Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007889.1 Hibiscus syriacus cultivar Beakdansim tig00110271_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: 1663484
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1594350 original size:2 final size:2
Alignment explanation
Indices: 1594343--1594373 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1594333 TGTCAGAAAG
1594343 AT AT AT 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 AT AT AT A
1594374 GCTTTTGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1596396 original size:22 final size:22
Alignment explanation
Indices: 1596345--1596405 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
1596335 TTCAAAAATG
*
1596345 GTATCGATACCATA-T-T-ATA
1 GTATCGATACCATAGTATGGTA
*
1596364 GTATTGATACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
* *
1596386 GTATCGCTACCATGGTATGG
1 GTATCGATACCATAGTATGG
1596406 GTACCGATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 13 0.38
20 1 0.03
21 1 0.03
22 19 0.56
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:1596894 original size:45 final size:45
Alignment explanation
Indices: 1596830--1597286 Score: 774
Period size: 45 Copynumber: 10.2 Consensus size: 45
1596820 TGAAAATAAT
* * * *
1596830 AATGCATATGGGTGCATTATCAACAGAAAAATATACCATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
1596875 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
1596920 AATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
1596965 AATGCATATGGGTGCATTATCAACA-AAAAATATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
1597009 AATGCATATGGGTGCATTATCAATATAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
1597054 AATGCATATGGGTGCATTATCAACAGAAAATTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
1597099 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
1597144 AATGCATATGGGTGCATTATCAACATAAAAGTATGCAATAGTTAA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
1597189 AATG-ATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
1597233 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTG-A
1597279 AATGCATA
1 AATGCATA
1597287 ATGGTTCATT
Statistics
Matches: 391, Mismatches: 18, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
44 83 0.21
45 299 0.76
46 9 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
Found at i:1597051 original size:134 final size:135
Alignment explanation
Indices: 1596830--1597286 Score: 783
Period size: 134 Copynumber: 3.4 Consensus size: 135
1596820 TGAAAATAAT
* *
1596830 AATGCATATGGGTGCATTATCAACAGAAAAATATACCATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
* *
1596895 CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCTATA
1596960 GTTGA
131 GTTGA
1596965 AATGCATATGGGTGCATTATCAACA-AAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
* * *
1597029 CAATATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAATTATGCTATA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCTATA
1597094 GTTGA
131 GTTGA
*
1597099 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
* *
1597164 CAACATAAAAGTATGCAATAGTTAAAATG-ATATGGGTGCATTATCAACATAAAAGTATGCTATA
66 CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCTATA
1597228 GTTGA
131 GTTGA
* *
1597233 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAAATGCATA
1 AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTG-AAATGCATA
1597287 ATGGTTCATT
Statistics
Matches: 306, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
134 208 0.68
135 98 0.32
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (135 bp):
AATGCATATGGGTGCATTATCAACAGAAAAATATGCTATAGTTGAAATGCATATGGGTGCATTAT
CAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCTATA
GTTGA
Found at i:1597131 original size:179 final size:180
Alignment explanation
Indices: 1596830--1597286 Score: 783
Period size: 179 Copynumber: 2.5 Consensus size: 180
1596820 TGAAAATAAT
* * * *
1596830 AATGCATATGGGTGCATTATCAACAGAAAAATATACCATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
*
1596895 CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATA
66 CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCCATA
* *
1596960 GTTGAAATGCATATGGGTGCATTATCAACA-AAAAATATGCTATAGTTGA
131 GTTGAAATGCATATGGGTGCATTATCAACATAAAAATATGCAATAGTTAA
*
1597009 AATGCATATGGGTGCATTATCAATATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
* *
1597074 CAACAGAAAATTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATA
66 CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCCATA
*
1597139 GTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCAATAGTTAA
131 GTTGAAATGCATATGGGTGCATTATCAACATAAAAATATGCAATAGTTAA
1597189 AATG-ATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
*
1597253 CAACATAAAAGTATGCTATAGTTGAAAATGCATA
66 CAACAGAAAAGTATGCTATAGTTG-AAATGCATA
1597287 ATGGTTCATT
Statistics
Matches: 262, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
179 233 0.89
180 29 0.11
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (180 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTAT
CAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCCATA
GTTGAAATGCATATGGGTGCATTATCAACATAAAAATATGCAATAGTTAA
Found at i:1599228 original size:17 final size:17
Alignment explanation
Indices: 1599208--1599266 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1599198 TTTAGGGAAG
1599208 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
1599225 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
1599241 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
1599258 TAGTTCATT
1 TAGTTCATT
1599267 GAATAAAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:1606805 original size:20 final size:20
Alignment explanation
Indices: 1606779--1606830 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1606769 TGATTCAATT
1606779 GGTATCGATACCGAAGGG-A
1 GGTATCGATACCGAAGGGAA
*
1606798 GAGTATCGATACTGAAGGGAA
1 G-GTATCGATACCGAAGGGAA
1606819 GGTATCGATACC
1 GGTATCGATACC
1606831 ATTTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (20 bp):
GGTATCGATACCGAAGGGAA
Found at i:1606881 original size:19 final size:19
Alignment explanation
Indices: 1606854--1606912 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
1606844 TGCAAAAATG
1606854 GTATCGATACCATAGTATA
1 GTATCGATACCATAGTATA
*
1606873 GTATTGATACCATAGTATGGTA
1 GTATCGATACCATAGTA---TA
*
1606895 GTATCGATACCATGGTAT
1 GTATCGATACCATAGTAT
1606913 GGGTATCGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 17 0.50
22 17 0.50
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (19 bp):
GTATCGATACCATAGTATA
Found at i:1606903 original size:22 final size:22
Alignment explanation
Indices: 1606854--1606914 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
1606844 TGCAAAAATG
1606854 GTATCGATACCATAGTA---TA
1 GTATCGATACCATAGTATGGTA
*
1606873 GTATTGATACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
*
1606895 GTATCGATACCATGGTATGG
1 GTATCGATACCATAGTATGG
1606915 GTATCGTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 16 0.44
22 20 0.56
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:1610893 original size:34 final size:33
Alignment explanation
Indices: 1610841--1610908 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
1610831 CGTTCCATAC
* *
1610841 AGCATCCGTGATAAGGGCTGAATAAGTAAAACT
1 AGCATCCGTAATAAGGGCTGAATAAGAAAAACT
1610874 AGCATCCGTTAATAAGGGCTGAATAAGAAAAACT
1 AGCATCCG-TAATAAGGGCTGAATAAGAAAAACT
1610908 A
1 A
1610909 TATGGTGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 8 0.25
34 24 0.75
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (33 bp):
AGCATCCGTAATAAGGGCTGAATAAGAAAAACT
Found at i:1617677 original size:7 final size:7
Alignment explanation
Indices: 1617665--1617730 Score: 132
Period size: 7 Copynumber: 9.4 Consensus size: 7
1617655 AGGAAGGAAG
1617665 GAATTTA
1 GAATTTA
1617672 GAATTTA
1 GAATTTA
1617679 GAATTTA
1 GAATTTA
1617686 GAATTTA
1 GAATTTA
1617693 GAATTTA
1 GAATTTA
1617700 GAATTTA
1 GAATTTA
1617707 GAATTTA
1 GAATTTA
1617714 GAATTTA
1 GAATTTA
1617721 GAATTTA
1 GAATTTA
1617728 GAA
1 GAA
1617731 CACACGCTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (7 bp):
GAATTTA
Found at i:1618625 original size:34 final size:30
Alignment explanation
Indices: 1618587--1618655 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
