Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007863.1 Hibiscus syriacus cultivar Beakdansim tig00110234_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: 1653362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1535933 original size:41 final size:38
Alignment explanation
Indices: 1535850--1536085 Score: 186
Period size: 38 Copynumber: 6.3 Consensus size: 38
1535840 TGAAACTACG
* * * *
1535850 TATATAATATATAGTTTTT-AATA-GTTTT-TAAAA-C
1 TATATAATATATAGTTTTTAAAAACATTTTAGAAAATA
1535884 TATATAATATATAGTTTTTAAAAAAAACATTTTAGAAAATA
1 TATATAATATATAGTTTTT---AAAAACATTTTAGAAAATA
* * *
1535925 TATGTAATATATAATTTTTAAAATCATTTTA-AAAACTTA
1 TATATAATATATAGTTTTTAAAAACATTTTAGAAAA--TA
* * *
1535964 TATATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATA-ATATATAGTTTTTAAAAACATTTTAGAAAATA
* * *
1536003 TATAT-AT-TATAG-TTTTGAAAACATTTTAAAAACATT
1 TATATAATATATAGTTTTTAAAAACATTTTAGAAA-ATA
* * *
1536039 TATATATTATATAGTTTTT-AAAACGTTTTTGAAAACT-
1 TATATAATATATAGTTTTTAAAAACATTTTAGAAAA-TA
1536076 TATATAATAT
1 TATATAATAT
1536086 TTTTGAAAAC
Statistics
Matches: 164, Mismatches: 22, Indels: 29
0.76 0.10 0.13
Matches are distributed among these distances:
34 19 0.12
35 18 0.11
36 11 0.07
37 17 0.10
38 32 0.20
39 21 0.13
40 25 0.15
41 21 0.13
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (38 bp):
TATATAATATATAGTTTTTAAAAACATTTTAGAAAATA
Found at i:1535934 original size:75 final size:75
Alignment explanation
Indices: 1535850--1536061 Score: 202
Period size: 75 Copynumber: 2.8 Consensus size: 75
1535840 TGAAACTACG
*
1535850 TATATAATATATAGTTTTTAATAGTTTTTAAAAC-TATATAATATATAGTTTTTAAAAAAAACAT
1 TATATAATATATAGTTTTTAATA-TTTTAAAAACTTATATAATATATAGTTTTTAAAAAAAACAT
*
1535914 TTTAGAAAATA
65 TTTAGAAAACA
* * *
1535925 TATGTAATATATAATTTTTAAAATCATTTTAAAAACTTATATATATATATATAGTTTTT---GAA
1 TATATAATATATAGTTTTT--AAT-ATTTTAAAAAC-T-TATATA-ATATATAGTTTTTAAAAAA
*
1535987 AACATTTTTGAAAACA
60 AACATTTTAGAAAACA
* * *
1536003 TATAT-AT-TATAGTTTTGAAAACATTTTAAAAACATTTATATATTATATAGTTTTTAAAA
1 TATATAATATATAGTTTT--TAATATTTTAAAAAC--TTATATAATATATAGTTTTTAAAA
1536062 CGTTTTTGAA
Statistics
Matches: 112, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
74 12 0.11
75 34 0.30
76 12 0.11
77 14 0.12
78 21 0.19
80 6 0.05
81 13 0.12
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (75 bp):
TATATAATATATAGTTTTTAATATTTTAAAAACTTATATAATATATAGTTTTTAAAAAAAACATT
TTAGAAAACA
Found at i:1535994 original size:12 final size:12
Alignment explanation
Indices: 1535979--1536003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1535969 ATATATATAG
1535979 TTTTTGAAAACA
1 TTTTTGAAAACA
1535991 TTTTTGAAAACA
1 TTTTTGAAAACA
1536003 T
1 T
1536004 ATATATTATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:1536097 original size:71 final size:74
Alignment explanation
Indices: 1535884--1536122 Score: 247
Period size: 71 Copynumber: 3.2 Consensus size: 74
1535874 TTTTTAAAAC
* * * * *
1535884 TATATAATATATAGTTTTTAAAAAAAACATTTTAGAAAATATATGTAATATATAATTTTT-AAAA
1 TATATATTATATAGTTTTT---GAAAACATTTTTGAAAACATATAT-ATA-AT-ATTTTTGAAAA
1535948 TCATTTTAAAAAC-TT
60 -CATTTTAAAAACATT
* *
1535963 ATATATATATATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAACATT
1 -TATATAT-TATATAGTTTTTGAAAACATTTTTGAAAACATATATATAATATTTTTGAAAACATT
1536028 TTAAAAACATT
64 TTAAAAACATT
*
1536039 TATATATTATATAGTTTTT-AAAACGTTTTTGAAAAC-T-TATATAATATTTTTGAAAACATGTT
1 TATATATTATATAGTTTTTGAAAACATTTTTGAAAACATATATATAATATTTTTGAAAACAT-TT
*
1536101 GAAAAA-ATT
65 TAAAAACATT
**
1536110 CGTATATTATATA
1 TATATATTATATA
1536123 TGTTGAGTTA
Statistics
Matches: 142, Mismatches: 13, Indels: 17
0.83 0.08 0.10
Matches are distributed among these distances:
71 34 0.24
72 8 0.06
73 16 0.11
74 12 0.08
75 24 0.17
76 8 0.06
77 2 0.01
78 20 0.14
80 6 0.04
81 12 0.08
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (74 bp):
TATATATTATATAGTTTTTGAAAACATTTTTGAAAACATATATATAATATTTTTGAAAACATTTT
AAAAACATT
Found at i:1536123 original size:73 final size:74
Alignment explanation
Indices: 1535884--1536123 Score: 222
Period size: 73 Copynumber: 3.2 Consensus size: 74
1535874 TTTTTAAAAC
* * * * * * *
1535884 TATATAATATATAGTTTTTAAAAAAAACATTTTAGAAAATATATGTAATATATAATTTTTAAAAT
1 TATATTATATATAGTTTTT---GAAAACATTTTTGAAAACATATAT-ATA-ATAGTTTTGAAAA-
*
1535949 CATTTTAAAAAC-TT
60 CATTTGAAAAACATT
*
1535963 ATATATATATATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAACATT
1 -TATAT-TATATATAGTTTTTGAAAACATTTTTGAAAACATATATATAATAGTTTTGAAAACATT
*
1536028 TTAAAAACATT
64 TGAAAAACATT
* *
1536039 TATA-TATTATATAGTTTTT-AAAACGTTTTTGAAAAC-T-TATATAATATTTTTGAAAACATGT
1 TATATTA-TATATAGTTTTTGAAAACATTTTTGAAAACATATATATAATAGTTTTGAAAACAT-T
1536100 TGAAAAA-ATT
64 TGAAAAACATT
1536110 CGTATATTATATAT
1 --TATATTATATAT
1536124 GTTGAGTTAA
Statistics
Matches: 141, Mismatches: 12, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
71 23 0.16
72 8 0.06
73 27 0.19
74 14 0.10
75 16 0.11
76 13 0.09
77 2 0.01
78 20 0.14
80 5 0.04
81 13 0.09
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (74 bp):
TATATTATATATAGTTTTTGAAAACATTTTTGAAAACATATATATAATAGTTTTGAAAACATTTG
AAAAACATT
Found at i:1539556 original size:21 final size:21
Alignment explanation
Indices: 1539530--1539569 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1539520 CAGAACCCTA
*
1539530 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1539551 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1539570 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1539598 original size:20 final size:21
Alignment explanation
Indices: 1539552--1539612 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1539542 TTCCCCTGTG
1539552 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1539575 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1539595 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1539613 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1545719 original size:3 final size:3
Alignment explanation
Indices: 1545711--1545762 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1545701 TATATATATC
