Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005868.1 Hibiscus syriacus cultivar Beakdansim tig00013795_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: 101581
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:444 original size:29 final size:31
Alignment explanation
Indices: 393--450 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
383 AATTTAAGGC
393 AAATGGTTTTTGGACTTGAATTGAATTTACA
1 AAATGGTTTTTGGACTTGAATTGAATTTACA
424 AAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAATGGTTTTTGGACTTGAATTGAATTTA
451 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.41
30 12 0.44
31 4 0.15
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (31 bp):
AAATGGTTTTTGGACTTGAATTGAATTTACA
Found at i:570 original size:21 final size:20
Alignment explanation
Indices: 540--616 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
530 TTCAAGATTG
* *
540 CCCAGGGGTATAGATTCCCC
1 CCCAGGGGTACAGATACCCC
560 CCCAGGGGGTACAGATA---C
1 CCCA-GGGGTACAGATACCCC
*
578 CCC--GGGTACAAATA-CCC
1 CCCAGGGGTACAGATACCCC
595 CCCAGGGGGTACAGATACCCC
1 CCCA-GGGGTACAGATACCCC
616 C
1 C
617 TGCAGGTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
15 10 0.22
17 4 0.09
18 4 0.09
20 14 0.30
21 14 0.30
ACGTcount: A:0.25, C:0.36, G:0.26, T:0.13
Consensus pattern (20 bp):
CCCAGGGGTACAGATACCCC
Found at i:580 original size:20 final size:20
Alignment explanation
Indices: 557--616 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
547 GTATAGATTC
557 CCCCCCAGGGGGTACAGATA
1 CCCCCCAGGGGGTACAGATA
*
577 --CCCC---GGGTACAAATA
1 CCCCCCAGGGGGTACAGATA
592 CCCCCCAGGGGGTACAGATA
1 CCCCCCAGGGGGTACAGATA
612 CCCCC
1 CCCCC
617 TGCAGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 10 0.30
17 4 0.12
18 4 0.12
20 15 0.45
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (20 bp):
CCCCCCAGGGGGTACAGATA
Found at i:586 original size:15 final size:15
Alignment explanation
Indices: 566--595 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
556 CCCCCCCAGG
*
566 GGGTACAGATACCCC
1 GGGTACAAATACCCC
581 GGGTACAAATACCCC
1 GGGTACAAATACCCC
596 CCAGGGGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (15 bp):
GGGTACAAATACCCC
Found at i:676 original size:20 final size:20
Alignment explanation
Indices: 651--688 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
641 CAGAATGTCT
651 AGGGGTACCAATTCCCCCCC
1 AGGGGTACCAATTCCCCCCC
*
671 AGGGGTACCGATTCCCCC
1 AGGGGTACCAATTCCCCC
689 TGTTCAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (20 bp):
AGGGGTACCAATTCCCCCCC
Found at i:762 original size:22 final size:21
Alignment explanation
Indices: 724--767 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
714 ATTTGAATAT
* *
724 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGGACCGATTCCC
745 TATGAAGGGGGGACCGATTCCC
1 TATGAA-GGGGGACCGATTCCC
767 T
1 T
768 CTATTCTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (21 bp):
TATGAAGGGGGACCGATTCCC
Found at i:1089 original size:34 final size:32
Alignment explanation
Indices: 1050--1113 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
1040 AAAGGGTTTT
*
1050 GGTTCTAGCTTAGCCCGTGTAAAAGCTAGGGAAA
1 GGTTCTAGCTTAGCCCG-G-AAAAACTAGGGAAA
*
1084 GGTTCTAGTTTAGCCCGGAAAAACTAGGGA
1 GGTTCTAGCTTAGCCCGGAAAAACTAGGGA
1114 GTTTGTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 11 0.39
33 1 0.04
34 16 0.57
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (32 bp):
GGTTCTAGCTTAGCCCGGAAAAACTAGGGAAA
Found at i:3947 original size:29 final size:30
Alignment explanation
Indices: 3877--3936 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
3867 CAATTTAAGG
3877 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
3908 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
3937 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:4052 original size:20 final size:19
Alignment explanation
Indices: 4023--4098 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 19
4013 TTCAAGATTG
* *
4023 CCCAGGGGTATAGATTCCC
1 CCCAGGGGTACAGATACCC
4042 CCCAGGGGGTACAGATA--C
1 CCCA-GGGGTACAGATACCC
4060 CCC--GGGTA-AGATACCCC
1 CCCAGGGGTACAGATA-CCC
4077 CCCAGGGGGTACAGATACCC
1 CCCA-GGGGTACAGATACCC
4097 CC
1 CC
4099 TGCAGGTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
14 5 0.11
15 5 0.11
17 4 0.09
18 4 0.09
19 4 0.09
20 20 0.43
21 5 0.11
ACGTcount: A:0.24, C:0.36, G:0.28, T:0.13
Consensus pattern (19 bp):
CCCAGGGGTACAGATACCC
Found at i:4077 original size:15 final size:15
Alignment explanation
Indices: 4048--4076 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4038 TCCCCCCAGG
4048 GGGTACAGATACCCC
1 GGGTACAGATACCCC
4063 GGGTA-AGATACCCC
1 GGGTACAGATACCCC
4077 CCCAGGGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:4172 original size:20 final size:21
Alignment explanation
Indices: 4132--4174 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4122 AACAGAATGT
4132 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
4153 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
4174 C
1 C
4175 TTATTCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:4237 original size:21 final size:21
Alignment explanation
Indices: 4211--4253 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4201 ATTTGAATAT
*
4211 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
4232 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
4253 T
1 T
4254 CTATTCTGGG
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:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:6859 original size:14 final size:13
Alignment explanation
Indices: 6837--6869 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
6827 AAAAGTGAAG
6837 AAAAAATAATAAT
1 AAAAAATAATAAT
6850 AAAAATATAATAAT
1 AAAAA-ATAATAAT
6864 AAAAAA
1 AAAAAA
6870 ACACATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:7204 original size:20 final size:20
Alignment explanation
Indices: 7181--7218 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7171 GAGTTAGAAA
*
7181 TTCGCAACTCGAATTTCTTT
1 TTCGCAACACGAATTTCTTT
*
7201 TTCGCAACACGATTTTCT
1 TTCGCAACACGAATTTCT
7219 AAATTCGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
TTCGCAACACGAATTTCTTT
Found at i:7269 original size:20 final size:20
Alignment explanation
Indices: 7220--7269 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
7210 CGATTTTCTA
*
7220 AATTCGCAAAGCGAATATGT
