Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007930.1 Hibiscus syriacus cultivar Beakdansim tig00110338_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: 2280901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1531427 original size:20 final size:20
Alignment explanation
Indices: 1531382--1531459 Score: 120
Period size: 20 Copynumber: 3.7 Consensus size: 20
1531372 GCATGTGTAG
1531382 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
1531406 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
1531426 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
1531446 TGCATCGATGCACT
1 TGCATCGATGCACT
1531460 TCAAGGGGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
20 38 0.70
22 1 0.02
23 2 0.04
24 13 0.24
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1531454 original size:40 final size:43
Alignment explanation
Indices: 1531366--1531459 Score: 126
Period size: 40 Copynumber: 2.3 Consensus size: 43
1531356 TGAGTTGTGT
*
1531366 ATCGATGCA-TGTGTAGTGCATCGATGCACATGTTAAAGAATGC
1 ATCGATGCACTGTGTAATGCATCGATGCACATGTT-AAGAATGC
1531409 ATCGATGCACTGTAG-AATGCATCGATGCAC-TG-T-AGAATGC
1 ATCGATGCACTGT-GTAATGCATCGATGCACATGTTAAGAATGC
1531449 ATCGATGCACT
1 ATCGATGCACT
1531460 TCAAGGGGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
40 18 0.38
42 1 0.02
43 11 0.23
44 17 0.35
45 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (43 bp):
ATCGATGCACTGTGTAATGCATCGATGCACATGTTAAGAATGC
Found at i:1533105 original size:2 final size:2
Alignment explanation
Indices: 1533092--1533123 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1533082 AATATGTATG
1533092 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
1533124 TATGTTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1539864 original size:30 final size:31
Alignment explanation
Indices: 1539825--1539883 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
1539815 CTTATTTGAC
*
1539825 AAATCAACTTTATTTTAT-GATTTTTTTACT
1 AAATAAACTTTATTTTATGGATTTTTTTACT
1539855 AAATAAACTTTATTTTATGGATTTTTTTA
1 AAATAAACTTTATTTTATGGATTTTTTTA
1539884 TAAGGAGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (31 bp):
AAATAAACTTTATTTTATGGATTTTTTTACT
Found at i:1543706 original size:52 final size:51
Alignment explanation
Indices: 1543636--1543737 Score: 123
Period size: 52 Copynumber: 2.0 Consensus size: 51
1543626 TGGAAAAATC
** *
1543636 ATTATATGTGACACCACTATTCTGGATCGATGGCTCGATTGAAATAAAAACA
1 ATTATATGTGACACCACTATTCTAAACCGATGGCTCGATTGAAA-AAAAACA
* * * * *
1543688 ATTATTTGTGGCATCACTATTCTAAACCGATGGCTCGTTTGAGAAAAAAC
1 ATTATATGTGACACCACTATTCTAAACCGATGGCTCGATTGAAAAAAAAC
1543738 CACTATCAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
51 6 0.14
52 36 0.86
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (51 bp):
ATTATATGTGACACCACTATTCTAAACCGATGGCTCGATTGAAAAAAAACA
Found at i:1545632 original size:18 final size:18
Alignment explanation
Indices: 1545597--1545657 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
1545587 TTAGCATGTT
*
1545597 TAAAAATAAAACTTAAAA
1 TAAAAATAAAACTGAAAA
1545615 TAAAAATGAAAAC-GAAAA
1 TAAAAAT-AAAACTGAAAA
* *
1545633 GAAAAACAAAAACTTGAAAA
1 TAAAAA-TAAAAC-TGAAAA
*
1545653 GAAAA
1 TAAAA
1545658 GAAATAACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 21 0.58
19 5 0.14
20 10 0.28
ACGTcount: A:0.72, C:0.07, G:0.08, T:0.13
Consensus pattern (18 bp):
TAAAAATAAAACTGAAAA
Found at i:1557006 original size:20 final size:20
Alignment explanation
Indices: 1556981--1557020 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1556971 AATTTTTTTT
1556981 ATCATAACTGA-ACATATACC
1 ATCATAACTGACA-ATATACC
1557001 ATCATAACTGACAATATACC
1 ATCATAACTGACAATATACC
1557021 TACATCCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (20 bp):
ATCATAACTGACAATATACC
Found at i:1557131 original size:16 final size:16
Alignment explanation
Indices: 1557101--1557131 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1557091 TTAGAAATAA
*
1557101 ATTAAATATAAAAAAT
1 ATTAAATAAAAAAAAT
1557117 ATTAAATAAAAAAAA
1 ATTAAATAAAAAAAA
1557132 CTAAAATCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAATAAAAAAAAT
Found at i:1562571 original size:23 final size:23
Alignment explanation
Indices: 1562545--1562589 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1562535 GAACAAACAT
1562545 TAAAAGGATATAATTT-TTAAATA
1 TAAAAGGATA-AATTTATTAAATA
* *
1562568 TAAAATGTTAAATTTATTAAAT
1 TAAAAGGATAAATTTATTAAAT
1562590 TATTTTGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
TAAAAGGATAAATTTATTAAATA
Found at i:1563956 original size:22 final size:22
Alignment explanation
Indices: 1563926--1563967 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1563916 CTTGATGTTG
1563926 TGGACTTTCAAGTTCAAAGTAA
1 TGGACTTTCAAGTTCAAAGTAA
*
1563948 TGGAGTTTCAAGTTCAAAGT
1 TGGACTTTCAAGTTCAAAGT
1563968 GGTGATGGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (22 bp):
TGGACTTTCAAGTTCAAAGTAA
Found at i:1564412 original size:24 final size:24
Alignment explanation
Indices: 1564359--1564412 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1564349 AACCGGTGAA
*
1564359 CCAGTACCTTCACCGGTTTAAGGC
1 CCAGTCCCTTCACCGGTTTAAGGC
*
1564383 CCAGTCCCTTCACCGGTTTAAGGT
1 CCAGTCCCTTCACCGGTTTAAGGC
1564407 CCAGTC
1 CCAGTC
1564413 ATTGATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.35, G:0.20, T:0.26
Consensus pattern (24 bp):
CCAGTCCCTTCACCGGTTTAAGGC
Found at i:1565897 original size:16 final size:16
Alignment explanation
Indices: 1565854--1565898 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1565844 TAATAAATAA
**
1565854 ACGAACATAAAAAAAC
1 ACGAACATAAACGAAC
1565870 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1565886 ACGAACATAAACG
1 ACGAACATAAACG
1565899 TTCCTACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.60, C:0.22, G:0.11, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1566181 original size:34 final size:34
Alignment explanation
Indices: 1566105--1566182 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
1566095 CACTCGATTA
* * *
1566105 AAGCTCAATTTTGAGTTCGATTCAAGCTCAATTC
1 AAGCTCGATTTTGAGCTCGATTAAAGCTCAATTC
**
1566139 AATATCGATTTTGAGCTCGATTAAAGCTCAATTC
1 AAGCTCGATTTTGAGCTCGATTAAAGCTCAATTC
1566173 AAGCTCGATT
1 AAGCTCGATT
1566183 GACCCAATCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (34 bp):
AAGCTCGATTTTGAGCTCGATTAAAGCTCAATTC
Found at i:1566543 original size:14 final size:14
Alignment explanation
Indices: 1566526--1566581 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
1566516 AATGAACATA
1566526 AACGAACATAACCG
1 AACGAACATAACCG
1566540 AACGAACAT----G
1 AACGAACATAACCG
1566550 AACGAACATAACCG
1 AACGAACATAACCG
1566564 AACGAACATAACCG
1 AACGAACATAACCG
1566578 AACG
1 AACG
1566582 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.26
14 28 0.74
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1566546 original size:24 final size:24
Alignment explanation
Indices: 1566519--1566580 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1566509 ATAAATGAAT
1566519 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
1566543 GAACATGAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
1566567 GAACATAACCGAAC
1 GAACATAAACGAAC
1566581 GTTCACGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:1566825 original size:12 final size:12
Alignment explanation
Indices: 1566808--1566833 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1566798 AACAAAGGAA
1566808 AGGACCATATAT
1 AGGACCATATAT
1566820 AGGACCATATAT
