Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003369.1 Hibiscus syriacus cultivar Beakdansim tig00007083_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: 74071
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3568 original size:17 final size:17
Alignment explanation
Indices: 3546--3582 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3536 ATATTTTGTA
3546 TTAATTTA-TTTAAGTAT
1 TTAATTTATTTTAA-TAT
3563 TTAATTTATTTTAATAT
1 TTAATTTATTTTAATAT
3580 TTA
1 TTA
3583 CTTATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTAATTTATTTTAATAT
Found at i:5580 original size:3 final size:3
Alignment explanation
Indices: 5572--5603 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5562 AGCTACTCAG
*
5572 GAC GAC GAC GAC GAC GAC GAC GAC GAT GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
5604 TTATGATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.34, T:0.03
Consensus pattern (3 bp):
GAC
Found at i:11079 original size:17 final size:18
Alignment explanation
Indices: 11053--11097 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
11043 TATGAAATTT
*
11053 GATTCAAATTCC-TGACA
1 GATTCAAATTCCTTCACA
*
11070 GATTCCAATTCCTTCACA
1 GATTCAAATTCCTTCACA
*
11088 GATTCTAATT
1 GATTCAAATT
11098 TACTCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCAAATTCCTTCACA
Found at i:17002 original size:22 final size:21
Alignment explanation
Indices: 16974--17039 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
16964 ATTATATGGT
*
16974 ATGAACAGTATCGTGAACATTA
1 ATGAACAGTA-CGTGAACAGTA
* *
16996 ATGAACAATACTGTAAACAGTA
1 ATGAACAGTAC-GTGAACAGTA
17018 ATGAACAGTACCGTGAACAGTA
1 ATGAACAGTA-CGTGAACAGTA
17040 CCGACTACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (21 bp):
ATGAACAGTACGTGAACAGTA
Found at i:17098 original size:21 final size:21
Alignment explanation
Indices: 17073--17115 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
17063 TGCTATAGGG
*
17073 GTATCGATACCTTGCTACAGT
1 GTATCGATACCCTGCTACAGT
17094 GTATCGATACCCTGCTACAGT
1 GTATCGATACCCTGCTACAGT
17115 G
1 G
17116 ATTTCGGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (21 bp):
GTATCGATACCCTGCTACAGT
Found at i:17872 original size:32 final size:32
Alignment explanation
Indices: 17795--17891 Score: 144
Period size: 31 Copynumber: 3.1 Consensus size: 32
17785 GCTCGTATAA
* *
17795 TAAT-TTGTCCATATGTCCCTAAGAACATAGA
1 TAATCTTGTCCATATGTCCCGAAGAACATAGG
*
17826 TAAAC-TGTCCATATGTCCCGAAGAACATAGG
1 TAATCTTGTCCATATGTCCCGAAGAACATAGG
*
17857 TAATCTTGTCCATATGTTCCGAAGAACATAGG
1 TAATCTTGTCCATATGTCCCGAAGAACATAGG
17889 TAA
1 TAA
17892 CCCTCGACTC
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
31 31 0.53
32 28 0.47
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (32 bp):
TAATCTTGTCCATATGTCCCGAAGAACATAGG
Found at i:22060 original size:18 final size:18
Alignment explanation
Indices: 22028--22064 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
22018 TATCACAAAT
22028 ATTATAATAATTTAATCA
1 ATTATAATAATTTAATCA
22046 ATTA-AATAATATTAATCA
1 ATTATAATAAT-TTAATCA
22064 A
1 A
22065 CGTAGAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAATAATTTAATCA
Found at i:27230 original size:26 final size:24
Alignment explanation
Indices: 27191--27238 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
27181 ATTTATTTTT
27191 AAATTAATTAAAATACTATTAAATCA
1 AAATTAATTAAAATA-TA-TAAATCA
27217 AAATTATATT-AAATATATAAAT
1 AAATTA-ATTAAAATATATAAAT
27239 TTTAACAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 2 0.10
26 11 0.52
27 3 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATTAATTAAAATATATAAATCA
Found at i:27601 original size:21 final size:22
Alignment explanation
Indices: 27562--27619 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
27552 AAAGAATAAA
27562 TAAATTGAATTT-T-ATTAATT
1 TAAATTGAATTTATAATTAATT
27582 T-AATTGAATTTATAATTAATT
1 TAAATTGAATTTATAATTAATT
*
27603 TAAATT-ACTTTATAATT
1 TAAATTGAATTTATAATT
27620 TAAAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 18 0.53
22 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (22 bp):
TAAATTGAATTTATAATTAATT
Found at i:27604 original size:11 final size:11
Alignment explanation
Indices: 27582--27619 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27572 TTTATTAATT
27582 TAATTGAATTTA
1 TAATT-AATTTA
27594 TAATTAATTTA
1 TAATTAATTTA
*
27605 -AATTACTTTA
1 TAATTAATTTA
27615 TAATT
1 TAATT
27620 TAAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 10 0.42
12 5 0.21
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (11 bp):
TAATTAATTTA
Found at i:27676 original size:22 final size:22
Alignment explanation
Indices: 27651--27695 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
27641 AAAATTTTGA
*
27651 TTAT-AATATGATTTTTAAAAAT
1 TTATCAAT-TGATATTTAAAAAT
*
27673 TTATCACTTGATATTTAAAAAT
1 TTATCAATTGATATTTAAAAAT
27695 T
1 T
27696 CTAAAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
TTATCAATTGATATTTAAAAAT
Found at i:36693 original size:2 final size:2
Alignment explanation