1 AATTCGCAACGCGAATATGT
* *
7240 AAATCGCAACGCGAATTTGT
1 AATTCGCAACGCGAATATGT
*
7260 AATTCACAAC
1 AATTCGCAAC
7270 ACAGAAGTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (20 bp):
AATTCGCAACGCGAATATGT
Found at i:8885 original size:42 final size:42
Alignment explanation
Indices: 8821--8925 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
8811 TGAGCACCCC
* * *
8821 CCACTTCGAGAGCCATCACCTGATCAAGTC-GATTCTGCAGCT
1 CCACATCGAGAGCCATCACCTGATCAAG-CAGATTATACAGCT
* * *
8863 CGACATCGAGAGCCATCACCTGATCGAGCAGATTATACATCT
1 CCACATCGAGAGCCATCACCTGATCAAGCAGATTATACAGCT
*
8905 CCACACCGAGAGCCATCACCT
1 CCACATCGAGAGCCATCACCT
8926 ATTACATCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 1 0.02
42 53 0.98
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (42 bp):
CCACATCGAGAGCCATCACCTGATCAAGCAGATTATACAGCT
Found at i:9066 original size:21 final size:21
Alignment explanation
Indices: 9039--9091 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
9029 GTTAGGGGAG
*
9039 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* * *
9060 TTGCGTGATAAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
9081 TTACGTGATGA
1 TTACGTGATGA
9092 CATGGTGAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:9292 original size:4 final size:4
Alignment explanation
Indices: 9283--9316 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
9273 GGCATTATTA
* *
9283 TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
9317 TTAGCGTCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:9486 original size:21 final size:21
Alignment explanation
Indices: 9461--9557 Score: 149
Period size: 21 Copynumber: 4.6 Consensus size: 21
9451 ATTCACCTGT
* *
9461 CATCGTTCAAGAGGCTCCTCA
1 CATCGTTCAAGAGGCCCCTCC
*
9482 TATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
9503 CATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
9524 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
9545 CACCGTTCAAGAG
1 CATCGTTCAAGAG
9558 CCTGATTCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:12573 original size:23 final size:23
Alignment explanation
Indices: 12547--12607 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
12537 CACCACAACT
12547 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
12570 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
12593 CGTAGAATTGCACCG
1 CATATAATTGCACCG
12608 TAGTTCCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:12802 original size:103 final size:103
Alignment explanation
Indices: 12623--12848 Score: 373
Period size: 103 Copynumber: 2.2 Consensus size: 103
12613 CCATATAATA
*
12623 ATGT-CCATAAGGACCACATATAATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
* *
12687 GTCTCACCAGACTTCACACATGTTCCAATGAATACATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAACACATAT
* * *
12726 ATGTCCCAAATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
12791 TCTCACCAGACTTCACACATGTTCCAAAGAACACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAACACATAT
*
12829 ATGTCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
12849 GACCCTCGAC
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 111 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAACACATAT
Found at i:16668 original size:24 final size:24
Alignment explanation
Indices: 16634--16687 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
16624 CTGAAACATC
* *
16634 ATCAAAATCAGAGTATTGACTAAG
1 ATCAAAATCAGAGCATTGACCAAG
* *
16658 ATCAAAGTCAGGGCATTGACCAAG
1 ATCAAAATCAGAGCATTGACCAAG
16682 ATCAAA
1 ATCAAA
16688 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCAGAGCATTGACCAAG
Found at i:17649 original size:20 final size:20
Alignment explanation
Indices: 17624--17691 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
17614 AAATAAAAGC
17624 TGTTGCGAAATTAAAATTTG
1 TGTTGCGAAATTAAAATTTG
*
17644 TGTTGCG-AATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTTG
* **
17664 AGTTGCGAAAACAAAATTTG
1 TGTTGCGAAATTAAAATTTG
17684 TGTTGCGA
1 TGTTGCGA
17692 TTTAGAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 8 0.21
20 24 0.63
21 6 0.16
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTTG
Found at i:17714 original size:40 final size:40
Alignment explanation
Indices: 17625--17701 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
17615 AATAAAAGCT
** *
17625 GTTGCGAAATTAAAATTTGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTTGTGTTGCGAATTAGAAAATCGA
*
17665 GTTGCGAAAACAAAATTTGTGTTGCGATTTAGAAAAT
1 GTTGCGAAAACAAAATTTGTGTTGCGAATTAGAAAAT
17702 TTTGTTGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.32
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTTGTGTTGCGAATTAGAAAATCGA
Found at i:17802 original size:41 final size:41
Alignment explanation
Indices: 17757--17842 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
17747 TGTGAATTCA
* * *
17757 GAAATCAAGTTGCGAATTT-GAAATTCCGTGTTGCGAATTTG
1 GAAATCAAGTTGCGAATTTGGAAAAT-CGCGTTACGAATTTG
**
17798 GAAATCGCGTTGCGAATTTGGAAAATCGCGTTACGAATTTG
1 GAAATCAAGTTGCGAATTTGGAAAATCGCGTTACGAATTTG
17839 GAAA
1 GAAA
17843 ATCGCGTTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 34 0.87
42 5 0.13
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (41 bp):
GAAATCAAGTTGCGAATTTGGAAAATCGCGTTACGAATTTG
Found at i:17811 original size:20 final size:20
Alignment explanation
Indices: 17736--17853 Score: 121
Period size: 21 Copynumber: 5.7 Consensus size: 20
17726 TTACGAAAAA
* **
17736 GAAATTCGCGTTGTGAATTCA
1 GAAA-TCGCGTTGCGAATTTG
**
17757 GAAATCAAGTTGCGAATTT-
1 GAAATCGCGTTGCGAATTTG
*
17776 GAAATTCCGTGTTGCGAATTTG
1 GAAA-T-CGCGTTGCGAATTTG
17798 GAAATCGCGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTG
*
17818 GAAAATCGCGTTACGAATTTG
1 G-AAATCGCGTTGCGAATTTG
17839 GAAAATCGCGTTGCG
1 G-AAATCGCGTTGCG
17854 GAAAAGAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
19 4 0.05
20 27 0.32
21 49 0.58
22 4 0.05
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (20 bp):
GAAATCGCGTTGCGAATTTG
Found at i:18151 original size:26 final size:25
Alignment explanation
Indices: 18122--18194 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 25
18112 CAGTGTTTGA
18122 CTCGTGCTCGTTAAGAAAATTTGTTG
1 CTCGTGCTCGTTAA-AAAATTTGTTG
**
18148 CTCGTTTAGCTCGTT-AAATTTTTGTTTG
1 CTCG--T-GCTCGTTAAAAAATTTG-TTG
18176 ACTCGTGCTCGTTAAAAAA
1 -CTCGTGCTCGTTAAAAAA
