Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 24
Found at i:1121860 original size:44 final size:44
Alignment explanation
Indices: 1121797--1121886 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
1121787 TGGGATGCTC
1121797 TTCTATGTTTCTTAGTCATGTGGGATTATTTTGTTCTCATATTT
1 TTCTATGTTTCTTAGTCATGTGGGATTATTTTGTTCTCATATTT
1121841 TTCTATGTTTCTTAGTCATGTGGGATTATTTTGTTCTCATATTT
1 TTCTATGTTTCTTAGTCATGTGGGATTATTTTGTTCTCATATTT
1121885 TT
1 TT
1121887 ACTCTTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (44 bp):
TTCTATGTTTCTTAGTCATGTGGGATTATTTTGTTCTCATATTT
Found at i:1123680 original size:21 final size:21
Alignment explanation
Indices: 1123656--1123697 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1123646 AAATAAAGTA
*
1123656 AAGTTCAGTTACAAAATTTGT
1 AAGTTAAGTTACAAAATTTGT
*
1123677 AAGTTAAGTTACCAAATTTGT
1 AAGTTAAGTTACAAAATTTGT
1123698 GCTTTACCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
AAGTTAAGTTACAAAATTTGT
Found at i:1128145 original size:21 final size:21
Alignment explanation
Indices: 1128121--1128163 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1128111 AAAATAAATT
**
1128121 ACTGAAATTTAAATTACTGGA
1 ACTGAAAAATAAATTACTGGA
*
1128142 ACTGAAAAATGAATTACTGGA
1 ACTGAAAAATAAATTACTGGA
1128163 A
1 A
1128164 TTTGAATTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (21 bp):
ACTGAAAAATAAATTACTGGA
Found at i:1128177 original size:14 final size:15
Alignment explanation
Indices: 1128151--1128187 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1128141 AACTGAAAAA
*
1128151 TGAATTACTGGAATT
1 TGAATTACTGGAAAT
1128166 TGAATT-CTGGAAAT
1 TGAATTACTGGAAAT
1128180 TGAATTAC
1 TGAATTAC
1128188 ATTTCAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (15 bp):
TGAATTACTGGAAAT
Found at i:1128424 original size:24 final size:25
Alignment explanation
Indices: 1128385--1128456 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 25
1128375 CTTAATATTA
*
1128385 TTATTTTA-AAAT-AATAAAATAAT
1 TTATTTTATTAATAAATAAAATAAT
* ** *
1128408 TTA-TTTATTATTAAATATTAT-TT
1 TTATTTTATTAATAAATAAAATAAT
1128431 TTATTTTATTAATAAA-AAAATAAT
1 TTATTTTATTAATAAATAAAATAAT
1128455 TT
1 TT
1128457 TTGTATATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
22 4 0.11
23 12 0.33
24 20 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATTTTATTAATAAATAAAATAAT
Found at i:1128561 original size:21 final size:20
Alignment explanation
Indices: 1128516--1128561 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1128506 AGTAATAGTA
*
1128516 TATTATATTTTAAAAATATT
1 TATTATATATTAAAAATATT
* *
1128536 AATTAGTATATTAAAAATCTT
1 TATTA-TATATTAAAAATATT
1128557 TATTA
1 TATTA
1128562 AAATATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTATATATTAAAAATATT
Found at i:1128567 original size:21 final size:21
Alignment explanation
Indices: 1128525--1128569 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1128515 ATATTATATT
**
1128525 TTAAAAATATTAATTAGTATA
1 TTAAAAATATTAATTAAAATA
* *
1128546 TTAAAAATCTTTATTAAAATA
1 TTAAAAATATTAATTAAAATA
1128567 TTA
1 TTA
1128570 TTTAAATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAAAAATATTAATTAAAATA
Found at i:1128587 original size:52 final size:50
Alignment explanation
Indices: 1128526--1128633 Score: 121
Period size: 52 Copynumber: 2.1 Consensus size: 50
1128516 TATTATATTT
*
1128526 TAAAAATATTAATTAGTATAT-TA-AAAATCTTTATTAAAATATTATTTAAATA
1 TAAAAATATTAATTAGTAAATATATAAAATCTTTATT---ATATTATTTAAA-A
* * * *
1128578 TAAATATATTCATTATTAAATATATAAAATTTTTATTATATTATTTAAAA
1 TAAAAATATTAATTAGTAAATATATAAAATCTTTATTATATTATTTAAAA
1128628 TAAAAA
1 TAAAAA
1128634 AATAATATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
50 6 0.12
51 12 0.25
52 17 0.35
53 2 0.04
54 11 0.23
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (50 bp):
TAAAAATATTAATTAGTAAATATATAAAATCTTTATTATATTATTTAAAA
Found at i:1128615 original size:23 final size:22
Alignment explanation
Indices: 1128565--1128616 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1128555 TTTATTAAAA
*
1128565 TATTATTTAAATATAAATATATT
1 TATTA-TTAAATATAAAAATATT
* *
1128588 CATTATTAAATATATAAAATTTT
1 TATTATTAAATATA-AAAATATT
1128611 TATTAT
1 TATTAT
1128617 ATTATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTATTAAATATAAAAATATT
Found at i:1128667 original size:46 final size:45
Alignment explanation
Indices: 1128617--1128704 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
1128607 TTTTTATTAT
*
1128617 ATTA-TTTAAAATAAAAAAATAATATCTATATTATTATAAATAATTG
1 ATTATTTTAAAATAAAAAAAT-AT-TATATATTATTATAAATAATTG
* **
1128663 ATTATTTTTATAATATTAAAATATTATATATTATTATAAATA
1 ATTA-TTTTAAAATAAAAAAATATTATATATTATTATAAATA
1128705 TTAATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
46 21 0.58
47 2 0.06
48 13 0.36
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (45 bp):
ATTATTTTAAAATAAAAAAATATTATATATTATTATAAATAATTG
Found at i:1128687 original size:19 final size:20
Alignment explanation
Indices: 1128665--1128706 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1128655 AATAATTGAT
*
1128665 TATTTTTATAATATTA-AAA
1 TATTTATATAATATTATAAA
*
1128684 TA-TTATATATTATTATAAA
1 TATTTATATAATATTATAAA
1128703 TATT
1 TATT
1128707 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 11 0.58
19 7 0.37
20 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTATATAATATTATAAA
Found at i:1128697 original size:18 final size:19
Alignment explanation
Indices: 1128671--1128707 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1128661 TGATTATTTT
1128671 TATAATATTA-AAATATTA
1 TATAATATTATAAATATTA
*
1128689 TATATTATTATAAATATTA
1 TATAATATTATAAATATTA
1128708 ATTAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATAATATTATAAATATTA
Found at i:1128704 original size:27 final size:27
Alignment explanation
Indices: 1128643--1128708 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
1128633 AAATAATATC
* *
1128643 TATATTATTATAAATAATTGATTATTTT
1 TATAATATTA-AAATAATTGATTATTAT
1128671 TATAATATTAAAAT-ATT-ATATATTAT
1 TATAATATTAAAATAATTGAT-TATTAT
1128697 TATAAATATTAA
1 TAT-AATATTAA
1128709 TTAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 2 0.06
26 11 0.32
27 12 0.35
28 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TATAATATTAAAATAATTGATTATTAT
Found at i:1128959 original size:42 final size:42
Alignment explanation
Indices: 1128904--1129020 Score: 189
Period size: 42 Copynumber: 2.8 Consensus size: 42
1128894 AATTACATTT
* * *
1128904 CGGAAAACCAATTACGTTAAACAAACATGGGAAAACATTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
*
1128946 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTT
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
*
1128988 TGGAAAACGAATTACGTGAAACAAACACGGGAA
1 CGGAAAACGAATTACGTGAAACAAACACGGGAA
1129021 TTCGGGAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.18
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
Found at i:1135467 original size:49 final size:46
Alignment explanation
Indices: 1135390--1135486 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 46
1135380 TAGGTCCGAC
*
1135390 GTTGCTCGGACTCCGAATTTTTCTCCAAGTATATAATAAGTCTGATATT
1 GTTGCTCGGACTCCGAATTTTTCACCAAG--TAT-ATAAGTCTGATATT
*
1135439 GTTGCTCGGACTCCGAGTTTTTCACCAAGTATATAAGTCTGATATT
1 GTTGCTCGGACTCCGAATTTTTCACCAAGTATATAAGTCTGATATT
1135485 GT
1 GT
1135487 GTTCGATGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 16 0.35
47 3 0.07
49 27 0.59
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (46 bp):
GTTGCTCGGACTCCGAATTTTTCACCAAGTATATAAGTCTGATATT
Found at i:1136567 original size:19 final size:19
Alignment explanation
Indices: 1136543--1136580 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1136533 ACCAATAAAA
* *
1136543 TCGCAATGCGATTTCTAAT
1 TCGCAACGCGATCTCTAAT
1136562 TCGCAACGCGATCTCTAAT
1 TCGCAACGCGATCTCTAAT
1136581 ATTGCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
TCGCAACGCGATCTCTAAT
Found at i:1136658 original size:21 final size:21
Alignment explanation
Indices: 1136634--1136700 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1136624 TTCCATTTCG
1136634 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * * *
1136655 CGTTGC-A-ATTTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
1136673 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
1136696 CGTTG
1 CGTTG
1136701 TGATTGGTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 7 0.21
21 12 0.36
22 5 0.15
23 2 0.06
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:1136699 original size:41 final size:41
Alignment explanation
Indices: 1136589--1136705 Score: 191
Period size: 41 Copynumber: 2.9 Consensus size: 41
1136579 ATATTGCAAA
* *