1618577 TTGATATGAC
*
1618587 AATTTAAGGCAAAATGGTTTTTGTACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1618621 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1618650 AATTTA
1 AATTTA
1618656 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1618666 original size:29 final size:30
Alignment explanation
Indices: 1618596--1618655 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1618586 CAATTTAAGG
*
1618596 CAAAATGGTTTTTGTACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1618627 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1618656 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1618973 original size:21 final size:21
Alignment explanation
Indices: 1618940--1618979 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1618930 TTTGAGTAGA
*
1618940 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1618962 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1618980 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1620143 original size:19 final size:20
Alignment explanation
Indices: 1620119--1620166 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1620109 AACGATTTTC
*
1620119 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1620138 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1620158 TTTTGAAAA
1 TTTTGAAAA
1620167 GGATTTAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1621466 original size:34 final size:30
Alignment explanation
Indices: 1621428--1621496 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1621418 TTGATATAAC
1621428 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1621462 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1621491 AATTTA
1 AATTTA
1621497 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1621507 original size:29 final size:30
Alignment explanation
Indices: 1621437--1621496 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1621427 CAATTTAAGG
1621437 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1621468 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1621497 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1621602 original size:21 final size:21
Alignment explanation
Indices: 1621576--1621633 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1621566 AGGGTGTCAA
1621576 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1621597 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
1621618 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
1621634 TGCACTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1621877 original size:20 final size:22
Alignment explanation
Indices: 1621839--1621878 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1621829 TTTGAGTAGA
1621839 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1621861 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1621879 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1625158 original size:3 final size:3
Alignment explanation
Indices: 1625143--1625228 Score: 66
Period size: 3 Copynumber: 28.7 Consensus size: 3
1625133 CTTTTCTTTT
* * * * *
1625143 TTA TTA TTT TTA TTA TTA TAA TAA TAA TTA TAA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** *
1625190 TAA TTA TAA TTA TTA TTA CCA TTA CTA TTAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TT
1625229 CTTAATAAAT
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1625192 original size:29 final size:30
Alignment explanation
Indices: 1625145--1625207 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
1625135 TTTCTTTTTT
*
1625145 ATTATTTTTATTATTATAATAATAATTATA
1 ATTATTATTATTATTATAATAATAATTATA
* *
1625175 ATTATTATT-TTATTATAATTATAATTATT
1 ATTATTATTATTATTATAATAATAATTATA
1625204 ATTA
1 ATTA
1625208 CCATTACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTATTATTATTATTATAATAATAATTATA
Found at i:1626402 original size:2 final size:2
Alignment explanation
Indices: 1626395--1626438 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1626385 TTATAAAACC
*
1626395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1626437 TA
1 TA
1626439 ATTGAACCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1631854 original size:46 final size:47