18195 AATTTATTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
26 11 0.30
27 10 0.27
28 5 0.14
29 11 0.30
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.41
Consensus pattern (25 bp):
CTCGTGCTCGTTAAAAAATTTGTTG
Found at i:18233 original size:16 final size:16
Alignment explanation
Indices: 18209--18243 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18199 TATTGCTCAA
*
18209 CTCGTTGCTCATTAAG
1 CTCGATGCTCATTAAG
*
18225 CTCGATGCTCGTTAAG
1 CTCGATGCTCATTAAG
18241 CTC
1 CTC
18244 ACCGAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.29, G:0.20, T:0.34
Consensus pattern (16 bp):
CTCGATGCTCATTAAG
Found at i:20256 original size:209 final size:209
Alignment explanation
Indices: 19696--20713 Score: 1572
Period size: 202 Copynumber: 4.9 Consensus size: 209
19686 ATACCCCTCG
* * * * *
19696 TTATATGTTGGCTCCGCGTGCACAACCTTAAATATTTATTCACTAATCTTAATGTATTAAATTTA
1 TTATA-GTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAA
* * *
19761 ATATT--T-TTTTTCTAAAATAATAGATTGTTTCCATCTCTCCATACATTTGCCACTGATACGAG
65 AT-TTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAG
* * ** * *
19823 CTCTCGATGCTTTCACACAAAAATGTGTTTTTATTGAATAATTAAACCCTAAACTTTAAACCTTA
129 CTCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAA--C----C-TTAAACCCTA
*
19888 AATTTATAAAAATATCATAAATA
187 AATTTATAAAAATATCATAAACA
* * * *
19911 TTATATGTTGGCTCCGTTTGCACAACCTTAAATATTTATTCACTAATCTTAATATGTTAAATTAA
1 TTATA-GTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAA
* *
19976 ATTTAATAATTTCTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAA
65 ATTTAAT-ATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAG
20041 CTCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCTTAAACCCTAAATTTAT
129 CTCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCTTAAACCCTAAATTTAT
20106 AAAAATATCATAAACA
194 AAAAATATCATAAACA
*
20122 TTATAGTCGGCTCTGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
1 TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
*
20187 TTTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATGCATTTGCCACTGATATGAGCT
66 TTTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAGCT
20252 CTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATG-----A--TTAAACCCTAAATTTATAA
131 CTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCTTAAACCCTAAATTTATAA
*
20310 AAATATCATACACA
196 AAATATCATAAACA
20324 TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
1 TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
20389 TTTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAGCT
66 TTTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAGCT
*
20454 CTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCCTAAACCCTAAATTTATAA
131 CTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCTTAAACCCTAAATTTATAA
20519 AAATATCATAAACA
196 AAATATCATAAACA
20533 TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
1 TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
*
20598 TTTAATATTTTTTCTAAAATAATAGATTGTTTCCACCCCTACATACATTTGCCACTGATATGAGC
66 TTTAATA-TTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAGC
* * **
20663 TCTCGATGCTTTCACCCAAAAGTGTGTTTTTATTGAATGATTTAAA-CTTAA
130 TCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGA-TTAAACCTTAA
20714 TCAATAACTT
Statistics
Matches: 754, Mismatches: 36, Indels: 31
0.92 0.04 0.04
Matches are distributed among these distances:
202 198 0.26
204 1 0.00
207 1 0.00
209 197 0.26
210 157 0.21
211 41 0.05
212 1 0.00
214 2 0.00
215 62 0.08
216 2 0.00
218 92 0.12
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (209 bp):
TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
TTTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAGCT
CTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCTTAAACCCTAAATTTATAA
AAATATCATAAACA
Found at i:20490 original size:411 final size:414
Alignment explanation
Indices: 19696--20709 Score: 1599
Period size: 411 Copynumber: 2.4 Consensus size: 414
19686 ATACCCCTCG
* * * * *
19696 TTATATGTTGGCTCCGCGTGCACAACCTTAAATATTTATTCACTAATCTTAATGTATTAAATTTA
1 TTATA-GTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAA
* * *
19761 ATATT--T-TTTTTCTAAAATAATAGATTGTTTCCATCTCTCCATACATTTGCCACTGATACGAG
65 AT-TTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAG
* * *
19823 CTCTCGATGCTTTCACACAAAAATGTGTTTTTATTGAATAATTAAACCCTAAACTTTAAACCTTA
129 CTCTCGATGCTTTCACCCAAAAATGTG---TT-TT---T-ATTAAA---T-GA-TTTAAACCCTA
* * *
19888 AATTTATAAAAATATCATAAATATTATATGTTGGCTCCGTTTGCACAACCTTAAATATTTATTCA
181 AATTTATAAAAATATCATAAACATTATATGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCA
*
19953 CTAATCTTAATATGTTAAATTAAATTTAATAATTTCTCTAAAATAATAGATTGTTTCCACCTCTA
246 CTAATCCTAATATGTTAAATTAAATTTAATAATTTCTCTAAAATAATAGATTGTTTCCACCTCTA
20018 CATACATTTGCCACTGATATGAACTCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGAT
311 CATACATTTGCCACTGATATGAACTCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGAT
*
20083 TAAACCTTAAACCCTAAATTTATAAAAATATCATAAACA
376 TAAACCCTAAACCCTAAATTTATAAAAATATCATAAACA
*
20122 TTATAGTCGGCTCTGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
1 TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
*
20187 TTTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATGCATTTGCCACTGATATGAGCT
66 TTTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAGCT
* *
20252 CTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGA-TTAAACCCTAAATTTATAAAAATAT
131 CTCGATGCTTTCACCCAAAAATGTGTTTTTATTAAATGATTTAAACCCTAAATTTATAAAAATAT
* *
20316 CATACACATTATA-GTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGT
196 CATAAACATTATATGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATATGT
*
20380 TAAATTAAATTTAAT-ATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACT
261 TAAATTAAATTTAATAATTTCTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACT
*
20444 GATATGAGCTCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCCTAAACCCT
326 GATATGAACTCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCCTAAACCCT
20509 AAATTTATAAAAATATCATAAACA
391 AAATTTATAAAAATATCATAAACA
20533 TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
1 TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
*
20598 TTTAATATTTTTTCTAAAATAATAGATTGTTTCCACCCCTACATACATTTGCCACTGATATGAGC