*
1545711 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTA TTT TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
1545755 TTT TTA TT
1 TTA TTA TT
1545763 TATTTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (3 bp):
TTA
Found at i:1545764 original size:15 final size:15
Alignment explanation
Indices: 1545711--1545768 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
1545701 TATATATATC
1545711 TTATTATTA-TTATT
1 TTATTATTATTTATT
1545725 ATTATTATTATTTA--
1 -TTATTATTATTTATT
1545739 TT-TTATT-TTTATT
1 TTATTATTATTTATT
*
1545752 TTATTTTTATTTATT
1 TTATTATTATTTATT
1545767 TT
1 TT
1545769 TTTTGTCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
11 4 0.11
12 5 0.14
13 4 0.11
14 4 0.11
15 17 0.46
16 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTATTATTTATT
Found at i:1545765 original size:21 final size:24
Alignment explanation
Indices: 1545693--1545769 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 24
1545683 TTTGAAAATA
1545693 TTTATGTATATATATATCTTATTATTATT
1 TTTAT-TAT-TAT-TAT-TTATT-TTATT
*
1545722 ATTATTATTATTATTTATTTTATT
1 TTTATTATTATTATTTATTTTATT
1545746 TTTATT-TTATT-TTTA-TTTATT
1 TTTATTATTATTATTTATTTTATT
1545767 TTT
1 TTT
1545770 TTTGTCTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.20
22 4 0.09
23 5 0.11
24 10 0.22
25 5 0.11
26 3 0.07
27 3 0.07
28 3 0.07
29 4 0.09
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (24 bp):
TTTATTATTATTATTTATTTTATT
Found at i:1545770 original size:11 final size:11
Alignment explanation
Indices: 1545711--1545769 Score: 75
Period size: 12 Copynumber: 5.2 Consensus size: 11
1545701 TATATATATC
*
1545711 TTATTATTATTA
1 TTATT-TTATTT
1545723 TTATTATTATTAT
1 TTATT-TTATT-T
1545736 TTATTTTATTT
1 TTATTTTATTT
1545747 TTATTTTATTT
1 TTATTTTATTT
1545758 TTA-TTTATTT
1 TTATTTTATTT
1545768 TT
1 TT
1545770 TTTGTCTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
10 9 0.20
11 15 0.33
12 16 0.36
13 5 0.11
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:1546703 original size:214 final size:214
Alignment explanation
Indices: 1546334--1546764 Score: 862
Period size: 214 Copynumber: 2.0 Consensus size: 214
1546324 AGAACAGAAG
1546334 CATAAAAGTAAAAGGTCGAGACTTTTGGCTTAGATCTACGCCAATAGGAGATTTGTTTGGAGAAA
1 CATAAAAGTAAAAGGTCGAGACTTTTGGCTTAGATCTACGCCAATAGGAGATTTGTTTGGAGAAA
1546399 TAGGTATCGGATTTGGGATCGGGGGGTGGAGACGAACATTCGGTGAGGTTTCGATTTTTCCGGCC
66 TAGGTATCGGATTTGGGATCGGGGGGTGGAGACGAACATTCGGTGAGGTTTCGATTTTTCCGGCC
1546464 GTCGCGACGTTTGACGCTGGTCGGACATTAGCCTGGGTAGAGAGAGAGGAGAGAAATTTGATCTC
131 GTCGCGACGTTTGACGCTGGTCGGACATTAGCCTGGGTAGAGAGAGAGGAGAGAAATTTGATCTC
1546529 TCTTATTTTTAGAGAGAGA
196 TCTTATTTTTAGAGAGAGA
1546548 CATAAAAGTAAAAGGTCGAGACTTTTGGCTTAGATCTACGCCAATAGGAGATTTGTTTGGAGAAA
1 CATAAAAGTAAAAGGTCGAGACTTTTGGCTTAGATCTACGCCAATAGGAGATTTGTTTGGAGAAA
1546613 TAGGTATCGGATTTGGGATCGGGGGGTGGAGACGAACATTCGGTGAGGTTTCGATTTTTCCGGCC
66 TAGGTATCGGATTTGGGATCGGGGGGTGGAGACGAACATTCGGTGAGGTTTCGATTTTTCCGGCC
1546678 GTCGCGACGTTTGACGCTGGTCGGACATTAGCCTGGGTAGAGAGAGAGGAGAGAAATTTGATCTC
131 GTCGCGACGTTTGACGCTGGTCGGACATTAGCCTGGGTAGAGAGAGAGGAGAGAAATTTGATCTC
1546743 TCTTATTTTTAGAGAGAGA
196 TCTTATTTTTAGAGAGAGA
1546762 CAT
1 CAT
1546765 TTTGAATTTA
Statistics
Matches: 217, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 217 1.00
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (214 bp):
CATAAAAGTAAAAGGTCGAGACTTTTGGCTTAGATCTACGCCAATAGGAGATTTGTTTGGAGAAA
TAGGTATCGGATTTGGGATCGGGGGGTGGAGACGAACATTCGGTGAGGTTTCGATTTTTCCGGCC
GTCGCGACGTTTGACGCTGGTCGGACATTAGCCTGGGTAGAGAGAGAGGAGAGAAATTTGATCTC
TCTTATTTTTAGAGAGAGA
Found at i:1547203 original size:14 final size:14
Alignment explanation
Indices: 1547186--1547219 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1547176 ATTTATTATT
1547186 ATTTTCTATCTAAC
1 ATTTTCTATCTAAC
1547200 ATTTTCTATCTAAC
1 ATTTTCTATCTAAC
1547214 ATTTTC
1 ATTTTC
1547220 GTCTCATTTT
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:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTCTATCTAAC
Found at i:1548001 original size:17 final size:17
Alignment explanation
Indices: 1547979--1548037 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
1547969 GAGAGAGAGA
1547979 GAGAGAGGTAATTCGGG
1 GAGAGAGGTAATTCGGG
* ** *
1547996 GAGAGAGGGAA-GAGAGA
1 GAGAGAGGTAATTCG-GG
1548013 GAGAGAGGTAATTCGGG
1 GAGAGAGGTAATTCGGG
*
1548030 GAAAGAGG
1 GAGAGAGG
1548038 GAAGGGAGGG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
16 1 0.03
17 29 0.94
18 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.49, T:0.10
Consensus pattern (17 bp):
GAGAGAGGTAATTCGGG
Found at i:1548010 original size:34 final size:34
Alignment explanation
Indices: 1547972--1548041 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
1547962 TGTGTGAGAG
*
1547972 AGAGAGAGAGAGAGGTAATTCGGGGAGAGAGGGA
1 AGAGAGAGAGAGAGGTAATTCGGGGAAAGAGGGA
1548006 AGAGAGAGAGAGAGGTAATTCGGGGAAAGAGGGA
1 AGAGAGAGAGAGAGGTAATTCGGGGAAAGAGGGA
1548040 AG
1 AG
1548042 GGAGGGGAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.03, G:0.49, T:0.09
Consensus pattern (34 bp):
AGAGAGAGAGAGAGGTAATTCGGGGAAAGAGGGA
Found at i:1550931 original size:20 final size:21
Alignment explanation
Indices: 1550906--1550957 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1550896 TTTTCCCAAT
*
1550906 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1550926 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1550947 TCGCAATGCGA
1 TCGCAATGCGA
1550958 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1550971 original size:20 final size:20
Alignment explanation
Indices: 1550946--1551059 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
1550936 AATTGGGAAA
*
1550946 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1550966 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1550986 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1551007 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1551027 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1551047 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1551060 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1550990 original size:61 final size:61
