAAAA-AAT
*
61013 AAAGAA-GAAAAGAAGAAAAGG
1 AAA-AATG--AA-AA-AAAA-T
*
61034 AAAAATGAGAAAAAAT
1 AAAAATGAAAAAAAAT
*
61050 AAAAATGAGAAAAAAT
1 AAAAATGAAAAAAAAT
* *
61066 AAAAATTTAAAAAAAAG
1 AAAAA-TGAAAAAAAAT
61083 AAAAAT-AAAAA
1 AAAAATGAAAAA
61094 GAGAAAATGA
Statistics
Matches: 82, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
15 5 0.06
16 22 0.27
17 29 0.35
18 12 0.15
19 6 0.07
20 4 0.05
21 4 0.05
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAAATGAAAAAAAAT
Found at i:61015 original size:16 final size:15
Alignment explanation
Indices: 60965--61113 Score: 69
Period size: 16 Copynumber: 9.6 Consensus size: 15
60955 AAGAAGAAAT
* *
60965 AAAAGGAAAAAACGA
1 AAAAAGAAAAAATGA
* *
60980 AAAATGAAAAAATAA
1 AAAAAGAAAAAATGA
60995 TAAAAATGAGAAAAA-G-
1 -AAAAA-GA-AAAAATGA
61011 AAAAAGAAGAAAA-GA
1 AAAAAGAA-AAAATGA
*
61026 AGAAAAGGAAAAATGA
1 A-AAAAGAAAAAATGA
61042 GAAAAA-ATAAAAATGA
1 -AAAAAGA-AAAAATGA
*
61058 GAAAAA-ATAAAAATTTA
1 -AAAAAGA-AAAAA-TGA
*
61075 AAAAAAAGAAAAAT--
1 AAAAAGA-AAAAATGA
*
61089 AAAAAGAGAAAATGAA
1 AAAAAGAAAAAATG-A
61105 AAAAAGAAA
1 AAAAAGAAA
61114 TAAAAGGAGG
Statistics
Matches: 108, Mismatches: 12, Indels: 27
0.73 0.08 0.18
Matches are distributed among these distances:
13 6 0.06
14 13 0.12
15 22 0.20
16 51 0.47
17 11 0.10
18 5 0.05
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.09
Consensus pattern (15 bp):
AAAAAGAAAAAATGA
Found at i:61023 original size:23 final size:23
Alignment explanation
Indices: 61003--61054 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
60993 AATAAAAATG
61003 AGAAAAAGAAAAA-GAAGAAAAGA
1 AGAAAAAGAAAAATG-AGAAAAGA
*
61026 AGAAAAGGAAAAATGAGAAAA-A
1 AGAAAAAGAAAAATGAGAAAAGA
*
61048 ATAAAAA
1 AGAAAAA
61055 TGAGAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 6 0.24
23 18 0.72
24 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AGAAAAAGAAAAATGAGAAAAGA
Found at i:61069 original size:23 final size:24
Alignment explanation
Indices: 61043--61109 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 24
61033 GAAAAATGAG
61043 AAAAA-ATAAAAATGAGAAAAAAT
1 AAAAAGATAAAAATGAGAAAAAAT
** **
61066 AAAAATTTAAAAAAAAG-AAAAAT
1 AAAAAGATAAAAATGAGAAAAAAT
*
61089 AAAAAGA-GAAAATGA-AAAAAA
1 AAAAAGATAAAAATGAGAAAAAA
61110 GAAATAAAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
22 10 0.29
23 16 0.47
24 8 0.24
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (24 bp):
AAAAAGATAAAAATGAGAAAAAAT
Found at i:61098 original size:54 final size:55
Alignment explanation
Indices: 60954--61109 Score: 151
Period size: 55 Copynumber: 2.8 Consensus size: 55
60944 TATTTCGCTT
* *
60954 AAAGAAGAAATAAAAGGAAAAAACGAAAAATGAAAAAATAATAAAAATGAGAAAAAGAA
1 AAAGAAGAAA-AGAA-G-AAAAA-GAAAAATGAGAAAATAATAAAAATGAGAAAAAGAA
* *
61013 AAAGAAGAAAAGAAGAAAAGGAAAAATGAGAAAA-AATAAAAATGAGAAAAAATAA
1 AAAGAAGAAAAGAAGAAAAAGAAAAATGAGAAAATAATAAAAATGAG-AAAAAGAA
* *
61068 AAATTTAA-AAAA-AAGAAAAATAAAAA-GAGAAAATGAA-AAAAA
1 AAA--GAAGAAAAGAAGAAAAAGAAAAATGAGAAAAT-AATAAAAA
61110 GAAATAAAAG
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
54 19 0.22
55 40 0.47
56 10 0.12
57 3 0.04
58 3 0.04
59 10 0.12
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.09
Consensus pattern (55 bp):
AAAGAAGAAAAGAAGAAAAAGAAAAATGAGAAAATAATAAAAATGAGAAAAAGAA
Found at i:62488 original size:51 final size:51
Alignment explanation
Indices: 62427--62832 Score: 659
Period size: 51 Copynumber: 7.9 Consensus size: 51
62417 AAATTCGTTT
62427 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
62478 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
62529 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
62580 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
62631 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
62682 GTTGAAGATTGAGTCCTATATTCTCTGAAGGAATAGGGAGCGGACTAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * ** *
62733 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
62784 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
62833 CCATTTTATT
Statistics
Matches: 336, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
51 303 0.90
54 2 0.01
55 31 0.09
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:62553 original size:102 final size:102
Alignment explanation
Indices: 62427--62939 Score: 670
Period size: 102 Copynumber: 4.9 Consensus size: 102
62417 AAATTCGTTT
*
62427 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
62492 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
62529 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
*
62594 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
62631 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