66 TTTAATA-TTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAGC
* *
20663 TCTCGATGCTTTCACCCAAAAGTGTGTTTTTATTGAATGATTTAAAC
130 TCTCGATGCTTTCACCCAAAAATGTGTTTTTATTAAATGATTTAAAC
20710 TTAATCAATA
Statistics
Matches: 552, Mismatches: 31, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
411 206 0.37
412 153 0.28
413 41 0.07
415 1 0.00
416 1 0.00
419 5 0.01
420 1 0.00
423 2 0.00
424 4 0.01
425 55 0.10
426 6 0.01
427 77 0.14
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.38
Consensus pattern (414 bp):
TTATAGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATGTGTTAAATTAAA
TTTAATATTTTTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACTGATATGAGCT
CTCGATGCTTTCACCCAAAAATGTGTTTTTATTAAATGATTTAAACCCTAAATTTATAAAAATAT
CATAAACATTATATGTCGGCTCCGCTTGCACAACCTTAAATATTTATTCACTAATCCTAATATGT
TAAATTAAATTTAATAATTTCTCTAAAATAATAGATTGTTTCCACCTCTACATACATTTGCCACT
GATATGAACTCTCGATGCTTTCACCCAAAAATATGTTTTTATCAAATGATTAAACCCTAAACCCT
AAATTTATAAAAATATCATAAACA
Found at i:21933 original size:521 final size:513
Alignment explanation
Indices: 20960--21989 Score: 1830
Period size: 521 Copynumber: 2.0 Consensus size: 513
20950 CTAATATTGA
*
20960 TATTAATTAACATACAATTTGATACATGATTGTAAGTTAGCTAATAAATATTAAATATATTGATT
1 TATTAATTAACATACAATTTGATACATCATTGTAAGTTAGCTAATAAATATTAAATATATTGATT
* *
21025 TAGAGATGTAATAAATAGTAGCCATACATAGGGGTGAGCAAAACTCGACTCAACTCGAAAATAAA
66 TAGAGATGTAATAAATAGTACCCATACATAGGGGTGAGCAAAACTCGACTCAACTCAAAAATAAA
* * * *
21090 AAAACATTAATTTCATGTTATTCGAGTTGAGTTATTCGAGTCAACTTGAATTATAAATTCGGTTT
131 AAAACATTAATTTCATGTTATTCGAGTCGAGTTATTCAAGTAAACTTGAATTATAAAATCGGTTT
21155 TCAAGTTCGAGTCGAGTTGAAATTTTGAATTTTCAAGTTATACATGGTTTTGTTTAGTGCAAGAG
196 TCAAGTTCGAGTCGAGTTGAAATTTTGAATTTTCAAGTTATACATGGTTTTGTTTAGTGCAAGAG
* *
21220 GTTGGAGAAGATTTCGAAGCTAAGGGGAAGGAAAAGTCTACTTTGGGTTGAGTCTGACGTTTCCA
261 GTTGGAGAAGATTTCAAAGCTAAGGGGAAGGAAAAGTCTACTTTGGGATGAGTCTGACGTTTCCA
21285 ACAATATAGCATCAAAGGTAACTCACTCTTGACTCAACTATACCTTATGTAAGTCATTTAGATAA
326 ACAATATAGCATCAAAGGTAACTCACTCTTGACTCAACTATACCTTATGTAAGTCATTTAGATAA
21350 AATGTAGTAGGTTGCATAAGCTTGAAGCATTCTCATGGTAGATTTCATGTTTTAGAGTTATAAAC
391 AATGTAGTAGGTTGCATAAGCTTGAAGCATTCTCATGGTAGATTTCATGTTTTAGAGTTATAAAC
*
21415 ATGTCTAAGGCCCTATTTATGCTCCTTTGTATCTTCATAAAACTTTAATAATGTAAGT
456 ATGTCTAAGGCCCTATTTATGCTCCTTTGTATCTTCATAAAACATTAATAATGTAAGT
21473 TATTAATTAACATACAATTTGATACATCATTGTAAGTTAGCTAATAAATATTAAATATATTGATT
1 TATTAATTAACATACAATTTGATACATCATTGTAAGTTAGCTAATAAATATTAAATATATTGATT
21538 TAGAGATGTAATAAATAGTACCCATACATAGGGGTGAGC-AAACTCGACTCAACTCAAAAAATAA
66 TAGAGATGTAATAAATAGTACCCATACATAGGGGTGAGCAAAACTCGACTCAACTC-AAAAATAA
21602 AAAAA-ATTAATTTCATGTTATTCGAGTCGAGTTATTCAAGTAAACTTGAATTATAAAATCGGTT
130 AAAAACATTAATTTCATGTTATTCGAGTCGAGTTATTCAAGTAAACTTGAATTATAAAATCGGTT
** *
21666 TTTGAGTTTGAGTCGAGTTGAAATTTTGAATTTTGAATTTTCAAGTTATACATGGTTTTGTTTAG
195 TTCAAGTTCGAGTCGAGTTG--A-----AATTTTGAATTTTCAAGTTATACATGGTTTTGTTTAG
21731 TGCAAGAGGTTGGAGAAGATTTCAAAGCTAAGGGGAAGGAAAAGTCTACTTTGGGATGAGTCTTT
253 TGCAAGAGGTTGGAGAAGATTTCAAAGCTAAGGGGAAGGAAAAGTCTACTTTGGGATGAGTC--T
21796 GACGTTTCCAACAATATAGCATCAAAGGTAACTCACTCTTGACTCAACTATACCTTATGTAAGTC
316 GACGTTTCCAACAATATAGCATCAAAGGTAACTCACTCTTGACTCAACTATACCTTATGTAAGTC
*
21861 ATTTAGATAAAATGTAGTAGGTTGCATAAGCTTGCAGCATTCTCATGGTAGATTTCATGTTTTAG
381 ATTTAGATAAAATGTAGTAGGTTGCATAAGCTTGAAGCATTCTCATGGTAGATTTCATGTTTTAG
21926 AGTTATAAACATGTCTAAGGCCCTATTTATGCTCCTTTGTATCTTCATAAAACATTAATAATGT
446 AGTTATAAACATGTCTAAGGCCCTATTTATGCTCCTTTGTATCTTCATAAAACATTAATAATGT
21990 TTGGGAACCT
Statistics
Matches: 493, Mismatches: 14, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
512 88 0.18
513 114 0.23
514 1 0.00
519 97 0.20
521 193 0.39
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (513 bp):
TATTAATTAACATACAATTTGATACATCATTGTAAGTTAGCTAATAAATATTAAATATATTGATT
TAGAGATGTAATAAATAGTACCCATACATAGGGGTGAGCAAAACTCGACTCAACTCAAAAATAAA
AAAACATTAATTTCATGTTATTCGAGTCGAGTTATTCAAGTAAACTTGAATTATAAAATCGGTTT
TCAAGTTCGAGTCGAGTTGAAATTTTGAATTTTCAAGTTATACATGGTTTTGTTTAGTGCAAGAG
GTTGGAGAAGATTTCAAAGCTAAGGGGAAGGAAAAGTCTACTTTGGGATGAGTCTGACGTTTCCA
ACAATATAGCATCAAAGGTAACTCACTCTTGACTCAACTATACCTTATGTAAGTCATTTAGATAA
AATGTAGTAGGTTGCATAAGCTTGAAGCATTCTCATGGTAGATTTCATGTTTTAGAGTTATAAAC
ATGTCTAAGGCCCTATTTATGCTCCTTTGTATCTTCATAAAACATTAATAATGTAAGT
Found at i:30697 original size:21 final size:20
Alignment explanation
Indices: 30669--30707 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
30659 TTGATTTAAT
30669 TAAAATTTATAAATCATAAA
1 TAAAATTTATAAATCATAAA
* *
30689 TAAACATTTTTAACTCATA
1 TAAA-ATTTATAAATCATA
30708 GTAAAACGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATTTATAAATCATAAA
Found at i:37769 original size:17 final size:18
Alignment explanation
Indices: 37747--37780 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37737 TCAGTCCGTC
37747 TGGTTC-GAACGGTTCAG
1 TGGTTCTGAACGGTTCAG
*
37764 TGGTTCTGACCGGTTCA
1 TGGTTCTGAACGGTTCA
37781 CTAGTAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (18 bp):
TGGTTCTGAACGGTTCAG
Found at i:38125 original size:17 final size:17
Alignment explanation
Indices: 38103--38137 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
38093 ATCAATTATT
38103 AAAATTTCAAAATATAA
1 AAAATTTCAAAATATAA
*
38120 AAAATTTCAAAATTTAA
1 AAAATTTCAAAATATAA
38137 A
1 A
38138 CTTTGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTTCAAAATATAA
Found at i:38812 original size:51 final size:51
Alignment explanation
Indices: 38736--38837 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
38726 ATCTATCCCC
38736 GCCAGTGAGTAGTGTACGCACTATCAATATCACATGATCATTCGTGCCGGT
1 GCCAGTGAGTAGTGTACGCACTATCAATATCACATGATCATTCGTGCCGGT
38787 GCCAGTGAGTAGTGTACGCACTATCAATATCACATGATCATTCGTGCCGGT
1 GCCAGTGAGTAGTGTACGCACTATCAATATCACATGATCATTCGTGCCGGT
38838 TTAATTTGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (51 bp):
GCCAGTGAGTAGTGTACGCACTATCAATATCACATGATCATTCGTGCCGGT
Found at i:39913 original size:28 final size:29
Alignment explanation
Indices: 39881--39941 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
39871 AGGGCTATTG
* **
39881 TTTAGCCTAATACTCTATAAAA-AAATTA
1 TTTAGCATAATACAATATAAAATAAATTA
39909 TTTAGCATAATACAATATAAAATAAATTA
1 TTTAGCATAATACAATATAAAATAAATTA
39938 TTTA
1 TTTA
39942 ACAATTTACG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTAGCATAATACAATATAAAATAAATTA
