Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009644.1 Hibiscus syriacus cultivar Beakdansim tig00117060_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: 611714
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:549966 original size:20 final size:21
Alignment explanation
Indices: 549941--549992 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
549931 TTTTCCCAAT
*
549941 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
549961 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
549982 TCGCAATGCGA
1 TCGCAATGCGA
549993 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:549986 original size:41 final size:40
Alignment explanation
Indices: 549941--550136 Score: 148
Period size: 41 Copynumber: 4.8 Consensus size: 40
549931 TTTTCCCAAT
**
549941 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTACG-AAA
* * * * * *
549982 TCGCAATGCG-AT-ACTGACTATTGCAATGCGATTTACGTAT
1 TCGCAATGCGAATAAGT-A-AATCGCAATGCGAATTACGAAA
** * * * *
550022 TCGCGTTGTGATTTTCA-TAATTCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGA--ATAAGTAAATCGCAATGCGAATTACG-AAA
* *
550063 TCGCAATGCGATTAAGTAAATCGCAATGCGAATTAGGGAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTA-CGAAA
*
550104 TCGCAATGCGAATACGTAAATCGCAATGCGAAT
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAAT
550137 CTTACTATCG
Statistics
Matches: 119, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
39 5 0.04
40 30 0.25
41 79 0.66
42 2 0.02
43 2 0.02
44 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTACGAAA
Found at i:550068 original size:20 final size:20
Alignment explanation
Indices: 550043--550154 Score: 145
Period size: 20 Copynumber: 5.5 Consensus size: 20
550033 TTTTCATAAT
550043 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
550063 TCGCAATGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
550083 TCGCAATGCGAATTAGGGAAA
1 TCGCAATGCGAA-TACGTAAA
550104 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
550124 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
550144 TCGCAATGCGA
1 TCGCAATGCGA
550155 TTTACATAGC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.04
20 60 0.74
21 18 0.22
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:550069 original size:61 final size:61
Alignment explanation
Indices: 549941--550134 Score: 180
Period size: 61 Copynumber: 3.2 Consensus size: 61
549931 TTTTCCCAAT
* ** *
549941 TCGCAATGCGAATAAGTAAATCGCAATGCGAATT-GGGAAAATCGCAATGCG-ATAC-TGACTA
1 TCGCAATGCGATTAAGTAAATCGCAATGCGAATTACAG-AAATCGCAATGCGAATACGT-A-AA
* * * ** * * * * *
550002 TTGCAATGCGATTTACGT-ATTCGCGTTGTGATTTTCATAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGA-TTAAGTAAATCGCAATGCGAATTACAGAAATCGCAATGCGAATACGTAAA
**
550063 TCGCAATGCGATTAAGTAAATCGCAATGCGAATTAGGGAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTAAGTAAATCGCAATGCGAATTACAGAAATCGCAATGCGAATACGTAAA
550124 TCGCAATGCGA
1 TCGCAATGCGA
550135 ATCTTACTAT
Statistics
Matches: 103, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
60 5 0.05
61 88 0.85
62 9 0.09
63 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (61 bp):
TCGCAATGCGATTAAGTAAATCGCAATGCGAATTACAGAAATCGCAATGCGAATACGTAAA
Found at i:550110 original size:102 final size:102
Alignment explanation
Indices: 549923--550114 Score: 253
Period size: 102 Copynumber: 1.9 Consensus size: 102
549913 TCTACAGTGT
* **
549923 CGTTGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGAAAATCGCAA
1 CGTTGCGATTTTCACAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTAAGAAAATCGCAA
* * *
549988 TGCGATACTGACTATTGCAATGCGATTTACGTATTCG
66 TGCGATACGGACAATCGCAATGCGATTTACGTATTCG
* * * *
550025 CGTTGTGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATGCG-ATTAAGTAAATCGCAA
1 CGTTGCGATTTTCACAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTAAGAAAATCGCAA
*
550089 TGCGAATTAGGGA-AATCGCAATGCGA
66 TGCG-A-TACGGACAATCGCAATGCGA
550115 ATACGTAAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
101 17 0.22
102 56 0.73
103 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (102 bp):
CGTTGCGATTTTCACAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTAAGAAAATCGCAA
TGCGATACGGACAATCGCAATGCGATTTACGTATTCG
Found at i:550766 original size:19 final size:19
Alignment explanation
Indices: 550716--550828 Score: 92
Period size: 19 Copynumber: 6.1 Consensus size: 19
550706 GAAACCAAAA
* *
550716 TCGCATTGCGATGTTCATT
1 TCGCGTTGCGATTTTCATT