Indices: 36686--36717 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36676 CATGAGAAGA
36686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36718 GTTTAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38577 original size:40 final size:40
Alignment explanation
Indices: 38496--38643 Score: 219
Period size: 40 Copynumber: 3.8 Consensus size: 40
38486 TTTGAATGGA
* *
38496 GTACTAAAATGAAACAAAAACTAGAGTTTTTAAGGGC-GG
1 GTACTAAAATGAAACAAAAACTAAAGTTTTTTAGGGCGGG
* *
38535 GTACTAAAATAAAACAAAAACTATAGTTTTTTAGGGCGGG
1 GTACTAAAATGAAACAAAAACTAAAGTTTTTTAGGGCGGG
*
38575 GTACTAAAATGAAACAAAAACTAAAGTTTTTTAGGGCGGA
1 GTACTAAAATGAAACAAAAACTAAAGTTTTTTAGGGCGGG
* *
38615 ATACTAAAATGAAACAAAAGCTAAA-TTTT
1 GTACTAAAATGAAACAAAAACTAAAGTTTT
38644 ATGTATCATT
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 38 0.38
40 62 0.62
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (40 bp):
GTACTAAAATGAAACAAAAACTAAAGTTTTTTAGGGCGGG
Found at i:43686 original size:21 final size:20
Alignment explanation
Indices: 43600--43757 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
43590 AAATGACCAA
**
43600 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
43619 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
43639 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
43659 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
43680 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
43701 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
43721 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
43742 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
43758 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:43786 original size:20 final size:20
Alignment explanation
Indices: 43724--43917 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
43714 CGATTTTCCA
* ** *
43724 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
43744 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
43764 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
43784 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
43804 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
43824 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
43844 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
43864 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
43884 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
43905 AAATCGCAACGCG
1 AAATCGCAACGCG
43918 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:43808 original size:60 final size:60
Alignment explanation
Indices: 43724--43917 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
43714 CGATTTTCCA
* ** * *
43724 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
43784 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
43844 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
43905 AAATCGCAACGCG
1 AAATCGCAACGCG
43918 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:44340 original size:33 final size:33
Alignment explanation
Indices: 44301--44371 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
44291 TTCACTTAGA
*
44301 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
44334 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
44367 TTTCA
1 TTTCA
44372 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:44477 original size:21 final size:20
Alignment explanation
Indices: 44451--44557 Score: 93
Period size: 21 Copynumber: 5.6 Consensus size: 20
44441 TGCAGAAGAG
44451 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
44472 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
44492 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
44513 TCACAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
44527 TCGCAACG-GGAAATGAAAA
1 TCGCAACGAGAAAATGAAAA
44546 TCGCAACGAGAA
1 TCGCAACGAGAA
44558 TCGCAACGCG
Statistics
Matches: 67, Mismatches: 11, Indels: 17
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.01
14 9 0.13
16 2 0.03
17 2 0.03
19 10 0.15
20 18 0.27
21 25 0.37
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:44508 original size:41 final size:36
Alignment explanation
Indices: 44449--44556 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 36
44439 TTTGCAGAAG
*
44449 AGTCGCAACGAGATAAATGAAAATCGCAACGAGAGAA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAG-A
*
44486 TGACTGTCGCAACGAGAGAAATGAAAATCACAACGAGAGA
1 --A--GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGA
44526 A-TCGCAACG-G-GAAATGAAAATCGCAACGAGA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGA
44557 ATCGCAACGC
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
33 20 0.31
34 1 0.02
35 8 0.12
38 1 0.02
39 1 0.02
40 1 0.02
41 32 0.50
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (36 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGA
Found at i:44560 original size:31 final size:32
Alignment explanation
Indices: 44492--44581 Score: 110
Period size: 31 Copynumber: 2.8 Consensus size: 32
44482 AGAATGACTG
*
44492 TCGCAACGAGAGAAATGAAAATCACAACGAGAGAA
1 TCGCAACG-G-GAAATGAAAATCGCAAC-AGAGAA
44527 TCGCAACGGGAAATGAAAATCGCAAC-GAGAA