Found at i:40568 original size:16 final size:16
Alignment explanation
Indices: 40547--40580 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40537 TTTTTATATG
40547 AATTAAAA-TATTATTA
1 AATTAAAATTA-TATTA
40563 AATTAAAATTATATTA
1 AATTAAAATTATATTA
40579 AA
1 AA
40581 AAAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAAAATTATATTA
Found at i:48659 original size:19 final size:18
Alignment explanation
Indices: 48637--48672 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
48627 AAATTTTGGC
48637 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
48656 TTTTTTTGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
48673 TTTGCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:48660 original size:20 final size:20
Alignment explanation
Indices: 48637--48705 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 20
48627 AAATTTTGGC
* *
48637 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTTTTTTTTTGT
*
48657 TTTTTTGCCTTTTTTTTTTGCC
1 TTTTTTGCC-TTTTTTTTTG-T
**
48679 TTTTTTGTTTTTTTTTTTGT
1 TTTTTTGCCTTTTTTTTTGT
48699 TTTTTTG
1 TTTTTTG
48706 AAAAAAATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 15 0.37
21 19 0.46
22 7 0.17
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.80
Consensus pattern (20 bp):
TTTTTTGCCTTTTTTTTTGT
Found at i:48672 original size:13 final size:13
Alignment explanation
Indices: 48656--48689 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
48646 TCTTTTTTTG
48656 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
48669 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
48682 TTTGTTTT
1 TTT-TTTT
48690 TTTTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:48694 original size:12 final size:12
Alignment explanation
Indices: 48679--48704 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48669 TTTTTTTGCC
48679 TTTTTTGTTTTT
1 TTTTTTGTTTTT
48691 TTTTTTGTTTTT
1 TTTTTTGTTTTT
48703 TT
1 TT
48705 GAAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:56359 original size:16 final size:15
Alignment explanation
Indices: 56327--56388 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 15
56317 TTTACTTCAA
56327 AATGATT-AAACGCTG
1 AATGATTCAAA-GCTG
56342 AATGATTCAAATGCTG
1 AATGATTCAAA-GCTG
56358 AATGATTCAGAAGCTG
1 AATGATTCA-AAGCTG
56374 AATGATTCAGAAGCT
1 AATGATTCA-AAGCT
56389 CTGTATGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
15 7 0.16
16 35 0.80
17 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (15 bp):
AATGATTCAAAGCTG
Found at i:56575 original size:20 final size:20
Alignment explanation
Indices: 56562--56599 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
56552 TTCAACGCTT
56562 AATGGTTCCATTCAGAGCTG
1 AATGGTTCCATTCAGAGCTG
56582 AATGGTTCCATTCAGAGC
1 AATGGTTCCATTCAGAGC
56600 CAAACAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
AATGGTTCCATTCAGAGCTG
Found at i:56997 original size:2 final size:2
Alignment explanation
Indices: 56990--57036 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
56980 TCAAGTTTTG
56990 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
57032 AT AT A
1 AT AT A
57037 AAAATTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65291 original size:29 final size:29
Alignment explanation
Indices: 65249--65360 Score: 197
Period size: 29 Copynumber: 3.9 Consensus size: 29
65239 TACCGGGGGT
* *
65249 AGGTCGTCATGCACGCCCGGCGACCAACA
1 AGGTCGCCATGCACGCCCGGCGACCAACC
65278 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
65307 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
65336 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
65361 TACCCCACGA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.21, C:0.43, G:0.28, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:65403 original size:30 final size:30
Alignment explanation
Indices: 65367--65476 Score: 175
Period size: 30 Copynumber: 3.7 Consensus size: 30
65357 GACCTACCCC
65367 ACGACCTCCATGCACGCCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
* * *
65397 ACGACCTCCATGCATGCCCAGGCACGTCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
* *
65427 ACGACCTCCATGCACGGCCATGCACGGCCA
1 ACGACCTCCATGCACGCCCATGCACGCCCA
65457 ACGACCTCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCA
65477 GCTCGCCAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.24, C:0.46, G:0.19, T:0.11
Consensus pattern (30 bp):
ACGACCTCCATGCACGCCCATGCACGCCCA
Found at i:66097 original size:21 final size:21
Alignment explanation
Indices: 66072--66115 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
66062 AATTTAGTTA
66072 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
66093 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
66114 AT
1 AT
66116 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:66129 original size:28 final size:28
Alignment explanation
Indices: 66092--66145 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
66082 TAGTATAAAT
*
66092 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
66120 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
66146 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:67709 original size:11 final size:10
Alignment explanation
Indices: 67693--67960 Score: 53
Period size: 10 Copynumber: 26.7 Consensus size: 10
67683 AATGATTTGA
67693 TAGTAATGATT
1 TAGTAATGA-T
67704 TAGTAATGAT
1 TAGTAATGAT
*
67714 TAGTAAT-AA
1 TAGTAATGAT
* *
67723 T-GAAATTAT
1 TAGTAATGAT
* *
67732 TATTAATTAT
1 TAGTAATGAT
*
67742 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
67753 TAGTAATGACT
1 TAGTAATGA-T
67764 TAGTAATGAT
1 TAGTAATGAT
*
67774 TAGTAAT-AA
1 TAGTAATGAT
* *
67783 T-GAAATTAT
1 TAGTAATGAT
* *
67792 TATTAATTAT
1 TAGTAATGAT
*
67802 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
67813 TAGTAATGATT
1 TAGTAATGA-T
67824 TAGTAATGAT
1 TAGTAATGAT
*
67834 TAGTAAT-AA
1 TAGTAATGAT
* *
67843 T-GAAATTAT
1 TAGTAATGAT
* **
67852 TATTAATTTT
1 TAGTAATGAT
* *
67862 TAATGATTTGA-
1 TAGT-A-ATGAT
67873 TAGTAATGATT
1 TAGTAATGA-T
67884 TAGTAATGAT
1 TAGTAATGAT
*
67894 TAGTAAT-AA
1 TAGTAATGAT
* *
67903 T-GAAATTAT
1 TAGTAATGAT
* *
67912 TATTAATTAT
1 TAGTAATGAT
*
67922 GTA-TGATTTGA-
1 -TAGT-A-ATGAT
67933 TAGTAATGATT
1 TAGTAATGA-T
67944 TAGTAATGAT
1 TAGTAATGAT
67954 TAGTAAT
1 TAGTAAT
67961 AATGAAATTA
Statistics
Matches: 191, Mismatches: 36, Indels: 61
0.66 0.12 0.21