550735 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
550754 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
550768 TCTCGTTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
550787 TCCGCATTGCGATTATCATT
1 T-CGCGTTGCGATTTTCATT
*
550807 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
550827 TC
1 TC
550829 AACCAAATGA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 3 0.04
19 31 0.42
20 28 0.38
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:552990 original size:42 final size:42
Alignment explanation
Indices: 552911--552999 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
552901 GACTCGACTG
* * * *
552911 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
* * * * *
552953 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAAAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
552995 TCATC
1 TCATC
553000 GTTGAAGAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
Found at i:554417 original size:14 final size:14
Alignment explanation
Indices: 554382--554408 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
554372 ATTGTTTAAT
554382 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
554396 TGATTTGTAAAAG
1 TGATTTGTAAAAG
554409 TTTATTTGTT
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:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:554512 original size:19 final size:19
Alignment explanation
Indices: 554488--554546 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
554478 AAAAAGTACT
554488 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
554507 ATCGCAAT--G--AT-AGA
1 ATCGCAATGCGAAATGAAA
*
554521 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
554540 ATCGCAA
1 ATCGCAA
554547 CGAGAGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 17 0.53
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:554533 original size:33 final size:33
Alignment explanation
Indices: 554488--554568 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
554478 AAAAAGTACT
* * *
554488 ATCGCAATGCGAAATGAAAATCGCAATGATAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
554521 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
554554 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
554569 TCAATTCGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:554614 original size:33 final size:33
Alignment explanation
Indices: 554577--554703 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
554567 ATTCAATTCG
554577 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* * *
554610 CGTTGCGATTTTCATTTCGCATTACAAAAT-AC-
1 CGTTGCGATTTTCATTTCGCATTGC-GATTCACT
* *
554642 CATATGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGT-TGCGATTTTCATTTCGCATTGCGATTCACT
554676 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
554704 AGTAATTTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
32 4 0.05
33 73 0.90
34 4 0.05
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:556499 original size:20 final size:21
Alignment explanation
Indices: 556474--556516 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
556464 CCAGATTGCT
556474 CATA-GGGAACCGATTCCCCC
1 CATAGGGGAACCGATTCCCCC
*
556494 CATAGGGGGTACCGATTCCCCC
1 CATA-GGGGAACCGATTCCCCC
556516 C
1 C
556517 TGAATGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
22 16 0.80
ACGTcount: A:0.21, C:0.40, G:0.23, T:0.16
Consensus pattern (21 bp):
CATAGGGGAACCGATTCCCCC
Found at i:562373 original size:21 final size:21
Alignment explanation
Indices: 562336--562391 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
562326 TTTGTGCAGA
**
562336 GGGAATCGATT-CCCCCATGG
1 GGGAATCGATTCCCCCCACAG
*
562356 GGGAACCGATTCCCCCCACAG
1 GGGAATCGATTCCCCCCACAG
*
562377 GGGAATCGATACCCC
1 GGGAATCGATTCCCC
562392 TTGGGGTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.23, C:0.36, G:0.27, T:0.14
Consensus pattern (21 bp):
GGGAATCGATTCCCCCCACAG
Found at i:566519 original size:12 final size:12
Alignment explanation
Indices: 566502--566526 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
566492 TCTTCGGGGA
566502 CTTTTTCTTCTT
1 CTTTTTCTTCTT
566514 CTTTTTCTTCTT
1 CTTTTTCTTCTT
566526 C
1 C
566527 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:566740 original size:24 final size:24
Alignment explanation
Indices: 566713--566759 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
566703 CAAAATCCGA
*
566713 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