1 AGGACCATATAT
1566832 AG
1 AG
1566834 CTTTTAACCC
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:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (12 bp):
AGGACCATATAT
Found at i:1570378 original size:19 final size:20
Alignment explanation
Indices: 1570344--1570383 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1570334 GTTCTGCTAA
1570344 CCAGTTGGACCGATCT-GAC
1 CCAGTTGGACCGATCTAGAC
* *
1570363 CCAGTTGGGCCTATCTAGAC
1 CCAGTTGGACCGATCTAGAC
1570383 C
1 C
1570384 GAACTGAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
CCAGTTGGACCGATCTAGAC
Found at i:1576927 original size:32 final size:32
Alignment explanation
Indices: 1576891--1576969 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
1576881 TCTAAGGTGA
*
1576891 CCTTGGGTAGGTTCTGAGGCCTCAAGGTATTT
1 CCTTGGGTAGGCTCTGAGGCCTCAAGGTATTT
* * **
1576923 CCTTGGGTAGGCTCTTAGGCCTTAAGGTA-AA
1 CCTTGGGTAGGCTCTGAGGCCTCAAGGTATTT
1576954 CACTTGGGTAGGCTCT
1 C-CTTGGGTAGGCTCT
1576970 CATGCCCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 1 0.02
32 40 0.98
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTGAGGCCTCAAGGTATTT
Found at i:1580000 original size:30 final size:30
Alignment explanation
Indices: 1579966--1580085 Score: 213
Period size: 30 Copynumber: 4.0 Consensus size: 30
1579956 CCTAAAGGAC
1579966 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1579996 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1580026 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1580056 CTGTCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1580086 ACTGTCCATA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 86 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1580888 original size:64 final size:63
Alignment explanation
Indices: 1580816--1580959 Score: 163
Period size: 64 Copynumber: 2.3 Consensus size: 63
1580806 CATCCCTTGA
*
1580816 CAGGTGCATCGATGCACTATCC-ATGCATCGGTGCA-TAAATCCTATTCGATGTT-TTCATTTTA
1 CAGGTGCATCGATGCAC--TCCTATGCATCGATGCACTAAATCC-ATTCGATGTTATTCA-TTTA
1580878 AG
62 AG
* * *
1580880 CAGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTCATTTATTTAAG
1 CAGGTGCATCGATGCACTCC-TATGCATCGATGCACTAAATCCATTCGATGTT-ATTCATTTAAG
1580945 -A-GTGCATCGATGCAC
1 CAGGTGCATCGATGCAC
1580960 ATTGAAGATG
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
62 3 0.04
63 14 0.20
64 40 0.56
65 11 0.15
66 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (63 bp):
CAGGTGCATCGATGCACTCCTATGCATCGATGCACTAAATCCATTCGATGTTATTCATTTAAG
Found at i:1590743 original size:14 final size:14
Alignment explanation
Indices: 1590726--1590777 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1590716 GACTCGAATG
1590726 AGTTGACTCAGTCT
1 AGTTGACTCAGTCT
* * *
1590740 AGTTTAACTCAGGCG
1 AG-TTGACTCAGTCT
1590755 AGTTGACTCAGT-T
1 AGTTGACTCAGTCT
1590768 GAGTTGACTC
1 -AGTTGACTC
1590778 GGTTCAGCCG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (14 bp):
AGTTGACTCAGTCT
Found at i:1591368 original size:2 final size:2
Alignment explanation
Indices: 1591361--1591397 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1591351 TCAACTGATT
1591361 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1591398 TCAAGAGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1593179 original size:12 final size:12
Alignment explanation
Indices: 1593162--1593186 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1593152 ACATTGGTAG
1593162 TTTAAAACATAT
1 TTTAAAACATAT
1593174 TTTAAAACATAT
1 TTTAAAACATAT
1593186 T
1 T
1593187 AATACCCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAAACATAT
Found at i:1595808 original size:14 final size:15
Alignment explanation
Indices: 1595773--1595812 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
1595763 TGACTCGGAT
1595773 GAGTTGACTCAGTTC
1 GAGTTGACTCAGTTC
1595788 G-GTTTGACTCA-TTC
1 GAG-TTGACTCAGTTC
1595802 GAGTTGACTCA
1 GAGTTGACTCA
1595813 ATTTAGATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (15 bp):
GAGTTGACTCAGTTC
Found at i:1602846 original size:24 final size:24
Alignment explanation
Indices: 1602814--1602859 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1602804 GGTGATAACA
1602814 ATTTTGTTATATTGTTGTTGTACG
1 ATTTTGTTATATTGTTGTTGTACG
1602838 ATTTTGTTATATTGTTGTTGTA
1 ATTTTGTTATATTGTTGTTGTA
1602860 TGTGGATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (24 bp):
ATTTTGTTATATTGTTGTTGTACG
Found at i:1605991 original size:2 final size:2
Alignment explanation
Indices: 1605984--1606018 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1605974 AACTTAAAAT
1605984 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1606019 TTAAAAAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1606257 original size:30 final size:33
Alignment explanation
Indices: 1606223--1606301 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
1606213 GCAAATATTT
*
1606223 CAAATGCGTTAATATT-C-C-ACGAATTGCATC
1 CAAATGCGTTAATATTCCGCAAAGAATTGCATC
1606253 CAAATGCGTTAA-ATTCCGCAAAGAATTGCATC
1 CAAATGCGTTAATATTCCGCAAAGAATTGCATC
*
1606285 CAAATGTGTTAAATATT
1 CAAATGCGTT-AATATT
1606302 TCACCCAGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 3 0.07
30 13 0.31
31 1 0.02
32 20 0.48
33 2 0.05
34 3 0.07
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (33 bp):
CAAATGCGTTAATATTCCGCAAAGAATTGCATC
Found at i:1608423 original size:21 final size:21
Alignment explanation
Indices: 1608393--1608455 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1608383 ATATAAAATT
*
1608393 TGTCCCGAATGACCTCATGTA
1 TGTCCCGAATGACCTCATATA
*
1608414 TGTCCAGAATGACCTCATATA
1 TGTCCCGAATGACCTCATATA
*
1608435 TGTCCCGAAGGACCTCATATA
1 TGTCCCGAATGACCTCATATA
1608456 ACCCTGGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
TGTCCCGAATGACCTCATATA
Found at i:1616456 original size:21 final size:21
Alignment explanation
Indices: 1616431--1616483 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1616421 TTGTCCCGGG
*
1616431 GACCTCATGTATGTCCAGAAA
1 GACCTCATATATGTCCAGAAA
* * *
1616452 GACCTCGTATATGTCCCGAAG
1 GACCTCATATATGTCCAGAAA
*
1616473 GACCTCCTATA
1 GACCTCATATA
1616484 ACCCTCGACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (21 bp):
GACCTCATATATGTCCAGAAA
Found at i:1619003 original size:16 final size:17
Alignment explanation
Indices: 1618972--1619004 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1618962 GATGTCAAAA
1618972 AAAAATATGACTTTTTG
1 AAAAATATGACTTTTTG
*
1618989 AAAAATTTGACTTTTT
1 AAAAATATGACTTTTT
1619005 AGTCAAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (17 bp):
AAAAATATGACTTTTTG
Found at i:1619082 original size:15 final size:15
Alignment explanation
Indices: 1619060--1619100 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1619050 ATCAACGGTT
1619060 AAAGTCTAAACTCAA
1 AAAGTCTAAACTCAA
** *
1619075 CGAGTCTAAACTTAA
1 AAAGTCTAAACTCAA
1619090 AAAGTCTAAAC
1 AAAGTCTAAAC
1619101 ATTTTAGTCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.22
Consensus pattern (15 bp):
AAAGTCTAAACTCAA
Found at i:1624421 original size:81 final size:82
Alignment explanation
Indices: 1624320--1624472 Score: 272
Period size: 81 Copynumber: 1.9 Consensus size: 82
1624310 TCACAAATAT
1624320 AATTTCAGTGATATTATGTGTTTCATTCAGGATTTAGAATTATAGGTTTTATAATTTAAAATGTA
1 AATTTCAGTGATATTATGTGTTTCATTCAGGATTTAGAATTATAGGTTTTATAATTTAAAATGTA
*
1624385 TGTTTCACTAAAATTAA
66 TGATTCACTAAAATTAA
* *
1624402 AATTT-AGTGATATTGTGTGTTTCATTCAGGATTTAGAATTATAGGTTTTATAATTTAAAATTTA
1 AATTTCAGTGATATTATGTGTTTCATTCAGGATTTAGAATTATAGGTTTTATAATTTAAAATGTA
