Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004955.1 Hibiscus syriacus cultivar Beakdansim tig00011141_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: 100659
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2485 original size:20 final size:20
Alignment explanation
Indices: 2439--2486 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2429 TTGTTGCGAT
*
2439 TGTTGCGAAAGTCAAATTTG
1 TGTTGCGAAAGTCAAATTCG
***
2459 CAATGCGAAAGTCAAATTCG
1 TGTTGCGAAAGTCAAATTCG
2479 TGTTGCGA
1 TGTTGCGA
2487 TTATTACGAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAAGTCAAATTCG
Found at i:2707 original size:13 final size:13
Alignment explanation
Indices: 2674--2708 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2664 ATCAATTAAA
*
2674 AAATCAACTTTAC
1 AAATCAATTTTAC
2687 AAATCAATTTTAC
1 AAATCAATTTTAC
2700 AAATCAATT
1 AAATCAATT
2709 AAACAAGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATCAATTTTAC
Found at i:2714 original size:13 final size:13
Alignment explanation
Indices: 2664--2714 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
2654 TTATTTACAC
2664 ATCAATTAAA-AA
1 ATCAATTAAACAA
*
2676 ATCAACTT-TACAA
1 ATCAA-TTAAACAA
**
2689 ATCAATTTTACAA
1 ATCAATTAAACAA
2702 ATCAATTAAACAA
1 ATCAATTAAACAA
2715 GCAAAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 8 0.24
13 25 0.76
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (13 bp):
ATCAATTAAACAA
Found at i:2760 original size:74 final size:74
Alignment explanation
Indices: 2610--2778 Score: 261
Period size: 74 Copynumber: 2.3 Consensus size: 74
2600 ATTTAAAACA
2610 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGATTATTTACACATCAATTAAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAT-AGATTATTTACACATCAATTAAAA
2675 AATCAACTTT
65 AATCAACTTT
** * *
2685 ACAAATCAA-TTTTACAAATCAATTAAACAAGCAAAAAAT-TCTTATTTCCTCATCAATTAAACA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAGATTATTTACACATCAATTAAA-A
2748 AATCAACTTTT
65 AATCAAC-TTT
2759 ACAAATCAACTTTTACAAAT
1 ACAAATCAACTTTTACAAAT
2779 ACATCAAATT
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
72 18 0.21
73 8 0.09
74 42 0.48
75 19 0.22
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (74 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAGATTATTTACACATCAATTAAAAA
ATCAACTTT
Found at i:2764 original size:14 final size:14
Alignment explanation
Indices: 2745--2778 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2735 CATCAATTAA
2745 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2759 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2773 ACAAAT
1 ACAAAT
2779 ACATCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3728 original size:2 final size:2
Alignment explanation
Indices: 3717--3754 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3707 TATGCTGTTT
3717 TA TA -A 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 TA TA TA T
3755 TAGTGAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4204 original size:21 final size:21
Alignment explanation
Indices: 4178--4250 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
4168 CGATGACAGA
4178 GCCTCTTGAATGGTGGGAAGG
1 GCCTCTTGAATGGTGGGAAGG
** *
4199 GCCTCTTGAA-GGATGACAGGG
1 GCCTCTTGAATGG-TGGGAAGG
* *
4220 GCCTCTTGAATGATAGG-AGAG
1 GCCTCTTGAATGGTGGGAAG-G
4241 GCCTCTTGAA
1 GCCTCTTGAA
4251 CGATGACAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
20 3 0.07
21 37 0.90
22 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (21 bp):
GCCTCTTGAATGGTGGGAAGG
Found at i:4244 original size:42 final size:42
Alignment explanation
Indices: 4161--4260 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
4151 GGGAGGGACT
* *
4161 TCTTGAACGATGACA-GAGCCTCTTGAATGGTGGGAAGGGCC
1 TCTTGAACGATGACAGGAGCCTCTTGAATGATAGGAAGGGCC
* *
4202 TCTTGAAGGATGACAGGGGCCTCTTGAATGATAGG-AGAGGCC
1 TCTTGAACGATGACAGGAGCCTCTTGAATGATAGGAAG-GGCC
4244 TCTTGAACGATGACAGG
1 TCTTGAACGATGACAGG
4261 TGAATCAGGC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
41 16 0.31
42 36 0.69
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (42 bp):
TCTTGAACGATGACAGGAGCCTCTTGAATGATAGGAAGGGCC
Found at i:4650 original size:21 final size:21
Alignment explanation
Indices: 4560--4675 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
4550 AACACCATTT
* * * *
4560 TCATCGCGTAAAACATCTACC
1 TCATCACGTAAAGCACCGACC
* *
4581 TCACCACGTAAAG-ATCGAACC
1 TCATCACGTAAAGCACCG-ACC
* * **
4602 TCATCACGTCATGCACC-ATTG