Alignment explanation
Indices: 1550943--1551059 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1550933 GCGAATTGGG
* * * * *
1550943 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1551004 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
1551060 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1551632 original size:18 final size:18
Alignment explanation
Indices: 1551573--1551652 Score: 78
Period size: 18 Copynumber: 4.5 Consensus size: 18
1551563 TTCGAGAATG
1551573 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGC-GAAAT
* *
1551592 AACTATCGCAA--CGAGAT
1 AA-AATCGCAACGCGAAAT
1551609 --AATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAAT
*
1551625 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-T
1551644 AAAATCGCA
1 AAAATCGCA
1551653 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 16 0.32
19 11 0.22
20 7 0.14
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:1551670 original size:19 final size:19
Alignment explanation
Indices: 1551648--1551832 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1551638 GAAACCAAAA
*
1551648 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1551667 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1551686 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
1551705 TTGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1551725 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1551741 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1551758 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1551772 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1551791 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1551811 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1551831 TC
1 TC
1551833 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 48 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1551719 original size:39 final size:38
Alignment explanation
Indices: 1551648--1551832 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
1551638 GAAACCAAAA
*
1551648 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1551686 TCGCGTTGCGATTTTTATTTTGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1551725 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
1551758 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1551791 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1551831 TC
1 TC
1551833 AACCAAAAGA
Statistics
Matches: 123, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.02
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 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1551809 original size:20 final size:20
Alignment explanation
Indices: 1551775--1551832 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1551765 GCGATTCTCT
**
1551775 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1551795 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1551815 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1551833 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1553908 original size:41 final size:41
Alignment explanation
Indices: 1553829--1553949 Score: 111
Period size: 41 Copynumber: 2.9 Consensus size: 41
1553819 GCCCGACTCG
* * * * *
1553829 CCTATCATCCCTCAAGAGTCCACTCCTATCGTT-GAGAGGCC
1 CCTATCATTCCTCGAGAGTCC-CTCCCACCGTTCAAGAGGCC
1553870 CCTATCATTCCTCGAGAGTCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCTCCCACCGTTCAAGAGGCC
* * * * *
1553911 ACTGTCA-TCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCTCCCACCGTTCAAGAG
1553950 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
40 13 0.19
41 34 0.51
42 20 0.30
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (41 bp):
CCTATCATTCCTCGAGAGTCCCTCCCACCGTTCAAGAGGCC
Found at i:1553948 original size:21 final size:21
Alignment explanation
Indices: 1553887--1553949 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1553877 TTCCTCGAGA
1553887 GTCCCTCCCACCGTTCAAGAG
1 GTCCCTCCCACCGTTCAAGAG
** * *
1553908 G-CCACTGTCATCGTTGAAGAG
1 GTCC-CTCCCACCGTTCAAGAG
*
1553929 GTCCCTCCCACCATTCAAGAG
1 GTCCCTCCCACCGTTCAAGAG
1553950 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.21
Consensus pattern (21 bp):
GTCCCTCCCACCGTTCAAGAG
Found at i:1555319 original size:14 final size:14
Alignment explanation
Indices: 1555300--1555335 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1555290 ATTGTTTAAT
1555300 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1555314 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1555328 TGATTTGT
1 TGATTTGT
1555336 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:1555577 original size:19 final size:19
Alignment explanation
Indices: 1555553--1555644 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
1555543 AATTCCCTCG
1555553 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
1555572 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
1555586 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1555605 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1555619 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1555638 TTGCGAT
1 TTGCGAT
1555645 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 17 0.31
16 7 0.13
17 7 0.13
19 24 0.44
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1555607 original size:66 final size:66
Alignment explanation
Indices: 1555511--1555643 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1555501 ACGCGAAATT
* *
1555511 AAATTCGCGTTGTGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1555576 G
66 G
* *
1555577 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1555642 G
66 G
1555643 A
1 A
1555644 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1555642 original size:33 final size:33
Alignment explanation
Indices: 1555518--1555644 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1555508 ATTAAATTCG
* * *