1 TCGCAACGGGAAATGAAAATCGCAACAGAGAA
* **
44558 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGGGAAATGAAAATCGCA
44582 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 26 0.51
33 16 0.31
34 1 0.02
35 8 0.16
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (32 bp):
TCGCAACGGGAAATGAAAATCGCAACAGAGAA
Found at i:44599 original size:19 final size:19
Alignment explanation
Indices: 44577--44674 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
44567 GAAACCAAAA
*
44577 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
44596 TCGCGTTGCGATTCTC--T
1 TCGCGTTGCGATTTTCATT
44613 T---GTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
44629 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
44643 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
44662 TCGCGTTGCGATT
1 TCGCGTTGCGATT
44675 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 21 0.33
16 4 0.06
17 5 0.08
19 33 0.52
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:44619 original size:14 final size:14
Alignment explanation
Indices: 44600--44688 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
44590 TTCATTTCGC
44600 GTTGCGATTCTCTT
1 GTTGCGATTCTCTT
*
44614 GTTGCGATTTTCATTT
1 GTTGCGATTCTC--TT
*
44630 CGCGTTGCGATTCTCTC
1 ---GTTGCGATTCTCTT
*
44647 GTTGCGATTGTCATTT
1 GTTGCGATTCTC--TT
*
44663 CGCGTTGCGATTCTCTC
1 ---GTTGCGATTCTCTT
44680 GTTGCGATT
1 GTTGCGATT
44689 TTCATTTCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 31 0.53
16 3 0.05
17 2 0.03
19 22 0.38
ACGTcount: A:0.09, C:0.22, G:0.24, T:0.45
Consensus pattern (14 bp):
GTTGCGATTCTCTT
Found at i:44624 original size:33 final size:33
Alignment explanation
Indices: 44582--44696 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
44572 CAAAATCGCA
*
44582 TTGCGATTTTCATTTCGCGTTGCGATTCTCTTG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
44615 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
44648 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
44681 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
44697 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:46551 original size:93 final size:93
Alignment explanation
Indices: 46392--46952 Score: 1099
Period size: 93 Copynumber: 6.1 Consensus size: 93
46382 TAGATTGCTT
*
46392 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46457 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46485 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46550 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46578 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46643 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46671 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46736 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46764 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46829 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46857 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46921 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46948 AGTAA
1 AGTAA
46953 TGCAATCCAT
Statistics
Matches: 467, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
91 6 0.01
92 77 0.16
93 384 0.82
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:47040 original size:19 final size:19
Alignment explanation
Indices: 47000--47128 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
46990 TAGTTTACTT
* *
47000 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
47020 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
47039 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
47058 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
47072 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
47091 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
47105 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
47124 TCGCA
1 TCGCA
47129 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:47079 original size:33 final size:32
Alignment explanation
Indices: 47036--47128 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
47026 CGCGAAACCA
**
47036 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
47068 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
47101 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
47129 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:47126 original size:52 final size:52
Alignment explanation
Indices: 47000--47128 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
46990 TAGTTTACTT
**
47000 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
47052 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
47105 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
47129 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:47146 original size:19 final size:19
Alignment explanation
Indices: 47124--47258 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
47114 GAAACCAAAA
*
47124 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
47143 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
47159 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