1 TCATCACGTAAAGCACCGA-CC
* *
4623 TCTTCACGTAAAGTACCGACC
1 TCATCACGTAAAGCACCGACC
* * **
4644 TCCTCACGCAAAGCATTGACC
1 TCATCACGTAAAGCACCGACC
4665 TCATCACGTAA
1 TCATCACGTAA
4676 CTCCCCTAAC
Statistics
Matches: 68, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
20 4 0.06
21 61 0.90
22 3 0.04
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.22
Consensus pattern (21 bp):
TCATCACGTAAAGCACCGACC
Found at i:6313 original size:20 final size:20
Alignment explanation
Indices: 6290--6330 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6280 TCGCAACGCT
6290 ATTTTCATTTTCGCGTTGCG
1 ATTTTCATTTTCGCGTTGCG
* *
6310 ATTTTCATTTTTGTGTTGCG
1 ATTTTCATTTTCGCGTTGCG
6330 A
1 A
6331 ATTTAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.54
Consensus pattern (20 bp):
ATTTTCATTTTCGCGTTGCG
Found at i:6706 original size:20 final size:21
Alignment explanation
Indices: 6667--6716 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
6657 GATAGATGGA
6667 TTTCGCCGGAGATAGGGACGG
1 TTTCGCCGGAGATAGGGACGG
*
6688 TTTCGTCGGAGAT-GGGACGG
1 TTTCGCCGGAGATAGGGACGG
*
6708 ATGTCGCCG
1 -TTTCGCCG
6717 TAGAGAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.16, C:0.20, G:0.42, T:0.22
Consensus pattern (21 bp):
TTTCGCCGGAGATAGGGACGG
Found at i:6904 original size:20 final size:20
Alignment explanation
Indices: 6881--6967 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
6871 TGACTTATGT
*
6881 GTTGCGAATTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
6901 GTTGCGATTTACAGATTCGT
1 GTTGCGATTTACAAATTCGC
*
6921 ATTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
6941 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
6961 GTTGCGA
1 GTTGCGA
6968 ATTTGGAAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:6926 original size:40 final size:40
Alignment explanation
Indices: 6882--6970 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
6872 GACTTATGTG
*
6882 TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGTA
1 TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGCA
* * *
6922 TTGCGATTTACAAATTCGCGTTGCGATTTACATATTCGCG
1 TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGCA
6962 TTGCGAATT
1 TTGCGAATT
6971 TGGAAACTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (40 bp):
TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGCA
Found at i:6985 original size:40 final size:40
Alignment explanation
Indices: 6882--6987 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 40
6872 GACTTATGTG
* * * *
6882 TTGCGAATTACAAATTCGCGTTGCGATTTACAGATTCGTA
1 TTGCGATTTACAAACTCGAGTTGCGATTTACAGATTCGCA
* * * *
6922 TTGCGATTTACAAATTCGCGTTGCGATTTACATATTCGCG
1 TTGCGATTTACAAACTCGAGTTGCGATTTACAGATTCGCA
**
6962 TTGCGAATTTGGAAACT-GAGTTGCGA
1 TTGCG-ATTTACAAACTCGAGTTGCGA
6988 AATTGGAGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 49 0.86
41 8 0.14
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (40 bp):
TTGCGATTTACAAACTCGAGTTGCGATTTACAGATTCGCA
Found at i:25557 original size:21 final size:22
Alignment explanation
Indices: 25527--25568 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
25517 ATGTTATTAT
* *
25527 TTTAAGGATT-TTTTTTCTCTC
1 TTTAAAGATTGTTTATTCTCTC
25548 TTTAAAGATTGTTTATTCTCT
1 TTTAAAGATTGTTTATTCTCT
25569 GAACTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (22 bp):
TTTAAAGATTGTTTATTCTCTC
Found at i:32689 original size:34 final size:33
Alignment explanation
Indices: 32651--32755 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 33
32641 TTAATCAAGG
32651 AGGGTTATAGTGTAATTCGTATCTTATGTATTTC
1 AGGGTTATAGTGTAATT-GTATCTTATGTATTTC
*
32685 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTT-
1 AGGGTTATAGTGTAAT-TGTATCTTATGT-ATTTC
* * *
32719 AGGGTT-TGAGTGCATTTTGTATCTTATGTAATTC
1 AGGGTTAT-AGTGTA-ATTGTATCTTATGTATTTC
32753 AGG
1 AGG
32756 TTAATTAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
33 3 0.05
34 52 0.85
35 6 0.10
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.45
Consensus pattern (33 bp):
AGGGTTATAGTGTAATTGTATCTTATGTATTTC
Found at i:41402 original size:34 final size:34
Alignment explanation
Indices: 41362--41428 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
41352 TTCAAAGCAT
* *
41362 ATATTTATTTAGTGTCAAAATATAAGGCTTATAG
1 ATATTTATTGAGTATCAAAATATAAGGCTTATAG
41396 ATATTTATTGAGTATCAAAATATAAGGCTTATA
1 ATATTTATTGAGTATCAAAATATAAGGCTTATA
41429 CATGAGCCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (34 bp):