Alignment explanation
Indices: 1631798--1631936 Score: 145
Period size: 54 Copynumber: 2.8 Consensus size: 47
1631788 TGATTGAGAA
* * * *
1631798 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTGTC-TGCGAAC
1 ATCTGTGCAGAAACCACAAGAAATGATGAATGTGTTGTCTTACGAAC
* *
1631844 ATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAATTATTTTACGAAC
1 ATCTGTGCAGAAACCACAAGAAATGATGAATGTGTTGTC-------TTACGAAC
*
1631898 ATCTGTACAGAAACCACAAGAAATGATGAATGTGTTGTC
1 ATCTGTGCAGAAACCACAAGAAATGATGAATGTGTTGTC
1631937 AAATATTTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
46 35 0.45
54 42 0.55
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.26
Consensus pattern (47 bp):
ATCTGTGCAGAAACCACAAGAAATGATGAATGTGTTGTCTTACGAAC
Found at i:1631903 original size:54 final size:54
Alignment explanation
Indices: 1631839--1631951 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
1631829 GTGTTGTCTG
* * *
1631839 CGAACATCTGTGCAGAAACCACATGAAAGGATGAATGTGTTGTCAATTATTTTA
1 CGAACATCTGTACAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATATTTTA
*
1631893 CGAACATCTGTACAGAAACCACAAGAAATGATGAATGTGTTGTCAAATATTTTA
1 CGAACATCTGTACAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATATTTTA
*
1631947 TGAAC
1 CGAAC
1631952 CAGTGGTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (54 bp):
CGAACATCTGTACAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATATTTTA
Found at i:1633642 original size:217 final size:218
Alignment explanation
Indices: 1633001--1633909 Score: 1322
Period size: 219 Copynumber: 4.2 Consensus size: 218
1632991 CTATTTCCCT
* * *
1633001 AGATGATAAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1 AGATGATAAAG-CCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTT
* *
1633066 AGAAACTAAGCCTTCGAGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
65 AGAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
* * * * * *
1633131 CAAAGGGGTTCCTTTACAACTAATAAACTAAGCCTTCGGAAGTTTCTTGATTTGTAAATCCTTCG
130 CAAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGAGTTTCTTAATTTTTAAATCCTTCG
* *
1633196 GGTCATATGTAAGCCTTTCGAGTA
195 GGTCATCTGTAAGCCTTTCGAGCA
* * *
1633220 TGAAAGATAAAGCCTTCGGGTCATCCATATGACCTTCAATGCTGGATGTTTTCAAATGAGATTTT
1 AG-ATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTT
1633285 AGAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
65 AGAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAA
* * *
1633350 CAAAGGGGTTCATTTACAACTAATAAACTAAGCCTTCGGGAGTTTCTTAATTTATAAATCCTTCG
130 CAAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGAGTTTCTTAATTTTTAAATCCTTCG
*
1633415 AGTCATCTGTAAGCCTTTCGAGCA
195 GGTCATCTGTAAGCCTTTCGAGCA
* *
1633439 GGATGATAAAGCCTTCGGGTTATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTTA
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTTA
*
1633504 GAAACTAAGCTTTCGGGGGTTTGCT-ATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAC
66 GAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAC
* * *
1633568 AAAGGGGTTCATTGACAACTTAGAAACTAAGCCTTCGGGGGTTTCTTAATTTTTAAATTCTTCGG
131 AAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGAGTTTCTTAATTTTTAAATCCTTCGG
* * * *
1633633 GTTATCTGTAAGCTTTTGGAACA
196 GTCATCTGTAAGCCTTTCGAGCA
* * * *
1633656 AGATGATAAAGCCTTTGGGTCATCCATAAGACCTTCAGTGATGAATGTTTTCAAATGAGATTTTA
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTTA
* ** * *
1633721 GAAACTAAGCCTTT-GGGGGTTTCTTAATTATCTTGAAAGAGTTGCTAAA-GAATGCTAGGCCTA
66 GAAACTAAG-CTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAA-GCTAAGCCTA
* * * * *
1633784 ACAAAGGTGTTCCTTGACAATTAAGAAACTAAGCCTTTAGGG-GTTTCTTGATTTTTAAATCCTT
129 ACAAAGGGGTTCATTGACAACTAAGAAACTAAGCC-TTCGGGAGTTTCTTAATTTTTAAATCCTT
* *
1633848 CGGGGTCATCTGTAAACCTTTCGAGAA
193 C-GGGTCATCTGTAAGCCTTTCGAGCA
1633875 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTT
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTT
1633910 GATAACTAAG
Statistics
Matches: 627, Mismatches: 57, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
217 196 0.31
218 169 0.27
219 254 0.41
220 8 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (218 bp):
AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCTGGATGTTTTCAAATGAGATTTTA
GAAACTAAGCTTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAC
AAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGGAGTTTCTTAATTTTTAAATCCTTCGG
GTCATCTGTAAGCCTTTCGAGCA
Found at i:1634337 original size:3 final size:3
Alignment explanation
Indices: 1634329--1634411 Score: 82
Period size: 3 Copynumber: 28.3 Consensus size: 3
1634319 CCCTTTTCTT
* * *
1634329 TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTT TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1634376 TTA TTT TTA TTA TTA -AA TAA TT- TTA TTTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA T
1634412 AGGCCCGAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
2 5 0.07
3 60 0.88
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1634377 original size:20 final size:20
Alignment explanation
Indices: 1634330--1634412 Score: 105
Period size: 20 Copynumber: 4.1 Consensus size: 20
1634320 CCTTTTCTTT
* *
1634330 TATTATTATTATTATTATAA
1 TATTATTATTTTTATTATTA
1634350 TAATTATTATTTTTATTATTA
1 T-ATTATTATTTTTATTATTA
1634371 TATTATTATTTTTATTATTA
1 TATTATTATTTTTATTATTA
* *
1634391 AATAATT-TTATTTATTATTA
1 TATTATTATT-TTTATTATTA
1634411 TA
1 TA
1634413 GGCCCGAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 2 0.04
20 36 0.64
21 18 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATTTTTATTATTA
Found at i:1637135 original size:54 final size:54
Alignment explanation
Indices: 1637005--1637369 Score: 446
Period size: 54 Copynumber: 6.8 Consensus size: 54
1636995 CCAAATAGGA
* * * * *
1637005 ACTAAGTGTGCAATTCATGGAATTCTTCATATGTTGATGAAAAACCATTTC-AG
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
*
1637058 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAATCATTTCGAC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * *
1637112 AATATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * *
1637166 ACTAAGTTTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGAC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * * * * *
1637220 ACTATGTGTGCTACTCACGAAATTCATCATTTGTTGATGAACAATCGTTTC-AGC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGA-C
* * * * ** *
1637274 AATATATGTGCAACTCACGAAATTCATCATATGTTGATGAACAACTGTTTCGGC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * * *
1637328 ACTAAGTGTGCAATTCATGAAATTCATCATATTTTGATGAAC
1 ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAAC
1637370 GATCGCATAG
Statistics
Matches: 271, Mismatches: 38, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
53 47 0.17
54 224 0.83
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (54 bp):
ACTATGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGAC
Found at i:1637286 original size:162 final size:160
Alignment explanation
Indices: 1637005--1637369 Score: 534
Period size: 162 Copynumber: 2.3 Consensus size: 160
1636995 CCAAATAGGA
* * * *
1637005 ACTAAGTGTGCAATTCATGGAATTCTTCATATGTTGATGAAAAACCATTTCAGACTATGTGTGCA
1 ACTAAGTGTGCAATTCA-AGAATTCATCATATGTTGATGAACAACCATTTCACACTATGTGTGCA
* * * *
1637070 ATTCACGGAATTCATCATATGTTGATGAACAATCATTTCGACAATATGTGTGCAACTCACGGAAT
65 ACTCACGAAATTCATCATATGTTGATGAACAATCATTTCGACAATATATGTGCAACTCACGAAAT
1637135 TCATCATATGTTGATGAACAACCATTTCGGC
130 TCATCATATGTTGATGAACAACCATTTCGGC
*
1637166 ACTAAGTTTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGACACTATGTGTGC
1 ACTAAGTGTGCAATTCA-AGAATTCATCATATGTTGATGAACAACCATTTC-ACACTATGTGTGC
* * *
1637231 TACTCACGAAATTCATCATTTGTTGATGAACAATCGTTTC-AGCAATATATGTGCAACTCACGAA
64 AACTCACGAAATTCATCATATGTTGATGAACAATCATTTCGA-CAATATATGTGCAACTCACGAA
**
1637295 ATTCATCATATGTTGATGAACAACTGTTTCGGC
128 ATTCATCATATGTTGATGAACAACCATTTCGGC
* *
1637328 ACTAAGTGTGCAATTCATGAAATTCATCATATTTTGATGAAC
1 ACTAAGTGTGCAATTCAAG-AATTCATCATATGTTGATGAAC
1637370 GATCGCATAG
Statistics
Matches: 183, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
161 48 0.26
162 135 0.74
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (160 bp):
ACTAAGTGTGCAATTCAAGAATTCATCATATGTTGATGAACAACCATTTCACACTATGTGTGCAA
CTCACGAAATTCATCATATGTTGATGAACAATCATTTCGACAATATATGTGCAACTCACGAAATT