1555518 CGTTGTGATTTTCATTTCGCATTGCAATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* **
1555551 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
1555584 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1555617 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1555645 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 2 0.02
33 79 0.95
34 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1558763 original size:19 final size:19
Alignment explanation
Indices: 1558741--1558796 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
1558731 GAAAATTAAA
1558741 ATCGCAATGCGAAATGACT
1 ATCGCAATGCGAAATGACT
* * *
1558760 ATCGAAACGCGGAAATGGCT
1 ATCGCAATGC-GAAATGACT
1558780 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
1558797 AAATCGCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:1558802 original size:19 final size:19
Alignment explanation
Indices: 1558733--1558837 Score: 69
Period size: 19 Copynumber: 5.8 Consensus size: 19
1558723 CGCAACACGA
*
1558733 AAATTAAAATCGCAATGCG
1 AAATGAAAATCGCAATGCG
** * *
1558752 AAATGACTATCGAAACGCGG
1 AAATGAAAATCGCAATGC-G
***
1558772 AAATGGCTATCGCAATGCG
1 AAATGAAAATCGCAATGCG
1558791 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAATGCG
* *
1558808 --A-CAAAATTGCAATGCG
1 AAATGAAAATCGCAATGCG
1558824 AAATG-AAATCGCAA
1 AAATGAAAATCGCAA
1558838 CGACAAAATC
Statistics
Matches: 65, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 9 0.14
19 26 0.40
20 16 0.25
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (19 bp):
AAATGAAAATCGCAATGCG
Found at i:1558819 original size:14 final size:14
Alignment explanation
Indices: 1558796--1558853 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1558786 ATGCGAAATG
1558796 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1558810 AAAATTGCAATGCGAA
1 AAAATCGCAA--CGAC
1558826 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1558842 AAAATCGCAACG
1 AAAATCGCAACG
1558854 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1558838 original size:32 final size:33
Alignment explanation
Indices: 1558780--1558858 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1558770 GGAAATGGCT
1558780 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1558813 ATTGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1558845 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1558859 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 28 0.65
33 15 0.35
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1558887 original size:19 final size:18
Alignment explanation
Indices: 1558865--1558929 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
1558855 GAAACACAAA
1558865 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
1558884 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
1558900 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
1558916 TCGCATTGCGATTT
1 TCGCATTGCGATTT
1558930 TGTCGTTGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.23
16 8 0.21
18 12 0.31
19 10 0.26
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:1558906 original size:14 final size:14
Alignment explanation
Indices: 1558887--1558944 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1558877 TTTCATTTCG
1558887 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1558901 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1558917 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1558933 CGTTGTGATTTT
1 CGTTGCGATTTT
1558945 TATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1558955 original size:33 final size:33
Alignment explanation
Indices: 1558870--1558960 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
1558860 ACAAATCGCA
*
1558870 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1558903 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
1558935 TTGTGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1558961 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1558979 original size:20 final size:20
Alignment explanation
Indices: 1558954--1558999 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1558944 TTATTTCGCA
1558954 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
1558974 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
1558994 TTGCGA
1 TTGCGA
1559000 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1559507 original size:18 final size:18
Alignment explanation
Indices: 1559481--1559525 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1559471 GTCGATCAGA
*
1559481 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1559499 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1559517 TGATGGCTC
1 TGATGGCTC
1559526 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1560869 original size:20 final size:20
Alignment explanation
Indices: 1560844--1560881 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1560834 AATAGTTTCT
1560844 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1560864 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1560882 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1561172 original size:22 final size:22
Alignment explanation
Indices: 1561145--1561188 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1561135 GATGGAGATA
*
1561145 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
1561167 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
1561189 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:1561401 original size:20 final size:20
Alignment explanation
Indices: 1561376--1561428 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1561366 GATTATGTAT
*
1561376 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
1561396 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
1561416 TATCTCGTTGCGA
1 TATCGCGTTGCGA
1561429 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:1561462 original size:20 final size:20
Alignment explanation
Indices: 1561356--1561470 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
1561346 CGCTTTGAAA
*