ATATTTATTGAGTATCAAAATATAAGGCTTATAG
Found at i:44613 original size:20 final size:20
Alignment explanation
Indices: 44588--44661 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
44578 TTTTCCCAAT
*
44588 TCGCAATGCGAATAAATAAA
1 TCGCAACGCGAATAAATAAA
**
44608 TCGCAACGCGAATTGGGA-AAA
1 TCGCAACGCGAA-T-AAATAAA
* *
44629 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAATAAA
44649 TCGCAACGCGAAT
1 TCGCAACGCGAAT
44662 TGGGAAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 27 0.63
21 15 0.35
22 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAATAAA
Found at i:44631 original size:21 final size:21
Alignment explanation
Indices: 44605--44680 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
44595 GCGAATAAAT
44605 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
44626 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
44646 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
44667 AAATCGCAATGCGA
1 AAATCGCAACGCGA
44681 TACTTACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:44633 original size:41 final size:41
Alignment explanation
Indices: 44588--44680 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
44578 TTTTCCCAAT
44588 TCGCAATGCGAATAAATAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAATAAATCGCAACGCGAATTGGGAAAA
*
44629 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAATAAATCGCAACGCGAATTGGGAAAA
44670 TCGCAATGCGA
1 TCGCAATGCGA
44681 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAATAAATCGCAACGCGAATTGGGAAAA
Found at i:44693 original size:41 final size:41
Alignment explanation
Indices: 44607--44741 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
44597 GAATAAATAA
** *
44607 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
44648 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
44689 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
44730 TTCGCAACGCGA
1 ATCGCAACGCGA
44742 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:44694 original size:20 final size:20
Alignment explanation
Indices: 44669--44760 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
44659 AATTGGGAAA
*
44669 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
44689 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
44710 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
44730 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
44750 TTCGCAACGCG
1 ATCGCAACGCG
44761 GTTTACATAG
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 42 0.70
21 12 0.20
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:45320 original size:19 final size:19
Alignment explanation
Indices: 45282--45348 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
45272 TTCGAGAATG
45282 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
45302 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
45321 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
45340 AAAATCGCA
1 AAAATCGCA
45349 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:45366 original size:19 final size:19
Alignment explanation
Indices: 45344--45528 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
45334 GAAACCAAAA
*
45344 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45363 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
45382 TCGCGTTGAGATTTTTATT
1 TCGCGTTGCGATTTTCATT
45401 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
45421 TCGCGTTGCGATTTTC---
1 TCGCGTTGCGATTTTCATT
* **
45437 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
45454 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
45468 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
45487 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
45507 ATCTCGTTGTGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
45527 TC
1 TC
45529 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 47 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45419 original size:39 final size:38
Alignment explanation
Indices: 45344--45528 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
45334 GAAACCAAAA
*
45344 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
45382 TCGCGTTGAGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* **
45421 TCGCGTTGCGATTTTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
45454 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
45487 TCCGCGTTGCGATTCTCATTATCTCGTTGTGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
45527 TC
1 TC