1136589 TTCGCGTTGCGATAGTCTACAGTGTTGTAGAGATTTTCCAT
1 TTCGCGTTGCGATAGTCTACAGTGTCGTTGAGATTTTCCAT
1136630 TTCGCGTTGCGATAGTCTACAGTGTCGTTGCA-ATTTTCCAT
1 TTCGCGTTGCGATAGTCTACAGTGTCGTTG-AGATTTTCCAT
*
1136671 TTCGCGTTGCGATAGTCTACAGTGTCGTTGTGATT
1 TTCGCGTTGCGATAGTCTACAGTGTCGTTGAGATT
1136706 GGTATTGCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
41 70 0.99
42 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTCTACAGTGTCGTTGAGATTTTCCAT
Found at i:1136789 original size:6 final size:6
Alignment explanation
Indices: 1136778--1136810 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1136768 AGACACGTAT
*
1136778 GACCAC GACCAC GACCAC GATCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1136811 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.30, C:0.48, G:0.18, T:0.03
Consensus pattern (6 bp):
GACCAC
Found at i:1137660 original size:20 final size:20
Alignment explanation
Indices: 1137635--1137809 Score: 112
Period size: 20 Copynumber: 8.6 Consensus size: 20
1137625 TTTTAAAACT
*
1137635 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
1137655 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
1137676 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
1137696 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
*
1137717 ATCGTAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
**
1137737 ATCGCAA--C-AACACTGTAGACT
1 ATCGCAACGCGAA-A-TG--GAAA
1137758 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1137778 ACCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1137798 ATCGCAACGCGA
1 ATCGCAACGCGA
1137810 TTTTCAACTA
Statistics
Matches: 117, Mismatches: 21, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
17 2 0.02
18 7 0.06
19 8 0.07
20 56 0.48
21 26 0.22
22 8 0.07
23 8 0.07
24 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1137681 original size:21 final size:21
Alignment explanation
Indices: 1137655--1137766 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 21
1137645 GAAATGGAAA
1137655 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
1137676 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
1137696 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* * **
1137717 ATCGTAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
*
1137737 ATCGCAACAACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
1137758 ATCGCAACG
1 ATCGCAACG
1137767 CGAAATGGAA
Statistics
Matches: 65, Mismatches: 16, Indels: 20
0.64 0.16 0.20
Matches are distributed among these distances:
19 6 0.09
20 22 0.34
21 31 0.48
22 6 0.09
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:1137690 original size:41 final size:41
Alignment explanation
Indices: 1137632--1137786 Score: 274
Period size: 41 Copynumber: 3.8 Consensus size: 41
1137622 CAATTTTAAA
*
1137632 ACTATCGCAACGTGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1137673 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* *
1137714 ACTATCGTAACGCGAAATGGAAAATCGCAACAACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
1137755 ACTATCGCAACGCGAAATGGAAAACCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
1137787 CGAAATGGAA
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:1137826 original size:82 final size:81
Alignment explanation
Indices: 1137635--1137809 Score: 228
Period size: 82 Copynumber: 2.1 Consensus size: 81
1137625 TTTTAAAACT
* * * *
1137635 ATCGCAACGTGAAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGCGAAATGCAAAATCGCAACAACACTGTAGACTATCGCAACGCGAAATGGAAAACCG
* **
1137700 CAACGACACTGTAGACT
66 CAACGACAATG-AGAAA
* *
1137717 ATCGTAACGCGAAATGGAAAATCGCAACAACACTGTAGACTATCGCAACGCGAAATGGAAAACCG
1 ATCGCAACGCGAAATGCAAAATCGCAACAACACTGTAGACTATCGCAACGCGAAATGGAAAACCG
1137782 CAACG-CGAAATG-GAAA
66 CAACGAC--AATGAGAAA
1137798 ATCGCAACGCGA
1 ATCGCAACGCGA
1137810 TTTTCAACTA
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
81 14 0.17
82 66 0.80
83 3 0.04
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (81 bp):
ATCGCAACGCGAAATGCAAAATCGCAACAACACTGTAGACTATCGCAACGCGAAATGGAAAACCG
CAACGACAATGAGAAA
Found at i:1146046 original size:18 final size:19
Alignment explanation
Indices: 1146011--1146048 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1146001 CACGGAATGT
1146011 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1146031 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
1146049 GATTACTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1155579 original size:23 final size:23
Alignment explanation
Indices: 1155553--1155600 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1155543 ATAAAGTACA
*
1155553 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1155576 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1155599 AT
1 AT
1155601 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1156053 original size:23 final size:23
Alignment explanation
Indices: 1156027--1156089 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1156017 ATATAACCAC
1156027 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1156050 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1156073 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1156090 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1156467 original size:429 final size:429
Alignment explanation
Indices: 1155667--1156721 Score: 1986
Period size: 429 Copynumber: 2.5 Consensus size: 429
1155657 TATTACATTA
*
1155667 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1155732 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
* * * *
1155797 TTTTCACAAAAAATTATTTAATTGTTTTGATATTTTATAAAATATTTTTTAGAATTTTTAATTTA
131 TTTGCACAAAAAATTATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
*
1155862 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCTTATAATTACTAAATTAATATC
195 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
*
1155927 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAAAAAAGTATGGACACTT
260 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
1155992 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
325 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
1156057 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
1156097 TATTATATTGAAAGTGTCCATACTGTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
1156162 TTATGTTTCAATATTTTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTC
66 TTATGTTTCAAT-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
1156227 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAA-TTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
1156291 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
195 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
1156356 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
260 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
1156421 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
325 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
1156486 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
1156526 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1156591 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
1156656 ATTTGCACAAAAAATTATTTGATTATTTGATGTTTTATAAAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
1156721 A
195 A
1156722 CAACATTAAC
Statistics
Matches: 610, Mismatches: 12, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
429 422 0.69
430 115 0.19
431 73 0.12
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (429 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:1156482 original size:23 final size:23
Alignment explanation
Indices: 1156456--1156518 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1156446 ATATAACCAC
1156456 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1156479 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1156502 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1156519 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1156984 original size:39 final size:39
Alignment explanation
Indices: 1156930--1157015 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
1156920 CAAGTTGTAG
* *
1156930 ATTTTGATTTCCTTTTGCTTGGTATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
1156969 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
1157008 ATTTTGAT
1 ATTTTGAT
1157016 GAGCATCGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.50
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:1157297 original size:18 final size:18
Alignment explanation
Indices: 1157274--1157310 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1157264 CGAAATATAT
1157274 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1157292 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1157310 A