566737 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
566760 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:566768 original size:24 final size:24
Alignment explanation
Indices: 566717--566768 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
566707 ATCCGAGTAT
* ** *
566717 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
566741 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
566765 TGAC
1 TGAC
566769 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:567523 original size:20 final size:20
Alignment explanation
Indices: 567498--567548 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
567488 TGTATTATCT
567498 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
567518 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
567538 CGTTGCGAAAG
1 CGTTGCGAAAG
567549 GCAATCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:567790 original size:19 final size:18
Alignment explanation
Indices: 567766--567824 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
567756 TCATTTGACC
567766 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
*
567785 ATCGCAA-CG--AT-AGA
1 ATCGCAATCGAAATGAAA
567799 ATCGCAATACGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
567818 ATCGCAA
1 ATCGCAA
567825 CGAGGGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 9 0.27
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 16 0.48
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (18 bp):
ATCGCAATCGAAATGAAA
Found at i:567803 original size:14 final size:14
Alignment explanation
Indices: 567784--567852 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
567774 GCGAAATGAA
*
567784 AATCGCAACGATAG
1 AATCGCAACGAGAG
*
567798 AATCGCAATACGAAATGAA
1 AATCGC-A-ACG--A-GAG
*
567817 AATCGCAACGAGGG
1 AATCGCAACGAGAG
*
567831 AATCGCAACGAGGG
1 AATCGCAACGAGAG
567845 AATCGCAA
1 AATCGCAA
567853 AGCGAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
14 29 0.63
15 2 0.04
16 3 0.07
17 3 0.07
18 2 0.04
19 7 0.15
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:567812 original size:33 final size:33
Alignment explanation
Indices: 567766--567838 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
567756 TCATTTGACC
* *
567766 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
567799 ATCGCAATACGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
567832 ATCGCAA
1 ATCGCAA
567839 CGAGGGAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:567838 original size:47 final size:47
Alignment explanation
Indices: 567784--567873 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
567774 GCGAAATGAA
* *
567784 AATCGCAACGATAGAATCGCAATA-CGAAATGAAAATCGCAACGAGGG
1 AATCGCAACGAGAGAATCGCAA-AGCGAAATAAAAATCGCAACGAGGG
*
567831 AATCGCAACGAGGGAATCGCAAAGCGAAATAAAAATCGCAACG
1 AATCGCAACGAGAGAATCGCAAAGCGAAATAAAAATCGCAACG
567874 CGATTTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 1 0.03
47 38 0.97
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (47 bp):
AATCGCAACGAGAGAATCGCAAAGCGAAATAAAAATCGCAACGAGGG
Found at i:567898 original size:19 final size:19
Alignment explanation
Indices: 567874--567917 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
567864 AATCGCAACG
567874 CGATTTTAGTTTCACGTTA
1 CGATTTTAGTTTCACGTTA
* *
567893 CGA-TTTAGTTTCGCGTTG
1 CGATTTTAGTTTCACGTTA
567911 CGATTTT
1 CGATTTT
567918 CATTTCGCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (19 bp):
CGATTTTAGTTTCACGTTA
Found at i:567925 original size:19 final size:19
Alignment explanation
Indices: 567901--568000 Score: 85
Period size: 19 Copynumber: 5.8 Consensus size: 19
567891 TACGATTTAG
567901 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
567920 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
567936 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
567953 TTTCACATTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
567969 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
567986 TTTCGCATTGCGATT
1 TTTCGCGTTGCGATT
568001 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.30
16 6 0.09
17 6 0.09
19 33 0.52
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:567944 original size:14 final size:14
Alignment explanation
Indices: 567925--568013 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
567915 TTTCATTTCG
567925 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
567939 CGTTGCGATTTTCATTTCA
1 CGTTGCGA--TTC---TCT