1561356 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1561377 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1561397 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1561417 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1561438 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
1561458 ATCGCATTACGAT
1 ATCGCATTGCGAT
1561471 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.65
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1561471 original size:41 final size:41
Alignment explanation
Indices: 1561396--1561473 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1561386 CGAAAGTCAG
* * * *
1561396 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTTTAT
* *
1561437 TATCGCATTGCGATAGTCAGTATCGCATTACGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTT
1561474 CCCAATTCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTTTAT
Found at i:1561493 original size:21 final size:21
Alignment explanation
Indices: 1561467--1561534 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
1561457 TATCGCATTA
*
1561467 CGATTTTCCCAATTCACGTTG
1 CGATTTTCCCAATTCGCGTTG
* ** *
1561488 CGA-TTTACTTATTCGCATTG
1 CGATTTTCCCAATTCGCGTTG
1561508 CGATTTTCCCAATTCGCGTTG
1 CGATTTTCCCAATTCGCGTTG
1561529 CGATTT
1 CGATTT
1561535 ACTTATTCGC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (21 bp):
CGATTTTCCCAATTCGCGTTG
Found at i:1561508 original size:20 final size:20
Alignment explanation
Indices: 1561485--1561551 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1561475 CCAATTCACG
1561485 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
1561505 TTGCGATTTTCCCAATTCGCG
1 TTGCGA-TTTACTTATTCGCA
1561526 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
1561546 TTGCGA
1 TTGCGA
1561552 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:1561548 original size:41 final size:41
Alignment explanation
Indices: 1561459--1561551 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
1561449 ATAGTCAGTA
*
1561459 TCGCATTACGATTTTCCCAATTCACGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
*
1561500 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
1561541 TCGCATTGCGA
1 TCGCATTGCGA
1561552 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
Found at i:1562651 original size:7 final size:7
Alignment explanation
Indices: 1562616--1562676 Score: 94
Period size: 7 Copynumber: 9.3 Consensus size: 7
1562606 TGTGTCTCCC
1562616 TCCCC-T
1 TCCCCTT
1562622 TCCCC-T
1 TCCCCTT
1562628 TCCCC-T
1 TCCCCTT
1562634 TCCCC-T
1 TCCCCTT
1562640 TCCCCTT
1 TCCCCTT
1562647 TCCCCTT
1 TCCCCTT
1562654 TCCCCTT
1 TCCCCTT
1562661 TCCCCTT
1 TCCCCTT
1562668 TCCCCTT
1 TCCCCTT
1562675 TC
1 TC
1562677 TATAGCTACC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 23 0.43
7 31 0.57
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (7 bp):
TCCCCTT
Found at i:1564002 original size:3 final size:3
Alignment explanation
Indices: 1563971--1564033 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
1563961 TCTATAAAAA
1563971 TAT TA- TAT TA- TAT TA- TAT TA- TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
1564013 TATT TAT T-T TAT TAT TTT TAT
1 TA-T TAT TAT TAT TAT TAT TAT
1564034 AAGCTCCACA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 10 0.20
3 36 0.71
4 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1564119 original size:33 final size:33
Alignment explanation
Indices: 1564077--1564178 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
1564067 ATTTAGAAAA
*
1564077 TAAAT-CAACGTATTTGAATCTTATTAAAACAC
1 TAAATCCAACGTATTTGAATCATATTAAAACAC
* *
1564109 TAACA-CCAACGTATTTGAGTCATATTGAAACAC
1 TAA-ATCCAACGTATTTGAATCATATTAAAACAC
* * * * *
1564142 TAAATCTAACGTATTTGAGTAATATTGAAACAA
1 TAAATCCAACGTATTTGAATCATATTAAAACAC
1564175 TAAA
1 TAAA
1564179 AACAAAGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
32 4 0.07
33 57 0.93
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (33 bp):
TAAATCCAACGTATTTGAATCATATTAAAACAC
Found at i:1565238 original size:64 final size:64
Alignment explanation
Indices: 1565038--1565247 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
1565028 TTTTTCAAAG
* **
1565038 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATCAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTCATG-AT-ATTTTGAAACATCGAATGCA
1565101 TT
63 TT
* * * * *
1565103 TTATGCATCGATGCA-CATACCAAGCATCGATGCACTGAGGAT-TTTATAAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACTCATGATATTT-T-GAAACATCGAATGCA
1565166 TT
63 TT
* * * *
1565168 TGATGCATCGATGCACCAACCATGCATCGATACACTCTTGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCATGATATTTTGAAACATCGAATGCATT
1565232 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1565248 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 50 0.41
65 64 0.53
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCATGATATTTTGAAACATCGAATGCATT
Found at i:1565247 original size:17 final size:19
Alignment explanation
Indices: 1565219--1565267 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1565209 TATTTTGAAA
1565219 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1565237 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1565256 CACCGATGCACT
1 CATCGATGCACT
1565268 AAGGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1566926 original size:45 final size:45
Alignment explanation
Indices: 1566872--1566975 Score: 199
Period size: 45 Copynumber: 2.3 Consensus size: 45
1566862 GCACCAATCT
1566872 ATGCATCGATGCACCATGAATCAAATTGAACATCGAATGCATTTC
1 ATGCATCGATGCACCATGAATCAAATTGAACATCGAATGCATTTC
*
1566917 ATGCATCGATGCACCATGTATCAAATTGAACATCGAATGCATTTC
1 ATGCATCGATGCACCATGAATCAAATTGAACATCGAATGCATTTC
1566962 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1566976 ATACCATGCA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (45 bp):
ATGCATCGATGCACCATGAATCAAATTGAACATCGAATGCATTTC
Found at i:1566985 original size:19 final size:19
Alignment explanation
Indices: 1566961--1567013 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1566951 GAATGCATTT
1566961 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
*