1 A
1157311 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1157587 original size:25 final size:25
Alignment explanation
Indices: 1157559--1157609 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1157549 TTAATCCAAA
*
1157559 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
1157584 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
1157609 T
1 T
1157610 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:1157903 original size:21 final size:22
Alignment explanation
Indices: 1157878--1157929 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1157868 ACACTTTACA
*
1157878 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1157901 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1157924 ATATAA
1 ATATAA
1157930 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1157914 original size:23 final size:23
Alignment explanation
Indices: 1157888--1157950 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1157878 ATATAACCAC
1157888 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1157911 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1157934 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1157951 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1159290 original size:17 final size:18
Alignment explanation
Indices: 1159268--1159310 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1159258 ATATATCCGG
1159268 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1159285 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1159305 TATCAT
1 TATCAT
1159311 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1159328 original size:20 final size:19
Alignment explanation
Indices: 1159273--1159319 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1159263 TCCGGTATCA
1159273 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1159292 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1159313 TTTTACC
1 TTTTACC
1159320 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1159466 original size:20 final size:20
Alignment explanation
Indices: 1159440--1159485 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1159430 CACTTTTAAA
1159440 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1159459 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1159480 TTTACC
1 TTTACC
1159486 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1159952 original size:229 final size:228
Alignment explanation
Indices: 1159551--1159999 Score: 808
Period size: 229 Copynumber: 2.0 Consensus size: 228
1159541 TTAAAACTGC
1159551 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
1159616 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
1159681 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
*
1159746 GTATGAACACTTTTATAAAAATGATATATACTTT
195 GTATGAACACTTTTATAAAAAGGATATATACTTT
1159780 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
1159845 TTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
1159910 TTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
*
1159975 TATGGACACTTTTATAAAAAGGATA
196 TATGAACACTTTTATAAAAAGGATA
1160000 GATAATTTAC
Statistics
Matches: 211, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
228 36 0.17
229 175 0.83
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGAACACTTTTATAAAAAGGATATATACTTT
Found at i:1166382 original size:6 final size:6
Alignment explanation
Indices: 1166362--1166394 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1166352 TGGTTTCGTT
*
1166362 ATTCA- ATTTAC ATTCAC ATTCAC ATTCAC ATTC
1 ATTCAC ATTCAC ATTCAC ATTCAC ATTCAC ATTC
1166395 TGCTCCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (6 bp):
ATTCAC
Found at i:1175888 original size:23 final size:22
Alignment explanation
Indices: 1175862--1175910 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1175852 TAACTTATAT
* *
1175862 CTCAGGTTTTCATCTATATTCAA
1 CTCAGGTTTT-ATATACATTCAA
1175885 CTCA-GTTTTATATACATTCAA
1 CTCAGGTTTTATATACATTCAA
1175906 CTCAG
1 CTCAG
1175911 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.61
22 5 0.22
23 4 0.17
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (22 bp):
CTCAGGTTTTATATACATTCAA
Found at i:1185482 original size:2 final size:2
Alignment explanation
Indices: 1185475--1185499 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1185465 AACTTAAATA
1185475 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
1185500 ATGTAGAAAT
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:1187828 original size:25 final size:25
Alignment explanation
Indices: 1187800--1187849 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1187790 TCCTGAACAT
1187800 TCGTTATCTCGAATAAACCAGAAAG
1 TCGTTATCTCGAATAAACCAGAAAG
1187825 TCGTTATCTCGAATAAACCAGAAAG
1 TCGTTATCTCGAATAAACCAGAAAG
1187850 GTTTCGGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
TCGTTATCTCGAATAAACCAGAAAG
Found at i:1190362 original size:33 final size:32
Alignment explanation
Indices: 1190325--1190403 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
1190315 AGTTTGATAT
1190325 TCGGGTCTGGTTTTTTAAAAAAAAATATCGGGA
1 TCGGGTCTGGTTTTTTAAAAAAAAAT-TCGGGA
* * * * *
1190358 TCGGGACTGATTTTTTTTAAAAAAAATTTGGGT
1 TCGGGTCTG-GTTTTTTAAAAAAAAATTCGGGA
*
1190391 TCGGGTCAGGTTT
1 TCGGGTCTGGTTT
1190404 GTGTTGGGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
32 3 0.08
33 19 0.51
34 15 0.41
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (32 bp):
TCGGGTCTGGTTTTTTAAAAAAAAATTCGGGA
Found at i:1190451 original size:33 final size:34
Alignment explanation
Indices: 1190409--1190481 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
1190399 GGTTTGTGTT
1190409 GGGTTTTTTTAAGTGTGATATTCGGGTCGGG-TC
1 GGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTC
*
1190442 GGGTTTTTTTAAGTGTGATATTTGGGTCGGGTTC
1 GGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTC
1190476 GGGTTT
1 GGGTTT
1190482 AGGGTGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 30 0.79
34 8 0.21
ACGTcount: A:0.11, C:0.07, G:0.37, T:0.45
Consensus pattern (34 bp):
GGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTC
Found at i:1191035 original size:18 final size:16
Alignment explanation
Indices: 1190993--1191037 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
1190983 TCAGATTCAT
1190993 ATTCCAATTCCTACAG
1 ATTCCAATTCCTACAG
**
1191009 ATTTAAATTCCTTCACAG
1 ATTCCAATTCC-T-ACAG
1191027 ATTCCAATTCC
1 ATTCCAATTCC
1191038 CTCAGAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.39
17 1 0.04
18 13 0.57
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (16 bp):
ATTCCAATTCCTACAG
Found at i:1192838 original size:9 final size:9
Alignment explanation
Indices: 1192821--1192894 Score: 61
Period size: 9 Copynumber: 8.8 Consensus size: 9
1192811 CCCCGCCCCG
1192821 ATTATATAT
1 ATTATATAT
1192830 A-TA-ATAT
1 ATTATATAT
1192837 ATTATAT-T
1 ATTATATAT
*
1192845 TTTATATAT
1 ATTATATAT
1192854 A-TA-ATAT
1 ATTATATAT
*
1192861 TTTATATAT
1 ATTATATAT
*
1192870 TTTATAT-T
1 ATTATATAT
1192878 AATTATATAT
1 -ATTATATAT
*
1192888 ATAATAT
1 ATTATAT
1192895 TTTTGGGTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
7 9 0.17
8 16 0.30
9 27 0.51
10 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTATATAT
Found at i:1192854 original size:24 final size:24
Alignment explanation
Indices: 1192822--1192898 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 24
1192812 CCCGCCCCGA
1192822 TTATATATATAATATATTATATTT
1 TTATATATATAATATATTATATTT
*
1192846 TTATATATATAATATTTTATATATT
1 TTATATATATAATATATTATAT-TT
*
1192871 TTATAT-TAATTATATATATAATATTT
1 TTATATAT-A-TA-ATATATTATATTT
1192897 TT
1 TT
1192899 GGGTTCGGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 22 0.48
25 9 0.20
26 6 0.13
27 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATATATATAATATATTATATTT
Found at i:1192889 original size:34 final size:33
Alignment explanation
Indices: 1192833--1192897 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
1192823 TATATATATA
*
1192833 ATATATTATATTTTTATATATATAATATTTTAT
1 ATATATTATATTATTATATATATAATATTTTAT
*
1192866 ATATTTTATATTAATTATATATATAATATTTT
1 ATATATTATATT-ATTATATATATAATATTTT
1192898 TGGGTTCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
ATATATTATATTATTATATATATAATATTTTAT
Found at i:1194588 original size:23 final size:22
Alignment explanation
Indices: 1194560--1194613 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
1194550 GCACAAAGAA
1194560 TATATTTTAAAAAATATATATT
1 TATATTTTAAAAAATATATATT
***
1194582 TAGTATTTTCTCAAATATATATT
1 TA-TATTTTAAAAAATATATATT
1194605 TAT-TTTTAA
1 TATATTTTAA
1194614 TATAAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.15