*
567958 CATTGCGATTCTCT
1 CGTTGCGATTCTCT
*
567972 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
567989 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
568005 CGTTGCGAT
1 CGTTGCGAT
568014 AGTCAGTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 24 0.41
16 10 0.17
17 10 0.17
19 15 0.25
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:567948 original size:33 final size:33
Alignment explanation
Indices: 567906--568013 Score: 198
Period size: 33 Copynumber: 3.3 Consensus size: 33
567896 TTTAGTTTCG
*
567906 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
567939 CGTTGCGATTTTCATTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
567972 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
568005 CGTTGCGAT
1 CGTTGCGAT
568014 AGTCAGTTTC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:570043 original size:20 final size:19
Alignment explanation
Indices: 570020--570087 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
570010 GAAACTTAAA
570020 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
570040 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
570060 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
570079 ATCGCAACG
1 ATCGCAACG
570088 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:570095 original size:14 final size:14
Alignment explanation
Indices: 570076--570134 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
570066 ATGCGAAATG
570076 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
570090 AAAATCGCAAAGCGAAATG
1 AAAATCGC-AA-CG--A-C
570109 AAAATCGCAACGAC
1 AAAATCGCAACGAC
570123 AAAATCGCAACG
1 AAAATCGCAACG
570135 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 20 0.53
15 3 0.08
16 2 0.05
17 2 0.05
18 3 0.08
19 8 0.21
ACGTcount: A:0.51, C:0.24, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:570150 original size:33 final size:33
Alignment explanation
Indices: 570060--570139 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
570050 GGAAATGGCT
*
570060 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
570093 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
*
570126 ATCGCAACGCGAAA
1 ATCGCAAAGCGAAA
570140 CACAAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.49, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
Found at i:570168 original size:19 final size:19
Alignment explanation
Indices: 570146--570262 Score: 76
Period size: 19 Copynumber: 6.6 Consensus size: 19
570136 GAAACACAAA
570146 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
570165 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
570181 TCG--TTGCGATTATCATT
1 TCGCATTGCGATTTTCATT
*
570198 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
570214 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
570231 TCG-ATTTGCGATAGCCATT
1 TCGCA-TTGCGATTTTCATT
570250 TCCGCATTGCGAT
1 T-CGCATTGCGAT
570263 AGTCATTTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
14 12 0.16
15 5 0.07
16 8 0.11
17 8 0.11
18 5 0.07
19 28 0.37
20 9 0.12
21 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:570187 original size:14 final size:14
Alignment explanation
Indices: 570168--570226 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
570158 TTTCATTTCG
570168 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
570182 CGTTGCGATTATCATTT
1 CGTTGCGATT-T--TGT
570199 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
570215 CGTTGCGATTTT
1 CGTTGCGATTTT
570227 CATTTCGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 20 0.53
15 1 0.03
16 4 0.11
17 4 0.11
18 1 0.03
19 8 0.21
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:570197 original size:33 final size:33
Alignment explanation
Indices: 570151--570242 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
570141 ACAAATCGCA
*
570151 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
570184 TTGCGATTATCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
570217 TTGCGATTTTCATTTCG-ATTTGCGAT
1 TTGCGATTTTCATTTCGCA-TTGCGAT
570243 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 1 0.02
33 54 0.98
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:572175 original size:20 final size:20
Alignment explanation
Indices: 572127--572185 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
572117 AATAGTTTCT
** *
572127 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
572147 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