* *
62696 CCTATATTCTCTGAAGGAATAGGGAGCGGACTAGTTC
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * ** **
62733 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
* * * * *
62798 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTT
62 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CAAGTTC
* * * * * * *
62840 ATTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTT-TTATGAAGAT
1 GTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-TGAAGA-
*
62904 TGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
60 --TT-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
62940 AGGCTCGTCA
Statistics
Matches: 369, Mismatches: 31, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
102 252 0.68
105 2 0.01
106 31 0.08
107 13 0.04
110 2 0.01
111 69 0.19
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:62867 original size:56 final size:55
Alignment explanation
Indices: 62437--62939 Score: 252
Period size: 51 Copynumber: 9.6 Consensus size: 55
62427 GTTGAAGATT
* * *** **
62437 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * *** **
62488 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * *** **
62539 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * *** **
62590 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * *** **
62641 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * *** **
62692 GAGTCCTATATTCTCTGAAGGAATAGGGAGCGGACTAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * * *
62743 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGA-CCTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCT-TTTATTGAAGATTGTTC
*
62798 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCC-TTTTATTGAAGATTGTTC
* * * *
62854 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGAC-CCTTTTATTGAAGATTGTTC
*
62909 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
62940 AGGCTCGTCA
Statistics
Matches: 415, Mismatches: 26, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
51 291 0.70
54 3 0.01
55 66 0.16
56 52 0.13
57 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
Found at i:62956 original size:55 final size:55
Alignment explanation
Indices: 62744--62967 Score: 188
Period size: 55 Copynumber: 4.1 Consensus size: 55
62734 TTGAAGATTG
* * * * * * *
62744 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-CTGT-TTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC-GTATTA-TGAAGATTGTTCA
* * * * *
62799 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTAAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTA-TGAAGATTGTTCA
* * *
62855 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCA
* * * *
62910 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATT-TGAAGATTTTTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACGT-ATTATGAAGATTGTTCA
62965 AGT
1 AGT
62968 ATTTATCCTG
Statistics
Matches: 142, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
54 1 0.01
55 87 0.61
56 53 0.37
57 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (55 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCA
Found at i:65331 original size:8 final size:8
Alignment explanation
Indices: 65318--65364 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
65308 AACCCGACCC
65318 GACCCGTT
1 GACCCGTT
65326 GACCC---
1 GACCCGTT
65331 GACCCGTT
1 GACCCGTT
65339 GA-CCGTT
1 GACCCGTT
65346 GACCCGTT
1 GACCCGTT
65354 GA-CCGTT
1 GACCCGTT
65361 GACC
1 GACC
65365 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:65331 original size:13 final size:13
Alignment explanation
Indices: 65313--65357 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
65303 GTCACAACCC
65313 GACCCGACCCGTT
1 GACCCGACCCGTT
65326 GACCCGACCCGTT
1 GACCCGACCCGTT
*
65339 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
65354 GACC
1 GACC
65358 GTTGACCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:65346 original size:7 final size:7
Alignment explanation
Indices: 65334--65365 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
65324 TTGACCCGAC
65334 CCGTTGA
1 CCGTTGA
65341 CCGTTGA
1 CCGTTGA
65348 CCCGTTGA
1 -CCGTTGA
65356 CCGTTGA
1 CCGTTGA
65363 CCG
1 CCG
65366 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:65351 original size:15 final size:15
Alignment explanation
Indices: 65318--65364 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
65308 AACCCGACCC
*
65318 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
65331 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
65346 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
65361 GACC
1 GACC
65365 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Done.