22 3 0.12
23 19 0.73
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (22 bp):
TATATTTTAAAAAATATATATT
Found at i:1195907 original size:27 final size:27
Alignment explanation
Indices: 1195826--1195907 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
1195816 AGATATAATA
* *
1195826 TCTTTTTATTTAAATATTTAAAATGTT
1 TCTTTTTATATAAATATTTAAAATATT
* *
1195853 T-TTATTTACATAATTATTT-AAATCATT
1 TCTT-TTTATATAAATATTTAAAAT-ATT
* *
1195880 TCTTTTTGTGTAAATATTTAAAATATT
1 TCTTTTTATATAAATATTTAAAATATT
1195907 T
1 T
1195908 TTGTTAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
26 6 0.14
27 31 0.72
28 6 0.14
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (27 bp):
TCTTTTTATATAAATATTTAAAATATT
Found at i:1195925 original size:54 final size:54
Alignment explanation
Indices: 1195826--1195929 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
1195816 AGATATAATA
* * * *
1195826 TCTTTTTATTTAAATATTTAAAATGTTTTTATTTACATAATTATTTAAATCATT
1 TCTTTTTATGTAAATATTTAAAATATTTTTATTAAAATAATTATTTAAATCATT
* *
1195880 TCTTTTTGTGTAAATATTTAAAATATTTTTGTTAAAATAGA-TATTTAAAT
1 TCTTTTTATGTAAATATTTAAAATATTTTTATTAAAATA-ATTATTTAAAT
1195930 TATATAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 42 0.98
55 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.55
Consensus pattern (54 bp):
TCTTTTTATGTAAATATTTAAAATATTTTTATTAAAATAATTATTTAAATCATT
Found at i:1197363 original size:2 final size:2
Alignment explanation
Indices: 1197358--1197389 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1197348 ATTTTTTTGC
1197358 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
1197390 TAATTCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1200897 original size:14 final size:15
Alignment explanation
Indices: 1200873--1200901 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1200863 ATAATAATTT
1200873 TAAATTTTTTTAAAA
1 TAAATTTTTTTAAAA
1200888 TAAA-TTTTTTAAAA
1 TAAATTTTTTTAAAA
1200902 AATTATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAATTTTTTTAAAA
Found at i:1200902 original size:15 final size:15
Alignment explanation
Indices: 1200873--1200902 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1200863 ATAATAATTT
*
1200873 TAAATTTTTTTAAAA
1 TAAATTTTTTAAAAA
1200888 TAAATTTTTTAAAAA
1 TAAATTTTTTAAAAA
1200903 ATTATAAATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTTTTTAAAAA
Found at i:1232351 original size:31 final size:31
Alignment explanation
Indices: 1232278--1232343 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1232268 CAAACAGTCA
* *
1232278 GGGACCATATTGCAAATAGACTAAATGTTTG
1 GGGACCATATTGCAAACAGACTAAATGTTAG
1232309 GGGACCATATTGCAAACAGACTAAATGTTAG
1 GGGACCATATTGCAAACAGACTAAATGTTAG
1232340 GGGA
1 GGGA
1232344 TTGTATTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTAG
Found at i:1236055 original size:14 final size:14
Alignment explanation
Indices: 1236036--1236077 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
1236026 TCGGATGCTC
1236036 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1236050 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1236064 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1236078 ATGCCCAGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:1236080 original size:10 final size:10
Alignment explanation
Indices: 1236016--1236049 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1236006 CATAGCTCGG
1236016 TCGGATGGCC
1 TCGGATGGCC
1236026 TCGGAT-GCTC
1 TCGGATGGC-C
1236036 TCGGATGGCC
1 TCGGATGGCC
1236046 TCGG
1 TCGG
1236050 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:1241960 original size:10 final size:10
Alignment explanation
Indices: 1241945--1241976 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1241935 CTTATCCAAA
1241945 AAAAAATAAT
1 AAAAAATAAT
1241955 AAAAAATAAT
1 AAAAAATAAT
*
1241965 ATAAAATAAT
1 AAAAAATAAT
1241975 AA
1 AA
1241977 TAATTTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:1241960 original size:13 final size:13
Alignment explanation
Indices: 1241942--1241980 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1241932 TTACTTATCC
*
1241942 AAAAAAAAATAAT
1 AAAAAATAATAAT
1241955 AAAAAATAAT-AT
1 AAAAAATAATAAT
1241967 AAAATAATAATAAT
1 AAAA-AATAATAAT
1241981 TTATTGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 15 0.65
14 2 0.09
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:1243040 original size:2 final size:2
Alignment explanation
Indices: 1243033--1243068 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1243023 AAATATTTGG
1243033 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
1243069 TAAAGTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1243249 original size:18 final size:18
Alignment explanation
Indices: 1243228--1243269 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1243218 AATTTTAAGA
1243228 TAAAATAAAAATATA-ATT
1 TAAAATAAAAATATATA-T
* *
1243246 TAAACTAAATATATATAT
1 TAAAATAAAAATATATAT
1243264 TAAAAT
1 TAAAAT
1243270 TACCAGGTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATAAAAATATATAT
Found at i:1245607 original size:16 final size:16
Alignment explanation
Indices: 1245556--1245607 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1245546 CTAGTATATT
*
1245556 TTAATTATTTATTATAT
1 TTAATTA-TTATTATAA
* * *
1245573 TTAATAATTAATATTA
1 TTAATTATTATTATAA
1245589 TTAATTATTATTATAA
1 TTAATTATTATTATAA
1245605 TTA
1 TTA
1245608 TTAAAACAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 22 0.79
17 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATTATTATTATAA
Found at i:1245780 original size:16 final size:16
Alignment explanation
Indices: 1245729--1245790 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
1245719 CTAGTATATT
*
1245729 TTAATTATTTATTATAT
1 TTAATTA-TTATTATAA
* * *
1245746 TTAATAATTAATATTA
1 TTAATTATTATTATAA
1245762 TTAATTATTATTATAA
1 TTAATTATTATTATAA
* *
1245778 TTATTTGTTATTA
1 TTAATTATTATTA
1245791 ATTTCAATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
16 30 0.83
17 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTAATTATTATTATAA
Found at i:1248960 original size:3 final size:3
Alignment explanation
Indices: 1248952--1248988 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1248942 TCTTGGAGAT
1248952 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1248989 ATGTGCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1250550 original size:27 final size:27
Alignment explanation
Indices: 1250497--1250552 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1250487 TATGTTGGAA
* * *
1250497 AATAAATTTATAAAAAATTATAGGAAT
1 AATAAAGTTATAAAAAATTAAAAGAAT
**
1250524 AATAAAGTTATAAAATCTTAAAAGAAT
1 AATAAAGTTATAAAAAATTAAAAGAAT
1250551 AA
1 AA
1250553 AAATATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (27 bp):
AATAAAGTTATAAAAAATTAAAAGAAT
Found at i:1262235 original size:7 final size:7
Alignment explanation
Indices: 1262225--1262257 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1262215 TTATAAACAT
1262225 TAAACCC
1 TAAACCC
1262232 TAAACCC
1 TAAACCC
1262239 TAAACCC
1 TAAACCC
1262246 TAAACCC
1 TAAACCC
1262253 TAAAC
1 TAAAC
1262258 TCCAACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:1262235 original size:14 final size:14
Alignment explanation
Indices: 1262218--1262257 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1262208 CCCTAAATTA
*
1262218 TAAACATTAAACCC
1 TAAACACTAAACCC
*
1262232 TAAACCCTAAACCC
1 TAAACACTAAACCC
*
1262246 TAAACCCTAAAC
1 TAAACACTAAAC
1262258 TCCAACTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAACACTAAACCC
Found at i:1262242 original size:21 final size:21
Alignment explanation
Indices: 1262218--1262257 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1262208 CCCTAAATTA
*
1262218 TAAACATTAAACCCTAAACCC
1 TAAACACTAAACCCTAAACCC
*
1262239 TAAACCCTAAACCCTAAAC
1 TAAACACTAAACCCTAAAC
1262258 TCCAACTTAA
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:0.47, C:0.35, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACACTAAACCCTAAACCC
Found at i:1266352 original size:31 final size:31
Alignment explanation
Indices: 1266306--1266375 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
1266296 ATTTTAAATG
* * *
1266306 TAACAAACTGGTTACTAACATTATCAATTTA
1 TAACAAATTGATTACTAACATCATCAATTTA
** **
1266337 TAACAAATTGATTACTGTCATCATTGATTTA
1 TAACAAATTGATTACTAACATCATCAATTTA
1266368 TAACAAAT
1 TAACAAAT
1266376 CAGTCATTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (31 bp):
TAACAAATTGATTACTAACATCATCAATTTA
Found at i:1276155 original size:77 final size:78
Alignment explanation
Indices: 1275993--1276148 Score: 242
Period size: 77 Copynumber: 2.0 Consensus size: 78