572167 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
572186 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:572476 original size:22 final size:22
Alignment explanation
Indices: 572449--572492 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
572439 GATGGAGATA
572449 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
572471 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
572493 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:572706 original size:20 final size:20
Alignment explanation
Indices: 572681--572732 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
572671 ATTATGTATT
572681 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
**
572701 ATCGCGTTGCGAAAGTCATT
1 ATCGCGTTGCGAAAGTCAGA
*
572721 ATCTCGTTGCGA
1 ATCGCGTTGCGA
572733 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:572766 original size:20 final size:20
Alignment explanation
Indices: 572741--572794 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
572731 GATTTTGTAT
572741 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
572761 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
572781 TATCGCATTGCGAT
1 TATCGCATTGCGAT
572795 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:572766 original size:61 final size:61
Alignment explanation
Indices: 572660--572797 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
572650 CGCTTTGAAA
* * * * *
572660 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCATT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
572721 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
572782 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
572798 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:572936 original size:20 final size:20
Alignment explanation
Indices: 572911--572956 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
572901 GCACACGAAT
*
572911 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
572931 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
572950 TTGCGAT
1 TTGCGAT
572957 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:573751 original size:24 final size:24
Alignment explanation
Indices: 573693--573743 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
573683 AACGGGACTA
573693 CTTAATAATTCAATCCTTTCTTCT
1 CTTAATAATTCAATCCTTTCTTCT
*
573717 CTTAATAATTCATTCCTTTCTTCT
1 CTTAATAATTCAATCCTTTCTTCT
573741 CTT
1 CTT
573744 CTCCATTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (24 bp):
CTTAATAATTCAATCCTTTCTTCT
Found at i:580979 original size:23 final size:23
Alignment explanation
Indices: 580953--581000 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
580943 GTTAAGTGTT
*
580953 GCCGATGCATATGTATATGTTTA
1 GCCGATACATATGTATATGTTTA
*
580976 GCCGATATATATGTATATGTTTA
1 GCCGATACATATGTATATGTTTA
580999 GC
1 GC
581001 ATTGGTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (23 bp):
GCCGATACATATGTATATGTTTA
Found at i:588328 original size:35 final size:35
Alignment explanation
Indices: 588280--588504 Score: 114
Period size: 36 Copynumber: 6.3 Consensus size: 35
588270 ATAAATAATA
588280 ATAATATATTATATAT-AAAATATATCTAAAAACTAT
1 ATAATATA-TATATATCAAAA-ATATCTAAAAACTAT
* * *
588316 ATAATATATATATTTCAAAAATATTTTAAAACTAT
1 ATAATATATATATATCAAAAATATCTAAAAACTAT
* * ** * * *
588351 ATATTATATATATTTTTTAAAATGTTTTCAAAACTAT
1 ATAATATATATA-TATCAAAAAT-ATCTAAAAACTAT
* * * * *
588388 ATATTATATAGT-TTTCAAAAATGTTTTAAAACTAT
1 ATAATATATA-TATATCAAAAATATCTAAAAACTAT
* * * * * *
588423 ATATTATATATGTTTTCAAAAATGTTTTAAAACTAT
1 ATAATATATAT-ATATCAAAAATATCTAAAAACTAT
* * * * *
588459 ATATTATATA-AGTTTTAAAAATGATTTCAAAACTAT
1 ATAATATATATA-TATCAAAAAT-ATCTAAAAACTAT
*
588495 ATATTATATA
1 ATAATATATA
588505 AGTTTTTAAA
Statistics
Matches: 165, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
34 1 0.01
35 60 0.36
36 82 0.50
37 21 0.13
38 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (35 bp):
ATAATATATATATATCAAAAATATCTAAAAACTAT
Found at i:588346 original size:36 final size:35
Alignment explanation
Indices: 588308--588623 Score: 318
Period size: 36 Copynumber: 8.6 Consensus size: 35
588298 AATATATCTA
* *
588308 AAAACTATATAATATATATATTTCAAAAATATTTT
1 AAAACTATATATTATATATATTTCAAAAATGTTTT
**
588343 AAAACTATATATTATATATATTTTTTAAAATGTTTT
1 AAAACTATATATTATATATA-TTTCAAAAATGTTTT
588379 CAAAACTATATATTATATAGT-TTTCAAAAATGTTTT
1 -AAAACTATATATTATATA-TATTTCAAAAATGTTTT