45529 AACCAAAAGA
Statistics
Matches: 123, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
31 4 0.03
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 20 0.16
39 30 0.24
40 17 0.14
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:45505 original size:20 final size:19
Alignment explanation
Indices: 45471--45528 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
45461 GCGATTCTCT
**
45471 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
* *
45491 CGTTGCGATTCTCATTATCT
1 CGTTGCGATTTTCATT-TCG
*
45511 CGTTGTGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
45529 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.06
20 29 0.91
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:47609 original size:21 final size:21
Alignment explanation
Indices: 47585--47651 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
47575 TCATTCCTCG
47585 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
47606 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
47627 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
47648 AGAG
1 AGAG
47652 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:47609 original size:42 final size:42
Alignment explanation
Indices: 47529--47651 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
47519 GCCCGACTCG
* * * * * *
47529 CCTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
*
47571 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
47613 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
47652 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:49059 original size:14 final size:14
Alignment explanation
Indices: 49040--49075 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
49030 ATTGTTTAAT
49040 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
49054 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
49068 TGATTTGT
1 TGATTTGT
49076 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:49226 original size:33 final size:34
Alignment explanation
Indices: 49184--49260 Score: 113
Period size: 33 Copynumber: 2.3 Consensus size: 34
49174 AAAAGTACTA
49184 TCGCATTGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
* **
49217 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
49250 TCGCATTGCGA
1 TCGCATTGCGA
49261 TAGTAATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 2 0.05
33 37 0.95
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (34 bp):
TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
Found at i:49227 original size:19 final size:19
Alignment explanation
Indices: 49203--49261 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
49193 GAAATTAGCG
49203 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
49222 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
49236 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
49255 TTGCGAT
1 TTGCGAT
49262 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:51569 original size:12 final size:12
Alignment explanation
Indices: 51552--51576 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51542 TTCTTCGGGA
51552 CTTTTTCTTCTT
1 CTTTTTCTTCTT
51564 CTTTTTCTTCTT
1 CTTTTTCTTCTT
51576 C
1 C
51577 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:51784 original size:24 final size:24
Alignment explanation
Indices: 51750--51803 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
51740 CTGAAACATC
* *
51750 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
51774 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
51798 ATCAAA
1 ATCAAA
51804 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:54394 original size:20 final size:19
Alignment explanation
Indices: 54359--54425 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
54349 CGAACTTAAA
54359 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
54378 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
54398 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
54417 ATCGCAACG
1 ATCGCAACG
54426 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:54433 original size:14 final size:14
Alignment explanation
Indices: 54414--54471 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
54404 ATGCGAAATG
54414 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
54428 AAAATCGCAACGTGAA
1 AAAATCGCAAC--GAC
54444 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
54460 AAAATCGCAACG
1 AAAATCGCAACG
54472 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.58