1624466 TGATTCA
66 TGATTCA
1624473 AGATTTAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
81 63 0.93
82 5 0.07
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.46
Consensus pattern (82 bp):
AATTTCAGTGATATTATGTGTTTCATTCAGGATTTAGAATTATAGGTTTTATAATTTAAAATGTA
TGATTCACTAAAATTAA
Found at i:1627547 original size:60 final size:56
Alignment explanation
Indices: 1627393--1627553 Score: 160
Period size: 60 Copynumber: 2.8 Consensus size: 56
1627383 ATAGTTTGGG
* * * * ** *
1627393 ATAAAATTGGAATATTCAAAACGTTTGGGGACCAATTTGGAATGGTTATAGTTTGGGG
1 ATAAAATTGAAATATTCAAAA-GTTT-GGGACCAATTTGAAATAGTAATAGTTTAAGA
* * *
1627451 ATGAAATTGAAATACTCAAAAGTTTGAGGACTAATTTAGAATACTAGTAATAGTTTAAGA
1 ATAAAATTGAAATATTCAAAAGTTTG-GGACCAATTT-GAA-A-TAGTAATAGTTTAAGA
*
1627511 ATAAAATTGAAATATTTAAAAGTTTAGGGACCAATTTGAAATA
1 ATAAAATTGAAATATTCAAAAGTTT-GGGACCAATTTGAAATA
1627554 AAAGTCATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
56 1 0.01
57 15 0.18
58 21 0.25
59 4 0.05
60 42 0.50
61 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (56 bp):
ATAAAATTGAAATATTCAAAAGTTTGGGACCAATTTGAAATAGTAATAGTTTAAGA
Found at i:1633652 original size:213 final size:214
Alignment explanation
Indices: 1633285--1633712 Score: 849
Period size: 213 Copynumber: 2.0 Consensus size: 214
1633275 TGCTCGATTC
1633285 TTGATGCAGAGTTCTAGGATATCTACAAGGAAGTTGGAACTCTTTCCGCGACTAGTTAGGAAAGA
1 TTGATGCAGAGTTCTAGGATATCTACAAGGAAGTTGGAACTCTTTCCGCGACTAGTTAGGAAAGA
1633350 AACCAAGAGGGGACTCATCTTTGATGGTACACATAATAGACCTTACTAGACGTTGTTGGAATTTG
66 AACCAAGAGGGGACTCATCTTTGATGGTACACATAATAGACCTTACTAGACGTTGTTGGAATTTG
1633415 GATGTTGTTTACATCTCTCGAGAGTGTAACAAGGTTGTGGATGGTATGTCTAAACTTGCTT-GGC
131 GATGTTGTTTACATCTCTCGAGAGTGTAACAAGGTTGTGGATGGTATGTCTAAACTTGCTTGGGC
1633479 TCTTCCGGTCGGATTCCTT
196 TCTTCCGGTCGGATTCCTT
1633498 TTGATGCAGAGTTCTAGGATATCTACAAGGAAGTTGGAACTCTTTCCGCGACTAGTTAGGAAAGA
1 TTGATGCAGAGTTCTAGGATATCTACAAGGAAGTTGGAACTCTTTCCGCGACTAGTTAGGAAAGA
1633563 AACCAAGAGGGGACTCATCTTTGATGGTACACATAATAGACCTTACTAGACGTTGTTGGAATTTG
66 AACCAAGAGGGGACTCATCTTTGATGGTACACATAATAGACCTTACTAGACGTTGTTGGAATTTG
1633628 GATGTTGTTTACATCTCTCGAGAGTGTAACAAGGTTGTGGATGGTATGTCTAAACTTGCTTGGGC
131 GATGTTGTTTACATCTCTCGAGAGTGTAACAAGGTTGTGGATGGTATGTCTAAACTTGCTTGGGC
1633693 TCTTCCGGTCGGATTCCTT
196 TCTTCCGGTCGGATTCCTT
1633712 T
1 T
1633713 CTTTCCACGC
Statistics
Matches: 214, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
213 191 0.89
214 23 0.11
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (214 bp):
TTGATGCAGAGTTCTAGGATATCTACAAGGAAGTTGGAACTCTTTCCGCGACTAGTTAGGAAAGA
AACCAAGAGGGGACTCATCTTTGATGGTACACATAATAGACCTTACTAGACGTTGTTGGAATTTG
GATGTTGTTTACATCTCTCGAGAGTGTAACAAGGTTGTGGATGGTATGTCTAAACTTGCTTGGGC
TCTTCCGGTCGGATTCCTT
Found at i:1634400 original size:23 final size:21
Alignment explanation
Indices: 1634373--1634427 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
1634363 TAGTCTAATA
1634373 ATATTATAAAAATTTATTAAAAT
1 ATATTATAAAAA-TT-TTAAAAT
*
1634396 ATATTTATTAATAATTTTAAAAT
1 ATA-TTA-TAAAAATTTTAAAAT
*
1634419 ATAATATAA
1 ATATTATAA
1634428 TATTTTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 2 0.07
23 13 0.46
24 5 0.18
25 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTATAAAAATTTTAAAAT
Found at i:1634428 original size:21 final size:23
Alignment explanation
Indices: 1634389--1634435 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
1634379 TAAAAATTTA
*
1634389 TTAAAATATATTTATTAATAATT
1 TTAAAATATATATATTAATAATT
*
1634412 TTAAAATATA-ATA-TAATATTT
1 TTAAAATATATATATTAATAATT
1634433 TTA
1 TTA
1634436 GTGTTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 2 0.09
23 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAAATATATATATTAATAATT
Found at i:1635389 original size:22 final size:22
Alignment explanation
Indices: 1635364--1635425 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
1635354 ACATCCGTCT
1635364 CCATCTCCGACGAAATCAGTCC
1 CCATCTCCGACGAAATCAGTCC
* *
1635386 CCATCTCCGACGATATCAGTCT
1 CCATCTCCGACGAAATCAGTCC
*
1635408 CCATCTCCGGCGAAATCA
1 CCATCTCCGACGAAATCA
1635426 TTCACGGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.26, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCC
Found at i:1635848 original size:20 final size:20
Alignment explanation
Indices: 1635823--1635862 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1635813 GTTACGATAG
* *
1635823 TCATTTTCTTGTTGTGATTT
1 TCATTTTCGTGTTGCGATTT
1635843 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
1635863 AAAGTTTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.12, G:0.17, T:0.60
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:1637771 original size:20 final size:20
Alignment explanation
Indices: 1637746--1637795 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1637736 AGAATAGTTT
1637746 ACTATCGCAATGAGAAAATG
1 ACTATCGCAATGAGAAAATG
* **
1637766 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGAGAAAATG
1637786 ACTATCGCAA
1 ACTATCGCAA
1637796 CGAAAGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
ACTATCGCAATGAGAAAATG
Found at i:1637933 original size:60 final size:60
Alignment explanation
Indices: 1637840--1637968 Score: 222
Period size: 60 Copynumber: 2.1 Consensus size: 60
1637830 GCGATTCTCT
*
1637840 CGTTGCGATAGTCAAATTCGTATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
**
1637900 CGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
*
1637960 TGTTGCGAT
1 CGTTGCGAT
1637969 TTTAAGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (60 bp):
CGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
Found at i:1637968 original size:20 final size:20
Alignment explanation
Indices: 1637842--1637959 Score: 200
Period size: 20 Copynumber: 5.9 Consensus size: 20
1637832 GATTCTCTCG
** *
1637842 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCA
1637862 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1637882 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1637902 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1637922 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1637942 TTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCG
1637960 TGTTGCGATT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 93 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1639955 original size:14 final size:14
Alignment explanation
Indices: 1639936--1639971 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1639926 ATTGTTTAAT
1639936 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1639950 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1639964 TGATTTGT
1 TGATTTGT
1639972 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1640190 original size:14 final size:14
Alignment explanation
Indices: 1640171--1640238 Score: 82
Period size: 14 Copynumber: 4.5 Consensus size: 14
1640161 CATTTTCGCA
1640171 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
1640185 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1640199 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1640216 TATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1640232 TTGCGAT
1 TTGCGAT
1640239 AGTCATTTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
14 27 0.57
16 7 0.15
17 7 0.15
19 6 0.13
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.46
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1640227 original size:33 final size:33
Alignment explanation