*
588415 AAAACTATATATTATATATGTTTTCAAAAATGTTTT
1 AAAACTATATATTATATAT-ATTTCAAAAATGTTTT
* *
588451 AAAACTATATATTATATA-AGTTTTAAAAATGATTTC
1 AAAACTATATATTATATATA-TTTCAAAAATG-TTTT
**
588487 AAAACTATATATTATATA-AGTTTTTAAAATGTTTT
1 AAAACTATATATTATATATA-TTTCAAAAATGTTTT
*
588522 CAAAAACTTTATATTATATATATTTTTTTC-AAAATGTTTT
1 --AAAACTATATATTATATATA----TTTCAAAAATGTTTT
*
588562 CAAAAACTATATATTATATATATTTTCAAAATAT-TTTCG
1 --AAAACTATATATTATATATA-TTTCAAAA-ATGTTT-T
588601 AAAACTATATTATATATATATAT
1 AAAACTATA-TAT-TATATATAT
588624 ATATATTTTC
Statistics
Matches: 247, Mismatches: 16, Indels: 33
0.83 0.05 0.11
Matches are distributed among these distances:
34 1 0.00
35 50 0.20
36 91 0.37
37 49 0.20
38 12 0.05
39 10 0.04
40 31 0.13
41 3 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (35 bp):
AAAACTATATATTATATATATTTCAAAAATGTTTT
Found at i:588640 original size:35 final size:36
Alignment explanation
Indices: 588283--588638 Score: 233
Period size: 37 Copynumber: 9.8 Consensus size: 36
588273 AATAATAATA
* *
588283 ATATATTATATATAAAATA-TATCTAAAAACTATATAAT
1 ATATA-TAT-TATAAAATATTTTC-AAAAACTATATATT
588321 ATATATATT-TCAAAAATATTTT--AAAACTATATATT
1 ATATATATTAT--AAAATATTTTCAAAAACTATATATT
* *
588356 ATATATATTTTTTAAAATGTTTTC-AAAACTATATATT
1 ATATATA--TTATAAAATATTTTCAAAAACTATATATT
* *
588393 ATATAGTTTTCA-AAAATGTTTT--AAAACTATATATT
1 ATATA-TATT-ATAAAATATTTTCAAAAACTATATATT
* * *
588428 ATATATGTTTTCAAAA-ATGTTT-TAAAACTATATATT
1 ATATATATTAT-AAAATAT-TTTCAAAAACTATATATT
*
588464 ATATA-AGTTTTAAAA-ATGATTTC-AAAACTATATATT
1 ATATATA-TTATAAAATAT--TTTCAAAAACTATATATT
* * *
588500 ATATA-AGTTTTTAAAATGTTTTCAAAAACTTTATATT
1 ATATATA--TTATAAAATATTTTCAAAAACTATATATT
* *
588537 ATATATATTTTTTTCAAAATGTTTTCAAAAACTATATATT
1 ATATATA---TTAT-AAAATATTTTCAAAAACTATATATT
* *
588577 ATATATATTTTCAAAATATTTTCGAAAAC--TATATT
1 ATATATATTAT-AAAATATTTTCAAAAACTATATATT
*
588612 ATATATA-TATATATATATTTTCAAAAA
1 ATATATATTATA-AAATATTTTCAAAAA
588639 ACATTTGCAA
Statistics
Matches: 275, Mismatches: 20, Indels: 50
0.80 0.06 0.14
Matches are distributed among these distances:
33 1 0.00
34 19 0.07
35 64 0.23
36 70 0.25
37 74 0.27
38 11 0.04
39 5 0.02
40 31 0.11
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATATATTATAAAATATTTTCAAAAACTATATATT
Found at i:588656 original size:2 final size:2
Alignment explanation
Indices: 588651--588680 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
588641 ATTTGCAAAC
588651 TA TA TA -A 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 T
588681 TCAAAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:588663 original size:47 final size:47
Alignment explanation
Indices: 588569--588714 Score: 183
Period size: 45 Copynumber: 3.1 Consensus size: 47
588559 TTTCAAAAAC
* * *
588569 TATATAT-TATATATATTTTCAAAATA-TTTTCGAAAACTATAT--TA
1 TATATATATATATATATTTTCAAAAAACATTT-GCAAACTATATAATA
588613 TATATATATATATATATTTTCAAAAAACATTTGCAAACTATATAATA
1 TATATATATATATATATTTTCAAAAAACATTTGCAAACTATATAATA
* *
588660 TATATATATATATATATATATTCAAAAATCATTTTCAAAGCTATATAATA
1 TATATATATATATATAT-T-TTCAAAAAACATTTGCAAA-CTATATAATA
588710 TATAT
1 TATAT
588715 TTTTAAAAAC
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
44 7 0.08
45 28 0.31
46 3 0.03
47 19 0.21
48 1 0.01
49 17 0.19
50 15 0.17
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (47 bp):
TATATATATATATATATTTTCAAAAAACATTTGCAAACTATATAATA
Found at i:588731 original size:37 final size:35
Alignment explanation
Indices: 588664--588809 Score: 102
Period size: 36 Copynumber: 4.0 Consensus size: 35
588654 ATAATATATA
* * *
588664 TATATATATATATATATTCAAAAATCATTTTCAAAGC
1 TATATA-ATATATATTTTTAAAAACCATTTTCAAA-C
*
588701 TATATAATATATATTTTTAAAAACCGATTTTTTAAAC
1 TATATAATATATATTTTTAAAAACC-A-TTTTCAAAC
*
588738 -AGTATAAT-TATATGTTTTCAAAAACCATTTTCTAAAA
1 TA-TATAATATATAT-TTTT-AAAAACCATTTTC-AAAC
* *
588775 AAT-TATATATTATATTTTTCAAAAA-TATTTTCAAA
1 TATATA-ATA-TATATTTTT-AAAAACCATTTTCAAA
588810 AATTACATTA
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
36 31 0.34
37 31 0.34
38 25 0.27
39 5 0.05
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (35 bp):
TATATAATATATATTTTTAAAAACCATTTTCAAAC
Found at i:588750 original size:38 final size:37
Alignment explanation
Indices: 588703--588811 Score: 118
Period size: 38 Copynumber: 2.9 Consensus size: 37
588693 TTCAAAGCTA
* *
588703 TATAATATATATTTTT-AAAAACCGATTTT-TTAAACAG
1 TATAAT-TATATTTTTCAAAAACC-ATTTTCTAAAAAAG