47176 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
47192 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
47209 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
47228 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
47248 TCGTGTTGCGA
1 TCGCGTTGCGA
47259 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:47165 original size:14 final size:14
Alignment explanation
Indices: 47146--47202 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
47136 TTTCATTTCG
47146 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
47160 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
47177 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
47193 CGTTGCGATT
1 CGTTGCGATT
47203 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:47171 original size:33 final size:33
Alignment explanation
Indices: 47129--47221 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
47119 CAAAATCGCA
*
47129 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
47162 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
47195 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
47222 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:49203 original size:14 final size:14
Alignment explanation
Indices: 49184--49219 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
49174 ATTGTTTAAT
49184 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
49198 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
49212 TGATTTGT
1 TGATTTGT
49220 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:49342 original size:19 final size:19
Alignment explanation
Indices: 49326--49423 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
49316 AAAAATGACT
49326 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
49345 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
49364 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
49378 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
49397 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
49417 ATCGCAA
1 ATCGCAA
49424 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:49455 original size:53 final size:53
Alignment explanation
Indices: 49326--49441 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
49316 AAAAATGACT
49326 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
49378 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
49431 ATCGCAATGCG
1 ATCGCAATGCG
49442 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:49505 original size:52 final size:54
Alignment explanation
Indices: 49448--49681 Score: 239
Period size: 52 Copynumber: 4.6 Consensus size: 54
49438 TGCGTTTATA
49448 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
49500 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * *
49554 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * *
49606 GTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCA--T-G--TTGGGATT-T-TC
1 ATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCGCATTGCGATTCTCTC
49652 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
49682 GTAATTTCCG
Statistics
Matches: 163, Mismatches: 10, Indels: 23
0.83 0.05 0.12
Matches are distributed among these distances:
46 9 0.06
47 13 0.08
48 9 0.06
49 2 0.01
50 1 0.01
51 2 0.01
52 101 0.62
53 17 0.10
54 9 0.06
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (54 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:49527 original size:14 final size:14
Alignment explanation
Indices: 49508--49562 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
49498 TCATTTCGCA
49508 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
49522 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
49539 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
49555 TTGCGATT
1 TTGCGATT
49563 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:49548 original size:85 final size:85
Alignment explanation
Indices: 49448--49667 Score: 397
Period size: 85 Copynumber: 2.6 Consensus size: 85
49438 TGCGTTTATA
49448 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
49513 ATTCTCTCGTTGCGATTTTC
66 ATTCTCTCGTTGCGATTTTC
49533 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
49598 ATTCTCTCGTTGCGATTTTC
66 ATTCTCTCGTTGCGATTTTC
* *
49618 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
49668 CTCTCGTTGC
Statistics
Matches: 131, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
85 89 0.68
86 41 0.31
87 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (85 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTC
Found at i:49689 original size:33 final size:33
Alignment explanation
Indices: 49448--49681 Score: 185
Period size: 33 Copynumber: 6.9 Consensus size: 33
49438 TGCGTTTATA
49448 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
49481 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
49521 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTCTCTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATT-T-TC
* * * * *
49554 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