Matches are distributed among these distances:
8 16 0.08
9 28 0.15
10 79 0.41
11 61 0.32
12 7 0.04
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:67837 original size:21 final size:20
Alignment explanation
Indices: 67813--67961 Score: 60
Period size: 21 Copynumber: 7.4 Consensus size: 20
67803 TATGATTTGA
67813 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
67834 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * * *
67852 TATTAATTTTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
67873 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
67894 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
67912 TATTAATTATGTA-TGATTTGA-
1 TAGTAA-TATTTAGT-A-ATGAT
67933 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
67954 TAGTAATA
1 TAGTAATA
67962 ATGAAATTAT
Statistics
Matches: 89, Mismatches: 25, Indels: 29
0.62 0.17 0.20
Matches are distributed among these distances:
18 23 0.26
19 5 0.06
20 11 0.12
21 40 0.45
22 10 0.11
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:67996 original size:22 final size:22
Alignment explanation
Indices: 67968--68032 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
67958 AATAATGAAA
*
67968 TTATTATTAATTTTTTAATAAT
1 TTATTATTAATTATTTAATAAT
*
67990 TTATTATTAA-TATTTAATGAT
1 TTATTATTAATTATTTAATAAT
* *
68011 TTGA-TATTAATGATTTAGTAAT
1 TT-ATTATTAATTATTTAATAAT
68033 GATTTGATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATTATTAATTATTTAATAAT
Found at i:68005 original size:60 final size:60
Alignment explanation
Indices: 67640--67979 Score: 612
Period size: 60 Copynumber: 5.7 Consensus size: 60
67630 GTATTTATAA
* *
67640 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
67700 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
67760 GACTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
*
67820 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
67880 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
67940 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT
67980 TTTTAATAAT
Statistics
Matches: 271, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
59 2 0.01
60 265 0.98
61 4 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
Found at i:68020 original size:14 final size:14
Alignment explanation
Indices: 68004--68051 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
67994 TATTAATATT
*
68004 TAATGATTTGATAT
1 TAATGATTTGATAG
68018 TAATGA-TT--TAG
1 TAATGATTTGATAG
68029 TAATGATTTGATAG
1 TAATGATTTGATAG
68043 TAATGATTT
1 TAATGATTT
68052 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:68033 original size:25 final size:25
Alignment explanation
Indices: 68004--68052 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
67994 TATTAATATT
*
68004 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
68029 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
68053 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:68136 original size:7 final size:7
Alignment explanation
Indices: 68124--68150 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
68114 ATTTTTGGTT
68124 CAATGAA
1 CAATGAA
68131 CAATGAA
1 CAATGAA
68138 CAATGAA
1 CAATGAA
68145 CAATGA
1 CAATGA
68151 TTTAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
CAATGAA
Found at i:68185 original size:26 final size:26
Alignment explanation
Indices: 68146--68283 Score: 103
Period size: 26 Copynumber: 5.5 Consensus size: 26
68136 AACAATGAAC
*
68146 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAATAATAATCATTATAAA
*
68172 AATGA-TT--TAATAATGATT-T--A
1 AATGATTTAATAATAATCATTATAAA
* * * **
68192 AAT-ATTTAATGATTTGATGATT-TAGT
1 AATGATTTAAT-A-ATAATCATTATAAA
* **
68218 AATGATTTGATAATAATCATTATAGT
1 AATGATTTAATAATAATCATTATAAA
*
68244 AATGATTTAGTAATAATCATTATAAA
1 AATGATTTAATAATAATCATTATAAA
68270 AATGATTTAATAAT
1 AATGATTTAATAAT
68284 GATTTAAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
20 6 0.07
22 2 0.02
23 11 0.12
24 8 0.09
25 8 0.09
26 48 0.53
27 6 0.07
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (26 bp):
AATGATTTAATAATAATCATTATAAA
Found at i:68315 original size:98 final size:98
Alignment explanation
Indices: 68146--68364 Score: 404
Period size: 98 Copynumber: 2.2 Consensus size: 98
68136 AACAATGAAC
68146 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
*
68211 ATTTAGTAATGATTTGATAATAATCATTATAGT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
68244 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
68309 ATTTAGTAATGATTTGATAATAATCATTATAAT
66 ATTTAGTAATGATTTGATAATAATCATTATAAT
*
68342 AATGATTTTA-TAATAATTATTAT
1 AATGA-TTTAGTAATAATCATTAT
68365 GTTATTATTT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
98 114 0.97
99 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (98 bp):
AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
ATTTAGTAATGATTTGATAATAATCATTATAAT
Found at i:68344 original size:26 final size:26
Alignment explanation
Indices: 68217--68364 Score: 121
Period size: 26 Copynumber: 5.9 Consensus size: 26
68207 GATGATTTAG
*
68217 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
68243 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
68269 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
68292 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
68315 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* *
68341 TAATGATTTTATAATAATTATTAT
1 TAATGATTTGATAATAATCATTAT
68365 GTTATTATTT
Statistics
Matches: 95, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.04
22 3 0.03
23 12 0.13
24 7 0.07
25 7 0.07
26 61 0.64
27 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:68398 original size:24 final size:24
Alignment explanation
Indices: 68326--68417 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
68316 AATGATTTGA
*
68326 TAATAATCATTA-TAATAATGATT
1 TAATAATTATTACTAATAATGATT
* * * * * *
68349 TTATAATAATTATTATGTTATTATT
1 TAATAATTATTACTA-ATAATGATT
*
68374 TAGTAATTATTTA-TAATAATGATT
1 TAATAATTA-TTACTAATAATGATT
68398 TAATAATTATTACTAATAAT
1 TAATAATTATTACTAATAAT
68418 TATAGAATAC
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
23 13 0.25
24 23 0.43
25 14 0.26
26 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (24 bp):
TAATAATTATTACTAATAATGATT
Found at i:68414 original size:13 final size:12
Alignment explanation