16 6 0.16
18 10 0.26
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:54456 original size:32 final size:33
Alignment explanation
Indices: 54398--54476 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
54388 GGAAATGGCT
*
54398 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
54431 ATCGCAACGTGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
54463 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
54477 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 29 0.67
33 14 0.33
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:54505 original size:19 final size:17
Alignment explanation
Indices: 54483--54578 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
54473 GAAACACAAA
54483 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
54502 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
54518 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
54534 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
54550 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
54567 TCGCATTGCGAT
1 TCGC-TTGCGAT
54579 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:54524 original size:14 final size:14
Alignment explanation
Indices: 54505--54562 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
54495 TTTCATTTCG
54505 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
54519 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
54535 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
54551 CGTTGCGATTTT
1 CGTTGCGATTTT
54563 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:54569 original size:33 final size:33
Alignment explanation
Indices: 54488--54578 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
54478 ACAAATCGCA
54488 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
54521 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
54553 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
54579 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:54597 original size:20 final size:19
Alignment explanation
Indices: 54563--54616 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
54553 TTGCGATTTT
*
54563 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
54582 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
54602 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
54617 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:54615 original size:19 final size:19
Alignment explanation
Indices: 54551--54616 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
54541 GCGATTTTGT
**
54551 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
54570 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
54590 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
54609 TGTTGCGA
1 CGTTGCGA
54617 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:55108 original size:18 final size:18
Alignment explanation
Indices: 55082--55126 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
55072 GTCGATCAGA
* *
55082 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
55100 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
55118 TGATGGCTC
1 TGATGGCTC
55127 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:56762 original size:22 final size:22
Alignment explanation
Indices: 56737--56780 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
56727 GATTTAGATA
56737 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
56759 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
56781 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:57061 original size:20 final size:20
Alignment explanation
Indices: 56968--57061 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
56958 GATTATGTAA
* *
56968 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
* *
56988 ATCGCGTTGCAAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
57008 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
57029 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
57049 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
57062 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 43 0.72
21 12 0.20
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:57079 original size:21 final size:21
Alignment explanation
Indices: 57050--57125 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
57040 ATAGTAAGTA
57050 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
57071 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