Indices: 1640185--1640247 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1640175 GATTCTCTCG
**
1640185 TTGCGATTCTCTCGTTGCGATTTTCATTTCGTA
1 TTGCGATTCTCTCGTTGCGATAGTCATTTCGTA
1640218 TTGCGATTCTCTCGTTGCGATAGTCATTTC
1 TTGCGATTCTCTCGTTGCGATAGTCATTTC
1640248 CGCGTTGCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATAGTCATTTCGTA
Found at i:1640255 original size:20 final size:20
Alignment explanation
Indices: 1640230--1640318 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
1640220 GCGATTCTCT
1640230 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1640250 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
1640270 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1640290 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
1640310 CATTGCGAT
1 CGTTGCGAT
1640319 TTCCGCGTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 61 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1642783 original size:24 final size:24
Alignment explanation
Indices: 1642749--1642802 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1642739 CTGAAAAATC
1642749 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1642773 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1642797 ATCAAA
1 ATCAAA
1642803 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1642816 original size:24 final size:24
Alignment explanation
Indices: 1642749--1642816 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1642739 CTGAAAAATC
* * *
1642749 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1642773 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1642797 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1642817 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1643670 original size:20 final size:20
Alignment explanation
Indices: 1643645--1643711 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1643635 AAATTCAGTA
1643645 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
1643665 TTGCGATAGTCATAATCTCA
1 TTGCGATAGTCAGAATCTCG
* *
1643685 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
1643705 TTGCGAT
1 TTGCGAT
1643712 TTACATATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:1643727 original size:40 final size:40
Alignment explanation
Indices: 1643644--1643731 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
1643634 GAAATTCAGT
* *
1643644 ATTGCGATAGTCAGAATCTCGTTGCGATAGTCATAATCTC
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGC
* * *
1643684 ATTGCGATAGTCAGATTCGCGTTGCGAT-TTACATATTCGC
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGT-CATAATCGC
1643724 ATTGCGAT
1 ATTGCGAT
1643732 TTAGGAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.98
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (40 bp):
ATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGC
Found at i:1643751 original size:21 final size:20
Alignment explanation
Indices: 1643727--1643773 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
1643717 TATTCGCATT
1643727 GCGATTTAGGAAAATCGCAAC
1 GCGATTT-GGAAAATCGCAAC
*
1643748 GCGAATTTGGAAAATCGCAAT
1 GCG-ATTTGGAAAATCGCAAC
1643769 GCGAT
1 GCGAT
1643774 AGTCAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (20 bp):
GCGATTTGGAAAATCGCAAC
Found at i:1648247 original size:3 final size:3
Alignment explanation
Indices: 1648236--1648274 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
1648226 TTTAATAATA
1648236 ATT ATTT ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT A
1648275 GTGGACAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1652237 original size:2 final size:2
Alignment explanation
Indices: 1652230--1652283 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1652220 AAATCAAATA
1652230 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
1652272 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
1652284 AAACCCTACC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1653646 original size:17 final size:17
Alignment explanation
Indices: 1653624--1653657 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1653614 ATATTTGGAT
*
1653624 AAAAAATGAAAAAATTA
1 AAAAAATCAAAAAATTA
*
1653641 AAAAAATCAATAAATTA
1 AAAAAATCAAAAAATTA
1653658 CGAAGAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAAATCAAAAAATTA
Found at i:1661550 original size:16 final size:16
Alignment explanation
Indices: 1661529--1661562 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1661519 AACAAACAGA
1661529 AGATAACTGAAGGTAC
1 AGATAACTGAAGGTAC
*
1661545 AGATAACTTAAGGTAC
1 AGATAACTGAAGGTAC
1661561 AG
1 AG
1661563 TCACCTGAGA
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:0.44, C:0.12, G:0.24, T:0.21
Consensus pattern (16 bp):
AGATAACTGAAGGTAC
Found at i:1667379 original size:12 final size:12
Alignment explanation
Indices: 1667362--1667391 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1667352 TAGGACCATT
1667362 AGTTTTACATCA
1 AGTTTTACATCA
*
1667374 AGTTTTACATTA
1 AGTTTTACATCA
1667386 AGTTTT
1 AGTTTT
1667392 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:1672222 original size:1 final size:1
Alignment explanation
Indices: 1672216--1672246 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1672206 TCTTTCATTG
*
1672216 AAAAAAAAGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1672247 GAAGCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1672302 original size:28 final size:28
Alignment explanation
Indices: 1672239--1672302 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
1672229 AAAAAAAAAA
1672239 AAAAAAAAGAAGCAAAATTGTGCAAATG
1 AAAAAAAAGAAGCAAAATTGTGCAAATG
* *
1672267 -AAATAAAGAAAG-AGAGATTGTGC-AATG
1 AAAAAAAAG-AAGCA-AAATTGTGCAAATG
1672294 AAAAAAAAG
1 AAAAAAAAG
1672303 TTATATGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.61, C:0.05, G:0.20, T:0.14
Consensus pattern (28 bp):
AAAAAAAAGAAGCAAAATTGTGCAAATG
Found at i:1673505 original size:8 final size:9
Alignment explanation
Indices: 1673479--1673517 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
1673469 TTTTAAAAAC
1673479 ACACTTAAA
1 ACACTTAAA
1673488 ACACTTAAA
1 ACACTTAAA
1673497 ACA-TTAAA
1 ACACTTAAA
1673505 ACACTTAAA
1 ACACTTAAA
1673514 ACAC
1 ACAC
1673518 ACTTCTCCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (9 bp):
ACACTTAAA
Found at i:1673505 original size:17 final size:17
Alignment explanation
Indices: 1673483--1673516 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1673473 AAAAACACAC
1673483 TTAAAACACTTAAAACA
1 TTAAAACACTTAAAACA
1673500 TTAAAACACTTAAAACA
1 TTAAAACACTTAAAACA
1673517 CACTTCTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TTAAAACACTTAAAACA
Found at i:1675798 original size:21 final size:20
Alignment explanation
Indices: 1675772--1675832 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 20
1675762 CAGAACCCCA
1675772 GGGGGGTATCGATTCCCCTGT
1 GGGGGGTATC-ATTCCCCTGT
1675793 GGGGGGTATCAATTCCCCTGT
1 GGGGGGTATC-ATTCCCCTGT
*
1675814 GGGGGGAATCAGTTCCCCT
1 GGGGGGTATCA-TTCCCCT
1675833 TCAAAGGGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.13, C:0.25, G:0.36, T:0.26
Consensus pattern (20 bp):
GGGGGGTATCATTCCCCTGT
Found at i:1679727 original size:22 final size:21
Alignment explanation
Indices: 1679685--1679724 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1679675 GTTTTTTTTT
*
1679685 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1679706 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1679725 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1682959 original size:12 final size:12