Indices: 68325--68420 Score: 81
Period size: 11 Copynumber: 7.9 Consensus size: 12
68315 TAATGATTTG
*
68325 ATAATAATCATT
1 ATAATAATTATT
*
68337 ATAATAATGATTTT
1 ATAATAAT--TATT
68351 ATAATAATTATT
1 ATAATAATTATT
* *
68363 AT-GTTATTATT
1 ATAATAATTATT
*
68374 -TAGTAATTATTT
1 ATAATAATTA-TT
*
68386 ATAATAATGATT
1 ATAATAATTATT
68398 -TAATAATTATT
1 ATAATAATTATT
68409 ACTAATAATTAT
1 A-TAATAATTAT
68421 AGAATACTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.01
11 23 0.34
12 17 0.25
13 17 0.25
14 10 0.15
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:68426 original size:24 final size:24
Alignment explanation
Indices: 68377--68426 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
68367 TATTATTTAG
**
68377 TAATTATTTATAATAATGATTTAA
1 TAATTATTTATAATAATGATAGAA
*
68401 TAATTA-TTACTAATAATTATAGAA
1 TAATTATTTA-TAATAATGATAGAA
68425 TA
1 TA
68427 CTAACAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TAATTATTTATAATAATGATAGAA
Found at i:68525 original size:14 final size:13
Alignment explanation
Indices: 68506--68570 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
68496 TTTAAATATT
68506 TAATGATTTGATAC
1 TAATGATTT-ATAC
68520 TAATGA-TT-TAC
1 TAATGATTTATAC
*
68531 TAAT--TAT-TAC
1 TAATGATTTATAC
68541 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
68555 TAATTATTTGATAC
1 TAATGATTT-ATAC
68569 TA
1 TA
68571 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:68542 original size:10 final size:11
Alignment explanation
Indices: 68517--68550 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
68507 AATGATTTGA
68517 TACTAATGATT
1 TACTAATGATT
*
68528 TACTAATTA-T
1 TACTAATGATT
68538 TACTAATGATT
1 TACTAATGATT
68549 TA
1 TA
68551 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:68560 original size:21 final size:21
Alignment explanation
Indices: 68517--68560 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
68507 AATGATTTGA
* *
68517 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
68538 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
68559 TA
1 TA
68561 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:68577 original size:17 final size:17
Alignment explanation
Indices: 68555--68587 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
68545 GATTTAATAC
68555 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
68572 TAATTATTTGATACTA
1 TAATTATTTGATACTA
68588 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:70746 original size:14 final size:14
Alignment explanation
Indices: 70724--70753 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
70714 TACAACACTA
*
70724 AACTTTAATATAAT
1 AACTATAATATAAT
70738 AACTATAATATAAT
1 AACTATAATATAAT
70752 AA
1 AA
70754 ACTAATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AACTATAATATAAT
Found at i:70882 original size:33 final size:32
Alignment explanation
Indices: 70814--70882 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
70804 ACCCTTAAAC
*
70814 AACTAATAAAATATTTTTTTATATAACTAAAACT
1 AACTAATAAAATATTTTTTCATATAACT--AACT
*
70848 AACTAATAAACTATTTTTTCATTATATACT-ACT
1 AACTAATAAAATATTTTTTCA-TATA-ACTAACT
70881 AA
1 AA
70883 TAAACTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 5 0.16
34 19 0.61
35 4 0.13
36 3 0.10
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (32 bp):
AACTAATAAAATATTTTTTCATATAACTAACT
Found at i:70894 original size:12 final size:12
Alignment explanation
Indices: 70878--70921 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
70868 ATTATATACT
*
70878 ACTAATAAACTT
1 ACTAATAAACTA
70890 ACTAACTAAAACTA
1 ACTAA-T-AAACTA
70904 ACTAATAAACTA
1 ACTAATAAACTA
70916 ACTAAT
1 ACTAAT
70922 TTTTTACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 17 0.59
13 2 0.07
14 10 0.34
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (12 bp):
ACTAATAAACTA
Found at i:71052 original size:46 final size:46
Alignment explanation
Indices: 70951--71039 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 46
70941 CAACAAACAA
70951 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
1 ATATAAC-TAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
* *
70998 TTATAACTAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTT
1 ATATAACTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTT
71040 AACTATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 11 0.28
44 11 0.28
45 5 0.13
46 6 0.15
47 6 0.15
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (46 bp):
ATATAACTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTT
Found at i:71108 original size:41 final size:39
Alignment explanation
Indices: 71021--71108 Score: 88
Period size: 41 Copynumber: 2.2 Consensus size: 39
71011 TTAACAAAAC
*
71021 AAACTAATTAATTATTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
71061 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATT-AATAATTTTTAA-CTATATA-ACTATAAACAT
71102 AAACTAA
1 AAACTAA
71109 CAATCATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
40 8 0.21
41 21 0.54
42 5 0.13
43 5 0.13
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (39 bp):
AAACTAATTAATAATTTTTAACTATATAACTATAAACAT
Found at i:71173 original size:16 final size:18
Alignment explanation
Indices: 71144--71182 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
71134 ACTAATTAAC
*
71144 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
71162 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
71178 ATTTA
1 ATTTA
71183 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:71214 original size:19 final size:19
Alignment explanation
Indices: 71192--71236 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
71182 ACCTTATCTC
*
71192 CCTTTCTTCTTCTTACTTT
1 CCTTTCTTCTCCTTACTTT
*
71211 CCTTTCTTTCTCCTTTCTTT
1 CCTTTC-TTCTCCTTACTTT
71231 -CTTTCT
1 CCTTTCT
71237 CGGCTGAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 11 0.48
20 11 0.48
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (19 bp):
CCTTTCTTCTCCTTACTTT
Found at i:71232 original size:15 final size:16
Alignment explanation
Indices: 71207--71237 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
71197 CTTCTTCTTA
71207 CTTTCCTTTCTTTCTC
1 CTTTCCTTTCTTTCTC
71223 CTTT-CTTTCTTTCTC
1 CTTTCCTTTCTTTCTC
71238 GGCTGAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTTCCTTTCTTTCTC
Found at i:71464 original size:50 final size:48