CATCATATGTTGATGAACAACCATTTCGGC
Found at i:1637734 original size:46 final size:46
Alignment explanation
Indices: 1637678--1637765 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
1637668 TTATATGAAG
*
1637678 AATAATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGTAT
1 AATAATGCATAATTGGCATGAAAGGATGCCACAAATGAAAATGTAT
*
1637724 AATAGTGCATAATTGGCATGAAAGGATGCCACAAATGAAAAT
1 AATAATGCATAATTGGCATGAAAGGATGCCACAAATGAAAAT
1637766 ACATAGCGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.24
Consensus pattern (46 bp):
AATAATGCATAATTGGCATGAAAGGATGCCACAAATGAAAATGTAT
Found at i:1641644 original size:22 final size:22
Alignment explanation
Indices: 1641617--1641658 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1641607 TGCAAAAATG
1641617 GTATCGATACCATAGTATGGTA
1 GTATCGATACCATAGTATGGTA
*
1641639 GTATCGATACCATGGTATGG
1 GTATCGATACCATAGTATGG
1641659 GAATCGATAC
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:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:1642157 original size:45 final size:45
Alignment explanation
Indices: 1642086--1642577 Score: 761
Period size: 45 Copynumber: 11.0 Consensus size: 45
1642076 AATAATAATA
* * * *
1642086 CATATGGGTGCATTATTAACAAAAAAGTATACCATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* * * *
1642131 AATATGGGTGCATTATAAATAGAAAAGTATGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
*
1642176 CATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* * *
1642221 CATATGGGTGCAATATCAACAGAAAAGTATGCTATAGTTGAATTG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* *
1642266 CATATGGGTACATTATCAACATAAGAGTATGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
*
1642311 CACATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* **
1642356 CATATGGGTGCATTATCAACAGAAAAGTATATTATAGTTGAAAT-
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
*
1642400 CATATGGGTGCATTATCAACATAAAAGTATGATATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* *
1642445 CATATGGGTGCATTATCAACATAAAAGTATGCAATATTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
* *
1642490 CTTATGGGTGCATTCTCAACATAAAAGTATGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
*
1642535 CATATAGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAA
1 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAA
1642578 AATCATAGTG
Statistics
Matches: 406, Mismatches: 40, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 0.10
45 365 0.90
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (45 bp):
CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATG
Found at i:1648490 original size:20 final size:21
Alignment explanation
Indices: 1648465--1648514 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1648455 ATTCAATCAA
*
1648465 TATCGATACCTAAGGGGGA-G
1 TATCGATACCTAAGGGGAAGG
*
1648485 TATCGATA-CTGAGGGGAAGG
1 TATCGATACCTAAGGGGAAGG
1648505 TATCGATACC
1 TATCGATACC
1648515 ATTTAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 8 0.31
20 17 0.65
21 1 0.04
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (21 bp):
TATCGATACCTAAGGGGAAGG
Found at i:1649159 original size:45 final size:45
Alignment explanation
Indices: 1649022--1649164 Score: 234
Period size: 45 Copynumber: 3.2 Consensus size: 45
1649012 TGAAAATAAT
*
1649022 AATGCATATGGGTACATTATCAACAGAAACGTATGCCATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
* *
1649067 AAAGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
* *
1649112 AATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
1649157 AATG-ATAT
1 AATGCATAT
1649165 AATTGAATTG
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 4 0.04
45 87 0.96
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
Found at i:1649200 original size:59 final size:60
Alignment explanation
Indices: 1649099--1649224 Score: 211
Period size: 59 Copynumber: 2.1 Consensus size: 60
1649089 ACAGAAAAGT
*
1649099 ATGC-TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAA
1 ATGCATATAATTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAA
* *
1649158 ATG-ATATAATTGAATTGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAA
1 ATGCATATAATTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAA
1649217 ATGCATAT
1 ATGCATAT
1649225 GGGTGCATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
59 58 0.94
60 4 0.06
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (60 bp):
ATGCATATAATTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAA
Found at i:1649222 original size:45 final size:45
Alignment explanation
Indices: 1649162--1649512 Score: 560
Period size: 45 Copynumber: 7.8 Consensus size: 45
1649152 GTTGAAATGA
* *
1649162 TATAATTGAATTGCATATGGGTGCATTATCAACATAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
*
1649207 TATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
*
1649252 TATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
*
1649297 TATAGTTGAAATGCATATGGGTGCATTATCAACATCAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
*
1649342 TATAGTTGAAATGCATATGGGTTCATTATCAACATAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
* * *
1649387 AATAGTTGAAATTCATATGAGTGCATTATCAACATAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
* *
1649432 TATAGTTAAAATGCATATGGTTGCATTATCAACATAAAAGTATGC
1 TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
* *
1649477 TATAGTTAAAAATGCATAAT-GGTGCATTATAAACAT
1 TATAGTT-GAAATGCAT-ATGGGTGCATTATCAACAT
1649513 GAATGGAGGT
Statistics
Matches: 286, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
45 261 0.91
46 23 0.08
47 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (45 bp):
TATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGC
Found at i:1649246 original size:104 final size:105
Alignment explanation
Indices: 1649070--1649269 Score: 357
Period size: 104 Copynumber: 1.9 Consensus size: 105
1649060 TAGTTGAAAA
1649070 GCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAA
1 GCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAA
*
1649135 CATAAAAGTATGCCATAGTTGAAATG-ATATAATTGAATT
66 CAGAAAAGTATGCCATAGTTGAAATGCATATAATTGAATT
* *
1649174 GCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAA
1 GCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAA
*
1649239 CAGAAAAGTATGCTATAGTTGAAATGCATAT
66 CAGAAAAGTATGCCATAGTTGAAATGCATAT
1649270 GGGTGCATTA
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 87 0.96
105 4 0.04
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (105 bp):
GCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGGTGCATTATCAA
CAGAAAAGTATGCCATAGTTGAAATGCATATAATTGAATT
Found at i:1651520 original size:22 final size:22
Alignment explanation
Indices: 1651451--1651521 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
1651441 ACTGAAAGGG
* * * *
1651451 AGTATCAGTACCATAGTGTAGT
1 AGTATCGGTACTATAGTATAGA
* *
1651473 AGTATCGATACTA-AG-AGA-A
1 AGTATCGGTACTATAGTATAGA
1651492 AGGTATCGGTACTATAGTATAGA
1 A-GTATCGGTACTATAGTATAGA
1651515 AGTATCG
1 AGTATCG
1651522 ATGCCATGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 12 0.32
21 4 0.11
22 18 0.49
23 2 0.05
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (22 bp):
AGTATCGGTACTATAGTATAGA
Found at i:1651984 original size:27 final size:27
Alignment explanation
Indices: 1651954--1652036 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
1651944 GAATTCATCA
*
1651954 TATGTTGATGAACAACCGTTTCGGCAC
1 TATGTTGATGAACAACCGTTTCGACAC
* * *
1651981 TATG-TG-TGCAACTCACGGAATTC-ATCA-
1 TATGTTGATG-AAC-AACCG-TTTCGA-CAC
1652008 TATGTTGATGAACAACCGTTTCGACAC
1 TATGTTGATGAACAACCGTTTCGACAC
1652035 TA
1 TA
1652037 AGTGTGCAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
25 2 0.05
26 10 0.24
27 17 0.41
28 10 0.24
29 2 0.05
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (27 bp):
TATGTTGATGAACAACCGTTTCGACAC
Found at i:1652119 original size:27 final size:27
Alignment explanation
Indices: 1652089--1652174 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
1652079 TTTTCGGCAC
1652089 TATGTATGCAACTCACGGAATTCATCA
1 TATGTATGCAACTCACGGAATTCATCA
* * * **
1652116 TATGTTGATG-AAC-AAC-CATTTCGGCA
1 TATG-T-ATGCAACTCACGGAATTCATCA
*
1652142 CTATGTGTGCAACTCACGGAATTCATCA
1 -TATGTATGCAACTCACGGAATTCATCA
1652170 TATGT
1 TATGT
1652175 TGATGAACAA
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