49585 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
49618 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
49652 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
49682 GTAATTTCCG
Statistics
Matches: 171, Mismatches: 16, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.05
32 6 0.04
33 95 0.56
34 29 0.17
35 6 0.04
36 4 0.02
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:51977 original size:12 final size:12
Alignment explanation
Indices: 51960--51984 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51950 TCTTCGGGGA
51960 CTTTTTCTTCTT
1 CTTTTTCTTCTT
51972 CTTTTTCTTCTT
1 CTTTTTCTTCTT
51984 C
1 C
51985 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:52193 original size:24 final size:24
Alignment explanation
Indices: 52159--52205 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
52149 CTGAAACATC
52159 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
52183 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
52206 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:52915 original size:20 final size:20
Alignment explanation
Indices: 52887--53156 Score: 256
Period size: 20 Copynumber: 13.5 Consensus size: 20
52877 AAATTTCAGT
* * *
52887 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
52907 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
52927 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
52947 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
* *
52967 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
52987 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
53007 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
53027 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
53047 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
53067 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
53087 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
53107 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
53127 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
53147 GTTGCGATTT
1 GTTGCGATTT
53157 TGGAAAATCG
Statistics
Matches: 221, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
19 3 0.01
20 213 0.96
21 5 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:52947 original size:40 final size:40
Alignment explanation
Indices: 52887--53156 Score: 289
Period size: 40 Copynumber: 6.8 Consensus size: 40
52877 AAATTTCAGT
* *
52887 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* *
52927 GTTGCGATTTACAGATTCTCGTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
52967 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * * *
53007 GTTGCGATATACGGATACGCGTTGCGATATACGGA-TA-C
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
** * *
53045 GCATTGCGATTTACCCATACGCGTTGCGATTTACGGA-TACAC
1 G--TTGCGATTTACAGATTCGCGTTGCGATTTACGGATTA-TC
* * * **
53087 GTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACG-GATTATC
*
53127 GTTGCGATTTTA-ATATTCGCGTTGCGATTT
1 GTTGCGA-TTTACAGATTCGCGTTGCGATTT
53157 TGGAAAATCG
Statistics
Matches: 203, Mismatches: 20, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 191 0.94
41 6 0.03
42 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
Found at i:53157 original size:20 final size:20
Alignment explanation
Indices: 53123--53220 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
53113 ATTTATGTGT
*
53123 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
53143 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
53164 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
53185 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
53206 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
53221 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:53216 original size:42 final size:43
Alignment explanation
Indices: 53123--53221 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
53113 ATTTATGTGT
* *
53123 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
53164 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
53206 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
53222 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:54519 original size:31 final size:31
Alignment explanation
Indices: 54483--54561 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
54473 ATAACGGTGG
*
54483 AGTGACAATTTTGTTACAAATTAATAACGCT
1 AGTGACAATTTTGTTACAAACTAATAACGCT
* * *
54514 AGTGACCATTTTGTTACAAACTGATAACGTT
1 AGTGACAATTTTGTTACAAACTAATAACGCT
*
54545 AGTGACTATTTTGTTAC
1 AGTGACAATTTTGTTAC
54562 TTTTGAAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (31 bp):
AGTGACAATTTTGTTACAAACTAATAACGCT
Found at i:55261 original size:25 final size:25
Alignment explanation
Indices: 55233--55280 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
55223 GTTAGGAGTG
* *
55233 AACTTATATAATTTTAGGAGGATAT
1 AACTTATAAAATTATAGGAGGATAT
55258 AACTTATAAAATTATAGGAGGAT
1 AACTTATAAAATTATAGGAGGAT
55281 GAAAACATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (25 bp):
AACTTATAAAATTATAGGAGGATAT
Found at i:55881 original size:3 final size:3