1566980 CATGCATCGATGCATATAC
1 CATGCATCGATGCACATAC
1566999 CATGCATCGATGCAC
1 CATGCATCGATGCAC
1567014 TGAGGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (19 bp):
CATGCATCGATGCACATAC
Found at i:1567070 original size:19 final size:19
Alignment explanation
Indices: 1567046--1567116 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
1567036 AATTCATTTG
1567046 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
1567065 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
1567084 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
1567103 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1567117 TCTGGCTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACCAGCC
Found at i:1567086 original size:103 final size:102
Alignment explanation
Indices: 1566961--1567161 Score: 255
Period size: 103 Copynumber: 2.0 Consensus size: 102
1566951 GAATGCATTT
* * *
1566961 CATGCATCGATGCACATACCATGCATCGATGCA-TATACCATGCATCGATGCACTGAGG-TTTTT
1 CATGCATCGATGCACATACCATGCATCGATGCACCA-ACCATGCATCGATGCACTCAGGCTATTT
* * * *
1567024 ATGAAAACATCGAATTCATTTGATGCATCGATGCACCAGC
65 -TG-AAACATCAAATGCACTTGATACATCGATGCACCAGC
* * *
1567064 CATGCATCGATGCACCA-GCCATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT
1 CATGCATCGATGCA-CATACCATGCATCGATGCACCAACCATGCATCGATGCACTCAGGCTATTT
1567128 TGAAACATCAAATGCACTTGATACATCGATGCAC
65 TGAAACATCAAATGCACTTGATACATCGATGCAC
1567162 TCTTGGTGCA
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
102 28 0.33
103 50 0.59
104 7 0.08
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (102 bp):
CATGCATCGATGCACATACCATGCATCGATGCACCAACCATGCATCGATGCACTCAGGCTATTTT
GAAACATCAAATGCACTTGATACATCGATGCACCAGC
Found at i:1572079 original size:110 final size:110
Alignment explanation
Indices: 1571455--1572917 Score: 2114
Period size: 110 Copynumber: 13.5 Consensus size: 110
1571445 CAAACCACTT
* * *
1571455 TTCAGAGTTAATTTCAACTTCATAGCGAATGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
*
1571520 CAGCGAAGGGACGACTGACTGTCAACAAAC-A------A-TTT--
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
*
1571555 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTTA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
** *
1571620 CAATGAAGGGGCGACTGGCTGTCAACAAACAA-----C---TT--
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * *
1571655 TTCAGAGTTAATTTCAACTACACAAGCGAAGGATATTGGACTCGAGACAACAGAAGCTCAACTTC
1 TTCAGAGTCAATTTCAACTTCAC-AGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
1571720 ACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
65 ACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * * *
1571766 TTCAGATTCAATTTCAACTTCATAAGCGAGGGATATTGGACTCGATACAACACAAGCTCAACTTC
1 TTCAGAGTCAATTTCAACTTCA-CAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
*
1571831 ACAGCGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCA
65 ACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * *
1571877 TTCAAAGTCAATTTCAACTTCACAAGCGAATGATATTGGACTCGAGACAACATAAGCTCAACTTC
1 TTCAGAGTCAATTTCAACTTCAC-AGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * * *
1571942 ATAGCGAAGGGGCGACTGACTGCCAACAAATAACTTTTTAGTTTCA
65 ACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
*
1571988 TTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * * *
1572053 TAACGAAGGGGAGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * * *
1572098 TTCAGGGTCAATTT-AACTTCACAGCGAAGGATATTGAACTCAATACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* *
1572162 CAACGAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* *
1572207 TTCAGAGTCAATTTTAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* *
1572272 CAGCGAAGGGGCGACTGATTGTCAACAAATAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
1572317 TTCAGAGTCAATTTCAACTTCACAAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
1 TTCAGAGTCAATTTCAACTTCAC-AGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * *
1572382 ATAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCA
65 ACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* *
1572428 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACATAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * *
1572493 CAACGAAGGGCCAACTGACTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* *
1572538 TTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACACAAGCTCACCTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* *
1572603 CAGCGAAAGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * * *
1572648 TTCAGAGTCAATTTCAACTTCACAGTGAATGATATTGGACTCAAGACAACACAAGCTTAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1572713 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
** *
1572758 TAT-AGAGTCAATTTCAACTTCACAGCGAAGGATATTAAACTCGAGACAATACAAGCTCAACTTC
1 T-TCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * * *
1572822 ACTGCGAAGGGGCAACTGACTGTCAACAAGCAACTTTCCAG-TT--
65 ACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * * *
1572865 TT-AGAGTCAATTTCAACTTCACGGCGAAGGATATTGGTCTCGAAACAATACAA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
1572918 ATATTTGGAT
Statistics
Matches: 1240, Mismatches: 105, Indels: 30
0.90 0.08 0.02
Matches are distributed among these distances:
100 110 0.09
101 70 0.06
106 48 0.04
107 1 0.00
109 105 0.08
110 576 0.46
111 330 0.27
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (110 bp):
TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:1572669 original size:551 final size:552
Alignment explanation
Indices: 1571455--1572917 Score: 2156
Period size: 551 Copynumber: 2.7 Consensus size: 552
1571445 CAAACCACTT
* * *
1571455 TTCAGAGTTAATTTCAACTTCATAGCGAATGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1571520 CAGCG-AAGGGACGACTGACTGTCAACAAAC-A------A-TTT--TTCAGAGTCAATTTCAACT
66 CAGCGAAAGGG-CGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACT
* * * *
1571574 TCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTTACAATGAAGGGGCGACTGGC
130 TCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGAC
* *