Alignment explanation
Indices: 1682942--1682971 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1682932 TAGAGCCATT
1682942 AGTTTTACATCA
1 AGTTTTACATCA
*
1682954 AGTTTTACATTA
1 AGTTTTACATCA
1682966 AGTTTT
1 AGTTTT
1682972 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:1685050 original size:21 final size:21
Alignment explanation
Indices: 1684990--1685041 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1684980 CATAGAGTAT
** *
1684990 GTTCACATCCACTAATTCAAA
1 GTTCACATTTACTGATTCAAA
*
1685011 GTTCATATTTACTGATTCAAA
1 GTTCACATTTACTGATTCAAA
1685032 GTTCACATTT
1 GTTCACATTT
1685042 CCATATTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (21 bp):
GTTCACATTTACTGATTCAAA
Found at i:1685518 original size:54 final size:54
Alignment explanation
Indices: 1685435--1685565 Score: 165
Period size: 54 Copynumber: 2.4 Consensus size: 54
1685425 GATATTTCCC
* ** *
1685435 TTTAAGGGTAT-ATATACCTCCTCATGGTACCGATACTGATATAACATTTGATGT
1 TTTAAGGGTATCA-ATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGT
* * **
1685489 TTTAAGGGTATCGATACCTCCTCAAGGTACTGATACCAATATGGCATTCGATGT
1 TTTAAGGGTATCAATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGT
1685543 TTTAAGGGTATCAATACCATCCT
1 TTTAAGGGTATCAATACC-TCCT
1685566 TCAGGTATCT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
54 62 0.94
55 4 0.06
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (54 bp):
TTTAAGGGTATCAATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGT
Found at i:1685586 original size:20 final size:21
Alignment explanation
Indices: 1685549--1685600 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
1685539 ATGTTTTAAG
*
1685549 GGTATCAATACCATCCTT-CA
1 GGTATCAATACCAACCTTACA
* *
1685569 GGTATCTATACTAACCTTACA
1 GGTATCAATACCAACCTTACA
*
1685590 -GTATCGATACC
1 GGTATCAATACC
1685601 TCTTCAACAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (21 bp):
GGTATCAATACCAACCTTACA
Found at i:1690726 original size:23 final size:23
Alignment explanation
Indices: 1690665--1690775 Score: 131
Period size: 23 Copynumber: 4.9 Consensus size: 23
1690655 AAACTCGTAA
1690665 TTTGCACTGAAGTGCCACATA--
1 TTTGCACTGAAGTGCCACATAGG
* *
1690686 ATTGTC-TTGAAG-GACCACATAGG
1 TTTG-CACTGAAGTG-CCACATAGG
1690709 TTTGCACTGAAGTGCCACATAGG
1 TTTGCACTGAAGTGCCACATAGG
*
1690732 TTTGCACCGAAGTGCCACATAGG
1 TTTGCACTGAAGTGCCACATAGG
**
1690755 TTTGCACCAAAGTGCCACATA
1 TTTGCACTGAAGTGCCACATA
1690776 TTTATCCCGA
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.01
21 15 0.19
22 2 0.03
23 59 0.76
24 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
TTTGCACTGAAGTGCCACATAGG
Found at i:1690795 original size:21 final size:21
Alignment explanation
Indices: 1690769--1690818 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1690759 CACCAAAGTG
*
1690769 CCACATATTTATCCCGAAAGA
1 CCACATAATTATCCCGAAAGA
*
1690790 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAAAGA
1690811 CCACATAA
1 CCACATAA
1690819 AACCCTCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.30, G:0.08, T:0.22
Consensus pattern (21 bp):
CCACATAATTATCCCGAAAGA
Found at i:1691461 original size:54 final size:54
Alignment explanation
Indices: 1691373--1691498 Score: 171
Period size: 54 Copynumber: 2.3 Consensus size: 54
1691363 GATACTTCCC
* * *
1691373 TTCAAGGGTATCGATACCTCCTCATGGTACCGATACCGATATAACATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGATACCGATACCAATATAACATTCGATGT
* * * **
1691427 TTCAAGGGTATCGATACCTCCTCAAGATATCGATATCAATCTGGCATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGATACCGATACCAATATAACATTCGATGT
*
1691481 TTTAAGGGTATCGATACC
1 TTCAAGGGTATCGATACC
1691499 ATCTTTCAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGATACCGATACCAATATAACATTCGATGT
Found at i:1691531 original size:20 final size:20
Alignment explanation
Indices: 1691508--1691557 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1691498 CATCTTTCAG
1691508 GTATCGATACTAACCTTACA
1 GTATCGATACTAACCTTACA
*
1691528 GTATCAATACTAACCTTACA
1 GTATCGATACTAACCTTACA
1691548 GTATCGATAC
1 GTATCGATAC
1691558 CTCTTCAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (20 bp):
GTATCGATACTAACCTTACA
Found at i:1710888 original size:14 final size:14
Alignment explanation
Indices: 1710871--1710915 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1710861 TATTACACCC
*
1710871 TAAACCCTACACTA
1 TAAACCCTAAACTA
**
1710885 TAAACTATAAACTA
1 TAAACCCTAAACTA
*
1710899 TAAACCCTAAATTA
1 TAAACCCTAAACTA
1710913 TAA
1 TAA
1710916 GTCATAAACC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:1710909 original size:21 final size:21
Alignment explanation
Indices: 1710885--1710932 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1710875 CCCTACACTA
1710885 TAAACTATAAACT-ATAAACCC
1 TAAACTAT-AACTCATAAACCC
* *
1710906 TAAATTATAAGTCATAAACCC
1 TAAACTATAACTCATAAACCC
1710927 TAAACT
1 TAAACT
1710933 CTTAATCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAACTATAACTCATAAACCC
Found at i:1711045 original size:21 final size:21
Alignment explanation
Indices: 1711016--1711063 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1711006 CCTAAACCCT
1711016 TAAACCCTAAACTAT-AAACCA
1 TAAACCCTAAA-TATCAAACCA
* *
1711037 TAAATCCTAAATATCAAACCC
1 TAAACCCTAAATATCAAACCA
1711058 TAAACC
1 TAAACC
1711064 GTATGACGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAATATCAAACCA
Found at i:1712155 original size:11 final size:11
Alignment explanation
Indices: 1712135--1712186 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
1712125 CGTGGTGAGC
*
1712135 ATCGAACTTAA
1 ATCGAGCTTAA
1712146 ATCGAGCTTAA
1 ATCGAGCTTAA
1712157 AT-GAGCTTAA
1 ATCGAGCTTAA
* *
1712167 ATTGAGCTTTGA
1 ATCGAGC-TTAA
1712179 ATCGAGCT
1 ATCGAGCT
1712187 AGAATTAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 10 0.28
11 17 0.47
12 9 0.25
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (11 bp):
ATCGAGCTTAA
Found at i:1713157 original size:31 final size:30
Alignment explanation
Indices: 1713111--1713190 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
1713101 CTTGATAATA
*
1713111 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
1713142 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
1713173 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
1713191 TTTTAAACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.86
32 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:1713158 original size:20 final size:20
Alignment explanation
Indices: 1713135--1713197 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
1713125 TAGTATTTAG
1713135 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
1713155 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
1713175 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
1713194 -TAAA
1 ATAAA
1713198 CTTTATTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.09
19 13 0.37
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:1713168 original size:19 final size:20
Alignment explanation
Indices: 1713144--1713193 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1713134 GATAAATTTA
*
1713144 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
1713163 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
1713184 TT-ATAATTTT
1 TTAATAATTTT
1713194 TAAACTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:1713956 original size:31 final size:29
Alignment explanation
Indices: 1713912--1713997 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 29
1713902 CAATAAAGTT