1275983 GTTCCTACTT
* ** *
1275993 TAGTTTTTCAGGAATAGATCGAGATAGAGATTAACAAGGTGATTATTCTTGAAAATTTTAAATTT
1 TAGTTTTTCAGGAATAGATAGAGATAGAGACCAAC-AGGTGATTATTCTTGAAAATTTTAAAATT
1276058 TTATATAATTTAAA
65 TTATATAATTTAAA
* *
1276072 TAGTTTTTCATGAATGGATAGAGATAGAGACCAAC-GGTGATTATTCTTGAAAATTTTAAAATTT
1 TAGTTTTTCAGGAATAGATAGAGATAGAGACCAACAGGTGATTATTCTTGAAAATTTTAAAATTT
1276136 TATATAATTTAAA
66 TATATAATTTAAA
1276149 ATGTTTTATT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
77 41 0.58
79 30 0.42
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (78 bp):
TAGTTTTTCAGGAATAGATAGAGATAGAGACCAACAGGTGATTATTCTTGAAAATTTTAAAATTT
TATATAATTTAAA
Found at i:1277346 original size:21 final size:21
Alignment explanation
Indices: 1277296--1277347 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1277286 TACTAAATAT
**
1277296 TTCAAGTTACTATTCGAGTTA
1 TTCAAGTTGTTATTCGAGTTA
1277317 TTCAAGTTGTTATTCGAGTTA
1 TTCAAGTTGTTATTCGAGTTA
1277338 TTCAAGTTGT
1 TTCAAGTTGT
1277348 ACTTTACAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCAAGTTGTTATTCGAGTTA
Found at i:1277471 original size:83 final size:83
Alignment explanation
Indices: 1277376--1277530 Score: 247
Period size: 83 Copynumber: 1.9 Consensus size: 83
1277366 AACTTGAAAT
* * **
1277376 TTTTTTGAGTCGAGTTGAATTTATGAAATTACAACTTGAAGTTAATTTGAGTCAAATTTCCACGA
1 TTTTTCGAGTCGAGTCGAATTTATGAAATTACAACTTGAAGTTAATTCAAGTCAAATTTCCACGA
1277441 GTCGAGTCTAAAAACCAA
66 GTCGAGTCTAAAAACCAA
* * *
1277459 TTTTTCGAGTCGAGTCGAGTTTATGAAATTACAACTTGAAGTTAATTCAAGTCAAGTTTTCACGA
1 TTTTTCGAGTCGAGTCGAATTTATGAAATTACAACTTGAAGTTAATTCAAGTCAAATTTCCACGA
1277524 GTCGAGT
66 GTCGAGT
1277531 AAAGTCGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (83 bp):
TTTTTCGAGTCGAGTCGAATTTATGAAATTACAACTTGAAGTTAATTCAAGTCAAATTTCCACGA
GTCGAGTCTAAAAACCAA
Found at i:1278687 original size:13 final size:13
Alignment explanation
Indices: 1278651--1278688 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1278641 CATGTAAAAT
*
1278651 AATAATAAAA-AA
1 AATAAGAAAATAA
1278663 AATAATGAAAATAA
1 AATAA-GAAAATAA
1278677 AATAAGAAAATA
1 AATAAGAAAATA
1278689 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 5 0.22
13 11 0.48
14 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (13 bp):
AATAAGAAAATAA
Found at i:1279071 original size:205 final size:207
Alignment explanation
Indices: 1278849--1279265 Score: 730
Period size: 205 Copynumber: 2.0 Consensus size: 207
1278839 AAAAAATAAA
1278849 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACATAT
*
1278914 ATACATATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATGTATA
66 ATACATATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATATATA
* *
1278979 CGAA-TGT-ATAAAAAACTAATAATAGTATAAAATATATATAAATATTATAATGTAATATAAAAA
131 CGAAGTGTAAGAAAAAACTAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAA
*
1279042 GGTAATTAAAAC
196 GATAATTAAAAC
*
1279054 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACATAT
* *
1279119 ATACATATATATATATATAATATAACATATAAGTGAAATAATACTATACTAATAATAAATATATA
66 ATACATATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATATATA
*
1279184 CGAATGTGTAAAGAAAAAACTAATAATAATATAGAATATATATAAATATTATAATGTAATATAAA
131 CGAA-GTGT-AAGAAAAAACTAATAATAATATAAAATATATATAAATATTATAATGTAATATAAA
1279249 AAGATAATTAAAAC
194 AAGATAATTAAAAC
1279263 TAA
1 TAA
1279266 AATCCCGAGA
Statistics
Matches: 200, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
205 130 0.65
207 3 0.01
209 67 0.34
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (207 bp):
TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACATAT
ATACATATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATATATA
CGAAGTGTAAGAAAAAACTAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAA
GATAATTAAAAC
Found at i:1279125 original size:8 final size:8
Alignment explanation
Indices: 1279112--1279149 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1279102 ACAAAATGTG
1279112 TACATATA
1 TACATATA
1279120 TACATATA
1 TACATATA
*
1279128 TATATATA
1 TACATATA
1279136 TA-ATATA
1 TACATATA
1279143 -ACATATA
1 TACATATA
1279150 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:1279934 original size:105 final size:105
Alignment explanation
Indices: 1279752--1280412 Score: 1196
Period size: 105 Copynumber: 6.3 Consensus size: 105
1279742 AGGTTTTACC
1279752 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1279817 ACGAAGGGACCGCTAGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1279857 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1279922 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1279962 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1280027 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1280067 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1280132 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
1280172 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1280237 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCCATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1280277 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* ** *
1280342 ACGAAGGGACCACTGGTTGTCATTAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
1280382 CAGAGCCAATTTCAACTTCACAATGAAGGAT
1 CAGAGCCAATTTCAACTTCACAACGAAGGAT
1280413 TTTCGGGCTC
Statistics
Matches: 542, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 542 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:1282021 original size:202 final size:199
Alignment explanation
Indices: 1281625--1282035 Score: 666
Period size: 202 Copynumber: 2.0 Consensus size: 199
1281615 TCTCGGGATT
* *
1281625 TTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATTATATTATTATTAGTTTTTT
1 TTAGTTTTAATTACCTTTTTATATTACATTATAATATTTATATATTATACTATTATTAG--TTTT
1281690 CTTTACACATTCGTATATTTATTATTAGTATAGTATTATTTCACTTATATGTTATATTATATATA
64 CTTTACACATTCGTATATTTATTATTAGTATAGTATTATTTCACTTATATGTTATATTATATATA
1281755 TATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATATTTA
129 TATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATATTTA
1281820 TTTACA
194 TTTACA
1281826 TTAG-TTTAATTACCTTTTTATATTACATTATAATATTTATATATTTTATACTATTATTAG-TTT
1 TTAGTTTTAATTACCTTTTTATATTACATTATAATATTTATATA--TTATACTATTATTAGTTTT
* * *
1281889 -TTTATACATTCGTATACATTTATTATTAGTATAGTATTATTTCATTTATGTGTTATATTATATA
64 CTTTACACATTCGTAT--ATTTATTATTAGTATAGTATTATTTCACTTATATGTTATA-T-TATA
*
1281953 TATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTTTTTACTTCTTTATTATTATA
125 TATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATA
1282018 TTTATTTACA
190 TTTATTTACA
*
1282028 TTATTTTT
1 TTAGTTTT
1282036 TTTCTATTAT
Statistics
Matches: 196, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
198 14 0.07
199 3 0.02
200 76 0.39
201 5 0.03
202 95 0.48
203 3 0.02
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.58
Consensus pattern (199 bp):
TTAGTTTTAATTACCTTTTTATATTACATTATAATATTTATATATTATACTATTATTAGTTTTCT
TTACACATTCGTATATTTATTATTAGTATAGTATTATTTCACTTATATGTTATATTATATATATA
TATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATATTTATT
TACA
Found at i:1282206 original size:13 final size:13
Alignment explanation
Indices: 1282188--1282229 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1282178 TATATATATA
1282188 TATTTTCTTATTT
1 TATTTTCTTATTT
1282201 TATTTTCATTATTT
1 TATTTTC-TTATTT
* *
1282215 TTTTTTATTATTT
1 TATTTTCTTATTT
1282228 TA
1 TA
1282230 CATGTACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTCTTATTT
Found at i:1284128 original size:13 final size:13
Alignment explanation
Indices: 1284092--1284129 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1284082 CATGTAAAAT
*
1284092 AATAATAAAA-AA
1 AATAAGAAAATAA
1284104 AATAATGAAAATAA
1 AATAA-GAAAATAA
1284118 AATAAGAAAATA
1 AATAAGAAAATA
1284130 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 5 0.22
13 11 0.48
14 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (13 bp):
AATAAGAAAATAA
Found at i:1284283 original size:18 final size:19
Alignment explanation
Indices: 1284260--1284312 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
1284250 AAGAGGGAGG
1284260 AAAAAATATAATAATAG-A
1 AAAAAATATAATAATAGTA
*
1284278 AAAAAAAATAAATAAT-GTA
1 AAAAAATAT-AATAATAGTA
*
1284297 AATAAATATAATAATA
1 AAAAAATATAATAATA
1284313 AAGAAGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAAAATATAATAATAGTA
Found at i:1284542 original size:198 final size:200
Alignment explanation
Indices: 1284290--1284691 Score: 645
Period size: 198 Copynumber: 2.0 Consensus size: 200
1284280 AAAAAATAAA
1284290 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
1 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
*