*
588740 TATAATTATATGTTTTCAAAAACCATTTTCTAAAAAAT
1 TATAATTATAT-TTTTCAAAAACCATTTTCTAAAAAAG
*
588778 TATATATTATATTTTTCAAAAA-TATTTTC-AAAAA
1 TATA-ATTATATTTTTCAAAAACCATTTTCTAAAAA
588812 TTACATTATA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
36 10 0.16
37 21 0.33
38 26 0.41
39 7 0.11
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
TATAATTATATTTTTCAAAAACCATTTTCTAAAAAAG
Found at i:588824 original size:38 final size:38
Alignment explanation
Indices: 588664--588811 Score: 117
Period size: 38 Copynumber: 3.9 Consensus size: 38
588654 ATAATATATA
* * * **
588664 TATATATATATATATATTCAAAAATCATTTTC--AAAGC
1 TATATAT-TATATGTTTTCAAAAACCATTTTCAAAAAAT
* * * ** * *
588701 TATATAATATATATTTTTAAAAACCGATTTTTTAAACAG
1 TATATATTATATGTTTTCAAAAACC-ATTTTCAAAAAAT
588740 TATA-ATTATATGTTTTCAAAAACCATTTTCTAAAAAAT
1 TATATATTATATGTTTTCAAAAACCATTTTC-AAAAAAT
*
588778 TATATATTATAT-TTTTCAAAAA-TATTTTCAAAAA
1 TATATATTATATGTTTTCAAAAACCATTTTCAAAAA
588812 TTACATTATA
Statistics
Matches: 90, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
36 20 0.22
37 22 0.24
38 35 0.39
39 13 0.14
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (38 bp):
TATATATTATATGTTTTCAAAAACCATTTTCAAAAAAT
Found at i:588832 original size:2 final size:2
Alignment explanation
Indices: 588825--588857 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
588815 CATTATATTA
588825 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 A
588858 AAAAATCCGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:589948 original size:47 final size:47
Alignment explanation
Indices: 589876--590075 Score: 230
Period size: 47 Copynumber: 4.3 Consensus size: 47
589866 CGCTTAACGA
*
589876 CCGTCACTTTCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAGTGT
1 CCGTCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAGTGT
* * * * *
589923 TCGTCACTTCCAACTAAGTGCGCTCAACAA--AGT-TCGCT-TAA-TGA
1 CCGTCACTTCCAAGTAAGTGTGCTCAA-AATTATTGTCG-TGTAAGTGT
*
589967 CCGCCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAGTGT
1 CCGTCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAGTGT
** * * *
590014 CCACCACTTTCAAGTAAGTGTGCTCAAAATTGTTGTCATGTAAGTGT
1 CCGTCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAGTGT
*
590061 CCATCACTTCCAAGT
1 CCGTCACTTCCAAGT
590076 GTGTTCAACA
Statistics
Matches: 128, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
43 2 0.02
44 25 0.20
45 9 0.07
46 9 0.07
47 81 0.63
48 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (47 bp):
CCGTCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAGTGT
Found at i:589975 original size:91 final size:91
Alignment explanation
Indices: 589855--590040 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 91
589845 TCCAAATCAA
* *
589855 TCAACAAAGTTCGCTTAACGACCGTCACTTTCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAG
1 TCAACAAAGTTCGCTTAACGACCGCCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAG
* **
589920 TGTTCGTCACTTCCAACTAAGTGCGC
66 TGTCCACCACTTCCAACTAAGTGCGC
*
589946 TCAACAAAGTTCGCTTAATGACCGCCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAG
1 TCAACAAAGTTCGCTTAACGACCGCCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAG
* * *
590011 TGTCCACCACTTTCAAGTAAGTGTGC
66 TGTCCACCACTTCCAACTAAGTGCGC
590037 TCAA
1 TCAA
590041 AATTGTTGTC
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (91 bp):
TCAACAAAGTTCGCTTAACGACCGCCACTTCCAAGTAAGTGTGCTCAAAATTATTGTCGTGTAAG
TGTCCACCACTTCCAACTAAGTGCGC
Found at i:589985 original size:44 final size:44
Alignment explanation
Indices: 589855--590161 Score: 165
Period size: 47 Copynumber: 6.9 Consensus size: 44
589845 TCCAAATCAA
* *
589855 TCAACAAAGTTCGCTTAACGACCGTCACTTTCAAGTAAGTGTGC
1 TCAACAAAGTTCGCTTAATGACCGTCACTTCCAAGTAAGTGTGC
* ** * *
589899 TCAA-AATTATTGTCG-TGTAAGTGTTCGTCACTTCCAACTAAGTGCGC
1 TCAACAA--AGT-TCGCT-TAA-TGACCGTCACTTCCAAGTAAGTGTGC
*
589946 TCAACAAAGTTCGCTTAATGACCGCCACTTCCAAGTAAGTGTGC
1 TCAACAAAGTTCGCTTAATGACCGTCACTTCCAAGTAAGTGTGC
* * ** *
589990 TCAA-AATTATTGTCG-TGTAAGTGTCCACCACTTTCAAGTAAGTGTGC
1 TCAACAA--AGT-TCGCT-TAA-TGACCGTCACTTCCAAGTAAGTGTGC
* * *
590037 TCAA-AATTGTT-GTCATGTAAGTGTCCATCACTTCCAAGT--GTGT--
1 TCAACAA-AGTTCG-C-T-TAA-TGACCGTCACTTCCAAGTAAGTGTGC
** * *
590080 TCAACAAAGCTT-G-TTAACAATCATCACTTCCAAGTAAGT-TGC
1 TCAACAAAG-TTCGCTTAATGACCGTCACTTCCAAGTAAGTGTGC
* *
590122 TCAACAAAGTTCGCTTAACGATCC-CCACTTCCAAGTAAGT
1 TCAACAAAGTTCGCTTAATGA-CCGTCACTTCCAAGTAAGT