1571639 TGTCAACAAACAA-----C---TT--TTCAGAGTTAATTTCAACTACACAAGCGAAGGATATTGG
195 TGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAA-CGAAGGATATTGG
*
1571694 ACTCGAGACAACAGAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTC
259 ACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTC
* * * *
1571759 AGTTTCATTCAGATTCAATTTCAACTTCATAAGCGAGGGATATTGGACTCGATACAACACAAGCT
324 AGTTTCATTCAGAGTCAATTTCAACTTCACAAGCGAAGGATATTGGACTCGAAACAACACAAGCT
* *
1571824 CAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAAAGTCAAT
389 CAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAAT
* * * * *
1571889 TTCAACTTCACAAGCGAATGATATTGGACTCGAGACAACATAAGCTCAACTTCATAGCGAAGGGG
454 TTCAACTTCACAAGCGAAGGATATTGGACTCGAGAAAACATAAGCTCAACTTCACAACGAAGGGC
* * *
1571954 CGACTGACTGCCAACAAATAACTTTTTAGTTTCA
519 CAACTGACTGCCAACAAACAACTTTTCAGTTTCA
*
1571988 TTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * * * * *
1572053 TAACGAAGGGGAGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGGGTCAATTT-AACTT
66 CAGCGAAAGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTT
* * *
1572117 CACAGCGAAGGATATTGAACTCAATACAACACAAGCTCAACTTCACAACGAAGGGGCGGCTGACT
131 CACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACT
*
1572182 GTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGATATTGGAC
196 GTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
1572247 TCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGATTGTCAACAAATAACTTTTCAG
261 TCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAG
*
1572312 TTTCATTCAGAGTCAATTTCAACTTCACAAGCGAAGGATATTGGACTCGAGACAACACAAGCTCA
326 TTTCATTCAGAGTCAATTTCAACTTCACAAGCGAAGGATATTGGACTCGAAACAACACAAGCTCA
* * *
1572377 ACTTCATAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCATTCAGAGTCAATTT
391 ACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAATTT
1572442 CAACTTCAC-AGCGAAGGATATTGGACTCGAGAAAACATAAGCTCAACTTCACAACGAAGGGCCA
456 CAACTTCACAAGCGAAGGATATTGGACTCGAGAAAACATAAGCTCAACTTCACAACGAAGGGCCA
*
1572506 ACTGACTGTCAACAAACAACTTTTCAGTTTCA
521 ACTGACTGCCAACAAACAACTTTTCAGTTTCA
* *
1572538 TTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACACAAGCTCACCTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
*
1572603 CAGCGAAAGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTT
66 CAGCGAAAGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTT
* * * *
1572668 CACAGTGAATGATATTGGACTCAAGACAACACAAGCTTAACTTCACAGCGAAGGGGCGACTGACT
131 CACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACT
* **
1572733 GTCAACAAACAACTTTTCAGTTTCATAT-AGAGTCAATTTCAACTTCACAGCGAAGGATATTAAA
196 GTCAACAAACAACTTTTCAGTTTCAT-TCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGA
* * * * *
1572797 CTCGAGACAATACAAGCTCAACTTCACTGCGAAGGGGCAACTGACTGTCAACAAGCAACTTTCCA
260 CTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCA
* * *
1572862 G-TT--TT-AGAGTCAATTTCAACTTCAC-GGCGAAGGATATTGGTCTCGAAACAATACAA
325 GTTTCATTCAGAGTCAATTTCAACTTCACAAGCGAAGGATATTGGACTCGAAACAACACAA
1572918 ATATTTGGAT
Statistics
Matches: 834, Mismatches: 73, Indels: 33
0.89 0.08 0.04
Matches are distributed among these distances:
533 81 0.10
534 5 0.01
540 1 0.00
541 3 0.00
542 75 0.09
543 13 0.02
546 27 0.03
547 21 0.03
548 2 0.00
550 196 0.24
551 387 0.46
552 23 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (552 bp):
TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
CAGCGAAAGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTT
CACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACT
GTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
TCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAG
TTTCATTCAGAGTCAATTTCAACTTCACAAGCGAAGGATATTGGACTCGAAACAACACAAGCTCA
ACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAATTT
CAACTTCACAAGCGAAGGATATTGGACTCGAGAAAACATAAGCTCAACTTCACAACGAAGGGCCA
ACTGACTGCCAACAAACAACTTTTCAGTTTCA
Found at i:1573303 original size:81 final size:79
Alignment explanation
Indices: 1573025--1573304 Score: 265
Period size: 81 Copynumber: 3.4 Consensus size: 79
1573015 ATCGTGCCCA
* * * * * *
1573025 CCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGA-TTCACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGC
* * *
1573090 GAGAAGAGCTGTCTG
65 AAGAAGGGCTATCTG
* * * * * *
1573105 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGATT-CACTCAGC-TCAAAGGCACATCATTTGCAGCATAGCTCAAGG
*
1573170 CTAA-AAGGGTTATCTG
64 C-AAGAAGGGCTATCTG
* * *
1573186 TCAACAAAGACCTTCGAGTTCGACTTCACTCTGCTCAAAGACACCATCTTTTGCAGCATAGCTCA
1 -C--CAAAGACCTTCGAGTTCGA-TTCACTCAGCTCAAAGGCA-CATCATTTGCAGCATAGCTCA
*
1573251 AGGCAAGAAGGGCTATTTG
61 AGGCAAGAAGGGCTATCTG
* *
1573270 CCAAAGACCTTAGAGTTCGATTCCATTCAGCTCAA
1 CCAAAGACCTTCGAGTTCGATT-CACTCAGCTCAA
1573305 GGGTGTATCA
Statistics
Matches: 161, Mismatches: 29, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
79 1 0.01
80 27 0.17
81 64 0.40
82 2 0.01
83 9 0.06
84 56 0.35
85 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (79 bp):
CCAAAGACCTTCGAGTTCGATTCACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
AGAAGGGCTATCTG
Found at i:1573658 original size:24 final size:21
Alignment explanation
Indices: 1573625--1573680 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 21
1573615 CTACAAAAAC
*
1573625 ATTTTATTATATTATATTTATTT
1 ATTTTATTAT-TAATATTT-TTT
1573648 ATTATTATTATTAATATTTTTT
1 ATT-TTATTATTAATATTTTTT
1573670 ATTTTATTATT
1 ATTTTATTATT
1573681 TTTGTAGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 8 0.26
22 6 0.19
23 10 0.32
24 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTATTATTAATATTTTTT
Found at i:1573682 original size:13 final size:13
Alignment explanation
Indices: 1573625--1573682 Score: 66
Period size: 13 Copynumber: 4.4 Consensus size: 13
1573615 CTACAAAAAC
1573625 ATTTTATTATATT
1 ATTTTATTATATT
1573638 ATATTTATT-TATT
1 AT-TTTATTATATT
1573651 ATTATTATTAATATT
1 ATT-TTATT-ATATT
*
1573666 -TTTTATTTTATT
1 ATTTTATTATATT
1573678 ATTTT
1 ATTTT
1573683 TGTAGACCCC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 5 0.13
13 22 0.56
14 8 0.21