1284355 TACATATATATATATAAATAACACATAAATGAAATAATACTATACTAATAATAAATGTATACGAA
66 TACATATATATATATAAATAACACAT-AATGAAATAATACTATACTAATAAT--ATATATACGAA
* * *
1284420 -TGTATA-AAAAACTAATAATAGTATAAAATATATATAAATATTATAATGTAATAT-AAAAGGTA
128 GTGTAAAGAAAAACTAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATA
1284482 ATTAAAAC
193 ATTAAAAC
1284490 TAATGTAAAT-AA-AT-ATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAA-AAATAGGGTAAAATACAAAATGTGTACATAT
* * *
1284552 ATACATATATATATATATATAACATATAGTGAAATAATACTATACTAATAATATATATACGAATG
65 ATACATATATATATATAAATAACACATAATGAAATAATACTATACTAATAATATATATACGAA-G
*
1284617 TGTAAAGAAAAACTAATAATAATATAGAATATATATAAATATTATAATGTAATATAAAAAGATAA
129 TGTAAAGAAAAACTAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAA
1284682 TTAAAAC
194 TTAAAAC
1284689 TAA
1 TAA
1284692 AATCCCGAGA
Statistics
Matches: 189, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
195 10 0.05
197 45 0.24
198 104 0.55
199 20 0.11
200 10 0.05
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.30
Consensus pattern (200 bp):
TAATGTAAATAAATATAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
TACATATATATATATAAATAACACATAATGAAATAATACTATACTAATAATATATATACGAAGTG
TAAAGAAAAACTAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATT
AAAAC
Found at i:1286083 original size:105 final size:105
Alignment explanation
Indices: 1285901--1286560 Score: 1187
Period size: 105 Copynumber: 6.3 Consensus size: 105
1285891 GAGCCCGAAA
* * ** *
1285901 ATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTAATGACAACCAGTGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
1285966 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
* * * *
1286006 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATGGGGAAATGTTTATTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
1286071 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
1286111 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
1286176 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
*
1286216 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
*
1286281 CTTCGTCGTG-AGTTGAACTTACGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
*
1286320 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
*
1286385 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
*
1286425 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACTAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
1286490 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
1286530 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1286561 GGTAAAACCT
Statistics
Matches: 540, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
104 103 0.19
105 437 0.81
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
Found at i:1286471 original size:314 final size:315
Alignment explanation
Indices: 1285901--1286560 Score: 1187
Period size: 314 Copynumber: 2.1 Consensus size: 315
1285891 GAGCCCGAAA
* * * *
1285901 ATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTAATGACAACCAGTGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCAATGACAACCAGCGGTCC
*
1285966 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * *
1286031 GCTCTGAAATGGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
131 GCTCTGAAATGGAGAAATGTTCATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGT
1286096 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
196 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
1286161 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
261 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
**
1286216 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCAATGACAACCAGCGGTCC
*
1286281 CTTCGTCGTG-AGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
66 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* *
1286345 GCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGT
131 GCTCTGAAATGGAGAAATGTTCATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGT
1286410 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
196 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
*
1286475 GACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
261 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
1286530 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1286561 GGTAAAACCT
Statistics
Matches: 331, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
314 262 0.79
315 69 0.21
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (315 bp):
ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCAATGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
GCTCTGAAATGGAGAAATGTTCATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGT
TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTT
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
Found at i:1287395 original size:16 final size:15
Alignment explanation
Indices: 1287353--1287394 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
1287343 TCTTTTTTTT
1287353 CTTTTTTTTTTTCAA
1 CTTTTTTTTTTTCAA
1287368 CTTTTTTTTTTTCAA
1 CTTTTTTTTTTTCAA
1287383 CTTTTTTTTTTT
1 CTTTTTTTTTTT
1287395 TTTTTTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTTTTTTTTCAA
Found at i:1298141 original size:18 final size:18
Alignment explanation
Indices: 1298120--1298183 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
1298110 AGAGGAGGAA
*
1298120 AAAATATAATAATAATAG
1 AAAATAAAATAATAATAG
*
1298138 AAAAAAAAATAATAAT-G
1 AAAATAAAATAATAATAG
*
1298155 TAAATAAATATAATAATA-
1 AAAATAAA-ATAATAATAG
*
1298173 AAAAAAAAATA
1 AAAATAAAATA
1298184 GGGTAAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 10 0.26
18 28 0.74
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAAAATAATAATAG
Found at i:1298463 original size:200 final size:201
Alignment explanation
Indices: 1298150--1298554 Score: 651
Period size: 200 Copynumber: 2.0 Consensus size: 201
1298140 AAAAAAATAA
1298150 TAATGTAAATAAATATAATAATAAAAAAAAAATAGGGTAAAATACAAAATGTGTACATATATACA
1 TAATGTAAATAAATATAATAATAAAAAAAAAATAGGGTAAAATACAAAATGTGTACATATATACA
*
1298215 TATATATATATATAAATAACACATAAATGAAATAATACTATACTAATAATAAATGTATACGAA-T
66 TATATATATATATAAATAACACATAAATGAAATAATACTATACTAATAATAAATATATACGAAGT
* * *
1298279 GT-ATAAAAAACTAATAATAGTATA-AA-ATATATAAATATTATAATGTAATATAAAAAGGTAAT
131 GTAAGAAAAAACTAATAATAATATAGAATATATATAAATATTATAATGTAATATAAAAAGATAAT
1298341 TAAAAC
196 TAAAAC
1298347 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATAC-AAATGTGTACATAT
1 TAATGTAAATAAATATAATAAT-AA-AA--AAA-AAATAGGGTAAAATACAAAATGTGTACATAT
* * *
1298411 ATACATATATATATATA-ATATAACATATAAGTGAAATAATACTATACTAATAATAAATATATAC
61 ATACATATATATATATATAAATAACACATAAATGAAATAATACTATACTAATAATAAATATATAC
1298475 GAATGTGTAAGAAAAAACTAATAATAATATAGAATATATATAAATATTATAATGTAATATAAAAA
126 GAA-GTGTAAGAAAAAACTAATAATAATATAGAATATATATAAATATTATAATGTAATATAAAAA
1298540 GATAATTAAAAC
190 GATAATTAAAAC
1298552 TAA
1 TAA
1298555 AATCCCGAGA
Statistics
Matches: 191, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
197 22 0.12
198 2 0.01
199 2 0.01
200 46 0.24
201 34 0.18
202 19 0.10
203 20 0.10
204 2 0.01
205 44 0.23
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (201 bp):
TAATGTAAATAAATATAATAATAAAAAAAAAATAGGGTAAAATACAAAATGTGTACATATATACA
TATATATATATATAAATAACACATAAATGAAATAATACTATACTAATAATAAATATATACGAAGT
GTAAGAAAAAACTAATAATAATATAGAATATATATAAATATTATAATGTAATATAAAAAGATAAT
TAAAAC
Found at i:1303160 original size:19 final size:17
Alignment explanation
Indices: 1303120--1303156 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1303110 GGATTCAAAA
*
1303120 GATTATATTTAGAACTT
1 GATTATATATAGAACTT
*
1303137 GATTATATATAGAATTT
1 GATTATATATAGAACTT
1303154 GAT
1 GAT
1303157 ATTACTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.46
Consensus pattern (17 bp):
GATTATATATAGAACTT
Found at i:1310961 original size:17 final size:18
Alignment explanation
Indices: 1310918--1310958 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1310908 GAATTATATT
1310918 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1310935 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1310953 ATTAAA
1 AGTAAA
1310959 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1311037 original size:10 final size:10
Alignment explanation
Indices: 1311006--1311039 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1310996 CAGAGAGAAT
1311006 ATTTGAGAGA
1 ATTTGAGAGA
* *
1311016 AATCGAGAGA
1 ATTTGAGAGA
1311026 ATTTGAGAGA
1 ATTTGAGAGA
1311036 ATTT
1 ATTT
1311040 AGTGTGATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.29
Consensus pattern (10 bp):
ATTTGAGAGA
Found at i:1312678 original size:2 final size:2
Alignment explanation