57091 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
57112 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
57126 ATTTATTCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:57080 original size:41 final size:41
Alignment explanation
Indices: 56989--57123 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
56979 AAAGTCAGTA
* * * * ** *
56989 TCGCGTTGCAAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
57029 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
57071 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
57112 TCGCGTTGCGAT
1 TCGCGTTGCGAT
57124 TTATTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:57094 original size:20 final size:20
Alignment explanation
Indices: 57050--57142 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
57040 ATAGTAAGTA
* **
57050 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
57071 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
57091 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
* *
57112 TCGCGTTGCGATTTATTTAT
1 TCGCATTGCGATTTACTTAT
57132 TCGCATTGCGA
1 TCGCATTGCGA
57143 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.54
21 26 0.46
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:57124 original size:41 final size:41
Alignment explanation
Indices: 57050--57142 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
57040 ATAGTAAGTA
57050 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
57091 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTATTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
57132 TCGCATTGCGA
1 TCGCATTGCGA
57143 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:58092 original size:2 final size:2
Alignment explanation
Indices: 58085--58110 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58075 TTTAAGATGA
58085 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
58111 TAATATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59211 original size:21 final size:21
Alignment explanation
Indices: 59153--59212 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
59143 TGGGGTTTTT
59153 TTTATT-AAAAT-A-ATATTA
1 TTTATTAAAAATAATATATTA
* * * *
59171 TTAATTAATAATATTTTATTA
1 TTTATTAAAAATAATATATTA
59192 TTTATTAAAAATAATATATTA
1 TTTATTAAAAATAATATATTA
59213 GTTAACTTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
21 22 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATTAAAAATAATATATTA
Found at i:59250 original size:38 final size:36
Alignment explanation
Indices: 59149--59294 Score: 122
Period size: 38 Copynumber: 3.9 Consensus size: 36
59139 GGGTTGGGGT
59149 TTTTTTTATT-A-AAATAAT-ATTATTAATTAATAATA
1 TTTTTTTATTAATAAATAATAATTATTAATTAAT--TA
* * *
59184 TTTTATTATTTATTAAA-AATAATATATTAGTTAACTTA
1 TTTTTTTA-TTAATAAATAATAAT-TATTAATTAA-TTA
*
59222 TTTTTTTATTAATAAATTAATAATTATTATTTAGATT-
1 TTTTTTTATTAATAAA-TAATAATTATTAATTA-ATTA
* *
59259 TATTATTTATTAATAAATTAATAATTATTTATTAAT
1 T-TTTTTTATTAATAAA-TAATAATTATTAATTAAT
59295 AAATTAACTT
Statistics
Matches: 92, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
35 7 0.08
36 2 0.02
37 13 0.14
38 53 0.58
39 16 0.17
40 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (36 bp):
TTTTTTTATTAATAAATAATAATTATTAATTAATTA
Found at i:61886 original size:21 final size:21
Alignment explanation
Indices: 61847--61885 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
61837 AAACAATTGG
61847 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
61868 TAACAATTGATAT-ATTTT
1 TAACAATTGATATCATTTT
61886 TCATTAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:62160 original size:23 final size:21
Alignment explanation
Indices: 62110--62188 Score: 76
Period size: 21 Copynumber: 3.7 Consensus size: 21
62100 AGGGTGTCAA
62110 AGTGCATCCATGCACC--CCTGT
1 AGTGCATCCATGCACCTGCC--T
62131 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTG-C-CT
*
62154 AGTGCATCGATGCACCATG--T
1 AGTGCATCCATGCACC-TGCCT
62174 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
62189 TCCATTTCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
20 15 0.29
21 16 0.31
23 16 0.31
24 3 0.06
25 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCTGCCT
Found at i:63593 original size:48 final size:49
Alignment explanation
Indices: 63409--63696 Score: 258
Period size: 49 Copynumber: 5.9 Consensus size: 49
63399 TATAGATGTA
* *
63409 GATGATTTAGCACGTCTGACGTCTTTGTGATGGTGGTGCTACTATTAAT