1713912 TTAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAATTATAAAATA-TTATTAAATTTA
*
1713942 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAA-ATTATAAAA-TATTATTAAATTTA
* *
1713973 TTTAAATACTATAAAATAATTATTA
1 -TTAAAAATTATAAAAT-ATTATTA
1713998 TATTATTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
30 7 0.15
31 34 0.71
32 7 0.15
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (29 bp):
TTAAAAATTATAAAATATTATTAAATTTA
Found at i:1718364 original size:4 final size:4
Alignment explanation
Indices: 1718357--1718395 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
1718347 TATATATATT
*
1718357 TTTA TTTA -TAA TATTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTT
1718396 GCATTGATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 26 0.84
5 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:1718376 original size:16 final size:16
Alignment explanation
Indices: 1718347--1718395 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1718337 TCAAGGAATA
1718347 TATATATATT-TTTATT
1 TATA-ATATTATTTATT
1718363 TATAATATTATTTATT
1 TATAATATTATTTATT
*
1718379 TAT-TTATTTATTTATT
1 TATAATA-TTATTTATT
1718395 T
1 T
1718396 GCATTGATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 7 0.23
16 23 0.77
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATAATATTATTTATT
Found at i:1718766 original size:16 final size:16
Alignment explanation
Indices: 1718745--1718784 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
1718735 AGAAAAATTC
1718745 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
*
1718761 AATTTAATTTTAAAAT
1 AATTTAAATTTAAAAT
1718777 AATATTAA
1 AAT-TTAA
1718785 TAAATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:1721327 original size:20 final size:20
Alignment explanation
Indices: 1721283--1721462 Score: 73
Period size: 20 Copynumber: 8.8 Consensus size: 20
1721273 AATGACCAAT
* *
1721283 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1721302 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* ** ***
1721322 AAAATCACAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1721342 AAAATCGCAA--CGATCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1721362 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1721383 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
*
1721406 AAAATCGCAATGCG-TTT-G
1 AAAATCGCAACGCGATTTAG
* *
1721424 ATAGAATCGCAATGCGATTGAG
1 A-A-AATCGCAACGCGATTTAG
* *
1721446 AGAGTCGCAACGCGATT
1 AAAATCGCAACGCGATT
1721463 GACGTTGAAA
Statistics
Matches: 119, Mismatches: 29, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
18 3 0.03
19 18 0.15
20 64 0.54
21 15 0.13
22 8 0.07
23 11 0.09
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1721463 original size:20 final size:20
Alignment explanation
Indices: 1721387--1721464 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
1721377 GCTTCCAAGT
*
1721387 TCGCAACGCGATTTAGAAGAAAA
1 TCGCAACGCGA-TT-G-AGAGAA
* * *
1721410 TCGCAATGCGTTTGATAGAA
1 TCGCAACGCGATTGAGAGAA
* *
1721430 TCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTGAGAGAA
1721450 TCGCAACGCGATTGA
1 TCGCAACGCGATTGA
1721465 CGTTGAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 35 0.74
21 1 0.02
22 2 0.04
23 9 0.19
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGATTGAGAGAA
Found at i:1721544 original size:6 final size:6
Alignment explanation
Indices: 1721533--1721569 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1721523 GAAGACACGT
1721533 ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC A
1721570 CGACCACGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:1721575 original size:6 final size:6
Alignment explanation
Indices: 1721566--1721607 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1721556 CATTACCATT
1721566 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1721608 CGAGACGACG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1721575 original size:12 final size:12
Alignment explanation
Indices: 1721536--1721587 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
1721526 GACACGTATT
**
1721536 ACCATTACCATT
1 ACCATTACCACG
**
1721548 ACCATTACCATT
1 ACCATTACCACG
1721560 ACCATTACCACG
1 ACCATTACCACG
**
1721572 ACCACGACCACG
1 ACCATTACCACG
1721584 ACCA
1 ACCA
1721588 CGACCCGACC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.35, C:0.40, G:0.06, T:0.19
Consensus pattern (12 bp):
ACCATTACCACG
Found at i:1721575 original size:18 final size:18
Alignment explanation
Indices: 1721536--1721575 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1721526 GACACGTATT
**
1721536 ACCATTACCATTACCATT
1 ACCATTACCATTACCACG
1721554 ACCATTACCATTACCACG
1 ACCATTACCATTACCACG
1721572 ACCA
1 ACCA
1721576 CGACCACGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.38, G:0.03, T:0.25
Consensus pattern (18 bp):
ACCATTACCATTACCACG
Found at i:1721598 original size:5 final size:5
Alignment explanation
Indices: 1721570--1721610 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
1721560 ACCATTACCA
1721570 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
1721611 GACGACGGCG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:1721616 original size:15 final size:16
Alignment explanation
Indices: 1721566--1721616 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
1721556 CATTACCATT
1721566 ACCACGACCACGACCACG
1 ACCACGACC-CGA-CACG
*
1721584 ACCACGACCCGACCCG
1 ACCACGACCCGACACG
*
1721600 ACC-CGACCCGAGACG
1 ACCACGACCCGACACG
1721615 AC
1 AC
1721617 GGCGGCGGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 12 0.40
16 6 0.20
17 3 0.10
18 9 0.30
ACGTcount: A:0.29, C:0.51, G:0.20, T:0.00
Consensus pattern (16 bp):
ACCACGACCCGACACG
Found at i:1723115 original size:46 final size:46
Alignment explanation
Indices: 1723048--1723137 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
1723038 ATGATTTAAA
* ** *
1723048 ACTGATTGATTTAGTAAAACAGTGTTGACTGATTTAGCAAAACAGT
1 ACTGACTGATTTAGTAAAACAGTACTGACTGATTCAGCAAAACAGT
1723094 ACTGACTGATTTAGTAAAACAGTACTGACTGATTCAGCAAAACA
1 ACTGACTGATTTAGTAAAACAGTACTGACTGATTCAGCAAAACA
1723138 ATATTGAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (46 bp):
ACTGACTGATTTAGTAAAACAGTACTGACTGATTCAGCAAAACAGT
Found at i:1723150 original size:46 final size:46
Alignment explanation
Indices: 1723048--1723150 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 46
1723038 ATGATTTAAA
* ** * *
1723048 ACTGATTGATTTAGTAAAACAGTGTTGACTGATTTAGCAAAACAGT
1 ACTGAATGATTTAGTAAAACAGTACTGACTGATTCAGCAAAACAAT
*
1723094 ACTGACTGATTTAGTAAAACAGTACTGACTGATTCAGCAAAACAAT
1 ACTGAATGATTTAGTAAAACAGTACTGACTGATTCAGCAAAACAAT
*
1723140 ATTGAATGATT
1 ACTGAATGATT
1723151 CAGGTGATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (46 bp):
ACTGAATGATTTAGTAAAACAGTACTGACTGATTCAGCAAAACAAT
Found at i:1723153 original size:23 final size:23
Alignment explanation
Indices: 1723048--1723137 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
1723038 ATGATTTAAA
* *
1723048 ACTGATTGATTTAGTAAAACAGT
1 ACTGACTGATTTAGCAAAACAGT
**
1723071 GTTGACTGATTTAGCAAAACAGT
1 ACTGACTGATTTAGCAAAACAGT
*
1723094 ACTGACTGATTTAGTAAAACAGT
1 ACTGACTGATTTAGCAAAACAGT
*
1723117 ACTGACTGATTCAGCAAAACA
1 ACTGACTGATTTAGCAAAACA
1723138 ATATTGAATG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (23 bp):
ACTGACTGATTTAGCAAAACAGT
Found at i:1723324 original size:13 final size:13
Alignment explanation
Indices: 1723308--1723347 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1723298 TTGATGTAAG
1723308 TTTTTCTCTTTTA