590162 ATGTTCAAAA
Statistics
Matches: 210, Mismatches: 29, Indels: 49
0.73 0.10 0.17
Matches are distributed among these distances:
39 14 0.07
40 4 0.02
41 5 0.02
42 10 0.05
43 30 0.14
44 36 0.17
45 17 0.08
46 17 0.08
47 75 0.36
48 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (44 bp):
TCAACAAAGTTCGCTTAATGACCGTCACTTCCAAGTAAGTGTGC
Found at i:590056 original size:26 final size:26
Alignment explanation
Indices: 589980--590060 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
589970 CCACTTCCAA
*
589980 GTAAGTGTGCTCAAAATTATTGTCGT
1 GTAAGTGTGCTCAAAATTATTGTCAT
** * *
590006 GTAAGTGT-C-CACCA--CTT-TCAA
1 GTAAGTGTGCTCAAAATTATTGTCAT
*
590027 GTAAGTGTGCTCAAAATTGTTGTCAT
1 GTAAGTGTGCTCAAAATTATTGTCAT
590053 GTAAGTGT
1 GTAAGTGT
590061 CCATCACTTC
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 10 0.24
22 3 0.07
23 3 0.07
24 3 0.07
25 3 0.07
26 19 0.46
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (26 bp):
GTAAGTGTGCTCAAAATTATTGTCAT
Found at i:596498 original size:30 final size:30
Alignment explanation
Indices: 596441--596508 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
596431 ATGCATAAGT
* **
596441 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
596471 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
596501 ATATGCAT
1 AAATGCAT
596509 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:604607 original size:38 final size:38
Alignment explanation
Indices: 604555--604630 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
604545 CATCAGCTGG
* * *
604555 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCGA
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCGA
* *
604593 CCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCCGA
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCGA
604631 TAACCATCGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (38 bp):
CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCGA
Found at i:604651 original size:40 final size:38
Alignment explanation
Indices: 604565--604655 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 38
604555 CCAGAACTCT
* * * *
604565 TCATCACGTATGAGCCGTGTCATCCCGACCAGATCTCC
1 TCATCACGTAGGAGCCGTGTCACCCCGACAACATCTCC
* *
604603 TCATCACGTAGGAGTCGTGTCACCCCGATAACCATCGTCC
1 TCATCACGTAGGAGCCGTGTCACCCCGACAA-CATC-TCC
604643 TCATCACGTAGGA
1 TCATCACGTAGGA
604656 ACCATGTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 26 0.58
39 3 0.07
40 16 0.36
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (38 bp):
TCATCACGTAGGAGCCGTGTCACCCCGACAACATCTCC
Found at i:604658 original size:23 final size:23
Alignment explanation
Indices: 604632--604705 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
604622 TCACCCCGAT
604632 AACCATCGTCCTCATCACGTAGG
1 AACCATCGTCCTCATCACGTAGG
** * * * *
604655 AACCAT-GTTATCACCCCATAGAT
1 AACCATCGTCCTCATCACGTAG-G
*
604678 AACCAGCTGTCCTCATCACGTAGG
1 AACCATC-GTCCTCATCACGTAGG
604702 AACC
1 AACC
604706 GTGTTATCAC
Statistics
Matches: 35, Mismatches: 13, Indels: 5
0.66 0.25 0.09
Matches are distributed among these distances:
22 10 0.29
23 11 0.31
24 4 0.11
25 10 0.29
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.22
Consensus pattern (23 bp):
AACCATCGTCCTCATCACGTAGG
Found at i:605981 original size:32 final size:32
Alignment explanation
Indices: 605940--606007 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
605930 GGCCAAATCG
605940 TTTAGATTTCACTGAAATAACAAAGAGTATAC
1 TTTAGATTTCACTGAAATAACAAAGAGTATAC
605972 TTTAGATTTCACTGAAATAACAAAGAGTATAC
1 TTTAGATTTCACTGAAATAACAAAGAGTATAC
606004 TTTA
1 TTTA
606008 AAATCAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (32 bp):
TTTAGATTTCACTGAAATAACAAAGAGTATAC
Found at i:608099 original size:29 final size:30
Alignment explanation
Indices: 608057--608114 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
608047 TGATTGATAC
608057 TTGTATCAATTATACAC-TTTTTTATTTAA
1 TTGTATCAATTATACACTTTTTTTATTTAA
*
608086 TTGTATCAATTATATACTTTTTTTATTTA
1 TTGTATCAATTATACACTTTTTTTATTTA
608115 GTTTTTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (30 bp):
TTGTATCAATTATACACTTTTTTTATTTAA
Found at i:609899 original size:2 final size:2
Alignment explanation
Indices: 609892--609927 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
609882 AAATGGTTAT
609892 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
609928 CAATCAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.