25 2 0.05
26 10 0.24
27 17 0.40
28 10 0.24
29 3 0.07
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (27 bp):
TATGTATGCAACTCACGGAATTCATCA
Found at i:1652473 original size:54 final size:54
Alignment explanation
Indices: 1651881--1652447 Score: 757
Period size: 54 Copynumber: 10.5 Consensus size: 54
1651871 ACTAAGTATA
* * *** *
1651881 CAATTCACGGAATTCATCATATGTTGATGAACAACTGTTTCAATACTATGTGTA
1 CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
1651935 CAACTT-AC-AGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
1 CAA-TTCACGA-AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
* * * *
1651989 CAACTCACGGAATTCATCATATGTTGATGAACAACCGTTTCGACACTAAGTGTG
1 CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
* * * * *
1652043 CAATTCATGGAATTCATCATATGTTGAAGAACAACCTTTTCGGCACTATGTATG
1 CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
* * *
1652097 CAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGCACTATGTGTG
1 CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
* * * *
1652151 CAACTCACGGAATTCATCATATGTTGATGAACAAACGTTTCGGCACTAAGTGTG
1 CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
*
1652205 CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTG
1 CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
* ** *
1652259 CAATTCAC-AGAATTCATCATATGTTAATGAACAACTATTTC-GCACTAAGTGTG
1 CAATTCACGA-AATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
* * * *
1652312 CAATTCAAGAAATTCATCATATATTGATGAACATCCGTTTCGGCATTATGTGTG
1 CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
* *
1652366 CAACTT-ACGAAATTCATCATATGTTGATGAACAACAGTTTCGGCACTAAGTGTG
1 CAA-TTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
*
1652420 CAATTCATGAAATTCATCATATGTTGAT
1 CAATTCACGAAATTCATCATATGTTGAT
1652448 AAACGTCCAT
Statistics
Matches: 454, Mismatches: 50, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
53 47 0.10
54 403 0.89
55 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
CAATTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTATGTGTG
Found at i:1656653 original size:10 final size:10
Alignment explanation
Indices: 1656624--1656665 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1656614 TATTAATAAT
*
1656624 AATAATAAT-
1 AATAAAAATA
1656633 AATAAACAATA
1 AATAAA-AATA
1656644 AATAAAAATA
1 AATAAAAATA
*
1656654 AATAAATATA
1 AATAAAAATA
1656664 AA
1 AA
1656666 AGACCCGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 5 0.17
10 18 0.62
11 6 0.21
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (10 bp):
AATAAAAATA
Found at i:1658108 original size:15 final size:15
Alignment explanation
Indices: 1658090--1658155 Score: 89
Period size: 16 Copynumber: 4.3 Consensus size: 15
1658080 CCTTTATTTA
1658090 TTTTTTC-TTTTCTT
1 TTTTTTCTTTTTCTT
1658104 TTTTTTCTTTTTCTT
1 TTTTTTCTTTTTCTT
*
1658119 TTTTTTCATTTTTCAT
1 TTTTTTC-TTTTTCTT
*
1658135 TTTTTTCATTTTTCAT
1 TTTTTTC-TTTTTCTT
1658151 TTTTT
1 TTTTT
1658156 AAGTGTAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
14 7 0.14
15 14 0.29
16 28 0.57
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTCTT
Found at i:1658121 original size:16 final size:16
Alignment explanation
Indices: 1658097--1658155 Score: 93
Period size: 16 Copynumber: 3.7 Consensus size: 16
1658087 TTATTTTTTC
1658097 TTTTCTTTTTTTTC-T
1 TTTTCTTTTTTTTCAT
1658112 TTTTCTTTTTTTTCAT
1 TTTTCTTTTTTTTCAT
*
1658128 TTTTCATTTTTTTCAT
1 TTTTCTTTTTTTTCAT
1658144 TTTTCATTTTTT
1 TTTTC-TTTTTT
1658156 AAGTGTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.35
16 21 0.52
17 5 0.12
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTTTTTTCAT
Found at i:1658139 original size:9 final size:9
Alignment explanation
Indices: 1658111--1658155 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
1658101 CTTTTTTTTC
*
1658111 TTTTTCTTT
1 TTTTTCATT
1658120 TTTTTCA--
1 TTTTTCATT
1658127 TTTTTCATT
1 TTTTTCATT
1658136 TTTTTCA--
1 TTTTTCATT
1658143 TTTTTCATT
1 TTTTTCATT
1658152 TTTT
1 TTTT
1658156 AAGTGTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
7 14 0.45
9 17 0.55
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCATT
Done.