1 GATGACTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTACTATTAAT
* * *
63458 GATGATTTAGCACGTCTGACGTCTTTGTGACGATGGTGTTACTATTAAT
1 GATGACTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTACTATTAAT
* ** *
63507 GATGACTTAGGATATCTGACGTCTTTGTGACAGTGGTGCTACTATTAAT
1 GATGACTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTACTATTAAT
** * * * * * *
63556 GAT-AAATAGCACGCCTGGCGTCTGTGTGACGGTGGTGCTATTATGAAC
1 GATGACTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTACTATTAAT
* * * * * * **
63604 GGT-ACCTAGCACGTCTGACTTCTGTGTGATGGTGGTGTTACTATCGAT
1 GATGACTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTACTATTAAT
* * * * *
63652 GGT-ACCTAGCATGTCTGATGTTACTTATGTAACGGTGGTGCTACT
1 GATGACTTAGCACGTCTGACG-T-CTT-TGTGACGGTGGTGCTACT
63697 TATGTATATG
Statistics
Matches: 195, Mismatches: 41, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
48 86 0.44
49 92 0.47
50 2 0.01
51 15 0.08
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.35
Consensus pattern (49 bp):
GATGACTTAGCACGTCTGACGTCTTTGTGACGGTGGTGCTACTATTAAT
Found at i:63831 original size:30 final size:29
Alignment explanation
Indices: 63755--63873 Score: 138
Period size: 30 Copynumber: 4.1 Consensus size: 29
63745 CATTGGGTTG
*
63755 TGAAATGAAAAAGTGAAT-AGTACATGCTA
1 TGAAATGAATAAGTGAATGA-TACATGCTA
63784 TG-AATGAA-AAGTGAATGATACATGCTA
1 TGAAATGAATAAGTGAATGATACATGCTA
* *
63811 CGAAATGAATTAAATGAATGATACATGCTA
1 TGAAATGAA-TAAGTGAATGATACATGCTA
*
63841 TGAAATAAATGAAGTGAATG-TAACATGCTA
1 TGAAATGAAT-AAGTGAATGAT-ACATGCTA
63871 TGA
1 TGA
63874 TATATATGAT
Statistics
Matches: 79, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
27 18 0.23
28 13 0.16
29 4 0.05
30 44 0.56
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (29 bp):
TGAAATGAATAAGTGAATGATACATGCTA
Found at i:78853 original size:13 final size:13
Alignment explanation
Indices: 78835--78874 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
78825 ACCGAGTCGA
*
78835 ACTGAGTCAATTC
1 ACTGAGTCAACTC
*
78848 ACTGAGTTAACTC
1 ACTGAGTCAACTC
*
78861 ACTAAGTCAACTC
1 ACTGAGTCAACTC
78874 A
1 A
78875 TTTCAGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (13 bp):
ACTGAGTCAACTC
Found at i:78960 original size:22 final size:22
Alignment explanation
Indices: 78930--78971 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
78920 GACATGATCG
*
78930 TTGATTTTGACCATAGTTGACT
1 TTGACTTTGACCATAGTTGACT
*
78952 TTGACTTTGACCATATTTGA
1 TTGACTTTGACCATAGTTGA
78972 ATTTAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (22 bp):
TTGACTTTGACCATAGTTGACT
Found at i:80460 original size:18 final size:19
Alignment explanation
Indices: 80437--80473 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
80427 CCAGTAATCC
80437 TATTCCC-TGGTAATCTTT
1 TATTCCCTTGGTAATCTTT
80455 TATTCCCTTTGGTAATCTT
1 TATTCCC-TTGGTAATCTT
80474 ACATTCCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.16, C:0.22, G:0.11, T:0.51
Consensus pattern (19 bp):
TATTCCCTTGGTAATCTTT
Found at i:95656 original size:21 final size:21
Alignment explanation
Indices: 95630--95791 Score: 130
Period size: 21 Copynumber: 7.7 Consensus size: 21
95620 GGTTCTATTT
95630 TGGTCCTTCGGGATATATATG
1 TGGTCCTTCGGGATATATATG
*
95651 TGGTCCTT-TGGA-ATATATG
1 TGGTCCTTCGGGATATATATG
* * * *
95670 AGGTCCTTCGAGACATATATT
1 TGGTCCTTCGGGATATATATG
* * *
95691 TGGTCCTTTGGAACATATATG
1 TGGTCCTTCGGGATATATATG
* * * *
95712 TGGTCCTTAGGCACAATTATATA
1 TGGTCCTTCGGGA-TA-TATATG
*
95735 TGGTTCTTCGGGATATATATG
1 TGGTCCTTCGGGATATATATG
** *
95756 TGGTTTTTCAGGATATATATG
1 TGGTCCTTCGGGATATATATG
* *
95777 AGGTCATTCGGGATA
1 TGGTCCTTCGGGATA
95792 ATTTATATGG
Statistics
Matches: 112, Mismatches: 25, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
19 14 0.12
20 5 0.04
21 76 0.68
22 2 0.02
23 15 0.13
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (21 bp):
TGGTCCTTCGGGATATATATG
Found at i:95688 original size:40 final size:42
Alignment explanation
Indices: 95631--95719 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 42
95621 GTTCTATTTT
* *
95631 GGTCCTTCGGGATATATATGTGGTCCTTTGG-A-ATATATGA
1 GGTCCTTCGAGACATATATGTGGTCCTTTGGAACATATATGA
* *
95671 GGTCCTTCGAGACATATATTTGGTCCTTTGGAACATATATGT
1 GGTCCTTCGAGACATATATGTGGTCCTTTGGAACATATATGA
95713 GGTCCTT
1 GGTCCTT
95720 AGGCACAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 28 0.65
41 1 0.02
42 14 0.33
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (42 bp):
GGTCCTTCGAGACATATATGTGGTCCTTTGGAACATATATGA
Done.