Alignment explanation
Indices: 55873--55904 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
55863 AAGTAAATTT
55873 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
55905 TGTGTTTCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56137 original size:3 final size:3
Alignment explanation
Indices: 56129--56162 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
56119 TAGATTTCGC
56129 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
56163 ACATAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:57430 original size:72 final size:72
Alignment explanation
Indices: 57305--57438 Score: 189
Period size: 72 Copynumber: 1.9 Consensus size: 72
57295 GGGCCTACTG
*** * * *
57305 AATTATCATATTTTTGGGTTTTTTAAATAAAAATGATGTTTAAAAATATTTTTTTAATTATTGGG
1 AATTATCATATTTTAAAGTATTTGAAATAAAAATGATATTTAAAAATATTTTTTTAATTATTGGG
57370 ATCACTA
66 ATCACTA
*
57377 AATTATCATATTTTAAAGTATTTGAAATAAAAATATATATTTAAAAATA-TTTTTTAATTATT
1 AATTATCATATTTTAAAGTATTTGAAATAAAAAT-GATATTTAAAAATATTTTTTTAATTATT
57439 AAACTTAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 42 0.78
73 12 0.22
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (72 bp):
AATTATCATATTTTAAAGTATTTGAAATAAAAATGATATTTAAAAATATTTTTTTAATTATTGGG
ATCACTA
Found at i:60918 original size:20 final size:20
Alignment explanation
Indices: 60893--60944 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
60883 ATGCAGGTAG
60893 AGTATCGATACTATAGGGAT
1 AGTATCGATACTATAGGGAT
60913 AGTATCGATACTATAGGGAT
1 AGTATCGATACTATAGGGAT
* *
60933 AATACCGATACT
1 AGTATCGATACT
60945 TGTTCTTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTATAGGGAT
Found at i:67955 original size:17 final size:17
Alignment explanation
Indices: 67933--67969 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
67923 AATCTTTATC
67933 ATTCAAATCAAAACATT
1 ATTCAAATCAAAACATT
67950 ATTCAAATCAAAACATT
1 ATTCAAATCAAAACATT
67967 ATT
1 ATT
67970 TTAGTGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTCAAATCAAAACATT
Found at i:68097 original size:7 final size:6
Alignment explanation
Indices: 68086--68115 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
68076 TTAAGTATTA
68086 AAATTG ACAATTG AAATTG AAATTG AAATT
1 AAATTG A-AATTG AAATTG AAATTG AAATT
68116 TTAGTGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.33
Consensus pattern (6 bp):
AAATTG
Found at i:68704 original size:12 final size:13
Alignment explanation
Indices: 68687--68715 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
68677 TAACATGTTG
68687 CCTTA-CACAAAA
1 CCTTACCACAAAA
68699 CCTTACCACAAAA
1 CCTTACCACAAAA
68712 CCTT
1 CCTT
68716 GGATAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (13 bp):
CCTTACCACAAAA
Found at i:70524 original size:2 final size:2
Alignment explanation
Indices: 70519--70568 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
70509 AACTATTTAA
70519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
70561 AT AT AT AT
1 AT AT AT AT
70569 GAAAAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71581 original size:148 final size:147
Alignment explanation
Indices: 71313--71604 Score: 433
Period size: 148 Copynumber: 2.0 Consensus size: 147
71303 TTCTTTGGGT
*
71313 TTTTTCCTTATTAAAGAACCTCAATTATATGATGTAAAATTTGCCTTTGGATTCGAGTTTAAAGC
1 TTTTTCCTTATTAAAGAACCTCAATTATATGATGTAAAATTTGCCCTTGGATTCGAGTTTAAAGC
* * * ** *
71378 TCTTATTGTTGGTAATTCCGCGTTTTTAGGATTTAATTACTGGATTAACTAGTTGAACATCATGT
66 TCTTATGGTCGGTAATTCCACGCATTTAGGATTTAATTACTGGATTAACTAGTTG-ACATAATGT
71443 ATTTGTTGATTGATACTG
130 ATTTGTTGATTGATACTG
* * * *
71461 TTTTTGCTTATTGAAGAACCTGAATTATGTGATGTAAAATTTGCCCTTGGATTCGAGCTTT-AAG
1 TTTTTCCTTATTAAAGAACCTCAATTATATGATGTAAAATTTGCCCTTGGATTCGAG-TTTAAAG
* * *
71525 CTCTTATGGTCGGTAATTCCACGCATTTAGGATTTCATTACTGGGTTAACTGGTTGACATAATGT
65 CTCTTATGGTCGGTAATTCCACGCATTTAGGATTTAATTACTGGATTAACTAGTTGACATAATGT
71590 ATTTGTTGATTGATA
130 ATTTGTTGATTGATA
71605 TATTACTCTT
Statistics
Matches: 129, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
147 23 0.18
148 103 0.80
149 3 0.02
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (147 bp):
TTTTTCCTTATTAAAGAACCTCAATTATATGATGTAAAATTTGCCCTTGGATTCGAGTTTAAAGC
TCTTATGGTCGGTAATTCCACGCATTTAGGATTTAATTACTGGATTAACTAGTTGACATAATGTA
TTTGTTGATTGATACTG
Found at i:73686 original size:59 final size:59
Alignment explanation
Indices: 73616--73770 Score: 161
Period size: 59 Copynumber: 2.6 Consensus size: 59
73606 GAGTTAATGG
* *
73616 CAAATACATCCCCAAACTATGACTTTATTCTAAATTGGTCC-CTAAACATTTGAACATTT
1 CAAATCCATCCCCAAACTATGACTTTATTCTAAATTGGTCCAC-AAACATTTGAACATTC
* * *** * * *
73675 CAATTTCATCCCTC-AACTATGACTCCCTTCTAAATTGGTCCACAAGCTTTTTAACATTC
1 CAAATCCATCCC-CAAACTATGACTTTATTCTAAATTGGTCCACAAACATTTGAACATTC
* *
73734 CAAATCCATCCTCAAACTATGACCCTTATTCTAAATT
1 CAAATCCATCCCCAAACTATGA-CTTTATTCTAAATT
73771 AGCCCAAAAC
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
58 1 0.01
59 63 0.83
60 12 0.16
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (59 bp):
CAAATCCATCCCCAAACTATGACTTTATTCTAAATTGGTCCACAAACATTTGAACATTC
Done.