Indices: 1312671--1312698 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1312661 AGTTAATACA
1312671 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
1312699 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1315519 original size:12 final size:12
Alignment explanation
Indices: 1315502--1315526 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1315492 TTTTTTAAAA
1315502 ATATAAAATTTT
1 ATATAAAATTTT
1315514 ATATAAAATTTT
1 ATATAAAATTTT
1315526 A
1 A
1315527 AAATTATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATAAAATTTT
Found at i:1323234 original size:18 final size:18
Alignment explanation
Indices: 1323213--1323248 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1323203 CGTGTTCATT
1323213 TGTTTAATGTTTGTGAAC
1 TGTTTAATGTTTGTGAAC
1323231 TGTTTAATGTTTGTGAAC
1 TGTTTAATGTTTGTGAAC
1323249 ATAATCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (18 bp):
TGTTTAATGTTTGTGAAC
Found at i:1323554 original size:19 final size:19
Alignment explanation
Indices: 1323530--1323568 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1323520 GTTTGTTTAT
1323530 TAAATGAACATTATACGAA
1 TAAATGAACATTATACGAA
1323549 TAAATGAACATTATACGAA
1 TAAATGAACATTATACGAA
1323568 T
1 T
1323569 GATTTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (19 bp):
TAAATGAACATTATACGAA
Found at i:1326797 original size:18 final size:19
Alignment explanation
Indices: 1326769--1326806 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1326759 AAATGGTTTG
1326769 ATTGTAAAGTTCAATGAGA
1 ATTGTAAAGTTCAATGAGA
*
1326788 ATTG-AAAGTTGAATGAGA
1 ATTGTAAAGTTCAATGAGA
1326806 A
1 A
1326807 AAAAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.29
Consensus pattern (19 bp):
ATTGTAAAGTTCAATGAGA
Found at i:1327684 original size:2 final size:2
Alignment explanation
Indices: 1327677--1327735 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1327667 AAATTAAAAT
1327677 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1327719 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1327736 TCTATTAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1333783 original size:64 final size:64
Alignment explanation
Indices: 1333706--1333842 Score: 222
Period size: 64 Copynumber: 2.2 Consensus size: 64
1333696 CACTTATATA
* * * *
1333706 TTTT-ATTGTACATAAAATACGATCGAATGAAAATCTAGGAATGGCAAGTGTCCAATATGTATT
1 TTTTAATTATACATAAAATACGATCGAATGAAAATCTAAGAATGGCAAGTGTCCAAAATGTAAT
*
1333769 TTTTAATTATACATAAAATACGATTGAATGAAAATCTAAGAATGGCAAGTGTCCAAAATGTAAT
1 TTTTAATTATACATAAAATACGATCGAATGAAAATCTAAGAATGGCAAGTGTCCAAAATGTAAT
1333833 TTTTAATTAT
1 TTTTAATTAT
1333843 TTAAATTTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 4 0.06
64 64 0.94
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (64 bp):
TTTTAATTATACATAAAATACGATCGAATGAAAATCTAAGAATGGCAAGTGTCCAAAATGTAAT
Found at i:1334147 original size:16 final size:16
Alignment explanation
Indices: 1334123--1334160 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1334113 TTTTATCAAC
*
1334123 AATTAGTTGATAACAT
1 AATTTGTTGATAACAT
1334139 AATTTGTTGATAACAT
1 AATTTGTTGATAACAT
1334155 ATATTT
1 A-ATTT
1334161 TGAATCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (16 bp):
AATTTGTTGATAACAT
Found at i:1335091 original size:16 final size:17
Alignment explanation
Indices: 1335051--1335092 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1335041 AATGATGGAT
*
1335051 ATATAAATTTTTTAAAA
1 ATATAAATTTTTAAAAA
1335068 ATATAAATTTTTAAAAA
1 ATATAAATTTTTAAAAA
1335085 ATA-AAATT
1 ATATAAATT
1335093 ATTATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAAATTTTTAAAAA
Found at i:1335091 original size:22 final size:23
Alignment explanation
Indices: 1335063--1335107 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1335053 ATAAATTTTT
*
1335063 TAAAAATATAAATTTTTAAAAAA
1 TAAAATTATAAATTTTTAAAAAA
* *
1335086 TAAAATTATTATTTTTTAAAAA
1 TAAAATTATAAATTTTTAAAAA
1335108 TTCCAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAATTATAAATTTTTAAAAAA
Found at i:1341325 original size:17 final size:16
Alignment explanation
Indices: 1341286--1341332 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1341276 ATTTATTTTA
* *
1341286 ATTACTATATTTATAT
1 ATTATTATATTTAAAT
1341302 ATTATTATATTTAAAT
1 ATTATTATATTTAAAT
*
1341318 ATTTATTACATTTAA
1 A-TTATTATATTTAA
1341333 TAATTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATTATATTTAAAT
Found at i:1341380 original size:18 final size:18
Alignment explanation
Indices: 1341251--1341538 Score: 53
Period size: 18 Copynumber: 16.7 Consensus size: 18
1341241 TTTCAAAATA
1341251 TATTATAAT-TA-TT-TT
1 TATTATAATATATTTATT
*
1341266 T-TTATAAAATATTTATT
1 TATTATAATATATTTATT
* * *
1341283 T-TAATTACTATATTTATA
1 TATTA-TAATATATTTATT
**
1341301 TATTAT--TATATTTAAA
1 TATTATAATATATTTATT
* * *
1341317 TATT-TATTACATTTAAT
1 TATTATAATATATTTATT
* * *
1341334 AATTAATATTATTAGTTATT
1 TATT-ATAATA-TATTTATT
1341354 T-TTAT--TATATTTATT
1 TATTATAATATATTTATT
1341369 TATTATAATATAATTT-TT
1 TATTATAATAT-ATTTATT
* **
1341387 CATTATTTCAA-A-ATTTACA
1 TATTA--T-AATATATTTATT
* * * *
1341406 AAATATATTATAATTATT
1 TATTATAATATATTTATT
* * *
1341424 TTTTATAAAATATCTATT
1 TATTATAATATATTTATT
* * *
1341442 T-TAATTACTATATTTATA
1 TATTA-TAATATATTTATT
*
1341460 TATTATTATAT-TTTAATT
1 TATTATAATATATTT-ATT
*
1341478 AATTAT--TATATTTAATT
1 TATTATAATATATTT-ATT
* * * *
1341495 TAATATTAT-TAATTA-A
1 TATTATAATATATTTATT
1341511 TATTAT--TATATTTATT
1 TATTATAATATATTTATT
1341527 TATTATAATATA
1 TATTATAATATA
1341539 ATTTTTCATT
Statistics
Matches: 195, Mismatches: 48, Indels: 57
0.65 0.16 0.19
Matches are distributed among these distances:
14 7 0.04
15 17 0.09
16 36 0.18
17 35 0.18
18 72 0.37
19 19 0.10
20 7 0.04
21 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATAATATATTTATT
Found at i:1341521 original size:33 final size:29
Alignment explanation
Indices: 1341438--1341528 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 29
1341428 ATAAAATATC
*
1341438 TATTTTAATTACTATATTTATATATTA-TT-A
1 TATTTTAATTAAT-TA-TTATAT-TTATTTAA
1341468 TATTTTAATTAATTATTATATTTAATTTAA
1 TATTTTAATTAATTATTATATTT-ATTTAA
1341498 TATTATTAATTAATATTATTATATTTATTTA
1 TATT-TTAATT-A-ATTATTATATTTATTTA
1341529 TTATAATATA
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
27 2 0.04
28 7 0.13
29 4 0.07
30 17 0.31
31 6 0.11
32 6 0.11
33 12 0.22
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTTTAATTAATTATTATATTTATTTAA
Found at i:1341545 original size:158 final size:158
Alignment explanation
Indices: 1341238--1341704 Score: 776
Period size: 158 Copynumber: 2.9 Consensus size: 158
1341228 ATTCAAATTC
*
1341238 AAATTT-CAAAATATATTATAATTATTTTTTTATAAAATATTTATTTTAATTACTATATTTATAT
1 AAATTTACAAAATATATTATAATTA-TTTTTTATAAAATATCTATTTTAATTACTATATTTATAT
* * * *
1341302 ATTATTATATTTAAATATTTATTACATTTAATAATTAATATTATTAGTTATTTTTATTATATTTA
65 ATTATTATATTTAATTATTTATTATATTTAAT-ATTAATATTATTAATTATTATTATTATATTTA
1341367 TTTATTATAATATAATTTTTCATTATTTCA
129 TTTATTATAATATAATTTTTCATTATTTCA
1341397 AAATTTACAAAATATATTATAATTATTTTTTATAAAATATCTATTTTAATTACTATATTTATATA
1 AAATTTACAAAATATATTATAATTATTTTTTATAAAATATCTATTTTAATTACTATATTTATATA
* *
1341462 TTATTATATTTTAATTAATTATTATATTTAAT-TTAATATTATTAATTAATATTATTATATTTAT
66 TTATTATA-TTTAATTATTTATTATATTTAATATTAATATTATTAATTATTATTATTATATTTAT
1341526 TTATTATAATATAATTTTTCATTATTTCA
130 TTATTATAATATAATTTTTCATTATTTCA
* *
1341555 AAATTTACAAAATATATCATAATTATTTTTTATAAAATTTCTATTTTAATTACTATATTTATATA
1 AAATTTACAAAATATATTATAATTATTTTTTATAAAATATCTATTTTAATTACTATATTTATATA
1341620 TTATTATATTTAATTATTTATTATATTTAATAATTAATATTATTATTATTATTATTATTATATTT
66 TTATTATATTTAATTATTTATTATATTTAAT-ATTAATATTATTA--ATTATTATTATTATATTT
*
1341685 ATTTATTATAATATGATTTT
128 ATTTATTATAATATAATTTT
1341705 ATTTATATGT
Statistics
Matches: 290, Mismatches: 12, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
157 22 0.08
158 129 0.44
159 65 0.22
160 38 0.13
161 36 0.12
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (158 bp):
AAATTTACAAAATATATTATAATTATTTTTTATAAAATATCTATTTTAATTACTATATTTATATA
TTATTATATTTAATTATTTATTATATTTAATATTAATATTATTAATTATTATTATTATATTTATT
TATTATAATATAATTTTTCATTATTTCA
Found at i:1341626 original size:3 final size:3
Alignment explanation
Indices: 1341613--1341693 Score: 55
Period size: 3 Copynumber: 27.3 Consensus size: 3
1341603 ATTACTATAT
* * *
1341613 TTA TATA TTA TTA -TA TT- TAA TTA TTTA TTA -TA TT- TAA TAA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
1341656 ATA TTA TTA TTA TTA TTA TTA TTA -TA TTTA TTTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA T
1341694 AATATGATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 8 0.12
3 44 0.69