15 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTATTATATT
Found at i:1573778 original size:33 final size:33
Alignment explanation
Indices: 1573741--1573833 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
1573731 AATCAACGCC
*
1573741 TTTGAGTCCTATTGAAAAACTAAAACTAACGTA
1 TTTGAGTCCTATTGAAAAACTAAAACCAACGTA
* *
1573774 TTTGAGTCATATT-AAAACACTAAAACCAACTTA
1 TTTGAGTCCTATTGAAAA-ACTAAAACCAACGTA
* *
1573807 TTTGAGTCCTAGTGAAACACTAAAACC
1 TTTGAGTCCTATTGAAAAACTAAAACC
1573834 GAAACATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 4 0.08
33 45 0.87
34 3 0.06
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (33 bp):
TTTGAGTCCTATTGAAAAACTAAAACCAACGTA
Found at i:1595519 original size:42 final size:42
Alignment explanation
Indices: 1595472--1595552 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
1595462 AGGGGTTAAA
*
1595472 TAATTTGATATCATTTAAGTGGAGTCTCAAATTTAAGTTTTT
1 TAATTTGATATCACTTAAGTGGAGTCTCAAATTTAAGTTTTT
*
1595514 TAATTTGATATCACTTAAGTGGAGTCTCTAATTTAAGTT
1 TAATTTGATATCACTTAAGTGGAGTCTCAAATTTAAGTT
1595553 CTTGTATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.46
Consensus pattern (42 bp):
TAATTTGATATCACTTAAGTGGAGTCTCAAATTTAAGTTTTT
Found at i:1597862 original size:15 final size:16
Alignment explanation
Indices: 1597839--1597880 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1597829 TCTAAACTTA
* *
1597839 ATAATATAAAATT-CT
1 ATAAAATAAAATTGAT
1597854 ATAAAATAAAATTGAT
1 ATAAAATAAAATTGAT
1597870 ATAAAACTAAA
1 ATAAAA-TAAA
1597881 TCATAATTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.52
16 7 0.30
17 4 0.17
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (16 bp):
ATAAAATAAAATTGAT
Found at i:1607054 original size:5 final size:5
Alignment explanation
Indices: 1607044--1607070 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1607034 TTAAGGTACC
1607044 TTGCA TTGCA TTGCA TTGCA TTGCA TT
1 TTGCA TTGCA TTGCA TTGCA TTGCA TT
1607071 TCATAGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTGCA
Found at i:1609953 original size:32 final size:32
Alignment explanation
Indices: 1609911--1609985 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1609901 TCTATATGCG
* * *
1609911 ATACTGACTCTACTGTGCATTATCTAAATATC
1 ATACTAACTCTACTGTGCATTATATAAATATA
* ** *
1609943 ATGCTAACTCTGTTGTGCATTATATGAATATA
1 ATACTAACTCTACTGTGCATTATATAAATATA
1609975 ATACTAACTCT
1 ATACTAACTCT
1609986 GTTGTGACTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (32 bp):
ATACTAACTCTACTGTGCATTATATAAATATA
Found at i:1609986 original size:32 final size:32
Alignment explanation
Indices: 1609924--1609991 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
1609914 CTGACTCTAC
* * *
1609924 TGTGCATTATCTAAATATCATGCTAACTCTGT
1 TGTGCATTATATAAATATAATACTAACTCTGT
*
1609956 TGTGCATTATATGAATATAATACTAACTCTGT
1 TGTGCATTATATAAATATAATACTAACTCTGT
1609988 TGTG
1 TGTG
1609992 ACTCATATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (32 bp):
TGTGCATTATATAAATATAATACTAACTCTGT
Found at i:1610000 original size:32 final size:32
Alignment explanation
Indices: 1609937--1610000 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1609927 GCATTATCTA
* * *
1609937 AATATCATGCTAACTCTGTTGTGCATTATATG
1 AATATAATACTAACTCTGTTGTGCATCATATG
1609969 AATATAATACTAACTCTGTTGTG-ACTCATATG
1 AATATAATACTAACTCTGTTGTGCA-TCATATG
1610001 CTAGCTCGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (32 bp):
AATATAATACTAACTCTGTTGTGCATCATATG
Found at i:1611258 original size:20 final size:21
Alignment explanation
Indices: 1611235--1611274 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1611225 TCGATATTGT
1611235 CCCT-GCAATATCGATACTCA
1 CCCTAGCAATATCGATACTCA
*
1611255 CCCTAGCATTATCGATACTC
1 CCCTAGCAATATCGATACTC
1611275 CCTTTGGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.35, G:0.10, T:0.28
Consensus pattern (21 bp):
CCCTAGCAATATCGATACTCA
Found at i:1617149 original size:29 final size:29
Alignment explanation
Indices: 1617117--1617194 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 29
1617107 AATATTGTGT
* *
1617117 TAATATTTTTTAATTATTTAATTTTTGTA
1 TAATATTTTTTAATTATTTAATTTATATA
** *
1617146 TAATCATTTGATAA-TGTTTAATTTATATA
1 TAAT-ATTTTTTAATTATTTAATTTATATA
*
1617175 TTATATTTGTTTTAATTATT
1 TAATA-TT-TTTTAATTATT
1617195 AAAATATTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
28 1 0.03
29 21 0.58
30 11 0.31
31 3 0.08
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (29 bp):
TAATATTTTTTAATTATTTAATTTATATA
Found at i:1618782 original size:16 final size:16
Alignment explanation
Indices: 1618761--1618794 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1618751 TTACTATTCA
*
1618761 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1618777 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1618793 CG
1 CG
1618795 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1624510 original size:2 final size:2
Alignment explanation
Indices: 1624503--1624527 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1624493 TAGAGGGCAA
1624503 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1624528 ATTCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1641599 original size:23 final size:23
Alignment explanation
Indices: 1641548--1641617 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1641538 GTTGGTTAGA
* ** *
1641548 ATATATATGTGGTCCTTAAGGAG
1 ATATCTATGTGGTCCTTCGGGAC
*
1641571 AAATCTATGTGGTCCTTCGGGAC
1 ATATCTATGTGGTCCTTCGGGAC
* *
1641594 ATATCTACGCGGTCCTTCGGGAC
1 ATATCTATGTGGTCCTTCGGGAC
1641617 A
1 A
1641618 ATTTTATATG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
ATATCTATGTGGTCCTTCGGGAC
Found at i:1645938 original size:23 final size:23
Alignment explanation
Indices: 1645887--1645939 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1645877 GTCAATTGGA
* *
1645887 ATATATATGTGGTCCTTAAGGAG
1 ATATCTATGTGGTCCTTAAGGAC
* **
1645910 AAATCTATGTGGTCCTTCGGGAC
1 ATATCTATGTGGTCCTTAAGGAC
1645933 ATATCTA
1 ATATCTA
1645940 CACGGTCATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (23 bp):
ATATCTATGTGGTCCTTAAGGAC
Done.