1 TTTTTCTCTTTTA
1723321 TTTTTCTCTTTTA
1 TTTTTCTCTTTTA
*
1723334 TTTTTCTCATTTA
1 TTTTTCTCTTTTA
1723347 T
1 T
1723348 GAATTTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTCTCTTTTA
Found at i:1723629 original size:24 final size:25
Alignment explanation
Indices: 1723572--1723632 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1723562 TTTTAAATAA
1723572 AAGT-TTAA-TTAAGATAAAACTTT
1 AAGTATTAATTTAAGATAAAACTTT
* * *
1723595 TATTATCTAATTTAATAT-AAACTTT
1 AAGTAT-TAATTTAAGATAAAACTTT
1723620 AAGTATTAATTTA
1 AAGTATTAATTTA
1723633 TATTACTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
23 2 0.07
24 8 0.27
25 14 0.47
26 6 0.20
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (25 bp):
AAGTATTAATTTAAGATAAAACTTT
Found at i:1724918 original size:12 final size:12
Alignment explanation
Indices: 1724903--1724933 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1724893 GTTATTTAAA
1724903 CGGGTATCGGGC
1 CGGGTATCGGGC
*
1724915 CGGGTATCGGGT
1 CGGGTATCGGGC
1724927 CGGGTAT
1 CGGGTAT
1724934 ATATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:1724994 original size:32 final size:34
Alignment explanation
Indices: 1724931--1725005 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
1724921 TCGGGTCGGG
1724931 TATATATA-TTTAAATTAAATATATAAATATT-A
1 TATATATATTTTAAATTAAATATATAAATATTAA
*
1724963 TATATATATTTTAAATTAAAT-TA-AATTTATTAA
1 TATATATATTTTAAATTAAATATATAA-ATATTAA
1724996 TATTATATAT
1 TA-TATATAT
1725006 ATAATAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
31 2 0.05
32 14 0.37
33 15 0.39
34 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATATATTTTAAATTAAATATATAAATATTAA
Found at i:1725145 original size:36 final size:35
Alignment explanation
Indices: 1725068--1725150 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 35
1725058 TAAACCCGTC
* *
1725068 CCCGTCTCCGTCCCCGTTTAACATAAACGGGTTTT
1 CCCGTCCCCGTCCCCGTTTAACATAAACAGGTTTT
**
1725103 CTCCGTCCCCGTCCCCGTTTAACATAAACAATTTTTT
1 C-CCGTCCCCGTCCCCGTTTAACATAAAC-AGGTTTT
1725140 CCCGTCCCCGT
1 CCCGTCCCCGT
1725151 TTAATTCGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.02
36 36 0.86
37 5 0.12
ACGTcount: A:0.17, C:0.39, G:0.13, T:0.31
Consensus pattern (35 bp):
CCCGTCCCCGTCCCCGTTTAACATAAACAGGTTTT
Found at i:1730204 original size:23 final size:23
Alignment explanation
Indices: 1730142--1730240 Score: 98
Period size: 23 Copynumber: 4.3 Consensus size: 23
1730132 GAGTCGAGGG
**
1730142 TTCTACGTGGTCCTTCAAGACAAT
1 TTCTACGTGGTCCTTCGGGAC-AT
1730166 TT-TACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
1730188 TTCTACGCGGTCCTTCGGGACA-
1 TTCTACGTGGTCCTTCGGGACAT
*
1730210 TTCTATGTGG-CACTTCGGTG-CAAT
1 TTCTACGTGGTC-CTTCGG-GAC-AT
1730234 TTCTACG
1 TTCTACG
1730241 CGGCACTTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.02
22 19 0.30
23 36 0.56
24 8 0.12
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:1730245 original size:24 final size:23
Alignment explanation
Indices: 1730177--1730249 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 23
1730167 TTACGTGGTC
1730177 CTTCGGGACATTTCTACGCGGTC-
1 CTTCGGGACATTTCTACGCGG-CA
* *
1730200 CTTCGGGACA-TTCTATGTGGCA
1 CTTCGGGACATTTCTACGCGGCA
1730222 CTTCGGTG-CAATTTCTACGCGGCA
1 CTTCGG-GAC-ATTTCTACGCGGCA
1730246 CTTC
1 CTTC
1730250 AACACATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.02
22 15 0.36
23 12 0.29
24 14 0.33
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.32
Consensus pattern (23 bp):
CTTCGGGACATTTCTACGCGGCA
Found at i:1733187 original size:36 final size:37
Alignment explanation
Indices: 1733132--1733207 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
1733122 CATGTGTTTG
* *
1733132 ATATGAGTATTTGTGATATATGCTAT-TGTATATGTT
1 ATATGAGTATTTGTGATATATGCTATGTGAATATGAT
* *
1733168 ATATGATTA-TTGTGAATATATGTTATGTGAATATGAT
1 ATATGAGTATTTGTG-ATATATGCTATGTGAATATGAT
1733205 ATA
1 ATA
1733208 AACCATGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 5 0.15
36 18 0.53
37 11 0.32
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.47
Consensus pattern (37 bp):
ATATGAGTATTTGTGATATATGCTATGTGAATATGAT
Found at i:1733196 original size:15 final size:17
Alignment explanation
Indices: 1733167--1733201 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
1733157 TTGTATATGT
1733167 TATATGATTATTGTGAA
1 TATATGATTATTGTGAA
1733184 TATATG-TTA-TGTGAA
1 TATATGATTATTGTGAA
1733199 TAT
1 TAT
1733202 GATATAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 3 0.17
17 6 0.33
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (17 bp):
TATATGATTATTGTGAA
Found at i:1733241 original size:2 final size:2
Alignment explanation
Indices: 1733234--1733274 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1733224 ACTATGTGAC
*
1733234 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1733275 ATGGTATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1733427 original size:15 final size:15
Alignment explanation
Indices: 1733407--1733451 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
1733397 GTGAATGATA
1733407 TGATAAGAATCTATG
1 TGATAAGAATCTATG
1733422 TGATAAGAATCTATG
1 TGATAAGAATCTATG
1733437 TGATAAGAATCTATG
1 TGATAAGAATCTATG
1733452 AGCATATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (15 bp):
TGATAAGAATCTATG
Found at i:1733476 original size:8 final size:8
Alignment explanation
Indices: 1733465--1733492 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1733455 ATATGTGATA
1733465 TGAATATG
1 TGAATATG
1733473 TGAATATG
1 TGAATATG
1733481 TGAATATG
1 TGAATATG
1733489 TGAA
1 TGAA
1733493 ATGATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (8 bp):
TGAATATG
Found at i:1737650 original size:15 final size:15
Alignment explanation
Indices: 1737630--1737659 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1737620 GTGAATGTTA
1737630 TGATAAGAAACTATG
1 TGATAAGAAACTATG
*
1737645 TGATAAGAATCTATG
1 TGATAAGAAACTATG
1737660 AGCATATGTG
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:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (15 bp):
TGATAAGAAACTATG
Found at i:1741301 original size:2 final size:2
Alignment explanation
Indices: 1741294--1741318 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1741284 TAATGAAATA
1741294 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
1741319 CTTTAGATGA
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:1744723 original size:35 final size:35
Alignment explanation
Indices: 1744616--1744724 Score: 182
Period size: 35 Copynumber: 3.1 Consensus size: 35
1744606 ATACAACCCC
* *
1744616 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGAA
1 AGTAAGGCTCTGAGCACAAAGCCGAGGAGCCTGCA
*
1744651 AGTAAGGCTTTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCTCTGAGCACAAAGCCGAGGAGCCTGCA
*
1744686 AGTAAGGCTCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCTCTGAGCACAAAGCCGAGGAGCCTGCA
1744721 AGTA
1 AGTA
1744725 TTCTTTCTCC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.33, C:0.25, G:0.30, T:0.12
Consensus pattern (35 bp):
AGTAAGGCTCTGAGCACAAAGCCGAGGAGCCTGCA
Found at i:1744828 original size:12 final size:12
Alignment explanation
Indices: 1744811--1744877 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
1744801 AGTCAAGTAT
1744811 CAGATCAGAATC
1 CAGATCAGAATC
*
1744823 CAGATCATGTAT-
1 CAGATCA-GAATC
1744835 CAGATCAGAATC
1 CAGATCAGAATC
1744847 CATG-TCA-ATAT-
1 CA-GATCAGA-ATC
*
1744858 CAGATCAGAACC
1 CAGATCAGAATC
*
1744870 CAGGTCAG
1 CAGATCAG