4 12 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1341648 original size:9 final size:9
Alignment explanation
Indices: 1341608--1341691 Score: 65
Period size: 9 Copynumber: 9.7 Consensus size: 9
1341598 TTTTAATTAC
1341608 TATATTTA-
1 TATATTTAT
1341616 TATA-TTAT
1 TATATTTAT
*
1341624 TATATTTAA
1 TATATTTAT
1341633 T-TATTTAT
1 TATATTTAT
*
1341641 TATATTTAA
1 TATATTTAT
1341650 TA-ATTAATAT
1 TATATT--TAT
1341660 TAT-TATTAT
1 TATAT-TTAT
1341669 TAT-TATTAT
1 TATAT-TTAT
1341678 TATATTTAT
1 TATATTTAT
1341687 T-TATT
1 TATATT
1341692 ATAATATGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
7 3 0.05
8 22 0.34
9 32 0.50
10 6 0.09
11 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATATTTAT
Found at i:1341707 original size:24 final size:25
Alignment explanation
Indices: 1341608--1341710 Score: 64
Period size: 24 Copynumber: 4.4 Consensus size: 25
1341598 TTTTAATTAC
*
1341608 TATATTTATATATTATT-ATAT--T
1 TATATTTATTTATTATTAATATGAT
1341630 TA-A-TTATTTATTATATTTAATA--AT
1 TATATTTATTTA-T-TA-TTAATATGAT
* *
1341654 TA-ATATTA-TTATTATTATTATTAT
1 TATAT-TTATTTATTATTAATATGAT
1341678 TATATTTATTTATTA-TAATATGAT
1 TATATTTATTTATTATTAATATGAT
*
1341702 TTTATTTAT
1 TATATTTAT
1341711 ATGTTTCAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
20 6 0.09
21 2 0.03
22 9 0.14
23 4 0.06
24 30 0.46
25 11 0.17
26 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (25 bp):
TATATTTATTTATTATTAATATGAT
Found at i:1345190 original size:53 final size:54
Alignment explanation
Indices: 1345110--1345221 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 54
1345100 TGCTATTAAA
1345110 ATTTCACAATCACAATACTTGTAGTGACTG-TCATCTGTTATGTTAACAATAGC
1 ATTTCACAATCACAATACTTGTAGTGACTGATCATCTGTTATGTTAACAATAGC
*
1345163 ATTTCACAATCACAATACTTGTAGTGACTGAAATATCATCTGTTATGTTAACAGTAGC
1 ATTTCACAATCACAATACTTGTAGTGACTG----ATCATCTGTTATGTTAACAATAGC
1345221 A
1 A
1345222 ATAAACGCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
53 30 0.57
58 23 0.43
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (54 bp):
ATTTCACAATCACAATACTTGTAGTGACTGATCATCTGTTATGTTAACAATAGC
Found at i:1348246 original size:22 final size:22
Alignment explanation
Indices: 1348218--1348269 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1348208 AGATCGTGTA
1348218 ATAACGGTTTTAGTATCATTAT
1 ATAACGGTTTTAGTATCATTAT
*
1348240 ATAACGGTTTTAGTATCGTTAT
1 ATAACGGTTTTAGTATCATTAT
1348262 ATAACGGT
1 ATAACGGT
1348270 CAATATTCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (22 bp):
ATAACGGTTTTAGTATCATTAT
Found at i:1352071 original size:16 final size:17
Alignment explanation
Indices: 1352047--1352078 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1352037 ACACAATTGG
1352047 CATATTCTATTTTATCA
1 CATATTCTATTTTATCA
1352064 CATA-TCTATTTTATC
1 CATATTCTATTTTATC
1352079 GATGTTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (17 bp):
CATATTCTATTTTATCA
Found at i:1357004 original size:23 final size:21
Alignment explanation
Indices: 1356966--1357007 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
1356956 TAGGGTTATA
1356966 ATTTTTTATTAAATTTAAATC
1 ATTTTTTATTAAATTTAAATC
1356987 ATTTATTTATTTAAATTTAAA
1 ATTT-TTTA-TTAAATTTAAA
1357008 GATTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTATTAAATTTAAATC
Found at i:1362110 original size:18 final size:18
Alignment explanation
Indices: 1362087--1362121 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1362077 TTCCATCCGG
*
1362087 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1362105 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1362122 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1363230 original size:7 final size:7
Alignment explanation
Indices: 1363218--1363255 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
1363208 GTCAACAGTA
1363218 GTCAACG
1 GTCAACG
1363225 GTCAACGG
1 GTCAAC-G
1363233 GTCAACG
1 GTCAACG
1363240 GTCAACGG
1 GTCAAC-G
1363248 GTCAACG
1 GTCAACG
1363255 G
1 G
1363256 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.13
Consensus pattern (7 bp):
GTCAACG
Found at i:1363237 original size:8 final size:8
Alignment explanation
Indices: 1363218--1363289 Score: 73
Period size: 8 Copynumber: 9.4 Consensus size: 8
1363208 GTCAACAGTA
1363218 GTCAAC-G
1 GTCAACGG
1363225 GTCAACGG
1 GTCAACGG
1363233 GTCAAC-G
1 GTCAACGG
1363240 GTCAACGG
1 GTCAACGG
1363248 GTCAACGG
1 GTCAACGG
1363256 GT---CGG
1 GTCAACGG
*
1363261 GTCAACGA
1 GTCAACGG
*
1363269 GTCGAGTCGG
1 GTC-A-ACGG
1363279 GTCAACGG
1 GTCAACGG
1363287 GTC
1 GTC
1363290 GGGTAAACGG
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
5 5 0.09
7 13 0.24
8 29 0.54
9 2 0.04
10 5 0.09
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:1363238 original size:15 final size:15
Alignment explanation
Indices: 1363218--1363255 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1363208 GTCAACAGTA
1363218 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
1363233 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
1363248 GTCAACGG
1 GTCAACGG
1363256 GTCGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.13
Consensus pattern (15 bp):
GTCAACGGTCAACGG
Found at i:1363263 original size:13 final size:13
Alignment explanation
Indices: 1363245--1363307 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
1363235 CAACGGTCAA
1363245 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1363258 CGGGTCAACGAGTCGAGT
1 CGGGTCAAC--G--G-GT
1363276 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
1363289 CGGGTAAACGGGT
1 CGGGTCAACGGGT
1363302 CGGGTC
1 CGGGTC
1363308 GGGTAAACGG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.65
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.26
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1363279 original size:18 final size:18
Alignment explanation
Indices: 1363256--1363290 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1363246 GGGTCAACGG
1363256 GTCGGGTCAACGAGTCGA
1 GTCGGGTCAACGAGTCGA
*
1363274 GTCGGGTCAACGGGTCG
1 GTCGGGTCAACGAGTCG
1363291 GGTAAACGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (18 bp):
GTCGGGTCAACGAGTCGA
Found at i:1363283 original size:31 final size:30
Alignment explanation
Indices: 1363230--1363325 Score: 124
Period size: 31 Copynumber: 3.2 Consensus size: 30
1363220 CAACGGTCAA
*
1363230 CGGGTCAACGGTC-A-ACGGGTCAACGGGT
1 CGGGTCAACGGTCGAGTCGGGTCAACGGGT
1363258 CGGGTCAACGAGTCGAGTCGGGTCAACGGGT
1 CGGGTCAACG-GTCGAGTCGGGTCAACGGGT
* * *
1363289 CGGGTAAACGGGTCGGGTCGGGTAAACGGGT
1 CGGGTCAAC-GGTCGAGTCGGGTCAACGGGT
1363320 CGGGTC
1 CGGGTC
1363326 GGTTGTGACC
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.17
29 3 0.05
30 1 0.02
31 44 0.75
32 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.44, T:0.16
Consensus pattern (30 bp):
CGGGTCAACGGTCGAGTCGGGTCAACGGGT
Found at i:1363305 original size:18 final size:18
Alignment explanation
Indices: 1363284--1363327 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
1363274 GTCGGGTCAA
1363284 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1363302 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1363320 CGGGTCGG
1 CGGGTCGG
1363328 TTGTGACCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.14, C:0.18, G:0.52, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1367101 original size:18 final size:18
Alignment explanation
Indices: 1367078--1367112 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1367068 TTCCATCCGG
*
1367078 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1367096 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1367113 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1368221 original size:7 final size:7
Alignment explanation
Indices: 1368209--1368246 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
1368199 GTCAACAGTA
1368209 GTCAACG
1 GTCAACG
1368216 GTCAACGG
1 GTCAAC-G
1368224 GTCAACG
1 GTCAACG
1368231 GTCAACGG
1 GTCAAC-G
1368239 GTCAACG
1 GTCAACG
1368246 G
1 G
1368247 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.13
Consensus pattern (7 bp):
GTCAACG
Found at i:1368228 original size:8 final size:8
Alignment explanation
Indices: 1368209--1368280 Score: 73
Period size: 8 Copynumber: 9.4 Consensus size: 8
1368199 GTCAACAGTA
1368209 GTCAAC-G
1 GTCAACGG
1368216 GTCAACGG
1 GTCAACGG
1368224 GTCAAC-G
1 GTCAACGG
1368231 GTCAACGG
1 GTCAACGG
1368239 GTCAACGG
1 GTCAACGG
1368247 GT---CGG
1 GTCAACGG
*
1368252 GTCAACGA
1 GTCAACGG
*
1368260 GTCGAGTCGG
1 GTC-A-ACGG
1368270 GTCAACGG
1 GTCAACGG
1368278 GTC
1 GTC
1368281 GGGTAACGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
5 5 0.09
7 13 0.24
8 29 0.54
9 2 0.04
10 5 0.09
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Done.