Alignment explanation
Indices: 71393--71499 Score: 173
Period size: 49 Copynumber: 2.2 Consensus size: 48
71383 TAGGATCACA
*
71393 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTAT-T
71442 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
71490 TGGC-TGCATG
1 TGGCATGCATG
71500 TGCATGCATG
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
47 6 0.11
48 5 0.09
49 32 0.57
50 13 0.23
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (48 bp):
TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATT
Found at i:71567 original size:29 final size:29
Alignment explanation
Indices: 71534--71628 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
71524 TGGACGCCGG
71534 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
71563 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
71592 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
71621 GGCGACCT
1 GGCGACCT
71629 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:71657 original size:32 final size:32
Alignment explanation
Indices: 71615--71686 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
71605 GTCGCCCAGA
*
71615 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
71647 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
71679 CTGCATGG
1 CTGCATGG
71687 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:71751 original size:24 final size:19
Alignment explanation
Indices: 71701--71738 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
71691 TATATGGCTT
71701 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
71720 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
71739 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:76024 original size:43 final size:42
Alignment explanation
Indices: 75945--76028 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 42
75935 AATGAGATGG
*
75945 ATGAATAGGGTAGAAGACAAAAGAGTGAAAAAAATAAAGATAA
1 ATGAATACGGTAGAAGACAAAAGAGTGAAAAAAAT-AAGATAA
* *
75988 ATGAATACGGTAGAAGACAAAAGAGTGAAGACAATAAGATA
1 ATGAATACGGTAGAAGACAAAAGAGTGAAAAAAATAAGATA
76029 TACACAGCCG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 6 0.16
43 32 0.84
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
ATGAATACGGTAGAAGACAAAAGAGTGAAAAAAATAAGATAA
Found at i:76686 original size:21 final size:21
Alignment explanation
Indices: 76656--76696 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
76646 AAATGTTAAA
* *
76656 AAATATTAATGTTTTAGGTAG
1 AAATAATAATATTTTAGGTAG
76677 AAATAATAATATTTTAGGTA
1 AAATAATAATATTTTAGGTA
76697 ATTTTTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATAATAATATTTTAGGTAG
Found at i:78244 original size:18 final size:20
Alignment explanation
Indices: 78201--78250 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 20
78191 CTCCTATAGG
*
78201 GAGTATCCATACTCGACCCT
1 GAGTATCGATACTCGACCCT
*
78221 GGGTATCGATACTC-A-CCT
1 GAGTATCGATACTCGACCCT
78239 GAGTATCGATAC
1 GAGTATCGATAC
78251 CAAATTTAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 14 0.52
19 1 0.04
20 12 0.44
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (20 bp):
GAGTATCGATACTCGACCCT
Found at i:80301 original size:43 final size:43
Alignment explanation
Indices: 80253--80338 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
80243 CTCCCGCAAC
80253 GATTGTAGGCTGTAAATGTTCTCGGTTTGAACAAATAAAATTG
1 GATTGTAGGCTGTAAATGTTCTCGGTTTGAACAAATAAAATTG
*
80296 GATTGTAGGTTGTAAATGTTCTCGGTTTGAACAAATAAAATTG
1 GATTGTAGGCTGTAAATGTTCTCGGTTTGAACAAATAAAATTG
80339 TATTTGTGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (43 bp):
GATTGTAGGCTGTAAATGTTCTCGGTTTGAACAAATAAAATTG
Found at i:80520 original size:123 final size:122
Alignment explanation
Indices: 80301--80538 Score: 359
Period size: 123 Copynumber: 1.9 Consensus size: 122
80291 AATTGGATTG
* *
80301 TAGGTTGTAAATGTTCTCGGTTTGAACAAATAAAATTGTATTTGTGTTCGTATATTAAATGAATA
1 TAGGTTGTAAATGATCTCAGTTTGAACAAATAAAATTGTATTTGTGTTCGTATATTAAATGAATA
* *
80366 TAAAAAATTTATTCATACTCATTTATTTAACTTAATAAAAAAAATATAAACAAACATT
66 TAAAAAATTTATTAATACCCATTTATTTAACTTAAT-AAAAAAATATAAACAAACATT
* * * *
80424 TAGGTTGTAAATGATCTCATTTTGAACAAATGAAATTGTGTTTGTGTTCGTTTATTAAATGAATA
1 TAGGTTGTAAATGATCTCAGTTTGAACAAATAAAATTGTATTTGTGTTCGTATATTAAATGAATA
*** *
80489 TAAATTTTTTATTAATACCCATTTATTTAACTTAATAAACAAATATAAAC
66 TAAAAAATTTATTAATACCCATTTATTTAACTTAATAAAAAAATATAAAC
80539 CATCGCTATA
Statistics
Matches: 103, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
122 13 0.13
123 90 0.87
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (122 bp):
TAGGTTGTAAATGATCTCAGTTTGAACAAATAAAATTGTATTTGTGTTCGTATATTAAATGAATA
TAAAAAATTTATTAATACCCATTTATTTAACTTAATAAAAAAATATAAACAAACATT
Found at i:82371 original size:30 final size:30
Alignment explanation
Indices: 82335--82399 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
82325 AGTGAACCGA
* *
82335 CGGTTCAAACCGGTTTTGTCGGTTTTCAGC
1 CGGTTCAAACCAGTTTTATCGGTTTTCAGC
** *
82365 CGGTTCACCCCAGTTTTATCGGTTTTCAGT
1 CGGTTCAAACCAGTTTTATCGGTTTTCAGC
82395 CGGTT
1 CGGTT
82400 TATTGCCAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (30 bp):
CGGTTCAAACCAGTTTTATCGGTTTTCAGC
Found at i:83385 original size:20 final size:20
Alignment explanation
Indices: 83357--83394 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
83347 TTTCCCTTGA
83357 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
* *
83377 AGTGTATCGATGCATTCT
1 AGTGCATCGATACATTCT
83395 TTAACATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:88119 original size:24 final size:23
Alignment explanation
Indices: 88090--88134 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
88080 TTGGTGAATC
88090 ATTGTTACCAACTATACAACCATT
1 ATTGTTACCAACT-TACAACCATT
* *
88114 ATTGTTGCCAACTTTCAACCA
1 ATTGTTACCAACTTACAACCA
88135 ATAAAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTGTTACCAACTTACAACCATT
Found at i:88201 original size:22 final size:23
Alignment explanation
Indices: 88176--88222 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
88166 GGCCACTTGA
88176 TAAT-CACTTACTTTACAACAAT
1 TAATGCACTTACTTTACAACAAT
88198 TAATGGCCACTTACTTTACAACAAT
1 TAAT-G-CACTTACTTTACAACAAT
88223 CTCCCACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.18
25 18 0.82
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.34
Consensus pattern (23 bp):
TAATGCACTTACTTTACAACAAT
Done.