1744878 GTACCATAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
10 1 0.02
11 10 0.23
12 29 0.66
13 4 0.09
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (12 bp):
CAGATCAGAATC
Found at i:1744834 original size:24 final size:22
Alignment explanation
Indices: 1744801--1744877 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 22
1744791 ACATAATTAA
1744801 AGTCAAGTATCAGATCAGAATCC
1 AGTC-AGTATCAGATCAGAATCC
1744824 AGATCATGTATCAGATCAGAATCC
1 AG-TCA-GTATCAGATCAGAATCC
* *
1744848 ATGTCAATATCAGATCAGAACCC
1 A-GTCAGTATCAGATCAGAATCC
1744871 AGGTCAG
1 A-GTCAG
1744878 GTACCATAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
23 23 0.49
24 23 0.49
25 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (22 bp):
AGTCAGTATCAGATCAGAATCC
Found at i:1744891 original size:47 final size:48
Alignment explanation
Indices: 1744802--1744892 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 48
1744792 CATAATTAAA
* * * *
1744802 GTCAAGTATCAGATCAGAATCCAGATCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAACCCAGATCAGGTACCAGAACAGAATCCAT
* *
1744850 GTCAA-TATCAGATCAGAACCCAGGTCAGGTACCATAACAGAAT
1 GTCAAGTATCAGATCAGAACCCAGATCAGGTACCAGAACAGAAT
1744893 TCAAATCGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 32 0.86
48 5 0.14
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAACCCAGATCAGGTACCAGAACAGAATCCAT
Found at i:1747402 original size:18 final size:18
Alignment explanation
Indices: 1747339--1747403 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
1747329 AACAGTCAAT
* *
1747339 GGGTCGGGTAAACGGGTC
1 GGGTCGGGTTAACTGGTC
*
1747357 GGGTCGGGTCAA-TAGGTC
1 GGGTCGGGTTAACT-GGTC
*
1747375 GGTTCGGGTTAACTGGTC
1 GGGTCGGGTTAACTGGTC
1747393 GGGTCGGGTTA
1 GGGTCGGGTTA
1747404 GAACCGGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 39 0.98
19 1 0.03
ACGTcount: A:0.14, C:0.15, G:0.46, T:0.25
Consensus pattern (18 bp):
GGGTCGGGTTAACTGGTC
Found at i:1749427 original size:35 final size:35
Alignment explanation
Indices: 1749388--1749479 Score: 121
Period size: 35 Copynumber: 2.6 Consensus size: 35
1749378 CCCTGAGCAT
*
1749388 AAAGCCGAGGATCCTACAAGTAAGGCTCTAAGAAC
1 AAAGCCGAGGAGCCTACAAGTAAGGCTCTAAGAAC
* * *
1749423 AAAGCCGAGGAGCCTGCAAGTAAGGCTCTGAGCAC
1 AAAGCCGAGGAGCCTACAAGTAAGGCTCTAAGAAC
* * *
1749458 AAAGCTGACGAGCCTCCAAGTA
1 AAAGCCGAGGAGCCTACAAGTA
1749480 TTCTTCCTCC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.36, C:0.25, G:0.26, T:0.13
Consensus pattern (35 bp):
AAAGCCGAGGAGCCTACAAGTAAGGCTCTAAGAAC
Found at i:1749590 original size:24 final size:23
Alignment explanation
Indices: 1749562--1749632 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
1749552 ATTCAATTCA
*
1749562 AGTATCAGATCAGAATCCAAGTC
1 AGTATCATATCAGAATCCAAGTC
*
1749585 ATGTATCATATCAGAATCCATGTC
1 A-GTATCATATCAGAATCCAAGTC
* *
1749609 AATATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAAGTC
1749632 A
1 A
1749633 AATACCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 22 0.51
24 21 0.49
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAAGTC
Found at i:1749641 original size:24 final size:24
Alignment explanation
Indices: 1749559--1749648 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
1749549 ATAATTCAAT
* *
1749559 TCAAGTATCAGATCAGAATCCAAG
1 TCAAATATCATATCAGAATCCAAG
** *
1749583 TCATGTATCATATCAGAATCCATG
1 TCAAATATCATATCAGAATCCAAG
*
1749607 TC-AATATCATATCAGAATCCAGG
1 TCAAATATCATATCAGAATCCAAG
* *
1749630 TCAAATACCATAACAGAAT
1 TCAAATATCATATCAGAAT
1749649 TCAAATCGGA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (24 bp):
TCAAATATCATATCAGAATCCAAG
Found at i:1752101 original size:13 final size:12
Alignment explanation
Indices: 1752079--1752108 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1752069 TGTGGTCAAC
1752079 GTCGGTCAACGG
1 GTCGGTCAACGG
1752091 GTCGAGTCAACGG
1 GTCG-GTCAACGG
1752104 GTCGG
1 GTCGG
1752109 GTCGGGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (12 bp):
GTCGGTCAACGG
Found at i:1754410 original size:51 final size:51
Alignment explanation
Indices: 1754329--1754425 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
1754319 TGATAAATGA
*
1754329 CTGTCTCTTGTTCTCATATGTGATGGGATAAGAGGAGGTAAGATAGAAGGT
1 CTGTCTCTTGTTCTCATATGTGATGAGATAAGAGGAGGTAAGATAGAAGGT
*
1754380 CTGTCTCTTGTTCTCATATGTGATGAGATAAGGGGAGGTAAGATAG
1 CTGTCTCTTGTTCTCATATGTGATGAGATAAGAGGAGGTAAGATAG
1754426 TAGGCCGTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.32
Consensus pattern (51 bp):
CTGTCTCTTGTTCTCATATGTGATGAGATAAGAGGAGGTAAGATAGAAGGT
Found at i:1771477 original size:3 final size:3
Alignment explanation
Indices: 1771469--1771494 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1771459 CACTTTTTAA
1771469 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1771495 AATACATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1772821 original size:19 final size:20
Alignment explanation
Indices: 1772782--1772830 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1772772 CATGTTAGCC
1772782 ATTATAATATTAAATAATTA
1 ATTATAATATTAAATAATTA
* *
1772802 ATTATAA-ATTAGATATTTA
1 ATTATAATATTAAATAATTA
*
1772821 ATTTTAATAT
1 ATTATAATAT
1772831 ATTCTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTATAATATTAAATAATTA
Found at i:1772984 original size:26 final size:27
Alignment explanation
Indices: 1772948--1772998 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1772938 ATTTAAGTTA
*
1772948 TATTTTAATTTAAATATTAATTATTAT
1 TATTTTAATTTAAATATAAATTATTAT
*
1772975 TATTTT-ATTTTAATATAAATTATT
1 TATTTTAATTTAAATATAAATTATT
1772999 TTAATCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TATTTTAATTTAAATATAAATTATTAT
Found at i:1773334 original size:46 final size:46
Alignment explanation
Indices: 1773244--1773334 Score: 105
Period size: 47 Copynumber: 2.0 Consensus size: 46
1773234 TTTTATATAT
* * *
1773244 ATTATAAATTAATATATTTTTCATATTATAACTTTGAAATAATAGG
1 ATTATAAATTAATATATTTTTAATATTATAAATTTCAAATAATAGG
* *
1773290 ATTATAAATTAAATATATTTTTGAAT-TTTTAAATTTCTAA-AATAG
1 ATTATAAATT-AATATATTTTT-AATATTATAAATTTCAAATAATAG
1773335 AGACAATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
46 15 0.39
47 21 0.55
48 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (46 bp):
ATTATAAATTAATATATTTTTAATATTATAAATTTCAAATAATAGG
Found at i:1780748 original size:83 final size:83
Alignment explanation
Indices: 1780643--1780957 Score: 465
Period size: 83 Copynumber: 3.8 Consensus size: 83
1780633 TATGACAATT
*
1780643 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGGT-TTAAAACCC
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGGTATTAAAACGC
1780706 CACAAAAGTACGTGTCTATA
64 CACAAAAGTACGTGTCTATA
* * *
1780726 GCGGCGTTTGTGTAAAAAACGCCACTAAAGTACGAATCTATAGCGACGTTTGGTATTAAAACGCC
1 GCGGCGTTTGTGT-AAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGGTATTAAAACGCC
1780791 ACAAAAGTACGTGTCTATA
65 ACAAAAGTACGTGTCTATA
* *
1780810 GCGGCGTTTGTGTAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGGTATTAAAACGCCA
*
1780875 CAAAAGTATGTGTCTATA
66 CAAAAGTACGTGTCTATA
** * * * *
1780893 GCGGCGTTTGAATAAAAACGCCACTAAAATACTAGTTTATAGCGGCATTT-GTATAAAAACGCCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGGTATTAAAACGCCA
1780957 C
66 C
1780958 TACATTACGA
Statistics
Matches: 213, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
82 14 0.07
83 155 0.73
84 43 0.20
85 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (83 bp):
GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGGTATTAAAACGCCA
CAAAAGTACGTGTCTATA
Done.